Merge branch 'dev' of https://github.com/pinellolab/simba into dev #133
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| name: CI | |
| on: [push, pull_request] | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - 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 defaults | |
| conda config --add channels bioconda | |
| conda config --add channels conda-forge | |
| conda config --set channel_priority strict | |
| # conda env update --file environment.yml --name base | |
| # conda install simba | |
| # conda install -c anaconda pip | |
| conda install jupyter pytorch pybedtools -y | |
| conda install r-essentials r-optparse bioconductor-jaspar2020 bioconductor-biostrings bioconductor-tfbstools bioconductor-motifmatchr bioconductor-summarizedexperiment r-doparallel bioconductor-rhdf5 bioconductor-hdf5array | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -e . | |
| - name: Lint with flake8 | |
| run: | | |
| conda install flake8 | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| conda install pytest pytest-cov | |
| pytest --cov | |
| - name: Coverage report | |
| run: | | |
| bash <(curl -s https://codecov.io/bash) |