anndata 0.12.0rc2__tar.gz → 0.12.0rc3__tar.gz

{anndata-0.12.0rc2 → anndata-0.12.0rc3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: anndata
-Version: 0.12.0rc2
+Version: 0.12.0rc3
 Summary: Annotated data.
 Project-URL: Documentation, https://anndata.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/anndata
@@ -32,7 +32,7 @@ Requires-Dist: numpy>=1.25
 Requires-Dist: packaging>=24.2
 Requires-Dist: pandas!=2.1.0rc0,!=2.1.2,>=2.0.0
 Requires-Dist: scipy>=1.11
-Requires-Dist: zarr!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,<3.0.7,>=2.18.7
+Requires-Dist: zarr!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3,!=3.0.4,!=3.0.5,!=3.0.6,!=3.0.7,>=2.18.7
 Provides-Extra: cu11
 Requires-Dist: cupy-cuda11x; extra == 'cu11'
 Provides-Extra: cu12

{anndata-0.12.0rc2 → anndata-0.12.0rc3}/docs/conf.py

@@ -112,8 +112,7 @@ intersphinx_mapping = dict(
     python=("https://docs.python.org/3", None),
     scipy=("https://docs.scipy.org/doc/scipy", None),
     sklearn=("https://scikit-learn.org/stable", None),
-    # TODO: move back to stable once `ObjectStore` is released
-    zarr=("https://zarr.readthedocs.io/en/latest/", None),
+    zarr=("https://zarr.readthedocs.io/en/stable/", None),
     xarray=("https://docs.xarray.dev/en/stable", None),
     obstore=("https://developmentseed.org/obstore/latest/", None),
     kvikio=("https://docs.rapids.ai/api/kvikio/stable/", None),

{anndata-0.12.0rc2 → anndata-0.12.0rc3}/docs/release-notes/0.12.0rc2.md

@@ -1,14 +1,14 @@
 (v0.12.0rc2)=
 ### 0.12.0rc2 {small}`2025-05-15`
 
-### Bug fixes
+#### Bug fixes
 
 - Convert 1d {class}`numpy.ndarray` and {class}`cupy.ndarray`s in {attr}`anndata.AnnData.obsm` and {attr}`anndata.AnnData.varm` to 2d {user}`ilan-gold` ({pr}`1962`)
 
-### Features
+#### Features
 
 - Allow xarray Datasets to be used for obs/var/obsm/varm. {user}`ilia-kats` ({pr}`1966`)
 
-### Performance
+#### Performance
 
 - Load AnnLoader lazily to prevent expensive unnecessary `torch` imports when its available on the system. {user}`Zethson` & {user}`flying-sheep` ({pr}`1950`)

anndata-0.12.0rc3/docs/release-notes/0.12.0rc3.md

@@ -0,0 +1,6 @@
+(v0.12.0rc3)=
+### 0.12.0rc3 {small}`2025-05-20`
+
+### Bug fixes
+
+- Update zarr v3 bound to >3.0.8 to prevent corrupted data {issue}`zarr-developers/zarr-python#3061` {user}`ilan-gold` ({pr}`1993`)

{anndata-0.12.0rc2 → anndata-0.12.0rc3}/pyproject.toml

@@ -46,7 +46,7 @@ dependencies = [
     "packaging>=24.2",
     "array_api_compat>=1.7.1",
     "legacy-api-wrap",
-    "zarr >=2.18.7, !=3.0.0, !=3.0.1, !=3.0.2, !=3.0.3, <3.0.7",
+    "zarr >=2.18.7, !=3.0.0, !=3.0.1, !=3.0.2, !=3.0.3, !=3.0.4, !=3.0.5, !=3.0.6, !=3.0.7",
 ]
 dynamic = [ "version" ]
 

{anndata-0.12.0rc2 → anndata-0.12.0rc3}/src/anndata/_io/zarr.py

@@ -141,7 +141,7 @@ def read_dataset(dataset: zarr.Array):
     elif len(value.dtype.descr) > 1:  # Compound dtype
         # For backwards compat, now strings are written as variable length
         value = _from_fixed_length_strings(value)
-    if value.shape == ():
+    if value.shape == () and not np.isscalar(value):
         value = value[()]
     return value