codecov.yml

name: MATLAB Tests and Code Coverage

on:
  pull_request:
    branches:
      - '**'

jobs:
  build:
    runs-on: self-hosted
    steps:

      - name: Checkout PR Code
        uses: actions/checkout@v4

      - name: Merge PR with Develop
        run: |
          git fetch origin develop
          git checkout -b test-branch
          git merge origin/develop --no-edit

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

      - name: Run MATLAB Tests
        run: |
          matlab -batch "run('cobratoolbox/initCobraToolbox.m'); diary('test_results.txt'); run('cobratoolbox/testAll.m'); diary off;"

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

      - name: Upload Coverage to Codecov
        if: always()  # Ensure it runs even if tests fail
        uses: codecov/codecov-action@v3
        with:
          files: CodeCovTestResults.xml
          token: ${{ secrets.CODECOV_TOKEN }}
          fail_ci_if_error: true
          flags: matlab
          comment: true

      - name: Upload Test Results to Codecov
        if: always()
        uses: codecov/test-results-action@v1
        with:
          token: ${{ secrets.CODECOV_TOKEN }}