Add ATLAS to scverse ecosystem

[LorenzoMartiniTini]

Name of the tool: ATLAS

Short description: ATLAS is a framework for multi-omic trajectory inference from paired single-cell RNA and ATAC sequencing data. By integrating transcriptional and chromatin accessibility information within a unified representation, ATLAS enables pseudotime reconstruction and cell fate prediction that directly incorporate regulatory dynamics.

How does the package use scverse data structures (please describe in a few sentences): ATLAS is based on MuData for multiomics-data representation (AnnData for single modalities). Then exploits CellRank and Palantir for TI.

• 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:

Zulip:
Discourse:
Mastodon:
Bluesky:
Twitter: @smiliespolito , @LorenzoGAGAM

• The package provides tutorials (or "vignettes") that help getting users started quickly
• The package uses the scverse cookiecutter template.

[LorenzoMartiniTini]

Hi maintainers, and thanks for the review process!

I wanted to flag the current CI status. In the latest validate-registry run, ATLAS itself validates cleanly — PyPI package, GitHub users, and home/docs/tutorial URLs all pass with no errors:

INFO:scverse-eco:Validated PyPI package for ATLAS: atlas-smilies
INFO:scverse-eco:Validated GitHub users for ATLAS: ['AlessiaLeclercq', 'LorenzoMartiniTini']
INFO:scverse-eco:Validated home URL for ATLAS: 'https://github.com/smilies-polito/atlas-smilies'

The job is failing only because of intermittent 403 errors that ReadTheDocs returns when its pages are requested from the GitHub Actions runners. These affect many already-registered packages (e.g. muon, scvi-tools, pertpy, decoupler, cell2location, schist, biolord, …), not this PR.

For reference, the ATLAS docs are in fact reachable (RTD returns HTTP 200 outside the runner): https://atlas-smilies.readthedocs.io/

Could you advise on how you'd like to proceed? Happy to make any further changes on my side if needed. Thanks!

[muskanhashim]

Hi @LorenzoMartiniTini, thanks for your submission. It looks to be in great shape: MuData/AnnData throughout, nice integration with CellRank and Palantir, solid method-level tests, CI, and API docs.

Just wanted to share a quick update. We recently tightened the registry schema (#392: controlled-vocabulary tags + new required primary_category and language fields). Since that's our registry metadata, I've gone ahead and updated the meta.yaml for you (tags mapped to the vocabulary (multimodal, trajectory inference, pseudotime, scRNA-seq, ATAC-seq), primary_category: Multimodal, language: Python). No action needed from your end but please feel free to let us know if you think a different tag/primary_category better fits.

Thanks again for a clean submission!

[LorenzoMartiniTini]

@muskanhashim Thank you for your review of the PR and thank you for updating the tags accordingly with the new schema. The tags you set fits perfectly for me. This means the PR is near to be accepted and merged in the scverse ecosystem?

Thank you again!

[muskanhashim]

@muskanhashim Thank you for your review of the PR and thank you for updating the tags accordingly with the new schema. The tags you set fits perfectly for me. This means the PR is near to be accepted and merged in the scverse ecosystem?

Thank you again!

yes :)

the only (small, non-blocking note) i could find unrelated to the listing is a small typo: in src/atlas/tl/init.py the all lists fate_concentrarion_index and terminal_state_sihlouette, but the actual functions (and your API docs) are spelled fate_concentration_index and terminal_state_silhouette. So from atlas.tl import * would error on those two entries. Just a heads-up for whenever you next touch that file, but doesn't affect the ecosystem listing!