bioinformatics-docker.yml

name: Bioinformatics Docker Build

permissions:
  contents: read
  packages: write

on:
  push:
    branches: [ docker ]
    paths:
      - 'docker/bioinformatics/**'
      - 'scripts/publish_docker_images.py'
      - '.github/workflows/bioinformatics-docker.yml'
  workflow_dispatch:
    inputs:
      publish_images:
        description: 'Publish images to Docker Hub'
        required: false
        default: 'false'
        type: boolean
      tools_to_build:
        description: 'Comma-separated list of tools to build (empty for all)'
        required: false
        default: ''
        type: string

env:
  DOCKER_HUB_USERNAME: tonic01
  DOCKER_HUB_REPO: deepcritical-bioinformatics
  DOCKER_TAG: ${{ github.sha }}

jobs:
  build-and-test-bioinformatics:
    name: Build and Test Bioinformatics Docker Images
    runs-on: ubuntu-latest

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

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3

      - name: Log in to Docker Hub
        if: github.event_name == 'push' || github.event.inputs.publish_images == 'true'
        uses: docker/login-action@v3
        with:
          username: ${{ secrets.DOCKER_HUB_USERNAME }}
          password: ${{ secrets.DOCKER_HUB_PASSWORD }}

      - name: Install Python for publishing script
        uses: actions/setup-python@v4
        with:
          python-version: '3.11'

      - name: Install publishing dependencies
        run: |
          pip install requests

      - name: Build bioinformatics Docker images
        run: |
          echo "🐳 Building bioinformatics Docker images..."
          make docker-build-bioinformatics

      - name: Test bioinformatics Docker images
        run: |
          echo "🧪 Testing bioinformatics Docker images..."
          make docker-test-bioinformatics

      - name: Run containerized bioinformatics tests
        run: |
          echo "🧬 Running containerized bioinformatics tests..."
          pip install uv
          uv sync --dev
          make test-bioinformatics-containerized

      - name: Publish bioinformatics Docker images
        if: (github.event_name == 'push' && github.ref == 'refs/heads/main') || github.event.inputs.publish_images == 'true'
        env:
          DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }}
          DOCKER_HUB_REPO: ${{ env.DOCKER_HUB_REPO }}
          DOCKER_TAG: ${{ env.DOCKER_TAG }}
        run: |
          echo "🚀 Publishing bioinformatics Docker images..."
          make docker-publish-bioinformatics

      - name: Generate build report
        if: always()
        run: |
          echo "## Bioinformatics Docker Build Report" > build_report.md
          echo "- **Status:** ${{ job.status }}" >> build_report.md
          echo "- **Branch:** ${{ github.ref }}" >> build_report.md
          echo "- **Commit:** ${{ github.sha }}" >> build_report.md
          echo "- **Published:** ${{ (github.event_name == 'push' && github.ref == 'refs/heads/main') || github.event.inputs.publish_images == 'true' }}" >> build_report.md
          echo "" >> build_report.md
          echo "### Build Details" >> build_report.md
          echo "- Docker Hub Repo: ${{ env.DOCKER_HUB_USERNAME }}/${{ env.DOCKER_HUB_REPO }}" >> build_report.md
          echo "- Tag: ${{ env.DOCKER_TAG }}" >> build_report.md

      - name: Upload build report
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: bioinformatics-docker-report
          path: build_report.md

  validate-bioinformatics-configs:
    name: Validate Bioinformatics Configurations
    runs-on: ubuntu-latest
    needs: build-and-test-bioinformatics

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

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: '3.11'

      - name: Install dependencies
        run: |
          pip install uv
          uv sync --dev

      - name: Validate bioinformatics server configurations
        run: |
          echo "🔍 Validating bioinformatics server configurations..."
          python -c "
          import yaml
          import os
          from pathlib import Path

          config_dir = Path('DeepResearch/src/tools/bioinformatics')
          valid_configs = 0
          invalid_configs = 0

          for config_file in config_dir.glob('*_server.py'):
              try:
                  # Basic syntax check by importing
                  module_name = config_file.stem
                  exec(f'from DeepResearch.src.tools.bioinformatics.{module_name} import *')
                  print(f'✅ {module_name}')
                  valid_configs += 1
              except Exception as e:
                  print(f'❌ {module_name}: {e}')
                  invalid_configs += 1

          print(f'\\n📊 Validation Summary:')
          print(f'✅ Valid configs: {valid_configs}')
          print(f'❌ Invalid configs: {invalid_configs}')

          if invalid_configs > 0:
              exit(1)
          "

      - name: Check Docker Hub images exist
        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
        run: |
          echo "🔍 Checking Docker Hub images exist..."
          python scripts/publish_docker_images.py --check-only || echo "⚠️  Some images may not be published yet"