pythonapp.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Mila-IQIA Covid-19 Simulator

on:
  push:
    branches: [ master, develop, experimental ]
  pull_request:
    branches: [ master, develop, experimental ]

jobs:
  test:
    name: Test on Python ${{ matrix.python_version }}
    runs-on: ubuntu-latest
    timeout-minutes: 25
    strategy:
      matrix:
        python_version: ['3.7', '3.8']

    steps:
    - name: Simulator source code checkout
      uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python_version }}
      uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python_version }}
    - name: Update pip wrt current Python version
      run: |
        python -m pip install --upgrade pip
    - name: Machine learning source code checkout
      uses: actions/checkout@v2
      with:
        repository: mila-iqia/COVI-ML
        ref: littlecrunch  # TODO: auto-select the name of the current simulator branch?
        token: ${{ secrets.ORG_REPOS_AUTH_TOKEN }}  # TODO: ONCE PUBLIC, REMOVE + DELETE TOKEN @@@
        path: downloads/COVI-ML
    - name: Machine learning package installation
      run: |
        # TODO: ctt should self-install its own requirements.txt...
        pip install -r downloads/COVI-ML/requirements-minimal.txt
        pip install -e downloads/COVI-ML
    - name: Simulator package installation
      run: |
        pip install -e .
    - name: Lint with flake8
      run: |
        pip install flake8
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
    - name: Test
      run: |
        pytest --cov-report=xml --cov=covid19sim --timeout=600 tests/
    - uses: codecov/codecov-action@v1
      with:
        file: ./coverage.xml # optional
        flags: unittests # optional
        name: codecov-umbrella # optional
        fail_ci_if_error: false # optional (default = false)