build-warp-tools.yml

name: Warp Tools CI

# Controls when the workflow will run
on:
  # Triggers the workflow on push or pull request events but only for the "develop" and "master" branch
  # Uncomment this block and add your branch name to test without creating a PR
  #push:
    #branches: [ "kp_github_actions_pd-2113" ] 
    #paths-ignore:
    #  - '**/README.md'
  pull_request:
    branches: [ "develop", "master" ]
    paths:
      - 'tools/**'
  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:
    inputs:
      image_tag:
        description: 'Docker Image Tag (default: branch_name)' 

env:
  PROJECT_NAME: WARP Tools
  # Github repo name
  REPOSITORY_NAME: ${{ github.event.repository.name }}
  # Region-specific Google Docker repository where GOOGLE_PROJECT/REPOSITORY_NAME can be found
  GOOGLE_CONTAINER_REGISTRY: us.gcr.io
  GCR_PATH: broad-gotc-prod/warp-tools
  ACR_PATH: warp-tools
  TAG: ${{ github.event.inputs.image_tag || github.head_ref || github.ref_name }}


# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
  # The job that builds our container
  build-for-gcr:
    # The type of runner that the job will run on
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: tools
    # Map a step output to a job output
    outputs:
      imagePath: ${{ steps.saveImagePath.outputs.url }}
    steps:
    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
    - uses: actions/checkout@v3
    - name: Build the Docker image for GCR
      run: docker build . --file Dockerfile --tag ${GOOGLE_CONTAINER_REGISTRY}/${GCR_PATH}:${TAG}
    - name: Check working directory'
      run: |
        echo "Current directory: "
        pwd
        ls -lht
    # Save the image path to an output
    - id: 'saveImagePath'
      run: echo "url=${GOOGLE_CONTAINER_REGISTRY}/${GCR_PATH}:${TAG}" >> $GITHUB_OUTPUT
    # Log into the Google Container registry
    - id: 'Auth'
      name: Login to GCR
      uses: docker/login-action@v2
      with:
        registry: ${{ env.GOOGLE_CONTAINER_REGISTRY }}
        username: _json_key
        password: ${{ secrets.GCR_CI_KEY }}
    # Push the image to the Google Container registry
    - name: Push image
      run: "docker push ${GOOGLE_CONTAINER_REGISTRY}/${GCR_PATH}:${TAG}"

  #Runs pytest on all python code in warp-tools/tools
  test-python:
    needs: build-for-gcr
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: tools
    strategy:
      matrix:
        python-version: ["3.9", "3.10"]

    steps:
      - uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install ruff pytest
          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
      - name: Lint with ruff
        run: |
          # default set of ruff rules with GitHub Annotations
          ruff --format=github --target-version=py37 .
        continue-on-error: true
      - name: Test with pytest
        run: |
          pytest

  test-c:
    runs-on: ubuntu-latest
    needs: build-for-gcr
    container:
      image: ${{needs.build-for-gcr.outputs.imagePath}}
      # volumes:
      #   - my_docker_volume:/volume_mount
      # options: --cpus 1
      options: "--entrypoint /bin/bash"
    steps:
      - name: Check for dockerenv file
        run: |
          (ls /.dockerenv && echo Found dockerenv && cat /.dockerenv) || (echo No dockerenv)
      - name: Check directory
        run: |
          apt-get install tree
          whoami
          pwd
          ls -lhta
          tree /warptools
      # if test is at the end of the file name in the the test dir -- it gets picked up
      - name: Test TagSort
        run: |
          cd /warptools/TagSort
          pwd
          ls -lhta
          ./fetch_gtest.sh && make test
          cd /warptools/TagSort/bin
          ls -lht
          for f in *test; do ./"$f"; done;
      - name: Test FastqPreprocessing
        run: |
          cd /warptools/fastqpreprocessing
          pwd
          ls -lhta
          ./fetch_gtest.sh && make test
          cd /warptools/fastqpreprocessing/bin
          ls -lht
          for f in *test; do ./"$f"; done;

  build-for-acr:
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: tools
    steps:
    # checkout the repo
    - name: 'Checkout GitHub Action'
      uses: actions/checkout@v3
      
    - name: 'Login via Azure CLI'
      uses: azure/login@v1
      with:
        creds: ${{ secrets.AZURE_CREDENTIALS }}
    
    - name: 'Build and push image'
      uses: azure/docker-login@v1
      with:
        login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
        username: ${{ secrets.REGISTRY_USERNAME }}
        password: ${{ secrets.REGISTRY_PASSWORD }}
    - run: |
        docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
        docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}