testall.yml

name: MATLAB Tests and Coverage
on:
  pull_request:
    branches:
      - '**'

jobs:  # jobs
  build:
    runs-on: self-hosted
    steps:
    - uses: actions/checkout@v2

    - name: Clone COBRA Toolbox
      run: |
        git clone https://github.com/opencobra/cobratoolbox.git cobratoolbox

    - name: Run MATLAB tests and generate coverage
      run: |
        matlab -batch "run('cobratoolbox/initCobraToolbox.m'); diary('test_results.txt'); \
        coverageFile = fullfile('coverage', 'coverage.xml'); \
        mkdir('coverage'); \
        run('cobratoolbox/test/runTestAndGenerateReport.m'); \
        coverageResults = matlab.unittest.TestSuite.fromFile('cobratoolbox/test/testall_ghActions.m'); \
        results = run(coverageResults); \
        xmlwrite(coverageFile, results.generateCoverageReport('cobertura')); \
        diary off;"

    - name: Upload Test Report
      uses: actions/upload-artifact@v4
      with:
        name: test-report
        path: test_results.txt

    - name: Upload Coverage Report to Codecov
      uses: codecov/codecov-action@v3
      with:
        file: ./coverage/coverage.xml
        flags: unittests
        token: ${{ secrets.CODECOV_TOKEN }} # Add your Codecov token to the repo secrets