build-test.yml

name: Build and Test

on: push

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

env:
  NDIP_DOCKER_REPOSITORY: "${{ secrets.NDIP_DOCKER_REPOSITORY }}"
  READTHEDOCS_WEBHOOK_URL: "${{ secrets.READTHEDOCS_WEBHOOK_URL }}"
  READTHEDOCS_WEBHOOK_SECRET: "${{ secrets.READTHEDOCS_WEBHOOK_SECRET }}"
  GALAXY_URL: "${{ secrets.GALAXY_URL }}"
  GALAXY_KEY: "${{ secrets.GALAXY_KEY }}"

jobs:
  build-and-test:
    runs-on: ubuntu-latest
    timeout-minutes: 60
    env:
      GIT_STRATEGY: clone
      IMAGE_NAME: "${NDIP_DOCKER_REPOSITORY}/${{ github.repository }}"
    steps:
      - name: Set up QEMU
        uses: docker/setup-qemu-action@v3
      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3
      - name: Checkout repo
        uses: actions/checkout@v4
        with:
          fetch-depth: 20
          lfs: true
      - name: Build
        uses: docker/build-push-action@v6
        id: build
        with:
          file: dockerfiles/Dockerfile
          load: true
          target: source
      - name: Run ruff check
        run: docker run --rm ${{ steps.build.outputs.imageid }} ruff check
      - name: Run format check
        run: docker run --rm ${{ steps.build.outputs.imageid }} ruff format --check
      - name: Run mypy
        run: docker run --rm ${{ steps.build.outputs.imageid }} mypy .
      - name: Unit tests
        run: docker run -e NOVA_GALAXY_TEST_GALAXY_KEY=${{ env.GALAXY_KEY }} -e NOVA_GALAXY_TEST_GALAXY_URL=${{ env.GALAXY_URL }} --rm ${{ steps.build.outputs.imageid }} pytest
      - name: Run coverage
        run: docker run -e NOVA_GALAXY_TEST_GALAXY_KEY=${{ env.GALAXY_KEY }} -e NOVA_GALAXY_TEST_GALAXY_URL=${{ env.GALAXY_URL }} --rm ${{ steps.build.outputs.imageid }} sh -c "coverage run && coverage report"
      - name: Docs test
        run: docker run --rm ${{ steps.build.outputs.imageid }} bash build_docs.sh