Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild

Signed-off-by: Fedora Release Engineering <releng@fedoraproject.org>

.gitignore

@@ -32,3 +32,10 @@ scipy-0.7.2.tar.gz
 /scipy-1.5.2.tar.gz
 /scipy-1.5.3.tar.gz
 /scipy-1.5.4.tar.gz
+/scipy-1.6.0.tar.gz
+/scipy-1.6.1.tar.gz
+/scipy-1.6.2.tar.gz
+/scipy-1.7.0.tar.gz
+/scipy-1.7.3.tar.gz
+/scipy-1.8.0.tar.gz
+/scipy-1.8.1.tar.gz

scipy-1.8.1-syevr-operator-order-explicit.patch

@@ -0,0 +1,69 @@
+--- scipy-1.8.1/scipy/linalg/flapack_sym_herm.pyf.src.debug	2022-04-30 06:14:37.965527300 +0900
++++ scipy-1.8.1/scipy/linalg/flapack_sym_herm.pyf.src	2022-07-01 22:51:14.057047006 +0900
+@@ -772,10 +772,10 @@
+     integer intent(hide),dimension(liwork),depend(liwork) :: iwork
+ 
+     <ftype2> intent(out),dimension(n),depend(n) :: w
+-    <ftype2> intent(out),dimension((compute_v?MAX(0,n):0),(compute_v?(*range=='I'?iu-il+1:MAX(1,n)):0)),depend(n,compute_v,range,iu,il) :: z
++    <ftype2> intent(out),dimension((compute_v?MAX(0,n):0),(compute_v?((*range=='I')?(iu-il+1):MAX(1,n)):0)),depend(n,compute_v,range,iu,il) :: z
+     integer intent(out) :: m
+     ! Only returned if range=='A' or range=='I' and il, iu = 1, n
+-    integer intent(out),dimension((compute_v?(2*(*range=='A'||(*range=='I' && iu-il+1==n)?n:0)):0)),depend(n,iu,il,compute_v,range) :: isuppz
++    integer intent(out),dimension((compute_v?(2*((*range=='A')||((*range=='I') && (iu-il+1==n))?n:0)):0)),depend(n,iu,il,compute_v,range) :: isuppz
+     integer intent(out) :: info
+ 
+ end subroutine <prefix2>syevr
+@@ -844,7 +844,7 @@
+     integer intent(hide),dimension(liwork),depend(liwork) :: iwork
+ 
+     <ftype2> intent(out),dimension(n),depend(n) :: w
+-    <ftype2c> intent(out),dimension((compute_v?MAX(0,n):0),(compute_v?(*range=='I'?iu-il+1:MAX(1,n)):0)),depend(n,compute_v,range,iu,il) :: z
++    <ftype2c> intent(out),dimension((compute_v?MAX(0,n):0),(compute_v?((*range=='I')?(iu-il+1):MAX(1,n)):0)),depend(n,compute_v,range,iu,il) :: z
+     integer intent(out) :: m
+     ! MKL implementation has a bug that still accesses isuppz array even if
+     ! range=='A' or range=='I' and il, iu = 1, n which is not the case for
+@@ -852,7 +852,7 @@
+     ! of the settings. It is wasteful but necessary. The bug is fixed in
+     ! mkl 2020 update 2 and when time comes change this line with
+     !
+-    ! integer intent(out),dimension((compute_v?(2*(*range=='A'||(*range=='I' && iu-il+1==n)?n:0)):0)),depend(n,iu,il,range,compute_v) :: isuppz
++    ! integer intent(out),dimension((compute_v?(2*(*range=='A'||((*range=='I') && (iu-il+1==n))?n:0)):0)),depend(n,iu,il,range,compute_v) :: isuppz
+     !
+     integer intent(out),dimension(2*max(1,n)),depend(n) :: isuppz
+     integer intent(out) :: info
+@@ -919,7 +919,7 @@
+     integer intent(hide),dimension(5*n),depend(n) :: iwork
+ 
+     <ftype2> intent(out),dimension(n),depend(n) :: w
+-    <ftype2> intent(out),dimension((compute_v?MAX(0,n):0),(compute_v?(*range=='I'?iu-il+1:MAX(1,n)):0)),depend(n,compute_v,range,iu,il) :: z
++    <ftype2> intent(out),dimension((compute_v?MAX(0,n):0),(compute_v?((*range=='I')?(iu-il+1):MAX(1,n)):0)),depend(n,compute_v,range,iu,il) :: z
+     integer intent(out) :: m
+     integer intent(out),dimension((compute_v?n:0)),depend(compute_v,n):: ifail
+     integer intent(out) :: info
+@@ -984,7 +984,7 @@
+     <ftype2> intent(hide),dimension(7*n),depend(n) :: rwork
+ 
+     <ftype2> intent(out),dimension(n),depend(n) :: w
+-    <ftype2c> intent(out),dimension((compute_v*n),(compute_v?(*range=='I'?iu-il+1:MAX(1,n)):0)),depend(compute_v,range,n,iu,il) :: z
++    <ftype2c> intent(out),dimension((compute_v*n),(compute_v?((*range=='I')?(iu-il+1):MAX(1,n)):0)),depend(compute_v,range,n,iu,il) :: z
+     integer intent(out) :: m
+     integer intent(out),dimension(compute_v*n),depend(compute_v,n):: ifail
+     integer intent(out) :: info
+@@ -1222,7 +1222,7 @@
+     integer intent(hide),dimension(5*n),depend(n) :: iwork
+ 
+     <ftype2> intent(out),dimension(n),depend(n) :: w
+-    <ftype2> intent(out),dimension((jobz[0]=='V'?MAX(0,n):0),(jobz[0]=='V'?(range[0]=='I'?iu-il+1:MAX(1,n)):0)),depend(n,jobz,range,iu,il) :: z
++    <ftype2> intent(out),dimension((jobz[0]=='V'?MAX(0,n):0),(jobz[0]=='V'?((range[0]=='I')?(iu-il+1):MAX(1,n)):0)),depend(n,jobz,range,iu,il) :: z
+     integer intent(out) :: m
+     integer intent(out),dimension((jobz[0]=='N'?0:n)),depend(jobz,n):: ifail
+     integer intent(out) :: info
+@@ -1293,7 +1293,7 @@
+     <ftype2> intent(hide),dimension(7*n),depend(n) :: rwork
+ 
+     <ftype2> intent(out),dimension(n),depend(n) :: w
+-    <ftype2c> intent(out),dimension((jobz[0]=='V'?MAX(0,n):0),(jobz[0]=='V'?(range[0]=='I'?iu-il+1:MAX(1,n)):0)),depend(n,jobz,range,iu,il) :: z
++    <ftype2c> intent(out),dimension((jobz[0]=='V'?MAX(0,n):0),(jobz[0]=='V'?((range[0]=='I')?(iu-il+1):MAX(1,n)):0)),depend(n,jobz,range,iu,il) :: z
+     integer intent(out) :: m
+     integer intent(out),dimension((jobz[0]=='N'?0:n)),depend(jobz,n):: ifail
+     integer intent(out) :: info

scipy.spec

@@ -1,6 +1,16 @@
 # without means enabled
 %bcond_with doc
 
+# Pythran is an optional build dependency.
+# When used, it makes some modules faster,
+# but it is usually not available soon enough for new major Python versions.
+%ifarch i686 || armv7hl
+# It seems pythran is broken on 32-bit arches, disable it
+%bcond_with pythran
+%else
+%bcond_without pythran
+%endif
+
 # Set to pre-release version suffix if building pre-release, else %%{nil}
 %global rcver %{nil}
 
@@ -14,8 +24,8 @@
 
 Summary:    Scientific Tools for Python
 Name:       scipy
-Version:    1.5.4
-Release:    2%{?dist}
+Version:    1.8.1
+Release:    6%{?dist}
 
 # BSD -- whole package except:
 # Boost -- scipy/special/cephes/scipy_iv.c
@@ -23,11 +33,10 @@ Release:    2%{?dist}
 License:    BSD and Boost and Public Domain
 Url:        http://www.scipy.org/scipylib/index.html
 Source0:    https://github.com/scipy/scipy/releases/download/v%{version}/scipy-%{version}.tar.gz
-
-# https://github.com/scipy/scipy/pull/12899
-Patch0:     skip-certain-tests-on-32-bit-arches.patch
-# https://github.com/scipy/scipy/pull/13130
-Patch1:     skip-factorial-float-tests-on-py310.patch
+# https://bugzilla.redhat.com/show_bug.cgi?id=2099102
+# https://github.com/scipy/scipy/issues/16527
+# https://github.com/scipy/scipy/pull/16528
+Patch0:     scipy-1.8.1-syevr-operator-order-explicit.patch
 
 BuildRequires: fftw-devel, suitesparse-devel
 BuildRequires: %{blaslib}-devel
@@ -44,6 +53,10 @@ BuildRequires:  python3-pytest
 BuildRequires:  python3-pytest-xdist
 BuildRequires:  python3-pytest-timeout
 
+%if %{with pythran}
+BuildRequires:  pythran
+%endif
+
 %if %{with doc}
 BuildRequires:  python3-sphinx
 BuildRequires:  python3-matplotlib
@@ -106,6 +119,8 @@ rm doc/sphinxext -r
 rm $(grep -rl '/\* Generated by Cython') PKG-INFO
 
 %build
+export SCIPY_USE_PYTHRAN=0%{?with_pythran}
+
 for PY in %{python3_version}; do
   # Adding -fallow-argument-mismatch workaround for https://github.com/scipy/scipy/issues/11611
   env CFLAGS="$RPM_OPT_FLAGS -lm" \
@@ -114,8 +129,12 @@ for PY in %{python3_version}; do
   %else
       FFLAGS="$RPM_OPT_FLAGS -fPIC" \
   %endif
-    OPENBLAS=%{_libdir} \
-    FFTW=%{_libdir} BLAS=%{_libdir} LAPACK=%{_libdir} \
+  %ifarch x86_64
+      # workaround for https://bugzilla.redhat.com/show_bug.cgi?id=2068530
+      LDFLAGS="%{__global_ldflags} -Wl,--no-as-needed -lmvec -Wl,--as-needed" \
+  %else
+      LDFLAGS="%{__global_ldflags}" \
+  %endif
     %{_bindir}/python$PY setup.py config_fc \
     --fcompiler=gnu95 --noarch \
     build
@@ -131,6 +150,8 @@ for PY in %{python3_version}; do
 done
 
 %install
+export SCIPY_USE_PYTHRAN=0%{?with_pythran}
+
 %py3_install
 # Some files got ambiguous python shebangs, we fix them after everything else is done
 pathfix.py -pni "%{__python3} %{py3_shbang_opts}" %{buildroot}%{python3_sitearch}
@@ -139,24 +160,42 @@ pathfix.py -pni "%{__python3} %{py3_shbang_opts}" %{buildroot}%{python3_sitearch
 # check against the reference BLAS/LAPACK
 export FLEXIBLAS=netlib
 
+# default test timeout
+TIMEOUT=500
+
+# skip failing TestSchur, it needs to be fixed to account for different
+# (but still valid) results from lapack >= 3.10
+# see: https://github.com/Reference-LAPACK/lapack/issues/628
+export PYTEST_ADDOPTS="-k 'not TestSchur'"
+
 %ifarch s390x
 # skip failing tests on s390x for now
-export PYTEST_ADDOPTS="-k '\
+export PYTEST_ADDOPTS="-k 'not TestSchur and \
     not (TestNoData and test_nodata) and \
-    not test_fortranfile_read_mixed_record and \
-    not test_kde_1d and \
-    not test_kde_1d_weighted and \
-    not test_kde_2d and \
-    not test_kde_2d_weighted and \
-    not test_gaussian_kde_subclassing and \
-    not test_gaussian_kde_covariance_caching and \
-    not test_kde_integer_input and \
-    not test_pdf_logpdf and \
-    not test_pdf_logpdf_weighted'"
+    not test_solve_discrete_are'"
+
+# some tests (namely test_logpdf_overflow) tend to run for a long time on s390x
+TIMEOUT=1000
+%endif
+
+%ifarch aarch64 || ppc64le
+# https://bugzilla.redhat.com/show_bug.cgi?id=1959353
+export PYTEST_ADDOPTS="-k 'not TestSchur and not test_solve_discrete_are'"
+TIMEOUT=1000
+%endif
+
+%ifarch x86_64
+# skip also failing test_sygst for now
+export PYTEST_ADDOPTS="-k 'not TestSchur and not test_sygst'"
+%endif
+
+%ifarch i686 || armv7hl
+# skip also test_cython_api: https://bugzilla.redhat.com/show_bug.cgi?id=2068496
+export PYTEST_ADDOPTS="-k 'not TestSchur and not test_sygst and not test_cython_api'"
 %endif
 
 pushd %{buildroot}/%{python3_sitearch}
-%{pytest} --timeout=500 scipy --numprocesses=auto
+%{pytest} --timeout=${TIMEOUT} scipy --numprocesses=auto
 # Remove test remnants
 rm -rf gram{A,B}
 popd
@@ -173,6 +212,79 @@ popd
 %endif
 
 %changelog
+* Sat Jul 23 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.8.1-6
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
+
+* Sun Jul  3 2022 Mamoru TASAKA <mtasaka@fedoraproject.org> - 1.8.1-5
+- Fix linalg.lapack syevr segfault (#2099102)
+
+* Fri Jun 17 2022 Python Maint <python-maint@redhat.com> - 1.8.1-4
+- Rebuilt for Python 3.11
+
+* Tue Jun 14 2022 Python Maint <python-maint@redhat.com> - 1.8.1-3
+- Bootstrap for Python 3.11
+
+* Tue Jun 14 2022 Python Maint <python-maint@redhat.com> - 1.8.1-2
+- Rebuilt for Python 3.11
+
+* Thu Jun 09 2022 Nikola Forró <nforro@redhat.com> - 1.8.1-1
+- New upstream release 1.8.1
+  resolves: #2088437
+
+* Sat Mar 26 2022 Nikola Forró <nforro@redhat.com> - 1.8.0-3
+- Skip test_cython_api also on armv7hl
+
+* Sat Mar 26 2022 Nikola Forró <nforro@redhat.com> - 1.8.0-2
+- Disable pythran on armv7hl as well
+
+* Mon Feb 07 2022 Nikola Forró <nforro@redhat.com> - 1.8.0-1
+- New upstream release 1.8.0
+  resolves: #2035126
+
+* Sat Jan 22 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.7.3-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
+
+* Tue Dec 21 2021 Nikola Forró <nforro@redhat.com> - 1.7.3-1
+- New upstream release 1.7.3
+  resolves: #1988883
+
+* Fri Jul 23 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.7.0-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
+
+* Wed Jul 14 2021 Miro Hrončok <mhroncok@redhat.com> - 1.7.0-2
+- Use the optional Pythran build dependency
+
+* Wed Jun 23 2021 Nikola Forró <nforro@redhat.com> - 1.7.0-1
+- New upstream release 1.7.0
+  resolves: #1953422
+
+* Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 1.6.2-4
+- Rebuilt for Python 3.10
+
+* Fri Apr 23 2021 Nikola Forró <nforro@redhat.com> - 1.6.2-3
+- Remove RPATH from certain shared object files
+
+* Tue Mar 30 2021 Jonathan Wakely <jwakely@redhat.com> - 1.6.2-2
+- Rebuilt for removed libstdc++ symbol (#1937698)
+
+* Thu Mar 25 2021 Nikola Forró <nforro@redhat.com> - 1.6.2-1
+- New upstream release 1.6.2
+  resolves: #1942896
+
+* Thu Feb 18 2021 Nikola Forró <nforro@redhat.com> - 1.6.1-1
+- New upstream release 1.6.1
+  resolves: #1929994
+
+* Wed Feb 03 2021 Nikola Forró <nforro@redhat.com> - 1.6.0-3
+- Increase test timeout on s390x
+
+* Wed Jan 27 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.6.0-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
+
+* Mon Jan 04 2021 Nikola Forró <nforro@redhat.com> - 1.6.0-1
+- New upstream release 1.6.0
+  resolves: #1906692
+
 * Wed Nov 25 2020 Nikola Forró <nforro@redhat.com> - 1.5.4-2
 - Skip factorial() float tests on Python 3.10
   resolves: #1898157

skip-certain-tests-on-32-bit-arches.patch

@@ -1,47 +0,0 @@
-From ea0a77cf8761a8b8636b93314139ed0fc0a9d1db Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Nikola=20Forr=C3=B3?= <nforro@redhat.com>
-Date: Wed, 30 Sep 2020 11:44:25 +0200
-Subject: [PATCH] TST: make a couple of tests expected to fail on 32-bit
- architectures
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-In TestConstructUtils.test_concatenate_int32_overflow
-and test_nnz_overflow, on a 32-bit architecture, in case
-check_free_memory() passes, ValueError is raised on an attempt
-to create a numpy array too large for a 32-bit architecture.
-
-Signed-off-by: Nikola Forró <nforro@redhat.com>
----
- scipy/sparse/tests/test_construct.py   | 1 +
- scipy/sparse/tests/test_sparsetools.py | 1 +
- 2 files changed, 2 insertions(+)
-
-diff --git a/scipy/sparse/tests/test_construct.py b/scipy/sparse/tests/test_construct.py
-index 3a882c6cc..5a2b92667 100644
---- a/scipy/sparse/tests/test_construct.py
-+++ b/scipy/sparse/tests/test_construct.py
-@@ -378,6 +378,7 @@ class TestConstructUtils(object):
-         excinfo.match(r'Got blocks\[0,1\]\.shape\[0\] == 1, expected 2')
- 
-     @pytest.mark.slow
-+    @pytest.mark.xfail_on_32bit("Can't create large array for test")
-     def test_concatenate_int32_overflow(self):
-         """ test for indptr overflow when concatenating matrices """
-         check_free_memory(30000)
-diff --git a/scipy/sparse/tests/test_sparsetools.py b/scipy/sparse/tests/test_sparsetools.py
-index 0c208ef44..e95df1ba0 100644
---- a/scipy/sparse/tests/test_sparsetools.py
-+++ b/scipy/sparse/tests/test_sparsetools.py
-@@ -61,6 +61,7 @@ def test_regression_std_vector_dtypes():
- 
- 
- @pytest.mark.slow
-+@pytest.mark.xfail_on_32bit("Can't create large array for test")
- def test_nnz_overflow():
-     # Regression test for gh-7230 / gh-7871, checking that coo_todense
-     # with nnz > int32max doesn't overflow.
--- 
-2.26.2
-

skip-factorial-float-tests-on-py310.patch

@@ -1,40 +0,0 @@
-From eabd8ea25fe291665f37fd069a1c574cd30d12cc Mon Sep 17 00:00:00 2001
-From: Victor Stinner <vstinner@python.org>
-Date: Wed, 25 Nov 2020 11:41:15 +0100
-Subject: [PATCH] GH-13122: Skip factorial() float tests on Python 3.10
-
-special.factorial() argument should be an array of integers.
-On Python 3.10, math.factorial() reject float.
-On Python 3.9, a DeprecationWarning is emitted.
-A numpy array casts all integers to float if the array contains a
-single NaN.
----
- scipy/special/tests/test_basic.py | 8 ++++++++
- 1 file changed, 8 insertions(+)
-
-diff --git a/scipy/special/tests/test_basic.py b/scipy/special/tests/test_basic.py
-index 9b7260e8435..e2ae29812a5 100644
---- a/scipy/special/tests/test_basic.py
-+++ b/scipy/special/tests/test_basic.py
-@@ -19,6 +19,7 @@
- 
- import itertools
- import platform
-+import sys
- 
- import numpy as np
- from numpy import (array, isnan, r_, arange, finfo, pi, sin, cos, tan, exp,
-@@ -1822,6 +1823,13 @@ def test_nan_inputs(self, x, exact):
-         result = special.factorial(x, exact=exact)
-         assert_(np.isnan(result))
- 
-+    # GH-13122: special.factorial() argument should be an array of integers.
-+    # On Python 3.10, math.factorial() reject float.
-+    # On Python 3.9, a DeprecationWarning is emitted.
-+    # A numpy array casts all integers to float if the array contains a
-+    # single NaN.
-+    @pytest.mark.skipif(sys.version_info >= (3, 10),
-+                        reason="Python 3.10+ math.factorial() requires int")
-     def test_mixed_nan_inputs(self):
-         x = np.array([np.nan, 1, 2, 3, np.nan])
-         with suppress_warnings() as sup:

sources

@@ -1 +1 @@
-SHA512 (scipy-1.5.4.tar.gz) = d23f68911a8880f87767819750d4d175ba8f9c72fcb9b8080305ee65722c046d4485fde4f0c85cc53c46247dd99813afe675a38b3b0569a683ddc2c2e021b8fc
+SHA512 (scipy-1.8.1.tar.gz) = f6fc71c209991fe82baa4b10d8ade0deb1057f6f5942a91dfb7ae45f3eb78a4535efa2861badf5e2d37239fa99dbd99de760aa7e4854b95991ade0263004e7ea