build.yml

# -----------------------------------------------------------------------------
#   - invoked on push, pull_request, manual trigger, or schedule
#   - test under at least 3 versions of python
# -----------------------------------------------------------------------------
name: build
on:
  push:
  pull_request:
  workflow_dispatch:
  schedule: 
    - cron: "0 8 * * *"

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9", "3.10", "3.11"]
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      - name: get upstream branch name
        run: |
          if "${{ github.event_name == 'pull_request' }}" ; then
          echo "branch_name=${GITHUB_HEAD_REF}" >> $GITHUB_ENV
          else
          echo "branch_name=${GITHUB_REF_NAME}" >> $GITHUB_ENV
          fi
      - name: Update pip
        run: |
          python -m pip install --upgrade pip
      - name: Install dependencies
        run: |
          pip install .[dev]
      - name: check for dependency branches and install if needed
        run: |
          cd ..
          git clone https://github.com/ihmeuw/vivarium_build_utils.git
          cd pseudopeople
          echo "Contents of install_dependency_branch.sh"
          echo "----------------------------------------"
          cat ../vivarium_build_utils/install_dependency_branch.sh
          echo ""
          echo "----------------------------------------"
          sh ../vivarium_build_utils/install_dependency_branch.sh layered_config_tree ${branch_name} github
      - name: print environment values
        run: |
          cat $GITHUB_ENV
      - name: Install dependencies
        run: |
          pip install .[dev]
      - name: Lint
        run: |
          pip install black==22.3.0 isort mypy
          isort . --check --verbose --only-modified --diff
          black . --check --diff
          mypy .
      - name: Test
        run: |
          if "${{ github.event_name == 'schedule' }}"; then
            pytest --runslow ./tests
          else
            pytest --limit=1 ./tests
          fi
      - name: Doc build
        run: |
          make html -C docs/ SPHINXOPTS="-W --keep-going -n"
      - name: Doctest
        run: |
          make doctest -C docs/
      - name: Send mail
        # Notify when cron job fails
        if: (github.event_name == 'schedule' && failure())
        uses: dawidd6/action-send-mail@v2
        with:
          # mail server settings
          server_address: smtp.gmail.com
          server_port: 465
          # user credentials
          username: ${{ secrets.NOTIFY_EMAIL }}
          password: ${{ secrets.NOTIFY_PASSWORD }}
          # email subject
          subject: ${{ github.job }} job of ${{ github.repository }} has ${{ job.status }}
          # email body as text
          body: ${{ github.job }} job in worflow ${{ github.workflow }} of ${{ github.repository }} has ${{ job.status }}
          # comma-separated string, send email to
          to: uw_ihme_simulationscience@uw.edu
          # from email name
          from: Pseudopeople Notifications