Bump to 3.12.3 for #196 multi-allele NetMHCpan parser fix #142
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - master | |
| pull_request: | |
| permissions: | |
| contents: read | |
| jobs: | |
| quality: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: pip | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -e ".[dev,pepsickle]" | |
| - name: Run lint checks | |
| run: ./lint.sh | |
| - name: Build distribution artifacts | |
| run: python -m build --sdist --wheel --no-isolation | |
| - name: Run public pytest subset | |
| run: | | |
| pytest -ra \ | |
| tests/test_binding_prediction.py \ | |
| tests/test_binding_prediction_collection.py \ | |
| tests/test_cli_parsing_helpers.py \ | |
| tests/test_cli_registry.py \ | |
| tests/test_class2_allele_formats.py \ | |
| tests/test_cli_filters.py \ | |
| tests/test_mhc_formats.py \ | |
| tests/test_netchop_parse.py \ | |
| tests/test_process_helpers.py \ | |
| tests/test_pred.py \ | |
| tests/test_processing_predictor.py \ | |
| tests/test_pepsickle.py \ | |
| tests/test_bigmhc.py \ | |
| tests/test_random.py | |
| integration-netmhc: | |
| if: github.repository == 'openvax/mhctools' | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: pip | |
| - name: Checkout private netmhc-bundle repo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: openvax/netmhc-bundle | |
| ref: v1.0.0 | |
| token: ${{ secrets.NETMHC_BUNDLE_ACCESS_TOKEN }} | |
| path: netmhc-bundle | |
| - name: Install netmhc-bundle dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y tcsh gawk python2 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -e ".[dev]" | |
| python -m pip install 'setuptools<81' | |
| - name: Install MHCflurry data | |
| run: mhcflurry-downloads fetch | |
| - name: Configure netMHC tool paths | |
| env: | |
| NETMHC_BUNDLE_HOME: ${{ github.workspace }}/netmhc-bundle | |
| run: | | |
| # Wrapper scripts have hardcoded /tools/src paths; symlink so they resolve | |
| sudo mkdir -p /tools | |
| sudo ln -s "$NETMHC_BUNDLE_HOME" /tools/src | |
| - name: Run full test suite | |
| env: | |
| NETMHC_BUNDLE_HOME: ${{ github.workspace }}/netmhc-bundle | |
| NETMHC_BUNDLE_TMPDIR: ${{ github.workspace }}/netmhc-bundle-tmp | |
| run: | | |
| mkdir -p "$NETMHC_BUNDLE_TMPDIR" | |
| export PATH="$PATH:$NETMHC_BUNDLE_HOME/bin" | |
| ./test.sh |