v0.3.0

New features

• New interface for pulling metadata (.obs/.var) from modalities and pushing it to modalities (#57)
  • Use mudata.set_options(pull_on_update=False) to adopt the new .update() behaviour
  • See documentation for examples
• mudata.concat() analogous to anndata.concat() (#58)
• Experimental mudata.to_anndata(mdata) (merging) and mudata.to_mudata(adata, key) (splitting) (#54)

as well as

• .mod_names attribute to match .obs_names and .var_names
• Pretty-print MuData.mod including axis information (#51)
• fsspec support for reading HDF5 files
  • See documentation for examples

Improvements

• Improve handling of intersecting .var_names across modalities when modalities are added to an existing MuData object
• Whenever possible, .update() uses bool dtype — and pd.BooleanArray when there are null values

Fixes

• Fix nested MuData dimensions in __repr__()
• Fix .uns contents for views
• Fix read_zarr() to use modality order
• Compatibility with anndata v0.11, pandas v2.0, numpy v2.0

Development

• Adopt the src layout
• Use hatch for the build process