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0.10.0rc1 {small}2023-09-09

anndata 0.10.0 is currently available as a release candidate for testing. You can install this version of anndata with:

```
pip install -U --pre anndata
```

We expect to make a full release by October.

GPU Support

  • Dense and sparse CuPy arrays are now supported {pr}1066 {user}ivirshup
    • Once you have CuPy arrays in your anndata, use it with: rapids-singlecell from v0.9+
  • anndata now has GPU enabled CI. Made possibly by a grant from CZI's EOSS program and managed via Cirun {pr}1066 {pr}1084 {user}Zethson {user}ivirshup

Out of core

  • Concatenate on-disk anndata objects with {func}anndata.experimental.concat_on_disk {pr}955 {user}selmanozleyen
  • AnnData can now hold dask arrays with scipy.sparse.spmatrix chunks {pr}1114 {user}ivirshup
  • Public API for interacting with on disk sparse arrays: {func}~anndata.experimental.sparse_dataset, {class}~anndata.experimental.CSRDataset, and {class}~anndata.experimental.CSCDataset {pr}765 {user}ilan-gold {user}ivirshup

Improved errors and warnings

  • Improved error messages when combining dataframes with duplicated column names {pr}1029 {user}ivirshup
  • Improved warnings when modifying views of AlingedMappings {pr}1016 {user}flying-sheep {user}ivirshup
  • AnnDataReadErrors have been removed. The original error is now thrown with additional information in a note {pr}1055 {user}ivirshup
  • {meth}anndata.AnnData.transpose no longer copies unnecessarily. If you rely on the copying behavior, call .copy on the resulting object. {pr}1114 {user}ivirshup
  • Removal of deprecated dtype argument to AnnData constructor {pr}1126 {user}ivirshup
  • Bump minimum python version to 3.9 {pr}1117 {user}flying-sheep
  • Deprecate anndata.read, which was just an alias for {func}anndata.read_h5ad {pr}1108 {user}ivirshup.
  • Fix shape inference on initialization when X=None is specified {pr}1121 {user}flying-sheep