testAllCI_step1.yml

name: cobratoolboxCI (merge, test, and upload)
on:
  pull_request:
    branches:
      - develop
      - master
    types: [opened, synchronize, reopened]
  workflow_dispatch:
permissions:
  contents: read
env:
  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
jobs:
  build:
    runs-on: self-hosted
    steps:
      - name: Cleanup orphaned MATLAB containers
        run: docker ps -q --filter ancestor=matlab | xargs -r docker rm -f
        continue-on-error: true

      - name: Check out merged PR code
        uses: actions/checkout@v6
        with:
          submodules: recursive
          fetch-depth: 0

      - name: Fix workspace ownership and permissions for Docker
        run: |
          sudo chown -R "$(id -u):$(id -g)" "${GITHUB_WORKSPACE}"
          chmod -R o+rwx "${GITHUB_WORKSPACE}"

      # MATLAB runs inside Docker
      - name: Run MATLAB Tests in Docker (licensed MAC, xvfb headless)
        env:
          QT_QPA_PLATFORM: offscreen
          JAVA_AWT_HEADLESS: "1"
        run: |
          set -euo pipefail
          # Confirm MATLAB image exists
          docker image inspect matlab >/dev/null
          docker run --rm \
            --mac-address="02:42:ac:11:00:02" \
            --platform linux/amd64 \
            -e HOME=/tmp \
            -e USER=matlab \
            -e LOGNAME=matlab \
            -e COBRA_CI=1 \
            -e QT_QPA_PLATFORM="${QT_QPA_PLATFORM}" \
            -e JAVA_AWT_HEADLESS="${JAVA_AWT_HEADLESS}" \
            -v "${GITHUB_WORKSPACE}:/work" \
            -w /work \
            --entrypoint bash \
            matlab \
            -lc '
              set -euo pipefail
              echo "Running inside container as:"
              id
              echo "HOME=$HOME"
              echo "USER=$USER"
              mkdir -p /tmp/.matlab /tmp/.MathWorks
              echo "Configuring git safe directory..."
              git config --global --add safe.directory /work
              git config --global --add safe.directory "*"
              echo "Starting MATLAB tests..."
              xvfb-run -a -s "-screen 0 1280x1024x24" \
                matlab -noFigureWindows -batch "try; \
                  run(\"initCobraToolbox.m\"); \
                  changeCobraSolver(\"gurobi\",\"all\",0); \
                  set(0,\"DefaultFigureVisible\",\"off\"); \
                  run(\"test/testAll.m\"); \
                catch ME; \
                  disp(getReport(ME,\"extended\")); \
                  exit(1); \
                end; \
                exit(0);"
            '

      - name: Fix workspace permissions after Docker run
        run: sudo chown -R "$(id -u):$(id -g)" "${GITHUB_WORKSPACE}"
        continue-on-error: true

      - name: Set up Node.js 20
        uses: actions/setup-node@v6
        with:
          node-version: '20'

      - name: Convert JUnit to CTRF
        run: |
          MAJOR="$(node -p "process.versions.node.split('.')[0]")"
          if [ "$MAJOR" -lt 20 ]; then
            echo "❌ Node.js version too old: $(node -v)"
            exit 1
          fi
          echo "✅ Node version: $(node -v)"
          echo "✅ npm version: $(npm -v)"
          mkdir -p ./ctrf
          echo "Converting JUnit XML to CTRF JSON..."
          npx --yes junit-to-ctrf@0.0.12 ./testReport.junit.xml -o ./ctrf/ctrf-report.json

      - name: Normalize CTRF Test Names
        run: |
          node -e '
            const fs = require("fs");
            const path = "./ctrf/ctrf-report.json";
            const report = JSON.parse(fs.readFileSync(path, "utf8"));
            for (const test of report.results?.tests || []) {
              if (typeof test.name === "string") {
                test.name = test.name.split(": ").pop();
              }
            }
            fs.writeFileSync(path, JSON.stringify(report, null, 2) + "\n");
          '

      - name: Upload CTRF Artifact
        uses: actions/upload-artifact@v6
        with:
          name: testReport
          path: ./ctrf/ctrf-report.json

      - name: Save PR Number
        run: echo "PR_NUMBER=${{ github.event.pull_request.number }}" >> $GITHUB_ENV

      - name: Upload PR Number as Artifact
        run: echo $PR_NUMBER > pr_number.txt

      - name: Upload PR Number Artifact
        uses: actions/upload-artifact@v6
        with:
          name: pr_number
          path: pr_number.txt