[Python-modules-commits] r24244 - in packages/scipy/trunk/debian (9 files)
jtaylor-guest at users.alioth.debian.org
jtaylor-guest at users.alioth.debian.org
Thu May 9 10:42:53 UTC 2013
Date: Thursday, May 9, 2013 @ 10:42:51
Author: jtaylor-guest
Revision: 24244
refresh patches and remove upstream applied
- BUG-fix-dependency-on-dict-ordering-in-test.patch
- BUG-remove-inline-statement-rejected-by-cython.patch
- fix-dbg-crash.patch
- fix-f2py-dependencies.patch
- fix-test_basic.py-cephes_vs_amos_mass_te.patch
- python3.3-incdir.diff
Modified:
packages/scipy/trunk/debian/changelog
packages/scipy/trunk/debian/patches/restore_sys_argv.patch
packages/scipy/trunk/debian/patches/series
Deleted:
packages/scipy/trunk/debian/patches/BUG-fix-dependency-on-dict-ordering-in-test.patch
packages/scipy/trunk/debian/patches/BUG-remove-inline-statement-rejected-by-cython.patch
packages/scipy/trunk/debian/patches/fix-dbg-crash.patch
packages/scipy/trunk/debian/patches/fix-f2py-dependencies.patch
packages/scipy/trunk/debian/patches/fix-test_basic.py-cephes_vs_amos_mass_te.patch
packages/scipy/trunk/debian/patches/python3.3-incdir.diff
Modified: packages/scipy/trunk/debian/changelog
===================================================================
--- packages/scipy/trunk/debian/changelog 2013-05-09 10:42:46 UTC (rev 24243)
+++ packages/scipy/trunk/debian/changelog 2013-05-09 10:42:51 UTC (rev 24244)
@@ -7,6 +7,13 @@
* print skipped tests and unused skips in autopkgtest scripts
* add-swig-filetypes.patch, reswig.patch:
reswigging from setup.py, dropped from debian/rules
+ * refresh patches and remove upstream applied:
+ - BUG-fix-dependency-on-dict-ordering-in-test.patch
+ - BUG-remove-inline-statement-rejected-by-cython.patch
+ - fix-dbg-crash.patch
+ - fix-f2py-dependencies.patch
+ - fix-test_basic.py-cephes_vs_amos_mass_te.patch
+ - python3.3-incdir.diff
[ Jakub Wilk ]
* Use canonical URIs for Vcs-* fields.
Deleted: packages/scipy/trunk/debian/patches/BUG-fix-dependency-on-dict-ordering-in-test.patch
===================================================================
--- packages/scipy/trunk/debian/patches/BUG-fix-dependency-on-dict-ordering-in-test.patch 2013-05-09 10:42:46 UTC (rev 24243)
+++ packages/scipy/trunk/debian/patches/BUG-fix-dependency-on-dict-ordering-in-test.patch 2013-05-09 10:42:51 UTC (rev 24244)
@@ -1,51 +0,0 @@
-From c91d47da9e9b03861a41b4bf24ceb96506c158ce Mon Sep 17 00:00:00 2001
-From: Matthew Brett <matthew.brett at gmail.com>
-Date: Mon, 22 Oct 2012 13:00:28 -0400
-Subject: [PATCH] BUG: fix dependency on dict ordering in test.
-Applied-Upstream: 0.12
-
-Python 3.3 discovered the dependency on dict ordering
----
- scipy/io/matlab/tests/test_mio.py | 22 ++++++++++++++--------
- 1 file changed, 14 insertions(+), 8 deletions(-)
-
---- a/scipy/io/matlab/tests/test_mio.py
-+++ b/scipy/io/matlab/tests/test_mio.py
-@@ -516,23 +516,29 @@ def test_use_small_element():
-
- def test_save_dict():
- # Test that dict can be saved (as recarray), loaded as matstruct
-- dict_types = (dict,)
-+ dict_types = ((dict, False),)
- try:
- from collections import OrderedDict
- except ImportError:
- pass
- else:
-- dict_types += (OrderedDict,)
-- exp_arr = np.zeros((1, 1), dtype = [('a', object), ('b', object)])
-- exp_arr['a'] = 1
-- exp_arr['b'] = 2
-- for dict_type in dict_types:
-+ dict_types += ((OrderedDict, True),)
-+ ab_exp = np.array([[(1, 2)]], dtype=[('a', object), ('b', object)])
-+ ba_exp = np.array([[(2, 1)]], dtype=[('b', object), ('a', object)])
-+ for dict_type, is_ordered in dict_types:
- d = dict_type(a=1, b=2)
- stream = BytesIO()
- savemat_future(stream, {'dict': d})
- stream.seek(0)
-- vals = loadmat(stream)
-- assert_array_equal(vals['dict'], exp_arr)
-+ vals = loadmat(stream)['dict']
-+ assert_equal(set(vals.dtype.names), set(['a', 'b']))
-+ if is_ordered: # Input was ordered, output in ab order
-+ assert_array_equal(vals, ab_exp)
-+ else: # Not ordered input, either order output
-+ if vals.dtype.names[0] == 'a':
-+ assert_array_equal(vals, ab_exp)
-+ else:
-+ assert_array_equal(vals, ba_exp)
-
-
- def test_1d_shape():
Deleted: packages/scipy/trunk/debian/patches/BUG-remove-inline-statement-rejected-by-cython.patch
===================================================================
--- packages/scipy/trunk/debian/patches/BUG-remove-inline-statement-rejected-by-cython.patch 2013-05-09 10:42:46 UTC (rev 24243)
+++ packages/scipy/trunk/debian/patches/BUG-remove-inline-statement-rejected-by-cython.patch 2013-05-09 10:42:51 UTC (rev 24244)
@@ -1,42 +0,0 @@
-From c0f0fa2a5bdf30f3a4d35fe78a1f9884d2e2896e Mon Sep 17 00:00:00 2001
-From: Matthew Brett <matthew.brett at gmail.com>
-Date: Sat, 20 Oct 2012 20:46:14 -0400
-Subject: [PATCH] BUG: remove inline statement rejected by cython
-Applied-Upstream: 0.12
-
-Cython 0.17.1 rejects inline in the function definition for cpdef
-functions.
----
- scipy/io/matlab/mio5_utils.pyx | 10 +++++-----
- 1 file changed, 5 insertions(+), 5 deletions(-)
-
---- a/scipy/io/matlab/mio5_utils.pyx
-+++ b/scipy/io/matlab/mio5_utils.pyx
-@@ -408,14 +408,14 @@ cdef class VarReader5:
- if mod8:
- self.cstream.seek(8 - mod8, 1)
- return 0
--
-- cpdef inline cnp.ndarray read_numeric(self, int copy=True):
-+
-+ cpdef cnp.ndarray read_numeric(self, int copy=True):
- ''' Read numeric data element into ndarray
-
-- Reads element, then casts to ndarray.
-+ Reads element, then casts to ndarray.
-
- The type of the array is given by the ``mdtype`` returned via
-- ``read_element``.
-+ ``read_element``.
- '''
- cdef cnp.uint32_t mdtype, byte_count
- cdef void *data_ptr
-@@ -440,7 +440,7 @@ cdef class VarReader5:
- Py_INCREF(<object> data)
- PyArray_Set_BASE(el, data)
- return el
--
-+
- cdef inline object read_int8_string(self):
- ''' Read, return int8 type string
-
Deleted: packages/scipy/trunk/debian/patches/fix-dbg-crash.patch
===================================================================
--- packages/scipy/trunk/debian/patches/fix-dbg-crash.patch 2013-05-09 10:42:46 UTC (rev 24243)
+++ packages/scipy/trunk/debian/patches/fix-dbg-crash.patch 2013-05-09 10:42:51 UTC (rev 24244)
@@ -1,77 +0,0 @@
-From 4d7e7be0b8cbab48f8a55bf3d23d5f1e2e785eb9 Mon Sep 17 00:00:00 2001
-From: Pauli Virtanen <pav at iki.fi>
-Date: Fri, 14 Dec 2012 20:56:26 +0200
-Subject: [PATCH 1/3] BUG: sparse.linalg: initialize variables correctly in
- init and dealloc
-Applied-Upstream: 0.12
-
----
- scipy/sparse/linalg/dsolve/_superluobject.c | 14 ++++++--------
- 1 file changed, 6 insertions(+), 8 deletions(-)
-
---- a/scipy/sparse/linalg/dsolve/_superluobject.c
-+++ b/scipy/sparse/linalg/dsolve/_superluobject.c
-@@ -131,11 +131,15 @@ SciPyLU_dealloc(SciPyLUObject *self)
- {
- SUPERLU_FREE(self->perm_r);
- SUPERLU_FREE(self->perm_c);
-+ self->perm_r = NULL;
-+ self->perm_c = NULL;
- if (self->L.Store != NULL) {
- Destroy_SuperNode_Matrix(&self->L);
-+ self->L.Store = NULL;
- }
- if (self->U.Store != NULL) {
- Destroy_CompCol_Matrix(&self->U);
-+ self->U.Store = NULL;
- }
- PyObject_Del(self);
- }
-@@ -390,7 +394,6 @@ newSciPyLUObject(SuperMatrix *A, PyObjec
- superlu_options_t options;
- SuperLUStat_t stat;
- int panel_size, relax;
-- int trf_finished = 0;
-
- n = A->ncol;
-
-@@ -407,8 +410,13 @@ newSciPyLUObject(SuperMatrix *A, PyObjec
- self->n = n;
- self->perm_r = NULL;
- self->perm_c = NULL;
-+ self->L.Store = NULL;
-+ self->U.Store = NULL;
- self->type = intype;
-
-+ memset(&AC, 0, sizeof(SuperMatrix));
-+ memset(&stat, 0, sizeof(SuperLUStat_t));
-+
- if (setjmp(_superlu_py_jmpbuf)) goto fail;
-
- /* Calculate and apply minimum degree ordering*/
-@@ -438,7 +446,6 @@ newSciPyLUObject(SuperMatrix *A, PyObjec
- etree, NULL, lwork, self->perm_c, self->perm_r,
- &self->L, &self->U, &stat, &info);
- }
-- trf_finished = 1;
-
- if (info) {
- if (info < 0)
-@@ -461,16 +468,10 @@ newSciPyLUObject(SuperMatrix *A, PyObjec
- return (PyObject *)self;
-
- fail:
-- if (!trf_finished) {
-- /* Avoid trying to free partially initialized matrices;
-- might leak some memory, but avoids a crash */
-- self->L.Store = NULL;
-- self->U.Store = NULL;
-- }
- SUPERLU_FREE(etree);
- Destroy_CompCol_Permuted(&AC);
- StatFree(&stat);
-- SciPyLU_dealloc(self);
-+ Py_DECREF(self);
- return NULL;
- }
-
Deleted: packages/scipy/trunk/debian/patches/fix-f2py-dependencies.patch
===================================================================
--- packages/scipy/trunk/debian/patches/fix-f2py-dependencies.patch 2013-05-09 10:42:46 UTC (rev 24243)
+++ packages/scipy/trunk/debian/patches/fix-f2py-dependencies.patch 2013-05-09 10:42:51 UTC (rev 24244)
@@ -1,105 +0,0 @@
-Description: add dependencies to variables
- fixes unintialized uses due to random dict ordering in python3.3
-Origin: https://github.com/scipy/scipy/pull/404
-Author: Ralf Gommers <ralf.gommers at googlemail.com>
-Date: Fri Jan 25 12:36:09 2013 -0800
-Applied-Upstream: 0.12
-
---- a/scipy/linalg/flapack.pyf.src
-+++ b/scipy/linalg/flapack.pyf.src
-@@ -1470,7 +1470,7 @@ subroutine <prefix2>sbevx(ab,ldab,comput
- !* If JOBZ = 'V', the N-by-N orthogonal matrix used in the
- !* reduction to tridiagonal form.
- !* If JOBZ = 'N', the array Q is not referenced.
-- integer intent(hide),depend(n) :: ldq=(compute_v?n:1)
-+ integer intent(hide),depend(n,compute_v) :: ldq=(compute_v?n:1)
- <ftype2> dimension(ldq,ldq),intent(hide),depend(ldq) :: q
-
-
-@@ -1495,8 +1495,8 @@ subroutine <prefix2>sbevx(ab,ldab,comput
-
- <ftype2> dimension(n),intent(out),depend(n) :: w
-
-- <ftype2> dimension(ldz,mmax),intent(out) :: z
-- integer intent(hide),depend(n) :: ldz=(compute_v?n:1)
-+ <ftype2> dimension(ldz,mmax),depend(ldz,mmax),intent(out) :: z
-+ integer intent(hide),depend(n,compute_v) :: ldz=(compute_v?n:1)
-
- ! We use the mmax parameter to fix the size of z
- ! (only if eigenvalues are requested)
-@@ -1507,12 +1507,12 @@ subroutine <prefix2>sbevx(ab,ldab,comput
- ! number of eigenvalues in the interval in advance.
- ! As default we use the maximum value
- ! but the user should use an appropriate mmax.
-- integer intent(in),depend(n) :: mmax=(compute_v?(range==2?(iu-il+1):n):1)
-+ integer intent(in),depend(n,iu,il,compute_v,range) :: mmax=(compute_v?(range==2?(iu-il+1):n):1)
- integer intent(out) :: m
-
-- <ftype2> dimension(7*n),intent(hide) :: work
-- integer dimension(5*n),intent(hide) :: iwork
-- integer dimension((compute_v?n:1)),intent(out) :: ifail
-+ <ftype2> dimension(7*n),depend(n),intent(hide) :: work
-+ integer dimension(5*n),depend(n),intent(hide) :: iwork
-+ integer dimension((compute_v?n:1)),depend(n,compute_v),intent(out) :: ifail
- integer intent(out):: info
- end subroutine <prefix2>sbevx
-
-@@ -1590,7 +1590,7 @@ subroutine <prefix2c>hbevx(ab,ldab,compu
- !* If JOBZ = 'V', the N-by-N orthogonal matrix used in the
- !* reduction to tridiagonal form.
- !* If JOBZ = 'N', the array Q is not referenced.
-- integer intent(hide),depend(n) :: ldq=(compute_v?n:1)
-+ integer intent(hide),depend(n,compute_v) :: ldq=(compute_v?n:1)
- <ftype2c> dimension(ldq,ldq),intent(hide),depend(ldq) :: q
-
-
-@@ -1615,8 +1615,8 @@ subroutine <prefix2c>hbevx(ab,ldab,compu
-
- <ftype2> dimension(n),intent(out),depend(n) :: w
-
-- <ftype2c> dimension(ldz,mmax),intent(out) :: z
-- integer intent(hide),depend(n) :: ldz=(compute_v?n:1)
-+ <ftype2c> dimension(ldz,mmax),depend(ldz,mmax),intent(out) :: z
-+ integer intent(hide),depend(n,compute_v) :: ldz=(compute_v?n:1)
-
- ! We use the mmax parameter to fix the size of z
- ! (only if eigenvalues are requested)
-@@ -1627,13 +1627,13 @@ subroutine <prefix2c>hbevx(ab,ldab,compu
- ! number of eigenvalues in the interval in advance.
- ! As default we use the maximum value
- ! but the user should use an appropriate mmax.
-- integer intent(in),depend(n) :: mmax=(compute_v?(range==2?(iu-il+1):n):1)
-+ integer intent(in),depend(n,iu,il,compute_v,range) :: mmax=(compute_v?(range==2?(iu-il+1):n):1)
- integer intent(out) :: m
-
-- <ftype2c> dimension(n),intent(hide) :: work
-- <ftype2> dimension(7*n),intent(hide) :: rwork
-- integer dimension(5*n),intent(hide) :: iwork
-- integer dimension((compute_v?n:1)),intent(out) :: ifail
-+ <ftype2c> dimension(n),depend(n),intent(hide) :: work
-+ <ftype2> dimension(7*n),depend(n),intent(hide) :: rwork
-+ integer dimension(5*n),depend(n),intent(hide) :: iwork
-+ integer dimension((compute_v?n:1)),depend(n,compute_v),intent(out) :: ifail
- integer intent(out):: info
- end subroutine <prefix2c>hbevx
-
---- a/scipy/sparse/linalg/eigen/arpack/arpack.pyf.src
-+++ b/scipy/sparse/linalg/eigen/arpack/arpack.pyf.src
-@@ -29,7 +29,7 @@ python module _arpack ! in
- character :: howmny
- logical dimension(ncv) :: select
- <_rd> dimension(nev),intent(out),depend(nev) :: d
-- <_rd> dimension(n,nev),intent(out),depend(nev) :: z
-+ <_rd> dimension(n,nev),intent(out),depend(n,nev) :: z
- integer optional,check(shape(z,0)==ldz),depend(z) :: ldz=shape(z,0)
- <_rd> :: sigma
- character :: bmat
-@@ -121,7 +121,7 @@ python module _arpack ! in
- character :: howmny
- logical dimension(ncv) :: select
- <_cd> dimension(nev),depend(nev),intent(out) :: d
-- <_cd> dimension(n,nev), depend(nev),intent(out) :: z
-+ <_cd> dimension(n,nev), depend(n,nev),intent(out) :: z
- integer optional,check(shape(z,0)==ldz),depend(z) :: ldz=shape(z,0)
- <_cd> :: sigma
- <_cd> dimension(3 * ncv),depend(ncv) :: workev
Deleted: packages/scipy/trunk/debian/patches/fix-test_basic.py-cephes_vs_amos_mass_te.patch
===================================================================
--- packages/scipy/trunk/debian/patches/fix-test_basic.py-cephes_vs_amos_mass_te.patch 2013-05-09 10:42:46 UTC (rev 24243)
+++ packages/scipy/trunk/debian/patches/fix-test_basic.py-cephes_vs_amos_mass_te.patch 2013-05-09 10:42:51 UTC (rev 24244)
@@ -1,46 +0,0 @@
-From 6c1cd446bb6c3ffcc131de5b81e21b481400c334
-From: Pauli Virtanen <pav at iki.fi>
-Date: Sat, 3 Nov 2012 17:13:30 +0200
-Subject: [PATCH] TST: special: fix test_basic.py:cephes_vs_amos_mass_test
-Applied-Upstream: 0.12
-
----
- scipy/special/tests/test_basic.py | 22 ++++++++++++++--------
- 1 file changed, 14 insertions(+), 8 deletions(-)
-
---- a/scipy/special/tests/test_basic.py
-+++ b/scipy/special/tests/test_basic.py
-@@ -1640,17 +1640,23 @@ class TestBessel(TestCase):
- x = np.random.pareto(0.2, N) * (-1)**np.random.randint(2, size=N)
-
- imsk = (np.random.randint(8, size=N) == 0)
-- v[imsk] = v.astype(int)
-+ v[imsk] = v[imsk].astype(int)
-
-- c1 = special.iv(v, x)
-- c2 = special.iv(v, x+0j)
--
-- # deal with differences in the inf cutoffs
-- c1[abs(c1) > 1e300] = np.inf
-- c2[abs(c2) > 1e300] = np.inf
--
-- dc = abs(c1/c2 - 1)
-- dc[np.isnan(dc)] = 0
-+ old_err = np.seterr(all='ignore')
-+ try:
-+ c1 = special.iv(v, x)
-+ c2 = special.iv(v, x+0j)
-+
-+ # deal with differences in the inf and zero cutoffs
-+ c1[abs(c1) > 1e300] = np.inf
-+ c2[abs(c2) > 1e300] = np.inf
-+ c1[abs(c1) < 1e-300] = 0
-+ c2[abs(c2) < 1e-300] = 0
-+
-+ dc = abs(c1/c2 - 1)
-+ dc[np.isnan(dc)] = 0
-+ finally:
-+ np.seterr(**old_err)
-
- k = np.argmax(dc)
-
Deleted: packages/scipy/trunk/debian/patches/python3.3-incdir.diff
===================================================================
--- packages/scipy/trunk/debian/patches/python3.3-incdir.diff 2013-05-09 10:42:46 UTC (rev 24243)
+++ packages/scipy/trunk/debian/patches/python3.3-incdir.diff 2013-05-09 10:42:51 UTC (rev 24244)
@@ -1,59 +0,0 @@
-Description: add platform specific include directories
-Author: Matthias Klose <doko at ubuntu.com>
-Forwarded: https://github.com/scipy/scipy/pull/379
-Applied-Upstream: 0.12
---- a/scipy/spatial/SConscript
-+++ b/scipy/spatial/SConscript
-@@ -7,7 +7,10 @@ from numscons import GetNumpyEnvironment
- from numscons import write_info
-
- env = GetNumpyEnvironment(ARGUMENTS)
--env.PrependUnique(CPPPATH=[get_numpy_include_dirs(), get_python_inc(),
-+inc_dirs = [get_python_inc()]
-+if inc_dirs[0] != get_python_inc(plat_specific=1):
-+ inc_dirs.append(get_python_inc(plat_specific=1))
-+env.PrependUnique(CPPPATH=[get_numpy_include_dirs(), inc_dirs,
- env["PYEXTCPPPATH"]])
-
- #=======================
---- a/scipy/spatial/setup.py
-+++ b/scipy/spatial/setup.py
-@@ -16,10 +16,14 @@ def configuration(parent_package = '', t
- 'random.c', 'rboxlib.c', 'stat.c', 'user.c', 'usermem.c',
- 'userprintf.c']
-
-+ inc_dirs = [get_python_inc()]
-+ if inc_dirs[0] != get_python_inc(plat_specific=1):
-+ inc_dirs.append(get_python_inc(plat_specific=1))
-+ inc_dirs.append(get_numpy_include_dirs())
-+
- config.add_library('qhull',
- sources=[join('qhull', 'src', x) for x in qhull_src],
-- include_dirs=[get_python_inc(),
-- get_numpy_include_dirs()],
-+ include_dirs=inc_dirs,
- # XXX: GCC dependency!
- #extra_compiler_args=['-fno-strict-aliasing'],
- )
---- a/scipy/special/setup.py
-+++ b/scipy/special/setup.py
-@@ -23,12 +23,17 @@ def configuration(parent_package='',top_
- # define_macros.append(('NONANS',None))
- define_macros.append(('_USE_MATH_DEFINES',None))
-
-+ inc_dirs = [get_python_inc()]
-+ if inc_dirs[0] != get_python_inc(plat_specific=1):
-+ inc_dirs.append(get_python_inc(plat_specific=1))
-+ inc_dirs.append(get_numpy_include_dirs())
-+
- # C libraries
- config.add_library('sc_c_misc',sources=[join('c_misc','*.c')],
-- include_dirs=[get_python_inc(), get_numpy_include_dirs()],
-+ include_dirs=inc_dirs,
- macros=define_macros)
- config.add_library('sc_cephes',sources=[join('cephes','*.c')],
-- include_dirs=[get_python_inc(), get_numpy_include_dirs()],
-+ include_dirs=inc_dirs,
- macros=define_macros)
-
- # Fortran libraries
Modified: packages/scipy/trunk/debian/patches/restore_sys_argv.patch
===================================================================
--- packages/scipy/trunk/debian/patches/restore_sys_argv.patch 2013-05-09 10:42:46 UTC (rev 24243)
+++ packages/scipy/trunk/debian/patches/restore_sys_argv.patch 2013-05-09 10:42:51 UTC (rev 24244)
@@ -3,7 +3,7 @@
--- a/scipy/weave/build_tools.py
+++ b/scipy/weave/build_tools.py
-@@ -283,6 +283,9 @@ def build_extension(module_path,compiler
+@@ -284,6 +284,9 @@ def build_extension(module_path,compiler
configure_python_path(build_dir)
except SyntaxError: #TypeError:
success = 0
Modified: packages/scipy/trunk/debian/patches/series
===================================================================
--- packages/scipy/trunk/debian/patches/series 2013-05-09 10:42:46 UTC (rev 24243)
+++ packages/scipy/trunk/debian/patches/series 2013-05-09 10:42:51 UTC (rev 24244)
@@ -1,10 +1,4 @@
restore_sys_argv.patch
blitz++.patch
-BUG-fix-dependency-on-dict-ordering-in-test.patch
-BUG-remove-inline-statement-rejected-by-cython.patch
-fix-test_basic.py-cephes_vs_amos_mass_te.patch
-python3.3-incdir.diff
-fix-dbg-crash.patch
-fix-f2py-dependencies.patch
add-swig-filetypes.patch
reswig.patch
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