0.0.10 🌈 Release

EHRData drops the .R field, and now supports 3D data storage in any slot of .layers. See the tutorials/getting_started tutorial for an introduction to this behaviour. In the future, .X will be enabled soon for 3D data storage as well.

Maintenance

• Enhanced tutorials/getting_started (#184) @eroell
• Move from zarr<3 to zarr>=3 (#185) @eroell

Modified

• EHRData drops the .R field in favor of using .layers for any 3D data arrays (#184) @eroell
• EHRData's shape property will always return a 3 dimensional shape. If an EHRData object has flat arrays only, the third dimension will be 1. (#184) @eroell @flying-sheep @Zethson
• The following functions now take a layer argument: ehrdata.io.read_csv, ehrdata.io.from_pandas, ehrdata.io.to_pandas, ehrdata.io.omop.setup_variables, ehrdata.io.omop.setup_interval_variables, ehrdata.dt.ehrdata_blobs, ehrdata.dt.physionet2012. If it is let to its default, None, the .X field of EHRData is used. Since .X is 2D in this release, in cases with 3D data, the layer argument needs to be used. (#184) @eroell
• ehrdata.io.write_zarr now writes an EHRData specific store encoding, with anndata as a substore. This change allows to use AnnData with its change to consolidated Zarr metadata, and better isolates AnnData's io. (#185) @eroell @flying-sheep
• ehrdata.io.read_zarr is adapted to read the new store encoding, and can also deal with AnnData stores. (#185) @eroell @flying-sheep