BUG fix testing #456
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| name: semibin_test | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python-version: | |
| - "3.7" | |
| - "3.8" | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| - "3.12" | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: test | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: false | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run : | | |
| conda install -c conda-forge numpy pandas pytest hypothesis python-igraph scikit-learn requests numexpr tqdm | |
| conda install -c conda-forge -c bioconda bedtools hmmer fraggenescan prodigal samtools mmseqs2 | |
| conda install -c pytorch -c nvidia pytorch pytorch-cuda=11.8 | |
| pip install . | |
| - name: Test with pytest | |
| shell: bash -l {0} | |
| run: | | |
| python -m pytest ./test | |
| - name: Test with SemiBin command | |
| shell: bash -l {0} | |
| run: | | |
| for t in integration-tests/*.py; do | |
| echo "Running $t ..." | |
| python $t | |
| done | |