Skip to content
CI

Deprecate get_most_severe_consequence_for_summary in favor of more flexible get_most_severe_csq_from_multiple_csq_lists #2179

Sign in to view logs

Deprecate get_most_severe_consequence_for_summary in favor of more flexible get_most_severe_csq_from_multiple_csq_lists

Deprecate get_most_severe_consequence_for_summary in favor of more flexible get_most_severe_csq_from_multiple_csq_lists #2179

Workflow file for this run

.github/workflows/ci.yml at aa9df9a
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-${{ hashFiles('**/requirements*.txt') }}
restore-keys: |
pip-
- name: Install dependencies
run: |
pip install wheel
pip install -r requirements.txt
pip install -r requirements-dev.txt
curl -sSL https://broad.io/install-gcs-connector | python3 - --auth-type UNAUTHENTICATED
- name: Check formatting
run: black --check gnomad tests
- name: Check imports
run: isort --check-only gnomad tests
- name: Check docstrings
run: pydocstyle gnomad tests
- name: Check comment formatting
run: autopep8 --exit-code --diff gnomad
- name: Run Pylint
run: ./lint
- name: Run tests
run: python -m pytest
docs:
name: Build documentation
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v3
- name: Setup Python 3.11
uses: actions/setup-python@v4
with:
python-version: 3.11
- name: Use pip cache
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: pip-${{ 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