Merge pull request #25 from ave-dcd/Input-outputs-formats #25
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| name: Python package | |
| on: [push] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Test with pytest | |
| env: | |
| PATH_TO_SEQREPO: ./tests/data/seqrepo/latest | |
| HG38_FILE: ./tests/data/hg38.2bit | |
| run: | | |
| export UTA_PASSWORD=uta | |
| export LRG_REFSEQGENE_PATH=./tests/data/LRG_RefSeqGene | |
| export MANE_SUMMARY_PATH=./tests/data/MANE.GRCh38.v1.1.summary.txt.gz | |
| export PYTHONPATH="${PYTHONPATH}:$(pwd)" | |
| pytest |