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anndata-rs Python bindings

anndata_rs is the Python package for the Rust anndata-rs backend. It provides a backed AnnData API for reading, writing, subsetting, and streaming AnnData objects without loading every field into memory.

The package follows the AnnData data model:

  • X: primary observations × variables matrix, dense or sparse.
  • obs / var: observation and variable annotations.
  • obsm / varm: multi-dimensional annotations.
  • obsp / varp: pairwise annotations.
  • layers: alternative matrices with the same shape as X.
  • uns: unstructured metadata.

Key differences from Python anndata

  1. AnnData is opened in backed mode by default.
  2. Elements are lazily loaded; arrays are read when requested.
  3. Subsetting writes/copies data instead of creating AnnData views.
  4. The current Python package is centered on HDF5/.h5ad workflows. Use the Rust API directly for the full set of Rust backend features, including object-store Zarr workflows.

Package layout note

The user-facing Python package is in the repository's python/ directory and is imported as anndata_rs. The pyanndata/ Rust crate contains the internal PyO3 implementation used by the package.

For details about the AnnData specification, see https://anndata.readthedocs.io/en/latest/.

.. toctree::
   :maxdepth: 3
   :hidden:

   install
   api