287 dynamically adjust minimum maf for hwe calculation and add option to set hwe p value threshold #499
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python package | |
| on: | |
| push: | |
| branches: [ default ] | |
| pull_request: | |
| branches: [ default ] | |
| jobs: | |
| build_docs: | |
| runs-on: ubuntu-latest | |
| if: "!startsWith(github.event.head_commit.message, 'noci') && startsWith(github.event.head_commit.message, 'docs')" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get Current tag | |
| id: current_tag | |
| uses: WyriHaximus/github-action-get-previous-tag@v1 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip poetry | |
| poetry version ${{ steps.current_tag.outputs.tag }} | |
| poetry install | |
| - name: Build Docs | |
| shell: bash | |
| run: | | |
| poetry run make -C docs html | |
| - name: Deploy gh-pages | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: ./docs/_build/html | |
| build_and_test: | |
| runs-on: ubuntu-latest | |
| if: "!startsWith(github.event.head_commit.message, 'noci') && !startsWith(github.event.head_commit.message, 'docs')" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: "recursive" | |
| - name: setup-conda | |
| uses: s-weigand/setup-conda@v1 | |
| with: | |
| # Whether to activate the conda base env (Default: 'true') | |
| activate-conda: true | |
| # If conda should be updated before running other commands (Default: 'false') | |
| update-conda: true | |
| # Python version which should be installed with conda (default: 'Default') | |
| python-version: 3.8 | |
| # Additional channels like 'conda-forge' which can be used to install packages | |
| conda-channels: conda-forge, bioconda, default | |
| - name: Install dependencies | |
| shell: bash | |
| run: | | |
| conda install -y mamba | |
| python -m pip install --upgrade pip | |
| python -m pip install poetry | |
| poetry env info | |
| poetry install | |
| - name: Lint with flake8 | |
| shell: bash | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| poetry run flake8 . --count --exit-zero --statistics | |
| - name: Run black --check --exclude=tests/data . | |
| shell: bash | |
| run: | | |
| poetry run black --check --exclude=tests/data . | |
| - name: If needed, commit black changes to the pull request | |
| if: failure() | |
| shell: bash | |
| run: | | |
| poetry run black --exclude=tests/data . | |
| git config --global user.name 'autoblack' | |
| git config --global user.email '1240432+jfear@users.noreply.github.com' | |
| git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY | |
| git checkout $GITHUB_HEAD_REF | |
| git commit -am "fixup: Format Python code with Black" | |
| git push | |
| - name: Test with pytest | |
| shell: bash | |
| run: | | |
| poetry run pytest |