test.yml

# Built from:
# https://docs.github.com/en/actions/guides/building-and-testing-python
# https://github.com/Sage-Bionetworks/challengeutils/blob/master/.github/workflows/pythonapp.yml
# https://github.com/snok/install-poetry#workflows-and-tips

name: Test schematic

on:
  push:
    branches: ['main']
  pull_request:
    branches: ['*']
  workflow_dispatch:  # Allow manually triggering the workflow
concurrency:
  # cancel the current running workflow from the same branch, PR when a new workflow is triggered
  # when the trigger is not a PR but a push, it will use the commit sha to generate the concurrency group
  # {{ github.workflow }}: the workflow name is used to generate the concurrency group. This allows you to have more than one workflows
  # {{ github.ref_type }}: the type of Git ref object created in the repository. Can be either branch or tag
  # {{ github.event.pull_request.number}}: get PR number
  # {{ github.sha }}: full commit sha
  # credit: https://github.com/Sage-Bionetworks-Workflows/sagetasks/blob/main/.github/workflows/ci.yml
  group: >-
    ${{ github.workflow }}-${{ github.ref_type }}-
    ${{ github.event.pull_request.number || github.sha }}
  cancel-in-progress: true
jobs:
  test:
    runs-on: ubuntu-22.04-4core-16GBRAM-150GBSSD
    env:
      POETRY_VERSION:  1.3.0
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.9", "3.10"]

    steps:

      #----------------------------------------------
      #       check-out repo and set-up python
      #----------------------------------------------
      - name: Check out repository
        uses: actions/checkout@v2

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}

      #----------------------------------------------
      #          install & configure poetry
      #----------------------------------------------
      - name: Install Poetry
        run: |
          curl -sSL https://install.python-poetry.org \
            | python3 - --version ${{ env.POETRY_VERSION }};
          poetry config virtualenvs.create true;
          poetry config virtualenvs.in-project true;
      #----------------------------------------------
      #       load cached venv if cache exists
      #----------------------------------------------
      - name: Load cached venv
        id: cached-poetry-dependencies
        uses: actions/cache@v2
        with:
          path: .venv
          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}

      #----------------------------------------------
      # install dependencies and root project
      #----------------------------------------------
      - name: Install dependencies and root project
        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
        run: poetry install --no-interaction --all-extras

      #----------------------------------------------
      #             perform linting
      #----------------------------------------------
      # Disabled until we agree to turn it on
      # - name: Lint with flake8
      #   run: |
      #     # 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

      #----------------------------------------------
      #             check formatting
      #----------------------------------------------
      - name: Code formatting with black
        run: |
          # ran only on certain files for now
          # add here when checked
          poetry run black schematic tests schematic_api --check

      #----------------------------------------------
      #             type checking/enforcement
      #----------------------------------------------
      - name: Type checking with mypy
        run: |
          # ran only on certain files for now
          # add here when checked
          # poetry run mypy --install-types --non-interactive
          # add here when enforced
          poetry run mypy --disallow-untyped-defs --install-types --non-interactive schematic/schemas/ schematic/configuration/ schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py schematic/visualization schematic/utils/

      #----------------------------------------------
      #             linting
      #----------------------------------------------
      - name: Lint with pylint
        run: |
          # ran only on certain files for now
          # add here when checked
          poetry run pylint schematic/visualization/* schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py schematic/utils/*.py schematic/schemas/*.py

      #----------------------------------------------
      #              run test suite
      #----------------------------------------------
      - name: Run tests
        env:
          SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
          SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }}
        run: >
          source .venv/bin/activate;
          pytest --durations=0 --cov-report=term --cov-report=html:htmlcov --cov=schematic/
          -m "not (google_credentials_needed or schematic_api or table_operations)" --reruns 2 -n auto

      - name: Upload pytest test results
        uses: actions/upload-artifact@v2
        with:
          name: pytest-results-${{ matrix.python-version }}
          path: htmlcov
        # Use always() to always run this step to publish test results when there are test failures
        if: ${{ always() }}