DEVELOPER.md

Developer guide

Warning

This section is only for developers.

Full install

git clone [email protected]:gao-lab/DECIPHER.git && cd DECIPHER
mamba create -p ./conda -c conda-forge -c rapidsai -c nvidia -c bioconda python=3.11 rapids=24.04 cuda-version=11.8 cudnn cutensor cusparselt pandoc snakemake==7.32.4 -y && conda activate ./conda
pip install -e ".[dev, docs]"
install_pyg_dependencies

Unit test

Not finish yet

pytest --cov -n 8

Build docs

cd docs
sphinx-build -b html ./ ./_build/html

Enable code style checking

pre-commit install

Time analysis

py-spy record -o profile.svg -- python -m <YOUR_SCRIPT.py>

Build docker image

# cd DECIPHER/
docker image build --no-cache . -t huhansan666666/decipher:v0.1.0 --network=host