sprocket_bio
A Python library for parsing and analyzing Workflow Description Language (WDL), powered by Sprocket.
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Installation
Sprocket's Python bindings are available on PyPI as
sprocket-bio. It requires Python 3.10 or greater, and
can be installed using Pip:
pip install sprocket-bio
Sprocket publishes precompiled
wheels for
many common platforms and Python versions. If you install sprocket-bio on a platform that does
not have a precompiled wheel, you will need the latest stable release of the Rust
compiler in order to build from source.
Release 0.31.0 ships wheels for CPython 3.10 through 3.15 (including the
free-threaded builds) and PyPy 3.11, covering macOS on x86-64 and Apple silicon,
manylinux and musllinux on x86-64 and aarch64, and Windows on x86-64 and
ARM64.
🐍 Minimum Supported Python Version
The minimum supported Python version is currently 3.10.
sprocket_bio supports the oldest Python version still receiving security updates. It will drop support for Python versions as they reach end-of-life. For more information, please see Python's Version Status page.
Usage
The package exposes three modules: sprocket_bio.grammar for parsing WDL,
sprocket_bio.ast for working with the resulting syntax tree, and
sprocket_bio.diagnostics for rendering diagnostics the way the command line
tool does. The package is typed, so it ships type stubs for editors and
mypy.
For example, parsing a document and printing any diagnostics:
from sprocket_bio.diagnostics import Mode, emit_diagnostics
from sprocket_bio.grammar import SupportedVersion
from sprocket_bio.grammar.grammar import document
from sprocket_bio.grammar.version import V1
with open("example.wdl", "rt", encoding="utf-8") as f:
source = f.read()
events, diagnostics = document(source, fallback_version=SupportedVersion.V1(V1.ZERO))
if diagnostics:
emit_diagnostics("example.wdl", source, diagnostics, report_mode=Mode.FULL, colorize=True)
Complete, runnable examples — emitting diagnostics, walking the parser event
stream, and building a syntax highlighter — live in
python/sprocket_bio/examples
in the Sprocket repository.
Documentation
You can find the Python binding's API docs and several examples online at https://sprocket-bio.readthedocs.io/.
🖥️ 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 and sort import statements.
black python/
isort 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, and import statement sorting is done by isort.
Code Coverage
To generate code coverage reports, first install the llvm-tools Rustup component and install cargo-llvm-cov. For example:
rustup component add llvm-tools
cargo install cargo-llvm-cov --version 0.8 --locked
Then, run the following commands with the virtual environment activated:
# Configure Rust to build with code coverage.
source <(cargo llvm-cov show-env --sh)
# Remove unwanted artifacts that may affect coverage results.
cargo llvm-cov clean --workspace
# Compile and install `sprocket_bio`.
maturin develop --group=cov
# Run tests and display Python code coverage.
pytest --cov=python/sprocket_bio
# Display Rust code coverage.
cargo llvm-cov report -p sprocket-py -p wdl-diagnostics -p wdl-grammar -p wdl-ast
Code coverage of Python code is generated using pytest-cov, which is installed as part of the cov dependency group. The Python report is printed when you run pytest with the --cov option. The Rust coverage data is generated when you run pytest as well, but the report must be printed after the fact using cargo-llvm-cov.
API Documentation
In order to build the API docs, you must have Python 3.12 or greater installed. You can then install the necessary dependencies and generate the website with the following commands:
# Install dependencies necessary to build API docs.
maturin develop --group docs
# Build website.
sphinx-build --fail-on-warning python/docs python/docs/_build
The API docs are built using Sphinx with the Read the Docs theme. The source is in python/docs, and the output is in python/docs/_build. The API docs are hosted online at https://sprocket-bio.readthedocs.io/.
📝 License and Legal
This project is licensed as either Apache 2.0 or MIT at your discretion. Additionally, please see the disclaimer that applies to all crates and command line tools made available by St. Jude Rust Labs.
Copyright © 2026-Present St. Jude Children's Research Hospital.
1 maintainer
Metadata
1 maintainer
Release files for sprocket-bio 0.32.0
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Built distributions (wheels)
Total release size: 61.6 MB
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