test-and-deploy.yml

name: Test and deploy
on: [ push, pull_request ]

env:
  # Version required to run itwêwina:
  ACTIONS_PYTHON_VERSION: '3.10'
  # Version required to run npm build:
  ACTIONS_NODE_VERSION: 22

jobs:
  # Originally, it skipped deploy if [skip deploy] is present in the commit message.
  # There is currently a github-provided implementation of this behaviour and the
  # original repo is unmaintained.  Thus the new behaviour is that actions won't trigger
  # when using [skip ci].  See
  # https://github.blog/changelog/2021-02-08-github-actions-skip-pull-request-and-push-workflows-with-skip-ci/
  should-deploy:
    runs-on: ubuntu-latest

    outputs:
      should-run: ${{github.repository_owner == 'UAlbertaALTLab' && github.ref == 'refs/heads/main' }}

    steps:
      - run: true

  should-update-dev:
    runs-on: ubuntu-latest

    outputs:
      should-run: ${{ github.repository_owner == 'UAlbertaALTLab' && github.ref == 'refs/heads/dev' }}

    steps:
      - run: true

  # Run Pytest unit tests
  unit-test:
    runs-on: ubuntu-22.04

    steps:
      - uses: actions/checkout@v4
      - name: 🐍 Set up Python ${{ env.ACTIONS_PYTHON_VERSION }}
        uses: actions/setup-python@v5
        # actions/cache below uses this id to get the exact python version
        id: setup-python
        with:
          python-version: ${{ env.ACTIONS_PYTHON_VERSION }}
      - name: 🖥 Install system dependencies
        run: sudo apt-get install -y libfoma0
      - name: ☤ Install pipenv
        run: python3 -m pip install pipenv==2021.11.9

      # This started out life as a copy-paste from
      # https://github.com/actions/cache/blob/main/examples.md#python---pipenv
      - uses: actions/cache@v4
        with:
          path: ~/.local/share/virtualenvs
          key: ${{ runner.os }}-python-${{ steps.setup-python.outputs.python-version }}-pipenv-${{ hashFiles('Pipfile.lock') }}
      - name: 📥 Install dependencies
        run: |
          pipenv install --dev
          # Install pytest plugin to show failed tests on the web
          pipenv run pip install pytest-github-actions-annotate-failures
      - name: Do LFS checkout
        # actions/checkout@v2 has a `with: lfs: true` option, but it only
        # knows how to talk to GitHub’s LFS server.
        #
        # These actions are automatic if you have run `git lfs install`
        # even once on your dev machine.
        run: git lfs install --local && git lfs fetch && git lfs checkout
      - name: 🧶 Run linters/static-analysis
        run: |
          pipenv run mypy src
      - name: 🩺 Run unit tests
        env:
          DEBUG: "True"
        run: pipenv run test -v --cov=src --cov-report=xml
      - name: Check working directory clean
        run: ./libexec/check-git-status
      - name: Check that generated files are up-to-date
        # A few auto-generated files are checked in for convenience; ensure
        # that they are up-to-date.
        if: github.ref != 'refs/heads/dev'
        run: "pipenv run docker/helper.py make-yaml
        && if ! ./libexec/check-git-status ; then
            echo Error: running make-yaml resulted in changed files. When
              changing template files, please ensure that updated generated
              files get checked in too. 1>&2 ;
            exit 1 ;
        fi"
      - name: 📤 Upload Codecov coverage report
        uses: codecov/codecov-action@v4
        with:
          token: ${{ secrets.CODECOV_TOKEN }}

  # Runs Cypress acceptance tests
  integration-test:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
      - name: 🐍 Set up Python ${{ env.ACTIONS_PYTHON_VERSION }}
        uses: actions/setup-python@v5
        id: setup-python
        with:
          python-version: ${{ env.ACTIONS_PYTHON_VERSION }}
      - name: Setup Node ${{ env.ACTIONS_NODE_VERSION }}
        uses: actions/setup-node@v4
        with:
          node-version: ${{ env.ACTIONS_NODE_VERSION }}
          cache: npm
      - name: 🖥 Install system dependencies
        run: sudo apt-get install -y libfoma0 libgtk2.0-0 libgtk-3-0 libgbm-dev libnotify-dev libgconf-2-4 libnss3 libxss1 libasound2 libxtst6 xauth xvfb
      - name: ☤ Install pipenv
        run: python3 -m pip install pipenv==2021.11.9

      # This started out life as a copy-paste from
      # https://github.com/actions/cache/blob/main/examples.md#python---pipenv
      - uses: actions/cache@v4
        with:
          path: ~/.local/share/virtualenvs
          key: ${{ runner.os }}-python-${{ steps.setup-python.outputs.python-version }}-pipenv-${{ hashFiles('Pipfile.lock') }}
      - name: 📥 Install Python dependencies
        run: |
          pipenv install --dev
      - name: Do LFS checkout
        # actions/checkout@v2 has a `with: lfs: true` option, but it only
        # knows how to talk to GitHub’s LFS server.
        #
        # These actions are automatic if you have run `git lfs install`
        # even once on your dev machine.
        run: git lfs install --local && git lfs fetch && git lfs checkout
      - name: 📥 Install Node dependencies
        run: npm ci
      - name: 🛑 Halt tests if Cypress tests are marked as '.only'
        run: npm run stop-only
      - name: 🏗 Build frontend
        run: npm run build
      - name: 🌲 Run Cypress tests
        env:
          DEBUG: "True"
          # NOTE: only set on the upstream repo, i.e., UAlbertaALTLab/morphodict
          CYPRESS_RECORD_KEY: "${{ secrets.CYPRESS_RECORD_KEY }}"
        run: |
          # Enables uploading test runs to Cypress Dashboard:
          if [ -n "$CYPRESS_RECORD_KEY" ] ; then export CYPRESS_OPTS="--key $CYPRESS_RECORD_KEY" ; fi
          pipenv run ./scripts/run-cypress --no-interactive
      - name: Archive cypress videos
        uses: actions/upload-artifact@v4
        with:
          name: cypress-videos
          path: |
            cypress/videos

  build-docker-image-dev:
    runs-on: ubuntu-latest

    # Only build the Docker Image when we're deploying!
    needs:
      - should-update-dev
    if: needs.should-update-dev.outputs.should-run == 'true'

    steps:
      - name: Login to GitHub Container Registry
        uses: docker/login-action@v3
        with:
          registry: ghcr.io
          username: ${{ github.repository_owner }}
          password: ${{ secrets.GHCR_PERSONAL_ACCESS_TOKEN }}
      - uses: actions/checkout@v4
      - name: Build and push Docker images
        uses: docker/build-push-action@v6
        with:
          # build-push-action with the default ‘git context’ ignores the
          # .dockerignore file
          # https://github.com/docker/build-push-action/issues/182
          context: .
          file: docker/Dockerfile
          push: true
          # hopefully this will speed up builds and save disk space by
          # sharing layers with the existing docker image, where possible
          cache-from: |
            type=registry,ref=ghcr.io/ualbertaaltlab/itwewina.altlab.app:dev
          tags: |
            ghcr.io/ualbertaaltlab/itwewina.altlab.app:${{ github.sha }}

  update-docker-dev-tag:
    runs-on: ubuntu-latest

    needs:
      - should-update-dev
      # - unit-test
      # - integration-test
      - build-docker-image-dev

    if: needs.should-update-dev.outputs.should-run == 'true'

    steps:
      - name: Login to GitHub Container Registry
        uses: docker/login-action@v3
        with:
          registry: ghcr.io
          username: ${{ github.repository_owner }}
          password: ${{ secrets.GHCR_PERSONAL_ACCESS_TOKEN }}
      - uses: actions/checkout@v4
      - name: 🐍 Set up Python ${{ env.ACTIONS_PYTHON_VERSION }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ env.ACTIONS_PYTHON_VERSION }}
      - name: Install requests
        run: pip install requests
      - name: Update tag
        run: docker/copy-registry-tag ${{ github.sha }} dev
        env:
          GHCR_PERSONAL_ACCESS_TOKEN: ${{ secrets.GHCR_PERSONAL_ACCESS_TOKEN }}

  build-docker-image:
    runs-on: ubuntu-latest

    # Only build the Docker Image when we're deploying!
    needs:
      - should-deploy
    if: needs.should-deploy.outputs.should-run == 'true'

    steps:
      - name: Login to GitHub Container Registry
        uses: docker/login-action@v3
        with:
          registry: ghcr.io
          username: ${{ github.repository_owner }}
          password: ${{ secrets.GHCR_PERSONAL_ACCESS_TOKEN }}
      - uses: actions/checkout@v4
      - name: Build and push Docker images
        uses: docker/build-push-action@v6
        with:
          # build-push-action with the default ‘git context’ ignores the
          # .dockerignore file
          # https://github.com/docker/build-push-action/issues/182
          context: .
          file: docker/Dockerfile
          push: true
          # hopefully this will speed up builds and save disk space by
          # sharing layers with the existing docker image, where possible
          cache-from: |
            type=registry,ref=ghcr.io/ualbertaaltlab/itwewina.altlab.app:latest
          tags: |
            ghcr.io/ualbertaaltlab/itwewina.altlab.app:${{ github.sha }}

  trigger-deployment:
    runs-on: ubuntu-latest

    needs:
      - should-deploy
      - unit-test
      - integration-test
      - build-docker-image

    if: needs.should-deploy.outputs.should-run == 'true'

    steps:
      - name: Login to GitHub Container Registry
        uses: docker/login-action@v3
        with:
          registry: ghcr.io
          username: ${{ github.repository_owner }}
          password: ${{ secrets.GHCR_PERSONAL_ACCESS_TOKEN }}
      - uses: actions/checkout@v4
      - name: 🐍 Set up Python ${{ env.ACTIONS_PYTHON_VERSION }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ env.ACTIONS_PYTHON_VERSION }}
      - name: Install requests
        run: pip install requests
      - name: Update tag
        run: docker/copy-registry-tag ${{ github.sha }} latest
        env:
          GHCR_PERSONAL_ACCESS_TOKEN: ${{ secrets.GHCR_PERSONAL_ACCESS_TOKEN }}
      - name: send HTTP request to deploy.altlab.dev webhook
        # Be careful with spacing here.
        #
        # What https://yaml-multiline.info *doesn’t* warn you about: although
        # `>-` means “replace newlines with spaces,” if you have an extra
        # space on the next line, the newline gets preserved!
        #
        # So although
        #
        #     foo: >-
        #       a
        #       a
        #
        # means `{ "foo": "a a" }`,
        #
        #     foo: >-
        #       a
        #        a
        #
        # turns into `{ "foo": "a\n a" }` !
        # run: >-
        #  curl -X POST https://deploy.altlab.dev/itwewina --fail
        #  -d '{ "secret": "${{ secrets.DEPLOY_ALTLAB_DEV_ITWEWINA_KEY }}" }'
        #  -H 'Content-Type: application/json'
        run: echo "This step has been temporarily disabled, call the deploy script."