This release is a pre-release and may not be stable for production use.
bioutils
Package Description
miscellaneous simple bioinformatics utilities and lookup tables
This project is a product of the biocommons community.
- Github repository: https://github.com/biocommons/bioutils/
- Documentation https://biocommons.github.io/bioutils/
Getting Help
- 🐛 Bug reports: Open an issue
- 💡 Feature requests: Open an issue
- ❓ Questions: Ask in biocommons/discussions
- 💬 General discussion: biocommons/discussions
Python Package Installation
Install from PyPI with pip install bioutils or uv pip install bioutils.
Developer Setup
Install Prerequisites
These tools are required to get started:
- git: Version control system
- GNU make: Current mechanism for consistent invocation of developer tools.
- uv: An extremely fast Python package and project manager, written in Rust.
MacOS or Linux Systems
- Install brew
brew install git make uv
Linux (Debian-based systems)
You may also install using distribution packages:
sudo apt install git make
Then install uv using the uv installation instructions.
One-time developer setup
Create a Python virtual environment, install dependencies, install git hooks (prek), and install an editable package:
make devready
Development
N.B. Developers are strongly encouraged to use make to invoke tools to
ensure consistency with the CI/CD pipelines. Type make to see a list of
supported targets. A subset are listed here:
» make
🌟🌟 biocommons conventional make targets 🌟🌟
Using these targets promots consistency between local development and ci/cd commands.
usage: make [target ...]
BASIC USAGE
help Display help message
SETUP, INSTALLATION, PACKAGING
devready Prepare local dev env: Create virtual env, install the git hooks (prek)
build Build package
publish publish package to PyPI
FORMATTING, TESTING, AND CODE QUALITY
cqa Run code quality assessments
test Test the code with pytest
test-coverage Test the code with pytest and generate coverage report
test-matrix Test with each supported Python version (via nox)
DOCUMENTATION
docs-serve Build and serve the documentation
docs-test Test if documentation can be built without warnings or errors
docs-deploy Deploy documentation to GitHub Pages
CLEANUP
clean Remove temporary and backup files
cleaner Remove files and directories that are easily rebuilt
cleanest Remove all files that can be rebuilt
distclean Remove untracked files and other detritus
Testing
make test # tests, no coverage
make test-coverage # tests with coverage; writes coverage.xml
make test-matrix # `make test` on each Python version listed in pyproject.toml classifiers (nox)
make test is the test command everywhere: locally, in each nox session, and in each CI matrix leg. One CI leg runs make test-coverage and uploads to Codecov instead.
Known limitation: nox does not forward arguments, so nox -- -k foo runs the full suite. Run one version with uv run nox -s tests-3.11, or a subset on one version with uv run --isolated --python 3.11 pytest -k foo (--isolated leaves .venv untouched).
VS Code
Testing → Configure Python Tests → pytest → root directory. No other settings are needed; coverage is off by default, so breakpoints work.
Coverage gate
Codecov's codecov/project status fails when coverage drops more than 0.5% from the base commit. Make codecov/project a required status check in branch protection, or the gate does nothing.
3 maintainers
Metadata
3 maintainers
Release files for bioutils 0.6.3a0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| bioutils-0.6.3a0.tar.gz | 700.3 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| bioutils-0.6.3a0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.0 MB
Release files / bioutils-0.6.3a0.tar.gz
| Download URL | bioutils-0.6.3a0.tar.gz |
|---|---|
| Size | 700.3 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
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Release files / bioutils-0.6.3a0-py3-none-any.whl
| Download URL | bioutils-0.6.3a0-py3-none-any.whl |
|---|---|
| Size | 316.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
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Security for bioutils 0.6.3a0
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