updated read me and docs with biorxiv link #80
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 | |
| jobs: | |
| test-fast: | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@master | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| # make orthohmm CLI available for tests | |
| make install | |
| # install deps for tests | |
| pip install pytest | |
| pip install pytest-cov | |
| - name: Install HMMER | |
| run: | | |
| brew install hmmer | |
| - name: Install MCL | |
| run: | | |
| mkdir installmcl | |
| cd installmcl | |
| wget https://raw.githubusercontent.com/micans/mcl/main/install-this-mcl.sh -o install-this-mcl | |
| chmod u+x install-this-mcl.sh | |
| ./install-this-mcl.sh | |
| PATH=$PATH:$HOME/local/bin | |
| mcl --version | |
| cd .. | |
| - name: Run tests | |
| run: | | |
| PATH=$PATH:$HOME/local/bin | |
| make test.fast | |
| test-full: | |
| runs-on: macos-latest | |
| env: | |
| PYTHON: '3.9' | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Setup Python | |
| uses: actions/setup-python@master | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| # make orthohmm CLI available for tests | |
| make install | |
| # install test dependencies | |
| pip install pytest | |
| pip install pytest-cov | |
| - name: Install HMMER | |
| run: | | |
| brew install hmmer | |
| - name: Install MCL | |
| run: | | |
| mkdir installmcl | |
| cd installmcl | |
| wget https://raw.githubusercontent.com/micans/mcl/main/install-this-mcl.sh -o install-this-mcl | |
| chmod u+x install-this-mcl.sh | |
| ./install-this-mcl.sh | |
| PATH=$PATH:$HOME/local/bin | |
| mcl --version | |
| cd .. | |
| - name: Generate coverage report | |
| run: | | |
| PATH=$PATH:$HOME/local/bin | |
| make test.coverage | |
| - name: Upload unit test coverage to Codecov | |
| uses: codecov/[email protected] | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./unit.coverage.xml | |
| flags: unit | |
| env_vars: PYTHON | |
| name: codecov-unit | |
| fail_ci_if_error: false | |
| - name: Upload integration test coverage to Codecov | |
| uses: codecov/[email protected] | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./integration.coverage.xml | |
| flags: integration | |
| env_vars: PYTHON | |
| name: codecov-integration | |
| fail_ci_if_error: false | |
| docs: | |
| runs-on: macos-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@master | |
| with: | |
| persist-credentials: false | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v4 | |
| with: | |
| enable-cache: true | |
| cache-dependency-glob: "docs/uv.lock" | |
| - name: Build docs | |
| run: | | |
| cd docs | |
| uv python install | |
| uv sync --all-extras --dev | |
| uv run python -m sphinx.cmd.build -b html . ./_build/html | |
| cd .. | |
| - name: Deploy | |
| uses: JamesIves/github-pages-deploy-action@releases/v3 | |
| with: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| BRANCH: gh-pages | |
| FOLDER: docs/_build/html |