Modify haploid Viterbi/FB to handle NONCOPY state in reference panel #115
Workflow file for this run
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| 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} |