main.yaml

# Built from:
# https://docs.github.com/en/actions/guides/building-and-testing-python
# https://github.com/snok/install-poetry#workflows-and-tips

name: Build and test

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]

jobs:
  lint:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [ '3.9', '3.10', '3.12' ]
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4.3.0
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          pip install tox
      - name: Check code quality with ruff
        run: tox -e lint

  test:
    strategy:
      fail-fast: false
      matrix:
        os: [ ubuntu-latest, windows-latest ]
        python-version: [ "3.9", "3.10", "3.11" ]
        exclude:
          - os: windows-latest
            python-version: "3.9"

    runs-on: ${{ matrix.os }}

    steps:

      #----------------------------------------------
      #       check-out repo and set-up python
      #----------------------------------------------
      - name: Check out repository
        uses: actions/checkout@v3

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}

      #----------------------------------------------
      #          install & configure poetry
      #----------------------------------------------
      - name: Install Poetry
        run: |
          pip install --upgrade pip
          pip install poetry
        # uses: snok/install-poetry@v1.3.3
        # with:
        #   virtualenvs-create: true
        #   virtualenvs-in-project: true

      #----------------------------------------------
      #       load cached venv if cache exists
      #----------------------------------------------
      # - name: Load cached venv
      #   id: cached-poetry-dependencies
      #   uses: actions/cache@v3
      #   with:
      #     path: .venv
      #     key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}

      #----------------------------------------------
      # install dependencies if cache does not exist
      #----------------------------------------------
      - name: Install dependencies
        # if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
        run: |
          poetry add setuptools@latest
          poetry install --no-interaction --no-root

      #----------------------------------------------
      #    install your root project, if required
      #----------------------------------------------
      - name: Install library
        run: poetry install --no-interaction --extras "gilda semsimian"

      - name: Get Gilda resources
        run: |
          poetry run python -c "import nltk; nltk.download('punkt_tab'); nltk.download('stopwords')"
          poetry run python -m adeft.download

      #----------------------------------------------
      #        run test suite + coverage report
      #----------------------------------------------
      - name: Generate coverage results
        run: |
          poetry run pip install -U pytest
          poetry run coverage run -p -m pytest tests/
          poetry run coverage combine
          poetry run coverage xml
          poetry run coverage report -m
        shell: bash
        env:
          BIOPORTAL_API_KEY: ${{ secrets.BIOPORTAL_API_KEY }}

      #----------------------------------------------
      #           upload coverage results
      #----------------------------------------------
      - name: Upload coverage report
        uses: codecov/codecov-action@v3.1.1
        with:
          name: codecov-results-${{ matrix.os }}-${{ matrix.python-version }}
          token: ${{ secrets.CODECOV_TOKEN }}
          file: ./coverage.xml
          fail_ci_if_error: false