Merge pull request #93 from jonasscheid/fix_netmhc_len_restriction #289
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| name: Unit tests external tools | |
| on: | |
| push: | |
| branches: [ main, develop ] | |
| pull_request: | |
| branches: [ main, develop ] | |
| jobs: | |
| tests-external: | |
| strategy: | |
| matrix: | |
| platform: [ubuntu-latest] | |
| python-version: [3.7] | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| path: epytope | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: kohlbacherlab/fred-tools | |
| token: ${{ secrets.FRED_CI_PAT }} | |
| path: epytope-tools | |
| - name: Install epytope-tools system dependencies | |
| run: | |
| apt-fast install -y tcsh | |
| - name: epytope-tools post scripts | |
| working-directory: ./epytope-tools/ | |
| run: | | |
| ./post.runner | |
| - name: Set conda package directory | |
| run: | | |
| mkdir /tmp/condapkgs | |
| echo "CONDA_PKGS_DIRS=/tmp/condapkgs" >> $GITHUB_ENV | |
| - name: Activate epytope-tools | |
| run: | | |
| echo "$PWD/epytope-tools/bin" >> $GITHUB_PATH | |
| echo "PATH=$PATH" | |
| - name: Set up Python ${{ matrix.python-version }} | |
| run: | | |
| $CONDA/bin/conda create -p /tmp/condaenv python==${{ matrix.python-version }}'.*' setuptools"==52.0" protobuf"<=3.20.1" | |
| - name: Activate conda environment | |
| run: | | |
| echo "/tmp/condaenv/bin" >> $GITHUB_PATH | |
| export PATH="/tmp/condaenv/bin:$PATH" | |
| - name: Install epytope | |
| run: | | |
| pip install ./epytope/ | |
| - name: Set up test environment | |
| run: | | |
| conda install -p /tmp/condaenv -c conda-forge -c bioconda nose | |
| - name: Run Tests - Cleavage Prediction | |
| working-directory: ./epytope/ | |
| continue-on-error: true | |
| run: nosetests -v epytope/test/external/TestExternalCleavagePrediction.py || echo "Cleavage Prediction" >> FAILED_TESTS | |
| - name: Run Tests - Epitope Prediction | |
| working-directory: ./epytope/ | |
| run: nosetests -v epytope/test/external/TestExternalEpitopePrediction.py || echo "Epitope Prediction" >> FAILED_TESTS | |
| - name: Validate Test Results | |
| working-directory: ./epytope/ | |
| run: | | |
| if [ -e FAILED_TESTS ]; then | |
| echo "FAILED TESTS:" >&2 | |
| cat FAILED_TESTS | |
| exit 1 | |
| fi |