cmaboss-ubuntu.yml

name: cMaBoSS Linux

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

jobs:
  cmaboss:
    name: cMaBoSS
    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@v4
    
    - name: Install dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -yq python3-pip python3-setuptools
        sudo pip3 install numpy pandas

    - 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-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 cMaBoSS
      run: |
        cd engine/src
        make
        cd ../python
        cp -r ../src cmaboss
        pip3 install .
        cd ../..
    
    - name: Test cMaBoSS
      run: bash scripts/run_cmaboss_tests.sh

  build_wheels_linux:
    name: Build linux wheels
    runs-on: ubuntu-22.04
    strategy:
      matrix:
        build: ["cp*-manylinux_x86_64", "pp*-manylinux_x86_64"]
    needs: cmaboss
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.10' 

      - name: Install cibuildwheel
        run: python -m pip install cibuildwheel numpy twine

      - name: Build wheels
        env: 
          CIBW_BUILD: ${{ matrix.build }}
          CIBW_BEFORE_ALL: >
            yum install wget libxml2-devel -y &&
            GCC=gcc CXX=g++ INSTALL_PATH=/usr/ BUILD_PATH=/tmp/ \
              LIBXML_LIBDIR=/usr/lib64/libxml2.so \
              LIBXML_INCLUDEDIR=/usr/include/libxml2 bash scripts/build_libsbml.sh &&
            BUILD_PATH=/tmp/ bash scripts/install_libsbml.sh
        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
        if: matrix.build == 'cp*-manylinux_x86_64'
        with:
          name: wheels-cpython
          path: wheelhouse/*.whl
          
      - uses: actions/upload-artifact@v4
        if: matrix.build == 'pp*-manylinux_x86_64'
        with:
          name: wheels-pypy
          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*
          
  cmaboss_conda_defaults:
    name: Build cMaBoSS Anaconda package
    runs-on: ubuntu-22.04

    needs: cmaboss

    strategy:
      matrix:
        version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
    
    defaults:
      run:
        shell: bash -el {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 conda-verify
      
    - name: Build cMaBoSS Anaconda package
      run: |
        conda build -c colomoto --variants "{\"python\": [\"${{ matrix.version.python }}\"], \"numpy\": [\"${{ matrix.version.numpy }}\"]}" conda/cmaboss;
        
    - name: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /home/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-cmaboss-conda-defaults-${{ github.run_id }}-${{ matrix.version.python }}
  
  cmaboss_conda:
    name: Build cMaBoSS Anaconda package (conda-forge)
    runs-on: ubuntu-22.04

    needs: cmaboss
    
    strategy:
      matrix:
        version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
    
    defaults:
      run:
        shell: bash -el {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 conda-verify
      
    - name: Build cMaBoSS Anaconda package
      run: |
        CUSTOM_BUILD_NUMBER=1 conda build -c conda-forge -c colomoto --variants "{\"python\": [\"${{ matrix.version.python }}\"], \"numpy\": [\"${{ matrix.version.numpy }}\"]}" conda/cmaboss;
        
    - name: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /home/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }}-${{ matrix.version.python }}
          
        
  cmaboss_conda_defaults_test:
    name: Test cMaBoSS Anaconda package
    runs-on: ubuntu-22.04

    needs: cmaboss_conda_defaults
    
    strategy:
      matrix:
        version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
    
    defaults:
      run:
        shell: bash -el {0}
                
    steps:
    - uses: actions/checkout@v4
    - uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        channels: defaults
        python-version: ${{ matrix.version.python }}
        miniforge-variant: Mambaforge
        use-mamba: true
    
    - name: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /home/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-cmaboss-conda-defaults-${{ github.run_id }}-${{ matrix.version.python }}
        
    - name: Install conda-build
      run: |
        conda install conda-build conda-index
     
    - name: Install package
      run: |
        python -m conda_index /home/runner/miniconda3/envs/test/conda-bld/
        conda install -c file:///home/runner/miniconda3/envs/test/conda-bld/ -c colomoto cmaboss
        
    - name: Install test dependencies
      run: |
        pip install pandas
        
    - name: Test package
      run: |
        cd engine/tests
        python -m unittest test
        python -m unittest test_128n
  
  cmaboss_conda_test:
    name: Test cMaBoSS Anaconda package (conda-forge)
    runs-on: ubuntu-22.04

    needs: cmaboss_conda
    
    strategy:
      matrix:
        version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
       
    defaults:
      run:
        shell: bash -el {0}
    
    steps:
    - uses: actions/checkout@v4
    - uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        channels: conda-forge
        python-version: ${{ matrix.version.python }}
        miniforge-variant: Mambaforge
        use-mamba: true
    
    - name: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /home/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }}-${{ matrix.version.python }}
        
    - name: Install conda-build
      run: |
        conda install conda-build conda-index
     
    - name: Install package
      run: |
        python -m conda_index /home/runner/miniconda3/envs/test/conda-bld/
        conda install -c file:///home/runner/miniconda3/envs/test/conda-bld/ -c colomoto cmaboss
        
    - name: Install test dependencies
      run: |
        pip install pandas
                
    - name: Test package
      run: |
        cd engine/tests
        python -m unittest test
        python -m unittest test_128n
        
  cmaboss_conda_publish_defaults:
    name: Publish cMaBoSS Anaconda package
    runs-on: ubuntu-22.04

    needs: cmaboss_conda_defaults_test
    
    strategy:
      matrix:
        version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
       
    defaults:
      run:
        shell: bash -el {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: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /home/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-cmaboss-conda-defaults-${{ github.run_id }}-${{ matrix.version.python }}
              
    - name: Install anaconda-client
      run: |
        conda install anaconda-client
     
    - name: Upload cMaBoSS Ananconda package on vincent-noel
      run: |
        anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;

    - name: Upload cMaBoSS Ananconda package on colomoto
      if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release'
      run: |
        anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;
        
  cmaboss_conda_publish:
    name: Publish cMaBoSS Anaconda package (conda-forge)
    runs-on: ubuntu-22.04

    needs: cmaboss_conda_test
    
    strategy:
      matrix:
        version: [{python: "3.8", numpy: "1.22"}, {python: "3.9", numpy: "1.22"}, {python: "3.10", numpy: "1.22"}, {python: "3.11", numpy: "1.23"}, {python: "3.12", numpy: "1.26"}]
       
    defaults:
      run:
        shell: bash -el {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: Caching produced conda package
      uses: actions/cache@v4
      with:
        path: |
          /home/runner/miniconda3/envs/test/conda-bld/*
        key: ${{ runner.os }}-cmaboss-conda-${{ github.run_id }}-${{ matrix.version.python }}
              
    - name: Install anaconda-client
      run: |
        conda install anaconda-client
     
    - name: Upload cMaBoSS Ananconda package on vincent-noel
      run: |
        anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;

    - name: Upload cMaBoSS Ananconda package on colomoto
      if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release'
      run: |
        anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;