[med-svn] [python-bx] 07/09: Removing generated files from upstream
Steffen Möller
moeller at moszumanska.debian.org
Sat Jan 14 11:13:03 UTC 2017
This is an automated email from the git hooks/post-receive script.
moeller pushed a commit to branch master
in repository python-bx.
commit 38f5afb596e94453a889f8cc2f456f945acc6057
Author: Steffen Moeller <moeller at debian.org>
Date: Sat Jan 14 11:42:58 2017 +0100
Removing generated files from upstream
---
lib/bx/_seqmapping.c | 5344 -----------
lib/bx/align/_core.c | 1673 ----
lib/bx/align/_epo.c | 10839 ---------------------
lib/bx/align/sitemask/_cpg.c | 3042 ------
lib/bx/arrays/array_tree.c | 16912 ---------------------------------
lib/bx/arrays/bed.c | 2584 -----
lib/bx/arrays/wiggle.c | 3684 -------
lib/bx/bbi/bbi_file.c | 15020 -----------------------------
lib/bx/bbi/bigbed_file.c | 8069 ----------------
lib/bx/bbi/bigwig_file.c | 9619 -------------------
lib/bx/bbi/bpt_file.c | 2868 ------
lib/bx/bbi/cirtree_file.c | 3901 --------
lib/bx/bitset.c | 5871 ------------
lib/bx/intervals/cluster.c | 2615 -----
lib/bx/intervals/intersection.c | 8477 -----------------
lib/bx/intseq/ngramcount.c | 2711 ------
lib/bx/misc/_seekbzip2.c | 3194 -------
lib/bx/misc/bgzf.c | 2331 -----
lib/bx/motif/_pwm.c | 2250 -----
lib/bx/pwm/_position_weight_matrix.c | 1620 ----
lib/bx/seq/_nib.c | 1922 ----
lib/bx/seq/_twobit.c | 3010 ------
22 files changed, 117556 deletions(-)
diff --git a/lib/bx/_seqmapping.c b/lib/bx/_seqmapping.c
deleted file mode 100644
index 3dce174..0000000
--- a/lib/bx/_seqmapping.c
+++ /dev/null
@@ -1,5344 +0,0 @@
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-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- return 0;
-#endif
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
- return 0;
-}
-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- continue;
- }
- name = first_kw_arg;
- #if PY_MAJOR_VERSION < 3
- if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
- while (*name) {
- if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
- && _PyString_Eq(**name, key)) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- if ((**argname == key) || (
- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
- }
- argname++;
- }
- }
- } else
- #endif
- if (likely(PyUnicode_Check(key))) {
- while (*name) {
- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**name, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) goto arg_passed_twice;
- argname++;
- }
- }
- } else
- goto invalid_keyword_type;
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
- }
- }
- return 0;
-arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
-}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
- Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- }
- #if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
- if (cause && cause != Py_None) {
- PyObject *fixed_cause;
- if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- }
- else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- }
- else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static CYTHON_INLINE long __Pyx_div_long(long a, long b) {
- long q = a / b;
- long r = a - q*b;
- q -= ((r != 0) & ((r ^ b) < 0));
- return q;
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import = 0;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
-#if PY_MAJOR_VERSION < 3
- PyErr_Format(PyExc_ImportError, "cannot import name %.230s",
- PyString_AsString(name));
-#else
- PyErr_Format(PyExc_ImportError, "cannot import name %S", name);
-#endif
-}
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/align/_core.c b/lib/bx/align/_core.c
deleted file mode 100644
index dfac5d7..0000000
--- a/lib/bx/align/_core.c
+++ /dev/null
@@ -1,1673 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
- #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define Py_TPFLAGS_CHECKTYPES 0
- #define Py_TPFLAGS_HAVE_INDEX 0
-#endif
-#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBaseString_Type PyUnicode_Type
- #define PyStringObject PyUnicodeObject
- #define PyString_Type PyUnicode_Type
- #define PyString_Check PyUnicode_Check
- #define PyString_CheckExact PyUnicode_CheckExact
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PyBytesObject PyStringObject
- #define PyBytes_Type PyString_Type
- #define PyBytes_Check PyString_Check
- #define PyBytes_CheckExact PyString_CheckExact
- #define PyBytes_FromString PyString_FromString
- #define PyBytes_FromStringAndSize PyString_FromStringAndSize
- #define PyBytes_FromFormat PyString_FromFormat
- #define PyBytes_DecodeEscape PyString_DecodeEscape
- #define PyBytes_AsString PyString_AsString
- #define PyBytes_AsStringAndSize PyString_AsStringAndSize
- #define PyBytes_Size PyString_Size
- #define PyBytes_AS_STRING PyString_AS_STRING
- #define PyBytes_GET_SIZE PyString_GET_SIZE
- #define PyBytes_Repr PyString_Repr
- #define PyBytes_Concat PyString_Concat
- #define PyBytes_ConcatAndDel PyString_ConcatAndDel
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
- #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
-#endif
-#ifndef PySet_CheckExact
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- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/align/_epo.c b/lib/bx/align/_epo.c
deleted file mode 100644
index b837bc3..0000000
--- a/lib/bx/align/_epo.c
+++ /dev/null
@@ -1,10839 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
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- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
- if (cause && cause != Py_None) {
- PyObject *fixed_cause;
- if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- }
- else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- }
- else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* exc_type = tstate->curexc_type;
- if (unlikely(exc_type)) {
- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#endif
-}
-
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
-}
-
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
- PyObject *local_type, *local_value, *local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- local_type = tstate->curexc_type;
- local_value = tstate->curexc_value;
- local_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(&local_type, &local_value, &local_tb);
-#endif
- PyErr_NormalizeException(&local_type, &local_value, &local_tb);
-#if CYTHON_COMPILING_IN_CPYTHON
- if (unlikely(tstate->curexc_type))
-#else
- if (unlikely(PyErr_Occurred()))
-#endif
- goto bad;
- #if PY_MAJOR_VERSION >= 3
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
- goto bad;
- #endif
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- /* Make sure tstate is in a consistent state when we XDECREF
- these objects (DECREF may run arbitrary code). */
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(local_type, local_value, local_tb);
-#endif
- return 0;
-bad:
- *type = 0;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
-}
-
-static CYTHON_INLINE int __Pyx_IsLittleEndian(void) {
- unsigned int n = 1;
- return *(unsigned char*)(&n) != 0;
-}
-static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx,
- __Pyx_BufFmt_StackElem* stack,
- __Pyx_TypeInfo* type) {
- stack[0].field = &ctx->root;
- stack[0].parent_offset = 0;
- ctx->root.type = type;
- ctx->root.name = "buffer dtype";
- ctx->root.offset = 0;
- ctx->head = stack;
- ctx->head->field = &ctx->root;
- ctx->fmt_offset = 0;
- ctx->head->parent_offset = 0;
- ctx->new_packmode = '@';
- ctx->enc_packmode = '@';
- ctx->new_count = 1;
- ctx->enc_count = 0;
- ctx->enc_type = 0;
- ctx->is_complex = 0;
- ctx->is_valid_array = 0;
- ctx->struct_alignment = 0;
- while (type->typegroup == 'S') {
- ++ctx->head;
- ctx->head->field = type->fields;
- ctx->head->parent_offset = 0;
- type = type->fields->type;
- }
-}
-static int __Pyx_BufFmt_ParseNumber(const char** ts) {
- int count;
- const char* t = *ts;
- if (*t < '0' || *t > '9') {
- return -1;
- } else {
- count = *t++ - '0';
- while (*t >= '0' && *t < '9') {
- count *= 10;
- count += *t++ - '0';
- }
- }
- *ts = t;
- return count;
-}
-static int __Pyx_BufFmt_ExpectNumber(const char **ts) {
- int number = __Pyx_BufFmt_ParseNumber(ts);
- if (number == -1) /* First char was not a digit */
- PyErr_Format(PyExc_ValueError,\
- "Does not understand character buffer dtype format string ('%c')", **ts);
- return number;
-}
-static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) {
- PyErr_Format(PyExc_ValueError,
- "Unexpected format string character: '%c'", ch);
-}
-static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) {
- switch (ch) {
- case 'c': return "'char'";
- case 'b': return "'signed char'";
- case 'B': return "'unsigned char'";
- case 'h': return "'short'";
- case 'H': return "'unsigned short'";
- case 'i': return "'int'";
- case 'I': return "'unsigned int'";
- case 'l': return "'long'";
- case 'L': return "'unsigned long'";
- case 'q': return "'long long'";
- case 'Q': return "'unsigned long long'";
- case 'f': return (is_complex ? "'complex float'" : "'float'");
- case 'd': return (is_complex ? "'complex double'" : "'double'");
- case 'g': return (is_complex ? "'complex long double'" : "'long double'");
- case 'T': return "a struct";
- case 'O': return "Python object";
- case 'P': return "a pointer";
- case 's': case 'p': return "a string";
- case 0: return "end";
- default: return "unparseable format string";
- }
-}
-static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) {
- switch (ch) {
- case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return 2;
- case 'i': case 'I': case 'l': case 'L': return 4;
- case 'q': case 'Q': return 8;
- case 'f': return (is_complex ? 8 : 4);
- case 'd': return (is_complex ? 16 : 8);
- case 'g': {
- PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g')..");
- return 0;
- }
- case 'O': case 'P': return sizeof(void*);
- default:
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
-}
-static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) {
- switch (ch) {
- case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return sizeof(short);
- case 'i': case 'I': return sizeof(int);
- case 'l': case 'L': return sizeof(long);
- #ifdef HAVE_LONG_LONG
- case 'q': case 'Q': return sizeof(PY_LONG_LONG);
- #endif
- case 'f': return sizeof(float) * (is_complex ? 2 : 1);
- case 'd': return sizeof(double) * (is_complex ? 2 : 1);
- case 'g': return sizeof(long double) * (is_complex ? 2 : 1);
- case 'O': case 'P': return sizeof(void*);
- default: {
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
- }
-}
-typedef struct { char c; short x; } __Pyx_st_short;
-typedef struct { char c; int x; } __Pyx_st_int;
-typedef struct { char c; long x; } __Pyx_st_long;
-typedef struct { char c; float x; } __Pyx_st_float;
-typedef struct { char c; double x; } __Pyx_st_double;
-typedef struct { char c; long double x; } __Pyx_st_longdouble;
-typedef struct { char c; void *x; } __Pyx_st_void_p;
-#ifdef HAVE_LONG_LONG
-typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong;
-#endif
-static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) {
- switch (ch) {
- case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short);
- case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int);
- case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long);
-#ifdef HAVE_LONG_LONG
- case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG);
-#endif
- case 'f': return sizeof(__Pyx_st_float) - sizeof(float);
- case 'd': return sizeof(__Pyx_st_double) - sizeof(double);
- case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double);
- case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*);
- default:
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
-}
-/* These are for computing the padding at the end of the struct to align
- on the first member of the struct. This will probably the same as above,
- but we don't have any guarantees.
- */
-typedef struct { short x; char c; } __Pyx_pad_short;
-typedef struct { int x; char c; } __Pyx_pad_int;
-typedef struct { long x; char c; } __Pyx_pad_long;
-typedef struct { float x; char c; } __Pyx_pad_float;
-typedef struct { double x; char c; } __Pyx_pad_double;
-typedef struct { long double x; char c; } __Pyx_pad_longdouble;
-typedef struct { void *x; char c; } __Pyx_pad_void_p;
-#ifdef HAVE_LONG_LONG
-typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong;
-#endif
-static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) {
- switch (ch) {
- case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short);
- case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int);
- case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long);
-#ifdef HAVE_LONG_LONG
- case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG);
-#endif
- case 'f': return sizeof(__Pyx_pad_float) - sizeof(float);
- case 'd': return sizeof(__Pyx_pad_double) - sizeof(double);
- case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double);
- case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*);
- default:
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
-}
-static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) {
- switch (ch) {
- case 'c':
- return 'H';
- case 'b': case 'h': case 'i':
- case 'l': case 'q': case 's': case 'p':
- return 'I';
- case 'B': case 'H': case 'I': case 'L': case 'Q':
- return 'U';
- case 'f': case 'd': case 'g':
- return (is_complex ? 'C' : 'R');
- case 'O':
- return 'O';
- case 'P':
- return 'P';
- default: {
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
- }
-}
-static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) {
- if (ctx->head == NULL || ctx->head->field == &ctx->root) {
- const char* expected;
- const char* quote;
- if (ctx->head == NULL) {
- expected = "end";
- quote = "";
- } else {
- expected = ctx->head->field->type->name;
- quote = "'";
- }
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch, expected %s%s%s but got %s",
- quote, expected, quote,
- __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex));
- } else {
- __Pyx_StructField* field = ctx->head->field;
- __Pyx_StructField* parent = (ctx->head - 1)->field;
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'",
- field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex),
- parent->type->name, field->name);
- }
-}
-static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
- char group;
- size_t size, offset, arraysize = 1;
- if (ctx->enc_type == 0) return 0;
- if (ctx->head->field->type->arraysize[0]) {
- int i, ndim = 0;
- if (ctx->enc_type == 's' || ctx->enc_type == 'p') {
- ctx->is_valid_array = ctx->head->field->type->ndim == 1;
- ndim = 1;
- if (ctx->enc_count != ctx->head->field->type->arraysize[0]) {
- PyErr_Format(PyExc_ValueError,
- "Expected a dimension of size %zu, got %zu",
- ctx->head->field->type->arraysize[0], ctx->enc_count);
- return -1;
- }
- }
- if (!ctx->is_valid_array) {
- PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d",
- ctx->head->field->type->ndim, ndim);
- return -1;
- }
- for (i = 0; i < ctx->head->field->type->ndim; i++) {
- arraysize *= ctx->head->field->type->arraysize[i];
- }
- ctx->is_valid_array = 0;
- ctx->enc_count = 1;
- }
- group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex);
- do {
- __Pyx_StructField* field = ctx->head->field;
- __Pyx_TypeInfo* type = field->type;
- if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') {
- size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex);
- } else {
- size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex);
- }
- if (ctx->enc_packmode == '@') {
- size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex);
- size_t align_mod_offset;
- if (align_at == 0) return -1;
- align_mod_offset = ctx->fmt_offset % align_at;
- if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset;
- if (ctx->struct_alignment == 0)
- ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type,
- ctx->is_complex);
- }
- if (type->size != size || type->typegroup != group) {
- if (type->typegroup == 'C' && type->fields != NULL) {
- size_t parent_offset = ctx->head->parent_offset + field->offset;
- ++ctx->head;
- ctx->head->field = type->fields;
- ctx->head->parent_offset = parent_offset;
- continue;
- }
- if ((type->typegroup == 'H' || group == 'H') && type->size == size) {
- } else {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return -1;
- }
- }
- offset = ctx->head->parent_offset + field->offset;
- if (ctx->fmt_offset != offset) {
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected",
- (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset);
- return -1;
- }
- ctx->fmt_offset += size;
- if (arraysize)
- ctx->fmt_offset += (arraysize - 1) * size;
- --ctx->enc_count; /* Consume from buffer string */
- while (1) {
- if (field == &ctx->root) {
- ctx->head = NULL;
- if (ctx->enc_count != 0) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return -1;
- }
- break; /* breaks both loops as ctx->enc_count == 0 */
- }
- ctx->head->field = ++field;
- if (field->type == NULL) {
- --ctx->head;
- field = ctx->head->field;
- continue;
- } else if (field->type->typegroup == 'S') {
- size_t parent_offset = ctx->head->parent_offset + field->offset;
- if (field->type->fields->type == NULL) continue; /* empty struct */
- field = field->type->fields;
- ++ctx->head;
- ctx->head->field = field;
- ctx->head->parent_offset = parent_offset;
- break;
- } else {
- break;
- }
- }
- } while (ctx->enc_count);
- ctx->enc_type = 0;
- ctx->is_complex = 0;
- return 0;
-}
-static CYTHON_INLINE PyObject *
-__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp)
-{
- const char *ts = *tsp;
- int i = 0, number;
- int ndim = ctx->head->field->type->ndim;
-;
- ++ts;
- if (ctx->new_count != 1) {
- PyErr_SetString(PyExc_ValueError,
- "Cannot handle repeated arrays in format string");
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- while (*ts && *ts != ')') {
- if (isspace(*ts))
- continue;
- number = __Pyx_BufFmt_ExpectNumber(&ts);
- if (number == -1) return NULL;
- if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i])
- return PyErr_Format(PyExc_ValueError,
- "Expected a dimension of size %zu, got %d",
- ctx->head->field->type->arraysize[i], number);
- if (*ts != ',' && *ts != ')')
- return PyErr_Format(PyExc_ValueError,
- "Expected a comma in format string, got '%c'", *ts);
- if (*ts == ',') ts++;
- i++;
- }
- if (i != ndim)
- return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d",
- ctx->head->field->type->ndim, i);
- if (!*ts) {
- PyErr_SetString(PyExc_ValueError,
- "Unexpected end of format string, expected ')'");
- return NULL;
- }
- ctx->is_valid_array = 1;
- ctx->new_count = 1;
- *tsp = ++ts;
- return Py_None;
-}
-static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) {
- int got_Z = 0;
- while (1) {
- switch(*ts) {
- case 0:
- if (ctx->enc_type != 0 && ctx->head == NULL) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- if (ctx->head != NULL) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return NULL;
- }
- return ts;
- case ' ':
- case 10:
- case 13:
- ++ts;
- break;
- case '<':
- if (!__Pyx_IsLittleEndian()) {
- PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler");
- return NULL;
- }
- ctx->new_packmode = '=';
- ++ts;
- break;
- case '>':
- case '!':
- if (__Pyx_IsLittleEndian()) {
- PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler");
- return NULL;
- }
- ctx->new_packmode = '=';
- ++ts;
- break;
- case '=':
- case '@':
- case '^':
- ctx->new_packmode = *ts++;
- break;
- case 'T': /* substruct */
- {
- const char* ts_after_sub;
- size_t i, struct_count = ctx->new_count;
- size_t struct_alignment = ctx->struct_alignment;
- ctx->new_count = 1;
- ++ts;
- if (*ts != '{') {
- PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'");
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0; /* Erase processed last struct element */
- ctx->enc_count = 0;
- ctx->struct_alignment = 0;
- ++ts;
- ts_after_sub = ts;
- for (i = 0; i != struct_count; ++i) {
- ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts);
- if (!ts_after_sub) return NULL;
- }
- ts = ts_after_sub;
- if (struct_alignment) ctx->struct_alignment = struct_alignment;
- }
- break;
- case '}': /* end of substruct; either repeat or move on */
- {
- size_t alignment = ctx->struct_alignment;
- ++ts;
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0; /* Erase processed last struct element */
- if (alignment && ctx->fmt_offset % alignment) {
- ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment);
- }
- }
- return ts;
- case 'x':
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->fmt_offset += ctx->new_count;
- ctx->new_count = 1;
- ctx->enc_count = 0;
- ctx->enc_type = 0;
- ctx->enc_packmode = ctx->new_packmode;
- ++ts;
- break;
- case 'Z':
- got_Z = 1;
- ++ts;
- if (*ts != 'f' && *ts != 'd' && *ts != 'g') {
- __Pyx_BufFmt_RaiseUnexpectedChar('Z');
- return NULL;
- } /* fall through */
- case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I':
- case 'l': case 'L': case 'q': case 'Q':
- case 'f': case 'd': case 'g':
- case 'O': case 's': case 'p':
- if (ctx->enc_type == *ts && got_Z == ctx->is_complex &&
- ctx->enc_packmode == ctx->new_packmode) {
- ctx->enc_count += ctx->new_count;
- } else {
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_count = ctx->new_count;
- ctx->enc_packmode = ctx->new_packmode;
- ctx->enc_type = *ts;
- ctx->is_complex = got_Z;
- }
- ++ts;
- ctx->new_count = 1;
- got_Z = 0;
- break;
- case ':':
- ++ts;
- while(*ts != ':') ++ts;
- ++ts;
- break;
- case '(':
- if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL;
- break;
- default:
- {
- int number = __Pyx_BufFmt_ExpectNumber(&ts);
- if (number == -1) return NULL;
- ctx->new_count = (size_t)number;
- }
- }
- }
-}
-static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) {
- buf->buf = NULL;
- buf->obj = NULL;
- buf->strides = __Pyx_zeros;
- buf->shape = __Pyx_zeros;
- buf->suboffsets = __Pyx_minusones;
-}
-static CYTHON_INLINE int __Pyx_GetBufferAndValidate(
- Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags,
- int nd, int cast, __Pyx_BufFmt_StackElem* stack)
-{
- if (obj == Py_None || obj == NULL) {
- __Pyx_ZeroBuffer(buf);
- return 0;
- }
- buf->buf = NULL;
- if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail;
- if (buf->ndim != nd) {
- PyErr_Format(PyExc_ValueError,
- "Buffer has wrong number of dimensions (expected %d, got %d)",
- nd, buf->ndim);
- goto fail;
- }
- if (!cast) {
- __Pyx_BufFmt_Context ctx;
- __Pyx_BufFmt_Init(&ctx, stack, dtype);
- if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail;
- }
- if ((unsigned)buf->itemsize != dtype->size) {
- PyErr_Format(PyExc_ValueError,
- "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)",
- buf->itemsize, (buf->itemsize > 1) ? "s" : "",
- dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : "");
- goto fail;
- }
- if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
- return 0;
-fail:;
- __Pyx_ZeroBuffer(buf);
- return -1;
-}
-static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) {
- if (info->buf == NULL) return;
- if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL;
- __Pyx_ReleaseBuffer(info);
-}
-
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
- if (unlikely(!type)) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (likely(PyObject_TypeCheck(obj, type)))
- return 1;
- PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
- Py_TYPE(obj)->tp_name, type->tp_name);
- return 0;
-}
-
-static void __Pyx_RaiseBufferFallbackError(void) {
- PyErr_Format(PyExc_ValueError,
- "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!");
-}
-
-static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
- const char *name, int exact)
-{
- if (!type) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (none_allowed && obj == Py_None) return 1;
- else if (exact) {
- if (Py_TYPE(obj) == type) return 1;
- }
- else {
- if (PyObject_TypeCheck(obj, type)) return 1;
- }
- PyErr_Format(PyExc_TypeError,
- "Argument '%s' has incorrect type (expected %s, got %s)",
- name, type->tp_name, Py_TYPE(obj)->tp_name);
- return 0;
-}
-
-static void __Pyx_RaiseBufferIndexError(int axis) {
- PyErr_Format(PyExc_IndexError,
- "Out of bounds on buffer access (axis %d)", axis);
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-}
-
-static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->exc_type;
- *value = tstate->exc_value;
- *tb = tstate->exc_traceback;
- Py_XINCREF(*type);
- Py_XINCREF(*value);
- Py_XINCREF(*tb);
-#else
- PyErr_GetExcInfo(type, value, tb);
-#endif
-}
-static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = type;
- tstate->exc_value = value;
- tstate->exc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
-}
-
-#if PY_MAJOR_VERSION < 3
-static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
- CYTHON_UNUSED PyObject *getbuffer_cobj;
- #if PY_VERSION_HEX >= 0x02060000
- if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
- #endif
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags);
- #if PY_VERSION_HEX < 0x02060000
- if (obj->ob_type->tp_dict &&
- (getbuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
- "__pyx_getbuffer"))) {
- getbufferproc func;
- #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
- func = (getbufferproc) PyCapsule_GetPointer(getbuffer_cobj, "getbuffer(obj, view, flags)");
- #else
- func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj);
- #endif
- Py_DECREF(getbuffer_cobj);
- if (!func)
- goto fail;
- return func(obj, view, flags);
- } else {
- PyErr_Clear();
- }
- #endif
- PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
-#if PY_VERSION_HEX < 0x02060000
-fail:
-#endif
- return -1;
-}
-static void __Pyx_ReleaseBuffer(Py_buffer *view) {
- PyObject *obj = view->obj;
- CYTHON_UNUSED PyObject *releasebuffer_cobj;
- if (!obj) return;
- #if PY_VERSION_HEX >= 0x02060000
- if (PyObject_CheckBuffer(obj)) {
- PyBuffer_Release(view);
- return;
- }
- #endif
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; }
- #if PY_VERSION_HEX < 0x02060000
- if (obj->ob_type->tp_dict &&
- (releasebuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
- "__pyx_releasebuffer"))) {
- releasebufferproc func;
- #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
- func = (releasebufferproc) PyCapsule_GetPointer(releasebuffer_cobj, "releasebuffer(obj, view)");
- #else
- func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj);
- #endif
- Py_DECREF(releasebuffer_cobj);
- if (!func)
- goto fail;
- func(obj, view);
- return;
- } else {
- PyErr_Clear();
- }
- #endif
- goto nofail;
-#if PY_VERSION_HEX < 0x02060000
-fail:
-#endif
- PyErr_WriteUnraisable(obj);
-nofail:
- Py_DECREF(obj);
- view->obj = NULL;
-}
-#endif /* PY_MAJOR_VERSION < 3 */
-
-
- static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import = 0;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
-#if PY_MAJOR_VERSION < 3
- PyErr_Format(PyExc_ImportError, "cannot import name %.230s",
- PyString_AsString(name));
-#else
- PyErr_Format(PyExc_ImportError, "cannot import name %S", name);
-#endif
-}
-
-static PyObject *
-__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
-{
- if (unlikely(op->func_doc == NULL)) {
- if (op->func.m_ml->ml_doc) {
-#if PY_MAJOR_VERSION >= 3
- op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
-#else
- op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
-#endif
- if (unlikely(op->func_doc == NULL))
- return NULL;
- } else {
- Py_INCREF(Py_None);
- return Py_None;
- }
- }
- Py_INCREF(op->func_doc);
- return op->func_doc;
-}
-static int
-__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp = op->func_doc;
- if (value == NULL)
- value = Py_None; /* Mark as deleted */
- Py_INCREF(value);
- op->func_doc = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
-{
- if (unlikely(op->func_name == NULL)) {
-#if PY_MAJOR_VERSION >= 3
- op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
-#else
- op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
-#endif
- if (unlikely(op->func_name == NULL))
- return NULL;
- }
- Py_INCREF(op->func_name);
- return op->func_name;
-}
-static int
-__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
-#if PY_MAJOR_VERSION >= 3
- if (unlikely(value == NULL || !PyUnicode_Check(value))) {
-#else
- if (unlikely(value == NULL || !PyString_Check(value))) {
-#endif
- PyErr_SetString(PyExc_TypeError,
- "__name__ must be set to a string object");
- return -1;
- }
- tmp = op->func_name;
- Py_INCREF(value);
- op->func_name = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op)
-{
- Py_INCREF(op->func_qualname);
- return op->func_qualname;
-}
-static int
-__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
-#if PY_MAJOR_VERSION >= 3
- if (unlikely(value == NULL || !PyUnicode_Check(value))) {
-#else
- if (unlikely(value == NULL || !PyString_Check(value))) {
-#endif
- PyErr_SetString(PyExc_TypeError,
- "__qualname__ must be set to a string object");
- return -1;
- }
- tmp = op->func_qualname;
- Py_INCREF(value);
- op->func_qualname = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
-{
- PyObject *self;
- self = m->func_closure;
- if (self == NULL)
- self = Py_None;
- Py_INCREF(self);
- return self;
-}
-static PyObject *
-__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
-{
- if (unlikely(op->func_dict == NULL)) {
- op->func_dict = PyDict_New();
- if (unlikely(op->func_dict == NULL))
- return NULL;
- }
- Py_INCREF(op->func_dict);
- return op->func_dict;
-}
-static int
-__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
- if (unlikely(value == NULL)) {
- PyErr_SetString(PyExc_TypeError,
- "function's dictionary may not be deleted");
- return -1;
- }
- if (unlikely(!PyDict_Check(value))) {
- PyErr_SetString(PyExc_TypeError,
- "setting function's dictionary to a non-dict");
- return -1;
- }
- tmp = op->func_dict;
- Py_INCREF(value);
- op->func_dict = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op)
-{
- PyObject* dict = PyModule_GetDict(__pyx_m);
- Py_XINCREF(dict);
- return dict;
-}
-static PyObject *
-__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op)
-{
- Py_INCREF(Py_None);
- return Py_None;
-}
-static PyObject *
-__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
-{
- PyObject* result = (op->func_code) ? op->func_code : Py_None;
- Py_INCREF(result);
- return result;
-}
-static PyObject *
-__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op)
-{
- if (op->defaults_tuple) {
- Py_INCREF(op->defaults_tuple);
- return op->defaults_tuple;
- }
- if (op->defaults_getter) {
- PyObject *res = op->defaults_getter((PyObject *) op);
- if (likely(res)) {
- Py_INCREF(res);
- op->defaults_tuple = res;
- }
- return res;
- }
- Py_INCREF(Py_None);
- return Py_None;
-}
-static PyGetSetDef __pyx_CyFunction_getsets[] = {
- {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0},
- {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
- {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
- {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
- {0, 0, 0, 0, 0}
-};
-#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
-#define PY_WRITE_RESTRICTED WRITE_RESTRICTED
-#endif
-static PyMemberDef __pyx_CyFunction_members[] = {
- {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0},
- {0, 0, 0, 0, 0}
-};
-static PyObject *
-__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args)
-{
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromString(m->func.m_ml->ml_name);
-#else
- return PyString_FromString(m->func.m_ml->ml_name);
-#endif
-}
-static PyMethodDef __pyx_CyFunction_methods[] = {
- {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
- {0, 0, 0, 0}
-};
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname,
- PyObject *closure, PyObject *module, PyObject* code) {
- __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
- if (op == NULL)
- return NULL;
- op->flags = flags;
- op->func_weakreflist = NULL;
- op->func.m_ml = ml;
- op->func.m_self = (PyObject *) op;
- Py_XINCREF(closure);
- op->func_closure = closure;
- Py_XINCREF(module);
- op->func.m_module = module;
- op->func_dict = NULL;
- op->func_name = NULL;
- Py_INCREF(qualname);
- op->func_qualname = qualname;
- op->func_doc = NULL;
- op->func_classobj = NULL;
- Py_XINCREF(code);
- op->func_code = code;
- op->defaults_pyobjects = 0;
- op->defaults = NULL;
- op->defaults_tuple = NULL;
- op->defaults_getter = NULL;
- PyObject_GC_Track(op);
- return (PyObject *) op;
-}
-static int
-__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
-{
- Py_CLEAR(m->func_closure);
- Py_CLEAR(m->func.m_module);
- Py_CLEAR(m->func_dict);
- Py_CLEAR(m->func_name);
- Py_CLEAR(m->func_qualname);
- Py_CLEAR(m->func_doc);
- Py_CLEAR(m->func_code);
- Py_CLEAR(m->func_classobj);
- Py_CLEAR(m->defaults_tuple);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_XDECREF(pydefaults[i]);
- PyMem_Free(m->defaults);
- m->defaults = NULL;
- }
- return 0;
-}
-static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
-{
- PyObject_GC_UnTrack(m);
- if (m->func_weakreflist != NULL)
- PyObject_ClearWeakRefs((PyObject *) m);
- __Pyx_CyFunction_clear(m);
- PyObject_GC_Del(m);
-}
-static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
-{
- Py_VISIT(m->func_closure);
- Py_VISIT(m->func.m_module);
- Py_VISIT(m->func_dict);
- Py_VISIT(m->func_name);
- Py_VISIT(m->func_qualname);
- Py_VISIT(m->func_doc);
- Py_VISIT(m->func_code);
- Py_VISIT(m->func_classobj);
- Py_VISIT(m->defaults_tuple);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_VISIT(pydefaults[i]);
- }
- return 0;
-}
-static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type)
-{
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) {
- Py_INCREF(func);
- return func;
- }
- if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) {
- if (type == NULL)
- type = (PyObject *)(Py_TYPE(obj));
- return PyMethod_New(func,
- type, (PyObject *)(Py_TYPE(type)));
- }
- if (obj == Py_None)
- obj = NULL;
- return PyMethod_New(func, obj, type);
-}
-static PyObject*
-__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
-{
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromFormat("<cyfunction %U at %p>",
- op->func_qualname, (void *)op);
-#else
- return PyString_FromFormat("<cyfunction %s at %p>",
- PyString_AsString(op->func_qualname), (void *)op);
-#endif
-}
-#if CYTHON_COMPILING_IN_PYPY
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyCFunctionObject* f = (PyCFunctionObject*)func;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
- Py_ssize_t size;
- switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
- case METH_VARARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0)
- return (*meth)(self, arg);
- break;
- case METH_VARARGS | METH_KEYWORDS:
- return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
- case METH_NOARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 0)
- return (*meth)(self, NULL);
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes no arguments (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- case METH_O:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 1)
- return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes exactly one argument (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- default:
- PyErr_SetString(PyExc_SystemError, "Bad call flags in "
- "__Pyx_CyFunction_Call. METH_OLDARGS is no "
- "longer supported!");
- return NULL;
- }
- PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
- f->m_ml->ml_name);
- return NULL;
-}
-#else
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- return PyCFunction_Call(func, arg, kw);
-}
-#endif
-static PyTypeObject __pyx_CyFunctionType_type = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
- sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- __Pyx_CyFunction_Call, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/
- (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_CyFunction_methods, /*tp_methods*/
- __pyx_CyFunction_members, /*tp_members*/
- __pyx_CyFunction_getsets, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- __Pyx_CyFunction_descr_get, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-};
-static int __Pyx_CyFunction_init(void) {
-#if !CYTHON_COMPILING_IN_PYPY
- __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
-#endif
- if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
- return -1;
- __pyx_CyFunctionType = &__pyx_CyFunctionType_type;
- return 0;
-}
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults = PyMem_Malloc(size);
- if (!m->defaults)
- return PyErr_NoMemory();
- memset(m->defaults, 0, sizeof(size));
- m->defaults_pyobjects = pyobjects;
- return m->defaults;
-}
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults_tuple = tuple;
- Py_INCREF(tuple);
-}
-
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_npy_uint64(npy_uint64 val) {
- const npy_uint64 neg_one = (npy_uint64)-1, const_zero = (npy_uint64)0;
- const int is_unsigned = const_zero < neg_one;
- if ((sizeof(npy_uint64) == sizeof(char)) ||
- (sizeof(npy_uint64) == sizeof(short))) {
- return PyInt_FromLong((long)val);
- } else if ((sizeof(npy_uint64) == sizeof(int)) ||
- (sizeof(npy_uint64) == sizeof(long))) {
- if (is_unsigned)
- return PyLong_FromUnsignedLong((unsigned long)val);
- else
- return PyInt_FromLong((long)val);
- } else if (sizeof(npy_uint64) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
- else
- return PyLong_FromLongLong((PY_LONG_LONG)val);
- } else {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(npy_uint64),
- little, !is_unsigned);
- }
-}
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return ::std::complex< float >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return x + y*(__pyx_t_float_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- __pyx_t_float_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrtf(z.real*z.real + z.imag*z.imag);
- #else
- return hypotf(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- float denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(a, a);
- case 3:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, a);
- case 4:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- }
- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_absf(a);
- theta = atan2f(a.imag, a.real);
- }
- lnr = logf(r);
- z_r = expf(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cosf(z_theta);
- z.imag = z_r * sinf(z_theta);
- return z;
- }
- #endif
-#endif
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return ::std::complex< double >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return x + y*(__pyx_t_double_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- __pyx_t_double_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrt(z.real*z.real + z.imag*z.imag);
- #else
- return hypot(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- double denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(a, a);
- case 3:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, a);
- case 4:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- }
- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_abs(a);
- theta = atan2(a.imag, a.real);
- }
- lnr = log(r);
- z_r = exp(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cos(z_theta);
- z.imag = z_r * sin(z_theta);
- return z;
- }
- #endif
-#endif
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
-#ifndef __PYX_HAVE_RT_ImportType
-#define __PYX_HAVE_RT_ImportType
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%s.%s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%s.%s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/align/sitemask/_cpg.c b/lib/bx/align/sitemask/_cpg.c
deleted file mode 100644
index db78fd4..0000000
--- a/lib/bx/align/sitemask/_cpg.c
+++ /dev/null
@@ -1,3042 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
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- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/arrays/array_tree.c b/lib/bx/arrays/array_tree.c
deleted file mode 100644
index 434bc32..0000000
--- a/lib/bx/arrays/array_tree.c
+++ /dev/null
@@ -1,16912 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
- #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
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- static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex);
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex);
- #endif
-#endif
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-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *);
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-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *);
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-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *);
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-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *);
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-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *);
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *);
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
-
-static void __Pyx_WriteUnraisable(const char *name, int clineno,
- int lineno, const char *filename); /*proto*/
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-static CYTHON_INLINE int __Pyx_StrEq(const char *, const char *); /*proto*/
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-static int __Pyx_check_binary_version(void);
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
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-#if !defined(__Pyx_PyIdentifier_FromString)
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
-#else
- #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
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-static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
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-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
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-} __Pyx_CodeObjectCacheEntry;
-struct __Pyx_CodeObjectCache {
- int count;
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-static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
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-
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename); /*proto*/
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-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
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-
-/* Module declarations from 'cpython.buffer' */
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-/* Module declarations from 'cpython.ref' */
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-/* Module declarations from 'libc.string' */
-
-/* Module declarations from 'libc.stdio' */
-
-/* Module declarations from 'cpython.object' */
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-/* Module declarations from '__builtin__' */
-
-/* Module declarations from 'cpython.type' */
-static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
-
-/* Module declarations from 'libc.stdlib' */
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-/* Module declarations from 'numpy' */
-
-/* Module declarations from 'numpy' */
-static PyTypeObject *__pyx_ptype_5numpy_dtype = 0;
-static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0;
-static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0;
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-static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
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-/* Module declarations from 'bx.arrays.wiggle' */
-static PyTypeObject *__pyx_ptype_2bx_6arrays_6wiggle_WiggleReader = 0;
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-/* Module declarations from 'bx.arrays' */
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-/* Module declarations from 'bx' */
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-/* Module declarations from 'bx.arrays.array_tree' */
-static PyTypeObject *__pyx_ptype_2bx_6arrays_10array_tree_FileArrayTreeDict = 0;
-static PyTypeObject *__pyx_ptype_2bx_6arrays_10array_tree_FileArrayTree = 0;
-static PyTypeObject *__pyx_ptype_2bx_6arrays_10array_tree_Summary = 0;
-static PyTypeObject *__pyx_ptype_2bx_6arrays_10array_tree_ArrayTreeNode = 0;
-static PyTypeObject *__pyx_ptype_2bx_6arrays_10array_tree_ArrayTreeLeaf = 0;
-static PyTypeObject *__pyx_ptype_2bx_6arrays_10array_tree_ArrayTree = 0;
-#define __Pyx_MODULE_NAME "bx.arrays.array_tree"
-int __pyx_module_is_main_bx__arrays__array_tree = 0;
-
-/* Implementation of 'bx.arrays.array_tree' */
-static PyObject *__pyx_builtin_ValueError;
-static PyObject *__pyx_builtin_range;
-static PyObject *__pyx_builtin_sum;
-static PyObject *__pyx_builtin_RuntimeError;
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_array_tree_dict_from_reader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_reader, PyObject *__pyx_v_sizes, PyObject *__pyx_v_default_size, PyObject *__pyx_v_block_size, PyObject *__pyx_v_no_leaves); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_17FileArrayTreeDict___init__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTreeDict *__pyx_v_self, PyObject *__pyx_v_file); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_17FileArrayTreeDict_2__getitem__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTreeDict *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_17FileArrayTreeDict_4dict_to_file(CYTHON_UNUSED PyObject *__pyx_v_Class, PyObject *__pyx_v_dict, PyObject *__pyx_v_file, PyObject *__pyx_v_is_little_endian, PyObject *__pyx_v_no_leaves); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree___init__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self, PyObject *__pyx_v_file, PyObject *__pyx_v_is_little_endian); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_2__getitem__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self, PyObject *__pyx_v_index); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_4get_summary(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_level); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_6get_leaf(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self, PyObject *__pyx_v_index); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_3max___get__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_3max_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_10block_size___get__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_10block_size_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_5dtype___get__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_5dtype_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_5dtype_4__del__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_6levels___get__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_6levels_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_6offset___get__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_6offset_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_11root_offset___get__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13FileArrayTree_11root_offset_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_7Summary_6counts___get__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_6counts_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_6counts_4__del__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_7Summary_11frequencies___get__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_11frequencies_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_11frequencies_4__del__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_7Summary_4mins___get__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_4mins_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_4mins_4__del__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_7Summary_4maxs___get__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_4maxs_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_4maxs_4__del__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_7Summary_4sums___get__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_4sums_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_4sums_4__del__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_7Summary_10sumsquares___get__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_10sumsquares_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_7Summary_10sumsquares_4__del__(struct __pyx_obj_2bx_6arrays_10array_tree_Summary *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_9ArrayTree___init__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self, int __pyx_v_max, int __pyx_v_block_size, PyObject *__pyx_v_dtype, PyObject *__pyx_v_no_leaves); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_2__setitem__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self, int __pyx_v_index, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_4set_range(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self, int __pyx_v_start, int __pyx_v_end, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_6__getitem__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self, int __pyx_v_index); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_8to_file(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self, PyObject *__pyx_v_f, PyObject *__pyx_v_is_little_endian, PyObject *__pyx_v_no_leaves); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_10from_file(PyObject *__pyx_v_Class, PyObject *__pyx_v_f, PyObject *__pyx_v_is_little_endian); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_12from_sequence(PyObject *__pyx_v_Class, PyObject *__pyx_v_s, PyObject *__pyx_v_block_size); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_3max___get__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_3max_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_10block_size___get__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_10block_size_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_5dtype___get__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_5dtype_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_5dtype_4__del__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_6levels___get__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_6levels_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_9no_leaves___get__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_9no_leaves_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_4root___get__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_4root_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_9ArrayTree_4root_4__del__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode___init__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self, struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_tree, int __pyx_v_min, int __pyx_v_max, int __pyx_v_block_size, int __pyx_v_level); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_2set(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self, int __pyx_v_index, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_4get(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self, int __pyx_v_index); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_6build_summary(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_8to_file_data_pass(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self, PyObject *__pyx_v_io, PyObject *__pyx_v_level); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_10to_file_offset_pass(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self, PyObject *__pyx_v_io); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_12from_file(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self, PyObject *__pyx_v_io); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_14get_from_file(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_io, PyObject *__pyx_v_index); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_7summary___get__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_7summary_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_7summary_4__del__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_12start_offset___get__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeNode_12start_offset_2__set__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeLeaf___init__(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *__pyx_v_self, struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *__pyx_v_tree, int __pyx_v_min, int __pyx_v_max); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeLeaf_2set(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeLeaf_4get(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *__pyx_v_self, PyObject *__pyx_v_index); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeLeaf_6to_file_data_pass(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *__pyx_v_self, PyObject *__pyx_v_io, PyObject *__pyx_v_level); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeLeaf_8to_file_offset_pass(CYTHON_UNUSED struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_io); /* proto */
-static PyObject *__pyx_pf_2bx_6arrays_10array_tree_13ArrayTreeLeaf_10from_file(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *__pyx_v_self, PyObject *__pyx_v_io); /* proto */
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- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_FileArrayTreeDict, /*tp_as_number*/
- &__pyx_tp_as_sequence_FileArrayTreeDict, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_FileArrayTreeDict, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_FileArrayTreeDict, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("\n Access to a file containing multiple array trees indexed by a string key.\n "), /*tp_doc*/
- __pyx_tp_traverse_2bx_6arrays_10array_tree_FileArrayTreeDict, /*tp_traverse*/
- __pyx_tp_clear_2bx_6arrays_10array_tree_FileArrayTreeDict, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_2bx_6arrays_10array_tree_FileArrayTreeDict, /*tp_methods*/
- 0, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pw_2bx_6arrays_10array_tree_17FileArrayTreeDict_1__init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_2bx_6arrays_10array_tree_FileArrayTreeDict, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-static struct __pyx_vtabstruct_2bx_6arrays_10array_tree_FileArrayTree __pyx_vtable_2bx_6arrays_10array_tree_FileArrayTree;
-
-static PyObject *__pyx_tp_new_2bx_6arrays_10array_tree_FileArrayTree(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *)o);
- p->__pyx_vtab = __pyx_vtabptr_2bx_6arrays_10array_tree_FileArrayTree;
- p->dtype = Py_None; Py_INCREF(Py_None);
- p->io = Py_None; Py_INCREF(Py_None);
- return o;
-}
-
-static void __pyx_tp_dealloc_2bx_6arrays_10array_tree_FileArrayTree(PyObject *o) {
- struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *p = (struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->dtype);
- Py_CLEAR(p->io);
- PyObject_GC_Track(o);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_2bx_6arrays_10array_tree_FileArrayTree(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *p = (struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *)o;
- if (p->dtype) {
- e = (*v)(p->dtype, a); if (e) return e;
- }
- if (p->io) {
- e = (*v)(p->io, a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_2bx_6arrays_10array_tree_FileArrayTree(PyObject *o) {
- struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *p = (struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->dtype);
- p->dtype = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->io);
- p->io = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *__pyx_sq_item_2bx_6arrays_10array_tree_FileArrayTree(PyObject *o, Py_ssize_t i) {
- PyObject *r;
- PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
- r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
- Py_DECREF(x);
- return r;
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_max(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_3max_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_max(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_3max_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_block_size(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_10block_size_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_block_size(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_10block_size_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_dtype(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_5dtype_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_dtype(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_5dtype_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_5dtype_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_levels(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_6levels_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_levels(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_6levels_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_offset(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_6offset_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_offset(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_6offset_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_root_offset(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_11root_offset_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_root_offset(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_11root_offset_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyMethodDef __pyx_methods_2bx_6arrays_10array_tree_FileArrayTree[] = {
- {__Pyx_NAMESTR("get_summary"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_5get_summary, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("get_leaf"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_7get_leaf, METH_O, __Pyx_DOCSTR(0)},
- {0, 0, 0, 0}
-};
-
-static struct PyGetSetDef __pyx_getsets_2bx_6arrays_10array_tree_FileArrayTree[] = {
- {(char *)"max", __pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_max, __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_max, 0, 0},
- {(char *)"block_size", __pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_block_size, __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_block_size, 0, 0},
- {(char *)"dtype", __pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_dtype, __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_dtype, 0, 0},
- {(char *)"levels", __pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_levels, __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_levels, 0, 0},
- {(char *)"offset", __pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_offset, __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_offset, 0, 0},
- {(char *)"root_offset", __pyx_getprop_2bx_6arrays_10array_tree_13FileArrayTree_root_offset, __pyx_setprop_2bx_6arrays_10array_tree_13FileArrayTree_root_offset, 0, 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_FileArrayTree = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_FileArrayTree = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- __pyx_sq_item_2bx_6arrays_10array_tree_FileArrayTree, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping_FileArrayTree = {
- 0, /*mp_length*/
- __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_3__getitem__, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_FileArrayTree = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-static PyTypeObject __pyx_type_2bx_6arrays_10array_tree_FileArrayTree = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("bx.arrays.array_tree.FileArrayTree"), /*tp_name*/
- sizeof(struct __pyx_obj_2bx_6arrays_10array_tree_FileArrayTree), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_2bx_6arrays_10array_tree_FileArrayTree, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_FileArrayTree, /*tp_as_number*/
- &__pyx_tp_as_sequence_FileArrayTree, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_FileArrayTree, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_FileArrayTree, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("\n Wrapper for ArrayTree stored in file that reads as little as possible\n "), /*tp_doc*/
- __pyx_tp_traverse_2bx_6arrays_10array_tree_FileArrayTree, /*tp_traverse*/
- __pyx_tp_clear_2bx_6arrays_10array_tree_FileArrayTree, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_2bx_6arrays_10array_tree_FileArrayTree, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_2bx_6arrays_10array_tree_FileArrayTree, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pw_2bx_6arrays_10array_tree_13FileArrayTree_1__init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_2bx_6arrays_10array_tree_FileArrayTree, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-
-static PyObject *__pyx_tp_new_2bx_6arrays_10array_tree_Summary(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_2bx_6arrays_10array_tree_Summary *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_2bx_6arrays_10array_tree_Summary *)o);
- p->counts = Py_None; Py_INCREF(Py_None);
- p->frequencies = Py_None; Py_INCREF(Py_None);
- p->mins = Py_None; Py_INCREF(Py_None);
- p->maxs = Py_None; Py_INCREF(Py_None);
- p->sums = Py_None; Py_INCREF(Py_None);
- p->sumsquares = Py_None; Py_INCREF(Py_None);
- return o;
-}
-
-static void __pyx_tp_dealloc_2bx_6arrays_10array_tree_Summary(PyObject *o) {
- struct __pyx_obj_2bx_6arrays_10array_tree_Summary *p = (struct __pyx_obj_2bx_6arrays_10array_tree_Summary *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->counts);
- Py_CLEAR(p->frequencies);
- Py_CLEAR(p->mins);
- Py_CLEAR(p->maxs);
- Py_CLEAR(p->sums);
- Py_CLEAR(p->sumsquares);
- PyObject_GC_Track(o);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_2bx_6arrays_10array_tree_Summary(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_2bx_6arrays_10array_tree_Summary *p = (struct __pyx_obj_2bx_6arrays_10array_tree_Summary *)o;
- if (p->counts) {
- e = (*v)(p->counts, a); if (e) return e;
- }
- if (p->frequencies) {
- e = (*v)(p->frequencies, a); if (e) return e;
- }
- if (p->mins) {
- e = (*v)(p->mins, a); if (e) return e;
- }
- if (p->maxs) {
- e = (*v)(p->maxs, a); if (e) return e;
- }
- if (p->sums) {
- e = (*v)(p->sums, a); if (e) return e;
- }
- if (p->sumsquares) {
- e = (*v)(p->sumsquares, a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_2bx_6arrays_10array_tree_Summary(PyObject *o) {
- struct __pyx_obj_2bx_6arrays_10array_tree_Summary *p = (struct __pyx_obj_2bx_6arrays_10array_tree_Summary *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->counts);
- p->counts = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->frequencies);
- p->frequencies = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->mins);
- p->mins = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->maxs);
- p->maxs = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->sums);
- p->sums = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->sumsquares);
- p->sumsquares = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_7Summary_counts(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_6counts_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_7Summary_counts(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_6counts_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_6counts_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_7Summary_frequencies(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_11frequencies_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_7Summary_frequencies(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_11frequencies_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_11frequencies_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_7Summary_mins(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_4mins_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_7Summary_mins(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_4mins_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_4mins_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_7Summary_maxs(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_4maxs_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_7Summary_maxs(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_4maxs_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_4maxs_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_7Summary_sums(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_4sums_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_7Summary_sums(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_4sums_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_4sums_5__del__(o);
- }
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-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_7Summary_sumsquares(PyObject *o, CYTHON_UNUSED void *x) {
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-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_7Summary_sumsquares(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_10sumsquares_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_6arrays_10array_tree_7Summary_10sumsquares_5__del__(o);
- }
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-static PyMethodDef __pyx_methods_2bx_6arrays_10array_tree_Summary[] = {
- {0, 0, 0, 0}
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-
-static struct PyGetSetDef __pyx_getsets_2bx_6arrays_10array_tree_Summary[] = {
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- {(char *)"mins", __pyx_getprop_2bx_6arrays_10array_tree_7Summary_mins, __pyx_setprop_2bx_6arrays_10array_tree_7Summary_mins, 0, 0},
- {(char *)"maxs", __pyx_getprop_2bx_6arrays_10array_tree_7Summary_maxs, __pyx_setprop_2bx_6arrays_10array_tree_7Summary_maxs, 0, 0},
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- {0, 0, 0, 0, 0}
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-
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-static PyBufferProcs __pyx_tp_as_buffer_Summary = {
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- 0, /*bf_releasebuffer*/
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-static PyTypeObject __pyx_type_2bx_6arrays_10array_tree_Summary = {
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- __Pyx_NAMESTR("bx.arrays.array_tree.Summary"), /*tp_name*/
- sizeof(struct __pyx_obj_2bx_6arrays_10array_tree_Summary), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_2bx_6arrays_10array_tree_Summary, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_Summary, /*tp_as_number*/
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- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_Summary, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("\n Summary for a non-leaf level of the tree, contains arrays of the min, max,\n valid count, sum, and sum-of-squares for each child.\n "), /*tp_doc*/
- __pyx_tp_traverse_2bx_6arrays_10array_tree_Summary, /*tp_traverse*/
- __pyx_tp_clear_2bx_6arrays_10array_tree_Summary, /*tp_clear*/
- 0, /*tp_richcompare*/
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- 0, /*tp_iternext*/
- __pyx_methods_2bx_6arrays_10array_tree_Summary, /*tp_methods*/
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- __pyx_getsets_2bx_6arrays_10array_tree_Summary, /*tp_getset*/
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- __pyx_tp_new_2bx_6arrays_10array_tree_Summary, /*tp_new*/
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- 0, /*tp_weaklist*/
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- 0, /*tp_version_tag*/
- #endif
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-
-static PyObject *__pyx_tp_new_2bx_6arrays_10array_tree_ArrayTreeNode(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
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- if (!o) return 0;
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- return o;
-}
-
-static void __pyx_tp_dealloc_2bx_6arrays_10array_tree_ArrayTreeNode(PyObject *o) {
- struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *p = (struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *)o;
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- Py_CLEAR(p->tree);
- Py_CLEAR(p->children);
- Py_CLEAR(p->summary);
- PyObject_GC_Track(o);
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-}
-
-static int __pyx_tp_traverse_2bx_6arrays_10array_tree_ArrayTreeNode(PyObject *o, visitproc v, void *a) {
- int e;
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- }
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- }
- return 0;
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-
-static int __pyx_tp_clear_2bx_6arrays_10array_tree_ArrayTreeNode(PyObject *o) {
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- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_13ArrayTreeNode_summary(PyObject *o, CYTHON_UNUSED void *x) {
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-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_13ArrayTreeNode_summary(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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- }
- else {
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- }
-}
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-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_13ArrayTreeNode_start_offset(PyObject *o, CYTHON_UNUSED void *x) {
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-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_13ArrayTreeNode_start_offset(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
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-static PyMethodDef __pyx_methods_2bx_6arrays_10array_tree_ArrayTreeNode[] = {
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- {__Pyx_NAMESTR("get"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeNode_5get, METH_O, __Pyx_DOCSTR(0)},
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-static PyBufferProcs __pyx_tp_as_buffer_ArrayTreeNode = {
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- 0, /*bf_getwritebuffer*/
- #endif
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- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
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- #if PY_VERSION_HEX >= 0x02060000
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- #endif
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- 0, /*bf_releasebuffer*/
- #endif
-};
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-static PyTypeObject __pyx_type_2bx_6arrays_10array_tree_ArrayTreeNode = {
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- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_2bx_6arrays_10array_tree_ArrayTreeNode, /*tp_dealloc*/
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- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_ArrayTreeNode, /*tp_as_number*/
- &__pyx_tp_as_sequence_ArrayTreeNode, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_ArrayTreeNode, /*tp_as_mapping*/
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- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_ArrayTreeNode, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("\n Internal node of an ArrayTree. Contains summary data and pointers to\n subtrees.\n "), /*tp_doc*/
- __pyx_tp_traverse_2bx_6arrays_10array_tree_ArrayTreeNode, /*tp_traverse*/
- __pyx_tp_clear_2bx_6arrays_10array_tree_ArrayTreeNode, /*tp_clear*/
- 0, /*tp_richcompare*/
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- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_2bx_6arrays_10array_tree_ArrayTreeNode, /*tp_methods*/
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- __pyx_getsets_2bx_6arrays_10array_tree_ArrayTreeNode, /*tp_getset*/
- 0, /*tp_base*/
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- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeNode_1__init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_2bx_6arrays_10array_tree_ArrayTreeNode, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
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- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
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- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-
-static PyObject *__pyx_tp_new_2bx_6arrays_10array_tree_ArrayTreeLeaf(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *)o);
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- p->values = ((PyArrayObject *)Py_None); Py_INCREF(Py_None);
- return o;
-}
-
-static void __pyx_tp_dealloc_2bx_6arrays_10array_tree_ArrayTreeLeaf(PyObject *o) {
- struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *p = (struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->tree);
- Py_CLEAR(p->values);
- PyObject_GC_Track(o);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_2bx_6arrays_10array_tree_ArrayTreeLeaf(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *p = (struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *)o;
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- }
- if (p->values) {
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- }
- return 0;
-}
-
-static int __pyx_tp_clear_2bx_6arrays_10array_tree_ArrayTreeLeaf(PyObject *o) {
- struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *p = (struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf *)o;
- PyObject* tmp;
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- Py_XDECREF(tmp);
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- Py_XDECREF(tmp);
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-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_frequency(PyObject *o, CYTHON_UNUSED void *x) {
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-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_frequency(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
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- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
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- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_values(PyObject *o, CYTHON_UNUSED void *x) {
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-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_values(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeLeaf_6values_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeLeaf_6values_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_start_offset(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeLeaf_12start_offset_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_start_offset(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeLeaf_12start_offset_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyMethodDef __pyx_methods_2bx_6arrays_10array_tree_ArrayTreeLeaf[] = {
- {__Pyx_NAMESTR("set"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeLeaf_3set, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("get"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeLeaf_5get, METH_O, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("to_file_data_pass"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeLeaf_7to_file_data_pass, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("to_file_offset_pass"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeLeaf_9to_file_offset_pass, METH_O, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("from_file"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeLeaf_11from_file, METH_O, __Pyx_DOCSTR(0)},
- {0, 0, 0, 0}
-};
-
-static struct PyGetSetDef __pyx_getsets_2bx_6arrays_10array_tree_ArrayTreeLeaf[] = {
- {(char *)"frequency", __pyx_getprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_frequency, __pyx_setprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_frequency, 0, 0},
- {(char *)"values", __pyx_getprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_values, __pyx_setprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_values, 0, 0},
- {(char *)"start_offset", __pyx_getprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_start_offset, __pyx_setprop_2bx_6arrays_10array_tree_13ArrayTreeLeaf_start_offset, 0, 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_ArrayTreeLeaf = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_ArrayTreeLeaf = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping_ArrayTreeLeaf = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_ArrayTreeLeaf = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-static PyTypeObject __pyx_type_2bx_6arrays_10array_tree_ArrayTreeLeaf = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("bx.arrays.array_tree.ArrayTreeLeaf"), /*tp_name*/
- sizeof(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeLeaf), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_2bx_6arrays_10array_tree_ArrayTreeLeaf, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_ArrayTreeLeaf, /*tp_as_number*/
- &__pyx_tp_as_sequence_ArrayTreeLeaf, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_ArrayTreeLeaf, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_ArrayTreeLeaf, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("\n Leaf node of an ArrayTree, contains data values.\n "), /*tp_doc*/
- __pyx_tp_traverse_2bx_6arrays_10array_tree_ArrayTreeLeaf, /*tp_traverse*/
- __pyx_tp_clear_2bx_6arrays_10array_tree_ArrayTreeLeaf, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_2bx_6arrays_10array_tree_ArrayTreeLeaf, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_2bx_6arrays_10array_tree_ArrayTreeLeaf, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pw_2bx_6arrays_10array_tree_13ArrayTreeLeaf_1__init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_2bx_6arrays_10array_tree_ArrayTreeLeaf, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-
-static PyObject *__pyx_tp_new_2bx_6arrays_10array_tree_ArrayTree(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *)o);
- p->dtype = Py_None; Py_INCREF(Py_None);
- p->root = ((struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *)Py_None); Py_INCREF(Py_None);
- return o;
-}
-
-static void __pyx_tp_dealloc_2bx_6arrays_10array_tree_ArrayTree(PyObject *o) {
- struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *p = (struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->dtype);
- Py_CLEAR(p->root);
- PyObject_GC_Track(o);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_2bx_6arrays_10array_tree_ArrayTree(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *p = (struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *)o;
- if (p->dtype) {
- e = (*v)(p->dtype, a); if (e) return e;
- }
- if (p->root) {
- e = (*v)(((PyObject*)p->root), a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_2bx_6arrays_10array_tree_ArrayTree(PyObject *o) {
- struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *p = (struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->dtype);
- p->dtype = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->root);
- p->root = ((struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTreeNode *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *__pyx_sq_item_2bx_6arrays_10array_tree_ArrayTree(PyObject *o, Py_ssize_t i) {
- PyObject *r;
- PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
- r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
- Py_DECREF(x);
- return r;
-}
-
-static int __pyx_mp_ass_subscript_2bx_6arrays_10array_tree_ArrayTree(PyObject *o, PyObject *i, PyObject *v) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_3__setitem__(o, i, v);
- }
- else {
- PyErr_Format(PyExc_NotImplementedError,
- "Subscript deletion not supported by %s", Py_TYPE(o)->tp_name);
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_max(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_3max_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_max(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_3max_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_block_size(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_10block_size_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_block_size(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_10block_size_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_dtype(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_5dtype_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_dtype(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_5dtype_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_5dtype_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_levels(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_6levels_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_levels(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_6levels_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_no_leaves(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_9no_leaves_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_no_leaves(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_9no_leaves_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_root(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_4root_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_root(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_4root_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_4root_5__del__(o);
- }
-}
-
-static PyMethodDef __pyx_methods_2bx_6arrays_10array_tree_ArrayTree[] = {
- {__Pyx_NAMESTR("set_range"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_5set_range, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("to_file"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_9to_file, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("from_file"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_11from_file, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("from_sequence"), (PyCFunction)__pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_13from_sequence, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_6arrays_10array_tree_9ArrayTree_12from_sequence)},
- {0, 0, 0, 0}
-};
-
-static struct PyGetSetDef __pyx_getsets_2bx_6arrays_10array_tree_ArrayTree[] = {
- {(char *)"max", __pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_max, __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_max, 0, 0},
- {(char *)"block_size", __pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_block_size, __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_block_size, 0, 0},
- {(char *)"dtype", __pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_dtype, __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_dtype, 0, 0},
- {(char *)"levels", __pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_levels, __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_levels, 0, 0},
- {(char *)"no_leaves", __pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_no_leaves, __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_no_leaves, 0, 0},
- {(char *)"root", __pyx_getprop_2bx_6arrays_10array_tree_9ArrayTree_root, __pyx_setprop_2bx_6arrays_10array_tree_9ArrayTree_root, 0, 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_ArrayTree = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_ArrayTree = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- __pyx_sq_item_2bx_6arrays_10array_tree_ArrayTree, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping_ArrayTree = {
- 0, /*mp_length*/
- __pyx_pw_2bx_6arrays_10array_tree_9ArrayTree_7__getitem__, /*mp_subscript*/
- __pyx_mp_ass_subscript_2bx_6arrays_10array_tree_ArrayTree, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_ArrayTree = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-static PyTypeObject __pyx_type_2bx_6arrays_10array_tree_ArrayTree = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("bx.arrays.array_tree.ArrayTree"), /*tp_name*/
- sizeof(struct __pyx_obj_2bx_6arrays_10array_tree_ArrayTree), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_2bx_6arrays_10array_tree_ArrayTree, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_ArrayTree, /*tp_as_number*/
- &__pyx_tp_as_sequence_ArrayTree, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_ArrayTree, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_ArrayTree, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("\n Stores a sparse array of data as a tree.\n \n An array of `self.max` values is stored in a tree in which each leaf\n contains `self.block_size` values and each internal node contains\n `self.block_size` children.\n \n Entirely empty subtrees are not stored. Thus, the storage is efficient for\n data that is block sparse -- having contiguous chunks of `self.block_size` or\n larger data. Currently it is not efficient if the data is strided (e.g. [...]
- __pyx_tp_traverse_2bx_6arrays_10array_tree_ArrayTree, /*tp_traverse*/
- __pyx_tp_clear_2bx_6arrays_10array_tree_ArrayTree, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
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- PyType_Modified(__pyx_ptype_2bx_6arrays_10array_tree_ArrayTree);
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- /* "bx/arrays/array_tree.pyx":1
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- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
-
- /* "numpy.pxd":975
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- goto __pyx_L0;
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- if (__pyx_m) {
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-static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
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- if (dict != __pyx_b) {
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- result = PyObject_GetAttr(__pyx_b, name);
- }
- if (!result) {
- PyErr_SetObject(PyExc_NameError, name);
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- }
- return result;
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-
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *more_or_less;
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
- num_expected = num_max;
- more_or_less = "at most";
- }
- if (exact) {
- more_or_less = "exactly";
- }
- PyErr_Format(PyExc_TypeError,
- "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
- func_name, more_or_less, num_expected,
- (num_expected == 1) ? "" : "s", num_found);
-}
-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- continue;
- }
- name = first_kw_arg;
- #if PY_MAJOR_VERSION < 3
- if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
- while (*name) {
- if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
- && _PyString_Eq(**name, key)) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- if ((**argname == key) || (
- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
- }
- argname++;
- }
- }
- } else
- #endif
- if (likely(PyUnicode_Check(key))) {
- while (*name) {
- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**name, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) goto arg_passed_twice;
- argname++;
- }
- }
- } else
- goto invalid_keyword_type;
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
- }
- }
- return 0;
-arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* exc_type = tstate->curexc_type;
- if (unlikely(exc_type)) {
- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#endif
-}
-
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-}
-
-static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) {
- if (t == Py_None) {
- __Pyx_RaiseNoneNotIterableError();
- } else if (PyTuple_GET_SIZE(t) < index) {
- __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t));
- } else {
- __Pyx_RaiseTooManyValuesError(index);
- }
-}
-
-static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2,
- int is_tuple, int has_known_size, int decref_tuple) {
- Py_ssize_t index;
- PyObject *value1 = NULL, *value2 = NULL, *iter = NULL;
- if (!is_tuple && unlikely(!PyTuple_Check(tuple))) {
- iternextfunc iternext;
- iter = PyObject_GetIter(tuple);
- if (unlikely(!iter)) goto bad;
- if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; }
- iternext = Py_TYPE(iter)->tp_iternext;
- value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; }
- value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; }
- if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad;
- Py_DECREF(iter);
- } else {
- if (!has_known_size && unlikely(PyTuple_GET_SIZE(tuple) != 2)) {
- __Pyx_UnpackTupleError(tuple, 2);
- goto bad;
- }
-#if CYTHON_COMPILING_IN_PYPY
- value1 = PySequence_ITEM(tuple, 0);
- if (unlikely(!value1)) goto bad;
- value2 = PySequence_ITEM(tuple, 1);
- if (unlikely(!value2)) goto bad;
-#else
- value1 = PyTuple_GET_ITEM(tuple, 0);
- value2 = PyTuple_GET_ITEM(tuple, 1);
- Py_INCREF(value1);
- Py_INCREF(value2);
-#endif
- if (decref_tuple) { Py_DECREF(tuple); }
- }
- *pvalue1 = value1;
- *pvalue2 = value2;
- return 0;
-unpacking_failed:
- if (!has_known_size && __Pyx_IterFinish() == 0)
- __Pyx_RaiseNeedMoreValuesError(index);
-bad:
- Py_XDECREF(iter);
- Py_XDECREF(value1);
- Py_XDECREF(value2);
- if (decref_tuple) { Py_XDECREF(tuple); }
- return -1;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name,
- Py_ssize_t* p_orig_length, int* p_source_is_dict) {
- is_dict = is_dict || likely(PyDict_CheckExact(iterable));
- *p_source_is_dict = is_dict;
-#if !CYTHON_COMPILING_IN_PYPY
- if (is_dict) {
- *p_orig_length = PyDict_Size(iterable);
- Py_INCREF(iterable);
- return iterable;
- }
-#endif
- *p_orig_length = 0;
- if (method_name) {
- PyObject* iter;
- iterable = PyObject_CallMethodObjArgs(iterable, method_name, NULL);
- if (!iterable)
- return NULL;
-#if !CYTHON_COMPILING_IN_PYPY
- if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable))
- return iterable;
-#endif
- iter = PyObject_GetIter(iterable);
- Py_DECREF(iterable);
- return iter;
- }
- return PyObject_GetIter(iterable);
-}
-static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t orig_length, Py_ssize_t* ppos,
- PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) {
- PyObject* next_item;
-#if !CYTHON_COMPILING_IN_PYPY
- if (source_is_dict) {
- PyObject *key, *value;
- if (unlikely(orig_length != PyDict_Size(iter_obj))) {
- PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration");
- return -1;
- }
- if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) {
- return 0;
- }
- if (pitem) {
- PyObject* tuple = PyTuple_New(2);
- if (unlikely(!tuple)) {
- return -1;
- }
- Py_INCREF(key);
- Py_INCREF(value);
- PyTuple_SET_ITEM(tuple, 0, key);
- PyTuple_SET_ITEM(tuple, 1, value);
- *pitem = tuple;
- } else {
- if (pkey) {
- Py_INCREF(key);
- *pkey = key;
- }
- if (pvalue) {
- Py_INCREF(value);
- *pvalue = value;
- }
- }
- return 1;
- } else if (PyTuple_CheckExact(iter_obj)) {
- Py_ssize_t pos = *ppos;
- if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0;
- *ppos = pos + 1;
- next_item = PyTuple_GET_ITEM(iter_obj, pos);
- Py_INCREF(next_item);
- } else if (PyList_CheckExact(iter_obj)) {
- Py_ssize_t pos = *ppos;
- if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0;
- *ppos = pos + 1;
- next_item = PyList_GET_ITEM(iter_obj, pos);
- Py_INCREF(next_item);
- } else
-#endif
- {
- next_item = PyIter_Next(iter_obj);
- if (unlikely(!next_item)) {
- return __Pyx_IterFinish();
- }
- }
- if (pitem) {
- *pitem = next_item;
- } else if (pkey && pvalue) {
- if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1))
- return -1;
- } else if (pkey) {
- *pkey = next_item;
- } else {
- *pvalue = next_item;
- }
- return 1;
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
-}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
- Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- }
- #if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
- if (cause && cause != Py_None) {
- PyObject *fixed_cause;
- if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- }
- else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- }
- else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static CYTHON_INLINE int __Pyx_div_int(int a, int b) {
- int q = a / b;
- int r = a - q*b;
- q -= ((r != 0) & ((r ^ b) < 0));
- return q;
-}
-
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
- if (unlikely(!type)) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (likely(PyObject_TypeCheck(obj, type)))
- return 1;
- PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
- Py_TYPE(obj)->tp_name, type->tp_name);
- return 0;
-}
-
-static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
- const char *name, int exact)
-{
- if (!type) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (none_allowed && obj == Py_None) return 1;
- else if (exact) {
- if (Py_TYPE(obj) == type) return 1;
- }
- else {
- if (PyObject_TypeCheck(obj, type)) return 1;
- }
- PyErr_Format(PyExc_TypeError,
- "Argument '%s' has incorrect type (expected %s, got %s)",
- name, type->tp_name, Py_TYPE(obj)->tp_name);
- return 0;
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import = 0;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
-#if PY_MAJOR_VERSION < 3
- PyErr_Format(PyExc_ImportError, "cannot import name %.230s",
- PyString_AsString(name));
-#else
- PyErr_Format(PyExc_ImportError, "cannot import name %S", name);
-#endif
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_pow_PY_LONG_LONG(PY_LONG_LONG b, PY_LONG_LONG e) {
- PY_LONG_LONG t = b;
- switch (e) {
- case 3:
- t *= b;
- case 2:
- t *= b;
- case 1:
- return t;
- case 0:
- return 1;
- }
- #if 1
- if (unlikely(e<0)) return 0;
- #endif
- t = 1;
- while (likely(e)) {
- t *= (b * (e&1)) | ((~e)&1); /* 1 or b */
- b *= b;
- e >>= 1;
- }
- return t;
-}
-
-static CYTHON_INLINE int __Pyx_pow_int(int b, int e) {
- int t = b;
- switch (e) {
- case 3:
- t *= b;
- case 2:
- t *= b;
- case 1:
- return t;
- case 0:
- return 1;
- }
- #if 1
- if (unlikely(e<0)) return 0;
- #endif
- t = 1;
- while (likely(e)) {
- t *= (b * (e&1)) | ((~e)&1); /* 1 or b */
- b *= b;
- e >>= 1;
- }
- return t;
-}
-
-static PyObject* __Pyx_Method_ClassMethod(PyObject *method) {
-#if CYTHON_COMPILING_IN_PYPY
- if (PyObject_TypeCheck(method, &PyWrapperDescr_Type)) { /* cdef classes */
- return PyClassMethod_New(method);
- }
-#else
- static PyTypeObject *methoddescr_type = NULL;
- if (methoddescr_type == NULL) {
- PyObject *meth = __Pyx_GetAttrString((PyObject*)&PyList_Type, "append");
- if (!meth) return NULL;
- methoddescr_type = Py_TYPE(meth);
- Py_DECREF(meth);
- }
- if (PyObject_TypeCheck(method, methoddescr_type)) { /* cdef classes */
- PyMethodDescrObject *descr = (PyMethodDescrObject *)method;
- #if PY_VERSION_HEX < 0x03020000
- PyTypeObject *d_type = descr->d_type;
- #else
- PyTypeObject *d_type = descr->d_common.d_type;
- #endif
- return PyDescr_NewClassMethod(d_type, descr->d_method);
- }
-#endif
- else if (PyMethod_Check(method)) { /* python classes */
- return PyClassMethod_New(PyMethod_GET_FUNCTION(method));
- }
- else if (PyCFunction_Check(method)) {
- return PyClassMethod_New(method);
- }
-#ifdef __Pyx_CyFunction_USED
- else if (PyObject_TypeCheck(method, __pyx_CyFunctionType)) {
- return PyClassMethod_New(method);
- }
-#endif
- PyErr_Format(PyExc_TypeError,
- "Class-level classmethod() can only be called on "
- "a method_descriptor or instance method.");
- return NULL;
-}
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return ::std::complex< float >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return x + y*(__pyx_t_float_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- __pyx_t_float_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrtf(z.real*z.real + z.imag*z.imag);
- #else
- return hypotf(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- float denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(a, a);
- case 3:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, a);
- case 4:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- }
- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_absf(a);
- theta = atan2f(a.imag, a.real);
- }
- lnr = logf(r);
- z_r = expf(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cosf(z_theta);
- z.imag = z_r * sinf(z_theta);
- return z;
- }
- #endif
-#endif
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return ::std::complex< double >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return x + y*(__pyx_t_double_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- __pyx_t_double_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrt(z.real*z.real + z.imag*z.imag);
- #else
- return hypot(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- double denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(a, a);
- case 3:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, a);
- case 4:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- }
- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_abs(a);
- theta = atan2(a.imag, a.real);
- }
- lnr = log(r);
- z_r = exp(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cos(z_theta);
- z.imag = z_r * sin(z_theta);
- return z;
- }
- #endif
-#endif
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
- CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) {
- PyObject *old_exc, *old_val, *old_tb;
- PyObject *ctx;
- __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
- #if PY_MAJOR_VERSION < 3
- ctx = PyString_FromString(name);
- #else
- ctx = PyUnicode_FromString(name);
- #endif
- __Pyx_ErrRestore(old_exc, old_val, old_tb);
- if (!ctx) {
- PyErr_WriteUnraisable(Py_None);
- } else {
- PyErr_WriteUnraisable(ctx);
- Py_DECREF(ctx);
- }
-}
-
-static CYTHON_INLINE int __Pyx_StrEq(const char *s1, const char *s2) {
- while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
- return *s1 == *s2;
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
-#ifndef __PYX_HAVE_RT_ImportType
-#define __PYX_HAVE_RT_ImportType
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%s.%s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%s.%s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/arrays/bed.c b/lib/bx/arrays/bed.c
deleted file mode 100644
index 8695f48..0000000
--- a/lib/bx/arrays/bed.c
+++ /dev/null
@@ -1,2584 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
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- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
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- if (unlikely(tstate->curexc_type))
-#else
- if (unlikely(PyErr_Occurred()))
-#endif
- goto bad;
- #if PY_MAJOR_VERSION >= 3
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
- goto bad;
- #endif
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- /* Make sure tstate is in a consistent state when we XDECREF
- these objects (DECREF may run arbitrary code). */
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(local_type, local_value, local_tb);
-#endif
- return 0;
-bad:
- *type = 0;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
-}
-
-static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->exc_type;
- *value = tstate->exc_value;
- *tb = tstate->exc_traceback;
- Py_XINCREF(*type);
- Py_XINCREF(*value);
- Py_XINCREF(*tb);
-#else
- PyErr_GetExcInfo(type, value, tb);
-#endif
-}
-static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = type;
- tstate->exc_value = value;
- tstate->exc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
-}
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/bbi/bbi_file.c b/lib/bx/bbi/bbi_file.c
deleted file mode 100644
index fe3f17b..0000000
--- a/lib/bx/bbi/bbi_file.c
+++ /dev/null
@@ -1,15020 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
- #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define Py_TPFLAGS_CHECKTYPES 0
- #define Py_TPFLAGS_HAVE_INDEX 0
-#endif
-#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBaseString_Type PyUnicode_Type
- #define PyStringObject PyUnicodeObject
- #define PyString_Type PyUnicode_Type
- #define PyString_Check PyUnicode_Check
- #define PyString_CheckExact PyUnicode_CheckExact
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PyBytesObject PyStringObject
- #define PyBytes_Type PyString_Type
- #define PyBytes_Check PyString_Check
- #define PyBytes_CheckExact PyString_CheckExact
- #define PyBytes_FromString PyString_FromString
- #define PyBytes_FromStringAndSize PyString_FromStringAndSize
- #define PyBytes_FromFormat PyString_FromFormat
- #define PyBytes_DecodeEscape PyString_DecodeEscape
- #define PyBytes_AsString PyString_AsString
- #define PyBytes_AsStringAndSize PyString_AsStringAndSize
- #define PyBytes_Size PyString_Size
- #define PyBytes_AS_STRING PyString_AS_STRING
- #define PyBytes_GET_SIZE PyString_GET_SIZE
- #define PyBytes_Repr PyString_Repr
- #define PyBytes_Concat PyString_Concat
- #define PyBytes_ConcatAndDel PyString_ConcatAndDel
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-#if PY_VERSION_HEX < 0x02060000
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- #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
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-#endif
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- #define PyIntObject PyLongObject
- #define PyInt_Type PyLong_Type
- #define PyInt_Check(op) PyLong_Check(op)
- #define PyInt_CheckExact(op) PyLong_CheckExact(op)
- #define PyInt_FromString PyLong_FromString
- #define PyInt_FromUnicode PyLong_FromUnicode
- #define PyInt_FromLong PyLong_FromLong
- #define PyInt_FromSize_t PyLong_FromSize_t
- #define PyInt_FromSsize_t PyLong_FromSsize_t
- #define PyInt_AsLong PyLong_AsLong
- #define PyInt_AS_LONG PyLong_AS_LONG
- #define PyInt_AsSsize_t PyLong_AsSsize_t
- #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
- #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
-#endif
-#if PY_VERSION_HEX < 0x03020000
- typedef long Py_hash_t;
- #define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
-#else
- #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
- #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
-#endif
-#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
- #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
- #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
-#else
- #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
- #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
-#endif
-#if PY_VERSION_HEX < 0x02050000
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
- #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
-#else
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
- #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
-#endif
-#if PY_VERSION_HEX < 0x02050000
- #define __Pyx_NAMESTR(n) ((char *)(n))
- #define __Pyx_DOCSTR(n) ((char *)(n))
-#else
- #define __Pyx_NAMESTR(n) (n)
- #define __Pyx_DOCSTR(n) (n)
-#endif
-
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
-#ifndef __PYX_EXTERN_C
- #ifdef __cplusplus
- #define __PYX_EXTERN_C extern "C"
- #else
- #define __PYX_EXTERN_C extern
- #endif
-#endif
-
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
-#define __PYX_HAVE__bx__bbi__bbi_file
-#define __PYX_HAVE_API__bx__bbi__bbi_file
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "numpy/arrayobject.h"
-#include "numpy/ufuncobject.h"
-#include "limits.h"
-#ifdef _OPENMP
-#include <omp.h>
-#endif /* _OPENMP */
-
-#ifdef PYREX_WITHOUT_ASSERTIONS
-#define CYTHON_WITHOUT_ASSERTIONS
-#endif
-
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
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- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
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-# define CYTHON_UNUSED
-# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
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-# define CYTHON_UNUSED
-# endif
-#endif
-typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
-#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-#if CYTHON_COMPILING_IN_CPYTHON
-#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#else
-#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
-#endif
-#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
-
-
-#ifdef __GNUC__
- /* Test for GCC > 2.95 */
- #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
- #else /* __GNUC__ > 2 ... */
- #define likely(x) (x)
- #define unlikely(x) (x)
- #endif /* __GNUC__ > 2 ... */
-#else /* __GNUC__ */
- #define likely(x) (x)
- #define unlikely(x) (x)
-#endif /* __GNUC__ */
-
-static PyObject *__pyx_m;
-static PyObject *__pyx_b;
-static PyObject *__pyx_empty_tuple;
-static PyObject *__pyx_empty_bytes;
-static int __pyx_lineno;
-static int __pyx_clineno = 0;
-static const char * __pyx_cfilenm= __FILE__;
-static const char *__pyx_filename;
-
-#if !defined(CYTHON_CCOMPLEX)
- #if defined(__cplusplus)
- #define CYTHON_CCOMPLEX 1
- #elif defined(_Complex_I)
- #define CYTHON_CCOMPLEX 1
- #else
- #define CYTHON_CCOMPLEX 0
- #endif
-#endif
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- #include <complex>
- #else
- #include <complex.h>
- #endif
-#endif
-#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__)
- #undef _Complex_I
- #define _Complex_I 1.0fj
-#endif
-
-
-static const char *__pyx_f[] = {
- "bbi_file.pyx",
- "bbi_file.pxd",
- "numpy.pxd",
- "bpt_file.pxd",
- "cirtree_file.pxd",
- "type.pxd",
-};
-#define IS_UNSIGNED(type) (((type) -1) > 0)
-struct __Pyx_StructField_;
-#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0)
-typedef struct {
- const char* name; /* for error messages only */
- struct __Pyx_StructField_* fields;
- size_t size; /* sizeof(type) */
- size_t arraysize[8]; /* length of array in each dimension */
- int ndim;
- char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject, c_H_ar */
- char is_unsigned;
- int flags;
-} __Pyx_TypeInfo;
-typedef struct __Pyx_StructField_ {
- __Pyx_TypeInfo* type;
- const char* name;
- size_t offset;
-} __Pyx_StructField;
-typedef struct {
- __Pyx_StructField* field;
- size_t parent_offset;
-} __Pyx_BufFmt_StackElem;
-typedef struct {
- __Pyx_StructField root;
- __Pyx_BufFmt_StackElem* head;
- size_t fmt_offset;
- size_t new_count, enc_count;
- size_t struct_alignment;
- int is_complex;
- char enc_type;
- char new_packmode;
- char enc_packmode;
- char is_valid_array;
-} __Pyx_BufFmt_Context;
-
-
-/* "types.pxd":1
- * ctypedef unsigned char UBYTE # <<<<<<<<<<<<<<
- * ctypedef signed char BYTE
- * ctypedef unsigned short UWORD
- */
-typedef unsigned char __pyx_t_2bx_3bbi_5types_UBYTE;
-
-/* "types.pxd":2
- * ctypedef unsigned char UBYTE
- * ctypedef signed char BYTE # <<<<<<<<<<<<<<
- * ctypedef unsigned short UWORD
- * ctypedef short WORD
- */
-typedef signed char __pyx_t_2bx_3bbi_5types_BYTE;
-
-/* "types.pxd":3
- * ctypedef unsigned char UBYTE
- * ctypedef signed char BYTE
- * ctypedef unsigned short UWORD # <<<<<<<<<<<<<<
- * ctypedef short WORD
- * ctypedef unsigned long long bits64
- */
-typedef unsigned short __pyx_t_2bx_3bbi_5types_UWORD;
-
-/* "types.pxd":4
- * ctypedef signed char BYTE
- * ctypedef unsigned short UWORD
- * ctypedef short WORD # <<<<<<<<<<<<<<
- * ctypedef unsigned long long bits64
- * ctypedef unsigned bits32
- */
-typedef short __pyx_t_2bx_3bbi_5types_WORD;
-
-/* "types.pxd":5
- * ctypedef unsigned short UWORD
- * ctypedef short WORD
- * ctypedef unsigned long long bits64 # <<<<<<<<<<<<<<
- * ctypedef unsigned bits32
- * ctypedef unsigned short bits16
- */
-typedef unsigned PY_LONG_LONG __pyx_t_2bx_3bbi_5types_bits64;
-
-/* "types.pxd":6
- * ctypedef short WORD
- * ctypedef unsigned long long bits64
- * ctypedef unsigned bits32 # <<<<<<<<<<<<<<
- * ctypedef unsigned short bits16
- * ctypedef unsigned char bits8
- */
-typedef unsigned int __pyx_t_2bx_3bbi_5types_bits32;
-
-/* "types.pxd":7
- * ctypedef unsigned long long bits64
- * ctypedef unsigned bits32
- * ctypedef unsigned short bits16 # <<<<<<<<<<<<<<
- * ctypedef unsigned char bits8
- * ctypedef int signed32
- */
-typedef unsigned short __pyx_t_2bx_3bbi_5types_bits16;
-
-/* "types.pxd":8
- * ctypedef unsigned bits32
- * ctypedef unsigned short bits16
- * ctypedef unsigned char bits8 # <<<<<<<<<<<<<<
- * ctypedef int signed32
- *
- */
-typedef unsigned char __pyx_t_2bx_3bbi_5types_bits8;
-
-/* "types.pxd":9
- * ctypedef unsigned short bits16
- * ctypedef unsigned char bits8
- * ctypedef int signed32 # <<<<<<<<<<<<<<
- *
- * ctypedef bint boolean
- */
-typedef int __pyx_t_2bx_3bbi_5types_signed32;
-
-/* "types.pxd":11
- * ctypedef int signed32
- *
- * ctypedef bint boolean # <<<<<<<<<<<<<<
- *
- */
-typedef int __pyx_t_2bx_3bbi_5types_boolean;
-
-/* "numpy.pxd":723
- * # in Cython to enable them only on the right systems.
- *
- * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t
- */
-typedef npy_int8 __pyx_t_5numpy_int8_t;
-
-/* "numpy.pxd":724
- *
- * ctypedef npy_int8 int8_t
- * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
- * ctypedef npy_int32 int32_t
- * ctypedef npy_int64 int64_t
- */
-typedef npy_int16 __pyx_t_5numpy_int16_t;
-
-/* "numpy.pxd":725
- * ctypedef npy_int8 int8_t
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
- * ctypedef npy_int64 int64_t
- * #ctypedef npy_int96 int96_t
- */
-typedef npy_int32 __pyx_t_5numpy_int32_t;
-
-/* "numpy.pxd":726
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t
- * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_int96 int96_t
- * #ctypedef npy_int128 int128_t
- */
-typedef npy_int64 __pyx_t_5numpy_int64_t;
-
-/* "numpy.pxd":730
- * #ctypedef npy_int128 int128_t
- *
- * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t
- */
-typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-
-/* "numpy.pxd":731
- *
- * ctypedef npy_uint8 uint8_t
- * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint32 uint32_t
- * ctypedef npy_uint64 uint64_t
- */
-typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-
-/* "numpy.pxd":732
- * ctypedef npy_uint8 uint8_t
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint64 uint64_t
- * #ctypedef npy_uint96 uint96_t
- */
-typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-
-/* "numpy.pxd":733
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t
- * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_uint96 uint96_t
- * #ctypedef npy_uint128 uint128_t
- */
-typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-
-/* "numpy.pxd":737
- * #ctypedef npy_uint128 uint128_t
- *
- * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
- * ctypedef npy_float64 float64_t
- * #ctypedef npy_float80 float80_t
- */
-typedef npy_float32 __pyx_t_5numpy_float32_t;
-
-/* "numpy.pxd":738
- *
- * ctypedef npy_float32 float32_t
- * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_float80 float80_t
- * #ctypedef npy_float128 float128_t
- */
-typedef npy_float64 __pyx_t_5numpy_float64_t;
-
-/* "numpy.pxd":747
- * # The int types are mapped a bit surprising --
- * # numpy.int corresponds to 'l' and numpy.long to 'q'
- * ctypedef npy_long int_t # <<<<<<<<<<<<<<
- * ctypedef npy_longlong long_t
- * ctypedef npy_longlong longlong_t
- */
-typedef npy_long __pyx_t_5numpy_int_t;
-
-/* "numpy.pxd":748
- * # numpy.int corresponds to 'l' and numpy.long to 'q'
- * ctypedef npy_long int_t
- * ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
- * ctypedef npy_longlong longlong_t
- *
- */
-typedef npy_longlong __pyx_t_5numpy_long_t;
-
-/* "numpy.pxd":749
- * ctypedef npy_long int_t
- * ctypedef npy_longlong long_t
- * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_ulong uint_t
- */
-typedef npy_longlong __pyx_t_5numpy_longlong_t;
-
-/* "numpy.pxd":751
- * ctypedef npy_longlong longlong_t
- *
- * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
- * ctypedef npy_ulonglong ulong_t
- * ctypedef npy_ulonglong ulonglong_t
- */
-typedef npy_ulong __pyx_t_5numpy_uint_t;
-
-/* "numpy.pxd":752
- *
- * ctypedef npy_ulong uint_t
- * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
- * ctypedef npy_ulonglong ulonglong_t
- *
- */
-typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-
-/* "numpy.pxd":753
- * ctypedef npy_ulong uint_t
- * ctypedef npy_ulonglong ulong_t
- * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_intp intp_t
- */
-typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-
-/* "numpy.pxd":755
- * ctypedef npy_ulonglong ulonglong_t
- *
- * ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
- * ctypedef npy_uintp uintp_t
- *
- */
-typedef npy_intp __pyx_t_5numpy_intp_t;
-
-/* "numpy.pxd":756
- *
- * ctypedef npy_intp intp_t
- * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_double float_t
- */
-typedef npy_uintp __pyx_t_5numpy_uintp_t;
-
-/* "numpy.pxd":758
- * ctypedef npy_uintp uintp_t
- *
- * ctypedef npy_double float_t # <<<<<<<<<<<<<<
- * ctypedef npy_double double_t
- * ctypedef npy_longdouble longdouble_t
- */
-typedef npy_double __pyx_t_5numpy_float_t;
-
-/* "numpy.pxd":759
- *
- * ctypedef npy_double float_t
- * ctypedef npy_double double_t # <<<<<<<<<<<<<<
- * ctypedef npy_longdouble longdouble_t
- *
- */
-typedef npy_double __pyx_t_5numpy_double_t;
-
-/* "numpy.pxd":760
- * ctypedef npy_double float_t
- * ctypedef npy_double double_t
- * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_cfloat cfloat_t
- */
-typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- typedef ::std::complex< float > __pyx_t_float_complex;
- #else
- typedef float _Complex __pyx_t_float_complex;
- #endif
-#else
- typedef struct { float real, imag; } __pyx_t_float_complex;
-#endif
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- typedef ::std::complex< double > __pyx_t_double_complex;
- #else
- typedef double _Complex __pyx_t_double_complex;
- #endif
-#else
- typedef struct { double real, imag; } __pyx_t_double_complex;
-#endif
-
-
-/*--- Type declarations ---*/
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock;
-struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler;
-struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile;
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData;
-struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel;
-struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile;
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile;
-
-/* "numpy.pxd":762
- * ctypedef npy_longdouble longdouble_t
- *
- * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
- * ctypedef npy_cdouble cdouble_t
- * ctypedef npy_clongdouble clongdouble_t
- */
-typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-
-/* "numpy.pxd":763
- *
- * ctypedef npy_cfloat cfloat_t
- * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
- * ctypedef npy_clongdouble clongdouble_t
- *
- */
-typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-
-/* "numpy.pxd":764
- * ctypedef npy_cfloat cfloat_t
- * ctypedef npy_cdouble cdouble_t
- * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_cdouble complex_t
- */
-typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-
-/* "numpy.pxd":766
- * ctypedef npy_clongdouble clongdouble_t
- *
- * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
- *
- * cdef inline object PyArray_MultiIterNew1(a):
- */
-typedef npy_cdouble __pyx_t_5numpy_complex_t;
-
-/* "bx/bbi/bbi_file.pyx":43
- * cdef inline int imin(int a, int b): return a if a <= b else b
- *
- * cdef enum summary_type: # <<<<<<<<<<<<<<
- * summary_type_mean = 0
- * summary_type_max = 1
- */
-enum __pyx_t_2bx_3bbi_8bbi_file_summary_type {
- __pyx_e_2bx_3bbi_8bbi_file_summary_type_mean = 0,
- __pyx_e_2bx_3bbi_8bbi_file_summary_type_max = 1,
- __pyx_e_2bx_3bbi_8bbi_file_summary_type_min = 2,
- __pyx_e_2bx_3bbi_8bbi_file_summary_type_coverage = 3,
- __pyx_e_2bx_3bbi_8bbi_file_summary_type_sd = 4
-};
-
-/* "bx/bbi/bbi_file.pxd":8
- * cimport numpy
- *
- * cdef class SummaryBlock: # <<<<<<<<<<<<<<
- * """
- * A block of summary data from disk
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock {
- PyObject_HEAD
- __pyx_t_2bx_3bbi_5types_bits32 chrom_id;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
- __pyx_t_2bx_3bbi_5types_bits32 valid_count;
- double min_val;
- double max_val;
- double sum_data;
- double sum_squares;
-};
-
-
-/* "bx/bbi/bbi_file.pxd":39
- * cdef class BBIFile
- *
- * cdef class BlockHandler: # <<<<<<<<<<<<<<
- * """
- * Callback for `BBIFile.visit_blocks_in_region`
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtab;
-};
-
-
-/* "cirtree_file.pxd":3
- * from types cimport *
- *
- * cdef class CIRTreeFile: # <<<<<<<<<<<<<<
- * cdef object file
- * cdef object reader
- */
-struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile {
- PyObject_HEAD
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- __pyx_t_2bx_3bbi_5types_bits64 root_offset;
- __pyx_t_2bx_3bbi_5types_bits32 block_size;
- __pyx_t_2bx_3bbi_5types_bits64 item_count;
- __pyx_t_2bx_3bbi_5types_bits32 start_chrom_ix;
- __pyx_t_2bx_3bbi_5types_bits32 start_base;
- __pyx_t_2bx_3bbi_5types_bits32 end_chrom_ix;
- __pyx_t_2bx_3bbi_5types_bits32 end_base;
- __pyx_t_2bx_3bbi_5types_bits64 file_size;
- __pyx_t_2bx_3bbi_5types_bits32 items_per_slot;
-};
-
-
-/* "bx/bbi/bbi_file.pxd":21
- * cdef public double sum_squares
- *
- * cdef class SummarizedData: # <<<<<<<<<<<<<<
- * """
- * The result of using SummaryBlocks read from the file to produce a
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtab;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
- int size;
- PyArrayObject *valid_count;
- PyArrayObject *min_val;
- PyArrayObject *max_val;
- PyArrayObject *sum_data;
- PyArrayObject *sum_squares;
-};
-
-
-/* "bx/bbi/bbi_file.pyx":279
- * return closest_level
- *
- * cdef class ZoomLevel: # <<<<<<<<<<<<<<
- * cdef BBIFile bbi_file
- * cdef public bits32 reduction_level
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_vtab;
- struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *bbi_file;
- __pyx_t_2bx_3bbi_5types_bits32 reduction_level;
- __pyx_t_2bx_3bbi_5types_bits32 reserved;
- __pyx_t_2bx_3bbi_5types_bits64 data_offset;
- __pyx_t_2bx_3bbi_5types_bits64 index_offset;
- int item_count;
-};
-
-
-/* "bx/bbi/bbi_file.pxd":37
- * cdef accumulate_interval_value( self, bits32 s, bits32 e, float val )
- *
- * cdef class BBIFile # <<<<<<<<<<<<<<
- *
- * cdef class BlockHandler:
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile *__pyx_vtab;
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_bits32 magic;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile *chrom_bpt;
- __pyx_t_2bx_3bbi_5types_bits16 version;
- __pyx_t_2bx_3bbi_5types_bits16 zoom_levels;
- __pyx_t_2bx_3bbi_5types_bits64 chrom_tree_offset;
- __pyx_t_2bx_3bbi_5types_bits64 unzoomed_data_offset;
- __pyx_t_2bx_3bbi_5types_bits64 unzoomed_index_offset;
- __pyx_t_2bx_3bbi_5types_bits16 field_count;
- __pyx_t_2bx_3bbi_5types_bits16 defined_field_count;
- __pyx_t_2bx_3bbi_5types_bits64 as_offset;
- __pyx_t_2bx_3bbi_5types_bits64 total_summary_offset;
- __pyx_t_2bx_3bbi_5types_bits32 uncompress_buf_size;
- PyObject *level_list;
-};
-
-
-/* "bpt_file.pxd":5
- * from types cimport *
- *
- * cdef class BPTFile: # <<<<<<<<<<<<<<
- * """
- * On disk B+ tree compatible with Jim Kent's bPlusTree.c
- */
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile {
- PyObject_HEAD
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- __pyx_t_2bx_3bbi_5types_bits32 block_size;
- __pyx_t_2bx_3bbi_5types_bits32 key_size;
- __pyx_t_2bx_3bbi_5types_bits32 value_size;
- __pyx_t_2bx_3bbi_5types_bits64 item_count;
- __pyx_t_2bx_3bbi_5types_bits64 root_offset;
-};
-
-
-
-/* "bx/bbi/bbi_file.pyx":110
- * pass
- *
- * cdef class BBIFile: # <<<<<<<<<<<<<<
- * """
- * A "big binary indexed" file. Stores blocks of raw data and numeric
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile {
- PyObject *(*visit_blocks_in_region)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *);
- PyObject *(*_get_chrom_id_and_size)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *);
- PyObject *(*_best_zoom_level)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, int);
- PyObject *(*summarize)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch);
- PyObject *(*summarize_from_full)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch);
- PyObject *(*query)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch);
- PyObject *(*_summarize_from_full)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int);
-};
-static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile *__pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile;
-
-
-/* "bx/bbi/bbi_file.pyx":103
- * min_val[j] = val
- *
- * cdef class BlockHandler: # <<<<<<<<<<<<<<
- * """
- * Callback for `BBIFile.visit_blocks_in_region`
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler {
- PyObject *(*handle_block)(struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *, PyObject *, struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *);
-};
-static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtabptr_2bx_3bbi_8bbi_file_BlockHandler;
-
-
-/* "bx/bbi/bbi_file.pyx":56
- * pass
- *
- * cdef class SummarizedData: # <<<<<<<<<<<<<<
- * """
- * The result of using SummaryBlocks read from the file to produce a
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData {
- PyObject *(*accumulate_interval_value)(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float);
-};
-static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData;
-
-
-/* "bx/bbi/bbi_file.pyx":279
- * return closest_level
- *
- * cdef class ZoomLevel: # <<<<<<<<<<<<<<
- * cdef BBIFile bbi_file
- * cdef public bits32 reduction_level
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_ZoomLevel {
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-static int __pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_8chrom_id_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_5start___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_5start_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_3end___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_3end_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_11valid_count___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_11valid_count_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_7min_val___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_7min_val_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_7max_val___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_7max_val_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_8sum_data___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_8sum_data_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_11sum_squares___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_12SummaryBlock_11sum_squares_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData___init__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_v_size); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_5start___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_5start_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_3end___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_3end_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_4size___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_4size_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_11valid_count___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_11valid_count_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_11valid_count_4__del__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_7min_val___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_7min_val_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_7min_val_4__del__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_7max_val___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_7max_val_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_7max_val_4__del__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_8sum_data___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_8sum_data_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_8sum_data_4__del__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_11sum_squares___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_11sum_squares_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_14SummarizedData_11sum_squares_4__del__(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_7BBIFile___init__(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, PyObject *__pyx_v_file, PyObject *__pyx_v_expected_sig, PyObject *__pyx_v_type_name); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_2open(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, PyObject *__pyx_v_file, PyObject *__pyx_v_expected_sig, CYTHON_UNUSED PyObject *__pyx_v_type_name); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_4summarize(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, char *__pyx_v_chrom, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_v_summary_size); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_6summarize_from_full(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, char *__pyx_v_chrom, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_v_summary_size); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_8query(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, char *__pyx_v_chrom, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end, int __pyx_v_summary_size); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_5magic___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_5magic_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_7version___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_7version_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_11zoom_levels___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_11zoom_levels_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_10level_list___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_10level_list_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_7BBIFile_10level_list_4__del__(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel__summary_blocks_in_region(struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_v_self, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_chrom_id, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_start, __pyx_t_2bx_3bbi_5types_bits32 __pyx_v_end); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel_15reduction_level___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel_15reduction_level_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel_11data_offset___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel_11data_offset_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel_12index_offset___get__(struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_v_self); /* proto */
-static int __pyx_pf_2bx_3bbi_8bbi_file_9ZoomLevel_12index_offset_2__set__(struct __pyx_obj_2bx_3bbi_8bbi_file_ZoomLevel *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
-static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
-static char __pyx_k_2[] = "find_overlapping_blocks";
-static char __pyx_k_5[] = "_summary_blocks_in_region";
-static char __pyx_k_6[] = "ndarray is not C contiguous";
-static char __pyx_k_8[] = "ndarray is not Fortran contiguous";
-static char __pyx_k_10[] = "Non-native byte order not supported";
-static char __pyx_k_12[] = "unknown dtype code in numpy.pxd (%d)";
-static char __pyx_k_13[] = "Format string allocated too short, see comment in numpy.pxd";
-static char __pyx_k_16[] = "Format string allocated too short.";
-static char __pyx_k_18[] = "\nCore implementation for reading UCSC \"big binary indexed\" files.\n\nThere isn't really any specification for the format beyond the code, so this\nmirrors Jim Kent's 'bbiRead.c' mostly. \n";
-static char __pyx_k_19[] = "bx.misc.binary_file";
-static char __pyx_k__B[] = "B";
-static char __pyx_k__H[] = "H";
-static char __pyx_k__I[] = "I";
-static char __pyx_k__L[] = "L";
-static char __pyx_k__O[] = "O";
-static char __pyx_k__Q[] = "Q";
-static char __pyx_k__b[] = "b";
-static char __pyx_k__d[] = "d";
-static char __pyx_k__f[] = "f";
-static char __pyx_k__g[] = "g";
-static char __pyx_k__h[] = "h";
-static char __pyx_k__i[] = "i";
-static char __pyx_k__l[] = "l";
-static char __pyx_k__q[] = "q";
-static char __pyx_k__II[] = "II";
-static char __pyx_k__Zd[] = "Zd";
-static char __pyx_k__Zf[] = "Zf";
-static char __pyx_k__Zg[] = "Zg";
-static char __pyx_k__end[] = "end";
-static char __pyx_k__max[] = "max";
-static char __pyx_k__min[] = "min";
-static char __pyx_k__nan[] = "nan";
-static char __pyx_k__file[] = "file";
-static char __pyx_k__find[] = "find";
-static char __pyx_k__math[] = "math";
-static char __pyx_k__mean[] = "mean";
-static char __pyx_k__open[] = "open";
-static char __pyx_k__read[] = "read";
-static char __pyx_k__seek[] = "seek";
-static char __pyx_k__size[] = "size";
-static char __pyx_k__skip[] = "skip";
-static char __pyx_k__sqrt[] = "sqrt";
-static char __pyx_k__zlib[] = "zlib";
-static char __pyx_k__chrom[] = "chrom";
-static char __pyx_k__deque[] = "deque";
-static char __pyx_k__dtype[] = "dtype";
-static char __pyx_k__numpy[] = "numpy";
-static char __pyx_k__query[] = "query";
-static char __pyx_k__range[] = "range";
-static char __pyx_k__start[] = "start";
-static char __pyx_k__zeros[] = "zeros";
-static char __pyx_k__unpack[] = "unpack";
-static char __pyx_k__float64[] = "float64";
-static char __pyx_k__max_val[] = "max_val";
-static char __pyx_k__min_val[] = "min_val";
-static char __pyx_k__popleft[] = "popleft";
-static char __pyx_k__std_dev[] = "std_dev";
-static char __pyx_k__StringIO[] = "StringIO";
-static char __pyx_k____main__[] = "__main__";
-static char __pyx_k____test__[] = "__test__";
-static char __pyx_k__chrom_id[] = "chrom_id";
-static char __pyx_k__coverage[] = "coverage";
-static char __pyx_k__sum_data[] = "sum_data";
-static char __pyx_k__cStringIO[] = "cStringIO";
-static char __pyx_k__summarize[] = "summarize";
-static char __pyx_k__type_name[] = "type_name";
-static char __pyx_k__ValueError[] = "ValueError";
-static char __pyx_k__decompress[] = "decompress";
-static char __pyx_k__read_float[] = "read_float";
-static char __pyx_k__collections[] = "collections";
-static char __pyx_k__read_uint16[] = "read_uint16";
-static char __pyx_k__read_uint32[] = "read_uint32";
-static char __pyx_k__read_uint64[] = "read_uint64";
-static char __pyx_k__sum_squares[] = "sum_squares";
-static char __pyx_k__valid_count[] = "valid_count";
-static char __pyx_k__RuntimeError[] = "RuntimeError";
-static char __pyx_k__expected_sig[] = "expected_sig";
-static char __pyx_k__summary_size[] = "summary_size";
-static char __pyx_k__byteswap_needed[] = "byteswap_needed";
-static char __pyx_k__BinaryFileReader[] = "BinaryFileReader";
-static char __pyx_k__is_little_endian[] = "is_little_endian";
-static char __pyx_k__summarize_from_full[] = "summarize_from_full";
-static PyObject *__pyx_kp_u_10;
-static PyObject *__pyx_kp_u_12;
-static PyObject *__pyx_kp_u_13;
-static PyObject *__pyx_kp_u_16;
-static PyObject *__pyx_n_s_19;
-static PyObject *__pyx_n_s_2;
-static PyObject *__pyx_n_s_5;
-static PyObject *__pyx_kp_u_6;
-static PyObject *__pyx_kp_u_8;
-static PyObject *__pyx_n_s__BinaryFileReader;
-static PyObject *__pyx_n_s__II;
-static PyObject *__pyx_n_s__RuntimeError;
-static PyObject *__pyx_n_s__StringIO;
-static PyObject *__pyx_n_s__ValueError;
-static PyObject *__pyx_n_s____main__;
-static PyObject *__pyx_n_s____test__;
-static PyObject *__pyx_n_s__byteswap_needed;
-static PyObject *__pyx_n_s__cStringIO;
-static PyObject *__pyx_n_s__chrom;
-static PyObject *__pyx_n_s__chrom_id;
-static PyObject *__pyx_n_s__collections;
-static PyObject *__pyx_n_s__coverage;
-static PyObject *__pyx_n_s__decompress;
-static PyObject *__pyx_n_s__deque;
-static PyObject *__pyx_n_s__dtype;
-static PyObject *__pyx_n_s__end;
-static PyObject *__pyx_n_s__expected_sig;
-static PyObject *__pyx_n_s__file;
-static PyObject *__pyx_n_s__find;
-static PyObject *__pyx_n_s__float64;
-static PyObject *__pyx_n_s__is_little_endian;
-static PyObject *__pyx_n_s__math;
-static PyObject *__pyx_n_s__max;
-static PyObject *__pyx_n_s__max_val;
-static PyObject *__pyx_n_s__mean;
-static PyObject *__pyx_n_s__min;
-static PyObject *__pyx_n_s__min_val;
-static PyObject *__pyx_n_s__nan;
-static PyObject *__pyx_n_s__numpy;
-static PyObject *__pyx_n_s__open;
-static PyObject *__pyx_n_s__popleft;
-static PyObject *__pyx_n_s__query;
-static PyObject *__pyx_n_s__range;
-static PyObject *__pyx_n_s__read;
-static PyObject *__pyx_n_s__read_float;
-static PyObject *__pyx_n_s__read_uint16;
-static PyObject *__pyx_n_s__read_uint32;
-static PyObject *__pyx_n_s__read_uint64;
-static PyObject *__pyx_n_s__seek;
-static PyObject *__pyx_n_s__size;
-static PyObject *__pyx_n_s__skip;
-static PyObject *__pyx_n_s__sqrt;
-static PyObject *__pyx_n_s__start;
-static PyObject *__pyx_n_s__std_dev;
-static PyObject *__pyx_n_s__sum_data;
-static PyObject *__pyx_n_s__sum_squares;
-static PyObject *__pyx_n_s__summarize;
-static PyObject *__pyx_n_s__summarize_from_full;
-static PyObject *__pyx_n_s__summary_size;
-static PyObject *__pyx_n_s__type_name;
-static PyObject *__pyx_n_s__unpack;
-static PyObject *__pyx_n_s__valid_count;
-static PyObject *__pyx_n_s__zeros;
-static PyObject *__pyx_n_s__zlib;
-static PyObject *__pyx_int_0;
-static PyObject *__pyx_int_1;
-static PyObject *__pyx_int_15;
-static PyObject *__pyx_int_28;
-static PyObject *__pyx_int_32;
-static PyObject *__pyx_int_64;
-static PyObject *__pyx_k_tuple_1;
-static PyObject *__pyx_k_tuple_3;
-static PyObject *__pyx_k_tuple_4;
-static PyObject *__pyx_k_tuple_7;
-static PyObject *__pyx_k_tuple_9;
-static PyObject *__pyx_k_tuple_11;
-static PyObject *__pyx_k_tuple_14;
-static PyObject *__pyx_k_tuple_15;
-static PyObject *__pyx_k_tuple_17;
-int big_wig_sig;
-int big_bed_sig;
-
-/* "bx/bbi/bbi_file.pyx":35
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-static int __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_size(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_4size_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_valid_count(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_11valid_count_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_valid_count(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_11valid_count_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_11valid_count_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_min_val(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_7min_val_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_min_val(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_7min_val_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_7min_val_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_max_val(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_7max_val_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_max_val(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_7max_val_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_7max_val_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_sum_data(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_8sum_data_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_sum_data(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_8sum_data_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_8sum_data_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_sum_squares(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_11sum_squares_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_sum_squares(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_11sum_squares_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_11sum_squares_5__del__(o);
- }
-}
-
-static PyMethodDef __pyx_methods_2bx_3bbi_8bbi_file_SummarizedData[] = {
- {0, 0, 0, 0}
-};
-
-static struct PyGetSetDef __pyx_getsets_2bx_3bbi_8bbi_file_SummarizedData[] = {
- {(char *)"start", __pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_start, __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_start, 0, 0},
- {(char *)"end", __pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_end, __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_end, 0, 0},
- {(char *)"size", __pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_size, __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_size, 0, 0},
- {(char *)"valid_count", __pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_valid_count, __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_valid_count, 0, 0},
- {(char *)"min_val", __pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_min_val, __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_min_val, 0, 0},
- {(char *)"max_val", __pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_max_val, __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_max_val, 0, 0},
- {(char *)"sum_data", __pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_sum_data, __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_sum_data, 0, 0},
- {(char *)"sum_squares", __pyx_getprop_2bx_3bbi_8bbi_file_14SummarizedData_sum_squares, __pyx_setprop_2bx_3bbi_8bbi_file_14SummarizedData_sum_squares, 0, 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_SummarizedData = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
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- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_SummarizedData = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping_SummarizedData = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_SummarizedData = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-static PyTypeObject __pyx_type_2bx_3bbi_8bbi_file_SummarizedData = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("bx.bbi.bbi_file.SummarizedData"), /*tp_name*/
- sizeof(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_2bx_3bbi_8bbi_file_SummarizedData, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_SummarizedData, /*tp_as_number*/
- &__pyx_tp_as_sequence_SummarizedData, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_SummarizedData, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_SummarizedData, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("\n The result of using SummaryBlocks read from the file to produce a \n aggregation over a particular range and resolution\n "), /*tp_doc*/
- __pyx_tp_traverse_2bx_3bbi_8bbi_file_SummarizedData, /*tp_traverse*/
- __pyx_tp_clear_2bx_3bbi_8bbi_file_SummarizedData, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_2bx_3bbi_8bbi_file_SummarizedData, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_2bx_3bbi_8bbi_file_SummarizedData, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pw_2bx_3bbi_8bbi_file_14SummarizedData_1__init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_2bx_3bbi_8bbi_file_SummarizedData, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile __pyx_vtable_2bx_3bbi_8bbi_file_BBIFile;
-
-static PyObject *__pyx_tp_new_2bx_3bbi_8bbi_file_BBIFile(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *)o);
- p->__pyx_vtab = __pyx_vtabptr_2bx_3bbi_8bbi_file_BBIFile;
- p->file = Py_None; Py_INCREF(Py_None);
- p->reader = Py_None; Py_INCREF(Py_None);
- p->chrom_bpt = ((struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile *)Py_None); Py_INCREF(Py_None);
- p->level_list = Py_None; Py_INCREF(Py_None);
- return o;
-}
-
-static void __pyx_tp_dealloc_2bx_3bbi_8bbi_file_BBIFile(PyObject *o) {
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- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->file);
- Py_CLEAR(p->reader);
- Py_CLEAR(p->chrom_bpt);
- Py_CLEAR(p->level_list);
- PyObject_GC_Track(o);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_2bx_3bbi_8bbi_file_BBIFile(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *p = (struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *)o;
- if (p->file) {
- e = (*v)(p->file, a); if (e) return e;
- }
- if (p->reader) {
- e = (*v)(p->reader, a); if (e) return e;
- }
- if (p->chrom_bpt) {
- e = (*v)(((PyObject*)p->chrom_bpt), a); if (e) return e;
- }
- if (p->level_list) {
- e = (*v)(p->level_list, a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_2bx_3bbi_8bbi_file_BBIFile(PyObject *o) {
- struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *p = (struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->file);
- p->file = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->reader);
- p->reader = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->chrom_bpt);
- p->chrom_bpt = ((struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->level_list);
- p->level_list = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyObject *__pyx_getprop_2bx_3bbi_8bbi_file_7BBIFile_magic(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_5magic_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_3bbi_8bbi_file_7BBIFile_magic(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_5magic_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_3bbi_8bbi_file_7BBIFile_version(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_7version_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_3bbi_8bbi_file_7BBIFile_version(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
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- }
-}
-
-static PyObject *__pyx_getprop_2bx_3bbi_8bbi_file_7BBIFile_zoom_levels(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_11zoom_levels_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_3bbi_8bbi_file_7BBIFile_zoom_levels(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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- }
- else {
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- }
-}
-
-static PyObject *__pyx_getprop_2bx_3bbi_8bbi_file_7BBIFile_level_list(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_10level_list_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_3bbi_8bbi_file_7BBIFile_level_list(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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- }
- else {
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- }
-}
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-static PyMethodDef __pyx_methods_2bx_3bbi_8bbi_file_BBIFile[] = {
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- {__Pyx_NAMESTR("summarize"), (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_5summarize, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_3bbi_8bbi_file_7BBIFile_4summarize)},
- {__Pyx_NAMESTR("summarize_from_full"), (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_7summarize_from_full, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_3bbi_8bbi_file_7BBIFile_6summarize_from_full)},
- {__Pyx_NAMESTR("query"), (PyCFunction)__pyx_pw_2bx_3bbi_8bbi_file_7BBIFile_9query, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_3bbi_8bbi_file_7BBIFile_8query)},
- {0, 0, 0, 0}
-};
-
-static struct PyGetSetDef __pyx_getsets_2bx_3bbi_8bbi_file_BBIFile[] = {
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- {(char *)"version", __pyx_getprop_2bx_3bbi_8bbi_file_7BBIFile_version, __pyx_setprop_2bx_3bbi_8bbi_file_7BBIFile_version, 0, 0},
- {(char *)"zoom_levels", __pyx_getprop_2bx_3bbi_8bbi_file_7BBIFile_zoom_levels, __pyx_setprop_2bx_3bbi_8bbi_file_7BBIFile_zoom_levels, 0, 0},
- {(char *)"level_list", __pyx_getprop_2bx_3bbi_8bbi_file_7BBIFile_level_list, __pyx_setprop_2bx_3bbi_8bbi_file_7BBIFile_level_list, 0, 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_BBIFile = {
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- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
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-
-static PySequenceMethods __pyx_tp_as_sequence_BBIFile = {
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- 0, /*sq_concat*/
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-
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- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_BBIFile = {
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- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
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- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
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- PyErr_Format(PyExc_TypeError,
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- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- continue;
- }
- name = first_kw_arg;
- #if PY_MAJOR_VERSION < 3
- if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
- while (*name) {
- if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
- && _PyString_Eq(**name, key)) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- if ((**argname == key) || (
- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
- }
- argname++;
- }
- }
- } else
- #endif
- if (likely(PyUnicode_Check(key))) {
- while (*name) {
- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**name, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) goto arg_passed_twice;
- argname++;
- }
- }
- } else
- goto invalid_keyword_type;
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
- }
- }
- return 0;
-arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
- if (unlikely(!type)) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (likely(PyObject_TypeCheck(obj, type)))
- return 1;
- PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
- Py_TYPE(obj)->tp_name, type->tp_name);
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_IsLittleEndian(void) {
- unsigned int n = 1;
- return *(unsigned char*)(&n) != 0;
-}
-static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx,
- __Pyx_BufFmt_StackElem* stack,
- __Pyx_TypeInfo* type) {
- stack[0].field = &ctx->root;
- stack[0].parent_offset = 0;
- ctx->root.type = type;
- ctx->root.name = "buffer dtype";
- ctx->root.offset = 0;
- ctx->head = stack;
- ctx->head->field = &ctx->root;
- ctx->fmt_offset = 0;
- ctx->head->parent_offset = 0;
- ctx->new_packmode = '@';
- ctx->enc_packmode = '@';
- ctx->new_count = 1;
- ctx->enc_count = 0;
- ctx->enc_type = 0;
- ctx->is_complex = 0;
- ctx->is_valid_array = 0;
- ctx->struct_alignment = 0;
- while (type->typegroup == 'S') {
- ++ctx->head;
- ctx->head->field = type->fields;
- ctx->head->parent_offset = 0;
- type = type->fields->type;
- }
-}
-static int __Pyx_BufFmt_ParseNumber(const char** ts) {
- int count;
- const char* t = *ts;
- if (*t < '0' || *t > '9') {
- return -1;
- } else {
- count = *t++ - '0';
- while (*t >= '0' && *t < '9') {
- count *= 10;
- count += *t++ - '0';
- }
- }
- *ts = t;
- return count;
-}
-static int __Pyx_BufFmt_ExpectNumber(const char **ts) {
- int number = __Pyx_BufFmt_ParseNumber(ts);
- if (number == -1) /* First char was not a digit */
- PyErr_Format(PyExc_ValueError,\
- "Does not understand character buffer dtype format string ('%c')", **ts);
- return number;
-}
-static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) {
- PyErr_Format(PyExc_ValueError,
- "Unexpected format string character: '%c'", ch);
-}
-static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) {
- switch (ch) {
- case 'c': return "'char'";
- case 'b': return "'signed char'";
- case 'B': return "'unsigned char'";
- case 'h': return "'short'";
- case 'H': return "'unsigned short'";
- case 'i': return "'int'";
- case 'I': return "'unsigned int'";
- case 'l': return "'long'";
- case 'L': return "'unsigned long'";
- case 'q': return "'long long'";
- case 'Q': return "'unsigned long long'";
- case 'f': return (is_complex ? "'complex float'" : "'float'");
- case 'd': return (is_complex ? "'complex double'" : "'double'");
- case 'g': return (is_complex ? "'complex long double'" : "'long double'");
- case 'T': return "a struct";
- case 'O': return "Python object";
- case 'P': return "a pointer";
- case 's': case 'p': return "a string";
- case 0: return "end";
- default: return "unparseable format string";
- }
-}
-static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) {
- switch (ch) {
- case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return 2;
- case 'i': case 'I': case 'l': case 'L': return 4;
- case 'q': case 'Q': return 8;
- case 'f': return (is_complex ? 8 : 4);
- case 'd': return (is_complex ? 16 : 8);
- case 'g': {
- PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g')..");
- return 0;
- }
- case 'O': case 'P': return sizeof(void*);
- default:
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
-}
-static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) {
- switch (ch) {
- case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return sizeof(short);
- case 'i': case 'I': return sizeof(int);
- case 'l': case 'L': return sizeof(long);
- #ifdef HAVE_LONG_LONG
- case 'q': case 'Q': return sizeof(PY_LONG_LONG);
- #endif
- case 'f': return sizeof(float) * (is_complex ? 2 : 1);
- case 'd': return sizeof(double) * (is_complex ? 2 : 1);
- case 'g': return sizeof(long double) * (is_complex ? 2 : 1);
- case 'O': case 'P': return sizeof(void*);
- default: {
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
- }
-}
-typedef struct { char c; short x; } __Pyx_st_short;
-typedef struct { char c; int x; } __Pyx_st_int;
-typedef struct { char c; long x; } __Pyx_st_long;
-typedef struct { char c; float x; } __Pyx_st_float;
-typedef struct { char c; double x; } __Pyx_st_double;
-typedef struct { char c; long double x; } __Pyx_st_longdouble;
-typedef struct { char c; void *x; } __Pyx_st_void_p;
-#ifdef HAVE_LONG_LONG
-typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong;
-#endif
-static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) {
- switch (ch) {
- case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short);
- case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int);
- case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long);
-#ifdef HAVE_LONG_LONG
- case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG);
-#endif
- case 'f': return sizeof(__Pyx_st_float) - sizeof(float);
- case 'd': return sizeof(__Pyx_st_double) - sizeof(double);
- case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double);
- case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*);
- default:
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
-}
-/* These are for computing the padding at the end of the struct to align
- on the first member of the struct. This will probably the same as above,
- but we don't have any guarantees.
- */
-typedef struct { short x; char c; } __Pyx_pad_short;
-typedef struct { int x; char c; } __Pyx_pad_int;
-typedef struct { long x; char c; } __Pyx_pad_long;
-typedef struct { float x; char c; } __Pyx_pad_float;
-typedef struct { double x; char c; } __Pyx_pad_double;
-typedef struct { long double x; char c; } __Pyx_pad_longdouble;
-typedef struct { void *x; char c; } __Pyx_pad_void_p;
-#ifdef HAVE_LONG_LONG
-typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong;
-#endif
-static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) {
- switch (ch) {
- case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short);
- case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int);
- case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long);
-#ifdef HAVE_LONG_LONG
- case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG);
-#endif
- case 'f': return sizeof(__Pyx_pad_float) - sizeof(float);
- case 'd': return sizeof(__Pyx_pad_double) - sizeof(double);
- case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double);
- case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*);
- default:
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
-}
-static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) {
- switch (ch) {
- case 'c':
- return 'H';
- case 'b': case 'h': case 'i':
- case 'l': case 'q': case 's': case 'p':
- return 'I';
- case 'B': case 'H': case 'I': case 'L': case 'Q':
- return 'U';
- case 'f': case 'd': case 'g':
- return (is_complex ? 'C' : 'R');
- case 'O':
- return 'O';
- case 'P':
- return 'P';
- default: {
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
- }
-}
-static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) {
- if (ctx->head == NULL || ctx->head->field == &ctx->root) {
- const char* expected;
- const char* quote;
- if (ctx->head == NULL) {
- expected = "end";
- quote = "";
- } else {
- expected = ctx->head->field->type->name;
- quote = "'";
- }
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch, expected %s%s%s but got %s",
- quote, expected, quote,
- __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex));
- } else {
- __Pyx_StructField* field = ctx->head->field;
- __Pyx_StructField* parent = (ctx->head - 1)->field;
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'",
- field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex),
- parent->type->name, field->name);
- }
-}
-static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
- char group;
- size_t size, offset, arraysize = 1;
- if (ctx->enc_type == 0) return 0;
- if (ctx->head->field->type->arraysize[0]) {
- int i, ndim = 0;
- if (ctx->enc_type == 's' || ctx->enc_type == 'p') {
- ctx->is_valid_array = ctx->head->field->type->ndim == 1;
- ndim = 1;
- if (ctx->enc_count != ctx->head->field->type->arraysize[0]) {
- PyErr_Format(PyExc_ValueError,
- "Expected a dimension of size %zu, got %zu",
- ctx->head->field->type->arraysize[0], ctx->enc_count);
- return -1;
- }
- }
- if (!ctx->is_valid_array) {
- PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d",
- ctx->head->field->type->ndim, ndim);
- return -1;
- }
- for (i = 0; i < ctx->head->field->type->ndim; i++) {
- arraysize *= ctx->head->field->type->arraysize[i];
- }
- ctx->is_valid_array = 0;
- ctx->enc_count = 1;
- }
- group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex);
- do {
- __Pyx_StructField* field = ctx->head->field;
- __Pyx_TypeInfo* type = field->type;
- if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') {
- size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex);
- } else {
- size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex);
- }
- if (ctx->enc_packmode == '@') {
- size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex);
- size_t align_mod_offset;
- if (align_at == 0) return -1;
- align_mod_offset = ctx->fmt_offset % align_at;
- if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset;
- if (ctx->struct_alignment == 0)
- ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type,
- ctx->is_complex);
- }
- if (type->size != size || type->typegroup != group) {
- if (type->typegroup == 'C' && type->fields != NULL) {
- size_t parent_offset = ctx->head->parent_offset + field->offset;
- ++ctx->head;
- ctx->head->field = type->fields;
- ctx->head->parent_offset = parent_offset;
- continue;
- }
- if ((type->typegroup == 'H' || group == 'H') && type->size == size) {
- } else {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return -1;
- }
- }
- offset = ctx->head->parent_offset + field->offset;
- if (ctx->fmt_offset != offset) {
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected",
- (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset);
- return -1;
- }
- ctx->fmt_offset += size;
- if (arraysize)
- ctx->fmt_offset += (arraysize - 1) * size;
- --ctx->enc_count; /* Consume from buffer string */
- while (1) {
- if (field == &ctx->root) {
- ctx->head = NULL;
- if (ctx->enc_count != 0) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return -1;
- }
- break; /* breaks both loops as ctx->enc_count == 0 */
- }
- ctx->head->field = ++field;
- if (field->type == NULL) {
- --ctx->head;
- field = ctx->head->field;
- continue;
- } else if (field->type->typegroup == 'S') {
- size_t parent_offset = ctx->head->parent_offset + field->offset;
- if (field->type->fields->type == NULL) continue; /* empty struct */
- field = field->type->fields;
- ++ctx->head;
- ctx->head->field = field;
- ctx->head->parent_offset = parent_offset;
- break;
- } else {
- break;
- }
- }
- } while (ctx->enc_count);
- ctx->enc_type = 0;
- ctx->is_complex = 0;
- return 0;
-}
-static CYTHON_INLINE PyObject *
-__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp)
-{
- const char *ts = *tsp;
- int i = 0, number;
- int ndim = ctx->head->field->type->ndim;
-;
- ++ts;
- if (ctx->new_count != 1) {
- PyErr_SetString(PyExc_ValueError,
- "Cannot handle repeated arrays in format string");
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- while (*ts && *ts != ')') {
- if (isspace(*ts))
- continue;
- number = __Pyx_BufFmt_ExpectNumber(&ts);
- if (number == -1) return NULL;
- if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i])
- return PyErr_Format(PyExc_ValueError,
- "Expected a dimension of size %zu, got %d",
- ctx->head->field->type->arraysize[i], number);
- if (*ts != ',' && *ts != ')')
- return PyErr_Format(PyExc_ValueError,
- "Expected a comma in format string, got '%c'", *ts);
- if (*ts == ',') ts++;
- i++;
- }
- if (i != ndim)
- return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d",
- ctx->head->field->type->ndim, i);
- if (!*ts) {
- PyErr_SetString(PyExc_ValueError,
- "Unexpected end of format string, expected ')'");
- return NULL;
- }
- ctx->is_valid_array = 1;
- ctx->new_count = 1;
- *tsp = ++ts;
- return Py_None;
-}
-static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) {
- int got_Z = 0;
- while (1) {
- switch(*ts) {
- case 0:
- if (ctx->enc_type != 0 && ctx->head == NULL) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- if (ctx->head != NULL) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return NULL;
- }
- return ts;
- case ' ':
- case 10:
- case 13:
- ++ts;
- break;
- case '<':
- if (!__Pyx_IsLittleEndian()) {
- PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler");
- return NULL;
- }
- ctx->new_packmode = '=';
- ++ts;
- break;
- case '>':
- case '!':
- if (__Pyx_IsLittleEndian()) {
- PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler");
- return NULL;
- }
- ctx->new_packmode = '=';
- ++ts;
- break;
- case '=':
- case '@':
- case '^':
- ctx->new_packmode = *ts++;
- break;
- case 'T': /* substruct */
- {
- const char* ts_after_sub;
- size_t i, struct_count = ctx->new_count;
- size_t struct_alignment = ctx->struct_alignment;
- ctx->new_count = 1;
- ++ts;
- if (*ts != '{') {
- PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'");
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0; /* Erase processed last struct element */
- ctx->enc_count = 0;
- ctx->struct_alignment = 0;
- ++ts;
- ts_after_sub = ts;
- for (i = 0; i != struct_count; ++i) {
- ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts);
- if (!ts_after_sub) return NULL;
- }
- ts = ts_after_sub;
- if (struct_alignment) ctx->struct_alignment = struct_alignment;
- }
- break;
- case '}': /* end of substruct; either repeat or move on */
- {
- size_t alignment = ctx->struct_alignment;
- ++ts;
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0; /* Erase processed last struct element */
- if (alignment && ctx->fmt_offset % alignment) {
- ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment);
- }
- }
- return ts;
- case 'x':
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->fmt_offset += ctx->new_count;
- ctx->new_count = 1;
- ctx->enc_count = 0;
- ctx->enc_type = 0;
- ctx->enc_packmode = ctx->new_packmode;
- ++ts;
- break;
- case 'Z':
- got_Z = 1;
- ++ts;
- if (*ts != 'f' && *ts != 'd' && *ts != 'g') {
- __Pyx_BufFmt_RaiseUnexpectedChar('Z');
- return NULL;
- } /* fall through */
- case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I':
- case 'l': case 'L': case 'q': case 'Q':
- case 'f': case 'd': case 'g':
- case 'O': case 's': case 'p':
- if (ctx->enc_type == *ts && got_Z == ctx->is_complex &&
- ctx->enc_packmode == ctx->new_packmode) {
- ctx->enc_count += ctx->new_count;
- } else {
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_count = ctx->new_count;
- ctx->enc_packmode = ctx->new_packmode;
- ctx->enc_type = *ts;
- ctx->is_complex = got_Z;
- }
- ++ts;
- ctx->new_count = 1;
- got_Z = 0;
- break;
- case ':':
- ++ts;
- while(*ts != ':') ++ts;
- ++ts;
- break;
- case '(':
- if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL;
- break;
- default:
- {
- int number = __Pyx_BufFmt_ExpectNumber(&ts);
- if (number == -1) return NULL;
- ctx->new_count = (size_t)number;
- }
- }
- }
-}
-static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) {
- buf->buf = NULL;
- buf->obj = NULL;
- buf->strides = __Pyx_zeros;
- buf->shape = __Pyx_zeros;
- buf->suboffsets = __Pyx_minusones;
-}
-static CYTHON_INLINE int __Pyx_GetBufferAndValidate(
- Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags,
- int nd, int cast, __Pyx_BufFmt_StackElem* stack)
-{
- if (obj == Py_None || obj == NULL) {
- __Pyx_ZeroBuffer(buf);
- return 0;
- }
- buf->buf = NULL;
- if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail;
- if (buf->ndim != nd) {
- PyErr_Format(PyExc_ValueError,
- "Buffer has wrong number of dimensions (expected %d, got %d)",
- nd, buf->ndim);
- goto fail;
- }
- if (!cast) {
- __Pyx_BufFmt_Context ctx;
- __Pyx_BufFmt_Init(&ctx, stack, dtype);
- if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail;
- }
- if ((unsigned)buf->itemsize != dtype->size) {
- PyErr_Format(PyExc_ValueError,
- "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)",
- buf->itemsize, (buf->itemsize > 1) ? "s" : "",
- dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : "");
- goto fail;
- }
- if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
- return 0;
-fail:;
- __Pyx_ZeroBuffer(buf);
- return -1;
-}
-static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) {
- if (info->buf == NULL) return;
- if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL;
- __Pyx_ReleaseBuffer(info);
-}
-
-static void __Pyx_RaiseBufferIndexError(int axis) {
- PyErr_Format(PyExc_IndexError,
- "Out of bounds on buffer access (axis %d)", axis);
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
-}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* exc_type = tstate->curexc_type;
- if (unlikely(exc_type)) {
- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#endif
-}
-
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
-}
-
-static CYTHON_INLINE long __Pyx_div_long(long a, long b) {
- long q = a / b;
- long r = a - q*b;
- q -= ((r != 0) & ((r ^ b) < 0));
- return q;
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
- Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- }
- #if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
- if (cause && cause != Py_None) {
- PyObject *fixed_cause;
- if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- }
- else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- }
- else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static void __Pyx_RaiseBufferFallbackError(void) {
- PyErr_Format(PyExc_ValueError,
- "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!");
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import = 0;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-#if PY_MAJOR_VERSION < 3
-static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
- CYTHON_UNUSED PyObject *getbuffer_cobj;
- #if PY_VERSION_HEX >= 0x02060000
- if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
- #endif
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags);
- #if PY_VERSION_HEX < 0x02060000
- if (obj->ob_type->tp_dict &&
- (getbuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
- "__pyx_getbuffer"))) {
- getbufferproc func;
- #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
- func = (getbufferproc) PyCapsule_GetPointer(getbuffer_cobj, "getbuffer(obj, view, flags)");
- #else
- func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj);
- #endif
- Py_DECREF(getbuffer_cobj);
- if (!func)
- goto fail;
- return func(obj, view, flags);
- } else {
- PyErr_Clear();
- }
- #endif
- PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
-#if PY_VERSION_HEX < 0x02060000
-fail:
-#endif
- return -1;
-}
-static void __Pyx_ReleaseBuffer(Py_buffer *view) {
- PyObject *obj = view->obj;
- CYTHON_UNUSED PyObject *releasebuffer_cobj;
- if (!obj) return;
- #if PY_VERSION_HEX >= 0x02060000
- if (PyObject_CheckBuffer(obj)) {
- PyBuffer_Release(view);
- return;
- }
- #endif
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; }
- #if PY_VERSION_HEX < 0x02060000
- if (obj->ob_type->tp_dict &&
- (releasebuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
- "__pyx_releasebuffer"))) {
- releasebufferproc func;
- #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
- func = (releasebufferproc) PyCapsule_GetPointer(releasebuffer_cobj, "releasebuffer(obj, view)");
- #else
- func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj);
- #endif
- Py_DECREF(releasebuffer_cobj);
- if (!func)
- goto fail;
- func(obj, view);
- return;
- } else {
- PyErr_Clear();
- }
- #endif
- goto nofail;
-#if PY_VERSION_HEX < 0x02060000
-fail:
-#endif
- PyErr_WriteUnraisable(obj);
-nofail:
- Py_DECREF(obj);
- view->obj = NULL;
-}
-#endif /* PY_MAJOR_VERSION < 3 */
-
-
- static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
-#if PY_MAJOR_VERSION < 3
- PyErr_Format(PyExc_ImportError, "cannot import name %.230s",
- PyString_AsString(name));
-#else
- PyErr_Format(PyExc_ImportError, "cannot import name %S", name);
-#endif
-}
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return ::std::complex< float >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return x + y*(__pyx_t_float_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- __pyx_t_float_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrtf(z.real*z.real + z.imag*z.imag);
- #else
- return hypotf(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- float denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(a, a);
- case 3:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, a);
- case 4:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- }
- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_absf(a);
- theta = atan2f(a.imag, a.real);
- }
- lnr = logf(r);
- z_r = expf(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cosf(z_theta);
- z.imag = z_r * sinf(z_theta);
- return z;
- }
- #endif
-#endif
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return ::std::complex< double >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return x + y*(__pyx_t_double_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- __pyx_t_double_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrt(z.real*z.real + z.imag*z.imag);
- #else
- return hypot(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- double denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(a, a);
- case 3:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, a);
- case 4:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- }
- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_abs(a);
- theta = atan2(a.imag, a.real);
- }
- lnr = log(r);
- z_r = exp(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cos(z_theta);
- z.imag = z_r * sin(z_theta);
- return z;
- }
- #endif
-#endif
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
-#ifndef __PYX_HAVE_RT_ImportType
-#define __PYX_HAVE_RT_ImportType
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%s.%s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%s.%s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/bbi/bigbed_file.c b/lib/bx/bbi/bigbed_file.c
deleted file mode 100644
index f4016b7..0000000
--- a/lib/bx/bbi/bigbed_file.c
+++ /dev/null
@@ -1,8069 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
- #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define Py_TPFLAGS_CHECKTYPES 0
- #define Py_TPFLAGS_HAVE_INDEX 0
-#endif
-#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBaseString_Type PyUnicode_Type
- #define PyStringObject PyUnicodeObject
- #define PyString_Type PyUnicode_Type
- #define PyString_Check PyUnicode_Check
- #define PyString_CheckExact PyUnicode_CheckExact
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PyBytesObject PyStringObject
- #define PyBytes_Type PyString_Type
- #define PyBytes_Check PyString_Check
- #define PyBytes_CheckExact PyString_CheckExact
- #define PyBytes_FromString PyString_FromString
- #define PyBytes_FromStringAndSize PyString_FromStringAndSize
- #define PyBytes_FromFormat PyString_FromFormat
- #define PyBytes_DecodeEscape PyString_DecodeEscape
- #define PyBytes_AsString PyString_AsString
- #define PyBytes_AsStringAndSize PyString_AsStringAndSize
- #define PyBytes_Size PyString_Size
- #define PyBytes_AS_STRING PyString_AS_STRING
- #define PyBytes_GET_SIZE PyString_GET_SIZE
- #define PyBytes_Repr PyString_Repr
- #define PyBytes_Concat PyString_Concat
- #define PyBytes_ConcatAndDel PyString_ConcatAndDel
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
- #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
-#endif
-#ifndef PySet_CheckExact
- #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
-#endif
-#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-#if PY_MAJOR_VERSION >= 3
- #define PyIntObject PyLongObject
- #define PyInt_Type PyLong_Type
- #define PyInt_Check(op) PyLong_Check(op)
- #define PyInt_CheckExact(op) PyLong_CheckExact(op)
- #define PyInt_FromString PyLong_FromString
- #define PyInt_FromUnicode PyLong_FromUnicode
- #define PyInt_FromLong PyLong_FromLong
- #define PyInt_FromSize_t PyLong_FromSize_t
- #define PyInt_FromSsize_t PyLong_FromSsize_t
- #define PyInt_AsLong PyLong_AsLong
- #define PyInt_AS_LONG PyLong_AS_LONG
- #define PyInt_AsSsize_t PyLong_AsSsize_t
- #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
- #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
-#endif
-#if PY_VERSION_HEX < 0x03020000
- typedef long Py_hash_t;
- #define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
-#else
- #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
- #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
-#endif
-#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
- #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
- #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
-#else
- #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
- #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
-#endif
-#if PY_VERSION_HEX < 0x02050000
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
- #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
-#else
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
- #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
-#endif
-#if PY_VERSION_HEX < 0x02050000
- #define __Pyx_NAMESTR(n) ((char *)(n))
- #define __Pyx_DOCSTR(n) ((char *)(n))
-#else
- #define __Pyx_NAMESTR(n) (n)
- #define __Pyx_DOCSTR(n) (n)
-#endif
-
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
-#ifndef __PYX_EXTERN_C
- #ifdef __cplusplus
- #define __PYX_EXTERN_C extern "C"
- #else
- #define __PYX_EXTERN_C extern
- #endif
-#endif
-
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
-#define __PYX_HAVE__bx__bbi__bigbed_file
-#define __PYX_HAVE_API__bx__bbi__bigbed_file
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "numpy/arrayobject.h"
-#include "numpy/ufuncobject.h"
-#ifdef _OPENMP
-#include <omp.h>
-#endif /* _OPENMP */
-
-#ifdef PYREX_WITHOUT_ASSERTIONS
-#define CYTHON_WITHOUT_ASSERTIONS
-#endif
-
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
-#endif
-#ifndef CYTHON_UNUSED
-# if defined(__GNUC__)
-# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-#endif
-typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
-#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-#if CYTHON_COMPILING_IN_CPYTHON
-#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#else
-#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
-#endif
-#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
-
-
-#ifdef __GNUC__
- /* Test for GCC > 2.95 */
- #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
- #else /* __GNUC__ > 2 ... */
- #define likely(x) (x)
- #define unlikely(x) (x)
- #endif /* __GNUC__ > 2 ... */
-#else /* __GNUC__ */
- #define likely(x) (x)
- #define unlikely(x) (x)
-#endif /* __GNUC__ */
-
-static PyObject *__pyx_m;
-static PyObject *__pyx_b;
-static PyObject *__pyx_empty_tuple;
-static PyObject *__pyx_empty_bytes;
-static int __pyx_lineno;
-static int __pyx_clineno = 0;
-static const char * __pyx_cfilenm= __FILE__;
-static const char *__pyx_filename;
-
-#if !defined(CYTHON_CCOMPLEX)
- #if defined(__cplusplus)
- #define CYTHON_CCOMPLEX 1
- #elif defined(_Complex_I)
- #define CYTHON_CCOMPLEX 1
- #else
- #define CYTHON_CCOMPLEX 0
- #endif
-#endif
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- #include <complex>
- #else
- #include <complex.h>
- #endif
-#endif
-#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__)
- #undef _Complex_I
- #define _Complex_I 1.0fj
-#endif
-
-
-static const char *__pyx_f[] = {
- "bigbed_file.pyx",
- "numpy.pxd",
- "bpt_file.pxd",
- "cirtree_file.pxd",
- "type.pxd",
- "bbi_file.pxd",
-};
-
-/* "types.pxd":1
- * ctypedef unsigned char UBYTE # <<<<<<<<<<<<<<
- * ctypedef signed char BYTE
- * ctypedef unsigned short UWORD
- */
-typedef unsigned char __pyx_t_2bx_3bbi_5types_UBYTE;
-
-/* "types.pxd":2
- * ctypedef unsigned char UBYTE
- * ctypedef signed char BYTE # <<<<<<<<<<<<<<
- * ctypedef unsigned short UWORD
- * ctypedef short WORD
- */
-typedef signed char __pyx_t_2bx_3bbi_5types_BYTE;
-
-/* "types.pxd":3
- * ctypedef unsigned char UBYTE
- * ctypedef signed char BYTE
- * ctypedef unsigned short UWORD # <<<<<<<<<<<<<<
- * ctypedef short WORD
- * ctypedef unsigned long long bits64
- */
-typedef unsigned short __pyx_t_2bx_3bbi_5types_UWORD;
-
-/* "types.pxd":4
- * ctypedef signed char BYTE
- * ctypedef unsigned short UWORD
- * ctypedef short WORD # <<<<<<<<<<<<<<
- * ctypedef unsigned long long bits64
- * ctypedef unsigned bits32
- */
-typedef short __pyx_t_2bx_3bbi_5types_WORD;
-
-/* "types.pxd":5
- * ctypedef unsigned short UWORD
- * ctypedef short WORD
- * ctypedef unsigned long long bits64 # <<<<<<<<<<<<<<
- * ctypedef unsigned bits32
- * ctypedef unsigned short bits16
- */
-typedef unsigned PY_LONG_LONG __pyx_t_2bx_3bbi_5types_bits64;
-
-/* "types.pxd":6
- * ctypedef short WORD
- * ctypedef unsigned long long bits64
- * ctypedef unsigned bits32 # <<<<<<<<<<<<<<
- * ctypedef unsigned short bits16
- * ctypedef unsigned char bits8
- */
-typedef unsigned int __pyx_t_2bx_3bbi_5types_bits32;
-
-/* "types.pxd":7
- * ctypedef unsigned long long bits64
- * ctypedef unsigned bits32
- * ctypedef unsigned short bits16 # <<<<<<<<<<<<<<
- * ctypedef unsigned char bits8
- * ctypedef int signed32
- */
-typedef unsigned short __pyx_t_2bx_3bbi_5types_bits16;
-
-/* "types.pxd":8
- * ctypedef unsigned bits32
- * ctypedef unsigned short bits16
- * ctypedef unsigned char bits8 # <<<<<<<<<<<<<<
- * ctypedef int signed32
- *
- */
-typedef unsigned char __pyx_t_2bx_3bbi_5types_bits8;
-
-/* "types.pxd":9
- * ctypedef unsigned short bits16
- * ctypedef unsigned char bits8
- * ctypedef int signed32 # <<<<<<<<<<<<<<
- *
- * ctypedef bint boolean
- */
-typedef int __pyx_t_2bx_3bbi_5types_signed32;
-
-/* "types.pxd":11
- * ctypedef int signed32
- *
- * ctypedef bint boolean # <<<<<<<<<<<<<<
- *
- */
-typedef int __pyx_t_2bx_3bbi_5types_boolean;
-
-/* "numpy.pxd":723
- * # in Cython to enable them only on the right systems.
- *
- * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t
- */
-typedef npy_int8 __pyx_t_5numpy_int8_t;
-
-/* "numpy.pxd":724
- *
- * ctypedef npy_int8 int8_t
- * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
- * ctypedef npy_int32 int32_t
- * ctypedef npy_int64 int64_t
- */
-typedef npy_int16 __pyx_t_5numpy_int16_t;
-
-/* "numpy.pxd":725
- * ctypedef npy_int8 int8_t
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
- * ctypedef npy_int64 int64_t
- * #ctypedef npy_int96 int96_t
- */
-typedef npy_int32 __pyx_t_5numpy_int32_t;
-
-/* "numpy.pxd":726
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t
- * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_int96 int96_t
- * #ctypedef npy_int128 int128_t
- */
-typedef npy_int64 __pyx_t_5numpy_int64_t;
-
-/* "numpy.pxd":730
- * #ctypedef npy_int128 int128_t
- *
- * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t
- */
-typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-
-/* "numpy.pxd":731
- *
- * ctypedef npy_uint8 uint8_t
- * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint32 uint32_t
- * ctypedef npy_uint64 uint64_t
- */
-typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-
-/* "numpy.pxd":732
- * ctypedef npy_uint8 uint8_t
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint64 uint64_t
- * #ctypedef npy_uint96 uint96_t
- */
-typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-
-/* "numpy.pxd":733
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t
- * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_uint96 uint96_t
- * #ctypedef npy_uint128 uint128_t
- */
-typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-
-/* "numpy.pxd":737
- * #ctypedef npy_uint128 uint128_t
- *
- * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
- * ctypedef npy_float64 float64_t
- * #ctypedef npy_float80 float80_t
- */
-typedef npy_float32 __pyx_t_5numpy_float32_t;
-
-/* "numpy.pxd":738
- *
- * ctypedef npy_float32 float32_t
- * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_float80 float80_t
- * #ctypedef npy_float128 float128_t
- */
-typedef npy_float64 __pyx_t_5numpy_float64_t;
-
-/* "numpy.pxd":747
- * # The int types are mapped a bit surprising --
- * # numpy.int corresponds to 'l' and numpy.long to 'q'
- * ctypedef npy_long int_t # <<<<<<<<<<<<<<
- * ctypedef npy_longlong long_t
- * ctypedef npy_longlong longlong_t
- */
-typedef npy_long __pyx_t_5numpy_int_t;
-
-/* "numpy.pxd":748
- * # numpy.int corresponds to 'l' and numpy.long to 'q'
- * ctypedef npy_long int_t
- * ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
- * ctypedef npy_longlong longlong_t
- *
- */
-typedef npy_longlong __pyx_t_5numpy_long_t;
-
-/* "numpy.pxd":749
- * ctypedef npy_long int_t
- * ctypedef npy_longlong long_t
- * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_ulong uint_t
- */
-typedef npy_longlong __pyx_t_5numpy_longlong_t;
-
-/* "numpy.pxd":751
- * ctypedef npy_longlong longlong_t
- *
- * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
- * ctypedef npy_ulonglong ulong_t
- * ctypedef npy_ulonglong ulonglong_t
- */
-typedef npy_ulong __pyx_t_5numpy_uint_t;
-
-/* "numpy.pxd":752
- *
- * ctypedef npy_ulong uint_t
- * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
- * ctypedef npy_ulonglong ulonglong_t
- *
- */
-typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-
-/* "numpy.pxd":753
- * ctypedef npy_ulong uint_t
- * ctypedef npy_ulonglong ulong_t
- * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_intp intp_t
- */
-typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-
-/* "numpy.pxd":755
- * ctypedef npy_ulonglong ulonglong_t
- *
- * ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
- * ctypedef npy_uintp uintp_t
- *
- */
-typedef npy_intp __pyx_t_5numpy_intp_t;
-
-/* "numpy.pxd":756
- *
- * ctypedef npy_intp intp_t
- * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_double float_t
- */
-typedef npy_uintp __pyx_t_5numpy_uintp_t;
-
-/* "numpy.pxd":758
- * ctypedef npy_uintp uintp_t
- *
- * ctypedef npy_double float_t # <<<<<<<<<<<<<<
- * ctypedef npy_double double_t
- * ctypedef npy_longdouble longdouble_t
- */
-typedef npy_double __pyx_t_5numpy_float_t;
-
-/* "numpy.pxd":759
- *
- * ctypedef npy_double float_t
- * ctypedef npy_double double_t # <<<<<<<<<<<<<<
- * ctypedef npy_longdouble longdouble_t
- *
- */
-typedef npy_double __pyx_t_5numpy_double_t;
-
-/* "numpy.pxd":760
- * ctypedef npy_double float_t
- * ctypedef npy_double double_t
- * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_cfloat cfloat_t
- */
-typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- typedef ::std::complex< float > __pyx_t_float_complex;
- #else
- typedef float _Complex __pyx_t_float_complex;
- #endif
-#else
- typedef struct { float real, imag; } __pyx_t_float_complex;
-#endif
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- typedef ::std::complex< double > __pyx_t_double_complex;
- #else
- typedef double _Complex __pyx_t_double_complex;
- #endif
-#else
- typedef struct { double real, imag; } __pyx_t_double_complex;
-#endif
-
-
-/*--- Type declarations ---*/
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock;
-struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile;
-struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile;
-struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler;
-struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler;
-struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile;
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData;
-struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler;
-struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler;
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile;
-
-/* "numpy.pxd":762
- * ctypedef npy_longdouble longdouble_t
- *
- * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
- * ctypedef npy_cdouble cdouble_t
- * ctypedef npy_clongdouble clongdouble_t
- */
-typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-
-/* "numpy.pxd":763
- *
- * ctypedef npy_cfloat cfloat_t
- * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
- * ctypedef npy_clongdouble clongdouble_t
- *
- */
-typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-
-/* "numpy.pxd":764
- * ctypedef npy_cfloat cfloat_t
- * ctypedef npy_cdouble cdouble_t
- * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_cdouble complex_t
- */
-typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-
-/* "numpy.pxd":766
- * ctypedef npy_clongdouble clongdouble_t
- *
- * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
- *
- * cdef inline object PyArray_MultiIterNew1(a):
- */
-typedef npy_cdouble __pyx_t_5numpy_complex_t;
-
-/* "bbi_file.pxd":8
- * cimport numpy
- *
- * cdef class SummaryBlock: # <<<<<<<<<<<<<<
- * """
- * A block of summary data from disk
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock {
- PyObject_HEAD
- __pyx_t_2bx_3bbi_5types_bits32 chrom_id;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
- __pyx_t_2bx_3bbi_5types_bits32 valid_count;
- double min_val;
- double max_val;
- double sum_data;
- double sum_squares;
-};
-
-
-/* "bbi_file.pxd":37
- * cdef accumulate_interval_value( self, bits32 s, bits32 e, float val )
- *
- * cdef class BBIFile # <<<<<<<<<<<<<<
- *
- * cdef class BlockHandler:
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile *__pyx_vtab;
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_bits32 magic;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile *chrom_bpt;
- __pyx_t_2bx_3bbi_5types_bits16 version;
- __pyx_t_2bx_3bbi_5types_bits16 zoom_levels;
- __pyx_t_2bx_3bbi_5types_bits64 chrom_tree_offset;
- __pyx_t_2bx_3bbi_5types_bits64 unzoomed_data_offset;
- __pyx_t_2bx_3bbi_5types_bits64 unzoomed_index_offset;
- __pyx_t_2bx_3bbi_5types_bits16 field_count;
- __pyx_t_2bx_3bbi_5types_bits16 defined_field_count;
- __pyx_t_2bx_3bbi_5types_bits64 as_offset;
- __pyx_t_2bx_3bbi_5types_bits64 total_summary_offset;
- __pyx_t_2bx_3bbi_5types_bits32 uncompress_buf_size;
- PyObject *level_list;
-};
-
-
-/* "bx/bbi/bigbed_file.pyx":85
- * self.intervals.append( ( s, e, rest ) )
- *
- * cdef class BigBedFile( BBIFile ): # <<<<<<<<<<<<<<
- * """
- * A "big binary indexed" file whose raw data is in BED format.
- */
-struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedFile {
- struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile __pyx_base;
-};
-
-
-/* "bbi_file.pxd":39
- * cdef class BBIFile
- *
- * cdef class BlockHandler: # <<<<<<<<<<<<<<
- * """
- * Callback for `BBIFile.visit_blocks_in_region`
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtab;
-};
-
-
-/* "bx/bbi/bigbed_file.pyx":20
- * return min( end1, end2 ) - max( start1, start2 )
- *
- * cdef class BigBedBlockHandler( BlockHandler ): # <<<<<<<<<<<<<<
- * """
- * BlockHandler that parses the block into a series of BED records
- */
-struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler {
- struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler __pyx_base;
- __pyx_t_2bx_3bbi_5types_bits32 chrom_id;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
-};
-
-
-/* "cirtree_file.pxd":3
- * from types cimport *
- *
- * cdef class CIRTreeFile: # <<<<<<<<<<<<<<
- * cdef object file
- * cdef object reader
- */
-struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile {
- PyObject_HEAD
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- __pyx_t_2bx_3bbi_5types_bits64 root_offset;
- __pyx_t_2bx_3bbi_5types_bits32 block_size;
- __pyx_t_2bx_3bbi_5types_bits64 item_count;
- __pyx_t_2bx_3bbi_5types_bits32 start_chrom_ix;
- __pyx_t_2bx_3bbi_5types_bits32 start_base;
- __pyx_t_2bx_3bbi_5types_bits32 end_chrom_ix;
- __pyx_t_2bx_3bbi_5types_bits32 end_base;
- __pyx_t_2bx_3bbi_5types_bits64 file_size;
- __pyx_t_2bx_3bbi_5types_bits32 items_per_slot;
-};
-
-
-/* "bbi_file.pxd":21
- * cdef public double sum_squares
- *
- * cdef class SummarizedData: # <<<<<<<<<<<<<<
- * """
- * The result of using SummaryBlocks read from the file to produce a
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtab;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
- int size;
- PyArrayObject *valid_count;
- PyArrayObject *min_val;
- PyArrayObject *max_val;
- PyArrayObject *sum_data;
- PyArrayObject *sum_squares;
-};
-
-
-/* "bx/bbi/bigbed_file.pyx":54
- * pass
- *
- * cdef class SummarizingBlockHandler( BigBedBlockHandler ): # <<<<<<<<<<<<<<
- * """
- * Accumulates intervals into a SummarizedData
- */
-struct __pyx_obj_2bx_3bbi_11bigbed_file_SummarizingBlockHandler {
- struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler __pyx_base;
- struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *sd;
-};
-
-
-/* "bx/bbi/bigbed_file.pyx":73
- * self.sd.accumulate_interval_value( s, e, 1 )
- *
- * cdef class IntervalAccumulatingBlockHandler( BigBedBlockHandler ): # <<<<<<<<<<<<<<
- * cdef list intervals
- * """
- */
-struct __pyx_obj_2bx_3bbi_11bigbed_file_IntervalAccumulatingBlockHandler {
- struct __pyx_obj_2bx_3bbi_11bigbed_file_BigBedBlockHandler __pyx_base;
- PyObject *intervals;
-};
-
-
-/* "bpt_file.pxd":5
- * from types cimport *
- *
- * cdef class BPTFile: # <<<<<<<<<<<<<<
- * """
- * On disk B+ tree compatible with Jim Kent's bPlusTree.c
- */
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile {
- PyObject_HEAD
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- __pyx_t_2bx_3bbi_5types_bits32 block_size;
- __pyx_t_2bx_3bbi_5types_bits32 key_size;
- __pyx_t_2bx_3bbi_5types_bits32 value_size;
- __pyx_t_2bx_3bbi_5types_bits64 item_count;
- __pyx_t_2bx_3bbi_5types_bits64 root_offset;
-};
-
-
-
-/* "bbi_file.pxd":37
- * cdef accumulate_interval_value( self, bits32 s, bits32 e, float val )
- *
- * cdef class BBIFile # <<<<<<<<<<<<<<
- *
- * cdef class BlockHandler:
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile {
- PyObject *(*visit_blocks_in_region)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *);
- PyObject *(*_get_chrom_id_and_size)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *);
- PyObject *(*_best_zoom_level)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, int);
- PyObject *(*summarize)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch);
- PyObject *(*summarize_from_full)(struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *, char *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, int, int __pyx_skip_dispatch);
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- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#endif
-}
-
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
-}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
- Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- }
- #if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
- if (cause && cause != Py_None) {
- PyObject *fixed_cause;
- if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- }
- else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- }
- else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-}
-
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
- if (unlikely(!type)) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (likely(PyObject_TypeCheck(obj, type)))
- return 1;
- PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
- Py_TYPE(obj)->tp_name, type->tp_name);
- return 0;
-}
-
-static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_dealloc != current_tp_dealloc)
- type = type->tp_base;
- while (type && type->tp_dealloc == current_tp_dealloc)
- type = type->tp_base;
- if (type)
- type->tp_dealloc(obj);
-}
-
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_traverse != current_tp_traverse)
- type = type->tp_base;
- while (type && type->tp_traverse == current_tp_traverse)
- type = type->tp_base;
- if (type && type->tp_traverse)
- return type->tp_traverse(obj, v, a);
- return 0;
-}
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_clear != current_tp_clear)
- type = type->tp_base;
- while (type && type->tp_clear == current_tp_clear)
- type = type->tp_base;
- if (type && type->tp_clear)
- type->tp_clear(obj);
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import = 0;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
-#if PY_MAJOR_VERSION < 3
- PyErr_Format(PyExc_ImportError, "cannot import name %.230s",
- PyString_AsString(name));
-#else
- PyErr_Format(PyExc_ImportError, "cannot import name %S", name);
-#endif
-}
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return ::std::complex< float >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return x + y*(__pyx_t_float_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- __pyx_t_float_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrtf(z.real*z.real + z.imag*z.imag);
- #else
- return hypotf(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- float denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(a, a);
- case 3:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, a);
- case 4:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- }
- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_absf(a);
- theta = atan2f(a.imag, a.real);
- }
- lnr = logf(r);
- z_r = expf(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cosf(z_theta);
- z.imag = z_r * sinf(z_theta);
- return z;
- }
- #endif
-#endif
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return ::std::complex< double >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return x + y*(__pyx_t_double_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- __pyx_t_double_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrt(z.real*z.real + z.imag*z.imag);
- #else
- return hypot(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- double denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(a, a);
- case 3:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, a);
- case 4:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- }
- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_abs(a);
- theta = atan2(a.imag, a.real);
- }
- lnr = log(r);
- z_r = exp(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cos(z_theta);
- z.imag = z_r * sin(z_theta);
- return z;
- }
- #endif
-#endif
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
-#ifndef __PYX_HAVE_RT_ImportType
-#define __PYX_HAVE_RT_ImportType
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%s.%s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%s.%s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static void* __Pyx_GetVtable(PyObject *dict) {
- void* ptr;
- PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
- if (!ob)
- goto bad;
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- ptr = PyCapsule_GetPointer(ob, 0);
-#else
- ptr = PyCObject_AsVoidPtr(ob);
-#endif
- if (!ptr && !PyErr_Occurred())
- PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
- Py_DECREF(ob);
- return ptr;
-bad:
- Py_XDECREF(ob);
- return NULL;
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/bbi/bigwig_file.c b/lib/bx/bbi/bigwig_file.c
deleted file mode 100644
index 1fd18d3..0000000
--- a/lib/bx/bbi/bigwig_file.c
+++ /dev/null
@@ -1,9619 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
- #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define Py_TPFLAGS_CHECKTYPES 0
- #define Py_TPFLAGS_HAVE_INDEX 0
-#endif
-#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBaseString_Type PyUnicode_Type
- #define PyStringObject PyUnicodeObject
- #define PyString_Type PyUnicode_Type
- #define PyString_Check PyUnicode_Check
- #define PyString_CheckExact PyUnicode_CheckExact
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PyBytesObject PyStringObject
- #define PyBytes_Type PyString_Type
- #define PyBytes_Check PyString_Check
- #define PyBytes_CheckExact PyString_CheckExact
- #define PyBytes_FromString PyString_FromString
- #define PyBytes_FromStringAndSize PyString_FromStringAndSize
- #define PyBytes_FromFormat PyString_FromFormat
- #define PyBytes_DecodeEscape PyString_DecodeEscape
- #define PyBytes_AsString PyString_AsString
- #define PyBytes_AsStringAndSize PyString_AsStringAndSize
- #define PyBytes_Size PyString_Size
- #define PyBytes_AS_STRING PyString_AS_STRING
- #define PyBytes_GET_SIZE PyString_GET_SIZE
- #define PyBytes_Repr PyString_Repr
- #define PyBytes_Concat PyString_Concat
- #define PyBytes_ConcatAndDel PyString_ConcatAndDel
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
- #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
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-#ifndef PySet_CheckExact
- #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
-#endif
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- #define PyIntObject PyLongObject
- #define PyInt_Type PyLong_Type
- #define PyInt_Check(op) PyLong_Check(op)
- #define PyInt_CheckExact(op) PyLong_CheckExact(op)
- #define PyInt_FromString PyLong_FromString
- #define PyInt_FromUnicode PyLong_FromUnicode
- #define PyInt_FromLong PyLong_FromLong
- #define PyInt_FromSize_t PyLong_FromSize_t
- #define PyInt_FromSsize_t PyLong_FromSsize_t
- #define PyInt_AsLong PyLong_AsLong
- #define PyInt_AS_LONG PyLong_AS_LONG
- #define PyInt_AsSsize_t PyLong_AsSsize_t
- #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
- #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
-#endif
-#if PY_VERSION_HEX < 0x03020000
- typedef long Py_hash_t;
- #define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
-#else
- #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
- #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
-#endif
-#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
- #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
- #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
-#else
- #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
- #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
-#endif
-#if PY_VERSION_HEX < 0x02050000
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
- #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
-#else
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
- #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
-#endif
-#if PY_VERSION_HEX < 0x02050000
- #define __Pyx_NAMESTR(n) ((char *)(n))
- #define __Pyx_DOCSTR(n) ((char *)(n))
-#else
- #define __Pyx_NAMESTR(n) (n)
- #define __Pyx_DOCSTR(n) (n)
-#endif
-
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
-#ifndef __PYX_EXTERN_C
- #ifdef __cplusplus
- #define __PYX_EXTERN_C extern "C"
- #else
- #define __PYX_EXTERN_C extern
- #endif
-#endif
-
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
-#define __PYX_HAVE__bx__bbi__bigwig_file
-#define __PYX_HAVE_API__bx__bbi__bigwig_file
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "numpy/arrayobject.h"
-#include "numpy/ufuncobject.h"
-#ifdef _OPENMP
-#include <omp.h>
-#endif /* _OPENMP */
-
-#ifdef PYREX_WITHOUT_ASSERTIONS
-#define CYTHON_WITHOUT_ASSERTIONS
-#endif
-
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
-#endif
-#ifndef CYTHON_UNUSED
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-# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
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-# else
-# define CYTHON_UNUSED
-# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
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-# define CYTHON_UNUSED
-# endif
-#endif
-typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
-#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-#if CYTHON_COMPILING_IN_CPYTHON
-#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#else
-#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
-#endif
-#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
-
-
-#ifdef __GNUC__
- /* Test for GCC > 2.95 */
- #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
- #else /* __GNUC__ > 2 ... */
- #define likely(x) (x)
- #define unlikely(x) (x)
- #endif /* __GNUC__ > 2 ... */
-#else /* __GNUC__ */
- #define likely(x) (x)
- #define unlikely(x) (x)
-#endif /* __GNUC__ */
-
-static PyObject *__pyx_m;
-static PyObject *__pyx_b;
-static PyObject *__pyx_empty_tuple;
-static PyObject *__pyx_empty_bytes;
-static int __pyx_lineno;
-static int __pyx_clineno = 0;
-static const char * __pyx_cfilenm= __FILE__;
-static const char *__pyx_filename;
-
-#if !defined(CYTHON_CCOMPLEX)
- #if defined(__cplusplus)
- #define CYTHON_CCOMPLEX 1
- #elif defined(_Complex_I)
- #define CYTHON_CCOMPLEX 1
- #else
- #define CYTHON_CCOMPLEX 0
- #endif
-#endif
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- #include <complex>
- #else
- #include <complex.h>
- #endif
-#endif
-#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__)
- #undef _Complex_I
- #define _Complex_I 1.0fj
-#endif
-
-
-static const char *__pyx_f[] = {
- "bigwig_file.pyx",
- "numpy.pxd",
- "bpt_file.pxd",
- "cirtree_file.pxd",
- "type.pxd",
- "bbi_file.pxd",
-};
-#define IS_UNSIGNED(type) (((type) -1) > 0)
-struct __Pyx_StructField_;
-#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0)
-typedef struct {
- const char* name; /* for error messages only */
- struct __Pyx_StructField_* fields;
- size_t size; /* sizeof(type) */
- size_t arraysize[8]; /* length of array in each dimension */
- int ndim;
- char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject, c_H_ar */
- char is_unsigned;
- int flags;
-} __Pyx_TypeInfo;
-typedef struct __Pyx_StructField_ {
- __Pyx_TypeInfo* type;
- const char* name;
- size_t offset;
-} __Pyx_StructField;
-typedef struct {
- __Pyx_StructField* field;
- size_t parent_offset;
-} __Pyx_BufFmt_StackElem;
-typedef struct {
- __Pyx_StructField root;
- __Pyx_BufFmt_StackElem* head;
- size_t fmt_offset;
- size_t new_count, enc_count;
- size_t struct_alignment;
- int is_complex;
- char enc_type;
- char new_packmode;
- char enc_packmode;
- char is_valid_array;
-} __Pyx_BufFmt_Context;
-
-
-/* "types.pxd":1
- * ctypedef unsigned char UBYTE # <<<<<<<<<<<<<<
- * ctypedef signed char BYTE
- * ctypedef unsigned short UWORD
- */
-typedef unsigned char __pyx_t_2bx_3bbi_5types_UBYTE;
-
-/* "types.pxd":2
- * ctypedef unsigned char UBYTE
- * ctypedef signed char BYTE # <<<<<<<<<<<<<<
- * ctypedef unsigned short UWORD
- * ctypedef short WORD
- */
-typedef signed char __pyx_t_2bx_3bbi_5types_BYTE;
-
-/* "types.pxd":3
- * ctypedef unsigned char UBYTE
- * ctypedef signed char BYTE
- * ctypedef unsigned short UWORD # <<<<<<<<<<<<<<
- * ctypedef short WORD
- * ctypedef unsigned long long bits64
- */
-typedef unsigned short __pyx_t_2bx_3bbi_5types_UWORD;
-
-/* "types.pxd":4
- * ctypedef signed char BYTE
- * ctypedef unsigned short UWORD
- * ctypedef short WORD # <<<<<<<<<<<<<<
- * ctypedef unsigned long long bits64
- * ctypedef unsigned bits32
- */
-typedef short __pyx_t_2bx_3bbi_5types_WORD;
-
-/* "types.pxd":5
- * ctypedef unsigned short UWORD
- * ctypedef short WORD
- * ctypedef unsigned long long bits64 # <<<<<<<<<<<<<<
- * ctypedef unsigned bits32
- * ctypedef unsigned short bits16
- */
-typedef unsigned PY_LONG_LONG __pyx_t_2bx_3bbi_5types_bits64;
-
-/* "types.pxd":6
- * ctypedef short WORD
- * ctypedef unsigned long long bits64
- * ctypedef unsigned bits32 # <<<<<<<<<<<<<<
- * ctypedef unsigned short bits16
- * ctypedef unsigned char bits8
- */
-typedef unsigned int __pyx_t_2bx_3bbi_5types_bits32;
-
-/* "types.pxd":7
- * ctypedef unsigned long long bits64
- * ctypedef unsigned bits32
- * ctypedef unsigned short bits16 # <<<<<<<<<<<<<<
- * ctypedef unsigned char bits8
- * ctypedef int signed32
- */
-typedef unsigned short __pyx_t_2bx_3bbi_5types_bits16;
-
-/* "types.pxd":8
- * ctypedef unsigned bits32
- * ctypedef unsigned short bits16
- * ctypedef unsigned char bits8 # <<<<<<<<<<<<<<
- * ctypedef int signed32
- *
- */
-typedef unsigned char __pyx_t_2bx_3bbi_5types_bits8;
-
-/* "types.pxd":9
- * ctypedef unsigned short bits16
- * ctypedef unsigned char bits8
- * ctypedef int signed32 # <<<<<<<<<<<<<<
- *
- * ctypedef bint boolean
- */
-typedef int __pyx_t_2bx_3bbi_5types_signed32;
-
-/* "types.pxd":11
- * ctypedef int signed32
- *
- * ctypedef bint boolean # <<<<<<<<<<<<<<
- *
- */
-typedef int __pyx_t_2bx_3bbi_5types_boolean;
-
-/* "numpy.pxd":723
- * # in Cython to enable them only on the right systems.
- *
- * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t
- */
-typedef npy_int8 __pyx_t_5numpy_int8_t;
-
-/* "numpy.pxd":724
- *
- * ctypedef npy_int8 int8_t
- * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
- * ctypedef npy_int32 int32_t
- * ctypedef npy_int64 int64_t
- */
-typedef npy_int16 __pyx_t_5numpy_int16_t;
-
-/* "numpy.pxd":725
- * ctypedef npy_int8 int8_t
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
- * ctypedef npy_int64 int64_t
- * #ctypedef npy_int96 int96_t
- */
-typedef npy_int32 __pyx_t_5numpy_int32_t;
-
-/* "numpy.pxd":726
- * ctypedef npy_int16 int16_t
- * ctypedef npy_int32 int32_t
- * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_int96 int96_t
- * #ctypedef npy_int128 int128_t
- */
-typedef npy_int64 __pyx_t_5numpy_int64_t;
-
-/* "numpy.pxd":730
- * #ctypedef npy_int128 int128_t
- *
- * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t
- */
-typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-
-/* "numpy.pxd":731
- *
- * ctypedef npy_uint8 uint8_t
- * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint32 uint32_t
- * ctypedef npy_uint64 uint64_t
- */
-typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-
-/* "numpy.pxd":732
- * ctypedef npy_uint8 uint8_t
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
- * ctypedef npy_uint64 uint64_t
- * #ctypedef npy_uint96 uint96_t
- */
-typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-
-/* "numpy.pxd":733
- * ctypedef npy_uint16 uint16_t
- * ctypedef npy_uint32 uint32_t
- * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_uint96 uint96_t
- * #ctypedef npy_uint128 uint128_t
- */
-typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-
-/* "numpy.pxd":737
- * #ctypedef npy_uint128 uint128_t
- *
- * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
- * ctypedef npy_float64 float64_t
- * #ctypedef npy_float80 float80_t
- */
-typedef npy_float32 __pyx_t_5numpy_float32_t;
-
-/* "numpy.pxd":738
- *
- * ctypedef npy_float32 float32_t
- * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
- * #ctypedef npy_float80 float80_t
- * #ctypedef npy_float128 float128_t
- */
-typedef npy_float64 __pyx_t_5numpy_float64_t;
-
-/* "numpy.pxd":747
- * # The int types are mapped a bit surprising --
- * # numpy.int corresponds to 'l' and numpy.long to 'q'
- * ctypedef npy_long int_t # <<<<<<<<<<<<<<
- * ctypedef npy_longlong long_t
- * ctypedef npy_longlong longlong_t
- */
-typedef npy_long __pyx_t_5numpy_int_t;
-
-/* "numpy.pxd":748
- * # numpy.int corresponds to 'l' and numpy.long to 'q'
- * ctypedef npy_long int_t
- * ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
- * ctypedef npy_longlong longlong_t
- *
- */
-typedef npy_longlong __pyx_t_5numpy_long_t;
-
-/* "numpy.pxd":749
- * ctypedef npy_long int_t
- * ctypedef npy_longlong long_t
- * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_ulong uint_t
- */
-typedef npy_longlong __pyx_t_5numpy_longlong_t;
-
-/* "numpy.pxd":751
- * ctypedef npy_longlong longlong_t
- *
- * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
- * ctypedef npy_ulonglong ulong_t
- * ctypedef npy_ulonglong ulonglong_t
- */
-typedef npy_ulong __pyx_t_5numpy_uint_t;
-
-/* "numpy.pxd":752
- *
- * ctypedef npy_ulong uint_t
- * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
- * ctypedef npy_ulonglong ulonglong_t
- *
- */
-typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-
-/* "numpy.pxd":753
- * ctypedef npy_ulong uint_t
- * ctypedef npy_ulonglong ulong_t
- * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_intp intp_t
- */
-typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-
-/* "numpy.pxd":755
- * ctypedef npy_ulonglong ulonglong_t
- *
- * ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
- * ctypedef npy_uintp uintp_t
- *
- */
-typedef npy_intp __pyx_t_5numpy_intp_t;
-
-/* "numpy.pxd":756
- *
- * ctypedef npy_intp intp_t
- * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_double float_t
- */
-typedef npy_uintp __pyx_t_5numpy_uintp_t;
-
-/* "numpy.pxd":758
- * ctypedef npy_uintp uintp_t
- *
- * ctypedef npy_double float_t # <<<<<<<<<<<<<<
- * ctypedef npy_double double_t
- * ctypedef npy_longdouble longdouble_t
- */
-typedef npy_double __pyx_t_5numpy_float_t;
-
-/* "numpy.pxd":759
- *
- * ctypedef npy_double float_t
- * ctypedef npy_double double_t # <<<<<<<<<<<<<<
- * ctypedef npy_longdouble longdouble_t
- *
- */
-typedef npy_double __pyx_t_5numpy_double_t;
-
-/* "numpy.pxd":760
- * ctypedef npy_double float_t
- * ctypedef npy_double double_t
- * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_cfloat cfloat_t
- */
-typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- typedef ::std::complex< float > __pyx_t_float_complex;
- #else
- typedef float _Complex __pyx_t_float_complex;
- #endif
-#else
- typedef struct { float real, imag; } __pyx_t_float_complex;
-#endif
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- typedef ::std::complex< double > __pyx_t_double_complex;
- #else
- typedef double _Complex __pyx_t_double_complex;
- #endif
-#else
- typedef struct { double real, imag; } __pyx_t_double_complex;
-#endif
-
-
-/*--- Type declarations ---*/
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock;
-struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile;
-struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile;
-struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler;
-struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler;
-struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler;
-struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler;
-struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile;
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData;
-struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler;
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile;
-
-/* "numpy.pxd":762
- * ctypedef npy_longdouble longdouble_t
- *
- * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
- * ctypedef npy_cdouble cdouble_t
- * ctypedef npy_clongdouble clongdouble_t
- */
-typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-
-/* "numpy.pxd":763
- *
- * ctypedef npy_cfloat cfloat_t
- * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
- * ctypedef npy_clongdouble clongdouble_t
- *
- */
-typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-
-/* "numpy.pxd":764
- * ctypedef npy_cfloat cfloat_t
- * ctypedef npy_cdouble cdouble_t
- * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
- *
- * ctypedef npy_cdouble complex_t
- */
-typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-
-/* "numpy.pxd":766
- * ctypedef npy_clongdouble clongdouble_t
- *
- * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
- *
- * cdef inline object PyArray_MultiIterNew1(a):
- */
-typedef npy_cdouble __pyx_t_5numpy_complex_t;
-
-/* "bbi_file.pxd":8
- * cimport numpy
- *
- * cdef class SummaryBlock: # <<<<<<<<<<<<<<
- * """
- * A block of summary data from disk
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummaryBlock {
- PyObject_HEAD
- __pyx_t_2bx_3bbi_5types_bits32 chrom_id;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
- __pyx_t_2bx_3bbi_5types_bits32 valid_count;
- double min_val;
- double max_val;
- double sum_data;
- double sum_squares;
-};
-
-
-/* "bbi_file.pxd":37
- * cdef accumulate_interval_value( self, bits32 s, bits32 e, float val )
- *
- * cdef class BBIFile # <<<<<<<<<<<<<<
- *
- * cdef class BlockHandler:
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BBIFile *__pyx_vtab;
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_bits32 magic;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile *chrom_bpt;
- __pyx_t_2bx_3bbi_5types_bits16 version;
- __pyx_t_2bx_3bbi_5types_bits16 zoom_levels;
- __pyx_t_2bx_3bbi_5types_bits64 chrom_tree_offset;
- __pyx_t_2bx_3bbi_5types_bits64 unzoomed_data_offset;
- __pyx_t_2bx_3bbi_5types_bits64 unzoomed_index_offset;
- __pyx_t_2bx_3bbi_5types_bits16 field_count;
- __pyx_t_2bx_3bbi_5types_bits16 defined_field_count;
- __pyx_t_2bx_3bbi_5types_bits64 as_offset;
- __pyx_t_2bx_3bbi_5types_bits64 total_summary_offset;
- __pyx_t_2bx_3bbi_5types_bits32 uncompress_buf_size;
- PyObject *level_list;
-};
-
-
-/* "bx/bbi/bigwig_file.pyx":122
- * array[ i ] = val
- *
- * cdef class BigWigFile( BBIFile ): # <<<<<<<<<<<<<<
- * """
- * A "big binary indexed" file whose raw data is in wiggle format.
- */
-struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigFile {
- struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile __pyx_base;
-};
-
-
-/* "bbi_file.pxd":39
- * cdef class BBIFile
- *
- * cdef class BlockHandler: # <<<<<<<<<<<<<<
- * """
- * Callback for `BBIFile.visit_blocks_in_region`
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtab;
-};
-
-
-/* "bx/bbi/bigwig_file.pyx":23
- * return min( end1, end2 ) - max( start1, start2 )
- *
- * cdef class BigWigBlockHandler( BlockHandler ): # <<<<<<<<<<<<<<
- * """
- * BlockHandler that parses the block into a series of wiggle records, and calls `handle_interval_value` for each.
- */
-struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler {
- struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler __pyx_base;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
-};
-
-
-/* "bx/bbi/bigwig_file.pyx":93
- * self.sd.accumulate_interval_value( s, e, val )
- *
- * cdef class IntervalAccumulatingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
- * cdef list intervals
- * """
- */
-struct __pyx_obj_2bx_3bbi_11bigwig_file_IntervalAccumulatingBlockHandler {
- struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler __pyx_base;
- PyObject *intervals;
-};
-
-
-/* "bx/bbi/bigwig_file.pyx":105
- * self.intervals.append( ( s, e, val ) )
- *
- * cdef class ArrayAccumulatingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
- * """
- * Accumulates intervals into a list of intervals with values
- */
-struct __pyx_obj_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler {
- struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler __pyx_base;
- PyArrayObject *array;
-};
-
-
-/* "cirtree_file.pxd":3
- * from types cimport *
- *
- * cdef class CIRTreeFile: # <<<<<<<<<<<<<<
- * cdef object file
- * cdef object reader
- */
-struct __pyx_obj_2bx_3bbi_12cirtree_file_CIRTreeFile {
- PyObject_HEAD
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- __pyx_t_2bx_3bbi_5types_bits64 root_offset;
- __pyx_t_2bx_3bbi_5types_bits32 block_size;
- __pyx_t_2bx_3bbi_5types_bits64 item_count;
- __pyx_t_2bx_3bbi_5types_bits32 start_chrom_ix;
- __pyx_t_2bx_3bbi_5types_bits32 start_base;
- __pyx_t_2bx_3bbi_5types_bits32 end_chrom_ix;
- __pyx_t_2bx_3bbi_5types_bits32 end_base;
- __pyx_t_2bx_3bbi_5types_bits64 file_size;
- __pyx_t_2bx_3bbi_5types_bits32 items_per_slot;
-};
-
-
-/* "bbi_file.pxd":21
- * cdef public double sum_squares
- *
- * cdef class SummarizedData: # <<<<<<<<<<<<<<
- * """
- * The result of using SummaryBlocks read from the file to produce a
- */
-struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData {
- PyObject_HEAD
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtab;
- __pyx_t_2bx_3bbi_5types_bits32 start;
- __pyx_t_2bx_3bbi_5types_bits32 end;
- int size;
- PyArrayObject *valid_count;
- PyArrayObject *min_val;
- PyArrayObject *max_val;
- PyArrayObject *sum_data;
- PyArrayObject *sum_squares;
-};
-
-
-/* "bx/bbi/bigwig_file.pyx":76
- * pass
- *
- * cdef class SummarizingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
- * """
- * Accumulates intervals into a SummarizedData
- */
-struct __pyx_obj_2bx_3bbi_11bigwig_file_SummarizingBlockHandler {
- struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler __pyx_base;
- struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *sd;
-};
-
-
-/* "bpt_file.pxd":5
- * from types cimport *
- *
- * cdef class BPTFile: # <<<<<<<<<<<<<<
- * """
- * On disk B+ tree compatible with Jim Kent's bPlusTree.c
- */
-struct __pyx_obj_2bx_3bbi_8bpt_file_BPTFile {
- PyObject_HEAD
- PyObject *file;
- PyObject *reader;
- __pyx_t_2bx_3bbi_5types_boolean is_byteswapped;
- __pyx_t_2bx_3bbi_5types_bits32 block_size;
- __pyx_t_2bx_3bbi_5types_bits32 key_size;
- __pyx_t_2bx_3bbi_5types_bits32 value_size;
- __pyx_t_2bx_3bbi_5types_bits64 item_count;
- __pyx_t_2bx_3bbi_5types_bits64 root_offset;
-};
-
-
-
-/* "bbi_file.pxd":39
- * cdef class BBIFile
- *
- * cdef class BlockHandler: # <<<<<<<<<<<<<<
- * """
- * Callback for `BBIFile.visit_blocks_in_region`
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler {
- PyObject *(*handle_block)(struct __pyx_obj_2bx_3bbi_8bbi_file_BlockHandler *, PyObject *, struct __pyx_obj_2bx_3bbi_8bbi_file_BBIFile *);
-};
-static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler *__pyx_vtabptr_2bx_3bbi_8bbi_file_BlockHandler;
-
-
-/* "bx/bbi/bigwig_file.pyx":23
- * return min( end1, end2 ) - max( start1, start2 )
- *
- * cdef class BigWigBlockHandler( BlockHandler ): # <<<<<<<<<<<<<<
- * """
- * BlockHandler that parses the block into a series of wiggle records, and calls `handle_interval_value` for each.
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigBlockHandler {
- struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_BlockHandler __pyx_base;
- PyObject *(*handle_interval_value)(struct __pyx_obj_2bx_3bbi_11bigwig_file_BigWigBlockHandler *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float);
-};
-static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigwig_file_BigWigBlockHandler;
-
-
-/* "bx/bbi/bigwig_file.pyx":105
- * self.intervals.append( ( s, e, val ) )
- *
- * cdef class ArrayAccumulatingBlockHandler( BigWigBlockHandler ): # <<<<<<<<<<<<<<
- * """
- * Accumulates intervals into a list of intervals with values
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler {
- struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigBlockHandler __pyx_base;
-};
-static struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler *__pyx_vtabptr_2bx_3bbi_11bigwig_file_ArrayAccumulatingBlockHandler;
-
-
-/* "bbi_file.pxd":21
- * cdef public double sum_squares
- *
- * cdef class SummarizedData: # <<<<<<<<<<<<<<
- * """
- * The result of using SummaryBlocks read from the file to produce a
- */
-
-struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData {
- PyObject *(*accumulate_interval_value)(struct __pyx_obj_2bx_3bbi_8bbi_file_SummarizedData *, __pyx_t_2bx_3bbi_5types_bits32, __pyx_t_2bx_3bbi_5types_bits32, float);
-};
-static struct __pyx_vtabstruct_2bx_3bbi_8bbi_file_SummarizedData *__pyx_vtabptr_2bx_3bbi_8bbi_file_SummarizedData;
-
-
-/* "bbi_file.pxd":37
- * cdef accumulate_interval_value( self, bits32 s, bits32 e, float val )
- *
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- __Pyx_GOTREF(__pyx_t_2);
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- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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- /* "bx/bbi/bigwig_file.pyx":1
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- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
-
- /* "numpy.pxd":975
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- goto __pyx_L0;
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- if (__pyx_m) {
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- }
- if (!result) {
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-
-static void __Pyx_RaiseArgtupleInvalid(
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-{
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- if (exact) {
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- PyErr_Format(PyExc_TypeError,
- "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
- func_name, more_or_less, num_expected,
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-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
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- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
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- continue;
- }
- name = first_kw_arg;
- #if PY_MAJOR_VERSION < 3
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- while (*name) {
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- && _PyString_Eq(**name, key)) {
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- if ((**argname == key) || (
- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
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- #endif
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- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**name, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) {
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- break;
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- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) goto arg_passed_twice;
- argname++;
- }
- }
- } else
- goto invalid_keyword_type;
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
- }
- }
- return 0;
-arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
- if (unlikely(!type)) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (likely(PyObject_TypeCheck(obj, type)))
- return 1;
- PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
- Py_TYPE(obj)->tp_name, type->tp_name);
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_IsLittleEndian(void) {
- unsigned int n = 1;
- return *(unsigned char*)(&n) != 0;
-}
-static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx,
- __Pyx_BufFmt_StackElem* stack,
- __Pyx_TypeInfo* type) {
- stack[0].field = &ctx->root;
- stack[0].parent_offset = 0;
- ctx->root.type = type;
- ctx->root.name = "buffer dtype";
- ctx->root.offset = 0;
- ctx->head = stack;
- ctx->head->field = &ctx->root;
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- ctx->head->parent_offset = 0;
- ctx->new_packmode = '@';
- ctx->enc_packmode = '@';
- ctx->new_count = 1;
- ctx->enc_count = 0;
- ctx->enc_type = 0;
- ctx->is_complex = 0;
- ctx->is_valid_array = 0;
- ctx->struct_alignment = 0;
- while (type->typegroup == 'S') {
- ++ctx->head;
- ctx->head->field = type->fields;
- ctx->head->parent_offset = 0;
- type = type->fields->type;
- }
-}
-static int __Pyx_BufFmt_ParseNumber(const char** ts) {
- int count;
- const char* t = *ts;
- if (*t < '0' || *t > '9') {
- return -1;
- } else {
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- while (*t >= '0' && *t < '9') {
- count *= 10;
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- }
- }
- *ts = t;
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-}
-static int __Pyx_BufFmt_ExpectNumber(const char **ts) {
- int number = __Pyx_BufFmt_ParseNumber(ts);
- if (number == -1) /* First char was not a digit */
- PyErr_Format(PyExc_ValueError,\
- "Does not understand character buffer dtype format string ('%c')", **ts);
- return number;
-}
-static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) {
- PyErr_Format(PyExc_ValueError,
- "Unexpected format string character: '%c'", ch);
-}
-static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) {
- switch (ch) {
- case 'c': return "'char'";
- case 'b': return "'signed char'";
- case 'B': return "'unsigned char'";
- case 'h': return "'short'";
- case 'H': return "'unsigned short'";
- case 'i': return "'int'";
- case 'I': return "'unsigned int'";
- case 'l': return "'long'";
- case 'L': return "'unsigned long'";
- case 'q': return "'long long'";
- case 'Q': return "'unsigned long long'";
- case 'f': return (is_complex ? "'complex float'" : "'float'");
- case 'd': return (is_complex ? "'complex double'" : "'double'");
- case 'g': return (is_complex ? "'complex long double'" : "'long double'");
- case 'T': return "a struct";
- case 'O': return "Python object";
- case 'P': return "a pointer";
- case 's': case 'p': return "a string";
- case 0: return "end";
- default: return "unparseable format string";
- }
-}
-static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) {
- switch (ch) {
- case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return 2;
- case 'i': case 'I': case 'l': case 'L': return 4;
- case 'q': case 'Q': return 8;
- case 'f': return (is_complex ? 8 : 4);
- case 'd': return (is_complex ? 16 : 8);
- case 'g': {
- PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g')..");
- return 0;
- }
- case 'O': case 'P': return sizeof(void*);
- default:
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
-}
-static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) {
- switch (ch) {
- case 'c': case 'b': case 'B': case 's': case 'p': return 1;
- case 'h': case 'H': return sizeof(short);
- case 'i': case 'I': return sizeof(int);
- case 'l': case 'L': return sizeof(long);
- #ifdef HAVE_LONG_LONG
- case 'q': case 'Q': return sizeof(PY_LONG_LONG);
- #endif
- case 'f': return sizeof(float) * (is_complex ? 2 : 1);
- case 'd': return sizeof(double) * (is_complex ? 2 : 1);
- case 'g': return sizeof(long double) * (is_complex ? 2 : 1);
- case 'O': case 'P': return sizeof(void*);
- default: {
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
- }
- }
-}
-typedef struct { char c; short x; } __Pyx_st_short;
-typedef struct { char c; int x; } __Pyx_st_int;
-typedef struct { char c; long x; } __Pyx_st_long;
-typedef struct { char c; float x; } __Pyx_st_float;
-typedef struct { char c; double x; } __Pyx_st_double;
-typedef struct { char c; long double x; } __Pyx_st_longdouble;
-typedef struct { char c; void *x; } __Pyx_st_void_p;
-#ifdef HAVE_LONG_LONG
-typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong;
-#endif
-static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) {
- switch (ch) {
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- case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short);
- case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int);
- case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long);
-#ifdef HAVE_LONG_LONG
- case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG);
-#endif
- case 'f': return sizeof(__Pyx_st_float) - sizeof(float);
- case 'd': return sizeof(__Pyx_st_double) - sizeof(double);
- case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double);
- case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*);
- default:
- __Pyx_BufFmt_RaiseUnexpectedChar(ch);
- return 0;
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-typedef struct { short x; char c; } __Pyx_pad_short;
-typedef struct { int x; char c; } __Pyx_pad_int;
-typedef struct { long x; char c; } __Pyx_pad_long;
-typedef struct { float x; char c; } __Pyx_pad_float;
-typedef struct { double x; char c; } __Pyx_pad_double;
-typedef struct { long double x; char c; } __Pyx_pad_longdouble;
-typedef struct { void *x; char c; } __Pyx_pad_void_p;
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- return 'I';
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- return 'U';
- case 'f': case 'd': case 'g':
- return (is_complex ? 'C' : 'R');
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- if (ctx->head == NULL || ctx->head->field == &ctx->root) {
- const char* expected;
- const char* quote;
- if (ctx->head == NULL) {
- expected = "end";
- quote = "";
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- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch, expected %s%s%s but got %s",
- quote, expected, quote,
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- } else {
- __Pyx_StructField* field = ctx->head->field;
- __Pyx_StructField* parent = (ctx->head - 1)->field;
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'",
- field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex),
- parent->type->name, field->name);
- }
-}
-static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
- char group;
- size_t size, offset, arraysize = 1;
- if (ctx->enc_type == 0) return 0;
- if (ctx->head->field->type->arraysize[0]) {
- int i, ndim = 0;
- if (ctx->enc_type == 's' || ctx->enc_type == 'p') {
- ctx->is_valid_array = ctx->head->field->type->ndim == 1;
- ndim = 1;
- if (ctx->enc_count != ctx->head->field->type->arraysize[0]) {
- PyErr_Format(PyExc_ValueError,
- "Expected a dimension of size %zu, got %zu",
- ctx->head->field->type->arraysize[0], ctx->enc_count);
- return -1;
- }
- }
- if (!ctx->is_valid_array) {
- PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d",
- ctx->head->field->type->ndim, ndim);
- return -1;
- }
- for (i = 0; i < ctx->head->field->type->ndim; i++) {
- arraysize *= ctx->head->field->type->arraysize[i];
- }
- ctx->is_valid_array = 0;
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- }
- group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex);
- do {
- __Pyx_StructField* field = ctx->head->field;
- __Pyx_TypeInfo* type = field->type;
- if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') {
- size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex);
- } else {
- size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex);
- }
- if (ctx->enc_packmode == '@') {
- size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex);
- size_t align_mod_offset;
- if (align_at == 0) return -1;
- align_mod_offset = ctx->fmt_offset % align_at;
- if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset;
- if (ctx->struct_alignment == 0)
- ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type,
- ctx->is_complex);
- }
- if (type->size != size || type->typegroup != group) {
- if (type->typegroup == 'C' && type->fields != NULL) {
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- ++ctx->head;
- ctx->head->field = type->fields;
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- continue;
- }
- if ((type->typegroup == 'H' || group == 'H') && type->size == size) {
- } else {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return -1;
- }
- }
- offset = ctx->head->parent_offset + field->offset;
- if (ctx->fmt_offset != offset) {
- PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected",
- (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset);
- return -1;
- }
- ctx->fmt_offset += size;
- if (arraysize)
- ctx->fmt_offset += (arraysize - 1) * size;
- --ctx->enc_count; /* Consume from buffer string */
- while (1) {
- if (field == &ctx->root) {
- ctx->head = NULL;
- if (ctx->enc_count != 0) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return -1;
- }
- break; /* breaks both loops as ctx->enc_count == 0 */
- }
- ctx->head->field = ++field;
- if (field->type == NULL) {
- --ctx->head;
- field = ctx->head->field;
- continue;
- } else if (field->type->typegroup == 'S') {
- size_t parent_offset = ctx->head->parent_offset + field->offset;
- if (field->type->fields->type == NULL) continue; /* empty struct */
- field = field->type->fields;
- ++ctx->head;
- ctx->head->field = field;
- ctx->head->parent_offset = parent_offset;
- break;
- } else {
- break;
- }
- }
- } while (ctx->enc_count);
- ctx->enc_type = 0;
- ctx->is_complex = 0;
- return 0;
-}
-static CYTHON_INLINE PyObject *
-__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp)
-{
- const char *ts = *tsp;
- int i = 0, number;
- int ndim = ctx->head->field->type->ndim;
-;
- ++ts;
- if (ctx->new_count != 1) {
- PyErr_SetString(PyExc_ValueError,
- "Cannot handle repeated arrays in format string");
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- while (*ts && *ts != ')') {
- if (isspace(*ts))
- continue;
- number = __Pyx_BufFmt_ExpectNumber(&ts);
- if (number == -1) return NULL;
- if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i])
- return PyErr_Format(PyExc_ValueError,
- "Expected a dimension of size %zu, got %d",
- ctx->head->field->type->arraysize[i], number);
- if (*ts != ',' && *ts != ')')
- return PyErr_Format(PyExc_ValueError,
- "Expected a comma in format string, got '%c'", *ts);
- if (*ts == ',') ts++;
- i++;
- }
- if (i != ndim)
- return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d",
- ctx->head->field->type->ndim, i);
- if (!*ts) {
- PyErr_SetString(PyExc_ValueError,
- "Unexpected end of format string, expected ')'");
- return NULL;
- }
- ctx->is_valid_array = 1;
- ctx->new_count = 1;
- *tsp = ++ts;
- return Py_None;
-}
-static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) {
- int got_Z = 0;
- while (1) {
- switch(*ts) {
- case 0:
- if (ctx->enc_type != 0 && ctx->head == NULL) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- if (ctx->head != NULL) {
- __Pyx_BufFmt_RaiseExpected(ctx);
- return NULL;
- }
- return ts;
- case ' ':
- case 10:
- case 13:
- ++ts;
- break;
- case '<':
- if (!__Pyx_IsLittleEndian()) {
- PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler");
- return NULL;
- }
- ctx->new_packmode = '=';
- ++ts;
- break;
- case '>':
- case '!':
- if (__Pyx_IsLittleEndian()) {
- PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler");
- return NULL;
- }
- ctx->new_packmode = '=';
- ++ts;
- break;
- case '=':
- case '@':
- case '^':
- ctx->new_packmode = *ts++;
- break;
- case 'T': /* substruct */
- {
- const char* ts_after_sub;
- size_t i, struct_count = ctx->new_count;
- size_t struct_alignment = ctx->struct_alignment;
- ctx->new_count = 1;
- ++ts;
- if (*ts != '{') {
- PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'");
- return NULL;
- }
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0; /* Erase processed last struct element */
- ctx->enc_count = 0;
- ctx->struct_alignment = 0;
- ++ts;
- ts_after_sub = ts;
- for (i = 0; i != struct_count; ++i) {
- ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts);
- if (!ts_after_sub) return NULL;
- }
- ts = ts_after_sub;
- if (struct_alignment) ctx->struct_alignment = struct_alignment;
- }
- break;
- case '}': /* end of substruct; either repeat or move on */
- {
- size_t alignment = ctx->struct_alignment;
- ++ts;
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_type = 0; /* Erase processed last struct element */
- if (alignment && ctx->fmt_offset % alignment) {
- ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment);
- }
- }
- return ts;
- case 'x':
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->fmt_offset += ctx->new_count;
- ctx->new_count = 1;
- ctx->enc_count = 0;
- ctx->enc_type = 0;
- ctx->enc_packmode = ctx->new_packmode;
- ++ts;
- break;
- case 'Z':
- got_Z = 1;
- ++ts;
- if (*ts != 'f' && *ts != 'd' && *ts != 'g') {
- __Pyx_BufFmt_RaiseUnexpectedChar('Z');
- return NULL;
- } /* fall through */
- case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I':
- case 'l': case 'L': case 'q': case 'Q':
- case 'f': case 'd': case 'g':
- case 'O': case 's': case 'p':
- if (ctx->enc_type == *ts && got_Z == ctx->is_complex &&
- ctx->enc_packmode == ctx->new_packmode) {
- ctx->enc_count += ctx->new_count;
- } else {
- if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
- ctx->enc_count = ctx->new_count;
- ctx->enc_packmode = ctx->new_packmode;
- ctx->enc_type = *ts;
- ctx->is_complex = got_Z;
- }
- ++ts;
- ctx->new_count = 1;
- got_Z = 0;
- break;
- case ':':
- ++ts;
- while(*ts != ':') ++ts;
- ++ts;
- break;
- case '(':
- if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL;
- break;
- default:
- {
- int number = __Pyx_BufFmt_ExpectNumber(&ts);
- if (number == -1) return NULL;
- ctx->new_count = (size_t)number;
- }
- }
- }
-}
-static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) {
- buf->buf = NULL;
- buf->obj = NULL;
- buf->strides = __Pyx_zeros;
- buf->shape = __Pyx_zeros;
- buf->suboffsets = __Pyx_minusones;
-}
-static CYTHON_INLINE int __Pyx_GetBufferAndValidate(
- Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags,
- int nd, int cast, __Pyx_BufFmt_StackElem* stack)
-{
- if (obj == Py_None || obj == NULL) {
- __Pyx_ZeroBuffer(buf);
- return 0;
- }
- buf->buf = NULL;
- if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail;
- if (buf->ndim != nd) {
- PyErr_Format(PyExc_ValueError,
- "Buffer has wrong number of dimensions (expected %d, got %d)",
- nd, buf->ndim);
- goto fail;
- }
- if (!cast) {
- __Pyx_BufFmt_Context ctx;
- __Pyx_BufFmt_Init(&ctx, stack, dtype);
- if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail;
- }
- if ((unsigned)buf->itemsize != dtype->size) {
- PyErr_Format(PyExc_ValueError,
- "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)",
- buf->itemsize, (buf->itemsize > 1) ? "s" : "",
- dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : "");
- goto fail;
- }
- if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
- return 0;
-fail:;
- __Pyx_ZeroBuffer(buf);
- return -1;
-}
-static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) {
- if (info->buf == NULL) return;
- if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL;
- __Pyx_ReleaseBuffer(info);
-}
-
-static void __Pyx_RaiseBufferIndexError(int axis) {
- PyErr_Format(PyExc_IndexError,
- "Out of bounds on buffer access (axis %d)", axis);
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
-}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* exc_type = tstate->curexc_type;
- if (unlikely(exc_type)) {
- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#endif
-}
-
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
- Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- }
- #if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
- if (cause && cause != Py_None) {
- PyObject *fixed_cause;
- if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- }
- else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- }
- else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-}
-
-static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_dealloc != current_tp_dealloc)
- type = type->tp_base;
- while (type && type->tp_dealloc == current_tp_dealloc)
- type = type->tp_base;
- if (type)
- type->tp_dealloc(obj);
-}
-
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_traverse != current_tp_traverse)
- type = type->tp_base;
- while (type && type->tp_traverse == current_tp_traverse)
- type = type->tp_base;
- if (type && type->tp_traverse)
- return type->tp_traverse(obj, v, a);
- return 0;
-}
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_clear != current_tp_clear)
- type = type->tp_base;
- while (type && type->tp_clear == current_tp_clear)
- type = type->tp_base;
- if (type && type->tp_clear)
- type->tp_clear(obj);
-}
-
-#if PY_MAJOR_VERSION < 3
-static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
- CYTHON_UNUSED PyObject *getbuffer_cobj;
- #if PY_VERSION_HEX >= 0x02060000
- if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
- #endif
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags);
- #if PY_VERSION_HEX < 0x02060000
- if (obj->ob_type->tp_dict &&
- (getbuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
- "__pyx_getbuffer"))) {
- getbufferproc func;
- #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
- func = (getbufferproc) PyCapsule_GetPointer(getbuffer_cobj, "getbuffer(obj, view, flags)");
- #else
- func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj);
- #endif
- Py_DECREF(getbuffer_cobj);
- if (!func)
- goto fail;
- return func(obj, view, flags);
- } else {
- PyErr_Clear();
- }
- #endif
- PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
-#if PY_VERSION_HEX < 0x02060000
-fail:
-#endif
- return -1;
-}
-static void __Pyx_ReleaseBuffer(Py_buffer *view) {
- PyObject *obj = view->obj;
- CYTHON_UNUSED PyObject *releasebuffer_cobj;
- if (!obj) return;
- #if PY_VERSION_HEX >= 0x02060000
- if (PyObject_CheckBuffer(obj)) {
- PyBuffer_Release(view);
- return;
- }
- #endif
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; }
- #if PY_VERSION_HEX < 0x02060000
- if (obj->ob_type->tp_dict &&
- (releasebuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
- "__pyx_releasebuffer"))) {
- releasebufferproc func;
- #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
- func = (releasebufferproc) PyCapsule_GetPointer(releasebuffer_cobj, "releasebuffer(obj, view)");
- #else
- func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj);
- #endif
- Py_DECREF(releasebuffer_cobj);
- if (!func)
- goto fail;
- func(obj, view);
- return;
- } else {
- PyErr_Clear();
- }
- #endif
- goto nofail;
-#if PY_VERSION_HEX < 0x02060000
-fail:
-#endif
- PyErr_WriteUnraisable(obj);
-nofail:
- Py_DECREF(obj);
- view->obj = NULL;
-}
-#endif /* PY_MAJOR_VERSION < 3 */
-
-
- static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import = 0;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
-#if PY_MAJOR_VERSION < 3
- PyErr_Format(PyExc_ImportError, "cannot import name %.230s",
- PyString_AsString(name));
-#else
- PyErr_Format(PyExc_ImportError, "cannot import name %S", name);
-#endif
-}
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return ::std::complex< float >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- return x + y*(__pyx_t_float_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
- __pyx_t_float_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
- __pyx_t_float_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrtf(z.real*z.real + z.imag*z.imag);
- #else
- return hypotf(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
- __pyx_t_float_complex z;
- float r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- float denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(a, a);
- case 3:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, a);
- case 4:
- z = __Pyx_c_prodf(a, a);
- return __Pyx_c_prodf(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- }
- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_absf(a);
- theta = atan2f(a.imag, a.real);
- }
- lnr = logf(r);
- z_r = expf(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cosf(z_theta);
- z.imag = z_r * sinf(z_theta);
- return z;
- }
- #endif
-#endif
-
-#if CYTHON_CCOMPLEX
- #ifdef __cplusplus
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return ::std::complex< double >(x, y);
- }
- #else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- return x + y*(__pyx_t_double_complex)_Complex_I;
- }
- #endif
-#else
- static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
- __pyx_t_double_complex z;
- z.real = x;
- z.imag = y;
- return z;
- }
-#endif
-
-#if CYTHON_CCOMPLEX
-#else
- static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- return (a.real == b.real) && (a.imag == b.imag);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real + b.real;
- z.imag = a.imag + b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real - b.real;
- z.imag = a.imag - b.imag;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- z.real = a.real * b.real - a.imag * b.imag;
- z.imag = a.real * b.imag + a.imag * b.real;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double denom = b.real * b.real + b.imag * b.imag;
- z.real = (a.real * b.real + a.imag * b.imag) / denom;
- z.imag = (a.imag * b.real - a.real * b.imag) / denom;
- return z;
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = -a.real;
- z.imag = -a.imag;
- return z;
- }
- static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
- return (a.real == 0) && (a.imag == 0);
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
- __pyx_t_double_complex z;
- z.real = a.real;
- z.imag = -a.imag;
- return z;
- }
- #if 1
- static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) {
- #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
- return sqrt(z.real*z.real + z.imag*z.imag);
- #else
- return hypot(z.real, z.imag);
- #endif
- }
- static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
- __pyx_t_double_complex z;
- double r, lnr, theta, z_r, z_theta;
- if (b.imag == 0 && b.real == (int)b.real) {
- if (b.real < 0) {
- double denom = a.real * a.real + a.imag * a.imag;
- a.real = a.real / denom;
- a.imag = -a.imag / denom;
- b.real = -b.real;
- }
- switch ((int)b.real) {
- case 0:
- z.real = 1;
- z.imag = 0;
- return z;
- case 1:
- return a;
- case 2:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(a, a);
- case 3:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, a);
- case 4:
- z = __Pyx_c_prod(a, a);
- return __Pyx_c_prod(z, z);
- }
- }
- if (a.imag == 0) {
- if (a.real == 0) {
- return a;
- }
- r = a.real;
- theta = 0;
- } else {
- r = __Pyx_c_abs(a);
- theta = atan2(a.imag, a.real);
- }
- lnr = log(r);
- z_r = exp(lnr * b.real - theta * b.imag);
- z_theta = theta * b.real + lnr * b.imag;
- z.real = z_r * cos(z_theta);
- z.imag = z_r * sin(z_theta);
- return z;
- }
- #endif
-#endif
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
-#ifndef __PYX_HAVE_RT_ImportType
-#define __PYX_HAVE_RT_ImportType
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%s.%s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%s.%s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static void* __Pyx_GetVtable(PyObject *dict) {
- void* ptr;
- PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
- if (!ob)
- goto bad;
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- ptr = PyCapsule_GetPointer(ob, 0);
-#else
- ptr = PyCObject_AsVoidPtr(ob);
-#endif
- if (!ptr && !PyErr_Occurred())
- PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
- Py_DECREF(ob);
- return ptr;
-bad:
- Py_XDECREF(ob);
- return NULL;
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/bbi/bpt_file.c b/lib/bx/bbi/bpt_file.c
deleted file mode 100644
index 8ae1465..0000000
--- a/lib/bx/bbi/bpt_file.c
+++ /dev/null
@@ -1,2868 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
- #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define Py_TPFLAGS_CHECKTYPES 0
- #define Py_TPFLAGS_HAVE_INDEX 0
-#endif
-#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBaseString_Type PyUnicode_Type
- #define PyStringObject PyUnicodeObject
- #define PyString_Type PyUnicode_Type
- #define PyString_Check PyUnicode_Check
- #define PyString_CheckExact PyUnicode_CheckExact
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PyBytesObject PyStringObject
- #define PyBytes_Type PyString_Type
- #define PyBytes_Check PyString_Check
- #define PyBytes_CheckExact PyString_CheckExact
- #define PyBytes_FromString PyString_FromString
- #define PyBytes_FromStringAndSize PyString_FromStringAndSize
- #define PyBytes_FromFormat PyString_FromFormat
- #define PyBytes_DecodeEscape PyString_DecodeEscape
- #define PyBytes_AsString PyString_AsString
- #define PyBytes_AsStringAndSize PyString_AsStringAndSize
- #define PyBytes_Size PyString_Size
- #define PyBytes_AS_STRING PyString_AS_STRING
- #define PyBytes_GET_SIZE PyString_GET_SIZE
- #define PyBytes_Repr PyString_Repr
- #define PyBytes_Concat PyString_Concat
- #define PyBytes_ConcatAndDel PyString_ConcatAndDel
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
- #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
-#endif
-#ifndef PySet_CheckExact
- #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
-#endif
-#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-#if PY_MAJOR_VERSION >= 3
- #define PyIntObject PyLongObject
- #define PyInt_Type PyLong_Type
- #define PyInt_Check(op) PyLong_Check(op)
- #define PyInt_CheckExact(op) PyLong_CheckExact(op)
- #define PyInt_FromString PyLong_FromString
- #define PyInt_FromUnicode PyLong_FromUnicode
- #define PyInt_FromLong PyLong_FromLong
- #define PyInt_FromSize_t PyLong_FromSize_t
- #define PyInt_FromSsize_t PyLong_FromSsize_t
- #define PyInt_AsLong PyLong_AsLong
- #define PyInt_AS_LONG PyLong_AS_LONG
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- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/bbi/cirtree_file.c b/lib/bx/bbi/cirtree_file.c
deleted file mode 100644
index 2c096ac..0000000
--- a/lib/bx/bbi/cirtree_file.c
+++ /dev/null
@@ -1,3901 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
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- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/bitset.c b/lib/bx/bitset.c
deleted file mode 100644
index fb9c844..0000000
--- a/lib/bx/bitset.c
+++ /dev/null
@@ -1,5871 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
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-static CYTHON_INLINE PyObject *__pyx_f_2bx_6bitset_bb_check_range_count(struct __pyx_obj_2bx_6bitset_BinnedBitSet *, PyObject *, PyObject *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_2bx_6bitset_bb_check_same_size(struct __pyx_obj_2bx_6bitset_BinnedBitSet *, struct __pyx_obj_2bx_6bitset_BinnedBitSet *); /*proto*/
-#define __Pyx_MODULE_NAME "bx.bitset"
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- __Pyx_AddTraceback("init bx.bitset", __pyx_clineno, __pyx_lineno, __pyx_filename);
- Py_DECREF(__pyx_m); __pyx_m = 0;
- } else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_ImportError, "init bx.bitset");
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- __Pyx_RefNannyFinishContext();
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-#if CYTHON_REFNANNY
-static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
- PyObject *m = NULL, *p = NULL;
- void *r = NULL;
- m = PyImport_ImportModule((char *)modname);
- if (!m) goto end;
- p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
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- Py_XDECREF(p);
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-static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
- PyObject *result;
- result = PyObject_GetAttr(dict, name);
- if (!result) {
- if (dict != __pyx_b) {
- PyErr_Clear();
- result = PyObject_GetAttr(__pyx_b, name);
- }
- if (!result) {
- PyErr_SetObject(PyExc_NameError, name);
- }
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- return result;
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-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
-}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
- Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
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- #if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
- if (cause && cause != Py_None) {
- PyObject *fixed_cause;
- if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- }
- else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- }
- else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- continue;
- }
- name = first_kw_arg;
- #if PY_MAJOR_VERSION < 3
- if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
- while (*name) {
- if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
- && _PyString_Eq(**name, key)) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- if ((**argname == key) || (
- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
- }
- argname++;
- }
- }
- } else
- #endif
- if (likely(PyUnicode_Check(key))) {
- while (*name) {
- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**name, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) goto arg_passed_twice;
- argname++;
- }
- }
- } else
- goto invalid_keyword_type;
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
- }
- }
- return 0;
-arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *more_or_less;
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
- num_expected = num_max;
- more_or_less = "at most";
- }
- if (exact) {
- more_or_less = "exactly";
- }
- PyErr_Format(PyExc_TypeError,
- "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
- func_name, more_or_less, num_expected,
- (num_expected == 1) ? "" : "s", num_found);
-}
-
-static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
- const char *name, int exact)
-{
- if (!type) {
- PyErr_Format(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (none_allowed && obj == Py_None) return 1;
- else if (exact) {
- if (Py_TYPE(obj) == type) return 1;
- }
- else {
- if (PyObject_TypeCheck(obj, type)) return 1;
- }
- PyErr_Format(PyExc_TypeError,
- "Argument '%s' has incorrect type (expected %s, got %s)",
- name, type->tp_name, Py_TYPE(obj)->tp_name);
- return 0;
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import = 0;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/intervals/cluster.c b/lib/bx/intervals/cluster.c
deleted file mode 100644
index 1feabe2..0000000
--- a/lib/bx/intervals/cluster.c
+++ /dev/null
@@ -1,2615 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
- #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define Py_TPFLAGS_CHECKTYPES 0
- #define Py_TPFLAGS_HAVE_INDEX 0
-#endif
-#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
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-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/intervals/intersection.c b/lib/bx/intervals/intersection.c
deleted file mode 100644
index 009960e..0000000
--- a/lib/bx/intervals/intersection.c
+++ /dev/null
@@ -1,8477 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
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-static int __pyx_pf_2bx_9intervals_12intersection_8Interval_5start_2__set__(struct __pyx_obj_2bx_9intervals_12intersection_Interval *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
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- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-static PyTypeObject __pyx_type_2bx_9intervals_12intersection_IntervalNode = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("bx.intervals.intersection.IntervalNode"), /*tp_name*/
- sizeof(struct __pyx_obj_2bx_9intervals_12intersection_IntervalNode), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_2bx_9intervals_12intersection_IntervalNode, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- __pyx_pw_2bx_9intervals_12intersection_12IntervalNode_1__repr__, /*tp_repr*/
- &__pyx_tp_as_number_IntervalNode, /*tp_as_number*/
- &__pyx_tp_as_sequence_IntervalNode, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IntervalNode, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IntervalNode, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("\n A single node of an `IntervalTree`.\n \n NOTE: Unless you really know what you are doing, you probably should us\n `IntervalTree` rather than using this directly. \n "), /*tp_doc*/
- __pyx_tp_traverse_2bx_9intervals_12intersection_IntervalNode, /*tp_traverse*/
- __pyx_tp_clear_2bx_9intervals_12intersection_IntervalNode, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_2bx_9intervals_12intersection_IntervalNode, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_2bx_9intervals_12intersection_IntervalNode, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_2bx_9intervals_12intersection_IntervalNode, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-
-static PyObject *__pyx_tp_new_2bx_9intervals_12intersection_Interval(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_2bx_9intervals_12intersection_Interval *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_2bx_9intervals_12intersection_Interval *)o);
- p->value = Py_None; Py_INCREF(Py_None);
- p->chrom = Py_None; Py_INCREF(Py_None);
- p->strand = Py_None; Py_INCREF(Py_None);
- return o;
-}
-
-static void __pyx_tp_dealloc_2bx_9intervals_12intersection_Interval(PyObject *o) {
- struct __pyx_obj_2bx_9intervals_12intersection_Interval *p = (struct __pyx_obj_2bx_9intervals_12intersection_Interval *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->value);
- Py_CLEAR(p->chrom);
- Py_CLEAR(p->strand);
- PyObject_GC_Track(o);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_2bx_9intervals_12intersection_Interval(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_2bx_9intervals_12intersection_Interval *p = (struct __pyx_obj_2bx_9intervals_12intersection_Interval *)o;
- if (p->value) {
- e = (*v)(p->value, a); if (e) return e;
- }
- if (p->chrom) {
- e = (*v)(p->chrom, a); if (e) return e;
- }
- if (p->strand) {
- e = (*v)(p->strand, a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_2bx_9intervals_12intersection_Interval(PyObject *o) {
- struct __pyx_obj_2bx_9intervals_12intersection_Interval *p = (struct __pyx_obj_2bx_9intervals_12intersection_Interval *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->value);
- p->value = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->chrom);
- p->chrom = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->strand);
- p->strand = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyObject *__pyx_getprop_2bx_9intervals_12intersection_8Interval_start(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_5start_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_9intervals_12intersection_8Interval_start(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_5start_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_9intervals_12intersection_8Interval_end(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_3end_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_9intervals_12intersection_8Interval_end(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_3end_3__set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_2bx_9intervals_12intersection_8Interval_value(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_5value_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_9intervals_12intersection_8Interval_value(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_5value_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_5value_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_9intervals_12intersection_8Interval_chrom(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_5chrom_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_9intervals_12intersection_8Interval_chrom(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_5chrom_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_5chrom_5__del__(o);
- }
-}
-
-static PyObject *__pyx_getprop_2bx_9intervals_12intersection_8Interval_strand(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_6strand_1__get__(o);
-}
-
-static int __pyx_setprop_2bx_9intervals_12intersection_8Interval_strand(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_6strand_3__set__(o, v);
- }
- else {
- return __pyx_pw_2bx_9intervals_12intersection_8Interval_6strand_5__del__(o);
- }
-}
-
-static PyMethodDef __pyx_methods_2bx_9intervals_12intersection_Interval[] = {
- {0, 0, 0, 0}
-};
-
-static struct PyGetSetDef __pyx_getsets_2bx_9intervals_12intersection_Interval[] = {
- {(char *)"start", __pyx_getprop_2bx_9intervals_12intersection_8Interval_start, __pyx_setprop_2bx_9intervals_12intersection_8Interval_start, 0, 0},
- {(char *)"end", __pyx_getprop_2bx_9intervals_12intersection_8Interval_end, __pyx_setprop_2bx_9intervals_12intersection_8Interval_end, 0, 0},
- {(char *)"value", __pyx_getprop_2bx_9intervals_12intersection_8Interval_value, __pyx_setprop_2bx_9intervals_12intersection_8Interval_value, 0, 0},
- {(char *)"chrom", __pyx_getprop_2bx_9intervals_12intersection_8Interval_chrom, __pyx_setprop_2bx_9intervals_12intersection_8Interval_chrom, 0, 0},
- {(char *)"strand", __pyx_getprop_2bx_9intervals_12intersection_8Interval_strand, __pyx_setprop_2bx_9intervals_12intersection_8Interval_strand, 0, 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_Interval = {
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- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
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- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
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- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_Interval = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping_Interval = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_Interval = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-static PyTypeObject __pyx_type_2bx_9intervals_12intersection_Interval = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("bx.intervals.intersection.Interval"), /*tp_name*/
- sizeof(struct __pyx_obj_2bx_9intervals_12intersection_Interval), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_2bx_9intervals_12intersection_Interval, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- __pyx_pw_2bx_9intervals_12intersection_8Interval_3__repr__, /*tp_repr*/
- &__pyx_tp_as_number_Interval, /*tp_as_number*/
- &__pyx_tp_as_sequence_Interval, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_Interval, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_Interval, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("\n Basic feature, with required integer start and end properties.\n Also accepts optional strand as +1 or -1 (used for up/downstream queries),\n a name, and any arbitrary data is sent in on the info keyword argument\n\n >>> from bx.intervals.intersection import Interval\n\n >>> f1 = Interval(23, 36)\n >>> f2 = Interval(34, 48, value={'chr':12, 'anno':'transposon'})\n >>> f2\n Interval(34, 48, value={'anno': 'transposon', 'chr': 12})\n\n "), /*tp_doc*/
- __pyx_tp_traverse_2bx_9intervals_12intersection_Interval, /*tp_traverse*/
- __pyx_tp_clear_2bx_9intervals_12intersection_Interval, /*tp_clear*/
- __pyx_pw_2bx_9intervals_12intersection_8Interval_5__richcmp__, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_2bx_9intervals_12intersection_Interval, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_2bx_9intervals_12intersection_Interval, /*tp_getset*/
- 0, /*tp_base*/
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- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pw_2bx_9intervals_12intersection_8Interval_1__init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_2bx_9intervals_12intersection_Interval, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-
-static PyObject *__pyx_tp_new_2bx_9intervals_12intersection_IntervalTree(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_2bx_9intervals_12intersection_IntervalTree *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_2bx_9intervals_12intersection_IntervalTree *)o);
- p->root = ((struct __pyx_obj_2bx_9intervals_12intersection_IntervalNode *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_2bx_9intervals_12intersection_12IntervalTree_1__cinit__(o, __pyx_empty_tuple, NULL) < 0) {
- Py_DECREF(o); o = 0;
- }
- return o;
-}
-
-static void __pyx_tp_dealloc_2bx_9intervals_12intersection_IntervalTree(PyObject *o) {
- struct __pyx_obj_2bx_9intervals_12intersection_IntervalTree *p = (struct __pyx_obj_2bx_9intervals_12intersection_IntervalTree *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->root);
- PyObject_GC_Track(o);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_2bx_9intervals_12intersection_IntervalTree(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_2bx_9intervals_12intersection_IntervalTree *p = (struct __pyx_obj_2bx_9intervals_12intersection_IntervalTree *)o;
- if (p->root) {
- e = (*v)(((PyObject*)p->root), a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_2bx_9intervals_12intersection_IntervalTree(PyObject *o) {
- struct __pyx_obj_2bx_9intervals_12intersection_IntervalTree *p = (struct __pyx_obj_2bx_9intervals_12intersection_IntervalTree *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->root);
- p->root = ((struct __pyx_obj_2bx_9intervals_12intersection_IntervalNode *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyMethodDef __pyx_methods_2bx_9intervals_12intersection_IntervalTree[] = {
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- {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pw_2bx_9intervals_12intersection_12IntervalTree_5find, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_9intervals_12intersection_12IntervalTree_4find)},
- {__Pyx_NAMESTR("before"), (PyCFunction)__pyx_pw_2bx_9intervals_12intersection_12IntervalTree_7before, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_9intervals_12intersection_12IntervalTree_6before)},
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- {__Pyx_NAMESTR("upstream_of_interval"), (PyCFunction)__pyx_pw_2bx_9intervals_12intersection_12IntervalTree_17upstream_of_interval, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_9intervals_12intersection_12IntervalTree_16upstream_of_interval)},
- {__Pyx_NAMESTR("downstream_of_interval"), (PyCFunction)__pyx_pw_2bx_9intervals_12intersection_12IntervalTree_19downstream_of_interval, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_2bx_9intervals_12intersection_12IntervalTree_18downstream_of_interval)},
- {__Pyx_NAMESTR("traverse"), (PyCFunction)__pyx_pw_2bx_9intervals_12intersection_12IntervalTree_21traverse, METH_O, __Pyx_DOCSTR(__pyx_doc_2bx_9intervals_12intersection_12IntervalTree_20traverse)},
- {0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_IntervalTree = {
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- 0, /*nb_absolute*/
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- #if PY_MAJOR_VERSION < 3
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- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
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-static PyBufferProcs __pyx_tp_as_buffer_IntervalTree = {
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- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
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- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
-}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
- CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) {
- PyObject *old_exc, *old_val, *old_tb;
- PyObject *ctx;
- __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
- #if PY_MAJOR_VERSION < 3
- ctx = PyString_FromString(name);
- #else
- ctx = PyUnicode_FromString(name);
- #endif
- __Pyx_ErrRestore(old_exc, old_val, old_tb);
- if (!ctx) {
- PyErr_WriteUnraisable(Py_None);
- } else {
- PyErr_WriteUnraisable(ctx);
- Py_DECREF(ctx);
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
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-static int __Pyx_PrintOne(PyObject* f, PyObject *o) {
- if (!f) {
- if (!(f = __Pyx_GetStdout()))
- return -1;
- }
- Py_INCREF(f);
- if (PyFile_SoftSpace(f, 0)) {
- if (PyFile_WriteString(" ", f) < 0)
- goto error;
- }
- if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0)
- goto error;
- if (PyFile_WriteString("\n", f) < 0)
- goto error;
- Py_DECREF(f);
- return 0;
-error:
- Py_DECREF(f);
- return -1;
- /* the line below is just to avoid C compiler
- * warnings about unused functions */
- return __Pyx_Print(f, NULL, 0);
-}
-#else /* Python 3 has a print function */
-static int __Pyx_PrintOne(PyObject* stream, PyObject *o) {
- int res;
- PyObject* arg_tuple = PyTuple_Pack(1, o);
- if (unlikely(!arg_tuple))
- return -1;
- res = __Pyx_Print(stream, arg_tuple, 1);
- Py_DECREF(arg_tuple);
- return res;
-}
-#endif
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
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- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
- Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- }
- #if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- }
- else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto bad;
- }
- if (cause && cause != Py_None) {
- PyObject *fixed_cause;
- if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- }
- else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- }
- else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import = 0;
- py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
- const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned char" :
- "value too large to convert to unsigned char");
- }
- return (unsigned char)-1;
- }
- return (unsigned char)val;
- }
- return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/misc/bgzf.c b/lib/bx/misc/bgzf.c
deleted file mode 100644
index 76f75b9..0000000
--- a/lib/bx/misc/bgzf.c
+++ /dev/null
@@ -1,2331 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
- #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define Py_TPFLAGS_CHECKTYPES 0
- #define Py_TPFLAGS_HAVE_INDEX 0
-#endif
-#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBaseString_Type PyUnicode_Type
- #define PyStringObject PyUnicodeObject
- #define PyString_Type PyUnicode_Type
- #define PyString_Check PyUnicode_Check
- #define PyString_CheckExact PyUnicode_CheckExact
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PyBytesObject PyStringObject
- #define PyBytes_Type PyString_Type
- #define PyBytes_Check PyString_Check
- #define PyBytes_CheckExact PyString_CheckExact
- #define PyBytes_FromString PyString_FromString
- #define PyBytes_FromStringAndSize PyString_FromStringAndSize
- #define PyBytes_FromFormat PyString_FromFormat
- #define PyBytes_DecodeEscape PyString_DecodeEscape
- #define PyBytes_AsString PyString_AsString
- #define PyBytes_AsStringAndSize PyString_AsStringAndSize
- #define PyBytes_Size PyString_Size
- #define PyBytes_AS_STRING PyString_AS_STRING
- #define PyBytes_GET_SIZE PyString_GET_SIZE
- #define PyBytes_Repr PyString_Repr
- #define PyBytes_Concat PyString_Concat
- #define PyBytes_ConcatAndDel PyString_ConcatAndDel
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
- #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
-#endif
-#ifndef PySet_CheckExact
- #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
-#endif
-#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-#if PY_MAJOR_VERSION >= 3
- #define PyIntObject PyLongObject
- #define PyInt_Type PyLong_Type
- #define PyInt_Check(op) PyLong_Check(op)
- #define PyInt_CheckExact(op) PyLong_CheckExact(op)
- #define PyInt_FromString PyLong_FromString
- #define PyInt_FromUnicode PyLong_FromUnicode
- #define PyInt_FromLong PyLong_FromLong
- #define PyInt_FromSize_t PyLong_FromSize_t
- #define PyInt_FromSsize_t PyLong_FromSsize_t
- #define PyInt_AsLong PyLong_AsLong
- #define PyInt_AS_LONG PyLong_AS_LONG
- #define PyInt_AsSsize_t PyLong_AsSsize_t
- #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
- #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
-#endif
-#if PY_VERSION_HEX < 0x03020000
- typedef long Py_hash_t;
- #define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
-#else
- #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
- #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
-#endif
-#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
- #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
- #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
-#else
- #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
- #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
-#endif
-#if PY_VERSION_HEX < 0x02050000
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
- #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
-#else
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
- #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
-#endif
-#if PY_VERSION_HEX < 0x02050000
- #define __Pyx_NAMESTR(n) ((char *)(n))
- #define __Pyx_DOCSTR(n) ((char *)(n))
-#else
- #define __Pyx_NAMESTR(n) (n)
- #define __Pyx_DOCSTR(n) (n)
-#endif
-
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
-#ifndef __PYX_EXTERN_C
- #ifdef __cplusplus
- #define __PYX_EXTERN_C extern "C"
- #else
- #define __PYX_EXTERN_C extern
- #endif
-#endif
-
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
-#define __PYX_HAVE__bx__misc__bgzf
-#define __PYX_HAVE_API__bx__misc__bgzf
-#include "bgzf.h"
-#ifdef _OPENMP
-#include <omp.h>
-#endif /* _OPENMP */
-
-#ifdef PYREX_WITHOUT_ASSERTIONS
-#define CYTHON_WITHOUT_ASSERTIONS
-#endif
-
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
-#endif
-#ifndef CYTHON_UNUSED
-# if defined(__GNUC__)
-# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
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-{
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-
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-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
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-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/motif/_pwm.c b/lib/bx/motif/_pwm.c
deleted file mode 100644
index dc10599..0000000
--- a/lib/bx/motif/_pwm.c
+++ /dev/null
@@ -1,2250 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
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-{
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-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
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-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
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- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
-#ifndef __PYX_HAVE_RT_ImportType
-#define __PYX_HAVE_RT_ImportType
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%s.%s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%s.%s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/pwm/_position_weight_matrix.c b/lib/bx/pwm/_position_weight_matrix.c
deleted file mode 100644
index 083b726..0000000
--- a/lib/bx/pwm/_position_weight_matrix.c
+++ /dev/null
@@ -1,1620 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
- #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define Py_TPFLAGS_CHECKTYPES 0
- #define Py_TPFLAGS_HAVE_INDEX 0
-#endif
-#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBaseString_Type PyUnicode_Type
- #define PyStringObject PyUnicodeObject
- #define PyString_Type PyUnicode_Type
- #define PyString_Check PyUnicode_Check
- #define PyString_CheckExact PyUnicode_CheckExact
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PyBytesObject PyStringObject
- #define PyBytes_Type PyString_Type
- #define PyBytes_Check PyString_Check
- #define PyBytes_CheckExact PyString_CheckExact
- #define PyBytes_FromString PyString_FromString
- #define PyBytes_FromStringAndSize PyString_FromStringAndSize
- #define PyBytes_FromFormat PyString_FromFormat
- #define PyBytes_DecodeEscape PyString_DecodeEscape
- #define PyBytes_AsString PyString_AsString
- #define PyBytes_AsStringAndSize PyString_AsStringAndSize
- #define PyBytes_Size PyString_Size
- #define PyBytes_AS_STRING PyString_AS_STRING
- #define PyBytes_GET_SIZE PyString_GET_SIZE
- #define PyBytes_Repr PyString_Repr
- #define PyBytes_Concat PyString_Concat
- #define PyBytes_ConcatAndDel PyString_ConcatAndDel
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
- #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
-#endif
-#ifndef PySet_CheckExact
- #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
-#endif
-#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-#if PY_MAJOR_VERSION >= 3
- #define PyIntObject PyLongObject
- #define PyInt_Type PyLong_Type
- #define PyInt_Check(op) PyLong_Check(op)
- #define PyInt_CheckExact(op) PyLong_CheckExact(op)
- #define PyInt_FromString PyLong_FromString
- #define PyInt_FromUnicode PyLong_FromUnicode
- #define PyInt_FromLong PyLong_FromLong
- #define PyInt_FromSize_t PyLong_FromSize_t
- #define PyInt_FromSsize_t PyLong_FromSsize_t
- #define PyInt_AsLong PyLong_AsLong
- #define PyInt_AS_LONG PyLong_AS_LONG
- #define PyInt_AsSsize_t PyLong_AsSsize_t
- #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
- #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
-#endif
-#if PY_VERSION_HEX < 0x03020000
- typedef long Py_hash_t;
- #define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
-#else
- #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
- #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
-#endif
-#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
- #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
- #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
-#else
- #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
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-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/seq/_nib.c b/lib/bx/seq/_nib.c
deleted file mode 100644
index 155b683..0000000
--- a/lib/bx/seq/_nib.c
+++ /dev/null
@@ -1,1922 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
- #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define Py_TPFLAGS_CHECKTYPES 0
- #define Py_TPFLAGS_HAVE_INDEX 0
-#endif
-#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
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- * NIB_I2C_TABLE_SECOND = "TCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxx"
- *
- */
- __pyx_v_2bx_3seq_4_nib_NIB_I2C_TABLE_FIRST = __pyx_k_1;
-
- /* "bx/seq/_nib.pyx":13
- * #NIB_I2C_TABLE = "TCAGNXXXtcagnxxx"
- * NIB_I2C_TABLE_FIRST = "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGNNNNNNNNNNNNNNNNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXttttttttttttttttccccccccccccccccaaaaaaaaaaaaaaaaggggggggggggggggnnnnnnnnnnnnnnnnxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
- * NIB_I2C_TABLE_SECOND = "TCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxx" # <<<<<<<<<<<<<<
- *
- * def translate_raw_data( data, int start, int length ):
- */
- __pyx_v_2bx_3seq_4_nib_NIB_I2C_TABLE_SECOND = __pyx_k_2;
-
- /* "bx/seq/_nib.pyx":15
- * NIB_I2C_TABLE_SECOND = "TCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxxTCAGNXXXtcagnxxx"
- *
- * def translate_raw_data( data, int start, int length ): # <<<<<<<<<<<<<<
- * """
- * Data is a block read from the file that needs to be unpacked, dealing
- */
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_2bx_3seq_4_nib_1translate_raw_data, NULL, __pyx_n_s_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__translate_raw_data, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
-
- /* "bx/seq/_nib.pyx":1
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- * object PyString_FromStringAndSize( char *, int )
- */
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- if (__pyx_m) {
- __Pyx_AddTraceback("init bx.seq._nib", __pyx_clineno, __pyx_lineno, __pyx_filename);
- Py_DECREF(__pyx_m); __pyx_m = 0;
- } else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_ImportError, "init bx.seq._nib");
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- __pyx_L0:;
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-#if CYTHON_REFNANNY
-static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
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-
-static void __Pyx_RaiseArgtupleInvalid(
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- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *more_or_less;
- if (num_found < num_min) {
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- num_expected = num_max;
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- if (exact) {
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- PyErr_Format(PyExc_TypeError,
- "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
- func_name, more_or_less, num_expected,
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-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
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- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
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- if (*name) {
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- continue;
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- #if PY_MAJOR_VERSION < 3
- if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
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- && _PyString_Eq(**name, key)) {
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- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
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- #endif
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- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
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- break;
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- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
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- argname++;
- }
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- } else
- goto invalid_keyword_type;
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- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
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- return 0;
-arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%s() got an unexpected keyword argument '%s'",
- function_name, PyString_AsString(key));
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-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
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- PyObject *module = 0;
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- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import = 0;
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- if (!py_import)
- goto bad;
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- goto bad;
- empty_dict = PyDict_New();
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- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
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- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
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- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
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- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
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- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
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- #endif
- }
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- #else
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- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
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-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
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- "value too large to convert to unsigned short");
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-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
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- "can't convert negative value to unsigned int" :
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-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
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-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
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-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
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-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
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-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
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- if (unlikely(Py_SIZE(x) < 0)) {
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- unsigned PY_LONG_LONG val;
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-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
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- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
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-#endif
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- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
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- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/lib/bx/seq/_twobit.c b/lib/bx/seq/_twobit.c
deleted file mode 100644
index 204373d..0000000
--- a/lib/bx/seq/_twobit.c
+++ /dev/null
@@ -1,3010 +0,0 @@
-/* Generated by Cython 0.18 on Mon Jul 15 13:25:44 2013 */
-
-#define PY_SSIZE_T_CLEAN
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #define __fastcall
- #endif
-#endif
-#ifndef DL_IMPORT
- #define DL_IMPORT(t) t
-#endif
-#ifndef DL_EXPORT
- #define DL_EXPORT(t) t
-#endif
-#ifndef PY_LONG_LONG
- #define PY_LONG_LONG LONG_LONG
-#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if PY_VERSION_HEX < 0x02050000
- typedef int Py_ssize_t;
- #define PY_SSIZE_T_MAX INT_MAX
- #define PY_SSIZE_T_MIN INT_MIN
- #define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
- #define PyInt_FromSsize_t(z) PyInt_FromLong(z)
- #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
- #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
- #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define Py_TPFLAGS_CHECKTYPES 0
- #define Py_TPFLAGS_HAVE_INDEX 0
-#endif
-#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
- #define Py_TPFLAGS_HAVE_NEWBUFFER 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBaseString_Type PyUnicode_Type
- #define PyStringObject PyUnicodeObject
- #define PyString_Type PyUnicode_Type
- #define PyString_Check PyUnicode_Check
- #define PyString_CheckExact PyUnicode_CheckExact
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PyBytesObject PyStringObject
- #define PyBytes_Type PyString_Type
- #define PyBytes_Check PyString_Check
- #define PyBytes_CheckExact PyString_CheckExact
- #define PyBytes_FromString PyString_FromString
- #define PyBytes_FromStringAndSize PyString_FromStringAndSize
- #define PyBytes_FromFormat PyString_FromFormat
- #define PyBytes_DecodeEscape PyString_DecodeEscape
- #define PyBytes_AsString PyString_AsString
- #define PyBytes_AsStringAndSize PyString_AsStringAndSize
- #define PyBytes_Size PyString_Size
- #define PyBytes_AS_STRING PyString_AS_STRING
- #define PyBytes_GET_SIZE PyString_GET_SIZE
- #define PyBytes_Repr PyString_Repr
- #define PyBytes_Concat PyString_Concat
- #define PyBytes_ConcatAndDel PyString_ConcatAndDel
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
- #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
-#endif
-#ifndef PySet_CheckExact
- #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
-#endif
-#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-#if PY_MAJOR_VERSION >= 3
- #define PyIntObject PyLongObject
- #define PyInt_Type PyLong_Type
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-
-static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
- const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned short" :
- "value too large to convert to unsigned short");
- }
- return (unsigned short)-1;
- }
- return (unsigned short)val;
- }
- return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
- const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(unsigned int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(unsigned int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to unsigned int" :
- "value too large to convert to unsigned int");
- }
- return (unsigned int)-1;
- }
- return (unsigned int)val;
- }
- return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
-}
-
-static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
- const char neg_one = (char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to char" :
- "value too large to convert to char");
- }
- return (char)-1;
- }
- return (char)val;
- }
- return (char)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
- const short neg_one = (short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to short" :
- "value too large to convert to short");
- }
- return (short)-1;
- }
- return (short)val;
- }
- return (short)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
- const signed char neg_one = (signed char)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed char) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed char)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed char" :
- "value too large to convert to signed char");
- }
- return (signed char)-1;
- }
- return (signed char)val;
- }
- return (signed char)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
- const signed short neg_one = (signed short)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed short) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed short)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed short" :
- "value too large to convert to signed short");
- }
- return (signed short)-1;
- }
- return (signed short)val;
- }
- return (signed short)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
- const signed int neg_one = (signed int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(signed int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(signed int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to signed int" :
- "value too large to convert to signed int");
- }
- return (signed int)-1;
- }
- return (signed int)val;
- }
- return (signed int)__Pyx_PyInt_AsSignedLong(x);
-}
-
-static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
- const int neg_one = (int)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (sizeof(int) < sizeof(long)) {
- long val = __Pyx_PyInt_AsLong(x);
- if (unlikely(val != (long)(int)val)) {
- if (!unlikely(val == -1 && PyErr_Occurred())) {
- PyErr_SetString(PyExc_OverflowError,
- (is_unsigned && unlikely(val < 0)) ?
- "can't convert negative value to int" :
- "value too large to convert to int");
- }
- return (int)-1;
- }
- return (int)val;
- }
- return (int)__Pyx_PyInt_AsLong(x);
-}
-
-static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
- const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned long");
- return (unsigned long)-1;
- }
- return (unsigned long)PyLong_AsUnsignedLong(x);
- } else {
- return (unsigned long)PyLong_AsLong(x);
- }
- } else {
- unsigned long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned long)-1;
- val = __Pyx_PyInt_AsUnsignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
- const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to unsigned PY_LONG_LONG");
- return (unsigned PY_LONG_LONG)-1;
- }
- return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- unsigned PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (unsigned PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
- const long neg_one = (long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long)-1;
- }
- return (long)PyLong_AsUnsignedLong(x);
- } else {
- return (long)PyLong_AsLong(x);
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long)-1;
- val = __Pyx_PyInt_AsLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
- const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to PY_LONG_LONG");
- return (PY_LONG_LONG)-1;
- }
- return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
- const signed long neg_one = (signed long)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed long");
- return (signed long)-1;
- }
- return (signed long)PyLong_AsUnsignedLong(x);
- } else {
- return (signed long)PyLong_AsLong(x);
- }
- } else {
- signed long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed long)-1;
- val = __Pyx_PyInt_AsSignedLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
- const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_VERSION_HEX < 0x03000000
- if (likely(PyInt_Check(x))) {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)val;
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to signed PY_LONG_LONG");
- return (signed PY_LONG_LONG)-1;
- }
- return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
- } else {
- return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
- }
- } else {
- signed PY_LONG_LONG val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (signed PY_LONG_LONG)-1;
- val = __Pyx_PyInt_AsSignedLongLong(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_VERSION_HEX < 0x03000000
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_VERSION_HEX < 0x03000000
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_VERSION_HEX < 0x03000000
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%s__ returned non-%s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject* x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
- unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
- if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
- return (size_t)-1;
- } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
- PyErr_SetString(PyExc_OverflowError,
- "value too large to convert to size_t");
- return (size_t)-1;
- }
- return (size_t)val;
-}
-
-
-#endif /* Py_PYTHON_H */
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-bx.git
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