mudata - v0.3.2

New functionality

• Empty MuData objects can be instantiated (#65)

Functionality improvements and fixes

• Improvements and fixes for slicing MuData objects and copying views (incl. #94)

• Improvements for adding new modalities via mdata.mod["new_modality"] = adata (#99)

Compatibility improvements

• Compatibility with newer zarr versions

• Compatibility with newer anndata versions (#100)

- Python
Published by gtca about 1 year ago

mudata - v0.3.1

Compatibility with anndata v0.10.9.

- Python
Published by gtca almost 2 years ago

mudata - 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

- Python
Published by gtca almost 2 years ago

mudata - v0.2.4

Compatibility improvements

• Compatible with the numpy 2.0.0 release — requires anndata 0.10.8 or newer
• Compatible with the dtype argument deprecation in the anndata 0.11

- Python
Published by gtca almost 2 years ago

mudata - v0.2.3

• Fixes and improvements for backed objects (#30) and views (#31, #32)
• Improved pandas 2.0 compatibility (#43)
• Improvements for nested MuData objects
• I/O and HTML representation improvements

- Python
Published by gtca almost 3 years ago

mudata - v0.2.2

• Together with the latest versions of anndata, required Python 3.8 or higher
• .read() now accepts filenames as pathlib.Path objects

- Python
Published by gtca about 3 years ago

mudata - v0.2.1

• .update() improvements and optimisations
• __len__() method that returns the total number of observations (https://github.com/scverse/mudata/issues/26)
• Using dict where older versions might have used OrderedDict (https://github.com/scverse/muon/issues/65)

- Python
Published by gtca over 3 years ago

mudata - v0.2.0

• Compatibility with the new I/O specification from AnnData v0.8
• New axes interface allows to use MuData object as containers with different shared dimensions
• .update() behaviour and performance improvements

- Python
Published by gtca almost 4 years ago

mudata - v0.1.2

• Enhanced zarr support (#7).
• There's a new page in the documentation describing the sharp bits.
• There's a new mod-order attribute.

- Python
Published by gtca about 4 years ago

mudata - v0.1.1

This version comes with stability improvements and fixes.

- Python
Published by gtca over 4 years ago