Metadata-Version: 2.1
Name: kb_python
Version: 0.2.0
Summary: Python wrapper around kallisto | bustools for scRNA-seq analysis
Home-page: https://github.com/pachterlab/kb_python
Author: Kyung Hoi (Joseph) Min
Author-email: phoenixter96@gmail.com
Maintainer: Pachter Lab
Maintainer-email: lsledd@caltech.edu
License: BSD
Description: # kb_python
        ![](https://img.shields.io/badge/Version-0.2.0-informational)
        ![](https://github.com/pachterlab/kb_python/workflows/CI/badge.svg)
        
        A friendly wrapper around the kallisto | bustools pipeline for scRNA-seq analysis.
        
        ## Prerequisites
        - ~~[kallisto](https://pachterlab.github.io/kallisto/) v0.46.0 and up.
        Must be accessible from the command-line as `kallisto`.~~
        - ~~[bustools](https://bustools.github.io/) 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.
        
Keywords: kallisto bustools
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Utilities
Requires-Python: >=3.6
Description-Content-Type: text/markdown
