Add anndata-duckdb extension

[honicky]

Adding anndata-duckdb

A DuckDB extension for reading AnnData (.h5ad) files, providing SQL access to single-cell genomics data.

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Mandatory

Name of the tool: anndata-duckdb

Short description: DuckDB extension that provides SQL access to AnnData (.h5ad) files, enabling queries on obs, var, X matrix, dimensional reductions, layers, and unstructured metadata.

How does the package use scverse data structures: The extension reads AnnData HDF5 files directly, providing SQL table access to all standard AnnData components: observation metadata (obs), variable metadata (var), expression matrix (X), dimensional reductions (obsm/varm like PCA/UMAP), pairwise matrices (obsp/varp), alternative expression layers, and unstructured metadata (uns).

• The code is publicly available under an OSI-approved license (MIT)
• The package provides versioned releases
• The package can be installed from a standard registry (DuckDB community extensions: INSTALL anndata FROM community; LOAD anndata)
• 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 (reads AnnData files natively)
• 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 following accounts:
  • Twitter: https://x.com/honicky?
  • BlueSky: https://bsky.app/profile/honicky.bsky.social
  • LinkedIn: https://www.linkedin.com/in/rj-honicky/
• The package provides tutorials (or "vignettes") that help getting users started quickly
• The package uses the scverse cookiecutter template

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Note on installation: This is a DuckDB extension, not a Python package. The install field in meta.yaml lists duckdb (available on PyPI and conda-forge) since the schema doesn't have a DuckDB extension registry option. It can be used from python like any duckdb extension.

Users can install the DuckDB CLI, then run INSTALL anndata FROM community; from within DuckDB to install and load the extension from the DuckDB community extension repository.