test v0.3.0 #38
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| name: build | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: test-env | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| # Remove tmp files | |
| sudo rm -rf /tmp/* | |
| # Install conda packages | |
| conda env list | |
| conda info | |
| conda config --add channels defaults | |
| conda config --add channels bioconda | |
| conda config --add channels conda-forge | |
| conda install pandas==2.2.2 | |
| conda install maturin | |
| conda install rust | |
| conda install pylint | |
| conda install coveralls | |
| conda install pytest | |
| conda install pytest-cov | |
| conda install pysam==0.22.1 | |
| conda install numpy==1.26.2 | |
| conda install r-base==4.4.1 | |
| Rscript -e 'install.packages("dplyr", repos="https://cloud.r-project.org/")' | |
| Rscript -e 'install.packages("ggplot2", repos="https://cloud.r-project.org/")' | |
| Rscript -e 'install.packages("optparse", repos="https://cloud.r-project.org/")' | |
| pip install pyensembl | |
| # Install vstol | |
| pip install . --verbose | |
| - name: Download ensembl data | |
| shell: bash -l {0} | |
| run: | | |
| pyensembl install --release 95 --species human | |
| - name: Run linter | |
| shell: bash -l {0} | |
| run: | | |
| chmod +x lint.sh | |
| bash lint.sh | |
| - name: Run unit tests | |
| shell: bash -l {0} | |
| run: | | |
| chmod +x unittest.sh | |
| bash unittest.sh |