test-build.yml

name: Test Build

on:
  workflow_dispatch:  # Manual trigger
  pull_request:
  push:
    branches:
      - master

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  test-build:
    name: Test build on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-22.04, windows-latest, macos-latest]
      fail-fast: false  # Continue testing other platforms even if one fails

    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.11'

      - name: Install system dependencies (Linux)
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update
          sudo apt-get install -y build-essential

      - name: Install Python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e .

      - name: Build executable (Linux)
        if: runner.os == 'Linux'
        run: bash scripts/build/build_linux.sh

      - name: Build executable (Windows)
        if: runner.os == 'Windows'
        run: scripts/build/build_windows.bat

      - name: Build executable (macOS)
        if: runner.os == 'macOS'
        run: bash scripts/build/build_macos.sh

      # Create installers
      - name: Create Linux packages (DEB/RPM)
        if: runner.os == 'Linux'
        run: bash scripts/build/create_linux_packages.sh

      - name: Create Windows installer
        if: runner.os == 'Windows'
        run: pwsh scripts/build/create_windows_installer.ps1

      - name: Create macOS DMG
        if: runner.os == 'macOS'
        run: bash scripts/build/create_macos_dmg.sh

      # Test the built executable
      - name: Test basic commands (Linux/macOS)
        if: runner.os != 'Windows'
        run: |
          echo "Testing --help and --version..."
          dist/pyprophet --help
          dist/pyprophet --version

      - name: Test basic commands (Windows)
        if: runner.os == 'Windows'
        run: |
          echo "Testing --help and --version..."
          dist\pyprophet.exe --help
          dist\pyprophet.exe --version

      - name: Test score commands (Linux/macOS)
        if: runner.os != 'Windows'
        run: |
          echo "Testing score at ms1ms2 level..."
          dist/pyprophet score --in tests/data/test_data.osw --level ms1ms2 --pi0_lambda 0 0 0
          
          echo "Testing score at transition level..."
          dist/pyprophet score --in tests/data/test_data.osw --level transition --pi0_lambda 0 0 0

      - name: Test score commands (Windows)
        if: runner.os == 'Windows'
        run: |
          echo "Testing score at ms1ms2 level..."
          dist\pyprophet.exe score --in tests/data/test_data.osw --level ms1ms2 --pi0_lambda 0 0 0
          
          echo "Testing score at transition level..."
          dist\pyprophet.exe score --in tests/data/test_data.osw --level transition --pi0_lambda 0 0 0

      - name: Test infer commands (Linux/macOS)
        if: runner.os != 'Windows'
        run: |
          echo "Testing infer peptide..."
          dist/pyprophet infer peptide --in tests/data/test_data.osw --context global
          
          echo "Testing infer peptidoform..."
          dist/pyprophet infer peptidoform --in tests/data/test_data.osw --no-ipf_ms1_scoring

      - name: Test infer commands (Windows)
        if: runner.os == 'Windows'
        run: |
          echo "Testing infer peptide..."
          dist\pyprophet.exe infer peptide --in tests/data/test_data.osw --context global
          
          echo "Testing infer peptidoform..."
          dist\pyprophet.exe infer peptidoform --in tests/data/test_data.osw --no-ipf_ms1_scoring

      - name: Test export commands (Linux/macOS)
        if: runner.os != 'Windows'
        run: |
          echo "Testing export score-report..."
          dist/pyprophet export score-report --in tests/data/test_data.osw
          
          echo "Testing export tsv..."
          dist/pyprophet export tsv --in tests/data/test_data.osw --out test_data.tsv
          
          # Verify output file was created
          if [ ! -f test_data.tsv ]; then
            echo "ERROR: test_data.tsv was not created!"
            exit 1
          fi
          echo "Output file created successfully: test_data.tsv"

      - name: Test export commands (Windows)
        if: runner.os == 'Windows'
        run: |
          echo "Testing export score-report..."
          dist\pyprophet.exe export score-report --in tests/data/test_data.osw
          
          echo "Testing export tsv..."
          dist\pyprophet.exe export tsv --in tests/data/test_data.osw --out test_data.tsv
          
          # Verify output file was created
          if (-not (Test-Path test_data.tsv)) {
            Write-Error "ERROR: test_data.tsv was not created!"
            exit 1
          }
          Write-Output "Output file created successfully: test_data.tsv"
        shell: pwsh

      # Test DEB package installation
      - name: Test DEB package installation
        if: runner.os == 'Linux'
        run: |
          echo "============================================"
          echo "Testing DEB Package Installation"
          echo "============================================"
          
          DEB_FILE=$(ls pyprophet_*.deb)
          echo "Installing: $DEB_FILE"
          
          # Install the package
          sudo dpkg -i "$DEB_FILE" || {
            echo "Installation failed, attempting to fix dependencies..."
            sudo apt-get install -f -y
          }
          
          # Verify installation
          if ! command -v pyprophet &> /dev/null; then
            echo "ERROR: pyprophet command not found after DEB installation!"
            exit 1
          fi
          
          # Test installed package
          echo "Testing installed pyprophet..."
          pyprophet --version
          pyprophet --help
          
          # Test with actual data
          pyprophet score --in tests/data/test_data.osw --level ms1ms2 --pi0_lambda 0 0 0
          
          # Clean up
          echo "Uninstalling package..."
          sudo dpkg -r pyprophet
          
          echo "✅ DEB package test passed!"

      # Test Windows installer
      - name: Test Windows installer
        if: runner.os == 'Windows'
        run: |
          Write-Host "============================================"
          Write-Host "Testing Windows Installer"
          Write-Host "============================================"
          
          $installerFile = Get-ChildItem pyprophet-setup-*.exe | Select-Object -First 1
          
          if (-not $installerFile) {
            Write-Error "No installer file found!"
            exit 1
          }
          
          Write-Host "Installer: $($installerFile.Name)"
          
          # Install silently
          Write-Host "Installing silently..."
          Start-Process -FilePath $installerFile.FullName -ArgumentList "/VERYSILENT", "/SUPPRESSMSGBOXES", "/NORESTART", "/DIR=$env:TEMP\PyProphet" -Wait
          
          # Verify installation
          $installPath = "$env:TEMP\PyProphet\pyprophet.exe"
          if (-not (Test-Path $installPath)) {
            Write-Error "pyprophet.exe not found at expected location: $installPath"
            exit 1
          }
          
          # Test installed executable
          Write-Host "Testing installed pyprophet..."
          & $installPath --version
          & $installPath --help
          
          # Test with actual data
          & $installPath score --in tests/data/test_data.osw --level ms1ms2 --pi0_lambda 0 0 0
          
          # Clean up - uninstall silently
          Write-Host "Uninstalling..."
          $uninstallPath = "$env:TEMP\PyProphet\unins000.exe"
          if (Test-Path $uninstallPath) {
            Start-Process -FilePath $uninstallPath -ArgumentList "/VERYSILENT", "/SUPPRESSMSGBOXES", "/NORESTART" -Wait
          }
          
          Write-Host "✅ Windows installer test passed!"
        shell: pwsh

      # Test macOS DMG
      - name: Test macOS DMG
        if: runner.os == 'macOS'
        run: |
          echo "============================================"
          echo "Testing macOS DMG"
          echo "============================================"
          
          DMG_FILE=$(ls pyprophet-*.dmg)
          echo "DMG file: $DMG_FILE"
          
          # Mount the DMG
          echo "Mounting DMG..."
          hdiutil attach "$DMG_FILE" -mountpoint /Volumes/PyProphet
          
          # Verify PyProphet directory exists
          if [ ! -d "/Volumes/PyProphet/PyProphet" ]; then
            echo "ERROR: PyProphet directory not found in DMG!"
            hdiutil detach /Volumes/PyProphet || true
            exit 1
          fi
          
          # Verify executable exists
          if [ ! -f "/Volumes/PyProphet/PyProphet/pyprophet" ]; then
            echo "ERROR: pyprophet executable not found!"
            ls -la /Volumes/PyProphet/PyProphet/
            hdiutil detach /Volumes/PyProphet || true
            exit 1
          fi
          
          # Test directly from mounted DMG
          echo "Testing pyprophet from DMG..."
          /Volumes/PyProphet/PyProphet/pyprophet --version
          /Volumes/PyProphet/PyProphet/pyprophet --help
          
          # Test with actual data
          echo "Running score test..."
          /Volumes/PyProphet/PyProphet/pyprophet score --in tests/data/test_data.osw --level ms1ms2 --pi0_lambda 0 0 0
          
          # Copy to temporary location (simulating installation)
          echo "Testing installation by copying to /tmp..."
          TEMP_DIR="/tmp/PyProphet-test"
          rm -rf "$TEMP_DIR"
          cp -r /Volumes/PyProphet/PyProphet "$TEMP_DIR"
          
          # Unmount DMG
          echo "Unmounting DMG..."
          hdiutil detach /Volumes/PyProphet
          
          # Test from copied location
          echo "Testing from installed location..."
          "$TEMP_DIR/pyprophet" --version
          "$TEMP_DIR/pyprophet" --help
          "$TEMP_DIR/pyprophet" score --in tests/data/test_data.osw --level ms1ms2 --pi0_lambda 0 0 0
          
          # Clean up
          echo "Cleaning up..."
          rm -rf "$TEMP_DIR"
          
          echo "✅ macOS DMG test passed!"

      - name: Upload test outputs as artifacts
        if: always()  # Upload even if tests fail
        uses: actions/upload-artifact@v4
        with:
          name: test-outputs-${{ matrix.os }}
          path: |
            test_data.tsv
            tests/data/test_data.osw
          if-no-files-found: ignore
          retention-days: 3

      - name: Summary
        if: success()
        run: |
          echo "✅ All tests passed on ${{ matrix.os }}!"
          echo "  - Executable tests: PASSED"
          echo "  - Installer tests: PASSED"