Add pyXenium to the scverse ecosystem

[hutaobo]

Summary

This PR proposes adding pyXenium to the scverse ecosystem packages list.

Proposed metadata file:

• packages/pyXenium/meta.yaml

Checklist for adding packages

Mandatory

Name of the tool: pyXenium

Short description:

pyXenium is a Python toolkit for 10x Genomics Xenium data that combines Xenium I/O, multimodal RNA+protein analysis, contour-aware spatial profiling, topology workflows, GMI inference, mechanostress analysis, and optional external workflow bridges.

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

pyXenium uses anndata.AnnData as its canonical analysis object for downstream RNA+protein and spatial workflows. Core loaders can return AnnData directly, and the package's multimodal, contour, pathway, benchmarking, and mechanostress modules operate on AnnData inputs or on XeniumSlide, a slide-level container whose main table is an AnnData. The project also keeps an optional interoperability bridge to SpatialData via XeniumSlide.to_spatialdata(), but does not require spatialdata as a core runtime dependency.

• 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)

• 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.

Additional notes

• Source: https://github.com/hutaobo/pyXenium
• Documentation: https://pyxenium.readthedocs.io/en/latest/
• Tutorials: https://pyxenium.readthedocs.io/en/latest/tutorials/index.html
• PyPI: https://pypi.org/project/pyXenium/
• Maintained by: SPATHO AB
• Current released version: 0.4.5

[Copilot]

Pull request overview

Adds pyXenium to the scverse ecosystem registry by introducing a new package metadata entry under packages/.

Changes:

• Added packages/pyXenium/meta.yaml with package description, links, tags, license, version, and test command.
• Registered PyPI installation identifier and maintainer contact.

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