Functions to process, filter, annotate and aggregate variants by transcript expression (get the pext scores per variant) #1809
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| jobs: | |
| pylint: | |
| name: Pylint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup Python 3.11 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.11 | |
| - name: Use pip cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-${{ hashFiles('**/requirements*.txt') }} | |
| restore-keys: | | |
| pip- | |
| - name: Install dependencies | |
| run: | | |
| pip install wheel | |
| pip install -r requirements.txt | |
| pip install -r requirements-dev.txt | |
| - name: Check formatting | |
| run: black --check gnomad tests | |
| - name: Check imports | |
| run: isort --check-only gnomad tests | |
| - name: Check docstrings | |
| run: pydocstyle gnomad tests | |
| - name: Check comment formatting | |
| run: autopep8 --exit-code --diff gnomad | |
| - name: Run Pylint | |
| run: ./lint | |
| - name: Run tests | |
| run: python -m pytest | |
| docs: | |
| name: Build documentation | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup Python 3.11 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.11 | |
| - name: Use pip cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-${{ hashFiles('**/requirements*.txt') }} | |
| restore-keys: | | |
| pip- | |
| - name: Install dependencies | |
| run: | | |
| pip install wheel | |
| pip install -r requirements.txt | |
| pip install -r docs/requirements.docs.txt | |
| - name: Build docs | |
| run: ./docs/build.sh | |
| - name: Publish to GitHub Pages | |
| if: github.event_name == 'push' | |
| run: | | |
| # Create empty gh-pages branch | |
| git checkout --orphan gh-pages | |
| # Remove files other than docs | |
| git rm -rf . | |
| find . -name __pycache__ | xargs rm -r | |
| # Move docs to root | |
| mv docs/html/* ./ | |
| rm -r docs | |
| # Tell GitHub not to treat this as a Jekyll site | |
| touch .nojekyll | |
| git config user.name "${GITHUB_ACTOR}" | |
| git config user.email "${GITHUB_ACTOR}@users.noreply.github.com" | |
| git add . | |
| git commit --allow-empty -m "Update docs" | |
| git push --force origin gh-pages | |
| # Restore the original working tree by checking out the | |
| # commit that triggered the workflow. | |
| # This restores requirements.txt so that @actions/cache | |
| # can use it for determining the cache key. | |
| git checkout ${GITHUB_SHA} | |
| gnomad_qc: | |
| name: gnomad_qc checks | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout gnomad_methods | |
| uses: actions/checkout@v3 | |
| with: | |
| path: gnomad_methods | |
| - name: Checkout gnomad_qc | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| repository: broadinstitute/gnomad_qc | |
| path: gnomad_qc | |
| - name: Setup Python 3.11 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.11 | |
| - name: Use pip cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-${{ hashFiles('gnomad_methods/**/requirements*.txt') }} | |
| restore-keys: | | |
| pip- | |
| - name: Install dependencies | |
| run: | | |
| pip install wheel | |
| pip install ./gnomad_methods | |
| cat gnomad_qc/requirements.txt | grep -v gnomad_methods > gnomad_qc/requirements-edited.txt | |
| pip install -r gnomad_qc/requirements-edited.txt | |
| pip install -r gnomad_methods/requirements-dev.txt | |
| - name: Run Pylint | |
| run: pylint --disable=R,C,W gnomad_qc | |
| working-directory: ./gnomad_qc |