Not building pypy wheels on macosx #2
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| name: Linux | |
| on: | |
| push: | |
| pull_request: | |
| release: | |
| types: [created] | |
| jobs: | |
| maboss: | |
| name: MaBoSS (gcc) | |
| runs-on: ubuntu-22.04 | |
| env: | |
| GCC: gcc | |
| CXX: g++ | |
| INSTALL_PATH: /usr/ | |
| BUILD_PATH: /tmp/ | |
| LIBXML_LIBDIR: /usr/lib/x86_64-linux-gnu/libxml2.so | |
| LIBXML_INCLUDEDIR: /usr/include/libxml2/ | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install flex bison | |
| pip install numpy | |
| - name: Cache compiled libSBML | |
| id: cache-libsbml-gcc | |
| uses: actions/cache@v3 | |
| with: | |
| path: /tmp/libsbml-5.20.2 | |
| key: ${{ runner.os }}-libSBML-5.20.2-gcc-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 | |
| make install SBML_COMPAT=1 | |
| make MAXNODES=128 install SBML_COMPAT=1 | |
| - name: Test MaBoSS | |
| run: bash scripts/run_tests.sh | |
| maboss_llvm: | |
| name: MaBoSS (clang) | |
| runs-on: ubuntu-22.04 | |
| env: | |
| GCC: clang | |
| CXX: clang++ | |
| INSTALL_PATH: /usr/ | |
| BUILD_PATH: /tmp/ | |
| LIBXML_LIBDIR: /usr/lib/x86_64-linux-gnu/libxml2.so | |
| LIBXML_INCLUDEDIR: /usr/include/libxml2/ | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run : | | |
| sudo apt-get install flex bison clang | |
| pip install numpy | |
| - name: Cache compiled libSBML | |
| id: cache-libsbml-clang | |
| uses: actions/cache@v3 | |
| with: | |
| path: /tmp/libsbml-5.20.2 | |
| key: ${{ runner.os }}-libSBML-5.20.2-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 GCC=clang CXX=clang++ install SBML_COMPAT=1 | |
| make GCC=clang CXX=clang++ MAXNODES=128 install SBML_COMPAT=1 | |
| - name: Test MaBoSS | |
| run: bash scripts/run_tests.sh | |
| maboss_mpi: | |
| name: MaBoSS MPI | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install flex bison libopenmpi-dev | |
| pip install numpy | |
| - name: Build MaBoSS | |
| run: | | |
| cd engine/src | |
| make clean | |
| make install CXX=mpic++ MPI_COMPAT=1 | |
| make install CXX=mpic++ MPI_COMPAT=1 MAXNODES=128 | |
| - name: Test MaBoSS | |
| run: bash scripts/run_mpi_tests.sh | |
| maboss_binary: | |
| name: Building MaBoSS linux64 binary | |
| runs-on: ubuntu-22.04 | |
| needs: [maboss, maboss_llvm, maboss_mpi] | |
| env: | |
| GCC: gcc | |
| CXX: g++ | |
| INSTALL_PATH: /usr/ | |
| BUILD_PATH: /tmp/ | |
| LIBXML_LIBDIR: /usr/lib/x86_64-linux-gnu/libxml2.so | |
| LIBXML_INCLUDEDIR: /usr/include/libxml2 | |
| # if: github.event.workflow_run.conclusion == 'success' && (github.ref == 'refs/heads/master' || github.event_name == 'release') | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install flex bison | |
| pip install numpy | |
| - name: Cache compiled libSBML | |
| id: cache-libsbml-gcc | |
| uses: actions/cache@v3 | |
| with: | |
| path: /tmp/libsbml-5.20.2 | |
| key: ${{ runner.os }}-libSBML-5.20.2-gcc-namespace | |
| - name: Compiling libSBML | |
| if: steps.cache-libsbml-gcc.outputs.cache-hit != 'true' | |
| run: | | |
| bash scripts/build_libsbml.sh | |
| - name: Install libSBML | |
| run: | | |
| sudo env BUILD_PATH=/tmp/ bash scripts/install_libsbml.sh | |
| - name: Build binary | |
| run: | | |
| rm -fr engine/pub/* | |
| cd engine/src | |
| make clean | |
| make install_static SBML_COMPAT=1 | |
| make install_static MAXNODES=128 SBML_COMPAT=1 | |
| make install_static MAXNODES=256 SBML_COMPAT=1 | |
| make install_static MAXNODES=512 SBML_COMPAT=1 | |
| make install_static MAXNODES=1024 SBML_COMPAT=1 | |
| cd ../pub | |
| zip MaBoSS-linux64.zip * | |
| - uses: actions/upload-artifact@v3 | |
| if: github.event_name != 'release' | |
| with: | |
| name: MaBoSS-linux64 | |
| path: /home/runner/work/MaBoSS-env-2.0/MaBoSS-env-2.0/engine/pub/MaBoSS-linux64.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-linux64.zip | |
| asset_path: /home/runner/work/MaBoSS-env-2.0/MaBoSS-env-2.0/engine/pub/MaBoSS-linux64.zip | |
| asset_content_type: application/zip | |
| maboss_library: | |
| name: Building MaBoSS linux64 library | |
| runs-on: ubuntu-22.04 | |
| needs: [maboss, maboss_llvm, maboss_mpi] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install flex bison | |
| - name: Build binary | |
| run: | | |
| rm -fr engine/pub/* | |
| cd engine/src | |
| make clean | |
| make install_lib | |
| make install_lib MAXNODES=128 | |
| make install_lib MAXNODES=256 | |
| make install_lib MAXNODES=512 | |
| make install_lib MAXNODES=1024 | |
| make install_alib | |
| make install_alib MAXNODES=128 | |
| make install_alib MAXNODES=256 | |
| make install_alib MAXNODES=512 | |
| make install_alib MAXNODES=1024 | |
| make clean | |
| cd ../../../ | |
| tar -zcvf libMaBoSS-linux64.tar.gz MaBoSS-env-2.0/README.md MaBoSS-env-2.0/LICENSE MaBoSS-env-2.0/engine/src MaBoSS-env-2.0/engine/include MaBoSS-env-2.0/engine/lib | |
| - uses: actions/upload-artifact@v3 | |
| if: github.event_name != 'release' | |
| with: | |
| name: libMaBoSS-linux64 | |
| path: /home/runner/work/MaBoSS-env-2.0/libMaBoSS-linux64.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-linux64.tar.gz | |
| asset_path: /home/runner/work/MaBoSS-env-2.0/libMaBoSS-linux64.tar.gz | |
| asset_content_type: application/gzip | |
| maboss_library_sbml: | |
| name: Building MaBoSS linux64 library with libSBML | |
| runs-on: ubuntu-22.04 | |
| needs: [maboss, maboss_llvm, maboss_mpi] | |
| env: | |
| GCC: gcc | |
| CXX: g++ | |
| INSTALL_PATH: /usr/ | |
| BUILD_PATH: /tmp/ | |
| LIBXML_LIBDIR: /usr/lib/x86_64-linux-gnu/libxml2.so | |
| LIBXML_INCLUDEDIR: /usr/include/libxml2 | |
| # if: github.event.workflow_run.conclusion == 'success' && (github.ref == 'refs/heads/master' || github.event_name == 'release') | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install flex bison | |
| - name: Cache compiled libSBML | |
| id: cache-libsbml-gcc | |
| uses: actions/cache@v3 | |
| with: | |
| path: /tmp/libsbml-5.20.2 | |
| key: ${{ runner.os }}-libSBML-5.20.2-gcc-namespace | |
| - name: Compiling libSBML | |
| if: steps.cache-libsbml-gcc.outputs.cache-hit != 'true' | |
| run: bash scripts/build_libsbml.sh | |
| - name: Install libSBML | |
| run: sudo env BUILD_PATH=/tmp/ bash scripts/install_libsbml.sh | |
| - name: Build binary | |
| run: | | |
| rm -fr engine/pub/* | |
| cd engine/src | |
| make clean | |
| make install_lib SBML_COMPAT=1 | |
| make install_lib SBML_COMPAT=1 MAXNODES=128 | |
| make install_lib SBML_COMPAT=1 MAXNODES=256 | |
| make install_lib SBML_COMPAT=1 MAXNODES=512 | |
| make install_lib SBML_COMPAT=1 MAXNODES=1024 | |
| make install_alib SBML_COMPAT=1 | |
| make install_alib SBML_COMPAT=1 MAXNODES=128 | |
| make install_alib SBML_COMPAT=1 MAXNODES=256 | |
| make install_alib SBML_COMPAT=1 MAXNODES=512 | |
| make install_alib SBML_COMPAT=1 MAXNODES=1024 | |
| make clean | |
| cd ../../../ | |
| tar -zcvf libMaBoSS-sbml-linux64.tar.gz MaBoSS-env-2.0/README.md MaBoSS-env-2.0/LICENSE MaBoSS-env-2.0/engine/src MaBoSS-env-2.0/engine/include MaBoSS-env-2.0/engine/lib | |
| - uses: actions/upload-artifact@v3 | |
| if: github.event_name != 'release' | |
| with: | |
| name: libMaBoSS-sbml-linux64 | |
| path: /home/runner/work/MaBoSS-env-2.0/libMaBoSS-sbml-linux64.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-linux64.tar.gz | |
| asset_path: /home/runner/work/MaBoSS-env-2.0/libMaBoSS-sbml-linux64.tar.gz | |
| asset_content_type: application/gzip | |
| test_docker: | |
| name: Docker MaBoSS Server | |
| runs-on: ubuntu-22.04 | |
| needs: [maboss, maboss_llvm, maboss_mpi] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install flex bison | |
| pip install numpy | |
| - name: Start MaBoSS docker server | |
| run: | | |
| docker-compose up -d maboss-server | |
| bash -c "cd engine/src; make client" | |
| - name: Test MaBoSS docker server | |
| run: | | |
| bash -c "cd engine/tests; bash ./test-container.sh" | |
| - name: Connect Docker Hub | |
| if: github.event_name == 'release' && github.event.action == 'created' && github.repository == 'sysbio-curie/MaBoSS-env-2.0' | |
| run: | | |
| echo ${{ secrets.DOCKERHUB_TOKEN }} | docker login --username ${{ secrets.DOCKERHUB_USERNAME }} --password-stdin | |
| - name: Upload Docker Hub | |
| if: github.event_name == 'release' && github.event.action == 'created' && github.repository == 'sysbio-curie/MaBoSS-env-2.0' | |
| run: | | |
| docker tag maboss-server:latest vnoel/maboss-server:latest | |
| docker push vnoel/maboss-server:latest | |
| test_singularity: | |
| name: Singularity MaBoSS Server | |
| runs-on: ubuntu-22.04 | |
| needs: [maboss, maboss_llvm, maboss_mpi] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| wget https://github.com/sylabs/singularity/releases/download/v3.11.1/singularity-ce_3.11.1-jammy_amd64.deb | |
| sudo apt-get install -yq ./singularity-ce_3.11.1-jammy_amd64.deb | |
| sudo apt-get install flex bison debootstrap | |
| pip install numpy | |
| - name: Start MaBoSS Singularity server | |
| run: | | |
| sudo singularity build maboss-server.simg containers/singularity/Singularity | |
| singularity run maboss-server.simg & | |
| bash -c "cd engine/src; make client" | |
| - name: Test MaBoSS | |
| run: | | |
| bash -c "cd engine/tests; bash ./test-container.sh" | |
| maboss_conda_defaults: | |
| name: Build MaBoSS Anaconda package | |
| runs-on: ubuntu-22.04 | |
| needs: [maboss, maboss_llvm, maboss_mpi] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| - name: Install conda-build | |
| run: | | |
| conda update conda | |
| conda update conda --all | |
| conda install conda-build anaconda-client conda-verify | |
| - name: Build Anaconda package | |
| run: | | |
| conda build -c colomoto conda/maboss | |
| - name: Caching produced conda package | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/share/miniconda/conda-bld/linux-64/* | |
| key: ${{ runner.os }}-maboss-conda-defaults-${{ github.run_id }} | |
| maboss_conda: | |
| name: Build MaBoSS Anaconda package (conda-forge) | |
| runs-on: ubuntu-22.04 | |
| needs: [maboss, maboss_llvm, maboss_mpi] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| - name: Install conda-build | |
| run: | | |
| conda update conda | |
| conda config --add channels conda-forge | |
| conda config --set channel_priority strict | |
| conda update conda --all | |
| conda install conda-build anaconda-client conda-verify | |
| - name: Build Anaconda package | |
| run: | | |
| CUSTOM_BUILD_NUMBER=1 conda build -c colomoto conda/maboss | |
| - name: Caching produced conda package | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/share/miniconda/conda-bld/linux-64/* | |
| key: ${{ runner.os }}-maboss-conda-${{ github.run_id }} | |
| maboss_conda_test_defaults: | |
| name: Test MaBoSS Anaconda package | |
| runs-on: ubuntu-22.04 | |
| needs: maboss_conda_defaults | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| - name: Caching produced conda package | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/share/miniconda/conda-bld/linux-64/* | |
| key: ${{ runner.os }}-maboss-conda-defaults-${{ github.run_id }} | |
| - name: Install conda-build | |
| run: | | |
| conda update conda | |
| conda config --set channel_priority strict | |
| conda update conda --all | |
| conda install conda-build | |
| - name: Install package | |
| run: | | |
| conda index /usr/share/miniconda/conda-bld | |
| conda install --use-local -c colomoto maboss | |
| - name: Test package | |
| run: | | |
| pip install numpy | |
| export MABOSS=/usr/share/miniconda/bin/MaBoSS | |
| export MABOSS_128n=/usr/share/miniconda/bin/MaBoSS_128n | |
| export MABOSS_CLIENT=/usr/share/miniconda/bin/MaBoSS-client | |
| export MABOSS_SERVER=/usr/share/miniconda/bin/MaBoSS-server | |
| export MABOSS_SERVER_128n=/usr/share/miniconda/bin/MaBoSS_128n-server | |
| bash -c "cd engine/tests; bash ./test-cellcycle.sh" | |
| bash -c "cd engine/tests; bash ./test-ensemble.sh" | |
| bash -c "cd engine/tests; bash ./test-ewing.sh" | |
| bash -c "cd engine/tests; bash ./test-server.sh" | |
| bash -c "cd engine/tests; bash ./test-prngs.sh" | |
| bash -c "cd engine/tests; bash ./test-rngs.sh" | |
| bash -c "cd engine/tests; bash ./test-sbml.sh" | |
| maboss_conda_test: | |
| name: Test MaBoSS Anaconda package (conda-forge) | |
| runs-on: ubuntu-22.04 | |
| needs: maboss_conda | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| - name: Caching produced conda package | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/share/miniconda/conda-bld/linux-64/* | |
| key: ${{ runner.os }}-maboss-conda-${{ github.run_id }} | |
| - name: Install conda-build | |
| run: | | |
| conda update conda | |
| conda config --add channels conda-forge | |
| conda config --set channel_priority strict | |
| conda update conda --all | |
| conda install conda-build | |
| - name: Install package | |
| run: | | |
| conda index /usr/share/miniconda/conda-bld | |
| conda install --use-local -c colomoto maboss | |
| - name: Test package | |
| run: | | |
| pip install numpy | |
| export MABOSS=/usr/share/miniconda/bin/MaBoSS | |
| export MABOSS_128n=/usr/share/miniconda/bin/MaBoSS_128n | |
| export MABOSS_CLIENT=/usr/share/miniconda/bin/MaBoSS-client | |
| export MABOSS_SERVER=/usr/share/miniconda/bin/MaBoSS-server | |
| export MABOSS_SERVER_128n=/usr/share/miniconda/bin/MaBoSS_128n-server | |
| bash -c "cd engine/tests; bash ./test-cellcycle.sh" | |
| bash -c "cd engine/tests; bash ./test-ensemble.sh" | |
| bash -c "cd engine/tests; bash ./test-ewing.sh" | |
| bash -c "cd engine/tests; bash ./test-server.sh" | |
| bash -c "cd engine/tests; bash ./test-prngs.sh" | |
| bash -c "cd engine/tests; bash ./test-rngs.sh" | |
| bash -c "cd engine/tests; bash ./test-sbml.sh" | |
| maboss_conda_publish_defaults: | |
| name: Publish MaBoSS Anaconda package | |
| runs-on: ubuntu-22.04 | |
| needs: maboss_conda_test_defaults | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| - name: Restoring cached conda package | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/share/miniconda/conda-bld/linux-64/* | |
| key: ${{ runner.os }}-maboss-conda-defaults-${{ github.run_id }} | |
| - name: Install anaconda-client | |
| run: | | |
| conda update conda | |
| conda update --all | |
| conda install anaconda-client | |
| - name: Upload MaBoSS Ananconda package on vincent-noel | |
| run: | | |
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /usr/share/miniconda/conda-bld/linux-64/*.tar.bz2 --force; | |
| - name: Upload MaBoSS Ananconda package on colomoto | |
| if: github.repository == 'sysbio-curie/MaBoSS-env-2.0' && github.event_name == 'release' | |
| run: | | |
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /usr/share/miniconda/conda-bld/linux-64/*.tar.bz2 --force; | |
| maboss_conda_publish: | |
| name: Publish MaBoSS Anaconda package (conda-forge) | |
| runs-on: ubuntu-22.04 | |
| needs: maboss_conda_test | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| - name: Restoring cached conda package | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/share/miniconda/conda-bld/linux-64/* | |
| key: ${{ runner.os }}-maboss-conda-${{ github.run_id }} | |
| - name: Install anaconda-client | |
| run: | | |
| conda update conda | |
| conda config --add channels conda-forge | |
| conda config --set channel_priority strict | |
| conda update --all | |
| conda install anaconda-client | |
| - name: Upload MaBoSS Ananconda package on vincent-noel | |
| run: | | |
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /usr/share/miniconda/conda-bld/linux-64/*.tar.bz2 --force; | |
| - name: Upload MaBoSS Ananconda package on colomoto | |
| if: github.repository == 'sysbio-curie/MaBoSS-env-2.0' && github.event_name == 'release' | |
| run: | | |
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /usr/share/miniconda/conda-bld/linux-64/*.tar.bz2 --force; | |