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"]
    defaults:
      run:
        shell: bash -le {0}
    steps:
      - uses: actions/checkout@v3
      - uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: test_env_python${{ matrix.python-version }}
          python-version: ${{ matrix.python-version }}
          auto-activate-base: false

      - name: Install hdf5 libs
        run: |
          sudo apt-get update
          sudo apt-get install libhdf5-dev
      
      - 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: Conda info
        run: |
          conda info
          conda list
          echo branch_name = ${branch_name}
      - name: check for upstream vivarium
        run: |
          if git ls-remote --exit-code --heads https://github.com/ihmeuw/vivarium.git ${branch_name} == "0"; then
            echo "upstream_vivarium_exist=true" >> $GITHUB_ENV
          else
            echo "upstream_vivarium_exist=false" >> $GITHUB_ENV
          fi
      - name: check for upstream vivarium_public_health
        run: |
          if git ls-remote --exit-code --heads https://github.com/ihmeuw/vivarium_public_health.git ${branch_name} == "0"; then
            echo "upstream_vivarium_public_health_exist=true" >> $GITHUB_ENV
          else
            echo "upstream_vivarium_public_health_exist=false" >> $GITHUB_ENV
          fi
      - name: check for upstream gbd_mapping
        run: |
          if git ls-remote --exit-code --heads https://github.com/ihmeuw/gbd_mapping.git ${branch_name} == "0"; then
            echo "upstream_gbd_mapping_exist=true" >> $GITHUB_ENV
          else
            echo "upstream_gbd_mapping_exist=false" >> $GITHUB_ENV
          fi

      - name: print environment values
        run: |
          cat $GITHUB_ENV

      - name: Retrieve upstream vivarium
        if: env.upstream_vivarium_exist == 'true'
        run: |
          echo "Cloning vivarium upstream branch: ${branch_name}"
          git clone --branch=${branch_name} https://github.com/ihmeuw/vivarium.git
          pushd vivarium
          pip install .
          popd
      - name: Retrieve upstream vivarium_public_health
        if: env.upstream_vivarium_public_health_exist == 'true'
        run: |
          echo "Cloning vivarium_public_health upstream branch: ${branch_name}"
          git clone --branch=${branch_name} https://github.com/ihmeuw/vivarium_public_health.git
          pushd vivarium_public_health
          pip install .
          popd
      - name: Retrieve upstream gbd_mapping
        if: env.upstream_gbd_mapping_exist == 'true'
        run: |
          echo "Cloning upstream gbd_mapping branch: ${branch_name}"
          git clone --branch=${branch_name} https://github.com/ihmeuw/gbd_mapping.git
          pushd gbd_mapping
          pip install .
          popd

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip        
          pip install .[docs,test]
      - name: Lint
        run: |
          pip install black==22.3.0 isort
          black . --check --diff
          isort . --check --verbose --only-modified --diff
      - name: Test
        run: |
          if github.event_name == 'schedule'; then
            pytest --runslow ./tests
          else
            pytest ./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: Dr Manhattan