Modify haploid Viterbi/FB to handle NONCOPY state in reference panel #106
Workflow file for this run
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
| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| jobs: | |
| checks: | |
| name: Checks | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Setup Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Use pip cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-${{ hashFiles('**/requirements*.txt') }} | |
| restore-keys: | | |
| pip- | |
| - name: Install development tools | |
| run: | | |
| pip install -r requirements.dev.txt | |
| pip install build twine nox | |
| - name: Check formatting | |
| run: nox -s format | |
| - name: Check for lint | |
| run: nox -s lint | |
| - name: Run tests | |
| run: nox -s test | |
| - name: Check distribution build | |
| run: | | |
| python3 -m build | |
| python3 -m twine check dist/* | |
| # Disabling for now. | |
| # docs: | |
| # name: Build documentation | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - name: Checkout | |
| # uses: actions/checkout@v2 | |
| # - name: Setup Python 3.8 | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.8 | |
| # - name: Use pip cache | |
| # uses: actions/cache@v2 | |
| # with: | |
| # path: ~/.cache/pip | |
| # key: pip-${{ hashFiles('**/requirements*.txt') }} | |
| # restore-keys: | | |
| # pip- | |
| # - name: Install nox | |
| # run: pip install nox | |
| # - name: Build docs | |
| # run: nox -s build_docs | |
| # - 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 . | |
| # rm -rf .nox | |
| # find . -name __pycache__ | xargs rm -r | |
| # # Move docs to root | |
| # mv docs/html/* ./ | |
| # rm -r docs | |
| # # Prevent GitHub from assuming that this is 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} |