Add scCellFie

[earmingol]

Checklist for adding packages

Mandatory

Name of the tool: scCellFie

Short description: scCellFie is a Python tool for analyzing metabolic activity at different resolutions, developed at the Vento Lab. It efficiently processes both single-cell and spatial data to predict metabolic task activities. Additionally, scCellFie offers downstream analyses such as marker selection, differential analysis, and cell-cell communication inference.

How does the package use scverse data structures (please describe in a few sentences): anndata is used as input (and output whenever appropriate); uses, squidpy's neighborhood graph format; and integrates scanpy's visualizations.

• 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)
• 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:

  • Bluesky: @erickarmingol.bsky.social‬
  • Twitter: @eagut; @roserventotormo

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

• The package uses the scverse cookiecutter template.

Footnotes

1. We recommend thtat tests cover at least all user facing (public) functions. Minimal tests ensure that the function does not fail on an example data set. Ideally, tests also ensure the correctness of the results, e.g. by comparing against a snapshot. ↩

2. Continuous integration means that software tests are automatically executed on every push to the git repository. This guarantees they are always run and that they are run in a clean environment. Scverse ecosystem packages most commonly use GitHub Actions for CI. For an example, check out our cookiecutter template. ↩

3. By API documentation, we mean an overview of all public functions provided a package, with documentation of their parameters. For an example, see the Scanpy documentation. In simple cases, this can be done manually in a README file. For anything more complex, we recommend the Sphinx Autodoc plugin ↩

[mikkelnrasmussen]

Hi @earmingol,

Thanks for submitting scCellFie - it looks like a super cool package! Everything looks good to me: good API documentation, clear tutorials and great test coverage.

Best regards,
Mikkel

[earmingol]

awesome, thank you 😊!