Automatic compression of the pairs. #112
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Build | |
| on: | |
| push: | |
| pull_request: | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.9'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Conda environment from metator.yaml | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| environment-file: metator.yaml | |
| extra-specs: | | |
| python=${{ matrix.python-version }} | |
| - name: Load apt packages | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -y install git make g++ default-jre default-jdk zlib1g-dev | |
| - name: Install Louvain | |
| run: | | |
| cd external | |
| tar -xzf louvain-generic.tar.gz | |
| cd gen-louvain | |
| make | |
| cd ../.. | |
| - name: Install Leiden | |
| run: | | |
| git clone https://github.com/vtraag/networkanalysis.git | |
| cd networkanalysis | |
| ./gradlew build | |
| cd .. | |
| - name: Test with pytest | |
| run: | | |
| micromamba activate metator | |
| export LOUVAIN_PATH=external/gen-louvain | |
| export LEIDEN_PATH=networkanalysis/build/libs/networkanalysis-1.2.0.jar | |
| PWD=$(pwd) | |
| export PATH="$PATH:$PWD/bwa:$PWD/pairix/bin/:$PWD/pairix/util:$PWD/pairix/util/bam2pairs:/root/.local/bin" | |
| pytest --pylint --pylint-error-types=EF --pylint-rcfile=.pylintrc --doctest-modules metator | |
| pytest --cov=metator | |
| codecov |