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Work on fixing auditwheel error on Linux (#368)
* Update cibuildwheel version to attempt to fix auditwheel error. * Bump version of OpenBLAS and SuiteSparse used in wheels. * Add libgmp to wheels, which is a new dependency for suitesparse * Fix typo and add MPFR to wheel dependencies. * Install the xz tool with yum when building wheels. * Only build static gmp and mpfr, since suitesparse is also static. * Build gmp and mpfr with PIC. Patch suitesparse to have correct linking order when doing static linking * Move wheel builds back to daily test.
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‎.github/workflows/deploy.yml‎

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@@ -59,7 +59,7 @@ jobs:
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python-version: '3.7'
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- name: Install cibuildwheel
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run: |
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python -m pip install twine cibuildwheel==1.5.0
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python -m pip install twine cibuildwheel==1.6.3
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- name: Build wheel
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run: |
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python -m cibuildwheel --output-dir wheelhouse
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python-version: '3.7'
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- name: Install cibuildwheel
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run: |
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python -m pip install twine cibuildwheel==1.5.0
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python -m pip install twine cibuildwheel==1.6.3
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- name: Build wheel
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run: |
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python -m cibuildwheel --output-dir wheelhouse
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CIBW_MANYLINUX_I686_IMAGE: manylinux2010
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CIBW_BUILD_VERBOSITY: 3
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CIBW_ENVIRONMENT_LINUX: "PATH=/usr/lib64/mpich-3.2/bin:${PATH} TOAST_BUILD_BLAS_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran' TOAST_BUILD_LAPACK_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran' TOAST_BUILD_CMAKE_VERBOSE_MAKEFILE=ON"
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CIBW_ENVIRONMENT_MACOS:
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CIBW_ENVIRONMENT_MACOS:
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CIBW_BEFORE_BUILD_LINUX: ./wheels/install_deps_linux.sh
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CIBW_BEFORE_BUILD_MACOS: ./wheels/install_deps_osx.sh
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CIBW_BEFORE_TEST: pip3 install numpy && pip3 install mpi4py
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python-version: '3.7'
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- name: Install cibuildwheel
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run: |
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python -m pip install twine cibuildwheel==1.5.0
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python -m pip install twine cibuildwheel==1.6.3
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- name: Build wheel
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run: |
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python -m cibuildwheel --output-dir wheelhouse

‎.github/workflows/wheels.yml‎

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@@ -56,7 +56,7 @@ jobs:
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python-version: '3.7'
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- name: Install cibuildwheel
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run: |
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python -m pip install cibuildwheel==1.5.0
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python -m pip install cibuildwheel==1.6.3
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- name: Build wheel
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run: |
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python -m cibuildwheel --output-dir wheelhouse
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python-version: '3.7'
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- name: Install cibuildwheel
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run: |
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python -m pip install cibuildwheel==1.5.0
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python -m pip install cibuildwheel==1.6.3
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- name: Build wheel
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run: |
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python -m cibuildwheel --output-dir wheelhouse
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python-version: '3.7'
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- name: Install cibuildwheel
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run: |
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python -m pip install cibuildwheel==1.5.0
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python -m pip install cibuildwheel==1.6.3
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- name: Build wheel
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run: |
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python -m cibuildwheel --output-dir wheelhouse

‎wheels/install_deps_linux.sh‎

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@@ -12,6 +12,10 @@ pushd $(dirname $0) >/dev/null 2>&1
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topdir=$(pwd)
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popd >/dev/null 2>&1
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# Install xz
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yum -y install xz
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# Get newer cmake with pip
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pip install cmake
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@@ -57,9 +61,64 @@ tar xzf ${mpich_pkg} \
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pip install mpi4py
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# libgmp
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gmp_version=6.2.0
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gmp_dir=gmp-${gmp_version}
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gmp_pkg=${gmp_dir}.tar.xz
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echo "Fetching libgmp"
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if [ ! -e ${gmp_pkg} ]; then
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curl -SL https://ftp.gnu.org/gnu/gmp/${gmp_pkg} -o ${gmp_pkg}
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fi
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echo "Building libgmp..."
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rm -rf ${gmp_dir}
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tar xf ${gmp_pkg} \
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&& pushd ${gmp_dir} >/dev/null 2>&1 \
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&& CC="${CC}" CFLAGS="${CFLAGS}" \
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./configure \
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--enable-static \
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--disable-shared \
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--with-pic \
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--prefix="${PREFIX}" \
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&& make -j ${MAKEJ} \
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&& make install \
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&& popd >/dev/null 2>&1
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# libmpfr
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mpfr_version=4.1.0
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mpfr_dir=mpfr-${mpfr_version}
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mpfr_pkg=${mpfr_dir}.tar.xz
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echo "Fetching libmpfr"
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if [ ! -e ${mpfr_pkg} ]; then
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curl -SL https://www.mpfr.org/mpfr-current/${mpfr_pkg} -o ${mpfr_pkg}
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fi
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echo "Building libmpfr..."
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rm -rf ${mpfr_dir}
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tar xf ${mpfr_pkg} \
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&& pushd ${mpfr_dir} >/dev/null 2>&1 \
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&& CC="${CC}" CFLAGS="${CFLAGS}" \
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./configure \
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--enable-static \
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--disable-shared \
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--with-pic \
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--with-gmp="${PREFIX}" \
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--prefix="${PREFIX}" \
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&& make -j ${MAKEJ} \
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&& make install \
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&& popd >/dev/null 2>&1
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# Install Openblas
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openblas_version=0.3.9
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openblas_version=0.3.10
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openblas_dir=OpenBLAS-${openblas_version}
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openblas_pkg=${openblas_dir}.tar.gz
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# Install SuiteSparse
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ssparse_version=5.7.2
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ssparse_version=5.8.1
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ssparse_dir=SuiteSparse-${ssparse_version}
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ssparse_pkg=${ssparse_dir}.tar.gz
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‎wheels/install_deps_osx.sh‎

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@@ -31,6 +31,62 @@ MAKEJ=2
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PREFIX=/usr/local
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# libgmp
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gmp_version=6.2.0
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gmp_dir=gmp-${gmp_version}
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gmp_pkg=${gmp_dir}.tar.xz
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echo "Fetching libgmp"
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if [ ! -e ${gmp_pkg} ]; then
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curl -SL https://ftp.gnu.org/gnu/gmp/${gmp_pkg} -o ${gmp_pkg}
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fi
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echo "Building libgmp..."
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rm -rf ${gmp_dir}
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tar xf ${gmp_pkg} \
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&& pushd ${gmp_dir} >/dev/null 2>&1 \
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&& CC="${CC}" CFLAGS="${CFLAGS}" \
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&& CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" \
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./configure \
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--enable-static \
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--disable-shared \
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--with-pic \
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--prefix="${PREFIX}" \
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&& make -j ${MAKEJ} \
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&& make install \
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&& popd >/dev/null 2>&1
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# libmpfr
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mpfr_version=4.1.0
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mpfr_dir=mpfr-${mpfr_version}
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mpfr_pkg=${mpfr_dir}.tar.xz
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echo "Fetching libmpfr"
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if [ ! -e ${mpfr_pkg} ]; then
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curl -SL https://www.mpfr.org/mpfr-current/${mpfr_pkg} -o ${mpfr_pkg}
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fi
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echo "Building libmpfr..."
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rm -rf ${mpfr_dir}
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tar xf ${mpfr_pkg} \
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&& pushd ${mpfr_dir} >/dev/null 2>&1 \
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&& CC="${CC}" CFLAGS="${CFLAGS}" \
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./configure \
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--enable-static \
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--disable-shared \
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--with-pic \
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--with-gmp="${PREFIX}" \
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--prefix="${PREFIX}" \
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&& make -j ${MAKEJ} \
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&& make install \
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&& popd >/dev/null 2>&1
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# Install FFTW
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fftw_version=3.3.8
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# Install SuiteSparse
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ssparse_version=5.7.2
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ssparse_version=5.8.1
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ssparse_dir=SuiteSparse-${ssparse_version}
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ssparse_pkg=${ssparse_dir}.tar.gz
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‎wheels/suitesparse.patch‎

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@@ -1,7 +1,7 @@
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diff -urN SuiteSparse-5.7.2_orig/Makefile SuiteSparse-5.7.2/Makefile
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--- SuiteSparse-5.7.2_orig/Makefile 2020-04-08 13:42:59.000000000 -0700
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+++ SuiteSparse-5.7.2/Makefile 2020-05-27 07:26:10.020688473 -0700
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@@ -266,6 +266,9 @@
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diff -urN SuiteSparse-5.8.1_orig/Makefile SuiteSparse-5.8.1/Makefile
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--- SuiteSparse-5.8.1_orig/Makefile 2020-07-14 16:04:44.000000000 -0700
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+++ SuiteSparse-5.8.1/Makefile 2020-10-13 16:16:26.558744640 -0700
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@@ -281,6 +281,9 @@
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# hardcoded below.
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include/metis.h:
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ifeq (,$(MY_METIS_LIB))
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- ( cd metis-5.1.0 && $(MAKE) config shared=1 prefix=$(SUITESPARSE) cc=$(CC) )
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- ( cd metis-5.1.0 && $(MAKE) )
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- ( cd metis-5.1.0 && $(MAKE) install )
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diff -urN SuiteSparse-5.8.1_orig/SLIP_LU/Demo/Makefile SuiteSparse-5.8.1/SLIP_LU/Demo/Makefile
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--- SuiteSparse-5.8.1_orig/SLIP_LU/Demo/Makefile 2020-07-14 16:04:44.000000000 -0700
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+++ SuiteSparse-5.8.1/SLIP_LU/Demo/Makefile 2020-10-14 12:07:18.326605012 -0700
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@@ -20,7 +20,7 @@
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# LDFLAGS = -L../../lib
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-LDLIBS += -lm -lgmp -lmpfr -lcolamd -lamd -lsliplu
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+LDLIBS += -lsliplu -lcolamd -lamd -lmpfr -lgmp -lm
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CS = $(LDLIBS)
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diff -urN SuiteSparse-5.8.1_orig/SLIP_LU/Lib/Makefile SuiteSparse-5.8.1/SLIP_LU/Lib/Makefile
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--- SuiteSparse-5.8.1_orig/SLIP_LU/Lib/Makefile 2020-07-14 16:04:44.000000000 -0700
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+++ SuiteSparse-5.8.1/SLIP_LU/Lib/Makefile 2020-10-14 12:07:50.250795155 -0700
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@@ -20,7 +20,7 @@
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# CFLAGS += -Wall -Wextra -Wpedantic -Werror
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# SLIP_LU depends on SuiteSparse_config, AMD, COLAMD, M, GMP, and MPFR
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-LDLIBS += -lsuitesparseconfig -lamd -lcolamd -lm -lgmp -lmpfr
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+LDLIBS += -lsuitesparseconfig -lamd -lcolamd -lmpfr -lgmp -lm
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C = $(CC) $(CF) -I../Include -I../../COLAMD/Include -I../../AMD/Include -I../../SuiteSparse_config
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diff -urN SuiteSparse-5.8.1_orig/SLIP_LU/Tcov/Makefile SuiteSparse-5.8.1/SLIP_LU/Tcov/Makefile
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--- SuiteSparse-5.8.1_orig/SLIP_LU/Tcov/Makefile 2020-07-14 16:04:44.000000000 -0700
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+++ SuiteSparse-5.8.1/SLIP_LU/Tcov/Makefile 2020-10-14 12:08:36.691080983 -0700
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@@ -21,7 +21,7 @@
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-I../../SuiteSparse_config -I../../COLAMD/Include -I../../AMD/Include \
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-DSLIP_GMP_LIST_INIT=2 -DSLIP_LU_TCOV
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-LDLIBS += -lm -lgmp -lmpfr -lcolamd -lamd -lsuitesparseconfig
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+LDLIBS += -lsuitesparseconfig -lcolamd -lamd -lmpfr -lgmp -lm
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# run all statement coverage tests, and then check for 100% coverage
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run: runtests

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