Add actinn-jax to the ecosystem package registry

[iandriver]

Mandatory

Name of the tool: actinn-jax

Short description: A JAX reimplementation of ACTINN for cell-type annotation of scRNA-seq data. It trains a neural-network classifier from a labelled AnnData reference and annotates query AnnData objects on CPU, with pre-trained human references bundled or downloaded on first use.

How does the package use scverse data structures (please describe in a few sentences): AnnData is the interface on both sides. train_reference reads counts from adata.X or adata.raw.X and labels from a column of adata.obs. annotate/predict write predictions back into adata.obs in place (celltype, celltype_probability, celltype_coarse), and predict_frame returns the same as a DataFrame indexed by adata.obs_names for callers who want the probabilities without mutating the object. Gene identifiers are matched between reference and query from adata.var_names, falling back to a column of adata.var when var_names do not overlap the reference. detect_novel_celltypes builds an AnnData internally and uses scanpy for normalisation, PCA, neighbours and Leiden clustering, writing its flags to adata.obs.

• 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
• I agree to abide by the scverse code of conduct on all scverse communication channels

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

• The package uses the scverse cookiecutter template.

• I would like to be invited to the scverse Github organization