Improvements in documentation #336
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| # This is a basic workflow to help you get started with Actions | |
| name: Testing | |
| # Controls when the workflow will run | |
| on: | |
| # Triggers the workflow on push or pull request events but only for the main branch | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| pull_request: | |
| branches: | |
| - main | |
| - dev | |
| workflow_dispatch: # make is manually start-able | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| # This workflow contains a single job called "test" | |
| test: | |
| runs-on: 'ubuntu-latest' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup Mamba | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: '3.10' | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: MPP | |
| use-mamba: true | |
| - name: Install environment | |
| shell: bash -l {0} | |
| run: | | |
| mamba install -c conda-forge -c bioconda -y numpy pandas networkx matplotlib pytest setuptools pyscipopt"<4.0.0" foldseek mmseqs2 cd-hit mash tmalign diamond cvxpy pytest-cov rdkit">=2023.09.1" pytest-cases scikit-learn pyyaml h5py | |
| pip install grakel | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| cd tests | |
| pytest -m "not todo and not issue" --cov=../datasail/ --cov-report=xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: false | |
| files: coverage.xml |