Merge remote-tracking branch 'origin/main' into html_rep

# Conflicts:
#	.vscode/settings.json
#	src/anndata/_settings.pyi
#	tests/test_repr.py

Author: katosh

.github/workflows/test-cpu.yml

@@ -41,6 +41,7 @@ jobs:
     needs: get-environments
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
         io_mark: ["zarr_io", "not zarr_io", "dask_distributed"] # dask_distributed should not be run with -n auto as it uses a client with processes

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
         id: ruff
         args: ["--preview", "--select=PLR0917"]
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.4.13
+    rev: v2.4.15
     hooks:
       - id: biome-format
   - repo: https://github.com/ComPWA/taplo-pre-commit

.vscode/settings.json

@@ -25,6 +25,6 @@
     ],
     "python.terminal.activateEnvironment": true,
     "python.analysis.include": ["src/**/*", "ci/scripts/**/*", "tests/**/*"],
-    "python-envs.defaultEnvManager": "ms-python.python:venv",
-    "python-envs.defaultPackageManager": "ms-python.python:pip",
+    "python-envs.defaultEnvManager": "pypa.hatch:hatch",
+    "python-envs.defaultPackageManager": "pypa.hatch:hatch",
 }

benchmarks/benchmarks/dataset2d.py

@@ -34,7 +34,7 @@ def setup_cache(self):
         for k, v in array_types.items():
             for store in [
                 h5py.File(f"data_{k}.h5ad", mode="w"),
-                zarr.open(f"data_{k}.zarr", mode="w", zarr_version=2),
+                zarr.open(f"data_{k}.zarr", mode="w", zarr_format=2),
             ]:
                 df = pd.DataFrame({"a": v}, index=[f"cell{i}" for i in range(n_obs)])
                 if writing_string_array_on_disk := (
@@ -48,7 +48,7 @@ def setup_cache(self):
                     assert store["df"]["a"].attrs["encoding-type"] == "string-array"
         for store in [
             h5py.File("data_all.h5ad", mode="w"),
-            zarr.open("data_all.zarr", mode="w", zarr_version=2),
+            zarr.open("data_all.zarr", mode="w", zarr_format=2),
         ]:
             df = pd.DataFrame(array_types, index=[f"cell{i}" for i in range(n_obs)])
             # write a string array by triggering:

docs/concatenation.rst

@@ -30,6 +30,7 @@ Let's start off with an example:
         obsm: 'X_pca', 'X_umap'
         varm: 'PCs'
         obsp: ...
+        layers: None
 
 If we split this object up by clusters of observations, then stack those subsets we'll obtain the same values – just ordered differently.
 
@@ -42,6 +43,7 @@ If we split this object up by clusters of observations, then stack those subsets
         var: 'n_counts', 'means', 'dispersions', 'dispersions_norm', 'highly_variable'
         obsm: 'X_pca', 'X_umap'
         varm: 'PCs'
+        layers: None
 
 Note that we concatenated along the observations by default, and that most elements aligned to the observations were concatenated as well.
 A notable exception is :attr:`~anndata.AnnData.obsp`, which can be re-enabled with the `pairwise` keyword argument.
@@ -168,6 +170,7 @@ First, our example case:
         uns: 'pca'
         obsm: 'X_pca'
         varm: 'PCs'
+        layers: None
 
 Now we will split this object by the categorical `"blobs"` and recombine it to illustrate different merge strategies.
 
@@ -184,6 +187,7 @@ Now we will split this object by the categorical `"blobs"` and recombine it to i
         uns: 'pca'
         obsm: 'X_pca', 'qc'
         varm: 'PCs', '0_qc'
+        layers: None
 
 `adatas` is now a list of datasets with disjoint sets of observations and a common set of variables.
 Each object has had QC metrics computed, with observation-wise metrics stored under `"qc"` in `.obsm`, and variable-wise metrics stored with a unique key for each subset.
@@ -193,16 +197,19 @@ Taking a look at how this affects concatenation:
     AnnData object with n_obs × n_vars = 640 × 30
         obs: 'blobs'
         obsm: 'X_pca', 'qc'
+        layers: None
     >>> ad.concat(adatas, merge="same")
     AnnData object with n_obs × n_vars = 640 × 30
         obs: 'blobs'
         obsm: 'X_pca', 'qc'
         varm: 'PCs'
+        layers: None
     >>> ad.concat(adatas, merge="unique")
     AnnData object with n_obs × n_vars = 640 × 30
         obs: 'blobs'
         obsm: 'X_pca', 'qc'
         varm: 'PCs', '0_qc', '1_qc', '2_qc', '3_qc', '4_qc'
+        layers: None
 
 Note that comparisons are made after indices are aligned.
 That is, if the objects only share a subset of indices on the alternative axis, it's only required that values for those indices match when using a strategy like `"same"`.

docs/conf.py

@@ -181,6 +181,7 @@ def res(
     ("py:class", "anndata.acc.GenericAlias"),
     ("py:obj", "typing.R"),
     ("py:class", "_M"),
+    ("py:class", "anndata.utils.Default"),
 ]
 
 # -- Social cards ---------------------------------------------------------

docs/release-notes/0.12.11.md

@@ -0,0 +1,12 @@
+(v0.12.11)=
+### 0.12.11 {small}`2026-04-21`
+
+#### Bug fixes
+
+- {attr}`anndata.settings.zarr_write_format` and {attr}`anndata.settings.auto_shard_zarr_v3` can now be set together {user}`ilan-gold` ({pr}`2342`)
+- Check `Raw` length on creation and fix associated `.adata` in `Raw` slicing {user}`P Angerer` ({pr}`2351`)
+- Ensure the index name along `obs` and `var` are not lost when reading/writing to disk after reading with {func}`~anndata.experimental.read_lazy` {user}`ilan-gold` ({pr}`2358`)
+
+#### Performance
+
+- Accelerate outer joins on dask-sparse matrices with unchunked minor axes in {func}`anndata.concat` {user}`ilan-gold` ({pr}`2395`)

docs/release-notes/1707.breaking.md

@@ -0,0 +1 @@
+Remove `dtype` argument from {class}`~anndata.AnnData` constructor. {user}`flying-sheep`

docs/release-notes/1707.feat.md

@@ -0,0 +1,3 @@
+Move {attr}`~anndata.AnnData.X` into {attr}`anndata.AnnData.layers` under the `None` key.
+As result, `layers: X` shows up in `AnnData`’s text representation, `None` appears in `.layers.items()`/`.keys()`, {func}`~anndata.concat` now works when some `AnnData`s have no `X`.
+{user}`flying-sheep` & {user}`ilan-gold`