Moved Jupter notebooks to be part of sphinx docs #2198
Workflow file for this run
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| # 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/[email protected] | |
| 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: ${{ matrix.python-version }} | |
| #---------------------------------------------- | |
| # install & configure poetry | |
| #---------------------------------------------- | |
| - name: Install Poetry | |
| run: | | |
| pip install --upgrade pip | |
| pip install poetry | |
| # uses: snok/[email protected] | |
| # with: | |
| # virtualenvs-create: true | |
| # virtualenvs-in-project: true | |
| #---------------------------------------------- | |
| # load cached venv if cache exists | |
| #---------------------------------------------- | |
| # - name: Load cached venv | |
| # id: cached-poetry-dependencies | |
| # uses: actions/cache@v3 | |
| # with: | |
| # path: .venv | |
| # key: venv-${{ 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 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: ${{ secrets.BIOPORTAL_API_KEY }} | |
| #---------------------------------------------- | |
| # upload coverage results | |
| #---------------------------------------------- | |
| - name: Upload coverage report | |
| uses: codecov/[email protected] | |
| with: | |
| name: codecov-results-${{ matrix.os }}-${{ matrix.python-version }} | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| fail_ci_if_error: false |