import CS python3.12-scipy-1.11.1-2.el8
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commit
d3d7c7d72c
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SOURCES/scipy-1.11.1.tar.gz
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02f7b6413c1719b860c34248dd1a8c6114039fd9 SOURCES/scipy-1.11.1.tar.gz
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From 3c89445b6439f3ce7bffc4cf11c6407c39faedc5 Mon Sep 17 00:00:00 2001
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From: Matus Valo <matusvalo@users.noreply.github.com>
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Date: Thu, 6 Jul 2023 16:55:25 +0200
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Subject: [PATCH] BLD: copy `cython_optimize.pxd` to build dir (#18810)
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Closes gh-18792
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[skip cirrus] [skip circle]
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---------
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Co-authored-by: Ralf Gommers <ralf.gommers@gmail.com>
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---
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scipy/optimize/cython_optimize.pxd | 2 +-
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scipy/optimize/cython_optimize/meson.build | 1 +
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scipy/optimize/meson.build | 8 +++++++-
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3 files changed, 9 insertions(+), 2 deletions(-)
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diff --git a/scipy/optimize/cython_optimize.pxd b/scipy/optimize/cython_optimize.pxd
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index d5a0bdd758e0..d35f8da68b34 100644
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--- a/scipy/optimize/cython_optimize.pxd
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+++ b/scipy/optimize/cython_optimize.pxd
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@@ -7,5 +7,5 @@
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# support. Changing it causes an ABI forward-compatibility break
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# (gh-11793), so we currently leave it as is (no further cimport
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# statements should be used in this file).
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-from .cython_optimize._zeros cimport (
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+from scipy.optimize.cython_optimize._zeros cimport (
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brentq, brenth, ridder, bisect, zeros_full_output)
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diff --git a/scipy/optimize/cython_optimize/meson.build b/scipy/optimize/cython_optimize/meson.build
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index 359ea8418ba3..ee8def39b4d3 100644
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--- a/scipy/optimize/cython_optimize/meson.build
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+++ b/scipy/optimize/cython_optimize/meson.build
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@@ -17,6 +17,7 @@ cy_opt_gen = generator(cython,
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arguments : cython_args,
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output : '@BASENAME@.c',
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depends : [_cython_tree,
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+ cython_optimize_pxd,
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_dummy_init_optimize,
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_dummy_init_cyoptimize])
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diff --git a/scipy/optimize/meson.build b/scipy/optimize/meson.build
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index 26458b05cd70..4c5ab798316b 100644
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--- a/scipy/optimize/meson.build
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+++ b/scipy/optimize/meson.build
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@@ -206,10 +206,16 @@ endif
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_dummy_init_optimize = fs.copyfile('__init__.py')
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+# Copying this .pxd file is only needed because of a Cython bug, see
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+# discussion on SciPy PR gh-18810.
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+cython_optimize_pxd = [
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+ fs.copyfile('cython_optimize.pxd'),
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+]
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+
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opt_gen = generator(cython,
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arguments : cython_args,
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output : '@BASENAME@.c',
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- depends : [_cython_tree, cython_blas_pxd, _dummy_init_optimize])
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+ depends : [_cython_tree, cython_blas_pxd, cython_optimize_pxd, _dummy_init_optimize])
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_bglu_dense_c = opt_gen.process('_bglu_dense.pyx')
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@ -0,0 +1,280 @@
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%global __python3 /usr/bin/python3.12
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%global python3_pkgversion 3.12
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# Pythran is an optional build dependency.
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# When used, it makes some modules faster,
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# but it is usually not available soon enough for new major Python versions.
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%bcond_with pythran
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# The code is not safe to build with LTO
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%global _lto_cflags %{nil}
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# Set to pre-release version suffix if building pre-release, else %%{nil}
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%global rcver %{nil}
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%if 0%{?fedora} >= 33 || 0%{?rhel} >= 9
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%global blaslib flexiblas
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%global blasvar %{nil}
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%else
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%global blaslib openblas
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%global blasvar p
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%endif
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%global modname scipy
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Summary: Scientific Tools for Python
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Name: python%{python3_pkgversion}-scipy
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Version: 1.11.1
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Release: 2%{?dist}
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# BSD (3-Clause) -- whole package except:
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# BSD (2-Clause) -- scipy/_lib/_pep440.py
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# scipy/_lib/decorator.py
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# scipy/optimize/lbfgsb_src
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# scipy/special/_ellip_harm.pxd
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# MIT -- scipy/cluster/_optimal_leaf_ordering.pyx
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# scipy/io/_idl.py
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# scipy/linalg/_basic.py (in part)
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# scipy/optimize/_highs
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# scipy/optimize/_lbfgsb_py.py
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# scipy/optimize/_tnc.py
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# scipy/optimize/_trlib
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# scipy/optimize/tnc
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# scipy/special/Faddeeva.{cc,hh}
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# Boost -- scipy/_lib/boost_math
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# scipy/special/cephes
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# Boehm-GC (MIT) -- scipy/sparse/linalg/_dsolve/SuperLU
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# Qhull -- scipy/spatial/qhull_src
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# Public Domain -- scipy/odr/__odrpack.c
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License: BSD and MIT and Boost and Qhull and Public Domain
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Url: http://www.scipy.org/scipylib/index.html
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Source0: https://github.com/scipy/scipy/releases/download/v%{version}/scipy-%{version}.tar.gz
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# Fix build failure with Cython 3 when scipy is already installed
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Patch1: https://github.com/scipy/scipy/commit/3c89445b6439f3ce7bffc4cf11c6407c39faedc5.patch
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BuildRequires: %{blaslib}-devel
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BuildRequires: gcc-gfortran, gcc-c++
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BuildRequires: python%{python3_pkgversion}-pybind11-devel
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BuildRequires: python%{python3_pkgversion}-pybind11 >= 2.4.0
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BuildRequires: python%{python3_pkgversion}-numpy, python%{python3_pkgversion}-devel, python%{python3_pkgversion}-numpy-f2py
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BuildRequires: python%{python3_pkgversion}-rpm-macros
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BuildRequires: python%{python3_pkgversion}-setuptools
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BuildRequires: python%{python3_pkgversion}-Cython
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BuildRequires: python%{python3_pkgversion}-pytest
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%if %{with pythran}
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BuildRequires: pythran
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%endif
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Requires: python%{python3_pkgversion}-numpy, python%{python3_pkgversion}-f2py
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Provides: bundled(arpack) = 3.3.0
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Provides: bundled(biasedurn)
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Provides: bundled(boost-math)
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Provides: bundled(coin-or-HiGHS) = 1.2
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Provides: bundled(Faddeeva)
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Provides: bundled(id)
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Provides: bundled(l-bfgs-b) = 3.0
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Provides: bundled(LAPJVsp)
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Provides: bundled(python3-decorator) = 4.0.5
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Provides: bundled(python3-pep440)
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Provides: bundled(python3-pypocketfft) = bf2c431c21213b7c5e23c2f542009b0bd3ec1445
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Provides: bundled(qhull) = 2019.1
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Provides: bundled(SuperLU) = 5.2.0
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Provides: bundled(unuran) = 1.8.1
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%global _description %{expand:
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Scipy is open-source software for mathematics, science, and
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engineering. The core library is NumPy which provides convenient and
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fast N-dimensional array manipulation. The SciPy library is built to
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work with NumPy arrays, and provides many user-friendly and efficient
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numerical routines such as routines for numerical integration and
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optimization. Together, they run on all popular operating systems, are
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quick to install, and are free of charge. NumPy and SciPy are easy to
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use, but powerful enough to be depended upon by some of the world's
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leading scientists and engineers.}
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%description %_description
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%package -n python%{python3_pkgversion}-scipy-tests
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Summary: Scientific Tools for Python - test files
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Requires: python%{python3_pkgversion}-scipy = %{version}-%{release}
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Requires: python%{python3_pkgversion}-pytest
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%description -n python%{python3_pkgversion}-scipy-tests
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Scipy test files
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%prep
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%autosetup -p1 -n %{modname}-%{version}%{?rcver}
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cat > site.cfg << EOF
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[amd]
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library_dirs = %{_libdir}
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include_dirs = /usr/include/suitesparse
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amd_libs = amd
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[umfpack]
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library_dirs = %{_libdir}
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include_dirs = /usr/include/suitesparse
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umfpack_libs = umfpack
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[openblas]
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libraries = %{blaslib}%{blasvar}
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library_dirs = %{_libdir}
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EOF
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rm $(grep -rl '/\* Generated by Cython') PKG-INFO
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%build
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export SCIPY_USE_PYTHRAN=0%{?with_pythran}
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for PY in %{python3_pkgversion}; do
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# Adding -fallow-argument-mismatch workaround for https://github.com/scipy/scipy/issues/11611
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env CFLAGS="$RPM_OPT_FLAGS -lm" \
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FFLAGS="$RPM_OPT_FLAGS -fPIC -cpp" \
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LDFLAGS="%{__global_ldflags}" \
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%{_bindir}/python$PY setup.py config_fc \
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--fcompiler=gnu95 --noarch \
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build
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done
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%install
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export SCIPY_USE_PYTHRAN=0%{?with_pythran}
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%py3_install
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# Some files got ambiguous python shebangs, we fix them after everything else is done
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%py3_shebang_fix %{buildroot}%{python3_sitearch}
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%check
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# check against the reference BLAS/LAPACK
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export FLEXIBLAS=netlib
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# default test timeout
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TIMEOUT=500
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%ifarch aarch64
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TIMEOUT=1000
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# this is flaky according to the original Fedora spec
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export PYTEST_ADDOPTS="-k 'not test_concatenate_int32_overflow'"
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%endif
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%ifarch ppc64le
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TIMEOUT=1000
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%if 0%{?rhel} == 8
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# this fails in rhel8 brew but not in c8s koji
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# it has already been deselected in python3.11-scipy
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export PYTEST_ADDOPTS="-k 'not TestFFTConvolve and \
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not TestDoubleFFT and \
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not TestSingleFFT and \
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not TestDoubleIFFT and \
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not TestSingleIFFT and \
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not test_tpsv and \
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not TestLinear and \
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not test_various_drivers_standard and \
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not test_Mx1_economic and \
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not test_hegst and \
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not test_tpqrt_tpmqrt and \
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not test_pteqr and \
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not test_pptrs_pptri_pptrf_ppsv_ppcon and \
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not test_against_numpy_convolve and \
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not test_convolve_method and \
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not test_rank1 and \
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not test_splu_smoketest and \
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not test_spilu_smoketest and \
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not test_threads_parallel and \
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not test_hermitian and \
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not test_convergence and \
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not test_precond_dummy and \
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not test_x0_equals_Mb and \
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not test_show and \
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not test_svdp and \
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not test_examples'"
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%endif
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%endif
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%ifarch s390x
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TIMEOUT=1000
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export PYTEST_ADDOPTS="-k 'not test_distance_transform_cdt05 and not (TestZlibInputStream and test_all_data_read_)'"
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%endif
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%ifarch x86_64
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# this sometimes failed in rhel8 brew, but not in c8s koji or rhel9/c9s
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# assuming it's flaky or hardware/kernel dependent and disabling unconditionally
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export PYTEST_ADDOPTS="-k 'not test_large_rank_deficient'"
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%endif
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%ifarch i686
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export PYTEST_ADDOPTS="-k 'not test_gh12218 and not test_x0_equals_Mb[bicgstab-nonsymposdef-F]'"
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%endif
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pushd %{buildroot}/%{python3_sitearch}
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# Ignoring the datasets tests as we don't have the optional pooch
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# dependency on RHEL.
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%{pytest} --ignore=scipy/datasets/tests/test_data.py scipy
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# Remove test remnants
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rm -rf gram{A,B}
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rm -rf scipy/.pytest_cache
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popd
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%files -n python%{python3_pkgversion}-scipy
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%license LICENSE.txt LICENSES_bundled.txt
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%{python3_sitearch}/scipy/
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%{python3_sitearch}/*.egg-info
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%exclude %{python3_sitearch}/scipy/*/tests/
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%exclude %{python3_sitearch}/scipy/*/*/tests/
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%exclude %{python3_sitearch}/scipy/*/*/*/tests/
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%exclude %{python3_sitearch}/scipy/*/*/*/*/tests/
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%files -n python%{python3_pkgversion}-scipy-tests
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%{python3_sitearch}/scipy/*/tests/
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%{python3_sitearch}/scipy/*/*/tests/
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%{python3_sitearch}/scipy/*/*/*/tests/
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%{python3_sitearch}/scipy/*/*/*/*/tests/
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%changelog
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* Tue Jan 23 2024 Miro Hrončok <mhroncok@redhat.com> - 1.11.1-2
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- Rebuilt for timestamp .pyc invalidation mode
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* Thu Nov 09 2023 Charalampos Stratakis <cstratak@redhat.com> - 1.11.1-1
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- Initial package
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- Fedora contributions by:
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Antonio Trande <anto.trande@gmail.com>
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Bill Nottingham <notting@fedoraproject.org>
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Björn Esser <me@besser82.io>
|
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Charalampos Stratakis <cstratak@redhat.com>
|
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Christian Dersch <lupinix@mailbox.org>
|
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David Malcolm <dmalcolm@redhat.com>
|
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Deji Akingunola <deji@fedoraproject.org>
|
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Dennis Gilmore <dennis@ausil.us>
|
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Elliott Sales de Andrade <quantum.analyst@gmail.com>
|
||||
Ignacio Vazquez-Abrams <ivazquez@fedoraproject.org>
|
||||
Igor Gnatenko <ignatenkobrain@fedoraproject.org>
|
||||
Iñaki Úcar <iucar@fedoraproject.org>
|
||||
Jef Spaleta <jspaleta@fedoraproject.org>
|
||||
Jerry James <loganjerry@gmail.com>
|
||||
Jesse Keating <jkeating@fedoraproject.org>
|
||||
Jitka Plesnikova <jplesnik@redhat.com>
|
||||
Jonathan Wakely <jwakely@redhat.com>
|
||||
Jon Ciesla <limb@fedoraproject.org>
|
||||
Kalev Lember <klember@redhat.com>
|
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Kevin Fenzi <kevin@scrye.com>
|
||||
Lumir Balhar <lbalhar@redhat.com>
|
||||
Mamoru TASAKA <mtasaka@fedoraproject.org>
|
||||
Marcel Plch <mplch@redhat.com>
|
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Miro Hrončok <miro@hroncok.cz>
|
||||
Nikola Forró <nforro@redhat.com>
|
||||
Nils Philippsen <nils@redhat.com>
|
||||
Orion Poplawski <orion@cora.nwra.com>
|
||||
Pavel Šimovec <psimovec@redhat.com>
|
||||
Peter Robinson <pbrobinson@fedoraproject.org>
|
||||
Petr Viktorin <pviktori@redhat.com>
|
||||
Robert Kuska <rkuska@redhat.com>
|
||||
Than Ngo <than@redhat.com>
|
||||
Thomas Spura <thomas.spura@gmail.com>
|
||||
Tomas Tomecek <ttomecek@redhat.com>
|
||||
Toshio Kuratomi <toshio@fedoraproject.org>
|
||||
Troy Dawson <tdawson@fedoraproject.org>
|
||||
Yaakov Selkowitz <yselkowi@redhat.com>
|
||||
Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl>
|
||||
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