Merge pull request #6 from VectorInstitute/add_procedures_method_mimiciv #13
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| name: docs | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - .pre-commit-config.yaml | |
| - .github/workflows/code_checks.yml | |
| - .github/workflows/docs_build.yml | |
| - .github/workflows/docs_deploy.yml | |
| - .github/workflows/integration_tests.yml | |
| - '**.py' | |
| - '**.ipynb' | |
| - poetry.lock | |
| - pyproject.toml | |
| - '**.rst' | |
| - '**.md' | |
| jobs: | |
| deploy: | |
| runs-on: [self-hosted, db] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: 'true' | |
| - name: Install dependencies, build docs and coverage report | |
| run: python3 -m pip install --upgrade pip && python3 -m pip install poetry | |
| - uses: actions/[email protected] | |
| with: | |
| python-version: '3.10' | |
| cache: 'poetry' | |
| - run: | | |
| poetry env use '3.10' | |
| source $(poetry env info --path)/bin/activate | |
| poetry install --with docs,test | |
| # pandoc README.md -f markdown -t rst -s -o docs/source/intro.rst | |
| cd docs && rm -rf source/reference/api/_autosummary && make html | |
| cd .. && coverage run -m pytest -m "not integration_test" && coverage xml && coverage report -m | |
| - name: Upload coverage to Codecov | |
| uses: Wandalen/[email protected] | |
| with: | |
| action: codecov/[email protected] | |
| with: | | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| name: codecov-umbrella | |
| fail_ci_if_error: true | |
| attempt_limit: 5 | |
| attempt_delay: 30000 | |
| - name: Deploy to GitHub Pages | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_branch: github_pages | |
| publish_dir: docs/build/html |