Add ggml-ot

[DaminK]

Name of the tool: ggml-ot

Short description: ggml-ot enables supervised optimal transport for classification, clustering and embedding of patient-level single-cell data across conditions, disease states and treatments.

How does the package use scverse data structures: ggml-ot works directly on AnnData via ggml_ot.from_anndata. Samples and labels are taken from .obs columns, and either .X or any .obsm representation can be used as the cell input, which can be optionally aggregated according to an .obs column (e.g "cell_type" or "leiden"). Learned results are written back in-place following scverse conventions: the learned map to a latent space in .uns, the corresponding gene-space loadings in .varm, and the projected cell embedding in .obsm. It is interoperable with Scanpy which we demonstrate in the tutorials using processing (sc.pp.*), clustering/embedding (sc.tl.*) and plotting (sc.pl.*) functions.

Mandatory

• 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
• Continuous integration (CI) automatically executes these tests on each push or pull request
• The package provides API documentation via a website or README
• 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)
  Note: Will be done upon acceptance into scverse ecosystem
• 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.