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Upgraded macos-12 runners to macos-13 #515

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Upgraded macos-12 runners to macos-13

Upgraded macos-12 runners to macos-13 #515

Workflow file for this run

.github/workflows/maboss-macos.yml at dda49aa
name: MacOS
on:
push:
pull_request:
release:
types: [created]
jobs:
maboss_macos:
name: MaBoSS
runs-on: macos-13
env:
CC: gcc-12
CXX: g++-12
INSTALL_PATH: /usr/local
BUILD_PATH: /tmp/
LIBXML_LIBDIR: /usr/local/opt/libxml2/lib/libxml2.2.dylib
LIBXML_INCLUDEDIR: /usr/local/opt/libxml2/include/libxml2/
MACOSX_DEPLOYMENT_TARGET: 12.0
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run : |
brew install gcc flex bison cmake
brew install libxml2 hdf5
pip install numpy
- name: Set cmake version variable
run: |
echo "CMAKE_VERSION=$(cmake --version | head -n 1)" >> $GITHUB_ENV
- name: Cache compiled libSBML
id: cache-libsbml-gcc
uses: actions/cache@v4
with:
path: /tmp/libsbml-5.20.4
key: ${{ runner.os }}-${{ env.CMAKE_VERSION }}.libSBML-5.20.4-g++12-namespace
- name: Compiling libSBML
if: steps.cache-libsbml-gcc.outputs.cache-hit != 'true'
run: bash scripts/build_libsbml.sh
- name: Install libSBML
run: sudo bash scripts/install_libsbml.sh
- name: Build MaBoSS
run: |
cd engine/src
make clean
export CXXFLAGS="${CXXFLAGS} -I/usr/local/include -I/usr/local/include/libxml2"
export LDFLAGS="${LDFLAGS} -L/usr/local/lib -lxml2"
make CXX=g++-12 CC=gcc-12 install SBML_COMPAT=1
make CXX=g++-12 CC=gcc-12 MAXNODES=128 install SBML_COMPAT=1
- name: Test MaBoSS
run: bash scripts/run_tests.sh
maboss_llvm_macos:
name: MaBoSS (clang)
runs-on: macos-13
env:
CC: clang
CXX: clang++
INSTALL_PATH: /usr/local
BUILD_PATH: /tmp/
LIBXML_LIBDIR: /usr/local/opt/libxml2/lib/libxml2.dylib
LIBXML_INCLUDEDIR: /usr/local/opt/libxml2/include/libxml2/
MACOSX_DEPLOYMENT_TARGET: 12.0
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run : |
brew install flex bison cmake hdf5 libxml2
pip install numpy
- name: Set cmake version variable
run: |
echo "CMAKE_VERSION=$(cmake --version | head -n 1)" >> $GITHUB_ENV
- name: Cache compiled libSBML
id: cache-libsbml-clang
uses: actions/cache@v4
with:
path: /tmp/libsbml-5.20.4
key: ${{ runner.os }}-${{ env.CMAKE_VERSION }}-libSBML-5.20.4-clang++-namespace
- name: Compiling libSBML
if: steps.cache-libsbml-clang.outputs.cache-hit != 'true'
run: bash scripts/build_libsbml.sh
- name: Install libSBML
run: |
sudo bash scripts/install_libsbml.sh
- name: Build MaBoSS
run: |
cd engine/src
make clean
make CXX=g++ install SBML_COMPAT=1
make CXX=g++ MAXNODES=128 install SBML_COMPAT=1
- name: Test MaBoSS
run: bash scripts/run_tests.sh
maboss_binary_macos:
name: MaBoSS MacOSX x86_64 binary
runs-on: macos-13
needs: [maboss_macos, maboss_llvm_macos]
env:
CC: clang
CXX: clang++
INSTALL_PATH: /usr/local
BUILD_PATH: /tmp/
LIBXML_LIBDIR: /usr/local/opt/libxml2/lib/libxml2.dylib
LIBXML_INCLUDEDIR: /usr/local/opt/libxml2/include/libxml2/
MACOSX_DEPLOYMENT_TARGET: 12.0
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run : |
brew install flex bison cmake libxml2
- name: Set cmake version variable
run: |
echo "CMAKE_VERSION=$(cmake --version | head -n 1)" >> $GITHUB_ENV
- name: Cache compiled libSBML
id: cache-libsbml-clang
uses: actions/cache@v4
with:
path: /tmp/libsbml-5.20.4
key: ${{ runner.os }}-${{ env.CMAKE_VERSION }}-libSBML-5.20.4-clang++-namespace
- name: Compiling libSBML
if: steps.cache-libsbml-clang.outputs.cache-hit != 'true'
run: bash scripts/build_libsbml.sh
- name: Install libSBML
run: sudo bash scripts/install_libsbml.sh
- name: Build binary
run: |
rm -fr engine/pub/*
cd engine/src
make clean
make install_static CC=clang CXX=clang++ SBML_COMPAT=1
make install_static CC=clang CXX=clang++ MAXNODES=128 SBML_COMPAT=1
make install_static CC=clang CXX=clang++ MAXNODES=256 SBML_COMPAT=1
make install_static CC=clang CXX=clang++ MAXNODES=512 SBML_COMPAT=1
make install_static CC=clang CXX=clang++ MAXNODES=1024 SBML_COMPAT=1
cd ../pub
zip MaBoSS-osx64.zip *
- name: Caching produced project binaries
uses: actions/cache@v4
with:
path: |
${{ github.workspace }}/engine/pub/MaBoSS-osx64.zip
key: ${{ runner.os }}-macos-MaBoSS-${{ github.run_id }}
- uses: actions/upload-artifact@v4
if: github.event_name != 'release'
with:
name: MaBoSS-osx64
path: /Users/runner/work/MaBoSS/MaBoSS/engine/pub/MaBoSS-osx64.zip
- uses: actions/upload-release-asset@v1
if: github.event_name == 'release'
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
upload_url: ${{ github.event.release.upload_url }}
asset_name: MaBoSS-osx64.zip
asset_path: /Users/runner/work/MaBoSS/MaBoSS/engine/pub/MaBoSS-osx64.zip
asset_content_type: application/zip
maboss_binary_macos_m1:
name: MaBoSS MacOSX arm64 binary
needs: [maboss_macos, maboss_llvm_macos]
runs-on: macos-14
env:
CC: clang
CXX: clang++
INSTALL_PATH: /usr/local
BUILD_PATH: /tmp/
LIBXML_LIBDIR: /opt/homebrew/opt/libxml2/lib/libxml2.dylib
LIBXML_INCLUDEDIR: /opt/homebrew/opt/libxml2/include/
MACOSX_DEPLOYMENT_TARGET: 12.0
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run : |
brew install flex bison cmake libxml2
- name: Set cmake version variable
run: |
echo "CMAKE_VERSION=$(cmake --version | head -n 1)" >> $GITHUB_ENV
- name: Cache compiled libSBML
id: cache-libsbml-clang
uses: actions/cache@v4
with:
path: /tmp/libsbml-5.20.4
key: ${{ runner.os }}-m1-${{ env.CMAKE_VERSION }}-libSBML-5.20.4-clang++-namespace
- name: Compiling libSBML
if: steps.cache-libsbml-clang.outputs.cache-hit != 'true'
run: bash scripts/build_libsbml.sh
- name: Install libSBML
run: sudo bash scripts/install_libsbml.sh
- name: Build binary
run: |
rm -fr engine/pub/*
cd engine/src
make clean
make install_static CC=clang CXX=clang++ SBML_COMPAT=1
make install_static CC=clang CXX=clang++ MAXNODES=128 SBML_COMPAT=1
make install_static CC=clang CXX=clang++ MAXNODES=256 SBML_COMPAT=1
make install_static CC=clang CXX=clang++ MAXNODES=512 SBML_COMPAT=1
make install_static CC=clang CXX=clang++ MAXNODES=1024 SBML_COMPAT=1
cd ../pub
zip MaBoSS-osx-arm64.zip *
- name: Caching produced project binaries
uses: actions/cache@v4
with:
path: |
${{ github.workspace }}/engine/pub/MaBoSS-osx-arm64.zip
key: ${{ runner.os }}-macosarm64-MaBoSS-${{ github.run_id }}
- uses: actions/upload-artifact@v4
if: github.event_name != 'release'
with:
name: MaBoSS-osx-arm64
path: /Users/runner/work/MaBoSS/MaBoSS/engine/pub/MaBoSS-osx-arm64.zip
- uses: actions/upload-release-asset@v1
if: github.event_name == 'release'
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
upload_url: ${{ github.event.release.upload_url }}
asset_name: MaBoSS-osx-arm64.zip
asset_path: /Users/runner/work/MaBoSS/MaBoSS/engine/pub/MaBoSS-osx-arm64.zip
asset_content_type: application/zip
maboss_binary_macos_universal:
name: MaBoSS MacOSX universal binary
needs: [maboss_binary_macos, maboss_binary_macos_m1]
runs-on: macos-13
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run : |
brew install unzip
- name: Caching produced project binaries
uses: actions/cache@v4
with:
path: |
${{ github.workspace }}/engine/pub/MaBoSS-osx-arm64.zip
key: ${{ runner.os }}-macosarm64-MaBoSS-${{ github.run_id }}
- name: Caching produced project binaries
uses: actions/cache@v4
with:
path: |
${{ github.workspace }}/engine/pub/MaBoSS-osx64.zip
key: ${{ runner.os }}-macos-MaBoSS-${{ github.run_id }}
- name: Create universal binaries
run : |
cd engine/pub
unzip MaBoSS-osx64.zip -d MaBoSS-osx64
unzip MaBoSS-osx-arm64.zip -d MaBoSS-osx-arm64
lipo -create -output MaBoSS MaBoSS-osx64/MaBoSS MaBoSS-osx-arm64/MaBoSS
lipo -create -output MaBoSS_128n MaBoSS-osx64/MaBoSS_128n MaBoSS-osx-arm64/MaBoSS_128n
lipo -create -output MaBoSS_256n MaBoSS-osx64/MaBoSS_256n MaBoSS-osx-arm64/MaBoSS_256n
lipo -create -output MaBoSS_512n MaBoSS-osx64/MaBoSS_512n MaBoSS-osx-arm64/MaBoSS_512n
lipo -create -output MaBoSS_1024n MaBoSS-osx64/MaBoSS_1024n MaBoSS-osx-arm64/MaBoSS_1024n
lipo -create -output PopMaBoSS MaBoSS-osx64/PopMaBoSS MaBoSS-osx-arm64/PopMaBoSS
lipo -create -output PopMaBoSS_128n MaBoSS-osx64/PopMaBoSS_128n MaBoSS-osx-arm64/PopMaBoSS_128n
lipo -create -output PopMaBoSS_256n MaBoSS-osx64/PopMaBoSS_256n MaBoSS-osx-arm64/PopMaBoSS_256n
lipo -create -output PopMaBoSS_512n MaBoSS-osx64/PopMaBoSS_512n MaBoSS-osx-arm64/PopMaBoSS_512n
lipo -create -output PopMaBoSS_1024n MaBoSS-osx64/PopMaBoSS_1024n MaBoSS-osx-arm64/PopMaBoSS_1024n
zip MaBoSS-osx-universal.zip MaBoSS MaBoSS_128n MaBoSS_256n MaBoSS_512n MaBoSS_1024n PopMaBoSS PopMaBoSS_128n PopMaBoSS_256n PopMaBoSS_512n PopMaBoSS_1024n
- uses: actions/upload-artifact@v4
if: github.event_name != 'release'
with:
name: MaBoSS-osx-universal
path: /Users/runner/work/MaBoSS/MaBoSS/engine/pub/MaBoSS-osx-universal.zip
- uses: actions/upload-release-asset@v1
if: github.event_name == 'release'
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
upload_url: ${{ github.event.release.upload_url }}
asset_name: MaBoSS-osx-universal.zip
asset_path: /Users/runner/work/MaBoSS/MaBoSS/engine/pub/MaBoSS-osx-universal.zip
asset_content_type: application/zip
maboss_library_macos:
name: Building MaBoSS osx library
runs-on: macos-13
needs: [maboss_macos, maboss_llvm_macos]
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run : |
brew install flex bison
- name: Build library
run: |
rm -fr engine/pub/*
cd engine/src
make clean
make install_lib CC=gcc-12 CXX=g++-12
make install_lib MAXNODES=128 CC=gcc-12 CXX=g++-12
make install_lib MAXNODES=256 CC=gcc-12 CXX=g++-12
make install_lib MAXNODES=512 CC=gcc-12 CXX=g++-12
make install_lib MAXNODES=1024 CC=gcc-12 CXX=g++-12
make install_alib CC=gcc-12 CXX=g++-12
make install_alib MAXNODES=128 CC=gcc-12 CXX=g++-12
make install_alib MAXNODES=256 CC=gcc-12 CXX=g++-12
make install_alib MAXNODES=512 CC=gcc-12 CXX=g++-12
make install_alib MAXNODES=1024 CC=gcc-12 CXX=g++-12
make clean
cd ../../../
tar -zcvf libMaBoSS-osx64.tar.gz MaBoSS/README.md MaBoSS/LICENSE MaBoSS/engine/src MaBoSS/engine/include MaBoSS/engine/lib
- uses: actions/upload-artifact@v4
if: github.event_name != 'release'
with:
name: libMaBoSS-osx64
path: /Users/runner/work/MaBoSS/libMaBoSS-osx64.tar.gz
- uses: actions/upload-release-asset@v1
if: github.event_name == 'release'
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
upload_url: ${{ github.event.release.upload_url }}
asset_name: libMaBoSS-osx64.tar.gz
asset_path: /Users/runner/work/MaBoSS/libMaBoSS-osx64.tar.gz
asset_content_type: application/gzip
maboss_library_macos_m1:
name: Building MaBoSS osx library for arm64
runs-on: macos-14
needs: [maboss_macos, maboss_llvm_macos]
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run : |
brew install flex bison
- name: Build library
run: |
rm -fr engine/pub/*
cd engine/src
make clean
make install_lib CC=gcc-12 CXX=g++-12
make install_lib MAXNODES=128 CC=gcc-12 CXX=g++-12
make install_lib MAXNODES=256 CC=gcc-12 CXX=g++-12
make install_lib MAXNODES=512 CC=gcc-12 CXX=g++-12
make install_lib MAXNODES=1024 CC=gcc-12 CXX=g++-12
make install_alib CC=gcc-12 CXX=g++-12
make install_alib MAXNODES=128 CC=gcc-12 CXX=g++-12
make install_alib MAXNODES=256 CC=gcc-12 CXX=g++-12
make install_alib MAXNODES=512 CC=gcc-12 CXX=g++-12
make install_alib MAXNODES=1024 CC=gcc-12 CXX=g++-12
make clean
cd ../../../
tar -zcvf libMaBoSS-macos-arm64.tar.gz MaBoSS/README.md MaBoSS/LICENSE MaBoSS/engine/src MaBoSS/engine/include MaBoSS/engine/lib
- uses: actions/upload-artifact@v4
if: github.event_name != 'release'
with:
name: libMaBoSS-macos-arm64
path: /Users/runner/work/MaBoSS/libMaBoSS-macos-arm64.tar.gz
- uses: actions/upload-release-asset@v1
if: github.event_name == 'release'
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
upload_url: ${{ github.event.release.upload_url }}
asset_name: libMaBoSS-macos-arm64.tar.gz
asset_path: /Users/runner/work/MaBoSS/libMaBoSS-macos-arm64.tar.gz
asset_content_type: application/gzip
maboss_library_sbml_macos:
name: Building MaBoSS osx library with libSBML
runs-on: macos-13
needs: [maboss_macos, maboss_llvm_macos]
env:
CC: gcc-12
CXX: g++-12
INSTALL_PATH: /usr/local/
BUILD_PATH: /tmp/
LIBXML_LIBDIR: /usr/local/opt/libxml2/lib/libxml2.dylib
LIBXML_INCLUDEDIR: /usr/local/opt/libxml2/include/libxml2
MACOSX_DEPLOYMENT_TARGET: 12.0
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run : |
brew install flex bison cmake libxml2
- name: Set cmake version variable
run: |
echo "CMAKE_VERSION=$(cmake --version | head -n 1)" >> $GITHUB_ENV
- name: Cache compiled libSBML
id: cache-libsbml-gcc12
uses: actions/cache@v4
with:
path: /tmp/libsbml-5.20.4
key: ${{ runner.os }}-${{ env.CMAKE_VERSION }}-libSBML-5.20.4-g++12-namespace
- name: Compiling libSBML
if: steps.cache-libsbml-gcc11.outputs.cache-hit != 'true'
run: bash scripts/build_libsbml.sh
- name: Install libSBML
run: sudo bash scripts/install_libsbml.sh
- name: Build library
run: |
export CXXFLAGS="${CXXFLAGS} -I/usr/local/include -I/usr/local/include/libxml2"
export LDFLAGS="${LDFLAGS} -L/usr/local/lib -lxml2"
rm -fr engine/pub/*
cd engine/src
make clean
make install CC=gcc-12 CXX=g++-12
make install_lib SBML_COMPAT=1 CC=gcc-12 CXX=g++-12
make install_lib SBML_COMPAT=1 CC=gcc-12 MAXNODES=128 CXX=g++-12
make install_lib SBML_COMPAT=1 CC=gcc-12 MAXNODES=256 CXX=g++-12
make install_lib SBML_COMPAT=1 CC=gcc-12 MAXNODES=512 CXX=g++-12
make install_lib SBML_COMPAT=1 CC=gcc-12 MAXNODES=1024 CXX=g++-12
make install_alib SBML_COMPAT=1 CC=gcc-12 CXX=g++-12
make install_alib SBML_COMPAT=1 CC=gcc-12 MAXNODES=128 CXX=g++-12
make install_alib SBML_COMPAT=1 CC=gcc-12 MAXNODES=256 CXX=g++-12
make install_alib SBML_COMPAT=1 CC=gcc-12 MAXNODES=512 CXX=g++-12
make install_alib SBML_COMPAT=1 CC=gcc-12 MAXNODES=1024 CXX=g++-12
make clean
cd ../../../
tar -zcvf libMaBoSS-sbml-osx64.tar.gz MaBoSS/README.md MaBoSS/LICENSE MaBoSS/engine/src MaBoSS/engine/include MaBoSS/engine/lib
- uses: actions/upload-artifact@v4
if: github.event_name != 'release'
with:
name: libMaBoSS-sbml-osx64
path: /Users/runner/work/MaBoSS/libMaBoSS-sbml-osx64.tar.gz
- uses: actions/upload-release-asset@v1
if: github.event_name == 'release'
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
upload_url: ${{ github.event.release.upload_url }}
asset_name: libMaBoSS-sbml-osx64.tar.gz
asset_path: /Users/runner/work/MaBoSS/libMaBoSS-sbml-osx64.tar.gz
asset_content_type: application/gzip
conda_maboss_macosx:
name: Build Conda MaBoSS package
needs: [maboss_macos, maboss_llvm_macos]
strategy:
fail-fast: false
matrix:
repo: [
{id: 0, name: "defaults"},
{id: 1, name: "conda-forge"}
]
runs-on: macos-13
defaults:
run:
shell: sh -l {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: ${{ matrix.repo.name }}
python-version: 3.12
use-mamba: true
- name: Installing conda-build
run: |
conda install conda-build conda-verify anaconda-client
- name: Installing MacOSX SDK
run: |
wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.13.sdk.tar.xz
sudo tar xf MacOSX10.13.sdk.tar.xz -C /opt
echo "conda_build:" > ~/.condarc
echo " config_file: ~/.conda/conda_build_config.yaml" >> ~/.condarc
echo "CONDA_BUILD_SYSROOT:" > ~/.conda/conda_build_config.yaml
echo " - /opt/MacOSX10.13.sdk # [osx]" >> ~/.conda/conda_build_config.yaml
- name: Build MaBoSS Anaconda package
run: |
CUSTOM_BUILD_NUMBER=${{ matrix.repo.id }} conda build -c ${{ matrix.repo.name }} -c colomoto conda/maboss
- name: Upload MaBoSS to Anaconda cloud on vincent-noel
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /usr/local/miniconda/envs/test/conda-bld/osx-64/*.tar.bz2 --force;
- name: Upload MaBoSS to Anaconda cloud on colomoto
if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release'
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /usr/local/miniconda/envs/test/conda-bld/osx-64/*.tar.bz2 --force;
conda_maboss_macosx_m1:
name: Build Conda MaBoSS package for arm64
needs: [maboss_macos, maboss_llvm_macos]
strategy:
fail-fast: false
matrix:
repo: [
{id: 0, name: "defaults", path: "/Users/runner/miniconda3"},
{id: 1, name: "conda-forge", path: "/Users/runner/miniconda3"}
]
runs-on: macos-14
defaults:
run:
shell: sh -l {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: ${{ matrix.repo.name }}
python-version: 3.12
use-mamba: true
- name: Installing conda-build
run: |
conda install conda-build conda-verify anaconda-client
- name: Installing MacOSX SDK
run: |
wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX11.0.sdk.tar.xz
sudo tar xf MacOSX11.0.sdk.tar.xz -C /opt
echo "conda_build:" > ~/.condarc
echo " config_file: ~/.conda/conda_build_config.yaml" >> ~/.condarc
echo "CONDA_BUILD_SYSROOT:" > ~/.conda/conda_build_config.yaml
echo " - /opt/MacOSX11.0.sdk # [osx]" >> ~/.conda/conda_build_config.yaml
- name: Build MaBoSS Anaconda package
run: |
CUSTOM_BUILD_NUMBER=${{ matrix.repo.id }} conda build -c ${{ matrix.repo.name }} -c colomoto conda/maboss
- name: Upload MaBoSS to Anaconda cloud on vincent-noel
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel ${{ matrix.repo.path }}/envs/test/conda-bld/osx-arm64/*.tar.bz2 --force;
- name: Upload MaBoSS to Anaconda cloud on colomoto
if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release'
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto ${{ matrix.repo.path }}/envs/test/conda-bld/osx-arm64/*.tar.bz2 --force;