Add CSV and FASTA input formats #71
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: Tests | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-22.04 | |
| env: | |
| HAS_NETMHC_TOKEN: ${{ secrets.NETMHC_BUNDLE_ACCESS_TOKEN != '' }} | |
| strategy: | |
| fail-fast: true | |
| 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@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Checkout private netmhc-bundle repo | |
| if: env.HAS_NETMHC_TOKEN == 'true' | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: openvax/netmhc-bundle | |
| token: ${{ secrets.NETMHC_BUNDLE_ACCESS_TOKEN }} | |
| path: netmhc-bundle | |
| - name: Install netmhc-bundle dependencies | |
| if: env.HAS_NETMHC_TOKEN == 'true' | |
| uses: awalsh128/cache-apt-pkgs-action@latest | |
| with: | |
| packages: tcsh gawk | |
| version: 1.0 | |
| - name: Verify netmhc-bundle tools | |
| if: env.HAS_NETMHC_TOKEN == 'true' | |
| run: | | |
| export NETMHC_BUNDLE_HOME=$PWD/netmhc-bundle | |
| mkdir -p $PWD/netmhc-bundle-tmp | |
| export NETMHC_BUNDLE_TMPDIR=$PWD/netmhc-bundle-tmp | |
| export PATH=$PATH:$NETMHC_BUNDLE_HOME/bin | |
| echo `which netMHC` && netMHC -h | |
| echo `which netMHCpan` && netMHCpan -h | |
| echo `which netMHCcons` && netMHCcons -h | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install pytest pytest-cov ruff | |
| pip install -e . | |
| - name: Lint with ruff | |
| run: | | |
| ./lint.sh | |
| - name: Download Ensembl data | |
| run: | | |
| echo "Before installing Ensembl releases" && df -h | |
| pyensembl install --release 75 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh37.75/ | |
| pyensembl install --release 102 --species mouse --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.102/ | |
| pyensembl install --release 93 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.93/ | |
| pyensembl install --release 93 --species mouse --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.93/ | |
| - name: Test with pytest | |
| if: env.HAS_NETMHC_TOKEN == 'true' | |
| run: | | |
| # configure netmhc-bundle paths | |
| export NETMHC_BUNDLE_HOME=$PWD/netmhc-bundle | |
| echo "NetMHC-bundle dir:" && ls -l $NETMHC_BUNDLE_HOME | |
| mkdir -p $PWD/netmhc-bundle-tmp | |
| export NETMHC_BUNDLE_TMPDIR=$PWD/netmhc-bundle-tmp | |
| export PATH=$PATH:$NETMHC_BUNDLE_HOME/bin | |
| ./test.sh | |
| - name: Publish coverage to Coveralls | |
| uses: coverallsapp/github-action@v2.2.3 | |
| with: | |
| parallel: true | |
| flag-name: python-${{ matrix.python-version }} | |
| coveralls-finish: | |
| needs: build | |
| runs-on: ubuntu-latest | |
| if: always() | |
| steps: | |
| - name: Finalize Coveralls | |
| uses: coverallsapp/github-action@v2.2.3 | |
| with: | |
| parallel-finished: true |