anndata - Annotated Data¶
Report issues and see the code on GitHub.
0.7 January 22, 2020¶
Breaking changes introduced between 0.6.22.post1 and 0.7:
Internal modules like
anndata.coreare private and their contents are not stable: See #174.
The old deprecated attributes
.datahave been removed.
Currently broken features
sc.pp.normalize_per_celldoesn’t work on dask arrays. It just doesn’t modify the matrix.
- View overhaul – PR #164
Indexing into a view no longer keeps a reference to intermediate view, see #62.
Views are now lazy. Elements of view of AnnData are not indexed until they’re accessed.
Indexing with scalars no longer reduces dimensionality of contained arrays, see #145.
All elements of AnnData should now follow the same rules about how they’re subset, see #145.
Can now index by observations and variables at the same time.
- IO overhaul – PR #167
Reading and writing has been overhauled for simplification and speed.
Time and memory usage can be half of previous in typical use cases
Zarr backend now supports sparse arrays, and generally is closer to having the same features as HDF5.
Backed mode should see significant speed and memory improvements for access along compressed dimensions and IO. PR #241.
- Mapping attributes overhaul (obsm, varm, layers, …)
These are intended to store values like cell-by-cell graphs, which are currently stored in
Sparse arrays are now allowed as values in all mapping attributes.
All mapping attributes now share an implementation and will have the same behaviour. PR #164.
- Miscellaneous improvements
better support for aligned mappings (obsm, varm, layers) 0.6.22 #155 thanks to I Virshup
compatibility with Scipy >=1.3 by removing
IndexMixindependency. 0.6.20 #151 thanks to P Angerer
bug fix for second-indexing into views. 0.6.19 0ab553f thanks to P Angerer
bug fix for reading excel files. 0.6.19 90bea2c thanks to A Wolf
maintain dtype upon copy. 0.6.13 534bea4 thanks to A Wolf
initialization from pandas DataFrames 0.6. 648bcc8 thanks to A Wolf
Version 0.6 May 1, 2018¶
compatibility with Seurat converter
tremendous speedup for
bug fix for deep copy of unstructured annotation after slicing
bug fix for reading HDF5 stored single-category annotations
“outer join” concatenation: adds zeros for concatenation of sparse data and nans for dense data
better memory efficiency in loom exports