Update of cmaboss. many things #507
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| name: cMaBoSS MacOS | |
| on: | |
| push: | |
| pull_request: | |
| release: | |
| types: [created] | |
| jobs: | |
| cmaboss_macos: | |
| name: cMaBoSS | |
| runs-on: macos-12 | |
| 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: Downgrading to XCode 13.1 | |
| run: | | |
| sudo xcode-select -s /Applications/Xcode_13.1.app/Contents/Developer | |
| - name: Install dependencies | |
| run: | | |
| brew install flex bison python3 cmake libxml2 | |
| python3 -m pip install --upgrade pip | |
| pip3 install numpy wheel delocate pandas | |
| - 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 cMaBoSS | |
| run: | | |
| cd engine/src | |
| make grammars | |
| cd ../python | |
| cp -r ../src cmaboss | |
| python3 -m pip wheel -w wheelhouse . | |
| delocate-wheel -w fixed_wheels -v `ls wheelhouse/cmaboss*.whl` | |
| pip3 install `ls fixed_wheels/cmaboss*.whl` | |
| - name: Test cMaBoSS | |
| run: bash scripts/run_cmaboss_tests.sh | |
| build_wheels_macos: | |
| name: Build MacOS wheels | |
| runs-on: macos-12 | |
| needs: cmaboss_macos | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Downgrading to XCode 13.1 | |
| run: | | |
| sudo xcode-select -s /Applications/Xcode_13.1.app/Contents/Developer | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Install cibuildwheel | |
| run: python -m pip install cibuildwheel numpy twine | |
| - name: Build wheels | |
| env: | |
| MACOSX_DEPLOYMENT_TARGET: 12.0 | |
| CIBW_ARCHS: x86_64 | |
| CIBW_BEFORE_ALL: > | |
| brew install libxml2 && | |
| 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/ \ | |
| bash scripts/build_libsbml.sh && | |
| BUILD_PATH=/tmp/ bash scripts/install_libsbml.sh | |
| CIBW_REPAIR_WHEEL_COMMAND_MACOS: > | |
| DYLD_LIBRARY_PATH=/usr/local/lib/ delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel} | |
| run: | | |
| cd engine/src | |
| make grammars | |
| cd ../../ | |
| cp -r engine/src engine/python/cmaboss/ | |
| python -m cibuildwheel --output-dir wheelhouse engine/python | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheels-macos-x86_64 | |
| path: wheelhouse/*.whl | |
| - name: Upload cMaBoSS to test Pypi | |
| if: github.repository == 'vincent-noel/MaBoSS' && github.ref == 'refs/heads/master' | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_TEST_TOKEN }} | |
| run: | | |
| python -m twine upload --repository testpypi --skip-existing wheelhouse/cmaboss* | |
| - name: Upload cMaBoSS to Pypi | |
| if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release' | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }} | |
| run: | | |
| python -m twine upload --skip-existing wheelhouse/cmaboss* | |
| build_wheels_macos_arm64: | |
| name: Build MacOS wheels | |
| runs-on: macos-14 | |
| needs: cmaboss_macos | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Install cibuildwheel | |
| run: python -m pip install cibuildwheel numpy twine | |
| - name: Build wheels | |
| env: | |
| MACOSX_DEPLOYMENT_TARGET: 14.0 | |
| CIBW_ARCHS: arm64 | |
| CIBW_BEFORE_ALL: > | |
| brew install libxml2 && | |
| 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/ \ | |
| bash scripts/build_libsbml.sh && | |
| BUILD_PATH=/tmp/ sudo bash scripts/install_libsbml.sh | |
| CIBW_REPAIR_WHEEL_COMMAND_MACOS: > | |
| DYLD_LIBRARY_PATH=/usr/local/lib/ delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel} | |
| run: | | |
| cd engine/src | |
| make grammars | |
| cd ../../ | |
| cp -r engine/src engine/python/cmaboss/ | |
| python -m cibuildwheel --output-dir wheelhouse engine/python | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheels-macos-arm64 | |
| path: wheelhouse/*.whl | |
| - name: Upload cMaBoSS to test Pypi | |
| if: github.repository == 'vincent-noel/MaBoSS' && github.ref == 'refs/heads/master' | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_TEST_TOKEN }} | |
| run: | | |
| python -m twine upload --repository testpypi --skip-existing wheelhouse/cmaboss* | |
| - name: Upload cMaBoSS to Pypi | |
| if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release' | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }} | |
| run: | | |
| python -m twine upload --skip-existing wheelhouse/cmaboss* | |
| conda_cmaboss_macosx_defaults: | |
| name: cMaBoSS Conda package (defaults) | |
| needs: cmaboss_macos | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| version: [{python: "3.8", numpy: "1.24"}, {python: "3.9", numpy: "2.0"}, {python: "3.10", numpy: "2.0"}, {python: "3.11", numpy: "2.0"}, {python: "3.12", numpy: "2.0"}] | |
| runs-on: macos-12 | |
| defaults: | |
| run: | |
| shell: sh -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channels: defaults | |
| python-version: 3.12 | |
| use-mamba: true | |
| - name: Install conda-build | |
| run: | | |
| conda install conda-build conda-verify anaconda-client | |
| - name: Installing MacOSX10.9 SDK | |
| run: | | |
| wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.9.sdk.tar.xz | |
| sudo tar xf MacOSX10.9.sdk.tar.xz -C /opt | |
| echo "conda_build:" > ~/.condarc | |
| echo " config_file: ~/.conda/conda_build_config.yaml" >> ~/.condarc | |
| echo "CONDA_BUILD_SYSROOT:" > ~/.conda/conda_build_config.yaml | |
| echo " - /opt/MacOSX10.9.sdk # [osx]" >> ~/.conda/conda_build_config.yaml | |
| - name: Build cMaBoSS Anaconda package | |
| env: | |
| MACOSX_DEPLOYMENT_TARGET: 10.9 | |
| run: | | |
| CUSTOM_BUILD_NUMBER=0 conda build -c defaults -c colomoto --variants "{\"python\": [\"${{ matrix.version.python }}\"], \"numpy\": [\"${{ matrix.version.numpy }}\"]}" conda/cmaboss; | |
| - 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 ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /usr/local/miniconda/envs/test/conda-bld/osx-64/*.tar.bz2 --force; | |
| conda_cmaboss_macosx_condaforge: | |
| name: cMaBoSS Conda package (conda-forge) | |
| needs: cmaboss_macos | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| version: [{python: "3.8", numpy: "1.24"}, {python: "3.9", numpy: "2.0"}, {python: "3.10", numpy: "2.1"}, {python: "3.11", numpy: "2.1"}, {python: "3.12", numpy: "2.1"}] | |
| runs-on: macos-12 | |
| defaults: | |
| run: | |
| shell: sh -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channels: conda-forge | |
| python-version: 3.12 | |
| use-mamba: true | |
| - name: Install conda-build | |
| run: | | |
| conda install conda-build conda-verify anaconda-client | |
| - name: Installing MacOSX10.13 SDK | |
| run: | | |
| wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.13.sdk.tar.xz | |
| sudo tar xf MacOSX10.13.sdk.tar.xz -C /opt | |
| echo "conda_build:" > ~/.condarc | |
| echo " config_file: ~/.conda/conda_build_config.yaml" >> ~/.condarc | |
| echo "CONDA_BUILD_SYSROOT:" > ~/.conda/conda_build_config.yaml | |
| echo " - /opt/MacOSX10.13.sdk # [osx]" >> ~/.conda/conda_build_config.yaml | |
| - name: Build cMaBoSS Anaconda package | |
| env: | |
| MACOSX_DEPLOYMENT_TARGET: 10.13 | |
| run: | | |
| CUSTOM_BUILD_NUMBER=1 conda build -c conda-forge -c colomoto --variants "{\"python\": [\"${{ matrix.version.python }}\"], \"numpy\": [\"${{ matrix.version.numpy }}\"]}" conda/cmaboss; | |
| - 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 ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /usr/local/miniconda/envs/test/conda-bld/osx-64/*.tar.bz2 --force; | |
| conda_cmaboss_macosx_M1_defaults: | |
| name: cMaBoSS Conda package for arm64 (defaults) | |
| needs: cmaboss_macos | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| version: [{python: "3.8", numpy: "1.24"}, {python: "3.9", numpy: "2.0"}, {python: "3.10", numpy: "2.0"}, {python: "3.11", numpy: "2.0"}, {python: "3.12", numpy: "2.0"}] | |
| runs-on: macos-14 | |
| defaults: | |
| run: | |
| shell: sh -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channels: defaults | |
| python-version: 3.12 | |
| use-mamba: true | |
| - name: Install conda-build | |
| run: | | |
| conda install conda-build conda-verify anaconda-client | |
| - name: Installing MacOSX11.1 SDK | |
| run: | | |
| wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX11.1.sdk.tar.xz | |
| sudo tar xf MacOSX11.1.sdk.tar.xz -C /opt | |
| echo "conda_build:" > ~/.condarc | |
| echo " config_file: ~/.conda/conda_build_config.yaml" >> ~/.condarc | |
| echo "CONDA_BUILD_SYSROOT:" > ~/.conda/conda_build_config.yaml | |
| echo " - /opt/MacOSX11.1.sdk # [osx]" >> ~/.conda/conda_build_config.yaml | |
| - name: Build cMaBoSS Anaconda package | |
| env: | |
| MACOSX_DEPLOYMENT_TARGET: 11.1 | |
| run: | | |
| CUSTOM_BUILD_NUMBER=0 conda build -c defaults -c colomoto --variants "{\"python\": [\"${{ matrix.version.python }}\"], \"numpy\": [\"${{ matrix.version.numpy }}\"]}" conda/cmaboss; | |
| - name: Upload MaBoSS to Anaconda cloud on vincent-noel | |
| run: | | |
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /Users/runner/miniconda3/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 ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /Users/runner/miniconda3/envs/test/conda-bld/osx-arm64/*.tar.bz2 --force; | |
| conda_cmaboss_macosx_M1_condaforge: | |
| name: cMaBoSS Conda package for arm64 (conda-forge) | |
| needs: cmaboss_macos | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| version: [{python: "3.8", numpy: "1.24"}, {python: "3.9", numpy: "2.0"}, {python: "3.10", numpy: "2.1"}, {python: "3.11", numpy: "2.1"}, {python: "3.12", numpy: "2.1"}] | |
| runs-on: macos-14 | |
| defaults: | |
| run: | |
| shell: sh -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channels: conda-forge | |
| python-version: 3.12 | |
| use-mamba: true | |
| - name: Install conda-build | |
| run: | | |
| conda install conda-build conda-verify anaconda-client | |
| - name: Installing MacOSX11.0 SDK | |
| run: | | |
| wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX11.0.sdk.tar.xz | |
| sudo tar xf MacOSX11.0.sdk.tar.xz -C /opt | |
| echo "conda_build:" > ~/.condarc | |
| echo " config_file: ~/.conda/conda_build_config.yaml" >> ~/.condarc | |
| echo "CONDA_BUILD_SYSROOT:" > ~/.conda/conda_build_config.yaml | |
| echo " - /opt/MacOSX11.0.sdk # [osx]" >> ~/.conda/conda_build_config.yaml | |
| - name: Build cMaBoSS Anaconda package | |
| env: | |
| MACOSX_DEPLOYMENT_TARGET: 11.0 | |
| run: | | |
| CUSTOM_BUILD_NUMBER=1 conda build -c conda-forge -c colomoto --variants "{\"python\": [\"${{ matrix.version.python }}\"], \"numpy\": [\"${{ matrix.version.numpy }}\"]}" conda/cmaboss; | |
| - name: Upload MaBoSS to Anaconda cloud on vincent-noel | |
| run: | | |
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /Users/runner/miniconda3/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 /Users/runner/miniconda3/envs/test/conda-bld/osx-arm64/*.tar.bz2 --force; | |