test: more tests for binning/zoomify/balance combinations #38
Workflow file for this run
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name: build | |
on: [push] | |
jobs: | |
build-linux: | |
runs-on: ubuntu-latest | |
strategy: | |
max-parallel: 5 | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Set up Python 3.9 | |
uses: actions/setup-python@v2 | |
with: | |
python-version: 3.9 | |
- name: Add conda to system path | |
run: | | |
# $CONDA is an environment variable pointing to the root of the miniconda directory | |
echo $CONDA/bin >> $GITHUB_PATH | |
- name: Install dependencies | |
run: | | |
conda config --add channels bioconda | |
conda install -c conda-forge python=3.9 minimap2 bowtie2=2.4.5 bwa samtools htslib pysam pytest cooler pytest-cov pylint codecov mappy | |
pip install -Ur requirements.txt | |
pip install pytest-pylint | |
- name: Lint and test | |
run: | | |
pytest --pylint --pylint-error-types=EF --pylint-rcfile=.pylintrc --doctest-modules --doctest-modules hicstuff | |
pytest --cov=hicstuff | |
codecov |