sprocket_bio

Python bindings to Sprocket, a bioinformatics toolkit for Workflow Description Language (WDL).

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🖥️ Development

sprocket_bio requires Python 3.10 or greater, which you can install from python.org or from your favorite package manager. Once you have Python installed, you can set up your development environment with the following commands:

# Create the Python virtual environment, installing the latest version of pip and setuptools.
python -m venv --upgrade-deps .venv

# Activate the virtual environment.
source .venv/bin/activate

# Install the build system, Maturin.
pip install maturin

# Compile and install `sprocket_bio` in the virtual environment.
maturin develop

# Run unit tests.
pytest

# Check types and type stubs.
mypy python/
python -m mypy.stubtest sprocket_bio

# Format code.
black python/

The Python package is located at python/sprocket_bio (in this folder), and the Python extension that it bundles is compiled from crates/sprocket-py using the Maturin build system. Dependencies and additional metadata are specified in pyproject.toml and crates/sprocket-py/Cargo.toml. Unit tests are defined in python/tests using the pytest framework. Type and stub checking is performed by mypy. Code formatting is performed by black.