big tree by @domivika #18
This file contains hidden or 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: Python package | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Important for setuptools_scm to determine the version | |
| - name: Set up Conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| activate-environment: barcode-constrained-phylogeny-backbone | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| - name: Install additional test dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda activate barcode-constrained-phylogeny-backbone | |
| pip install pytest pytest-cov flake8 | |
| pip install -e . | |
| - name: Test environment | |
| shell: bash -l {0} | |
| run: | | |
| conda activate barcode-constrained-phylogeny-backbone | |
| conda list | |
| which python | |
| which iqtree | |
| which raxml-ng | |
| which raxmlHPC | |
| - name: Lint with flake8 | |
| shell: bash -l {0} | |
| run: | | |
| conda activate barcode-constrained-phylogeny-backbone | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| shell: bash -l {0} | |
| run: | | |
| conda activate barcode-constrained-phylogeny-backbone | |
| pytest --cov=barcode-constrained-phylogeny-backbone --cov-report=xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| fail_ci_if_error: false |