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0.7.0 {small}22 January, 2020

Breaking changes introduced between `0.6.22.post1` and `0.7`:

- Elements of {class}`~anndata.AnnData`s don’t have their dimensionality reduced when the main object is subset.
  This is to maintain consistency when subsetting. See discussion in {issue}`145`.
- Internal modules like `anndata.core` are private and their contents are not stable: See {issue}`174`.
- The old deprecated attributes `.smp*`. `.add` and `.data` have been removed.
  • Indexing into a view no longer keeps a reference to intermediate view, see {issue}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 {issue}145.
  • All elements of AnnData should now follow the same rules about how they’re subset, see {issue}145.
  • Can now index by observations and variables at the same time.
  • 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 {pr}241.
  • {class}~pandas.Categoricals can now be ordered (PR {pr}230) and written to disk with a large number of categories (PR {pr}217).
  • New attributes {attr}~anndata.AnnData.obsp and {attr}~anndata.AnnData.varp have been added for two dimensional arrays where each axis corresponds to a single axis of the AnnData object. PR {pr}207.
  • These are intended to store values like cell-by-cell graphs, which are currently stored in {attr}~anndata.AnnData.uns.
  • Sparse arrays are now allowed as values in all mapping attributes.
  • DataFrames are now allowed as values in {attr}~anndata.AnnData.obsm and {attr}~anndata.AnnData.varm.
  • All mapping attributes now share an implementation and will have the same behaviour. PR {pr}164.
  • Mapping attributes now have ipython tab completion (e.g. adata.obsm["\\t can provide suggestions) PR {pr}183.
  • {class}~anndata.AnnData attributes are now delete-able (e.g. del adata.raw) PR {pr}242.
  • Many many bug fixes