add illico

[remydubois]

Mandatory

Name of the tool: illico

Short description: illico runs fast, CPU-based, wilcoxon rank-sum tests to identify differentially expressed genes for single-cell RNA-seq data.

How does the package use scverse data structures (please describe in a few sentences): illico uses AnnData objects as input data. It uses .X or .layers to read expression counts, and .obs to get the grouping variable.

• 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 README3
• The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
• 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: @remydubois, post is here: #announce > illico: x100 faster rank-sum tests on CPU in python @ 💬

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

• The package uses the scverse cookiecutter template.

[mikkelnrasmussen]

Hi @remydubois,

Thanks for submitting illico, it looks like a really nice tool! In general the package looks good, however I have one comment regarding API documentation. By API documentation, we mean a structured listing of all functions/classes/methods, including their arguments and expected inputs/outputs. A good example is the scirpy API docs. I recommend looking into Sphinx Autodoc plugin to generate this kind of documentation. I was not able to find this kind of API documentation for the package.

Looking forward to hearing from you.

Best regards,
Mikkel

[remydubois]

Hi,

Thanks for looking into this. I agree an API doc would be helpful.

Because only one function is meant at being user facing (illico.asymptotic_wilcoxon), I could be in favor of showing only this function in the doc, unless specific rules exist in the scverse ecosystem. What do you think ?

Rémy