[Python-modules-commits] r23414 - in packages/scipy/trunk/debian/patches (8 files)
jtaylor-guest at users.alioth.debian.org
jtaylor-guest at users.alioth.debian.org
Sun Jan 27 16:54:08 UTC 2013
Date: Sunday, January 27, 2013 @ 16:54:05
Author: jtaylor-guest
Revision: 23414
refresh all patches again
Modified:
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/blitz++.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
packages/scipy/trunk/debian/patches/restore_sys_argv.patch
Modified: 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 2013-01-27 16:54:00 UTC (rev 23413)
+++ packages/scipy/trunk/debian/patches/BUG-fix-dependency-on-dict-ordering-in-test.patch 2013-01-27 16:54:05 UTC (rev 23414)
@@ -2,14 +2,13 @@
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(-)
-diff --git a/scipy/io/matlab/tests/test_mio.py b/scipy/io/matlab/tests/test_mio.py
-index c4f8f5b..9d246e0 100644
--- 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():
@@ -50,6 +49,3 @@
def test_1d_shape():
---
-1.7.10.4
-
Modified: 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 2013-01-27 16:54:00 UTC (rev 23413)
+++ packages/scipy/trunk/debian/patches/BUG-remove-inline-statement-rejected-by-cython.patch 2013-01-27 16:54:05 UTC (rev 23414)
@@ -2,6 +2,7 @@
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.
@@ -9,8 +10,6 @@
scipy/io/matlab/mio5_utils.pyx | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
-diff --git a/scipy/io/matlab/mio5_utils.pyx b/scipy/io/matlab/mio5_utils.pyx
-index 1604a61..21b1386 100644
--- a/scipy/io/matlab/mio5_utils.pyx
+++ b/scipy/io/matlab/mio5_utils.pyx
@@ -408,14 +408,14 @@ cdef class VarReader5:
@@ -41,6 +40,3 @@
cdef inline object read_int8_string(self):
''' Read, return int8 type string
---
-1.7.10.4
-
Modified: packages/scipy/trunk/debian/patches/blitz++.patch
===================================================================
--- packages/scipy/trunk/debian/patches/blitz++.patch 2013-01-27 16:54:00 UTC (rev 23413)
+++ packages/scipy/trunk/debian/patches/blitz++.patch 2013-01-27 16:54:05 UTC (rev 23414)
@@ -4,10 +4,8 @@
Bug-Debian: http://bugs.debian.org/598520
Bug-Ubuntu: https://launchpad.net/bugs/302649
-Index: python-scipy-0.8.0+dfsg1/scipy/weave/blitz/blitz/blitz.h
-===================================================================
---- python-scipy-0.8.0+dfsg1.orig/scipy/weave/blitz/blitz/blitz.h 2010-07-26 10:48:37.000000000 -0400
-+++ python-scipy-0.8.0+dfsg1/scipy/weave/blitz/blitz/blitz.h 2010-12-23 18:39:27.000000000 -0500
+--- a/scipy/weave/blitz/blitz/blitz.h
++++ b/scipy/weave/blitz/blitz/blitz.h
@@ -65,6 +65,8 @@
#define BZ_THROW // Needed in <blitz/numinquire.h>
@@ -17,23 +15,8 @@
BZ_NAMESPACE(blitz)
#ifdef BZ_HAVE_STD
-Index: python-scipy-0.8.0+dfsg1/scipy/weave/blitz/blitz/mathfunc.h
-===================================================================
---- python-scipy-0.8.0+dfsg1.orig/scipy/weave/blitz/blitz/mathfunc.h 2010-07-26 10:48:37.000000000 -0400
-+++ python-scipy-0.8.0+dfsg1/scipy/weave/blitz/blitz/mathfunc.h 2010-12-23 18:39:27.000000000 -0500
-@@ -14,6 +14,8 @@
-
- #include <cstdlib>
-
-+#include <cstdlib>
-+
- BZ_NAMESPACE(blitz)
-
- // abs(P_numtype1) Absolute value
-Index: python-scipy-0.8.0+dfsg1/scipy/weave/blitz/blitz/prettyprint.h
-===================================================================
---- python-scipy-0.8.0+dfsg1.orig/scipy/weave/blitz/blitz/prettyprint.h 2010-07-26 10:48:37.000000000 -0400
-+++ python-scipy-0.8.0+dfsg1/scipy/weave/blitz/blitz/prettyprint.h 2010-12-23 18:39:27.000000000 -0500
+--- a/scipy/weave/blitz/blitz/prettyprint.h
++++ b/scipy/weave/blitz/blitz/prettyprint.h
@@ -22,6 +22,8 @@
#ifndef BZ_PRETTYPRINT_H
#define BZ_PRETTYPRINT_H
Modified: packages/scipy/trunk/debian/patches/fix-dbg-crash.patch
===================================================================
--- packages/scipy/trunk/debian/patches/fix-dbg-crash.patch 2013-01-27 16:54:00 UTC (rev 23413)
+++ packages/scipy/trunk/debian/patches/fix-dbg-crash.patch 2013-01-27 16:54:05 UTC (rev 23414)
@@ -3,16 +3,15 @@
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(-)
-diff --git a/scipy/sparse/linalg/dsolve/_superluobject.c b/scipy/sparse/linalg/dsolve/_superluobject.c
-index 4017a86..4496eea 100644
--- a/scipy/sparse/linalg/dsolve/_superluobject.c
+++ b/scipy/sparse/linalg/dsolve/_superluobject.c
-@@ -131,11 +131,15 @@
+@@ -131,11 +131,15 @@ SciPyLU_dealloc(SciPyLUObject *self)
{
SUPERLU_FREE(self->perm_r);
SUPERLU_FREE(self->perm_c);
@@ -28,7 +27,7 @@
}
PyObject_Del(self);
}
-@@ -390,7 +394,6 @@ int NCFormat_from_spMatrix(SuperMatrix *A, int m, int n, int nnz,
+@@ -390,7 +394,6 @@ newSciPyLUObject(SuperMatrix *A, PyObjec
superlu_options_t options;
SuperLUStat_t stat;
int panel_size, relax;
@@ -36,7 +35,7 @@
n = A->ncol;
-@@ -407,6 +410,8 @@ int NCFormat_from_spMatrix(SuperMatrix *A, int m, int n, int nnz,
+@@ -407,8 +410,13 @@ newSciPyLUObject(SuperMatrix *A, PyObjec
self->n = n;
self->perm_r = NULL;
self->perm_c = NULL;
@@ -44,8 +43,13 @@
+ 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;
-@@ -438,7 +443,6 @@ int NCFormat_from_spMatrix(SuperMatrix *A, int m, int n, int nnz,
+
+ /* 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);
}
@@ -53,7 +57,7 @@
if (info) {
if (info < 0)
-@@ -461,12 +465,6 @@ int NCFormat_from_spMatrix(SuperMatrix *A, int m, int n, int nnz,
+@@ -461,16 +468,10 @@ newSciPyLUObject(SuperMatrix *A, PyObjec
return (PyObject *)self;
fail:
@@ -66,61 +70,8 @@
SUPERLU_FREE(etree);
Destroy_CompCol_Permuted(&AC);
StatFree(&stat);
---
-1.7.10
-
-
-From e8295335e0ad73e1cc54fba8dac43b3bed772264 Mon Sep 17 00:00:00 2001
-From: Pauli Virtanen <pav at iki.fi>
-Date: Fri, 14 Dec 2012 20:57:05 +0200
-Subject: [PATCH 2/3] BUG: sparse.linalg: deallocate Python object correctly
- (fixes #1789)
-
----
- scipy/sparse/linalg/dsolve/_superluobject.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/scipy/sparse/linalg/dsolve/_superluobject.c b/scipy/sparse/linalg/dsolve/_superluobject.c
-index 4496eea..8060bc9 100644
---- a/scipy/sparse/linalg/dsolve/_superluobject.c
-+++ b/scipy/sparse/linalg/dsolve/_superluobject.c
-@@ -468,7 +468,7 @@ int NCFormat_from_spMatrix(SuperMatrix *A, int m, int n, int nnz,
- SUPERLU_FREE(etree);
- Destroy_CompCol_Permuted(&AC);
- StatFree(&stat);
- SciPyLU_dealloc(self);
+ Py_DECREF(self);
return NULL;
}
---
-1.7.10
-
-
-From da1864d3b47bfd39b7c6dc49475ca3dd8a93c3d0 Mon Sep 17 00:00:00 2001
-From: Pauli Virtanen <pav at iki.fi>
-Date: Fri, 14 Dec 2012 21:14:42 +0200
-Subject: [PATCH 3/3] BUG: sparse.linalg: initialize yet more variables in
- superlu
-
----
- scipy/sparse/linalg/dsolve/_superluobject.c | 3 +++
- 1 file changed, 3 insertions(+)
-
-diff --git a/scipy/sparse/linalg/dsolve/_superluobject.c b/scipy/sparse/linalg/dsolve/_superluobject.c
-index 8060bc9..078b131 100644
---- a/scipy/sparse/linalg/dsolve/_superluobject.c
-+++ b/scipy/sparse/linalg/dsolve/_superluobject.c
-@@ -414,6 +414,9 @@ int NCFormat_from_spMatrix(SuperMatrix *A, int m, int n, int nnz,
- 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*/
---
-1.7.10
-
Modified: packages/scipy/trunk/debian/patches/fix-f2py-dependencies.patch
===================================================================
--- packages/scipy/trunk/debian/patches/fix-f2py-dependencies.patch 2013-01-27 16:54:00 UTC (rev 23413)
+++ packages/scipy/trunk/debian/patches/fix-f2py-dependencies.patch 2013-01-27 16:54:05 UTC (rev 23414)
@@ -3,6 +3,7 @@
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
Modified: 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 2013-01-27 16:54:00 UTC (rev 23413)
+++ packages/scipy/trunk/debian/patches/fix-test_basic.py-cephes_vs_amos_mass_te.patch 2013-01-27 16:54:05 UTC (rev 23414)
@@ -2,13 +2,12 @@
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(-)
-diff --git a/scipy/special/tests/test_basic.py b/scipy/special/tests/test_basic.py
-index c4371bb..184f4c9 100644
--- a/scipy/special/tests/test_basic.py
+++ b/scipy/special/tests/test_basic.py
@@ -1640,17 +1640,23 @@ class TestBessel(TestCase):
@@ -20,22 +19,24 @@
- 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 cutoffs
-- c1[abs(c1) > 1e300] = np.inf
-- c2[abs(c2) > 1e300] = np.inf
++
+ # 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
++
+ dc = abs(c1/c2 - 1)
+ dc[np.isnan(dc)] = 0
+ finally:
@@ -43,6 +44,3 @@
k = np.argmax(dc)
---
-1.7.10.4
-
Modified: packages/scipy/trunk/debian/patches/python3.3-incdir.diff
===================================================================
--- packages/scipy/trunk/debian/patches/python3.3-incdir.diff 2013-01-27 16:54:00 UTC (rev 23413)
+++ packages/scipy/trunk/debian/patches/python3.3-incdir.diff 2013-01-27 16:54:05 UTC (rev 23414)
@@ -1,11 +1,10 @@
Description: add platform specific include directories
Author: Matthias Klose <doko at ubuntu.com>
Forwarded: https://github.com/scipy/scipy/pull/379
-Index: b/scipy/spatial/SConscript
-===================================================================
---- a/scipy/spatial/SConscript 2011-03-10 01:40:54.000000000 +0000
-+++ b/scipy/spatial/SConscript 2012-10-23 14:21:23.582321642 +0000
-@@ -7,7 +7,10 @@
+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)
@@ -17,11 +16,9 @@
env["PYEXTCPPPATH"]])
#=======================
-Index: b/scipy/spatial/setup.py
-===================================================================
---- a/scipy/spatial/setup.py 2011-03-10 01:40:54.000000000 +0000
-+++ b/scipy/spatial/setup.py 2012-10-23 14:19:14.842324162 +0000
-@@ -16,10 +16,14 @@
+--- 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']
@@ -38,11 +35,9 @@
# XXX: GCC dependency!
#extra_compiler_args=['-fno-strict-aliasing'],
)
-Index: b/scipy/special/setup.py
-===================================================================
---- a/scipy/special/setup.py 2011-09-25 16:06:47.000000000 +0000
-+++ b/scipy/special/setup.py 2012-10-23 14:23:42.110319714 +0000
-@@ -23,12 +23,17 @@
+--- 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))
Modified: packages/scipy/trunk/debian/patches/restore_sys_argv.patch
===================================================================
--- packages/scipy/trunk/debian/patches/restore_sys_argv.patch 2013-01-27 16:54:00 UTC (rev 23413)
+++ packages/scipy/trunk/debian/patches/restore_sys_argv.patch 2013-01-27 16:54:05 UTC (rev 23414)
@@ -1,11 +1,9 @@
Description: restore sys.argv in case of exception
Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=500814
-Index: python-scipy-0.10.1+dfsg1/scipy/weave/build_tools.py
-===================================================================
---- python-scipy-0.10.1+dfsg1.orig/scipy/weave/build_tools.py 2012-04-19 16:30:03.073017007 -0400
-+++ python-scipy-0.10.1+dfsg1/scipy/weave/build_tools.py 2012-04-19 16:30:12.712727587 -0400
-@@ -283,6 +283,9 @@
+--- a/scipy/weave/build_tools.py
++++ b/scipy/weave/build_tools.py
+@@ -283,6 +283,9 @@ def build_extension(module_path,compiler
configure_python_path(build_dir)
except SyntaxError: #TypeError:
success = 0
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