Add pycea

[colganwi]

Name of the tool: pycea

Short description: Pycea is a Python toolkit for single-cell lineage tracing analysis and visualization.

How does the package use scverse data structures (please describe in a few sentences): Pycea is built to use TreeData a lightweight wrapper around AnnData that adds support for storing trees. Since the TreeData object is a drop in replacement for AnnData pycea seamlessly integrates into the scverse ecosystem. Users easily perform analyses like clustering with scanpy then immediately plot those clusters on the lineage tree.

• 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.

[mikkelnrasmussen]

Hi @colganwi,

Thanks for submitting pycea - it looks super nice and integrates nicely with TreeData! Again everything looks good - nice documentation, tutorials and test coverage.

Best,
Mikkel