Add celltypist

[ChuanXu1]

Mandatory

Name of the tool: celltypist

Short description: CellTypist is an automated cell type annotation tool for scRNA-seq datasets.

How does the package use scverse data structures (please describe in a few sentences): CellTypist uses anndata for most analyses and is dependent on Scanpy.

• The code is publicly available under an OSI-approved license
• The package provides versioned releases
• The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda)
• The package uses automated software tests and runs them via continuous integration (CI)
• The package provides API documentation via a website or README
• The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
• I am an author or maintainer of the tool and agree on listing the package on the scverse website

Recommended

• Please announce this package on scverse communication channels (zulip, discourse, twitter)
• Please tag the author(s) these announcements. Handles (e.g. @scverse_team) to include are:
  • Twitter:
  • Zulip:
  • Discourse:
  • Mastodon:
• The package provides tutorials (or "vignettes") that help getting users started quickly
• The package uses the scverse cookiecutter template.

[grst]

The package uses automated software tests and runs them via continuous integration (CI)

I can't find any tests nor continous integration in the repo or am I overlooking something?
The rest is fine!

For a test/CI setup, you can check out how it's done in our cookiecutter template.
The probably lowest hanging fruit for test-cases are high-level "smoke tests", i.e. you just test the public interface on a test dataset and compare the results against a snapshot. Additionally lower level "unit test" could be implemented that test individual functions, including internal ones. Just having the former would be ok from our side, we mainly just want to make sure that there's an automated way to detect if something breaks.

[ChuanXu1]

I see. Will incorporate this and inform you then :)

[Zethson]

@ChuanXu1 just checking in, have you had a chance to look yet?

Thank you!