add scprint-2

[jkobject]

Mandatory

Name of the tool: scPRINT-2

Short description: A next generation single cell foundation model

How does the package use scverse data structures (please describe in a few sentences): XXX

• 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.

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. ↩

[Copilot]

Pull request overview

This PR adds metadata for five new packages to the scverse ecosystem: scPRINT-2 (a next-generation single cell foundation model), scPRINT (the original single cell foundation model), scDataLoader (a dataloader for large single cell databases), benGRN (a benchmarking tool for gene network inference), and GRnnData (an AnnData extension for gene networks). All packages are authored by jkobject (Jeremie Kalfon) and follow the required meta.yaml schema format.

• Added scPRINT-2 package metadata with GPL-3.0-or-later license
• Added four supporting packages (scPRINT, scDataLoader, benGRN, GRnnData) all with MIT license
• All packages include standard fields: project home, documentation, publications, installation instructions, tags, version, and test commands

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
packages/scPRINT-2/meta.yaml	Adds metadata for the next-generation scPRINT foundation model with additional features like species integration and counterfactual predictions
packages/scPRINT/meta.yaml	Adds metadata for the original scPRINT foundation model focused on gene network inference
packages/scDataLoader/meta.yaml	Adds metadata for a dataloader supporting weighted random sampling from large single cell databases
packages/benGRN/meta.yaml	Adds metadata for a gene network inference benchmarking tool using biological ground truth networks
packages/GRnnData/meta.yaml	Adds metadata for an AnnData extension providing utilities for working with gene networks

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[grst]

CI fails because usernames are now validated against the github api:

[03/21/26 19:13:03] ERROR    ERROR:ecosystem_scripts._logging:Validation error: GRnnData: Failed to validate GitHub users      validate_registry.py:48
                             ['jkobject (jeremie kalfon)']:                                                                                           
                             - Could not resolve to a User with the login of 'jkobject (jeremie kalfon)'. 

Please use plain github user IDs

[grst]

not sure what went wrong, but this issue is back.

[jkobject]

updated username

[grst]

I'm really sorry for the delay, I'm only getting back to reviewing these ecosystem PRs now.
Please fill and add the checklist to the main comment of this PR. Once it's there, we will proceeed with the package review.

[jkobject]

done

[jkobject]

I am not sure what is going on now...