Raspbian forward porter [Mon, 13 Feb 2023 15:21:51 +0000 (15:21 +0000)]
Merge scipy (1.10.0-4+rpi1) import into refs/heads/workingbranch
Evgeni Burovski [Thu, 5 Jan 2023 09:29:15 +0000 (12:29 +0300)]
[PATCH 1/2] BUG: interpolate/RGI: upcast float32 to float64
Gbp-Pq: Name fix_cast_PR17726.patch
Debian Python Team [Mon, 13 Feb 2023 15:21:51 +0000 (15:21 +0000)]
readonly_interpolate_PR17717
===================================================================
Gbp-Pq: Name readonly_interpolate_PR17717.patch
Debian Python Team [Mon, 13 Feb 2023 15:21:51 +0000 (15:21 +0000)]
fix_highs_atomic_PR17777
===================================================================
Gbp-Pq: Name fix_highs_atomic_PR17777.patch
Debian Python Team [Mon, 13 Feb 2023 15:21:51 +0000 (15:21 +0000)]
docs_no_sphinx_design
===================================================================
Gbp-Pq: Name docs_no_sphinx_design.patch
Debian Python Team [Mon, 13 Feb 2023 15:21:51 +0000 (15:21 +0000)]
manage_docs
===================================================================
Gbp-Pq: Name manage_docs.patch
Andreas Tille [Mon, 13 Feb 2023 15:21:51 +0000 (15:21 +0000)]
cython is actually cython3
Last-Update: Tue, 13 Dec 2022 14:11:49 +0100
Gbp-Pq: Name find_cython3.patch
Jochen Sprickerhof [Tue, 3 Jan 2023 13:35:03 +0000 (14:35 +0100)]
Drop intersphinx
Gbp-Pq: Name 0018-Drop-intersphinx.patch
Jochen Sprickerhof [Tue, 20 Dec 2022 18:29:15 +0000 (19:29 +0100)]
Allow test_svds_parameter_k_which to fail on armel
Gbp-Pq: Name 0010-Allow-test_svds_parameter_k_which-to-fail-on-armel.patch
Jochen Sprickerhof [Tue, 20 Dec 2022 08:45:22 +0000 (09:45 +0100)]
Remove some documentation referencing the source
These break in sbuild with:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/sphinx/cmd/build.py", line 281, in build_main
app.build(args.force_all, args.filenames)
File "/usr/lib/python3/dist-packages/sphinx/application.py", line 341, in build
self.builder.build_update()
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 310, in build_update
self.build(to_build,
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 376, in build
self.write(docnames, list(updated_docnames), method)
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 571, in write
self._write_serial(sorted(docnames))
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 574, in _write_serial
with logging.pending_warnings():
File "/usr/lib/python3.10/contextlib.py", line 142, in __exit__
next(self.gen)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 218, in pending_warnings
memhandler.flushTo(logger)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 183, in flushTo
logger.handle(record)
File "/usr/lib/python3.10/logging/__init__.py", line 1634, in handle
self.callHandlers(record)
File "/usr/lib/python3.10/logging/__init__.py", line 1696, in callHandlers
hdlr.handle(record)
File "/usr/lib/python3.10/logging/__init__.py", line 964, in handle
rv = self.filter(record)
File "/usr/lib/python3.10/logging/__init__.py", line 821, in filter
result = f.filter(record)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 499, in filter
record.location = get_node_location(location)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 519, in get_node_location
source = abspath(source)
File "/usr/lib/python3/dist-packages/sphinx/util/osutil.py", line 136, in abspath
pathdir = path.abspath(pathdir)
File "/usr/lib/python3.10/posixpath.py", line 378, in abspath
path = os.fspath(path)
TypeError: expected str, bytes or os.PathLike object, not StringList
Gbp-Pq: Name 0009-Remove-some-documentation-referencing-the-source.patch
Jochen Sprickerhof [Sun, 18 Dec 2022 09:33:23 +0000 (10:33 +0100)]
Don't treat warnings as errors in pytest
Gbp-Pq: Name 0008-Don-t-treat-warnings-as-errors-in-pytest.patch
serge-sans-paille [Tue, 19 Jul 2022 17:04:28 +0000 (19:04 +0200)]
[PATCH] Have get_index_dtype follow its documentation and return int32 or int64
This also avoids np.intc which is a portability pain.
Adjust group_sparse signature accordingly.
This should also fix https://github.com/serge-sans-paille/pythran/issues/2002
Gbp-Pq: Name pythran_type_PR16646.patch
Debian Python Team [Mon, 13 Feb 2023 15:21:51 +0000 (15:21 +0000)]
build_sh4_FE
Gbp-Pq: Name build_sh4_FE.patch
Debian Python Team [Mon, 13 Feb 2023 15:21:51 +0000 (15:21 +0000)]
manage_tests
===================================================================
Gbp-Pq: Name manage_tests.patch
Gard Spreemann [Sun, 29 Jan 2023 18:55:15 +0000 (19:55 +0100)]
Use system LBFGSB.
Gbp-Pq: Name Use-system-LBFGSB.patch
Julian Taylor [Mon, 12 Oct 2015 22:17:23 +0000 (15:17 -0700)]
enable large file support
probably not needed as the file open api of qhull is not available in python
Forwarded: no
Patch-Name: qhull-lfs.patch
Gbp-Pq: Name qhull-lfs.patch
SVN-Git Migration [Mon, 12 Oct 2015 22:17:20 +0000 (15:17 -0700)]
use_local_mathjax
Setting mathjax_path variable to use the local mathjax javascript library
Patch-Name: use_local_mathjax.patch
Gbp-Pq: Name use_local_mathjax.patch
Raspbian forward porter [Mon, 13 Feb 2023 15:21:51 +0000 (15:21 +0000)]
scipy (1.10.0-4+rpi1) bookworm-staging; urgency=medium
[changes brought forward from 1.8.1-14+rpi1 by Peter Michael Green <plugwash@raspbian.org> at Mon, 26 Sep 2022 01:12:43 +0000]
* Disable testsuite.
* Add build-conflicts on git, the documenation seems to fail to
build if it is installed.
[dgit import unpatched scipy 1.10.0-4+rpi1]
Raspbian forward porter [Mon, 13 Feb 2023 15:21:51 +0000 (15:21 +0000)]
Import scipy_1.10.0-4+rpi1.debian.tar.xz
[dgit import tarball scipy 1.10.0-4+rpi1 scipy_1.10.0-4+rpi1.debian.tar.xz]
Drew Parsons [Tue, 7 Feb 2023 08:49:03 +0000 (08:49 +0000)]
Merge scipy (1.10.0-4) import into refs/heads/workingbranch
Evgeni Burovski [Thu, 5 Jan 2023 09:29:15 +0000 (12:29 +0300)]
[PATCH 1/2] BUG: interpolate/RGI: upcast float32 to float64
Gbp-Pq: Name fix_cast_PR17726.patch
Debian Python Team [Tue, 7 Feb 2023 08:49:03 +0000 (08:49 +0000)]
readonly_interpolate_PR17717
===================================================================
Gbp-Pq: Name readonly_interpolate_PR17717.patch
Debian Python Team [Tue, 7 Feb 2023 08:49:03 +0000 (08:49 +0000)]
fix_highs_atomic_PR17777
===================================================================
Gbp-Pq: Name fix_highs_atomic_PR17777.patch
Debian Python Team [Tue, 7 Feb 2023 08:49:03 +0000 (08:49 +0000)]
docs_no_sphinx_design
===================================================================
Gbp-Pq: Name docs_no_sphinx_design.patch
Debian Python Team [Tue, 7 Feb 2023 08:49:03 +0000 (08:49 +0000)]
manage_docs
===================================================================
Gbp-Pq: Name manage_docs.patch
Andreas Tille [Tue, 7 Feb 2023 08:49:03 +0000 (08:49 +0000)]
cython is actually cython3
Last-Update: Tue, 13 Dec 2022 14:11:49 +0100
Gbp-Pq: Name find_cython3.patch
Jochen Sprickerhof [Tue, 3 Jan 2023 13:35:03 +0000 (14:35 +0100)]
Drop intersphinx
Gbp-Pq: Name 0018-Drop-intersphinx.patch
Jochen Sprickerhof [Tue, 20 Dec 2022 18:29:15 +0000 (19:29 +0100)]
Allow test_svds_parameter_k_which to fail on armel
Gbp-Pq: Name 0010-Allow-test_svds_parameter_k_which-to-fail-on-armel.patch
Jochen Sprickerhof [Tue, 20 Dec 2022 08:45:22 +0000 (09:45 +0100)]
Remove some documentation referencing the source
These break in sbuild with:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/sphinx/cmd/build.py", line 281, in build_main
app.build(args.force_all, args.filenames)
File "/usr/lib/python3/dist-packages/sphinx/application.py", line 341, in build
self.builder.build_update()
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 310, in build_update
self.build(to_build,
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 376, in build
self.write(docnames, list(updated_docnames), method)
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 571, in write
self._write_serial(sorted(docnames))
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 574, in _write_serial
with logging.pending_warnings():
File "/usr/lib/python3.10/contextlib.py", line 142, in __exit__
next(self.gen)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 218, in pending_warnings
memhandler.flushTo(logger)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 183, in flushTo
logger.handle(record)
File "/usr/lib/python3.10/logging/__init__.py", line 1634, in handle
self.callHandlers(record)
File "/usr/lib/python3.10/logging/__init__.py", line 1696, in callHandlers
hdlr.handle(record)
File "/usr/lib/python3.10/logging/__init__.py", line 964, in handle
rv = self.filter(record)
File "/usr/lib/python3.10/logging/__init__.py", line 821, in filter
result = f.filter(record)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 499, in filter
record.location = get_node_location(location)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 519, in get_node_location
source = abspath(source)
File "/usr/lib/python3/dist-packages/sphinx/util/osutil.py", line 136, in abspath
pathdir = path.abspath(pathdir)
File "/usr/lib/python3.10/posixpath.py", line 378, in abspath
path = os.fspath(path)
TypeError: expected str, bytes or os.PathLike object, not StringList
Gbp-Pq: Name 0009-Remove-some-documentation-referencing-the-source.patch
Jochen Sprickerhof [Sun, 18 Dec 2022 09:33:23 +0000 (10:33 +0100)]
Don't treat warnings as errors in pytest
Gbp-Pq: Name 0008-Don-t-treat-warnings-as-errors-in-pytest.patch
serge-sans-paille [Tue, 19 Jul 2022 17:04:28 +0000 (19:04 +0200)]
[PATCH] Have get_index_dtype follow its documentation and return int32 or int64
This also avoids np.intc which is a portability pain.
Adjust group_sparse signature accordingly.
This should also fix https://github.com/serge-sans-paille/pythran/issues/2002
Gbp-Pq: Name pythran_type_PR16646.patch
Debian Python Team [Tue, 7 Feb 2023 08:49:03 +0000 (08:49 +0000)]
build_sh4_FE
Gbp-Pq: Name build_sh4_FE.patch
Debian Python Team [Tue, 7 Feb 2023 08:49:03 +0000 (08:49 +0000)]
manage_tests
===================================================================
Gbp-Pq: Name manage_tests.patch
Gard Spreemann [Sun, 29 Jan 2023 18:55:15 +0000 (19:55 +0100)]
Use system LBFGSB.
Gbp-Pq: Name Use-system-LBFGSB.patch
Julian Taylor [Mon, 12 Oct 2015 22:17:23 +0000 (15:17 -0700)]
enable large file support
probably not needed as the file open api of qhull is not available in python
Forwarded: no
Patch-Name: qhull-lfs.patch
Gbp-Pq: Name qhull-lfs.patch
SVN-Git Migration [Mon, 12 Oct 2015 22:17:20 +0000 (15:17 -0700)]
use_local_mathjax
Setting mathjax_path variable to use the local mathjax javascript library
Patch-Name: use_local_mathjax.patch
Gbp-Pq: Name use_local_mathjax.patch
Drew Parsons [Tue, 7 Feb 2023 08:49:03 +0000 (08:49 +0000)]
scipy (1.10.0-4) unstable; urgency=medium
* Team upload.
* skip more build-time tests
- hurd-i386: test_find_peaks_exact test_find_peaks_withnoise
test_examples[True-float64] test_rv_sample
test_location_scale[pdf
- x32: test_basic
* update debian/tests
- armhf with openblas: skip test_array_smoothing
- i386 with blis: skip test_random_complex_exact
* debian patch fix_cast_PR17726.patch applies upstream PR17726
to fix 32-bit/64-bit casting. Closes: #
1029690.
* add Breaks: python3-skbio (<< 0.5.8-3~) to aid migration
[dgit import unpatched scipy 1.10.0-4]
Drew Parsons [Tue, 7 Feb 2023 08:49:03 +0000 (08:49 +0000)]
Import scipy_1.10.0-4.debian.tar.xz
[dgit import tarball scipy 1.10.0-4 scipy_1.10.0-4.debian.tar.xz]
Drew Parsons [Wed, 25 Jan 2023 14:32:10 +0000 (14:32 +0000)]
Merge scipy (1.8.1-22) import into refs/heads/workingbranch
Debian Python Team [Wed, 25 Jan 2023 14:32:10 +0000 (14:32 +0000)]
fix_numpy1.24_PR17035
===================================================================
Gbp-Pq: Name fix_numpy1.24_PR17035.patch
Tirth Patel [Fri, 28 Oct 2022 10:52:43 +0000 (03:52 -0700)]
DOC,MAINT: remove use of inspect.formatargspec dusing doc build (#17301)
Gbp-Pq: Name 0020-DOC-MAINT-remove-use-of-inspect.formatargspec-dusing.patch
Jochen Sprickerhof [Tue, 3 Jan 2023 17:44:06 +0000 (18:44 +0100)]
Ignore sphinx warnings
Gbp-Pq: Name 0019-Ignore-sphinx-warnings.patch
Jochen Sprickerhof [Tue, 3 Jan 2023 13:35:03 +0000 (14:35 +0100)]
Drop intersphinx
Gbp-Pq: Name 0018-Drop-intersphinx.patch
Ralf Gommers [Sun, 3 Jul 2022 11:12:56 +0000 (13:12 +0200)]
MAINT: fix umfpack test failure with numpy 1.23
The reason is a divide-by-zero warning that our test suite settings
convert to an error. So ignore these warnings, because they're
coming from inside `scikit-umfpack`.
This has been failing consistently in the Azure pre-release job.
Closes gh-16523
[skip github]
Gbp-Pq: Name 0017-MAINT-fix-umfpack-test-failure-with-numpy-1.23.patch
Jake Bowhay [Sat, 18 Jun 2022 07:39:32 +0000 (08:39 +0100)]
BUG: Fix power operator behaviour for sparse arrays to be consistent with numpy arrays
Gbp-Pq: Name 0016-BUG-Fix-power-operator-behaviour-for-sparse-arrays-t.patch
Ralf Gommers [Fri, 17 Jun 2022 05:12:24 +0000 (07:12 +0200)]
TST: fix test issues with casting-related warnings with numpy >1.23
Closes gh-16403
Gbp-Pq: Name 0015-TST-fix-test-issues-with-casting-related-warnings-wi.patch
Ralf Gommers [Fri, 17 Jun 2022 14:22:40 +0000 (16:22 +0200)]
MAINT: fix up `_sputils.get_index_dtype` for NEP 50 casting rules
The issue boiled down to `np.iinfo(np.int32).max` being a Python int,
and comparisons between numpy scalars and Python scalars changing
behavior - so avoid using Python scalars.
Also fix other sparse issues in the test suite turned up by NEP 50
And makes the tests more concise.
Gbp-Pq: Name 0014-MAINT-fix-up-_sputils.get_index_dtype-for-NEP-50-cas.patch
Tyler Reddy [Tue, 20 Dec 2022 03:22:21 +0000 (20:22 -0700)]
MAINT: casting errstate for NumPy 1.24
* Attempts to deal with the ARM-specific portion
of gh-17630 -- these issues appear to be the
result of NumPy 1.24.0 change:
https://numpy.org/devdocs/release/1.24.0-notes.html#numpy-now-gives-floating-point-errors-in-casts
* I was able to reproduce and fix the issues
in `scipy/sparse/tests/test_base` on an ARM node
* however, for `test_decomp_update` I actually saw more severe
problems when working on a Cavium ThunderX2 B0 node;
for the latter cases, I'll paste what I saw below
for some of the representative failures, but for now
I just tried to patch the less severe casting errors I see
in the CI for those tests to see if it helps (I'm hoping that
my own flavor of OpenBLAS is just throwing things off locally
and I can at least delay looking into that for now...)
```
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_neg_strides_economic_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_neg_strides_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_itemsize_strides_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_native_byte_order_economic_rank_1 - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_unit_strides_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_D::test_economic_rank_p - AssertionError:
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_native_byte_order_rank_1 - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_D::test_Mx1_economic_rank_p - AssertionError:
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_D::test_economic_rank_1 - AssertionError:
```
Gbp-Pq: Name 0013-MAINT-casting-errstate-for-NumPy-1.24.patch
warren [Wed, 12 Oct 2022 01:41:23 +0000 (21:41 -0400)]
MAINT: Handle numpy's deprecation of accepting out-of-bound integers.
After the change in https://github.com/numpy/numpy/pull/22385, numpy
raises a deprecation warning with calls such as np.int8(5000) and
np.uint32(-1). This change avoids such calls in the tests.
Gbp-Pq: Name 0012-MAINT-Handle-numpy-s-deprecation-of-accepting-out-of.patch
Mamoru TASAKA [Sun, 3 Jul 2022 07:11:18 +0000 (16:11 +0900)]
BUG: fix syevr series segfault by explicitly specifying operator priority
With numpy 1.22.x f2py, dimension of isuppz in syevr is mistranslated.
Avoid this by explicitly specifying operator priority with parenthesis.
Fixes #16527
Gbp-Pq: Name 0011-BUG-fix-syevr-series-segfault-by-explicitly-specifyi.patch
Jochen Sprickerhof [Tue, 20 Dec 2022 18:29:15 +0000 (19:29 +0100)]
Allow test_svds_parameter_k_which to fail on armel
Gbp-Pq: Name 0010-Allow-test_svds_parameter_k_which-to-fail-on-armel.patch
Jochen Sprickerhof [Tue, 20 Dec 2022 08:45:22 +0000 (09:45 +0100)]
Remove some documentation referencing the source
These break in sbuild with:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/sphinx/cmd/build.py", line 281, in build_main
app.build(args.force_all, args.filenames)
File "/usr/lib/python3/dist-packages/sphinx/application.py", line 341, in build
self.builder.build_update()
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 310, in build_update
self.build(to_build,
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 376, in build
self.write(docnames, list(updated_docnames), method)
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 571, in write
self._write_serial(sorted(docnames))
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 574, in _write_serial
with logging.pending_warnings():
File "/usr/lib/python3.10/contextlib.py", line 142, in __exit__
next(self.gen)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 218, in pending_warnings
memhandler.flushTo(logger)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 183, in flushTo
logger.handle(record)
File "/usr/lib/python3.10/logging/__init__.py", line 1634, in handle
self.callHandlers(record)
File "/usr/lib/python3.10/logging/__init__.py", line 1696, in callHandlers
hdlr.handle(record)
File "/usr/lib/python3.10/logging/__init__.py", line 964, in handle
rv = self.filter(record)
File "/usr/lib/python3.10/logging/__init__.py", line 821, in filter
result = f.filter(record)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 499, in filter
record.location = get_node_location(location)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 519, in get_node_location
source = abspath(source)
File "/usr/lib/python3/dist-packages/sphinx/util/osutil.py", line 136, in abspath
pathdir = path.abspath(pathdir)
File "/usr/lib/python3.10/posixpath.py", line 378, in abspath
path = os.fspath(path)
TypeError: expected str, bytes or os.PathLike object, not StringList
Gbp-Pq: Name 0009-Remove-some-documentation-referencing-the-source.patch
Jochen Sprickerhof [Sun, 18 Dec 2022 09:33:23 +0000 (10:33 +0100)]
Don't treat warnings as errors in pytest
Gbp-Pq: Name 0008-Don-t-treat-warnings-as-errors-in-pytest.patch
serge-sans-paille [Mon, 29 Aug 2022 06:15:49 +0000 (08:15 +0200)]
[PATCH] WIP
Gbp-Pq: Name pythran_type_PR16646.patch
Debian Python Team [Wed, 25 Jan 2023 14:32:10 +0000 (14:32 +0000)]
build_sh4_FE
===================================================================
Gbp-Pq: Name build_sh4_FE.patch
Debian Python Team [Wed, 25 Jan 2023 14:32:10 +0000 (14:32 +0000)]
manage_tests
===================================================================
Gbp-Pq: Name manage_tests.patch
Debian Python Team [Wed, 25 Jan 2023 14:32:10 +0000 (14:32 +0000)]
hppa-boost-long-double-config
===================================================================
Gbp-Pq: Name hppa-boost-long-double-config.patch
Gard Spreemann [Tue, 2 Apr 2019 09:25:26 +0000 (11:25 +0200)]
Use system LBFGSB.
Gbp-Pq: Name Use-system-LBFGSB.patch
Julian Taylor [Mon, 12 Oct 2015 22:17:23 +0000 (15:17 -0700)]
enable large file support
probably not needed as the file open api of qhull is not available in python
Forwarded: no
Patch-Name: qhull-lfs.patch
Gbp-Pq: Name qhull-lfs.patch
SVN-Git Migration [Mon, 12 Oct 2015 22:17:20 +0000 (15:17 -0700)]
use_local_mathjax
Setting mathjax_path variable to use the local mathjax javascript library
Patch-Name: use_local_mathjax.patch
Gbp-Pq: Name use_local_mathjax.patch
Drew Parsons [Wed, 25 Jan 2023 14:32:10 +0000 (14:32 +0000)]
scipy (1.8.1-22) unstable; urgency=medium
* Team upload.
* skip test_atol[bicg] on s390x. Closes: #
1029550.
[dgit import unpatched scipy 1.8.1-22]
Drew Parsons [Wed, 25 Jan 2023 14:32:10 +0000 (14:32 +0000)]
Import scipy_1.8.1-22.debian.tar.xz
[dgit import tarball scipy 1.8.1-22 scipy_1.8.1-22.debian.tar.xz]
Drew Parsons [Fri, 20 Jan 2023 10:47:47 +0000 (10:47 +0000)]
Import scipy_1.10.0.orig.tar.gz
[dgit import orig scipy_1.10.0.orig.tar.gz]
Drew Parsons [Fri, 20 Jan 2023 10:47:47 +0000 (10:47 +0000)]
Import scipy_1.10.0.orig-submodules.tar.gz
[dgit import orig scipy_1.10.0.orig-submodules.tar.gz]
Drew Parsons [Thu, 19 Jan 2023 13:54:51 +0000 (13:54 +0000)]
Merge scipy (1.8.1-21) import into refs/heads/workingbranch
Debian Python Team [Thu, 19 Jan 2023 13:54:51 +0000 (13:54 +0000)]
fix_numpy1.24_PR17035
===================================================================
Gbp-Pq: Name fix_numpy1.24_PR17035.patch
Tirth Patel [Fri, 28 Oct 2022 10:52:43 +0000 (03:52 -0700)]
DOC,MAINT: remove use of inspect.formatargspec dusing doc build (#17301)
Gbp-Pq: Name 0020-DOC-MAINT-remove-use-of-inspect.formatargspec-dusing.patch
Jochen Sprickerhof [Tue, 3 Jan 2023 17:44:06 +0000 (18:44 +0100)]
Ignore sphinx warnings
Gbp-Pq: Name 0019-Ignore-sphinx-warnings.patch
Jochen Sprickerhof [Tue, 3 Jan 2023 13:35:03 +0000 (14:35 +0100)]
Drop intersphinx
Gbp-Pq: Name 0018-Drop-intersphinx.patch
Ralf Gommers [Sun, 3 Jul 2022 11:12:56 +0000 (13:12 +0200)]
MAINT: fix umfpack test failure with numpy 1.23
The reason is a divide-by-zero warning that our test suite settings
convert to an error. So ignore these warnings, because they're
coming from inside `scikit-umfpack`.
This has been failing consistently in the Azure pre-release job.
Closes gh-16523
[skip github]
Gbp-Pq: Name 0017-MAINT-fix-umfpack-test-failure-with-numpy-1.23.patch
Jake Bowhay [Sat, 18 Jun 2022 07:39:32 +0000 (08:39 +0100)]
BUG: Fix power operator behaviour for sparse arrays to be consistent with numpy arrays
Gbp-Pq: Name 0016-BUG-Fix-power-operator-behaviour-for-sparse-arrays-t.patch
Ralf Gommers [Fri, 17 Jun 2022 05:12:24 +0000 (07:12 +0200)]
TST: fix test issues with casting-related warnings with numpy >1.23
Closes gh-16403
Gbp-Pq: Name 0015-TST-fix-test-issues-with-casting-related-warnings-wi.patch
Ralf Gommers [Fri, 17 Jun 2022 14:22:40 +0000 (16:22 +0200)]
MAINT: fix up `_sputils.get_index_dtype` for NEP 50 casting rules
The issue boiled down to `np.iinfo(np.int32).max` being a Python int,
and comparisons between numpy scalars and Python scalars changing
behavior - so avoid using Python scalars.
Also fix other sparse issues in the test suite turned up by NEP 50
And makes the tests more concise.
Gbp-Pq: Name 0014-MAINT-fix-up-_sputils.get_index_dtype-for-NEP-50-cas.patch
Tyler Reddy [Tue, 20 Dec 2022 03:22:21 +0000 (20:22 -0700)]
MAINT: casting errstate for NumPy 1.24
* Attempts to deal with the ARM-specific portion
of gh-17630 -- these issues appear to be the
result of NumPy 1.24.0 change:
https://numpy.org/devdocs/release/1.24.0-notes.html#numpy-now-gives-floating-point-errors-in-casts
* I was able to reproduce and fix the issues
in `scipy/sparse/tests/test_base` on an ARM node
* however, for `test_decomp_update` I actually saw more severe
problems when working on a Cavium ThunderX2 B0 node;
for the latter cases, I'll paste what I saw below
for some of the representative failures, but for now
I just tried to patch the less severe casting errors I see
in the CI for those tests to see if it helps (I'm hoping that
my own flavor of OpenBLAS is just throwing things off locally
and I can at least delay looking into that for now...)
```
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_neg_strides_economic_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_neg_strides_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_itemsize_strides_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_native_byte_order_economic_rank_1 - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_unit_strides_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_D::test_economic_rank_p - AssertionError:
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_native_byte_order_rank_1 - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_D::test_Mx1_economic_rank_p - AssertionError:
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_D::test_economic_rank_1 - AssertionError:
```
Gbp-Pq: Name 0013-MAINT-casting-errstate-for-NumPy-1.24.patch
warren [Wed, 12 Oct 2022 01:41:23 +0000 (21:41 -0400)]
MAINT: Handle numpy's deprecation of accepting out-of-bound integers.
After the change in https://github.com/numpy/numpy/pull/22385, numpy
raises a deprecation warning with calls such as np.int8(5000) and
np.uint32(-1). This change avoids such calls in the tests.
Gbp-Pq: Name 0012-MAINT-Handle-numpy-s-deprecation-of-accepting-out-of.patch
Mamoru TASAKA [Sun, 3 Jul 2022 07:11:18 +0000 (16:11 +0900)]
BUG: fix syevr series segfault by explicitly specifying operator priority
With numpy 1.22.x f2py, dimension of isuppz in syevr is mistranslated.
Avoid this by explicitly specifying operator priority with parenthesis.
Fixes #16527
Gbp-Pq: Name 0011-BUG-fix-syevr-series-segfault-by-explicitly-specifyi.patch
Jochen Sprickerhof [Tue, 20 Dec 2022 18:29:15 +0000 (19:29 +0100)]
Allow test_svds_parameter_k_which to fail on armel
Gbp-Pq: Name 0010-Allow-test_svds_parameter_k_which-to-fail-on-armel.patch
Jochen Sprickerhof [Tue, 20 Dec 2022 08:45:22 +0000 (09:45 +0100)]
Remove some documentation referencing the source
These break in sbuild with:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/sphinx/cmd/build.py", line 281, in build_main
app.build(args.force_all, args.filenames)
File "/usr/lib/python3/dist-packages/sphinx/application.py", line 341, in build
self.builder.build_update()
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 310, in build_update
self.build(to_build,
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 376, in build
self.write(docnames, list(updated_docnames), method)
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 571, in write
self._write_serial(sorted(docnames))
File "/usr/lib/python3/dist-packages/sphinx/builders/__init__.py", line 574, in _write_serial
with logging.pending_warnings():
File "/usr/lib/python3.10/contextlib.py", line 142, in __exit__
next(self.gen)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 218, in pending_warnings
memhandler.flushTo(logger)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 183, in flushTo
logger.handle(record)
File "/usr/lib/python3.10/logging/__init__.py", line 1634, in handle
self.callHandlers(record)
File "/usr/lib/python3.10/logging/__init__.py", line 1696, in callHandlers
hdlr.handle(record)
File "/usr/lib/python3.10/logging/__init__.py", line 964, in handle
rv = self.filter(record)
File "/usr/lib/python3.10/logging/__init__.py", line 821, in filter
result = f.filter(record)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 499, in filter
record.location = get_node_location(location)
File "/usr/lib/python3/dist-packages/sphinx/util/logging.py", line 519, in get_node_location
source = abspath(source)
File "/usr/lib/python3/dist-packages/sphinx/util/osutil.py", line 136, in abspath
pathdir = path.abspath(pathdir)
File "/usr/lib/python3.10/posixpath.py", line 378, in abspath
path = os.fspath(path)
TypeError: expected str, bytes or os.PathLike object, not StringList
Gbp-Pq: Name 0009-Remove-some-documentation-referencing-the-source.patch
Jochen Sprickerhof [Sun, 18 Dec 2022 09:33:23 +0000 (10:33 +0100)]
Don't treat warnings as errors in pytest
Gbp-Pq: Name 0008-Don-t-treat-warnings-as-errors-in-pytest.patch
serge-sans-paille [Mon, 29 Aug 2022 06:15:49 +0000 (08:15 +0200)]
[PATCH] WIP
Gbp-Pq: Name pythran_type_PR16646.patch
Debian Python Team [Thu, 19 Jan 2023 13:54:51 +0000 (13:54 +0000)]
build_sh4_FE
===================================================================
Gbp-Pq: Name build_sh4_FE.patch
Debian Python Team [Thu, 19 Jan 2023 13:54:51 +0000 (13:54 +0000)]
manage_tests
===================================================================
Gbp-Pq: Name manage_tests.patch
Debian Python Team [Thu, 19 Jan 2023 13:54:51 +0000 (13:54 +0000)]
hppa-boost-long-double-config
===================================================================
Gbp-Pq: Name hppa-boost-long-double-config.patch
Gard Spreemann [Tue, 2 Apr 2019 09:25:26 +0000 (11:25 +0200)]
Use system LBFGSB.
Gbp-Pq: Name Use-system-LBFGSB.patch
Julian Taylor [Mon, 12 Oct 2015 22:17:23 +0000 (15:17 -0700)]
enable large file support
probably not needed as the file open api of qhull is not available in python
Forwarded: no
Patch-Name: qhull-lfs.patch
Gbp-Pq: Name qhull-lfs.patch
SVN-Git Migration [Mon, 12 Oct 2015 22:17:20 +0000 (15:17 -0700)]
use_local_mathjax
Setting mathjax_path variable to use the local mathjax javascript library
Patch-Name: use_local_mathjax.patch
Gbp-Pq: Name use_local_mathjax.patch
Drew Parsons [Thu, 19 Jan 2023 13:54:51 +0000 (13:54 +0000)]
scipy (1.8.1-21) unstable; urgency=medium
* Team upload.
* debian patch fix_numpy1.24_PR17035.patch applies upstream PR17035
to fix build with numpy 1.24. Closes: #
1027244
[dgit import unpatched scipy 1.8.1-21]
Drew Parsons [Thu, 19 Jan 2023 13:54:51 +0000 (13:54 +0000)]
Import scipy_1.8.1-21.debian.tar.xz
[dgit import tarball scipy 1.8.1-21 scipy_1.8.1-21.debian.tar.xz]
Jochen Sprickerhof [Tue, 3 Jan 2023 20:59:59 +0000 (20:59 +0000)]
Merge scipy (1.8.1-20) import into refs/heads/workingbranch
Tirth Patel [Fri, 28 Oct 2022 10:52:43 +0000 (03:52 -0700)]
DOC,MAINT: remove use of inspect.formatargspec dusing doc build (#17301)
Gbp-Pq: Name 0020-DOC-MAINT-remove-use-of-inspect.formatargspec-dusing.patch
Jochen Sprickerhof [Tue, 3 Jan 2023 17:44:06 +0000 (18:44 +0100)]
Ignore sphinx warnings
Gbp-Pq: Name 0019-Ignore-sphinx-warnings.patch
Jochen Sprickerhof [Tue, 3 Jan 2023 13:35:03 +0000 (14:35 +0100)]
Drop intersphinx
Gbp-Pq: Name 0018-Drop-intersphinx.patch
Ralf Gommers [Sun, 3 Jul 2022 11:12:56 +0000 (13:12 +0200)]
MAINT: fix umfpack test failure with numpy 1.23
The reason is a divide-by-zero warning that our test suite settings
convert to an error. So ignore these warnings, because they're
coming from inside `scikit-umfpack`.
This has been failing consistently in the Azure pre-release job.
Closes gh-16523
[skip github]
Gbp-Pq: Name 0017-MAINT-fix-umfpack-test-failure-with-numpy-1.23.patch
Jake Bowhay [Sat, 18 Jun 2022 07:39:32 +0000 (08:39 +0100)]
BUG: Fix power operator behaviour for sparse arrays to be consistent with numpy arrays
Gbp-Pq: Name 0016-BUG-Fix-power-operator-behaviour-for-sparse-arrays-t.patch
Ralf Gommers [Fri, 17 Jun 2022 05:12:24 +0000 (07:12 +0200)]
TST: fix test issues with casting-related warnings with numpy >1.23
Closes gh-16403
Gbp-Pq: Name 0015-TST-fix-test-issues-with-casting-related-warnings-wi.patch
Ralf Gommers [Fri, 17 Jun 2022 14:22:40 +0000 (16:22 +0200)]
MAINT: fix up `_sputils.get_index_dtype` for NEP 50 casting rules
The issue boiled down to `np.iinfo(np.int32).max` being a Python int,
and comparisons between numpy scalars and Python scalars changing
behavior - so avoid using Python scalars.
Also fix other sparse issues in the test suite turned up by NEP 50
And makes the tests more concise.
Gbp-Pq: Name 0014-MAINT-fix-up-_sputils.get_index_dtype-for-NEP-50-cas.patch
Tyler Reddy [Tue, 20 Dec 2022 03:22:21 +0000 (20:22 -0700)]
MAINT: casting errstate for NumPy 1.24
* Attempts to deal with the ARM-specific portion
of gh-17630 -- these issues appear to be the
result of NumPy 1.24.0 change:
https://numpy.org/devdocs/release/1.24.0-notes.html#numpy-now-gives-floating-point-errors-in-casts
* I was able to reproduce and fix the issues
in `scipy/sparse/tests/test_base` on an ARM node
* however, for `test_decomp_update` I actually saw more severe
problems when working on a Cavium ThunderX2 B0 node;
for the latter cases, I'll paste what I saw below
for some of the representative failures, but for now
I just tried to patch the less severe casting errors I see
in the CI for those tests to see if it helps (I'm hoping that
my own flavor of OpenBLAS is just throwing things off locally
and I can at least delay looking into that for now...)
```
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_neg_strides_economic_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_neg_strides_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_itemsize_strides_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_native_byte_order_economic_rank_1 - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_unit_strides_rank_p - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_D::test_economic_rank_p - AssertionError:
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_d::test_non_native_byte_order_rank_1 - ValueError: array must not contain infs or NaNs
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_D::test_Mx1_economic_rank_p - AssertionError:
FAILED scipy/linalg/tests/test_decomp_update.py::TestQRupdate_D::test_economic_rank_1 - AssertionError:
```
Gbp-Pq: Name 0013-MAINT-casting-errstate-for-NumPy-1.24.patch
warren [Wed, 12 Oct 2022 01:41:23 +0000 (21:41 -0400)]
MAINT: Handle numpy's deprecation of accepting out-of-bound integers.
After the change in https://github.com/numpy/numpy/pull/22385, numpy
raises a deprecation warning with calls such as np.int8(5000) and
np.uint32(-1). This change avoids such calls in the tests.
Gbp-Pq: Name 0012-MAINT-Handle-numpy-s-deprecation-of-accepting-out-of.patch
Mamoru TASAKA [Sun, 3 Jul 2022 07:11:18 +0000 (16:11 +0900)]
BUG: fix syevr series segfault by explicitly specifying operator priority
With numpy 1.22.x f2py, dimension of isuppz in syevr is mistranslated.
Avoid this by explicitly specifying operator priority with parenthesis.
Fixes #16527
Gbp-Pq: Name 0011-BUG-fix-syevr-series-segfault-by-explicitly-specifyi.patch
Jochen Sprickerhof [Tue, 20 Dec 2022 18:29:15 +0000 (19:29 +0100)]
Allow test_svds_parameter_k_which to fail on armel
Gbp-Pq: Name 0010-Allow-test_svds_parameter_k_which-to-fail-on-armel.patch
projects / scipy.git / log