anndata 0.12.0rc3__tar.gz → 0.12.1__tar.gz

anndata-0.12.1/.github/workflows/test-cpu.yml

@@ -0,0 +1,125 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - "[0-9]+.[0-9]+.x"
+  pull_request:
+
+env:
+  FORCE_COLOR: "1"
+
+defaults:
+  run:
+    shell: bash -el {0}
+
+# Cancel the job if new commits are pushed
+# https://stackoverflow.com/questions/66335225/how-to-cancel-previous-runs-in-the-pr-when-you-push-new-commitsupdate-the-curre
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  get-environments:
+    runs-on: ubuntu-latest
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: false
+      - id: get-envs
+        run: |
+          ENVS_JSON=$(NO_COLOR=1 uvx hatch env show --json | jq -c 'to_entries
+            | map(
+              select(.key | startswith("hatch-test"))
+              | { name: .key, python: .value.python }
+            )')
+          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+  test:
+    needs: get-environments
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+        io_mark: ["zarr_io", "not zarr_io"]
+    env:  # environment variable for use in codecov’s env_vars tagging
+      ENV_NAME: ${{ matrix.env.name }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: blob:none
+
+      - name: Set up Python ${{ matrix.env.python }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.env.python }}
+
+      - name: Install UV
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+
+      - name: Install dependencies
+        run: uvx hatch -v env create ${{ matrix.env.name }}
+
+      - name: Run tests
+        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto --cov --cov-report=xml --junitxml=test-data/test-results.xml -m "${{matrix.io_mark}}"
+
+      - name: Upload coverage data
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          env_vars: ENV_NAME
+          fail_ci_if_error: true
+          files: test-data/coverage.xml
+
+  build:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: blob:none
+
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install build tools and requirements
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Display installed versions
+        run: pip list
+
+      - name: Build & Twine check
+        run: |
+          python -m build --sdist --wheel .
+          twine check dist/*
+
+      - name: Check runtime version
+        run: |
+          pip install dist/*.whl
+          python -c 'import anndata; print(anndata.__version__)'
+
+  check:
+    if: always()
+    needs:
+      - get-environments
+      - test
+      - build
+    runs-on: ubuntu-latest
+    steps:
+        - uses: re-actors/alls-green@release/v1
+          with:
+            jobs: ${{ toJSON(needs) }}

{anndata-0.12.0rc3 → anndata-0.12.1}/.gitignore

@@ -12,6 +12,7 @@ __pycache__/
 # Distribution / packaging
 /dist/
 /ci/min-deps.txt
+/ci/pre-deps.txt
 /requirements*.lock
 /.python-version
 

{anndata-0.12.0rc3 → anndata-0.12.1}/.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.4
+    rev: v0.12.4
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -10,7 +10,7 @@ repos:
         id: ruff
         args: ["--preview", "--select=PLR0917"]
   - repo: https://github.com/biomejs/pre-commit
-    rev: v1.9.4
+    rev: v2.1.2
     hooks:
       - id: biome-format
   - repo: https://github.com/ComPWA/taplo-pre-commit

{anndata-0.12.0rc3 → anndata-0.12.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: anndata
-Version: 0.12.0rc3
+Version: 0.12.1
 Summary: Annotated data.
 Project-URL: Documentation, https://anndata.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/anndata
@@ -28,11 +28,11 @@ Requires-Dist: array-api-compat>=1.7.1
 Requires-Dist: h5py>=3.8
 Requires-Dist: legacy-api-wrap
 Requires-Dist: natsort
-Requires-Dist: numpy>=1.25
+Requires-Dist: numpy>=1.26
 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,!=3.0.4,!=3.0.5,!=3.0.6,!=3.0.7,>=2.18.7
+Requires-Dist: pandas!=2.1.2,>=2.1.0
+Requires-Dist: scipy>=1.12
+Requires-Dist: zarr!=3.0.*,>=2.18.7
 Provides-Extra: cu11
 Requires-Dist: cupy-cuda11x; extra == 'cu11'
 Provides-Extra: cu12
@@ -40,31 +40,8 @@ Requires-Dist: cupy-cuda12x; extra == 'cu12'
 Provides-Extra: dask
 Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'dask'
 Provides-Extra: dev
-Requires-Dist: aiohttp; extra == 'dev'
-Requires-Dist: awkward>=2.3.2; extra == 'dev'
-Requires-Dist: boltons; extra == 'dev'
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'dev'
-Requires-Dist: dask[distributed]; extra == 'dev'
-Requires-Dist: filelock; extra == 'dev'
 Requires-Dist: hatch-vcs; extra == 'dev'
-Requires-Dist: httpx; extra == 'dev'
-Requires-Dist: joblib; extra == 'dev'
-Requires-Dist: loompy>=3.0.5; extra == 'dev'
-Requires-Dist: matplotlib; extra == 'dev'
-Requires-Dist: openpyxl; extra == 'dev'
-Requires-Dist: pandas>=2.1.0; extra == 'dev'
-Requires-Dist: pyarrow; extra == 'dev'
-Requires-Dist: pytest-cov; extra == 'dev'
-Requires-Dist: pytest-memray; extra == 'dev'
-Requires-Dist: pytest-mock; extra == 'dev'
-Requires-Dist: pytest-randomly; extra == 'dev'
-Requires-Dist: pytest-xdist[psutil]; extra == 'dev'
-Requires-Dist: pytest<8.3.4,>=8.2; extra == 'dev'
-Requires-Dist: requests; extra == 'dev'
-Requires-Dist: scanpy>=1.10; extra == 'dev'
-Requires-Dist: scikit-learn; extra == 'dev'
 Requires-Dist: towncrier>=24.8.0; extra == 'dev'
-Requires-Dist: xarray>=2025.04.0; extra == 'dev'
 Provides-Extra: dev-doc
 Requires-Dist: towncrier>=24.8.0; extra == 'dev-doc'
 Provides-Extra: doc
@@ -89,7 +66,7 @@ Provides-Extra: lazy
 Requires-Dist: aiohttp; extra == 'lazy'
 Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'lazy'
 Requires-Dist: requests; extra == 'lazy'
-Requires-Dist: xarray>=2025.04.0; extra == 'lazy'
+Requires-Dist: xarray>=2025.06.1; extra == 'lazy'
 Provides-Extra: test
 Requires-Dist: aiohttp; extra == 'test'
 Requires-Dist: awkward>=2.3.2; extra == 'test'
@@ -97,13 +74,12 @@ Requires-Dist: boltons; extra == 'test'
 Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'test'
 Requires-Dist: dask[distributed]; extra == 'test'
 Requires-Dist: filelock; extra == 'test'
-Requires-Dist: httpx; extra == 'test'
+Requires-Dist: httpx<1.0; extra == 'test'
 Requires-Dist: joblib; extra == 'test'
 Requires-Dist: loompy>=3.0.5; extra == 'test'
 Requires-Dist: matplotlib; extra == 'test'
 Requires-Dist: openpyxl; extra == 'test'
-Requires-Dist: pandas>=2.1.0; extra == 'test'
-Requires-Dist: pyarrow; extra == 'test'
+Requires-Dist: pyarrow<21; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
 Requires-Dist: pytest-memray; extra == 'test'
 Requires-Dist: pytest-mock; extra == 'test'
@@ -113,19 +89,19 @@ Requires-Dist: pytest<8.3.4,>=8.2; extra == 'test'
 Requires-Dist: requests; extra == 'test'
 Requires-Dist: scanpy>=1.10; extra == 'test'
 Requires-Dist: scikit-learn; extra == 'test'
-Requires-Dist: xarray>=2025.04.0; extra == 'test'
+Requires-Dist: xarray>=2025.06.1; extra == 'test'
 Provides-Extra: test-min
 Requires-Dist: awkward>=2.3.2; extra == 'test-min'
 Requires-Dist: boltons; extra == 'test-min'
 Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'test-min'
 Requires-Dist: dask[distributed]; extra == 'test-min'
 Requires-Dist: filelock; extra == 'test-min'
-Requires-Dist: httpx; extra == 'test-min'
+Requires-Dist: httpx<1.0; extra == 'test-min'
 Requires-Dist: joblib; extra == 'test-min'
 Requires-Dist: loompy>=3.0.5; extra == 'test-min'
 Requires-Dist: matplotlib; extra == 'test-min'
 Requires-Dist: openpyxl; extra == 'test-min'
-Requires-Dist: pyarrow; extra == 'test-min'
+Requires-Dist: pyarrow<21; extra == 'test-min'
 Requires-Dist: pytest-cov; extra == 'test-min'
 Requires-Dist: pytest-memray; extra == 'test-min'
 Requires-Dist: pytest-mock; extra == 'test-min'

{anndata-0.12.0rc3 → anndata-0.12.1}/benchmarks/asv.conf.json

@@ -70,6 +70,8 @@
         "pytoml": [""],
         "pytest": [""],
         "pooch": [""],
+        "xarray": [""],
+        "dask": [""],
         // "scanpy": [""],
         // "psutil": [""]
     },

anndata-0.12.1/benchmarks/benchmarks/dataset2d.py

@@ -0,0 +1,61 @@
+from __future__ import annotations
+
+import tempfile
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+import h5py
+import numpy as np
+import pandas as pd
+import zarr
+
+import anndata as ad
+
+if TYPE_CHECKING:
+    from collections.abc import Callable
+
+
+class Dataset2D:
+    param_names = ("gen_store", "chunks")
+    params = (
+        (
+            lambda: h5py.File(Path(tempfile.mkdtemp()) / "data.h5ad", mode="w"),
+            lambda: zarr.open(
+                Path(tempfile.mkdtemp()) / "data.zarr", mode="w", zarr_version=2
+            ),
+        ),
+        ((-1,), None),
+    )
+
+    def setup(
+        self, gen_store: Callable[[], zarr.Group | h5py.File], chunks: None | tuple[int]
+    ):
+        self.n_obs = 100000
+        df = pd.DataFrame(
+            {
+                "a": pd.Categorical(np.array(["a"] * self.n_obs)),
+                "b": np.arange(self.n_obs),
+            },
+            index=[f"cell{i}" for i in range(self.n_obs)],
+        )
+        store = gen_store()
+        ad.io.write_elem(store, "obs", df)
+        self.ds = ad.experimental.read_elem_lazy(store["obs"], chunks=chunks)
+
+    def time_getitem_slice(self, *_):
+        self.ds.iloc[0 : (self.n_obs // 2)].to_memory()
+
+    def peakmem_getitem_slice(self, *_):
+        self.ds.iloc[0 : (self.n_obs // 2)].to_memory()
+
+    def time_full_to_memory(self, *_):
+        self.ds.to_memory()
+
+    def peakmem_full_to_memory(self, *_):
+        self.ds.to_memory()
+
+    def time_getitem_bool_mask(self, *_):
+        self.ds.iloc[np.random.randint(0, self.n_obs, self.n_obs // 2)].to_memory()
+
+    def peakmem_getitem_bool_mask(self, *_):
+        self.ds.iloc[np.random.randint(0, self.n_obs, self.n_obs // 2)].to_memory()

{anndata-0.12.0rc3 → anndata-0.12.1}/benchmarks/benchmarks/sparse_dataset.py

@@ -4,11 +4,13 @@ from types import MappingProxyType
 
 import numpy as np
 import zarr
+from dask.array.core import Array as DaskArray
 from scipy import sparse
 
 from anndata import AnnData
 from anndata._core.sparse_dataset import sparse_dataset
 from anndata._io.specs import write_elem
+from anndata.experimental import read_elem_lazy
 
 
 def make_alternating_mask(n):
@@ -37,27 +39,36 @@ class SparseCSRContiguousSlice:
             # (10_000, 500)
         ],
         _slices.keys(),
+        [True, False],
     )
-    param_names = ("shape", "slice")
+    param_names = ("shape", "slice", "use_dask")
 
-    def setup(self, shape: tuple[int, int], slice: str):
+    def setup(self, shape: tuple[int, int], slice: str, use_dask: bool):  # noqa: FBT001
         X = sparse.random(
             *shape, density=0.01, format="csr", random_state=np.random.default_rng(42)
         )
         self.slice = self._slices[slice]
         g = zarr.group()
         write_elem(g, "X", X)
-        self.x = sparse_dataset(g["X"])
+        self.x = read_elem_lazy(g["X"]) if use_dask else sparse_dataset(g["X"])
         self.adata = AnnData(self.x)
 
     def time_getitem(self, *_):
-        self.x[self.slice]
+        res = self.x[self.slice]
+        if isinstance(res, DaskArray):
+            res.compute()
 
     def peakmem_getitem(self, *_):
-        self.x[self.slice]
+        res = self.x[self.slice]
+        if isinstance(res, DaskArray):
+            res.compute()
 
     def time_getitem_adata(self, *_):
-        self.adata[self.slice]
+        res = self.adata[self.slice]
+        if isinstance(res, DaskArray):
+            res.compute()
 
     def peakmem_getitem_adata(self, *_):
-        self.adata[self.slice]
+        res = self.adata[self.slice]
+        if isinstance(res, DaskArray):
+            res.compute()

{anndata-0.12.0rc3 → anndata-0.12.1}/biome.jsonc

@@ -1,9 +1,9 @@
 {
-    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "$schema": "https://biomejs.dev/schemas/2.1.1/schema.json",
     "formatter": { "useEditorconfig": true },
     "overrides": [
         {
-            "include": ["./.vscode/*.json", "**/*.jsonc", "**/asv.conf.json"],
+            "includes": ["./.vscode/*.json", "**/*.jsonc", "**/asv.conf.json"],
             "json": {
                 "formatter": {
                     "trailingCommas": "all",

{anndata-0.12.0rc3 → anndata-0.12.1}/docs/api.md

@@ -178,9 +178,10 @@ Types used by the former:
    experimental.ReadCallback
    experimental.WriteCallback
    experimental.StorageType
-   experimental.backed._lazy_arrays.MaskedArray
-   experimental.backed._lazy_arrays.CategoricalArray
-   _core.xarray.Dataset2D
+   experimental.backed.MaskedArray
+   experimental.backed.CategoricalArray
+   experimental.backed.Dataset2D
+   experimental.Dataset2DIlocIndexer
 ```
 
 (extensions-api)=

{anndata-0.12.0rc3 → anndata-0.12.1}/docs/conf.py

@@ -99,23 +99,45 @@ def setup(app: Sphinx):
     app.add_generic_role("small", partial(nodes.inline, classes=["small"]))
     app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"]))
 
+    # TODO: move to scanpydoc
+    if TYPE_CHECKING:
+        from docutils.nodes import TextElement, reference
+        from sphinx.addnodes import pending_xref
+        from sphinx.environment import BuildEnvironment
+
+    def res(
+        app: Sphinx, env: BuildEnvironment, node: pending_xref, contnode: TextElement
+    ) -> reference | None:
+        return env.domains["py"].resolve_xref(
+            env,
+            node["refdoc"],
+            app.builder,
+            node["reftype"],
+            node["reftarget"],
+            node,
+            contnode,
+        )
+
+    app.connect("missing-reference", res, priority=502)
+
 
 intersphinx_mapping = dict(
     awkward=("https://awkward-array.org/doc/stable", None),
     cupy=("https://docs.cupy.dev/en/stable", None),
     dask=("https://docs.dask.org/en/stable", None),
+    fsspec=("https://filesystem-spec.readthedocs.io/en/stable/", None),
     h5py=("https://docs.h5py.org/en/latest", None),
     hdf5plugin=("https://hdf5plugin.readthedocs.io/en/latest", None),
+    kvikio=("https://docs.rapids.ai/api/kvikio/stable/", None),
     loompy=("https://linnarssonlab.org/loompy", None),
     numpy=("https://numpy.org/doc/stable", None),
+    obstore=("https://developmentseed.org/obstore/latest/", None),
     pandas=("https://pandas.pydata.org/pandas-docs/stable", None),
     python=("https://docs.python.org/3", None),
     scipy=("https://docs.scipy.org/doc/scipy", None),
     sklearn=("https://scikit-learn.org/stable", 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),
+    zarr=("https://zarr.readthedocs.io/en/stable/", None),
     zarrs=("https://zarrs-python.readthedocs.io/en/stable/", None),
 )
 
@@ -133,6 +155,7 @@ qualname_overrides = {
     "anndata._types.WriteCallback": "anndata.experimental.WriteCallback",
     "anndata._types.Read": "anndata.experimental.Read",
     "anndata._types.Write": "anndata.experimental.Write",
+    "anndata._types.Dataset2DIlocIndexer": "anndata.experimental.Dataset2DIlocIndexer",
     "zarr.core.array.Array": "zarr.Array",
     "zarr.core.group.Group": "zarr.Group",
     # Buffer is not yet exported, so the buffer class registry is the closest thing
@@ -142,6 +165,7 @@ qualname_overrides = {
     "anndata.compat.CupyArray": "cupy.ndarray",
     "anndata.compat.CupySparseMatrix": "cupyx.scipy.sparse.spmatrix",
     "anndata.compat.XDataArray": "xarray.DataArray",
+    "anndata.compat.XDataset": "xarray.Dataset",
     "awkward.highlevel.Array": "ak.Array",
     "numpy.int64": ("py:attr", "numpy.int64"),
     "pandas.DataFrame.iloc": ("py:attr", "pandas.DataFrame.iloc"),

anndata-0.12.1/docs/extensions/autosummary_skip_inherited.py

@@ -0,0 +1,55 @@
+"""Extension to skip inherited methods and properties in autosummary."""
+
+from __future__ import annotations
+
+from traceback import walk_stack
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from typing import Literal
+
+    from sphinx.application import Sphinx
+    from sphinx.ext.autodoc import Options
+
+
+def skip_inherited(  # noqa: PLR0917
+    app: Sphinx,
+    what: Literal[
+        "module", "class", "exception", "function", "method", "attribute", "property"
+    ],
+    name: str,
+    obj: object,
+    skip: bool,  # noqa: FBT001
+    options: Options | dict[str, object],
+) -> bool | None:
+    """Skip inherited members."""
+    # Skip `getdoc` property
+    if what == "method" and name == "getdoc":
+        return True
+
+    # find parent class
+    for frame, _ in walk_stack(None):
+        if frame.f_code.co_name == "_get_members" and frame.f_code.co_filename.endswith(
+            "/generate.py"
+        ):
+            parent = frame.f_locals["obj"]
+            if not isinstance(parent, type):
+                return None
+            break
+    else:
+        return None
+
+    # return if it’s a member of the parent class
+    typ = parent
+    while typ is not type:
+        if name in typ.__dict__:
+            return None
+        typ = type(typ)
+
+    # skip since we know it’s not a member of the parent class
+    return True
+
+
+def setup(app: Sphinx) -> None:
+    """App setup hook."""
+    app.connect("autodoc-skip-member", skip_inherited)

anndata-0.12.1/docs/release-notes/0.12.0.md

@@ -0,0 +1,51 @@
+(v0.12.0)=
+### 0.12.0 {small}`2025-07-16`
+
+- (v0.12.0rc4)=
+  {guilabel}`rc4` 2025-06-18
+- (v0.12.0rc3)=
+  {guilabel}`rc3` 2025-05-20
+- (v0.12.0rc2)=
+  {guilabel}`rc2` 2025-05-15
+- (v0.12.0rc1)=
+  {guilabel}`rc1` 2025-04-09
+
+#### Breaking changes
+
+- {guilabel}`rc1` Remove `anndata.read` {user}`ilan-gold` ({pr}`1766`)
+- {guilabel}`rc1` Tighten usage of {class}`scipy.sparse.spmatrix` for describing sparse matrices in types and instance checks to only {class}`scipy.sparse.csr_matrix` and {class}`scipy.sparse.csc_matrix` {user}`ilan-gold` ({pr}`1768`)
+- {guilabel}`rc1` Disallow declaration of {class}`~anndata.AnnData` with non-`cs{r,c}` sparse data-structures {user}`ilan-gold` ({pr}`1829`)
+- {guilabel}`rc1` Upgrade all `DeprecationWarning`s to `FutureWarning`s {user}`ilan-gold` ({pr}`1874`)
+- {guilabel}`rc4` Lower bound `xarray` by `2025.06.01`.  {class}`pandas.arrays.StringArray` was previously used as the in-memory `nullable-string-array` container in `xarray`, but due to {issue}`pydata/xarray#10419` now uses {class}`numpy.ndarray` with an object data type.  {user}`ilan-gold` ({pr}`2008`)
+
+#### Bug fixes
+
+- Fix {func}`anndata.experimental.backed.Dataset2D.reindex` internal setting {user}`ilan-gold` ({pr}`2018`)
+- {guilabel}`rc1` Disallow writing of {class}`~anndata.experimental.backed.Dataset2D` objects {user}`ilan-gold` ({pr}`1887`)
+- {guilabel}`rc1` Upgrade old deprecation warning to a `FutureWarning` on `BaseCompressedSparseDataset.__setitem__`, showing our intent to remove the feature in the next release.  {user}`ilan-gold` ({pr}`1928`)
+- {guilabel}`rc1` Don't use {func}`asyncio.run` internally for any operations {user}`ilan-gold` ({pr}`1933`)
+- {guilabel}`rc1` Disallow forward slashes in keys for writing {user}`ilan-gold` ({pr}`1940`)
+- {guilabel}`rc2` 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`)
+- {guilabel}`rc3` Update zarr v3 bound to >3.0.8 to prevent corrupted data {issue}`zarr-developers/zarr-python#3061` {user}`ilan-gold` ({pr}`1993`)
+
+#### Features
+
+- {guilabel}`rc1` {data}`None` values can now be serialized to `.h5ad` and `.zarr`,
+  preserving e.g. {attr}`~anndata.AnnData.uns` structure through saving and loading {user}`flying-sheep` ({pr}`999`)
+- {guilabel}`rc1` Add {func}`~anndata.experimental.read_elem_lazy` (in place of `read_elem_as_dask`) to handle backed dataframes, sparse arrays, and dense arrays, as well as a {func}`~anndata.experimental.read_lazy` to handle reading in as much of the on-disk data as possible to produce a {class}`~anndata.AnnData` object {user}`ilan-gold` ({pr}`1247`)
+- {guilabel}`rc1` Support {mod}`zarr` version 3 python package {user}`ilan-gold` ({pr}`1726`)
+- {guilabel}`rc1` Adopt the Scientific Python [deprecation schedule](https://scientific-python.org/specs/spec-0000/) {user}`ilan-gold` ({pr}`1768`)
+- {guilabel}`rc1` Allow {mod}`zarr` v3 writing of data {user}`ilan-gold` ({pr}`1892`)
+- {guilabel}`rc1` {func}`anndata.register_anndata_namespace` functionality for adding custom functionality to an {class}`~anndata.AnnData` object {user}`srivarra` ({pr}`1870`)
+- {guilabel}`rc2` Allow xarray Datasets to be used for obs/var/obsm/varm. {user}`ilia-kats` ({pr}`1966`)
+- {guilabel}`rc4` {class}`anndata.experimental.backed.Dataset2D` now takes a compositional approach to wrapping {class}`xarray.Dataset` which may have breaking changes over the past release versions. {user}`ilan-gold` ({pr}`1997`)
+- {guilabel}`rc4` Use {attr}`numpy.dtypes.StringDType` with `na_object` set to {attr}`pandas.NA` for nullable string data with {class}`anndata.experimental.backed.Dataset2D` {user}`ilan-gold` ({pr}`2011`)
+
+#### Performance
+
+- {guilabel}`rc2` Load AnnLoader lazily to prevent expensive unnecessary `torch` imports when its available on the system. {user}`Zethson` & {user}`flying-sheep` ({pr}`1950`)
+- {guilabel}`rc4` Improve {func}`~anndata.experimental.read_elem_lazy` performance for `h5ad` files by not caching `indptr`. {user}`ilan-gold` ({pr}`2005`)
+
+#### Development
+
+- {guilabel}`rc4` Temporarily bound {mod}`zarr` to `<3.1` until {pr}`1995` is merged to handle the new data type structure.  {user}`ilan-gold` ({pr}`2013`)

anndata-0.12.1/docs/release-notes/0.12.1.md

@@ -0,0 +1,10 @@
+(v0.12.1)=
+### 0.12.1 {small}`2025-07-23`
+
+### Bug fixes
+
+- Fix `chunks` argument for {func}`anndata.experimental.read_elem_lazy` so that it uses the on-disk chunking when possible, and allow users to pass this argument through to the reading of {class}`anndata.experimental.backed.Dataset2D` {user}`ilan-gold` ({pr}`2033`)
+
+### Performance
+
+- Improve integer indexing performance of `h5` 1d arrays that are opened via {func}`anndata.experimental.read_elem_lazy` {user}`ilan-gold` ({pr}`2035`)

{anndata-0.12.0rc3 → anndata-0.12.1}/docs/tutorials/zarr-v3.md

@@ -4,6 +4,23 @@
 Users should notice a significant performance improvement, especially for cloud data, but also likely for local data as well.
 Here is a quick guide on some of our learnings so far:
 
+## Consolidated Metadata
+
+All `zarr` stores are now consolidated by default when written via {func}`anndata.io.write_zarr` or {meth}`anndata.AnnData.write_zarr`.  For more information on this topic, please seee {ref}`the zarr docs <zarr:user-guide-consolidated-metadata>`.  Practcally, this changes means that once a store has been written, it should be treated as immutable **unless you remove the consolidated metadata and/or rewrite after the mutating operation** i.e., if you wish to use `anndata.io.write_elem` to add a column to `obs`, a `layer` etc. to an existing store.  For example, to mutate an existing store on-disk, you may do:
+
+```python
+g = zarr.open_group(orig_path, mode="a", use_consolidated=False)
+ad.io.write_elem(
+    g,
+    "obs",
+    obs,
+    dataset_kwargs=dict(chunks=(250,)),
+)
+zarr.consolidate_metadata(g.store)
+```
+
+In this example, the store was opened unconsolidated (trying to open it as a consolidated store would error out), edited, and then reconsolidated.  Alternatively, one could simple delete the file containing the consolidated metadata first at the root, `.zmetadata`.
+
 ## Remote data
 
 We now provide the {func}`anndata.experimental.read_lazy` feature for reading as much of the {class}`~anndata.AnnData` object as lazily as possible, using `dask` and {mod}`xarray`.

{anndata-0.12.0rc3 → anndata-0.12.1}/hatch.toml

@@ -20,10 +20,14 @@ extra-dependencies = [ "ipykernel" ]
 env-vars.UV_CONSTRAINT = "ci/constraints.txt"
 overrides.matrix.deps.env-vars = [
     { if = [ "pre" ], key = "UV_PRERELEASE", value = "allow" },
+    { if = [ "pre" ], key = "UV_CONSTRAINT", value = "ci/pre-deps.txt" },
     { if = [ "min" ], key = "UV_CONSTRAINT", value = "ci/constraints.txt ci/min-deps.txt" },
 ]
 overrides.matrix.deps.pre-install-commands = [
     { if = [ "min" ], value = "uv run ci/scripts/min-deps.py pyproject.toml --all-extras -o ci/min-deps.txt" },
+    # To prevent situations like https://github.com/pydata/xarray/issues/10419 going forward
+    { if = [ "pre" ], value = "echo xarray @ git+https://github.com/pydata/xarray.git > ci/pre-deps.txt" },
+
 ]
 overrides.matrix.deps.python = [
     { if = [ "min" ], value = "3.11" },