13 inversion detection #231
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| name: build tests | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| jobs: | |
| build-and-test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Download assets | |
| uses: dsaltares/fetch-gh-release-asset@1.0.0 | |
| with: | |
| repo: 'WGLab/ContextSV' | |
| version: 'tags/v0.1.0' | |
| file: 'TestData.zip' | |
| - name: Unzip assets | |
| shell: bash --login {0} | |
| run: unzip TestData.zip | |
| - name: Set up conda (Miniconda only) | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-activate-base: true | |
| python-version: 3.10 | |
| - name: Configure conda channels and create environment | |
| shell: bash -l {0} | |
| run: | | |
| conda config --remove channels defaults || true | |
| conda config --add channels conda-forge | |
| conda config --add channels bioconda | |
| conda config --set channel_priority strict | |
| conda info # confirm the change | |
| conda env create -f environment.yml | |
| - name: Build C++ code | |
| shell: bash --login {0} # --login enables PATH variable access | |
| run: | | |
| make | |
| - name: Run unit tests | |
| shell: bash --login {0} | |
| run: | | |
| mkdir -p tests/output | |
| python -m pytest -s -v tests/test_general.py |