store-artefact.yml

name: Nightly build (binaries)

on:
  workflow_dispatch:
  schedule:
    - cron: "0 5 * * *"

env:
  BUILD_TYPE: Release

jobs:
  build:
    if: github.repository_owner == 'sbmlteam'
    name:
      ${{ matrix.platform }}, Parser option ${{ matrix.xml_parser_option }},
      with namespaces ${{ matrix.with_namespace}}, strict includes ${{
      matrix.strict }}, with examples ${{ matrix.with_examples}}, package option
      ${{ matrix.package_option}}
    strategy:
      fail-fast: false
      matrix:
        platform: [windows-latest, macos-latest, ubuntu-latest]
        xml_parser_option: ["-DWITH_EXPAT=ON"]
        with_namespace: ["True"]
        strict: ["True"]
        with_examples: ["True"]
        package_option: ["-DWITH_ALL_PACKAGES=ON", "-DWITH_STABLE_PACKAGES=ON"]
        language_bindings:
          [
            "-DWITH_JAVA=True -DWITH_PYTHON=True -DWITH_R=OFF",
          ]
    runs-on: ${{ matrix.platform }}

    steps:
      - uses: actions/checkout@v4
      - uses: seanmiddleditch/gha-setup-ninja@master

      - name: Add msbuild to PATH (Windows)
        if: matrix.platform == 'windows-latest'
        uses: ilammy/msvc-dev-cmd@v1

      ### configure the operating system ###
      - name: Cache Windows dependencies and SWIG
        # On Windows, the dependencies live inside the source folder, ie `.`.
        # For the CI, we put SWIG there too, for simplicity.
        if: matrix.platform == 'windows-latest'
        id: cache-win-dependencies-static
        uses: actions/cache@v4
        with:
          path: |
            ./dependencies
            ./swig
          key: ${{ runner.os }}-dependencies-static-2

      - name: Download pre-built Windows dependencies and SWIG
        # Windows dependencies have to be in a subfolder called `dependencies`, directly under the git repository root.
        # also gets SWIG, completing the set of dependencies needed for windows
        if:
          matrix.platform == 'windows-latest' &&
          steps.cache-win-dependencies-static.outputs.cache-hit != 'true'
        shell: bash
        run: |
          curl -L https://github.com/sbmlteam/libSBML-dependencies/releases/download/latest/libSBML-dependencies-1.0.1-x64-Release-static.zip > dependencies.zip
          unzip dependencies.zip
          mv libSBML-dependencies-1.0.1-x64-Release-static dependencies
          curl -L https://prdownloads.sourceforge.net/swig/swigwin-3.0.12.zip > swig.zip
          unzip -o swig.zip -d swig

      - name: setup Windows environment
        # this is separate from the SWIG download itself, because it needs to be added to the path also when SWIG is cached
        if: matrix.platform == 'windows-latest'
        shell: bash
        run: |
          echo $GITHUB_WORKSPACE"/swig/swigwin-3.0.12/" >> $GITHUB_PATH
          echo RUNTIME_LINKING_OPTION="-DWITH_STATIC_RUNTIME=ON" >> "${GITHUB_ENV}"
          echo CSHARP_OPTION="-DWITH_CSHARP=True" >> "${GITHUB_ENV}"
          ./dev/utilities/expdef/expdef64.exe -dRlib.def -l R.dll
          echo R_PLATFORM_SPECIFIC_OPTIONS="-DR_LIB=${GITHUB_WORKSPACE}\Rlib.lib" >> "${GITHUB_ENV}"

      - name: Find Windows R include path
        # robust to R version changing
        if: matrix.platform == 'windows-latest'
        shell: bash
        run: |
            cd /c/Program\ Files/R/
            R_INCLUDE_DIR_VERSION=$(ls -d *)
            echo R_INCLUDE_PATH="/c/Program Files/R/"$R_INCLUDE_DIR_VERSION"/include" >> "${GITHUB_ENV}"

      - name: Install Ubuntu dependencies
        # ubuntu already has SWIG but expat is too old
        if: matrix.platform == 'ubuntu-latest'
        shell: bash
        run: |
          sudo apt-get update
          sudo apt-get install -y check ccache
          echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
          echo CSHARP_OPTION="-DWITH_CSHARP=True" >> "${GITHUB_ENV}"
          git clone https://github.com/libexpat/libexpat
          cmake -G Ninja -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=./dependencies -B libexpat -S libexpat/expat 
          cmake --build libexpat
          cmake --install libexpat


      - name: Install MacOS dependencies
        # MacOS already has expat by default
        if: matrix.platform == 'macos-latest'
        shell: bash
        run: |
          brew install check swig ccache
          echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
          echo CSHARP_OPTION="-DWITH_CSHARP=OFF" >> "${GITHUB_ENV}"

      - name: Unix R options
        if: matrix.platform != 'windows-latest'
        shell: bash
        run:
          echo R_PLATFORM_SPECIFIC_OPTIONS="-DWITH_CREATE_R_SOURCE=ON
          -DWITH_SKIP_R_BINARY=ON" >> "${GITHUB_ENV}"

      ### setup ccache, not on Windows ###
      - name: Prepare ccache timestamp
        if: matrix.platform != 'windows-latest'
        id: ccache_cache_timestamp
        shell: cmake -P {0}
        run: |
          string(TIMESTAMP current_date "%Y-%m-%d-%H;%M;%S" UTC)
          message("::set-output name=timestamp::${current_date}")
      - name: Set ccache cache directory
        if: matrix.platform != 'windows-latest'
        shell: bash
        run: |
          echo "CCACHE_DIR=${{runner.workspace}}/.ccache" >> "${GITHUB_ENV}"
          echo "COMPILER_LAUNCHER=ccache" >> "${GITHUB_ENV}"
      - name: cache ccache files
        if: matrix.platform != 'windows-latest'
        uses: actions/cache@v4
        with:
          path: ${{runner.workspace}}/.ccache
          key:
            ${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp}}
          restore-keys: |
            ${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp }}
            ${{ runner.os }}-

      ### build the project ###
      - name: Create Build Environment
        run: cmake -E make_directory ${{runner.workspace}}/build

      - name: Configure CMake for XML_parser (expat)
        shell: bash
        working-directory: ${{runner.workspace}}/build
        run: |
          mkdir ../install
          cmake $GITHUB_WORKSPACE \
          -G "Ninja" \
          -DCMAKE_INSTALL_PREFIX=../install \
          -DCMAKE_BUILD_TYPE=$BUILD_TYPE \
          -DCMAKE_C_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \
          -DCMAKE_CXX_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \
          -DCMAKE_CXX_STANDARD=98 \
          -DWITH_CHECK=True \
          -DWITH_CPP_NAMESPACE=${{matrix.with_namespace}} \
          -DLIBSBML_USE_STRICT_INCLUDES=${{matrix.strict}} \
          -DWITH_EXAMPLES=${{matrix.with_examples}} \
          -DWITH_LIBXML=OFF \
          ${{matrix.xml_parser_option}} \
          ${{matrix.package_option}} \
          ${{matrix.language_bindings}} \
          ${R_PLATFORM_SPECIFIC_OPTIONS} \
          -DR_INCLUDE_DIRS="$R_INCLUDE_PATH" \
          ${RUNTIME_LINKING_OPTION} \
          ${PYTHON_LINKING_OPTION} \
          ${CSHARP_OPTION}

      - name: Build
        working-directory: ${{runner.workspace}}/build
        shell: bash
        run: |
          cmake --build . --config $BUILD_TYPE

      # - name: Build Unix R binaries from source package
        # if: matrix.platform != 'windows-latest'
        # shell: bash
        # working-directory: ${{runner.workspace}}/build
        # run: |
          # mkdir r-binaries
          # R CMD INSTALL -l r-binaries --build ./src/bindings/r/out/libSBML_5.19.3.tar.gz

      ### run tests ###
      - name: Test
        working-directory: ${{runner.workspace}}/build
        shell: bash
        run: ctest -C $BUILD_TYPE

      ### create binaries ###
      - name: Install
        working-directory: ${{runner.workspace}}/build
        shell: bash
        run: cmake --install . --config $BUILD_TYPE

      - name: Remove large .lib file on Windows
        ### file temporarily needed for bindings ###
        if: matrix.platform == 'windows-latest'
        working-directory: ${{runner.workspace}}/install
        shell: bash
        run: rm lib/libsbml-static.lib

      ### setup artifact environment ###
      - name: Store libSBML version in environment
        shell: bash
        run: echo "LIBSBML_VERSION=$( cat VERSION.txt)"  >> "${GITHUB_ENV}"

      - name: Set artifact name suffix to stable packages
        if: matrix.package_option=='-DWITH_STABLE_PACKAGES=ON'
        shell: bash
        run: |
          echo "ARTIFACT_NAME_SUFFIX=stable-packages" >> "${GITHUB_ENV}"

      - name: Set artifact name suffix to all packages
        if: matrix.package_option=='-DWITH_ALL_PACKAGES=ON'
        shell: bash
        run: |
          echo "ARTIFACT_NAME_SUFFIX=all-packages" >> "${GITHUB_ENV}"

      ### Upload installed versions ###
      - name: Upload Windows binary archive
        if: matrix.platform == 'windows-latest'
        uses: actions/upload-artifact@v4
        with:
          name:
            Windows (zip, libSBML ${{env.LIBSBML_VERSION}},
            ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
          path: ${{runner.workspace}}/install/*
          retention-days: 1
          if-no-files-found: error

      - name: Upload MacOS binary archive
        if: matrix.platform == 'macos-latest'
        uses: actions/upload-artifact@v4
        with:
          name:
            MacOS (zip, libSBML ${{env.LIBSBML_VERSION}},
            ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
          path: |
            ${{runner.workspace}}/install/*
            ${{runner.workspace}}/build/r-binaries/*
          retention-days: 1
          if-no-files-found: error

      - name: Upload Ubuntu binary archive
        if: matrix.platform == 'ubuntu-latest'
        uses: actions/upload-artifact@v4
        with:
          name:
            Ubuntu nightly (zip, libSBML ${{env.LIBSBML_VERSION}},
            ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
          path: |
            ${{runner.workspace}}/install/*
          retention-days: 1
          if-no-files-found: error
  manylinuxbuild:
    if: github.repository_owner == 'sbmlteam'
    name:
      ${{ matrix.container }}, Parser option ${{ matrix.xml_parser_option }},
      with namespaces ${{ matrix.with_namespace}}, strict includes ${{
      matrix.strict }}, with examples ${{ matrix.with_examples}}, package option
      ${{ matrix.package_option}}
    strategy:
      fail-fast: false
      matrix:
        platform: [ubuntu-latest]
        xml_parser_option: ["-DWITH_EXPAT=ON"]
        with_namespace: ["True"]
        strict: ["True"]
        with_examples: ["True"]
        package_option: ["-DWITH_ALL_PACKAGES=ON", "-DWITH_STABLE_PACKAGES=ON"]
        cpp_standard: [98]
        language_bindings:
          ["-DWITH_JAVA=True -DWITH_PYTHON=True"]
        container: ["quay.io/pypa/manylinux_2_28_x86_64"]
    runs-on: ${{ matrix.platform }}
    container: ${{ matrix.container}}

    steps:
      - uses: actions/checkout@v4
      - name: install Swig 4 from source
        run: |
          yum install -y pcre-devel
          echo "SWIG_DIR=/usr/local/swig/" >> "${GITHUB_ENV}"
          curl -L https://sourceforge.net/projects/swig/files/swig/swig-4.0.2/swig-4.0.2.tar.gz/download > swig.tar.gz
          tar -zxvf swig.tar.gz
          cd swig-4.0.2/
          ./configure --disable-dependency-tracking --prefix=$SWIG_DIR
          make clean
          make -j 2
          make install
          swig -version

      - name: install CMake using pip
        run: |
          /opt/python/cp38-cp38/bin/pip install cmake
          ln -s /opt/python/cp38-cp38/bin/cmake /usr/bin/cmake
          ln -s /opt/python/cp38-cp38/bin/ctest /usr/bin/ctest
          cmake --version
          ctest --version

      - name: Install dependencies, configure, build
        run: |
          yum install -y libxml2-devel check-devel java-devel
          git clone https://github.com/libexpat/libexpat
          cmake -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=./dependencies -B libexpat -S libexpat/expat 
          cmake --build libexpat
          cmake --install libexpat
          cd ..
          mkdir build
          cd build
          mkdir ../install
          cmake ../libsbml \
          -DCMAKE_INSTALL_PREFIX=../install \
          -DCMAKE_BUILD_TYPE=$BUILD_TYPE \
          -DCMAKE_CXX_STANDARD=${{matrix.cpp_standard}} \
          -DWITH_CHECK=True \
          -DWITH_CPP_NAMESPACE=${{matrix.with_namespace}} \
          -DLIBSBML_USE_STRICT_INCLUDES=${{matrix.strict}} \
          -DWITH_EXAMPLES=${{matrix.with_examples}} \
          -DWITH_LIBXML=OFF \
          ${{matrix.xml_parser_option}} \
          ${{matrix.package_option}} \
          ${{matrix.language_bindings}} \
          -DPYTHON_EXECUTABLE=/opt/python/cp38-cp38/bin/python \
          -DPYTHON_INCLUDE_DIR=/opt/python/cp38-cp38/include/python3.8/ \
          -DWITH_STATIC_RUNTIME=ON \
          -DPYTHON_USE_DYNAMIC_LOOKUP=ON
          cmake --build . --config $BUILD_TYPE

      - name: Test
        run: |
          cd ../build
          ctest -V -C $BUILD_TYPE

      ### create binaries ###
      - name: Install
        run: |
          cd ../build
          cmake --install . --config $BUILD_TYPE

      ### setup artifact environment ###
      - name: Store libSBML version in environment
        run: |
          echo  "LIBSBML_VERSION=$( cat VERSION.txt)"  >> "${GITHUB_ENV}"

      - name: Set artifact name suffix to stable packages
        if: matrix.package_option=='-DWITH_STABLE_PACKAGES=ON'
        run: |
          echo "ARTIFACT_NAME_SUFFIX=stable-packages" >> "${GITHUB_ENV}"

      - name: Set artifact name suffix to all packages
        if: matrix.package_option=='-DWITH_ALL_PACKAGES=ON'
        run: |
          echo "ARTIFACT_NAME_SUFFIX=all-packages" >> "${GITHUB_ENV}"

      - name: Upload Manylinux binary archive
        uses: actions/upload-artifact@v4
        with:
          name:
            Manylinux nightly (zip, libSBML ${{env.LIBSBML_VERSION}},
            ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }}
          path: ../install