copasi_se.yml

name: Build and Test 

on: 
  workflow_dispatch:
    inputs:
      build_type:
        description: CMake build type
        type: choice
        required: true
        default: Release
        options:
          - Release
          - Debug
          - RelWithDebInfo
          - MinSizeRel
      run_valgrind:
        description: Run tests under Valgrind (Ubuntu only)
        type: boolean
        required: false
        default: false
  push:
    paths:
        - "**"
        - "!.github/**"
        - ".github/workflows/copasi_se.yml"

env:
  BUILD_TYPE: ${{ github.event.inputs.build_type || 'Release' }}

jobs:
  build:
    name:
      ${{ matrix.platform }}
    strategy:
      fail-fast: false
      matrix:
        platform: [ubuntu-latest, macos-latest, windows-latest]

    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@v1.6.0

    - name: Create Build Environment
      # Some projects don't allow in-source building, so create a separate build directory
      # We'll use this as our working directory for all subsequent commands
      shell: bash
      run: |
        cmake --version
        curl -L https://github.com/copasi/copasi-dependencies/releases/latest/download/${{ matrix.platform }}.zip -o ${{ matrix.platform }}.zip
        unzip -n -qq ${{ matrix.platform }}.zip -d dependencies

    - name: Patch dependencies (windows)
      shell: bash
      if: matrix.platform == 'windows-latest'
      working-directory: ${{github.workspace}}/dependencies/lib/cmake
      run: |
        sed -i 's|D:/a/copasi-dependencies/copasi-dependencies/install/|${_IMPORT_PREFIX}/|g'  *.cmake
        
    - name: Patch dependencies (ubuntu)
      shell: bash
      if: matrix.platform == 'ubuntu-latest'
      working-directory: ${{github.workspace}}/dependencies/lib/cmake
      run: |
        sed -i 's|/home/runner/work/copasi-dependencies/copasi-dependencies/install/|${_IMPORT_PREFIX}/|g'  *.cmake
        sudo apt update
        sudo apt install -y uuid-dev

    - name: Patch dependencies (mac)
      shell: bash
      if: matrix.platform == 'macos-latest'
      working-directory: ${{github.workspace}}/dependencies/lib/cmake
      run: |
        sed -i '.tmp' 's|/Users/runner/work/copasi-dependencies/copasi-dependencies/install/|${_IMPORT_PREFIX}/|g'  *.cmake
        rm lapack*
        rm ../libblas.a
        rm ../liblapack.a
        rm ../libf2c.a
        rm ../../include/clapack.h
        rm ../../include/lapack.h
        rm ../../include/blaswrap.h
        rm ../../include/f2c.h
        

    - name: Update COPASI Version
      shell: bash
      working-directory: ${{github.workspace}}
      run: ./gitTools/UpdateCopasiVersion

    - name: Download SBML Test Suite cases
      shell: bash
      working-directory: ${{github.workspace}}
      run: |
        curl -L https://copasi.org/static/test-suite.zip -o test-suite.zip
        unzip -n -qq test-suite.zip

    - name: Configure COPASI (mac)
      shell: bash
      if: matrix.platform == 'macos-latest'
      run: |
        cmake -G Ninja -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCOPASI_INSTALL_C_API=ON -DSBML_TESTSUITE_RUN=ON -DBUILD_TESTS=ON -DBUILD_GUI=OFF -DENABLE_JIT=OFF -DCOPASI_DEPENDENCY_DIR=./dependencies/ -DCMAKE_INSTALL_PREFIX=./install/  -DBUILD_SBML_TESTSUITE:BOOL=ON -DSBML_TESTSUITE_CASES_DIR:PATH=$PWD/test-suite -S .  -B ./build_copasi

    - name: Configure COPASI
      shell: bash
      if: matrix.platform != 'macos-latest'
      run: |
        cmake -G Ninja -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCOPASI_INSTALL_C_API=ON -DSBML_TESTSUITE_RUN=ON -DBUILD_TESTS=ON -DBUILD_GUI=OFF -DCOPASI_DEPENDENCY_DIR=./dependencies/ -DCMAKE_INSTALL_PREFIX=./install/  -DBUILD_SBML_TESTSUITE:BOOL=ON -DSBML_TESTSUITE_CASES_DIR:PATH=$PWD/test-suite -S .  -B ./build_copasi

    - name: Build COPASI
      shell: bash
      working-directory: ${{github.workspace}}/build_copasi
      run: cmake --build . --config $BUILD_TYPE

    - name: Install COPASI
      shell: bash
      working-directory: ${{github.workspace}}/build_copasi
      run: cmake --build . --config $BUILD_TYPE --target install

    - name: Run test_api under GDB and valgrind
      if: matrix.platform == 'ubuntu-latest'  && github.event.inputs.run_valgrind == 'true'
      working-directory: ${{github.workspace}}/build_copasi
      shell: bash
      run: |
        export srcdir="${{github.workspace}}/tests"
        TEST_API="$PWD/tests/test_api"
        sudo apt-get install -y gdb valgrind
        gdb -batch \
          -ex "set pagination off" \
          -ex run \
          -ex "thread apply all bt full" \
          -ex quit \
          -- "$TEST_API" || true

        valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --error-exitcode=1 --error-limit=no $TEST_API

    - name: Test
      working-directory: ${{github.workspace}}/build_copasi
      shell: bash
      run: ctest -C $BUILD_TYPE -V

    - name: binary archive
      uses: actions/upload-artifact@v4
      with:
        name:
          copasi-se-${{ matrix.platform }}
        path: ${{github.workspace}}/install/*
        retention-days: 10
        if-no-files-found: error