Update README #211
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://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Python package | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install packagge | |
| run: | | |
| python -m pip install --upgrade pip pytest pytest-cov | |
| python -m pip install -e . | |
| - name: Create tasks needed for testing | |
| run: | | |
| python scripts/tasks_retrieval/gene2gene_task_creation.py --allow-downloads True | |
| python scripts/tasks_retrieval/Genecorpus_tasks_creation.py --allow-downloads True | |
| python scripts/tasks_retrieval/HLA_task_creation.py --allow-downloads True | |
| python scripts/tasks_retrieval/HPA_tasks_creation.py --allow-downloads True | |
| python scripts/tasks_retrieval/humantfs_task_creation.py --allow-downloads True | |
| python scripts/tasks_retrieval/Reactome_tasks_creation.py --allow-downloads True | |
| python scripts/tasks_retrieval/uniprot_keyword_tasks_creation.py --allow-downloads True | |
| - name: Test with pytest | |
| run: | | |
| python -m pytest -v --durations=40 --cov=gene_benchmark--cov-fail-under=70 gene_benchmark |