fix #6
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| name: dev-tests | |
| on: | |
| push: | |
| branches: | |
| - '**' | |
| - '!main' | |
| - '!master' | |
| tags-ignore: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - '**' | |
| - '!main' | |
| - '!master' | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: xpresspipe | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda clean --all | |
| conda install -c conda-forge mamba | |
| mamba env update --file requirements.yml --name xpresspipe | |
| conda activate xpresspipe | |
| pip install . | |
| pip install codecov flake8 | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage run -a tests/test_arguments.py | |
| coverage run -a tests/test_utils.py | |
| coverage run -a tests/test_bam.py | |
| coverage run -a tests/test_modifyGTF.py | |
| coverage run -a tests/test_truncateGTF.py | |
| coverage run -a tests/test_metagene.py | |
| coverage run -a tests/test_periodicity.py | |
| coverage run -a tests/test_complexity.py | |
| coverage run -a tests/test_rrnaProbe.py | |
| coverage run -a tests/test_help.py | |
| coverage run -a tests/test_pipelines.py | |
| - name: Generate coverage report | |
| shell: bash -l {0} | |
| run: | | |
| conda activate xpresspipe | |
| coverage report | |
| bash <(curl -s https://codecov.io/bash) -cF python |