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here is the log from the commit of package python-scipy for openSUSE:Factory
checked in at 2024-04-30 17:25:49
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-scipy (Old)
and /work/SRC/openSUSE:Factory/.python-scipy.new.1880 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-scipy"
Tue Apr 30 17:25:49 2024 rev:70 rq:1170765 version:1.13.0
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-scipy/python-scipy.changes
2024-03-01 23:34:20.886730700 +0100
+++ /work/SRC/openSUSE:Factory/.python-scipy.new.1880/python-scipy.changes
2024-04-30 17:26:07.991494898 +0200
@@ -1,0 +2,138 @@
+Wed Apr 24 11:41:51 UTC 2024 - Ben Greiner <c...@bnavigator.de>
+
+- Skip another test out of numeric precision for 32-bit
+- Fix HPC _version
+
+-------------------------------------------------------------------
+Fri Apr 19 10:55:20 UTC 2024 - Ben Greiner <c...@bnavigator.de>
+
+- Update to 1.13.0
+ ## Highlights of this release
+ * Support for NumPy 2.0.0.
+ * Interactive examples have been added to the documentation,
+ allowing users to run the examples locally on embedded
+ Jupyterlite notebooks in their browser.
+ * Preliminary 1D array support for the COO and DOK sparse
+ formats.
+ * Several scipy.stats functions have gained support for
+ additional axis, nan_policy, and keepdims arguments.
+ scipy.stats also has several performance and accuracy
+ improvements.
+ ## New features
+ * scipy.integrate improvements
+ * scipy.io improvements
+ * scipy.interpolate improvements
+ * scipy.signal improvements
+ * scipy.sparse improvements
+ * scipy.spatial improvements
+ * scipy.special improvements
+ * scipy.stats improvements
+ ## Deprecated features
+ * Complex dtypes in PchipInterpolator and Akima1DInterpolator
+ have been deprecated and will raise an error in SciPy 1.15.0.
+ If you are trying to use the real components of the passed
+ array, use np.real on y.
+ ## Other changes
+ * The second argument of scipy.stats.moment has been renamed to
+ order while maintaining backward compatibility.
+- Release 1.12.0
+ ## Highlights of this release
+ * Experimental support for the array API standard has been added
+ to part of scipy.special, and to all of scipy.fft and
+ scipy.cluster. There are likely to be bugs and early feedback
+ for usage with CuPy arrays, PyTorch tensors, and other array
+ API compatible libraries is appreciated. Use the
+ SCIPY_ARRAY_API environment variable for testing.
+ * A new class, ShortTimeFFT, provides a more versatile
+ implementation of the short-time Fourier transform (STFT), its
+ inverse (ISTFT) as well as the (cross-) spectrogram. It
+ utilizes an improved algorithm for calculating the ISTFT.
+ * Several new constructors have been added for sparse arrays, and
+ many operations now additionally support sparse arrays, further
+ facilitating the migration from sparse matrices.
+ * A large portion of the scipy.stats API now has improved support
+ for handling NaN values, masked arrays, and more fine-grained
+ shape-handling. The accuracy and performance of a number of
+ stats methods have been improved, and a number of new
+ statistical tests and distributions have been added.
+ ## New features
+ * scipy.cluster improvements
+ * scipy.fft improvements
+ * scipy.integrate improvements
+ * scipy.interpolate improvements
+ * scipy.linalg improvements
+ * scipy.ndimage improvements
+ * scipy.optimize improvements
+ * scipy.signal improvements
+ * scipy.sparse improvements
+ * scipy.spatial improvements
+ * scipy.special improvements
+ * scipy.stats improvements
+ ## Deprecated features
+ * Error messages have been made clearer for objects that donât
+ exist in the public namespace and warnings sharpened for
+ private attributes that are not supposed to be imported at all.
+ * scipy.signal.cmplx_sort has been deprecated and will be removed
+ in SciPy 1.15. A replacement you can use is provided in the
+ deprecation message.
+ * Values the argument initial of
+ scipy.integrate.cumulative_trapezoid other than 0 and None are
+ now deprecated.
+ * scipy.stats.rvs_ratio_uniforms is deprecated in favour of
+ scipy.stats.sampling.RatioUniforms
+ * scipy.integrate.quadrature and scipy.integrate.romberg have
+ been deprecated due to accuracy issues and interface
+ shortcomings. They will be removed in SciPy 1.15. Please use
+ scipy.integrate.quad instead.
+ * Coinciding with upcoming changes to function signatures (e.g.
+ removal of a deprecated keyword), we are deprecating positional
+ use of keyword arguments for the affected functions, which will
+ raise an error starting with SciPy 1.14. In some cases, this
+ has delayed the originally announced removal date, to give time
+ to respond to the second part of the deprecation. Affected
+ functions are:
+ - linalg.{eigh, eigvalsh, pinv}
+ - integrate.simpson
+ - signal.{firls, firwin, firwin2, remez}
+ - sparse.linalg.{bicg, bicgstab, cg, cgs, gcrotmk, gmres,
+ lgmres, minres, qmr, tfqmr}
+ - special.comb
+ - stats.kendalltau
+ * All wavelet functions have been deprecated, as PyWavelets
+ provides suitable implementations; affected functions are:
+ signal.{daub, qmf, cascade, morlet, morlet2, ricker, cwt}
+ * scipy.integrate.trapz, scipy.integrate.cumtrapz, and
+ scipy.integrate.simps have been deprecated in favour of
+ scipy.integrate.trapezoid,
+ scipy.integrate.cumulative_trapezoid, and
+ scipy.integrate.simpson respectively and will be removed in
+ SciPy 1.14.
+ * The tol argument of
+ scipy.sparse.linalg.{bcg,bicstab,cg,cgs,gcrotmk,gmres,lgmres,
+ minres,qmr,tfqmr}
+ is now deprecated in favour of rtol and will be removed in
+ SciPy 1.14. Furthermore, the default value of atol for these
+ functions is due to change to 0.0 in SciPy 1.14.
+ ## Expired Deprecations
+ * There is an ongoing effort to follow through on long-standing
+ deprecations. The following previously deprecated features are
+ affected:
+ * The centered keyword of scipy.stats.qmc.LatinHypercube has been
+ removed. Use scrambled=False instead of centered=True.
+ * scipy.stats.binom_test has been removed in favour of
+ scipy.stats.binomtest.
+ * In scipy.stats.iqr, the use of scale='raw' has been removed in
+ favour of scale=1.
+ * Functions from NumPyâs main namespace which were exposed in
+ SciPyâs main namespace, such as numpy.histogram exposed by
+ scipy.histogram, have been removed from SciPyâs main namespace.
+ Please use the functions directly from numpy.
+ ## Other changes
+ * The arguments used to compile and link SciPy are now available
+ via show_config.
+- Drop 8c96a1f742335bca283aae418763aaba62c03378.patch (merged
+ upstream)
+- Add scipy-pr20530-f2py_error.patch gh#scipy/scipy#20530, used to
+ find workaround for failing HPC build gh#scipy/scipy#20535
+
+-------------------------------------------------------------------
Old:
----
8c96a1f742335bca283aae418763aaba62c03378.patch
scipy-1.11.4.tar.gz
New:
----
scipy-1.13.0.tar.gz
scipy-pr20530-f2py_error.patch
BETA DEBUG BEGIN:
Old: via show_config.
- Drop 8c96a1f742335bca283aae418763aaba62c03378.patch (merged
upstream)
BETA DEBUG END:
BETA DEBUG BEGIN:
New: upstream)
- Add scipy-pr20530-f2py_error.patch gh#scipy/scipy#20530, used to
find workaround for failing HPC build gh#scipy/scipy#20535
BETA DEBUG END:
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-scipy.spec ++++++
--- /var/tmp/diff_new_pack.MzXTu6/_old 2024-04-30 17:26:10.931601808 +0200
+++ /var/tmp/diff_new_pack.MzXTu6/_new 2024-04-30 17:26:10.935601953 +0200
@@ -1,5 +1,5 @@
#
-# spec file
+# spec file for package python-scipy
#
# Copyright (c) 2024 SUSE LLC
#
@@ -18,7 +18,7 @@
%{?sle15_python_module_pythons}
%global flavor @BUILD_FLAVOR@%{nil}
-%define _ver 1_11_4
+%define _ver 1_13_0
%define shortname scipy
%define pname python-%{shortname}
%define hpc_upcase_trans_hyph() %(echo %{**} | tr [a-z] [A-Z] | tr '-' '_')
@@ -89,32 +89,35 @@
%endif
%{hpc_modules_init openblas}
%endif
+# make sure the generators get called with the flavored python --
gh#scipy/scipy#20535
+%define pybuildgenerators tools/generate_f2pymod.py
scipy/_build_utils/tempita.py
# TODO explore debundling Boost for standard and hpc
Name: %{package_name}
-Version: 1.11.4
+Version: 1.13.0
Release: 0
Summary: Scientific Tools for Python
License: BSD-3-Clause AND LGPL-2.0-or-later AND BSL-1.0
URL: https://www.scipy.org
Source0:
https://files.pythonhosted.org/packages/source/s/scipy/scipy-%{version}.tar.gz
-# Create with pooch: `python3 scipy-%{version}/scipy/datasets/_download_all.py
scipy-datasets/scipy-data; tar czf scipy-datasets.tar.gz scipy-datasets`
+# Create with pooch: `python3
scipy-%%{version}/scipy/datasets/_download_all.py scipy-datasets/scipy-data;
tar czf scipy-datasets.tar.gz scipy-datasets`
Source1: scipy-datasets.tar.gz
-Patch1: 8c96a1f742335bca283aae418763aaba62c03378.patch
-BuildRequires: %{python_module Cython >= 0.29.32}
-BuildRequires: %{python_module devel >= 3.8}
-BuildRequires: %{python_module meson-python >= 0.9.0}
+# PATCH-FIX-UPSTREAM scipy-pr20530-f2py_error.patch -- gh#scipy/scipy#20530
+Patch0: scipy-pr20530-f2py_error.patch
+BuildRequires: %{python_module Cython >= 3.0.8 with %python-Cython < 3.1}
+BuildRequires: %{python_module devel >= 3.9}
+BuildRequires: %{python_module meson-python >= 0.15.0 with
%python-meson-python < 0.18}
BuildRequires: %{python_module pip}
-BuildRequires: %{python_module pybind11 >= 2.4.3}
-BuildRequires: %{python_module pybind11-devel >= 2.4.3}
-BuildRequires: %{python_module pythran >= 0.9.12}
-BuildRequires: %{python_module wheel}
+BuildRequires: %{python_module pybind11-devel >= 2.12 with
%python-pybind11-devel < 2.13}
+BuildRequires: %{python_module pythran >= 0.14 with %python-pythran < 0.16}
BuildRequires: fdupes
BuildRequires: meson >= 0.62.2
BuildRequires: pkg-config
BuildRequires: python-rpm-macros >= 20220911
%if %{with test}
+BuildRequires: %{python_module hypothesis}
+BuildRequires: %{python_module matplotlib}
BuildRequires: %{python_module pooch}
BuildRequires: %{python_module pytest-timeout}
BuildRequires: %{python_module pytest-xdist}
@@ -123,7 +126,7 @@
BuildRequires: %{python_module threadpoolctl}
%endif
%if %{without hpc}
-BuildRequires: %{python_module numpy-devel >= 1.18.5}
+BuildRequires: %{python_module numpy-devel >= 1.18.5 with %python-numpy-devel
< 2.3}
%if 0%{?sle_version} && 0%{?sle_version} <= 150600
# The default gcc on SLE15 is gcc7 we need something newer
BuildRequires: gcc10-c++
@@ -132,8 +135,7 @@
BuildRequires: gcc-c++ >= 8
BuildRequires: gcc-fortran >= 8
%endif
-Requires: python-numpy >= 1.18.5
-Requires: python-pybind11 >= 2.4.3
+Requires: (python-numpy >= 1.22.4 with python-numpy < 2.3)
Suggests: python-pooch
%if %{with openblas}
BuildRequires: openblas-devel
@@ -166,6 +168,11 @@
sed -i '1{/env python/d}' scipy/sparse/linalg/_isolve/tests/test_gcrotmk.py
chmod a-x scipy/stats/tests/test_distributions.py
+# make sure the generators get called with the flavored python --
gh#scipy/scipy#20535
+for c in %pybuildgenerators; do
+ sed -E '1{s/^#!(.*)$/#!@MYFLAVORPYTHON@/}' $c > $c.flavorin
+done
+
%ifarch i586
# Limit double floating point precision for x87, triggered by GCC 12.
%global optflags %(echo "%{optflags} -ffloat-store")
@@ -189,6 +196,10 @@
# makes sure that the cython and pythran commands from the correct flavor are
in PATH
%python_flavored_alternatives
%{python_expand #
+# make sure the generators get called with the flavored python --
gh#scipy/scipy#20535
+for c in %pybuildgenerators; do
+ sed '1{s|@MYFLAVORPYTHON@|%{__$python}|}' $c.flavorin > $c
+done
%if %{with hpc}
py_ver=%{$python_version}
%hpc_setup
@@ -208,8 +219,7 @@
# https://github.com/scipy/scipy/issues/16310, delete in order to avoid
rpmlint errors
rm %{buildroot}%{p_python_sitearch_expand}/scipy/linalg/_blas_subroutines.h
rm %{buildroot}%{p_python_sitearch_expand}/scipy/linalg/_lapack_subroutines.h
-rm %{buildroot}%{p_python_sitearch_expand}/scipy/special/_ufuncs_cxx_defs.h
-rm %{buildroot}%{p_python_sitearch_expand}/scipy/special/_ufuncs_defs.h
+find %{buildroot}%{p_python_sitearch_expand}/scipy/special -name '*.h' -delete
%fdupes %{buildroot}%{p_python_sitearch_expand}
}
@@ -309,6 +319,7 @@
# not enough precison on 32 bits
if [ $(getconf LONG_BIT) -eq 32 ]; then
donttest+=" or (TestCheby1 and test_basic)"
+ donttest+=" or test_extreme_entropy"
fi
mv scipy scipy.dont-import-me
%pytest_arch --pyargs scipy -n auto -m "not (slow or xslow $mark32bit)" -k
"not ($donttest)"
++++++ scipy-1.11.4.tar.gz -> scipy-1.13.0.tar.gz ++++++
/work/SRC/openSUSE:Factory/python-scipy/scipy-1.11.4.tar.gz
/work/SRC/openSUSE:Factory/.python-scipy.new.1880/scipy-1.13.0.tar.gz differ:
char 5, line 1
++++++ scipy-datasets.tar.gz ++++++
++++++ scipy-pr20530-f2py_error.patch ++++++
>From 8dc60a00cfb428b530783d88b0aeb44a930ad3e0 Mon Sep 17 00:00:00 2001
From: Ben Greiner <c...@bnavigator.de>
Date: Fri, 19 Apr 2024 15:35:22 +0200
Subject: [PATCH 1/2] BLD: Fix error message for f2py generation fail
---
tools/generate_f2pymod.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/tools/generate_f2pymod.py b/tools/generate_f2pymod.py
index 5a8ba1389514..bb22fdb105cb 100644
--- a/tools/generate_f2pymod.py
+++ b/tools/generate_f2pymod.py
@@ -290,9 +290,9 @@ def main():
cwd=os.getcwd())
out, err = p.communicate()
if not (p.returncode == 0):
- raise RuntimeError(f"Writing {args.outfile} with f2py failed!\n"
- f"{out}\n"
- r"{err}")
+ raise RuntimeError(f"Writing {fname_pyf} with f2py failed!\n"
+ f"{out.decode()}\n"
+ f"{err.decode()}")
if __name__ == "__main__":
>From f7b532b4fbee2a2e54d9e357cf395c237a7ee894 Mon Sep 17 00:00:00 2001
From: Ralf Gommers <ralf.gomm...@gmail.com>
Date: Fri, 19 Apr 2024 17:38:04 +0200
Subject: [PATCH 2/2] MAINT: tweak message a bit more, and fix style issue
[skip ci]
---
tools/generate_f2pymod.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/tools/generate_f2pymod.py b/tools/generate_f2pymod.py
index bb22fdb105cb..4b4ce105a011 100644
--- a/tools/generate_f2pymod.py
+++ b/tools/generate_f2pymod.py
@@ -290,9 +290,9 @@ def main():
cwd=os.getcwd())
out, err = p.communicate()
if not (p.returncode == 0):
- raise RuntimeError(f"Writing {fname_pyf} with f2py failed!\n"
- f"{out.decode()}\n"
- f"{err.decode()}")
+ raise RuntimeError(f"Processing {fname_pyf} with f2py failed!\n"
+ f"{out.decode()}\n"
+ f"{err.decode()}")
if __name__ == "__main__":
