Update test_oligo_specificity_filter.py #151
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| name: test | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - 'README.md' | |
| - 'pyproject.toml' | |
| - 'docs/**' | |
| - 'tutorials/**' | |
| - '.github/workflows/**' | |
| pull_request: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - 'README.md' | |
| - 'pyproject.toml' | |
| - 'docs/**' | |
| - 'tutorials/**' | |
| - '.github/workflows/**' | |
| workflow_dispatch: | |
| workflow_call: | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 12 | |
| matrix: | |
| os: [ubuntu-latest] #, macos-latest, windows-latest | |
| python-version: ["3.9", "3.10"] # "3.10", "3.11", "3.12" | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Setup Conda for Ubuntu and Mac | |
| if: matrix.os != 'windows-latest' | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Setup Conda for Windows | |
| if: matrix.os == 'windows-latest' | |
| uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| conda-channels: anaconda, conda-forge | |
| - name: Update conda and add channels | |
| run: | | |
| conda config --add channels bioconda | |
| conda config --add channels conda-forge | |
| conda update --all | |
| - name: check python and conda version | |
| run: | | |
| conda --version | |
| conda config --show channels | |
| which python | |
| python --version | |
| - name: Check permissions | |
| run: | | |
| echo blablabla > test.txt | |
| ls -lh | |
| - name: Install conda dependencies | |
| run: | | |
| conda install "blast>=2.12" | |
| conda install "bedtools>=2.30" | |
| conda install "bowtie2>=2.5" | |
| conda install "bowtie>=1.3.1" | |
| - name: Install pip dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest | |
| pip install -e . | |
| - name: Test with pytest | |
| run: pytest | |