maboss-macos.yml

name: MacOS

on:
  push:
  pull_request:
  release:
    types: [created]

jobs:
  maboss_macos:
    name: MaBoSS
    runs-on: macos-11
    env:
      GCC: gcc-11
      CXX: g++-11
      INSTALL_PATH: /usr/local
      BUILD_PATH: /tmp/
      LIBXML_LIBDIR: /usr/local/opt/libxml2/lib/libxml2.dylib
      LIBXML_INCLUDEDIR: /usr/local/opt/libxml2/include/libxml2/
      
    steps:
    - uses: actions/checkout@v4
    - name: Install dependencies
      run : |
        brew install flex bison gcc cmake
        pip install numpy
        pwd

    - name: Manually install libxml2 2.11
      run: |
        wget https://github.com/Homebrew/homebrew-core/raw/38ba35404e3cdb398694419850179e0023158887/Formula/lib/libxml2.rb
        brew install -s libxml2.rb
        
    - name: Cache compiled libSBML
      id: cache-libsbml-gcc
      uses: actions/cache@v4
      with:
        path: /tmp/libsbml-5.20.2
        key: ${{ runner.os }}-libSBML-5.20.2-g++11-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++-11 GCC=gcc-11 install SBML_COMPAT=1
        make CXX=g++-11 GCC=gcc-11 MAXNODES=128 install SBML_COMPAT=1
        
    - name: Test MaBoSS
      run: bash scripts/run_tests.sh
        
  maboss_llvm_macos:
    name: MaBoSS (clang)
    runs-on: macos-11
    env:
      GCC: 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/
    
    steps:
    - uses: actions/checkout@v4
    - name: Install dependencies
      run : |
        brew install flex bison cmake
        pip install numpy

    - name: Manually install libxml2 2.11
      run: |
        wget https://github.com/Homebrew/homebrew-core/raw/38ba35404e3cdb398694419850179e0023158887/Formula/lib/libxml2.rb
        brew install -s libxml2.rb
        
    - name: Cache compiled libSBML
      id: cache-libsbml-clang
      uses: actions/cache@v4
      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 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 64 bits binary
    runs-on: macos-11
    needs: [maboss_macos, maboss_llvm_macos]
    env:
      GCC: 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/

    steps:
    - uses: actions/checkout@v4
    - name: Install dependencies
      run : |
        brew install flex bison cmake gcc@11
      
    - name: Manually install libxml2 2.11
      run: |
        wget https://github.com/Homebrew/homebrew-core/raw/38ba35404e3cdb398694419850179e0023158887/Formula/lib/libxml2.rb
        brew install -s libxml2.rb
    
    - name: Cache compiled libSBML
      id: cache-libsbml-clang
      uses: actions/cache@v4
      with:
        path: /tmp/libsbml-5.20.2
        key: ${{ runner.os }}-libSBML-5.20.2-clang++-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 binary
      run: |
        rm -fr engine/pub/*
        cd engine/src
        make clean
        make install_static GCC=clang CXX=clang++ SBML_COMPAT=1
        make install_static GCC=clang CXX=clang++ MAXNODES=128 SBML_COMPAT=1
        make install_static GCC=clang CXX=clang++ MAXNODES=256 SBML_COMPAT=1
        make install_static GCC=clang CXX=clang++ MAXNODES=512 SBML_COMPAT=1
        make install_static GCC=clang CXX=clang++ MAXNODES=1024 SBML_COMPAT=1
        cd ../pub
        zip MaBoSS-osx64.zip *
    
    - 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_library_macos:
    name: Building MaBoSS osx library
    runs-on: macos-11
    needs: [maboss_macos, maboss_llvm_macos]

    steps:
    - uses: actions/checkout@v4
    - name: Install dependencies
      run : |
        brew install flex bison gcc@11
              
    - name: Build library
      run: |
        rm -fr engine/pub/*
        cd engine/src
        make clean
        make install_lib GCC=gcc-11 CXX=g++-11
        make install_lib MAXNODES=128 GCC=gcc-11 CXX=g++-11
        make install_lib MAXNODES=256 GCC=gcc-11 CXX=g++-11
        make install_lib MAXNODES=512 GCC=gcc-11 CXX=g++-11
        make install_lib MAXNODES=1024 GCC=gcc-11 CXX=g++-11
        make install_alib GCC=gcc-11 CXX=g++-11
        make install_alib MAXNODES=128 GCC=gcc-11 CXX=g++-11
        make install_alib MAXNODES=256 GCC=gcc-11 CXX=g++-11
        make install_alib MAXNODES=512 GCC=gcc-11 CXX=g++-11
        make install_alib MAXNODES=1024 GCC=gcc-11 CXX=g++-11
        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: flyci-macos-large-latest-m1
    needs: [maboss_macos, maboss_llvm_macos]

    steps:
    - uses: actions/checkout@v4
  
    - name: Downgrade XCODE to 14.3.1
      run: sudo xcode-select -switch /Applications/Xcode_14.3.1.app
  
    - name: Install dependencies
      run : |
        brew install flex bison gcc@13
              
    - name: Build library
      run: |
        rm -fr engine/pub/*
        cd engine/src
        make clean
        make install_lib GCC=gcc-13 CXX=g++-13
        make install_lib MAXNODES=128 GCC=gcc-13 CXX=g++-13
        make install_lib MAXNODES=256 GCC=gcc-13 CXX=g++-13
        make install_lib MAXNODES=512 GCC=gcc-13 CXX=g++-13
        make install_lib MAXNODES=1024 GCC=gcc-13 CXX=g++-13
        make install_alib GCC=gcc-13 CXX=g++-13
        make install_alib MAXNODES=128 GCC=gcc-13 CXX=g++-13
        make install_alib MAXNODES=256 GCC=gcc-13 CXX=g++-13
        make install_alib MAXNODES=512 GCC=gcc-13 CXX=g++-13
        make install_alib MAXNODES=1024 GCC=gcc-13 CXX=g++-13
        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-11
    needs: [maboss_macos, maboss_llvm_macos]
    env:  
      GCC: gcc-11
      CXX: g++-11
      INSTALL_PATH: /usr/local/
      BUILD_PATH: /tmp/
      LIBXML_LIBDIR: /usr/local/opt/libxml2/lib/libxml2.dylib
      LIBXML_INCLUDEDIR: /usr/local/opt/libxml2/include/libxml2

    steps:
    - uses: actions/checkout@v4
    - name: Install dependencies
      run : |
        brew install flex bison gcc@11 cmake
        
    - name: Manually install libxml2 2.11
      run: |
        wget https://github.com/Homebrew/homebrew-core/raw/38ba35404e3cdb398694419850179e0023158887/Formula/lib/libxml2.rb
        brew install -s libxml2.rb
      
    - name: Cache compiled libSBML
      id: cache-libsbml-gcc11
      uses: actions/cache@v4
      with:
        path: /tmp/libsbml-5.20.2
        key: ${{ runner.os }}-libSBML-5.20.2-g++11-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 GCC=gcc-11 CXX=g++-11
        make install_lib SBML_COMPAT=1 GCC=gcc-11 CXX=g++-11
        make install_lib SBML_COMPAT=1 GCC=gcc-11 MAXNODES=128 CXX=g++-11
        make install_lib SBML_COMPAT=1 GCC=gcc-11 MAXNODES=256 CXX=g++-11
        make install_lib SBML_COMPAT=1 GCC=gcc-11 MAXNODES=512 CXX=g++-11
        make install_lib SBML_COMPAT=1 GCC=gcc-11 MAXNODES=1024 CXX=g++-11
        make install_alib SBML_COMPAT=1 GCC=gcc-11 CXX=g++-11
        make install_alib SBML_COMPAT=1 GCC=gcc-11 MAXNODES=128 CXX=g++-11
        make install_alib SBML_COMPAT=1 GCC=gcc-11 MAXNODES=256 CXX=g++-11
        make install_alib SBML_COMPAT=1 GCC=gcc-11 MAXNODES=512 CXX=g++-11
        make install_alib SBML_COMPAT=1 GCC=gcc-11 MAXNODES=1024 CXX=g++-11
        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
    runs-on: macos-12
    needs: [maboss_macos, maboss_llvm_macos]

    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
        miniforge-variant: Mambaforge
        use-mamba: true
              
    - name: Installing conda-build      
      run: |
        conda install conda-build conda-verify
    
    - name: Installing MacOSX10.10 SDK
      run: |
        wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.10.sdk.tar.xz
        sudo tar xf MacOSX10.10.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/MacOSX10.10.sdk        # [osx]" >> ~/.conda/conda_build_config.yaml
        
    - name: Build MaBoSS Anaconda package
      run: |
        conda build -c colomoto conda/maboss
          
    - name: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /Users/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-maboss-conda-${{ github.run_id }}
        
  conda_maboss_conda_forge_macosx:
    name: Build Conda MaBoSS package (conda-forge)
    runs-on: macos-12
    needs: [maboss_macos, maboss_llvm_macos]

    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
        miniforge-variant: Mambaforge
        use-mamba: true
              
    - name: Installing conda-build      
      run: |
        conda install conda-build conda-verify
    
    - name: Installing MacOSX10.10 SDK
      run: |
        wget https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.10.sdk.tar.xz
        sudo tar xf MacOSX10.10.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/MacOSX10.10.sdk        # [osx]" >> ~/.conda/conda_build_config.yaml
    
    - name: Build MaBoSS Anaconda package
      run: |
        CUSTOM_BUILD_NUMBER=1 conda build -c colomoto conda/maboss
          
    - name: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /Users/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-maboss-conda-forge-${{ github.run_id }}
   
  maboss_conda_test_macosx:
    name: MaBoSS Anaconda package test
    runs-on: macos-12
    needs: conda_maboss_macosx
    
    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
        miniforge-variant: Mambaforge
        use-mamba: true
              
    - name: Install conda-build
      run: |
        conda install conda-build anaconda-client
      
    - name: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /Users/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-maboss-conda-${{ github.run_id }}
        
    - name: Install package
      run: |
        python -m conda_index /Users/runner/miniconda3/envs/test/conda-bld/
        conda install -c file:///Users/runner/miniconda3/envs/test/conda-bld/ -c colomoto maboss
      
    - name: Test package
      run: |
        pip install numpy
        export MABOSS=/Users/runner/miniconda3/envs/test/bin/MaBoSS
        export MABOSS_128n=/Users/runner/miniconda3/envs/test/bin/MaBoSS_128n
        export MABOSS_CLIENT=/Users/runner/miniconda3/envs/test/bin/MaBoSS-client
        export MABOSS_SERVER=/Users/runner/miniconda3/envs/test/bin/MaBoSS-server
        export MABOSS_SERVER_128n=/Users/runner/miniconda3/envs/test/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_conda_forge_macosx:
    name: MaBoSS Anaconda package test (conda-forge)
    runs-on: macos-12
    needs: conda_maboss_conda_forge_macosx
    
    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
        miniforge-variant: Mambaforge
        use-mamba: true
              
    - name: Install conda-build
      run: |
        conda install conda-build anaconda-client
      
    - name: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /Users/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-maboss-conda-forge-${{ github.run_id }}
        
    - name: Install package
      run: |
        python -m conda_index /Users/runner/miniconda3/envs/test/conda-bld/
        conda install -c file:///Users/runner/miniconda3/envs/test/conda-bld/ -c colomoto maboss
      
    - name: Test package
      run: |
        pip install numpy
        export MABOSS=/Users/runner/miniconda3/envs/test/bin/MaBoSS
        export MABOSS_128n=/Users/runner/miniconda3/envs/test/bin/MaBoSS_128n
        export MABOSS_CLIENT=/Users/runner/miniconda3/envs/test/bin/MaBoSS-client
        export MABOSS_SERVER=/Users/runner/miniconda3/envs/test/bin/MaBoSS-server
        export MABOSS_SERVER_128n=/Users/runner/miniconda3/envs/test/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_macosx:
    name: MaBoSS Anaconda package publication
    runs-on: macos-12
    needs: maboss_conda_test_macosx
    
    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
        miniforge-variant: Mambaforge
        use-mamba: true
              
    - name: Install conda-build
      run: |
        conda install conda-build anaconda-client
      
    - name: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /Users/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-maboss-conda-${{ github.run_id }}
        
    
    - 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-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 /Users/runner/miniconda3/envs/test/conda-bld/osx-64/*.tar.bz2 --force;
 
  maboss_conda_publish_conda_forge_macosx:
    name: MaBoSS Anaconda package publication (conda-forge)
    runs-on: macos-12
    needs: maboss_conda_test_conda_forge_macosx
    
    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
        miniforge-variant: Mambaforge
        use-mamba: true
              
    - name: Install conda-build
      run: |
        conda install conda-build anaconda-client
      
    - name: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /Users/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-maboss-conda-forge-${{ github.run_id }}
        
    
    - 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-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 /Users/runner/miniconda3/envs/test/conda-bld/osx-64/*.tar.bz2 --force;