kb-python 0.2.1

Python wrapper around kallisto | bustools for scRNA-seq analysis

kb-python

A wrapper for the kallisto | bustools single-cell RNA-seq workflow.

Prerequisites

None. The kallisto and bustools binaries are included with the package.

Getting Started

Visit the Getting Started page.

Tutorials

• WIP...

Development

Documentation

Developer documentation is hosted on Read the Docs.

Code Quality

kb-python uses flake8 and yapf to ensure code quality and nose to run unittests. All necessary dependencies for development can be installed by running pip install -r dev-requirements.txt.

The CI workflow ensures all code passes code quality checks and unit tests. It is recommended to use pre-commit to make sure each commit satisfies code quality specifications. To do so, first install pre-commit by running pip install pre-commit, and then at the root run pre-commit install. Every future commit will pass through flake8 and yapf.

Bumpversion

Bumping versions is done with bumpversion. This should be installed from the dev-requirements.txt, but can be installed separately with pip. To bump version and release the new version to Pypi,

1. Run make bump_patch, make bump_minor or make bump_major depending on which version to bump. This will make a new commit and create a new tag with the new version.
2. Push the commit and tag with make push_release.
3. Go to the releases tab on Github. Select the version that was just commited. Edit tag, write a description, and Publish release.
4. A Github Actions workflow will be triggered to build and upload the updated package to Pypi.