add pyCrossTalkeR

[ruthvik07]

Mandatory

Name of the tool: pyCrossTalkeR

Short description: pyCrossTalkeR is a framework for network analysis and visualisation of LR networks. pyCrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological states: disease vs. homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of pyCrossTalkeR for characterisation of changes in cellular crosstalk in disease state.

How does the package use scverse data structures (please describe in a few sentences): The package uses AnnData data structure to read and store the analysis results.

• 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)
• Automated tests cover essential functions of the package and a reasonable range of inputs and conditions [^1]
• Continuous integration (CI) automatically executes these tests on each push or pull request [^2]
• The package provides API documentation via a website or README[^3]
• 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:

  • Zulip:
  • Discourse:
  • Mastodon:
  • Bluesky:
  • Twitter:

• The package provides tutorials (or "vignettes") that help getting users started quickly

• The package uses the scverse cookiecutter template.

Maintainers

https://github.com/jsnagai - James Nagai
https://github.com/vckraemer - Venessa Klocker
https://github.com/CostaLab

[mikkelnrasmussen]

Hi @ruthvik07,

Thanks for submitting pyCrossTalkeR! Overall the package looks nice and well documented. The only comment I have is the fact that a lot of the tests are commented out in e.g. test_single.py and test_comparative.py. Ideally, the tests should cover all the essential functions of the package - i.e. all of the functions that you provide API documentation for at least.

Looking forward to hearing from you.

Best,
Mikkel

[jsnagai]

@mikkelnrasmussen we wiill adequate this during this week.

Best

[jsnagai]

@mikkelnrasmussen we have refactor the test and the fuctions of pyCrossTalkeR are fully covered now :)

[mikkelnrasmussen]

@ruthvik07 it seems to me that the files with out-commented tests have just been deleted. What I meant by my previous comment was that there should be tests covering all of the functions you provide API documentation for.

Best,
Mikkel

[flying-sheep]

Suggested change

	documentation_home: https://pycrosstalker.readthedocs.io/en/stable/
	tutorials_home: https://pycrosstalker.readthedocs.io/en/stable/
	documentation_home: https://pycrosstalker.readthedocs.io/
	tutorials_home: https://pycrosstalker.readthedocs.io/

[jsnagai]

@ ruthvik07, the files without commented-out tests have just been deleted. What I meant by my previous comment was that there should be tests covering all the functions for which you provide API documentation.

Best, Mikkel (@mikkelnrasmussen)

Dear Mikkel @mikkelnrasmussen, the files were removed once the tool functionallity covered by tests in the other units. The removed files were deleted once they were old scripts generated by @ruthvik07 while developing the tool. Currently, the unit tests are passing in both Python 3.11 and 3.12.

Happy to clarify and provide more tests if needed.

Best,