ci-linux.yml

name: CI - Linux

on:
  workflow_call:
    inputs:
      hdf4_version:
        description: 'HDF4 version to use (default: hdf.version in pom.xml)'
        type: string
        required: false
        default: ''
      hdf5_version:
        description: 'HDF5 version to use (default: hdf5.version in pom.xml)'
        type: string
        required: false
        default: ''
  workflow_dispatch:
    inputs:
      hdf4_version:
        description: 'HDF4 version to use (default: hdf.version in pom.xml)'
        type: string
        required: false
        default: ''
      hdf5_version:
        description: 'HDF5 version to use (default: hdf5.version in pom.xml)'
        type: string
        required: false
        default: ''

permissions:
  contents: read
  checks: write
  pull-requests: write

env:
  # JVM configuration for CI performance
  # Note: java.awt.headless NOT set to true - SWT GUI tests need display (Xvfb)
  MAVEN_OPTS: >-
    -Xmx2g
    -Xms1g
    -XX:+UseParallelGC
    -XX:+TieredCompilation
    -XX:TieredStopAtLevel=1

jobs:
  build-and-test:
    name: Build and Test (Linux)
    runs-on: ubuntu-latest
    timeout-minutes: 40

    strategy:
      fail-fast: false

    steps:
    - name: Checkout Code
      uses: actions/checkout@v4
      with:
        fetch-depth: 0  # Full history for better analysis

    - name: Resolve HDF library versions
      uses: ./.github/actions/resolve-hdf-versions
      with:
        hdf4_version: ${{ inputs.hdf4_version }}
        hdf5_version: ${{ inputs.hdf5_version }}

    - name: Set up JDK 21
      uses: actions/setup-java@v4
      with:
        java-version: '21'
        distribution: 'temurin'

    - name: Cache Maven Dependencies
      uses: actions/cache@v4
      with:
        path: |
          ~/.m2/repository
          !~/.m2/repository/org/hdfgroup
        key: ${{ runner.os }}-maven-${{ hashFiles('pom.xml', 'object/pom.xml', 'hdfview/pom.xml', 'repository/pom.xml') }}
        restore-keys: |
          ${{ runner.os }}-maven-

    - name: Cache HDF Libraries
      id: cache-hdf
      uses: actions/cache@v4
      with:
        path: |
          ${{ github.workspace }}/hdf4
          ${{ github.workspace }}/hdf5
        key: ${{ runner.os }}-hdf-github-${{ github.run_id }}
        restore-keys: |
          ${{ runner.os }}-hdf-github-

    - name: Download and Install HDF4 from GitHub
      if: steps.cache-hdf.outputs.cache-hit != 'true'
      run: |
        HDF4_VERSION="${{ env.HDF4_VERSION }}"
        echo "Downloading HDF4 ${HDF4_VERSION} release..."

        PATTERN="hdf${HDF4_VERSION}-ubuntu-2404_gcc.tar.gz"
        echo "Using pattern $PATTERN"
        gh release download hdf${HDF4_VERSION} \
          --repo HDFGroup/hdf4 \
          --pattern "$PATTERN" \
          --clobber

        echo "After gh download"
        ls

        # Extract outer tar.gz (creates hdf4/ directory)
        tar -zxvf *-ubuntu-2404_gcc.tar.gz
        [ -d hdf4 ] || mv hdf4-* hdf4

        # Extract inner tar.gz into hdf4/ directory
        cd "${{ github.workspace }}/hdf4"
        echo "Before extracting inner tar.gz"
        ls
        tar -zxvf HDF-${HDF4_VERSION}-Linux.tar.gz --strip-components 1

        # Set HDF4 library path
        HDF4LIB_PATH=${{ github.workspace }}/hdf4/HDF_Group/HDF/${HDF4_VERSION}
        echo "HDF4LIB_PATH=$HDF4LIB_PATH" >> $GITHUB_ENV

        echo "HDF4 installed to: $HDF4LIB_PATH"
        ls -la "$HDF4LIB_PATH"
      env:
        GH_TOKEN: ${{ github.token }}

    - name: Download and Install HDF5 from GitHub
      if: steps.cache-hdf.outputs.cache-hit != 'true'
      run: |
        HDF5_VERSION="${{ env.HDF5_VERSION }}"
        echo "Downloading HDF5 ${HDF5_VERSION} release..."

        PATTERN="hdf5-${HDF5_VERSION}-ubuntu-2404_gcc.tar.gz"
        gh release download ${HDF5_VERSION} \
          --repo HDFGroup/hdf5 \
          --pattern "$PATTERN" \
          --clobber

        # Extract outer tar.gz (creates hdf5/ directory)
        tar -zxvf $PATTERN
        [ -d hdf5 ] || mv hdf5-* hdf5

        # Extract inner tar.gz into hdf5/ directory
        cd "${{ github.workspace }}/hdf5"
        tar -zxvf HDF5-${HDF5_VERSION}-Linux.tar.gz --strip-components 1

        # Set HDF5 library path
        HDF5LIB_PATH=${{ github.workspace }}/hdf5/HDF_Group/HDF5/${HDF5_VERSION}
        echo "HDF5LIB_PATH=$HDF5LIB_PATH" >> $GITHUB_ENV

        echo "HDF5 installed to: $HDF5LIB_PATH"
        ls -la "$HDF5LIB_PATH"
      env:
        GH_TOKEN: ${{ github.token }}

    - name: Set Environment Variables from Cache
      if: steps.cache-hdf.outputs.cache-hit == 'true'
      run: |
        HDF4_VERSION="${{ env.HDF4_VERSION }}"
        HDF5_VERSION="${{ env.HDF5_VERSION }}"

        HDF4LIB_PATH=${{ github.workspace }}/hdf4/HDF_Group/HDF/${HDF4_VERSION}
        echo "HDF4LIB_PATH=$HDF4LIB_PATH" >> $GITHUB_ENV

        HDF5LIB_PATH=${{ github.workspace }}/hdf5/HDF_Group/HDF5/${HDF5_VERSION}
        echo "HDF5LIB_PATH=$HDF5LIB_PATH" >> $GITHUB_ENV

        echo "Using cached HDF libraries:"
        echo "HDF4: $HDF4LIB_PATH"
        echo "HDF5: $HDF5LIB_PATH"

    - name: Install HDF JARs to Local Maven Repository
      run: |
        echo "Installing HDF JARs to local Maven repository..."

        # Copy HDF JARs from downloaded distributions
        mkdir -p repository/lib
        cp ${{ env.HDF4LIB_PATH }}/lib/*.jar repository/lib/ 2>/dev/null || echo "No HDF4 JARs found"
        cp ${{ env.HDF5LIB_PATH }}/lib/*.jar repository/lib/ 2>/dev/null || echo "No HDF5 JARs found"

        # List what we have
        echo "JARs in repository/lib:"
        ls -la repository/lib/*.jar 2>/dev/null || echo "No JARs found"

        # Install jarhdf5
        HDF5_VERSION="${{ env.HDF5_VERSION }}"
        if [ -f repository/lib/jarhdf5-*.jar ]; then
          JAR_FILE=$(ls repository/lib/jarhdf5-*.jar | head -1)
          mvn install:install-file -Dfile="$JAR_FILE" \
            -DgroupId=jarhdf5 -DartifactId=jarhdf5 -Dversion=${HDF5_VERSION} \
            -Dpackaging=jar -DgeneratePom=true
          echo "Installed: $JAR_FILE"
        fi

        # Install jarhdf (HDF4)
        HDF4_VERSION="${{ env.HDF4_VERSION }}"
        if [ -f repository/lib/jarhdf-*.jar ]; then
          JAR_FILE=$(ls repository/lib/jarhdf-*.jar | head -1)
          mvn install:install-file -Dfile="$JAR_FILE" \
            -DgroupId=jarhdf -DartifactId=jarhdf -Dversion=${HDF4_VERSION} \
            -Dpackaging=jar -DgeneratePom=true
          echo "Installed: $JAR_FILE"
        fi

        # Install fits.jar
        if [ -f repository/lib/fits.jar ]; then
          mvn install:install-file -Dfile=repository/lib/fits.jar \
            -DgroupId=fits -DartifactId=fits -Dversion=1.0.0 \
            -Dpackaging=jar -DgeneratePom=true
          echo "Installed: fits.jar"
        fi

        # Install netcdf.jar
        if [ -f repository/lib/netcdf.jar ]; then
          mvn install:install-file -Dfile=repository/lib/netcdf.jar \
            -DgroupId=netcdf -DartifactId=netcdf -Dversion=1.0.0 \
            -Dpackaging=jar -DgeneratePom=true
          echo "Installed: netcdf.jar"
        fi

        # Install slf4j-api if present
        if [ -f repository/lib/slf4j-api-*.jar ]; then
          JAR_FILE=$(ls repository/lib/slf4j-api-*.jar | head -1)
          VERSION=$(echo "$JAR_FILE" | grep -oP 'slf4j-api-\K[0-9.]+')
          mvn install:install-file -Dfile="$JAR_FILE" \
            -DgroupId=org.slf4j -DartifactId=slf4j-api -Dversion="$VERSION" \
            -Dpackaging=jar -DgeneratePom=true
          echo "Installed: $JAR_FILE"
        fi

        # Install SWTBot JARs for UI testing
        if [ -f repository/lib/org.eclipse.swtbot.swt.finder.jar ]; then
          mvn install:install-file -Dfile=repository/lib/org.eclipse.swtbot.swt.finder.jar \
            -DgroupId=org.eclipse.local -DartifactId=org.eclipse.swtbot.swt.finder -Dversion=4.2.1 \
            -Dpackaging=jar -DgeneratePom=true
          echo "Installed: org.eclipse.swtbot.swt.finder.jar"
        fi

        if [ -f repository/lib/org.eclipse.swtbot.nebula.nattable.finder.jar ]; then
          mvn install:install-file -Dfile=repository/lib/org.eclipse.swtbot.nebula.nattable.finder.jar \
            -DgroupId=org.eclipse.local -DartifactId=org.eclipse.swtbot.nebula.nattable.finder -Dversion=4.2.1 \
            -Dpackaging=jar -DgeneratePom=true
          echo "Installed: org.eclipse.swtbot.nebula.nattable.finder.jar"
        fi

    - name: Set up build.properties
      run: |
        cat > build.properties << EOF
        # CI Build Properties for HDFView
        # Generated automatically for GitHub Actions
        # Using HDF libraries from GitHub releases

        # HDF5 Configuration
        hdf5.lib.dir=${{ env.HDF5LIB_PATH }}/lib
        hdf5.plugin.dir=${{ env.HDF5LIB_PATH }}/lib/plugin

        # HDF4 Configuration
        hdf.lib.dir=${{ env.HDF4LIB_PATH }}/lib

        # Platform Configuration
        # Both library directories. This value becomes -Djava.library.path for the test
        # forks, which replaces the JVM's default.
        platform.hdf.lib=${{ env.HDF5LIB_PATH }}/lib:${{ env.HDF4LIB_PATH }}/lib

        # CI-specific settings
        ci.build=true
        skip.native.tests=false
        EOF

        echo "Generated build.properties for CI:"
        cat build.properties

        # Set LD_LIBRARY_PATH for test execution
        echo "LD_LIBRARY_PATH=${{ env.HDF5LIB_PATH }}/lib:${{ env.HDF4LIB_PATH }}/lib" >> $GITHUB_ENV

    - name: Validate Maven Configuration
      run: |
        mvn help:effective-pom -q > effective-pom.log
        echo "Maven configuration validated"
        echo "Active profiles:"
        mvn help:active-profiles

    - name: Maven Compile
      run: |
        echo "::group::Maven Compile"
        mvn clean compile -B \
          -Dmaven.compiler.showDeprecation=false \
          -Dmaven.compiler.showWarnings=false
        echo "::endgroup::"

    - name: Set up Xvfb for Headless GUI Testing
      run: |
        echo "Installing Xvfb, GTK and a window manager for headless SWT testing..."
        sudo apt-get update
        # metacity: SWTBot resolves widgets against Display.getActiveShell(), and on a bare X
        # server with no window manager nothing ever becomes active, so every lookup that waits
        # on shell activation would time out. x11-utils supplies xdpyinfo and xprop for the
        # readiness checks below.
        sudo apt-get install -y xvfb libgtk-3-0 libgtk-3-dev x11-xserver-utils x11-utils metacity
        echo "Xvfb, GTK and metacity installed successfully"

    - name: Run Tests
      run: |
        echo "::group::Run All Tests"
        # Install parent POM first (required for child module resolution)
        mvn install -B -N -Ddependency-check.skip=true

        # Compile repository module (sets up dependencies but don't install)
        mvn compile -B -pl repository -Ddependency-check.skip=true

        # Install object and hdfview modules (needed for testing)
        # Skip repository install (tries to install files that don't exist in CI)
        mvn install -B -pl object,hdfview -DskipTests -Ddependency-check.skip=true

        # Object module tests. These are blocking - they have passed on all three
        # OSes for a long time and a regression here is a real failure.
        mvn test -B -pl object -Dmaven.test.failure.ignore=false
        echo "::endgroup::"

    - name: Package Application
      run: |
        echo "::group::Package Application"
        mvn package -DskipTests -B
        echo "::endgroup::"

    - name: Verify Build Artifacts
      run: |
        echo "Build artifacts created:"
        find . -name "*.jar" -type f | head -10

        echo "Library artifacts:"
        ls -la libs/ || echo "No libs directory found"

        echo "Target artifacts:"
        find target -name "*.jar" -type f 2>/dev/null | head -5 || echo "No target JARs found"

    - name: Run UI Tests
      # TBD: This step will not be able to fail the job until
      # the underlying bugs that CI is detecting are fixed.
      # Once that is done, remove continue-on-error.
      continue-on-error: true
      timeout-minutes: 30
      run: |
        echo "::group::Run UI Tests (SWTBot under Xvfb)"
        # Started by hand rather than through xvfb-run because the window manager has to join
        # the same display, which xvfb-run's single-command wrapper does not allow.
        Xvfb :99 -screen 0 1280x1024x24 -nolisten tcp &
        export DISPLAY=:99

        for i in $(seq 1 30); do
          xdpyinfo -display :99 >/dev/null 2>&1 && break
          sleep 1
        done
        xdpyinfo -display :99 >/dev/null 2>&1 || { echo "Xvfb never accepted connections"; exit 1; }
        echo "Xvfb is up on :99"

        # Without a window manager no shell ever becomes active, and the waits on shell
        # activation in closeFile() and openDataObject() time out and fail the test.
        # Start metacity and wait for it to own the display before running the tests.
        metacity --sm-disable --display=:99 &
        for i in $(seq 1 20); do
          xprop -display :99 -root _NET_SUPPORTING_WM_CHECK 2>/dev/null | grep -q "window id" && break
          sleep 1
        done
        if xprop -display :99 -root _NET_SUPPORTING_WM_CHECK 2>/dev/null | grep -q "window id"; then
          echo "metacity is managing :99"
        else
          echo "WARNING: no window manager on :99 - shell activation waits will time out"
        fi

        mvn test -B -pl hdfview
        echo "::endgroup::"

    - name: UI Test Summary
      if: always()
      continue-on-error: true
      run: |
        # Surface the counts in the job log even when the step above was cut short, so a
        # run is never just a red X with no numbers attached.
        python3 - <<'EOF' >> $GITHUB_STEP_SUMMARY
        import glob, os, xml.etree.ElementTree as ET
        files = glob.glob("hdfview/target/surefire-reports/*.xml")
        print("## UI tests\n")
        if not files:
            print("No surefire XML was written - the suite did not get far enough to report.")
        else:
            tot = fail = err = skip = 0
            rows = []
            bad = []
            for f in sorted(files):
                # A fork killed by a timeout can leave a half-written XML behind. Report that
                # file as unreadable rather than letting ParseError abort the whole summary
                # halfway through the table, which looks like the suite simply stopped.
                try:
                    r = ET.parse(f).getroot()
                except Exception as exc:
                    bad.append((os.path.basename(f), type(exc).__name__))
                    continue
                t = int(r.get("tests", 0)); fl = int(r.get("failures", 0))
                e = int(r.get("errors", 0)); s = int(r.get("skipped", 0))
                tot += t; fail += fl; err += e; skip += s
                rows.append((r.get("name", f), t, fl, e, s))
            print(f"**{tot} tests, {fail} failures, {err} errors, {skip} skipped** "
                  f"across {len(rows)} classes\n")
            print("| Class | Tests | Failures | Errors | Skipped |")
            print("| --- | --- | --- | --- | --- |")
            for n, t, fl, e, s in rows:
                print(f"| {n} | {t} | {fl} | {e} | {s} |")
            for n, why in bad:
                print(f"| {n} | unreadable ({why}) | | | |")
        EOF
        cat $GITHUB_STEP_SUMMARY

    # Scoped to the object module on purpose. This action publishes a check run, and a check
    # is not covered by the step's continue-on-error - so globbing '**' would put the
    # UI failures into a failing check on every PR. The UI tier reports through the
    # summary step above and the uploaded surefire artifacts below.
    - name: Test Report
      uses: dorny/test-reporter@v1
      if: success() || failure()
      continue-on-error: true
      with:
        name: Maven Test Results (Linux)
        path: 'object/target/surefire-reports/*.xml'
        reporter: java-junit
        fail-on-error: false

    - name: Upload Test Results
      uses: actions/upload-artifact@v4
      if: always()
      with:
        name: test-results-linux-${{ github.run_number }}
        path: |
          **/target/surefire-reports/
          **/target/failsafe-reports/
        retention-days: 30

    - name: Upload Build Artifacts
      uses: actions/upload-artifact@v4
      if: success()
      with:
        name: build-artifacts-linux-${{ github.run_number }}
        path: |
          libs/*.jar
          target/*.jar
          hdfview/target/*.jar
          object/target/*.jar
        retention-days: 7

    - name: Create jpackage App Image
      run: |
        echo "::group::Create jpackage App Image"
        echo "Creating distributable application package with jpackage..."

        # Create app-image
        # -pl object,hdfview: Build object and hdfview modules (skip repository - causes install-file errors)
        # -Dmaven.test.skip=true: Skip test compilation and execution
        # -Djacoco.skip=true: Skip JaCoCo (code coverage already done in test step)
        # -Dpmd.skip=true: Skip PMD (static analysis already done in maven-quality.yml workflow)
        # Skip dependency-check (already runs in maven-security.yml workflow)
        mvn verify -Pjpackage-app-image -pl object,hdfview -Dmaven.test.skip=true -Djacoco.skip=true -Dpmd.skip=true -Ddependency-check.skip=true -B

        echo "Verifying jpackage output..."
        if [ -d hdfview/target/dist/HDFView ]; then
          echo "✓ jpackage app-image created successfully"
          echo "Package size: $(du -sh hdfview/target/dist/HDFView | cut -f1)"
          echo "Native libraries: $(find hdfview/target/dist/HDFView/lib/app -name "*.so" | wc -l) .so files"
          echo "JAR files: $(find hdfview/target/dist/HDFView/lib/app -name "*.jar" | wc -l) JARs"
          echo "HDF5 plugins: $(ls -1 hdfview/target/dist/HDFView/lib/app/plugin/*.so 2>/dev/null | wc -l) plugins"
        else
          echo "✗ jpackage app-image creation failed"
          exit 1
        fi
        echo "::endgroup::"

    - name: Upload jpackage App Image
      uses: actions/upload-artifact@v4
      if: success()
      with:
        name: hdfview-app-image-linux-${{ github.run_number }}
        path: hdfview/target/dist/HDFView/
        retention-days: 7

    - name: Build Summary
      if: always()
      run: |
        echo "## Build Summary (Linux)" >> $GITHUB_STEP_SUMMARY
        echo "- **Status**: ${{ job.status }}" >> $GITHUB_STEP_SUMMARY
        echo "- **Java Version**: $(java -version 2>&1 | head -n1)" >> $GITHUB_STEP_SUMMARY
        echo "- **Maven Version**: $(mvn --version | head -n1)" >> $GITHUB_STEP_SUMMARY
        echo "- **Build Time**: $(date)" >> $GITHUB_STEP_SUMMARY

        if [ -f target/surefire-reports/TEST-*.xml ]; then
          echo "- **Test Results**: Available in artifacts" >> $GITHUB_STEP_SUMMARY
        fi

        echo "" >> $GITHUB_STEP_SUMMARY
        echo "### Artifacts Generated" >> $GITHUB_STEP_SUMMARY
        find . -name "*.jar" -newer build.properties 2>/dev/null | \
          head -5 | sed 's/^/- /' >> $GITHUB_STEP_SUMMARY || \
          echo "- No JAR artifacts found" >> $GITHUB_STEP_SUMMARY

        # Add jpackage summary
        if [ -d hdfview/target/dist/HDFView ]; then
          echo "" >> $GITHUB_STEP_SUMMARY
          echo "### jpackage App Image" >> $GITHUB_STEP_SUMMARY
          echo "- **Size**: $(du -sh hdfview/target/dist/HDFView 2>/dev/null | cut -f1)" >> $GITHUB_STEP_SUMMARY
          echo "- **Native Libraries**: $(find hdfview/target/dist/HDFView/lib/app -name "*.so" 2>/dev/null | wc -l) .so files" >> $GITHUB_STEP_SUMMARY
          echo "- **JAR Files**: $(find hdfview/target/dist/HDFView/lib/app -name "*.jar" 2>/dev/null | wc -l) JARs" >> $GITHUB_STEP_SUMMARY
          echo "- **HDF5 Plugins**: $(ls -1 hdfview/target/dist/HDFView/lib/app/plugin/*.so 2>/dev/null | wc -l) compression plugins" >> $GITHUB_STEP_SUMMARY
        fi