kb-python 0.2.0

Python wrapper around kallisto | bustools for scRNA-seq analysis

kb_python

A friendly wrapper around the kallisto | bustools pipeline for scRNA-seq analysis.

Prerequisites

• kallisto v0.46.0 and up. Must be accessible from the command-line as kallisto.
• bustools v0.39.3 and up. Must be accessible from the command-line as bustools.

There are plans to include installers for both prerequisites.

Binaries are included with the package starting version 0.0.8. There are no prerequisites starting from this version.

Development

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 unittests. 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 git push --tag.
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.