added checks to make sure netmhc tools are executable #21
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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@v4 | |
| - 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: ${{ secrets.NETMHC_BUNDLE_ACCESS_TOKEN }} | |
| - name: Configure netmhc-bundle paths | |
| run: | | |
| export NETMHC_BUNDLE_HOME=$PWD/netmhc-bundle | |
| mkdir tmp | |
| export NETMHC_BUNDLE_TMPDIR=$PWD/tmp | |
| export PATH=$PATH:$NETMHC_BUNDLE_HOME/bin | |
| # make sure netmhc-bundle tools are actually installed | |
| echo `which netMHC` && echo `which netMHCpan` && echo `which netMHCcons` | |
| # make sure netmhc-bundle tools are executable | |
| netMHC -h | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest pytest-cov coveralls | |
| pip install -r requirements.txt | |
| pip install . | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Run default linting script | |
| run: | | |
| ./lint.sh | |
| - name: Install MHCflurry data | |
| run: | | |
| mhcflurry-downloads fetch | |
| - name: Run unit tests | |
| run: | | |
| ./test.sh | |
| - name: Publish coverage to Coveralls | |
| uses: coverallsapp/github-action@v2.2.3 |