allow wrong program name to be FileNotFoundError in test #36
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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 | |
| # TODO: | |
| # - cache this directory $HOME/.cache/pyensembl/ | |
| # - update coveralls | |
| # - get a badge for tests passing | |
| # - download binary dependencies from conda | |
| name: Tests | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11"] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| - name: Checkout private netmhc-bundle repo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: openvax/netmhc-bundle | |
| token: ${{ secrets.NETMHC_BUNDLE_ACCESS_TOKEN }} | |
| path: netmhc-bundle | |
| - name: Install netmhc-bundle dependencies | |
| uses: awalsh128/cache-apt-pkgs-action@latest | |
| with: | |
| packages: tcsh gawk python2-minimal | |
| version: 1.0 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest pytest-cov coveralls | |
| echo `pwd` && echo " || requirements:" && cat requirements.txt | |
| pip install -r requirements.txt | |
| pip install . | |
| - name: Run default linting script | |
| run: | | |
| ./lint.sh | |
| - name: Install MHCflurry data | |
| run: | | |
| mhcflurry-downloads fetch | |
| - name: Run unit tests | |
| run: | | |
| # configure netmhc-bundle paths | |
| export NETMHC_BUNDLE_HOME=$PWD/netmhc-bundle | |
| echo "NetMHC-bundle dir:" && ls -l $NETMHC_BUNDLE_HOME | |
| mkdir $PWD/netmhc-bundle-tmp | |
| export NETMHC_BUNDLE_TMPDIR=$PWD/netmhc-bundle-tmp | |
| export PATH=$PATH:$NETMHC_BUNDLE_HOME/bin | |
| # make sure netmhc-bundle tools are actually installed | |
| echo `which netMHC` && netMHC -h | |
| echo `which netMHCpan` && netMHCpan -h | |
| echo `which netMHCcons` && netMHCcons -h | |
| echo `which netMHCstab` && netMHCstab -h | |
| echo `which netMHCstabpan` && netMHCstabpan -h | |
| ./test.sh | |
| - name: Publish coverage to Coveralls | |
| uses: coverallsapp/[email protected] |