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Accepting request 906711 from home:bnavigator:branches:devel:languages:python:numeric

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- Fix segfault with subarray access
  * Add numpy-pr19326-fix-subarray-segfault.patch
  * Fixes python-zarr segfault
  * gh#numpy/numpy#19326

OBS-URL: https://build.opensuse.org/request/show/906711
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-numpy?expand=0&rev=92
This commit is contained in:
Matej Cepl 2021-07-17 06:27:46 +00:00 committed by Git OBS Bridge
parent c7e05108e5
commit 696375d29d
3 changed files with 136 additions and 4 deletions
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125
numpy-pr19326-fix-subarray-segfault.patch Normal file
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@ -0,0 +1,125 @@
From be09bb6ba4d27fbd1f667d34bb2f11cccb446d65 Mon Sep 17 00:00:00 2001
From: Gregory Lee <grlee77@gmail.com>
Date: Thu, 24 Jun 2021 08:37:01 -0400
Subject: [PATCH 1/4] BUG: protect against access an attribute of a NULL
pointer
Have PyArray_GetCastSafety return -1 if from is NULL
---
numpy/core/src/multiarray/convert_datatype.c | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/numpy/core/src/multiarray/convert_datatype.c b/numpy/core/src/multiarray/convert_datatype.c
index d197a4bea31..716e5dd3d11 100644
--- a/numpy/core/src/multiarray/convert_datatype.c
+++ b/numpy/core/src/multiarray/convert_datatype.c
@@ -417,6 +417,9 @@ PyArray_GetCastSafety(
if (to != NULL) {
to_dtype = NPY_DTYPE(to);
}
+ if (from == NULL) {
+ return -1;
+ }
PyObject *meth = PyArray_GetCastingImpl(NPY_DTYPE(from), to_dtype);
if (meth == NULL) {
return -1;
@@ -3293,8 +3296,10 @@ void_to_void_resolve_descriptors(
casting = NPY_NO_CASTING | _NPY_CAST_IS_VIEW;
}
}
- NPY_CASTING field_casting = PyArray_GetCastSafety(
- given_descrs[0]->subarray->base, given_descrs[1]->subarray->base, NULL);
+
+ PyArray_Descr *from_base = (from_sub == NULL) ? NULL : from_sub->base;
+ PyArray_Descr *to_base = (to_sub == NULL) ? NULL : to_sub->base;
+ NPY_CASTING field_casting = PyArray_GetCastSafety(from_base, to_base, NULL);
if (field_casting < 0) {
return -1;
}
From 3c901b49bd8715c93824c27682d81434d869498a Mon Sep 17 00:00:00 2001
From: Gregory Lee <grlee77@gmail.com>
Date: Thu, 24 Jun 2021 11:16:22 -0400
Subject: [PATCH 2/4] pass descriptor rather than null
---
numpy/core/src/multiarray/convert_datatype.c | 7 ++-----
1 file changed, 2 insertions(+), 5 deletions(-)
diff --git a/numpy/core/src/multiarray/convert_datatype.c b/numpy/core/src/multiarray/convert_datatype.c
index 716e5dd3d11..1bba276d2d1 100644
--- a/numpy/core/src/multiarray/convert_datatype.c
+++ b/numpy/core/src/multiarray/convert_datatype.c
@@ -417,9 +417,6 @@ PyArray_GetCastSafety(
if (to != NULL) {
to_dtype = NPY_DTYPE(to);
}
- if (from == NULL) {
- return -1;
- }
PyObject *meth = PyArray_GetCastingImpl(NPY_DTYPE(from), to_dtype);
if (meth == NULL) {
return -1;
@@ -3297,8 +3294,8 @@ void_to_void_resolve_descriptors(
}
}
- PyArray_Descr *from_base = (from_sub == NULL) ? NULL : from_sub->base;
- PyArray_Descr *to_base = (to_sub == NULL) ? NULL : to_sub->base;
+ PyArray_Descr *from_base = (from_sub == NULL) ? given_descrs[0] : from_sub->base;
+ PyArray_Descr *to_base = (to_sub == NULL) ? given_descrs[1] : to_sub->base;
NPY_CASTING field_casting = PyArray_GetCastSafety(from_base, to_base, NULL);
if (field_casting < 0) {
return -1;
From 8925fec4721b3a89e94d59b6149884d07fc581f4 Mon Sep 17 00:00:00 2001
From: Gregory Lee <grlee77@gmail.com>
Date: Thu, 24 Jun 2021 11:44:37 -0400
Subject: [PATCH 3/4] TST: test can_cast when only one argument has a subarray
---
numpy/core/tests/test_casting_unittests.py | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/numpy/core/tests/test_casting_unittests.py b/numpy/core/tests/test_casting_unittests.py
index 2cec1acd349..34f316d5ddc 100644
--- a/numpy/core/tests/test_casting_unittests.py
+++ b/numpy/core/tests/test_casting_unittests.py
@@ -646,3 +646,9 @@ def test_object_to_parametric_internal_error(self):
with pytest.raises(TypeError,
match="casting from object to the parametric DType"):
cast._resolve_descriptors((np.dtype("O"), None))
+
+ def test_void_to_structured_with_subarray(self):
+ # test case corresponding to gh-19325
+ dtype = np.dtype([("foo", "<f4", (3, 2))])
+ assert np.can_cast("V4", dtype, casting="unsafe")
+ assert not np.can_cast("V4", dtype, casting="no")
From 9bf60f5f8c5d0dde78b737932e61dec61b960d53 Mon Sep 17 00:00:00 2001
From: Gregory Lee <grlee77@gmail.com>
Date: Thu, 24 Jun 2021 13:41:03 -0400
Subject: [PATCH 4/4] TST: test both argument orders
---
numpy/core/tests/test_casting_unittests.py | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/numpy/core/tests/test_casting_unittests.py b/numpy/core/tests/test_casting_unittests.py
index 34f316d5ddc..d1924c1fda1 100644
--- a/numpy/core/tests/test_casting_unittests.py
+++ b/numpy/core/tests/test_casting_unittests.py
@@ -647,8 +647,10 @@ def test_object_to_parametric_internal_error(self):
match="casting from object to the parametric DType"):
cast._resolve_descriptors((np.dtype("O"), None))
- def test_void_to_structured_with_subarray(self):
+ @pytest.mark.parametrize("casting", ["no", "unsafe"])
+ def test_void_and_structured_with_subarray(self, casting):
# test case corresponding to gh-19325
dtype = np.dtype([("foo", "<f4", (3, 2))])
- assert np.can_cast("V4", dtype, casting="unsafe")
- assert not np.can_cast("V4", dtype, casting="no")
+ expected = casting == "unsafe"
+ assert np.can_cast("V4", dtype, casting=casting) == expected
+ assert np.can_cast(dtype, "V4", casting=casting) == expected

8
python-numpy.changes
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@ -1,3 +1,11 @@
-------------------------------------------------------------------
Fri Jul 16 15:14:36 UTC 2021 - Ben Greiner <code@bnavigator.de>
- Fix segfault with subarray access
* Add numpy-pr19326-fix-subarray-segfault.patch
* Fixes python-zarr segfault
* gh#numpy/numpy#19326
-------------------------------------------------------------------
Wed Jul 7 08:24:03 UTC 2021 - Antonio Larrosa <alarrosa@suse.com>

7
python-numpy.spec
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@ -79,6 +79,8 @@ Patch0: numpy-buildfix.patch
Patch1: numpy-1.9.0-remove-__declspec.patch
# PATCH-FIX-UPSTREAM 0001-BUG-Fix-infinite-loop-on-gcc11.patch
Patch2: 0001-BUG-Fix-infinite-loop-on-gcc11.patch
# PATCH-FIX-UPSTREAM numpy-pr19326-fix-subarray-segfault.patch -- gh#numpy/numpy#19326
Patch3: https://github.com/numpy/numpy/pull/19326.patch#/numpy-pr19326-fix-subarray-segfault.patch
BuildRequires: %{python_module Cython >= 0.29.23}
BuildRequires: %{python_module base >= 3.7}
BuildRequires: %{python_module devel}
@ -159,10 +161,7 @@ This package contains files for developing applications using numpy.
%{?with_hpc:%{hpc_python_master_package devel -a }}
%prep
%setup -q -n numpy-%{version}
%patch0 -p1
%patch1 -p1
%patch2 -p1
%autosetup -p1 -n numpy-%{version}
# Fix non-executable scripts
sed -i '1s/^#!.*$//' numpy/{compat/setup,random/_examples/cython/setup,distutils/{conv_template,cpuinfo,exec_command,from_template,setup,system_info},f2py/{__init__,auxfuncs,capi_maps,cb_rules,cfuncs,common_rules,crackfortran,diagnose,f2py2e,f90mod_rules,func2subr,rules,setup,use_rules},ma/{setup,bench},matrixlib/setup,setup,testing/{print_coercion_tables,setup}}.py
sed -i '1s/^#!.*$//' numpy/random/_examples/cython/*.pyx