Skip factorial() float tests on Python 3.10

- resolves: #1898157

.gitignore

@@ -24,3 +24,11 @@ scipy-0.7.2.tar.gz
 /scipy-0.19.1.tar.xz
 /scipy-1.0.0.tar.xz
 /scipy-1.1.0.tar.gz
+/scipy-1.2.0.tar.gz
+/scipy-1.2.1.tar.gz
+/scipy-1.3.1.tar.gz
+/scipy-1.4.1.tar.gz
+/scipy-1.5.0.tar.gz
+/scipy-1.5.2.tar.gz
+/scipy-1.5.3.tar.gz
+/scipy-1.5.4.tar.gz

acceptable_failure_rate.patch

@@ -1,28 +0,0 @@
-diff --git a/scipy/conftest.py b/scipy/conftest.py
-index b0edcdd..f5c3c0b 100644
---- a/scipy/conftest.py
-+++ b/scipy/conftest.py
-@@ -3,6 +3,7 @@ from __future__ import division, absolute_import, print_function
- 
- import os
- import pytest
-+import _pytest
- import warnings
- 
- from scipy._lib._fpumode import get_fpu_mode
-@@ -33,3 +34,15 @@ def check_fpu_mode(request):
-         warnings.warn("FPU mode changed from {0:#x} to {1:#x} during "
-                       "the test".format(old_mode, new_mode),
-                       category=FPUModeChangeWarning, stacklevel=0)
-+
-+
-+ACCEPTABLE_FAILURE_RATE = int(os.environ.get('ACCEPTABLE_FAILURE_RATE', 0))
-+
-+
-+@pytest.hookimpl()
-+def pytest_sessionfinish(session, exitstatus):
-+    if exitstatus != _pytest.main.EXIT_TESTSFAILED:
-+        return
-+    failure_rate = (100.0 * session.testsfailed) / session.testscollected
-+    if failure_rate <= ACCEPTABLE_FAILURE_RATE:
-+        session.exitstatus = 0

scipy.spec

@@ -1,15 +1,22 @@
 # without means enabled
-%bcond_without doc
+%bcond_with doc
 
 # Set to pre-release version suffix if building pre-release, else %%{nil}
 %global rcver %{nil}
 
+%if 0%{?fedora} >= 33 || 0%{?rhel} >= 9
+%global blaslib flexiblas
+%global blasvar %{nil}
+%else
+%global blaslib openblas
+%global blasvar p
+%endif
+
 Summary:    Scientific Tools for Python
 Name:       scipy
-Version:    1.1.0
-Release:    3%{?dist}
+Version:    1.5.4
+Release:    2%{?dist}
 
-Group:      Development/Libraries
 # BSD -- whole package except:
 # Boost -- scipy/special/cephes/scipy_iv.c
 # Public Domain -- scipy/odr/__odrpack.c
@@ -17,40 +24,33 @@ 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
 
-# Previously we ignored the tests results, because they don't always pass
-# Instead of ignoring the results entirely, we allow certain failure rate
-# https://stackoverflow.com/a/47731333/1839451
-Patch0:     acceptable_failure_rate.patch
+# 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
 
-BuildRequires: python2-numpy, python2-devel,python2-numpy-f2py
-BuildRequires: python2-pytest
-BuildRequires: python2-pytest-xdist
-BuildRequires: python2-pytest-timeout
-BuildRequires: fftw-devel, blas-devel, lapack-devel, suitesparse-devel
-%ifarch %{openblas_arches}
-BuildRequires: openblas-devel
-%else
-BuildRequires: atlas-devel
-%endif
+BuildRequires: fftw-devel, suitesparse-devel
+BuildRequires: %{blaslib}-devel
 BuildRequires: gcc-gfortran, swig, gcc-c++
 BuildRequires: qhull-devel
+BuildRequires: /usr/bin/pathfix.py
 
+BuildRequires:  pybind11-devel
+BuildRequires:  python3-pybind11 >= 2.4.0
 BuildRequires:  python3-numpy, python3-devel, python3-numpy-f2py
 BuildRequires:  python3-setuptools
+BuildRequires:  python3-Cython
 BuildRequires:  python3-pytest
 BuildRequires:  python3-pytest-xdist
 BuildRequires:  python3-pytest-timeout
 
 %if %{with doc}
-BuildRequires:  python2-sphinx
-BuildRequires:  python2-matplotlib
-BuildRequires:  python2-numpydoc
 BuildRequires:  python3-sphinx
 BuildRequires:  python3-matplotlib
 BuildRequires:  python3-numpydoc
-%endif # with doc
+%endif
 
-%description
+%global _description %{expand:
 Scipy is open-source software for mathematics, science, and
 engineering. The core library is NumPy which provides convenient and
 fast N-dimensional array manipulation. The SciPy library is built to
@@ -59,58 +59,23 @@ numerical routines such as routines for numerical integration and
 optimization. Together, they run on all popular operating systems, are
 quick to install, and are free of charge. NumPy and SciPy are easy to
 use, but powerful enough to be depended upon by some of the world's
-leading scientists and engineers.
+leading scientists and engineers.}
 
+%description %_description
 
-%package -n python2-scipy
+%package -n python3-scipy
 Summary:    Scientific Tools for Python
-Requires:   numpy, f2py
-%{?python_provide:%python_provide python2-scipy}
-# General provides of plain 'scipy' in F24
-Provides:       scipy = %{version}-%{release}
-Provides:       scipy%{?_isa} = %{version}-%{release}
-Obsoletes:      scipy <= 0.16.0
-%description -n python2-scipy
-Scipy is open-source software for mathematics, science, and
-engineering. The core library is NumPy which provides convenient and
-fast N-dimensional array manipulation. The SciPy library is built to
-work with NumPy arrays, and provides many user-friendly and efficient
-numerical routines such as routines for numerical integration and
-optimization. Together, they run on all popular operating systems, are
-quick to install, and are free of charge. NumPy and SciPy are easy to
-use, but powerful enough to be depended upon by some of the world's
-leading scientists and engineers.
+Requires:   python3-numpy, python3-f2py
+%{?python_provide:%python_provide python3-scipy}
+%description -n python3-scipy %_description
 
 %if %{with doc}
-%package -n python2-scipy-doc
-Summary:    Scientific Tools for Python - documentation
-Requires:   python2-scipy = %{version}-%{release}
-%description -n python2-scipy-doc
-HTML documentation for Scipy
-
 %package -n python3-scipy-doc
 Summary:    Scientific Tools for Python - documentation
 Requires:   python3-scipy = %{version}-%{release}
 %description -n python3-scipy-doc
 HTML documentation for Scipy
-%endif # with doc
-
-%package -n python3-scipy
-Summary:    Scientific Tools for Python
-Group:      Development/Libraries
-License:    BSD and LGPLv2+
-Requires:   python3-numpy, python3-f2py
-%{?python_provide:%python_provide python3-scipy}
-%description -n python3-scipy
-Scipy is open-source software for mathematics, science, and
-engineering. The core library is NumPy which provides convenient and
-fast N-dimensional array manipulation. The SciPy library is built to
-work with NumPy arrays, and provides many user-friendly and efficient
-numerical routines such as routines for numerical integration and
-optimization. Together, they run on all popular operating systems, are
-quick to install, and are free of charge. NumPy and SciPy are easy to
-use, but powerful enough to be depended upon by some of the world's
-leading scientists and engineers.
+%endif
 
 
 %prep
@@ -127,26 +92,29 @@ library_dirs = %{_libdir}
 include_dirs = /usr/include/suitesparse
 umfpack_libs = umfpack
 
-%ifarch %{openblas_arches}
 [openblas]
+libraries = %{blaslib}%{blasvar}
 library_dirs = %{_libdir}
-openblas_libs = openblasp
-%endif
 EOF
 
+# Docs won't build unless the .dat files are specified here
+sed -i 's/metadata = dict(/metadata = dict(package_data={"": ["*.dat"]},/' setup.py
+
 # remove bundled numpydoc
 rm doc/sphinxext -r
 
+rm $(grep -rl '/\* Generated by Cython') PKG-INFO
 
 %build
-for PY in %{python3_version} %{python2_version}; do
+for PY in %{python3_version}; do
+  # Adding -fallow-argument-mismatch workaround for https://github.com/scipy/scipy/issues/11611
   env CFLAGS="$RPM_OPT_FLAGS -lm" \
-      FFLAGS="$RPM_OPT_FLAGS -fPIC" \
-  %ifarch %{openblas_arches}
-    OPENBLAS=%{_libdir} \
+  %if 0%{?fedora} >= 32 || 0%{?rhel} >= 9
+      FFLAGS="$RPM_OPT_FLAGS -fPIC -fallow-argument-mismatch" \
   %else
-    ATLAS=%{_libdir}/atlas \
+      FFLAGS="$RPM_OPT_FLAGS -fPIC" \
   %endif
+    OPENBLAS=%{_libdir} \
     FFTW=%{_libdir} BLAS=%{_libdir} LAPACK=%{_libdir} \
     %{_bindir}/python$PY setup.py config_fc \
     --fcompiler=gnu95 --noarch \
@@ -164,52 +132,35 @@ done
 
 %install
 %py3_install
-%py2_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}
 
 %check
-# Skip all tests on s390x because they hangs unexpectedly and randomly
-# and pytest-timeout has no effect. Note that the outcome of the tests
-# was previously ignored anyway so by disabling the test for s390x we
-# are not doing anything more dangerous.
+# check against the reference BLAS/LAPACK
+export FLEXIBLAS=netlib
+
 %ifarch s390x
-exit 0
-%endif
-
-%ifarch x86_64
-export ACCEPTABLE_FAILURE_RATE=0
-%else
-# there are usually 10-21 test failing, so we allow 1% failure rate
-export ACCEPTABLE_FAILURE_RATE=1
-%endif
-
-%ifarch ppc64le
-# test_decomp segfaults on ppc64le
-export k="not test_denormals and not test_decomp"
-%else
-# test_denormals tends to stuck
-export k="not test_denormals"
+# skip failing tests on s390x for now
+export PYTEST_ADDOPTS="-k '\
+    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'"
 %endif
 
 pushd %{buildroot}/%{python3_sitearch}
-py.test-3 --timeout=300 -k "$k" scipy
+%{pytest} --timeout=500 scipy --numprocesses=auto
+# Remove test remnants
+rm -rf gram{A,B}
 popd
 
-pushd %{buildroot}/%{python2_sitearch}
-py.test-2 --timeout=300 -k "$k" scipy
-popd
-
-
-%files -n python2-scipy
-%doc LICENSE.txt
-%{python2_sitearch}/scipy/
-%{python2_sitearch}/*.egg-info
-
-%if %{with doc}
-%files -n python2-scipy-doc
-%license LICENSE.txt
-%doc doc/build-%{python2_version}/html
-%endif # with doc
-
 %files -n python3-scipy
 %doc LICENSE.txt
 %{python3_sitearch}/scipy/
@@ -219,9 +170,91 @@ popd
 %files -n python3-scipy-doc
 %license LICENSE.txt
 %doc doc/build-%{python3_version}/html
-%endif # with doc
+%endif
 
 %changelog
+* Wed Nov 25 2020 Nikola Forró <nforro@redhat.com> - 1.5.4-2
+- Skip factorial() float tests on Python 3.10
+  resolves: #1898157
+
+* Thu Nov 05 2020 Nikola Forró <nforro@redhat.com> - 1.5.4-1
+- New upstream release 1.5.4
+- Increase test timeout, 300 seconds is not always enough
+  for test_logpdf_overflow on s390x
+  resolves: #1894887
+
+* Mon Oct 19 2020 Nikola Forró <nforro@redhat.com> - 1.5.3-1
+- New upstream release 1.5.3
+  resolves: #1889132
+
+* Wed Sep 30 2020 Nikola Forró <nforro@redhat.com> - 1.5.2-2
+- Skip one more test expected to fail on 32-bit architectures
+
+* Mon Aug 31 2020 Nikola Forró <nforro@redhat.com> - 1.5.2-1
+- New upstream release 1.5.2
+  resolves: #1853871 and #1840077
+
+* Sun Aug 16 2020 Iñaki Úcar <iucar@fedoraproject.org> - 1.5.0-4
+- https://fedoraproject.org/wiki/Changes/FlexiBLAS_as_BLAS/LAPACK_manager
+
+* Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.5.0-3
+- Second attempt - Rebuilt for
+  https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Wed Jul 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.5.0-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Tue Jun 23 2020 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 1.5.0-1
+- Update to latest version
+
+* Mon May 25 2020 Miro Hrončok <mhroncok@redhat.com> - 1.4.1-2
+- Rebuilt for Python 3.9
+
+* Sun Mar 01 2020 Orion Poplawski <orion@nwra.com> - 1.4.1-1
+- Update to 1.4.1 (bz#1771154)
+- Workaround FTBFS with gcc 10 (bz#1800078)
+
+* Thu Jan 30 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.3.1-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
+
+* Fri Oct 18 2019 Miro Hrončok <mhroncok@redhat.com> - 1.3.1-1
+- Update to 1.3.1 (#1674101)
+- Drop Python 2 packages (not supported by SciPy >= 1.3)
+- Backported upstream patch for cKDTree (fixes FTBFS)
+
+* Thu Oct 03 2019 Miro Hrončok <mhroncok@redhat.com> - 1.2.1-8
+- Rebuilt for Python 3.8.0rc1 (#1748018)
+
+* Mon Aug 19 2019 Miro Hrončok <mhroncok@redhat.com> - 1.2.1-7
+- Rebuilt for Python 3.8
+
+* Tue Jul 30 2019 Petr Viktorin <pviktori@redhat.com> - 1.2.1-6
+- Remove build dependency on python2-pytest-xdist and python2-pytest-timeout
+- Enable parallel tests in Python 3 %%check
+- Use macros for Python interpreter in tests
+
+* Fri Jul 26 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.2.1-5
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
+
+* Mon Jun 10 2019 Marcel Plch <mplch@redhat.com> - 1.2.1-4
+- Fix FTBFS with Py3.8 (#1606315)
+
+* Thu May 16 2019 Orion Poplawski <orion@nwra.com> - 1.2.1-3
+- Build only against openblasp (bugz#1709161)
+
+* Fri Apr 26 2019 Orion Poplawski <orion@nwra.com> - 1.2.1-2
+- Do not create *-PYTEST.pyc files
+
+* Tue Apr 23 2019 Orion Poplawski <orion@nwra.com> - 1.2.1-1
+- Update to 1.2.1
+- Drop scipy2-doc
+
+* Wed Feb 06 2019 Charalampos Stratakis <cstratak@redhat.com> - 1.2.0-1
+- Update to 1.2.0
+
+* Sat Feb 02 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.1.0-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
+
 * Sat Jul 14 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.1.0-3
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
 
@@ -287,7 +320,7 @@ popd
 
 * Tue Jul 26 2016 Than Ngo <than@redhat.com> - 0.18.0-1
 - 0.18.0
-- %%check: make non-fatal as temporary workaround for scipy build on arm 
+- %%check: make non-fatal as temporary workaround for scipy build on arm
 
 * Tue Jul 19 2016 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.17.0-2
 - https://fedoraproject.org/wiki/Changes/Automatic_Provides_for_Python_RPM_Packages
@@ -577,4 +610,3 @@ popd
 - Add changelog
 - Removed Prefix, Vendor
 - Fix Source0
-

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

@@ -0,0 +1,47 @@
+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

@@ -0,0 +1,40 @@
+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-1.1.0.tar.gz) = 72fe32c6c009613cb78202598e5db14f8e630b3218839cfe18d43d40550d94cc5aa100c6f5d41f40e86ae148e9b6a13431bb91b0f9be44b0569ccd7b725fe973
+SHA512 (scipy-1.5.4.tar.gz) = d23f68911a8880f87767819750d4d175ba8f9c72fcb9b8080305ee65722c046d4485fde4f0c85cc53c46247dd99813afe675a38b3b0569a683ddc2c2e021b8fc