Expanded enrichment notebook (#692) #1772
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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' ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/[email protected] | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install tox | |
| - name: Check code quality with flake8 | |
| run: tox -e flake8 | |
| test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-latest, windows-latest ] | |
| python-version: [ "3.9", "3.10" ] | |
| 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: ${{ matrix.python-version }} | |
| #---------------------------------------------- | |
| # install & configure poetry | |
| #---------------------------------------------- | |
| - name: Install Poetry | |
| run: | | |
| pip install --upgrade pip | |
| pip install poetry | |
| # uses: snok/[email protected] | |
| # with: | |
| # virtualenvs-create: true | |
| # virtualenvs-in-project: true | |
| #---------------------------------------------- | |
| # load cached venv if cache exists | |
| #---------------------------------------------- | |
| # - name: Load cached venv | |
| # id: cached-poetry-dependencies | |
| # uses: actions/cache@v3 | |
| # with: | |
| # path: .venv | |
| # key: venv-${{ 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" | |
| - name: Get Gilda resources | |
| run: | | |
| poetry run python -c "import nltk; nltk.download('punkt'); 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: ${{ secrets.BIOPORTAL_API_KEY }} | |
| #---------------------------------------------- | |
| # upload coverage results | |
| #---------------------------------------------- | |
| - name: Upload coverage report | |
| uses: codecov/[email protected] | |
| with: | |
| name: codecov-results-${{ matrix.os }}-${{ matrix.python-version }} | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| fail_ci_if_error: false |