documented error message associated with khmer installation problems #357
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| on: push | |
| name: basic python | |
| jobs: | |
| example-1: | |
| name: (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| timeout-minutes: 120 | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: environment.yml | |
| - name: Conda info | |
| shell: bash -el {0} | |
| run: conda info | |
| - name: Conda env list | |
| shell: bash -el {0} | |
| run: | | |
| conda env list | |
| conda list | |
| - name: basic usage | |
| shell: bash -el {0} | |
| run: | | |
| which python | |
| python primerForge.py --help | |
| python primerForge.py --check_install | |
| - name: pip installation | |
| shell: bash -el {0} | |
| run: | | |
| pip install . | |
| primerForge --help | |
| primerForge --check_install | |
| - name: unit tests | |
| shell: bash -el {0} | |
| run: | | |
| python -m unittest discover -s ./bin/unit_tests/ -p "*_test.py" | |
| - name: upload pickles | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pickles | |
| path: test_dir/primerforge_*/*p | |
| - name: upload log | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: log | |
| path: test_dir/primerForge.log | |