anndata 0.12.0rc1__tar.gz → 0.12.0rc3__tar.gz

anndata-0.12.0rc3/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about “How to do X”, please ask them here.

anndata-0.12.0rc3/.github/ISSUE_TEMPLATE/question.yml

@@ -0,0 +1,14 @@
+name: Technical question
+description: You wonder about a design decision or implementation detail?
+#title: ...
+labels:
+  - question
+#assignees: []
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Question
+      description: If you have *usage* question, please visit the [Scverse Community Forum](https://discourse.scverse.org/) instead.
+    validations:
+      required: true

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/.github/workflows/test-cpu.yml

@@ -56,18 +56,18 @@ jobs:
 
       - name: Install dependencies
         if: matrix.dependencies-version == null
-        run: uv pip install --system --compile "anndata[dev,test-full] @ ." -c ci/constraints.txt
+        run: uv pip install --system --compile -r pyproject.toml --extra=dev --extra=test -e 'anndata @ .' -c ci/constraints.txt
 
       - name: Install minimum dependencies
         if: matrix.dependencies-version == 'minimum'
         run: |
           uv pip install --system --compile tomli packaging
-          deps=$(python3 ci/scripts/min-deps.py pyproject.toml --extra dev test)
-          uv pip install --system --compile $deps "anndata @ ."
+          deps=$(python3 ci/scripts/min-deps.py pyproject.toml --extras dev test-min)
+          uv pip install --system --compile $deps -e 'anndata @ .'
 
       - name: Install dependencies release candidates
         if: matrix.dependencies-version == 'pre-release'
-        run: uv pip install -v --system --compile --pre "anndata[dev,test-full] @ ." -c ci/constraints.txt
+        run: uv pip install -v --system --compile --pre -r pyproject.toml --extra=dev --extra=test -e 'anndata @ .' -c ci/constraints.txt
 
       - name: Display installed versions
         run: uv pip list

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/.pre-commit-config.yaml

@@ -5,6 +5,10 @@ repos:
       - id: ruff
         args: ["--fix"]
       - id: ruff-format
+      # The following can be removed once PLR0917 is out of preview
+      - name: ruff preview rules
+        id: ruff
+        args: ["--preview", "--select=PLR0917"]
   - repo: https://github.com/biomejs/pre-commit
     rev: v1.9.4
     hooks:

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: anndata
-Version: 0.12.0rc1
+Version: 0.12.0rc3
 Summary: Annotated data.
 Project-URL: Documentation, https://anndata.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/anndata
@@ -24,15 +24,15 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.11
-Requires-Dist: array-api-compat!=1.5,>1.4
+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: 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,>=2.18.7
+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
 Provides-Extra: cu11
 Requires-Dist: cupy-cuda11x; extra == 'cu11'
 Provides-Extra: cu12
@@ -40,7 +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: awkward>=2.3; 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'
@@ -51,6 +52,7 @@ 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'
@@ -58,9 +60,11 @@ 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
@@ -69,13 +73,12 @@ Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == '
 Requires-Dist: ipython; extra == 'doc'
 Requires-Dist: myst-nb; extra == 'doc'
 Requires-Dist: myst-parser; extra == 'doc'
-Requires-Dist: readthedocs-sphinx-search; extra == 'doc'
-Requires-Dist: scanpydoc[theme,typehints]>=0.15.1; extra == 'doc'
+Requires-Dist: scanpydoc[theme,typehints]>=0.15.3; extra == 'doc'
 Requires-Dist: sphinx-autodoc-typehints>=2.2.0; extra == 'doc'
 Requires-Dist: sphinx-book-theme>=1.1.0; extra == 'doc'
 Requires-Dist: sphinx-copybutton; extra == 'doc'
 Requires-Dist: sphinx-design>=0.5.0; extra == 'doc'
-Requires-Dist: sphinx-issues; extra == 'doc'
+Requires-Dist: sphinx-issues>=5.0.1; extra == 'doc'
 Requires-Dist: sphinx-toolbox>=3.8.0; extra == 'doc'
 Requires-Dist: sphinx>=8.2.1; extra == 'doc'
 Requires-Dist: sphinxext-opengraph; extra == 'doc'
@@ -86,9 +89,10 @@ 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>=2024.06.0; extra == 'lazy'
+Requires-Dist: xarray>=2025.04.0; extra == 'lazy'
 Provides-Extra: test
-Requires-Dist: awkward>=2.3; extra == 'test'
+Requires-Dist: aiohttp; extra == 'test'
+Requires-Dist: awkward>=2.3.2; extra == 'test'
 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'
@@ -98,6 +102,7 @@ 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: pytest-cov; extra == 'test'
 Requires-Dist: pytest-memray; extra == 'test'
@@ -105,31 +110,30 @@ Requires-Dist: pytest-mock; extra == 'test'
 Requires-Dist: pytest-randomly; extra == 'test'
 Requires-Dist: pytest-xdist[psutil]; extra == 'test'
 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'
-Provides-Extra: test-full
-Requires-Dist: aiohttp; extra == 'test-full'
-Requires-Dist: awkward>=2.3; extra == 'test-full'
-Requires-Dist: boltons; extra == 'test-full'
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'test-full'
-Requires-Dist: dask[distributed]; extra == 'test-full'
-Requires-Dist: filelock; extra == 'test-full'
-Requires-Dist: httpx; extra == 'test-full'
-Requires-Dist: joblib; extra == 'test-full'
-Requires-Dist: loompy>=3.0.5; extra == 'test-full'
-Requires-Dist: matplotlib; extra == 'test-full'
-Requires-Dist: openpyxl; extra == 'test-full'
-Requires-Dist: pyarrow; extra == 'test-full'
-Requires-Dist: pytest-cov; extra == 'test-full'
-Requires-Dist: pytest-memray; extra == 'test-full'
-Requires-Dist: pytest-mock; extra == 'test-full'
-Requires-Dist: pytest-randomly; extra == 'test-full'
-Requires-Dist: pytest-xdist[psutil]; extra == 'test-full'
-Requires-Dist: pytest<8.3.4,>=8.2; extra == 'test-full'
-Requires-Dist: requests; extra == 'test-full'
-Requires-Dist: scanpy>=1.10; extra == 'test-full'
-Requires-Dist: scikit-learn; extra == 'test-full'
-Requires-Dist: xarray>=2024.06.0; extra == 'test-full'
+Requires-Dist: xarray>=2025.04.0; 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: 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: pytest-cov; extra == 'test-min'
+Requires-Dist: pytest-memray; extra == 'test-min'
+Requires-Dist: pytest-mock; extra == 'test-min'
+Requires-Dist: pytest-randomly; extra == 'test-min'
+Requires-Dist: pytest-xdist[psutil]; extra == 'test-min'
+Requires-Dist: pytest<8.3.4,>=8.2; extra == 'test-min'
+Requires-Dist: scanpy>=1.10; extra == 'test-min'
+Requires-Dist: scikit-learn; extra == 'test-min'
 Description-Content-Type: text/markdown
 
 [![Tests](https://github.com/scverse/anndata/actions/workflows/test-cpu.yml/badge.svg)](https://github.com/scverse/anndata/actions)

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/benchmarks/benchmarks/readwrite.py

@@ -25,6 +25,7 @@ from __future__ import annotations
 import sys
 import tempfile
 from pathlib import Path
+from types import MappingProxyType
 
 import numpy as np
 import pooch
@@ -77,9 +78,9 @@ PBMC_3K_URL = "https://falexwolf.de/data/pbmc3k_raw.h5ad"
 
 
 class H5ADInMemorySizeSuite:
-    _urls = dict(pbmc3k=PBMC_3K_URL)
+    _urls = MappingProxyType(dict(pbmc3k=PBMC_3K_URL))
     params = _urls.keys()
-    param_names = ["input_data"]
+    param_names = ("input_data",)
 
     def setup(self, input_data: str):
         self.filepath = pooch.retrieve(url=self._urls[input_data], known_hash=None)
@@ -98,9 +99,9 @@ class H5ADInMemorySizeSuite:
 
 
 class H5ADReadSuite:
-    _urls = dict(pbmc3k=PBMC_3K_URL)
+    _urls = MappingProxyType(dict(pbmc3k=PBMC_3K_URL))
     params = _urls.keys()
-    param_names = ["input_data"]
+    param_names = ("input_data",)
 
     def setup(self, input_data: str):
         self.filepath = pooch.retrieve(url=self._urls[input_data], known_hash=None)
@@ -133,9 +134,9 @@ class H5ADReadSuite:
 
 
 class H5ADWriteSuite:
-    _urls = dict(pbmc3k=PBMC_3K_URL)
+    _urls = MappingProxyType(dict(pbmc3k=PBMC_3K_URL))
     params = _urls.keys()
-    param_names = ["input_data"]
+    param_names = ("input_data",)
 
     def setup(self, input_data: str):
         mem_recording, adata = memory_usage(
@@ -176,9 +177,9 @@ class H5ADWriteSuite:
 
 
 class H5ADBackedWriteSuite(H5ADWriteSuite):
-    _urls = dict(pbmc3k=PBMC_3K_URL)
+    _urls = MappingProxyType(dict(pbmc3k=PBMC_3K_URL))
     params = _urls.keys()
-    param_names = ["input_data"]
+    param_names = ("input_data",)
 
     def setup(self, input_data):
         mem_recording, adata = memory_usage(

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/benchmarks/benchmarks/sparse_dataset.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+from types import MappingProxyType
+
 import numpy as np
 import zarr
 from scipy import sparse
@@ -17,16 +19,18 @@ def make_alternating_mask(n):
 
 
 class SparseCSRContiguousSlice:
-    _slices = {
-        "0:1000": slice(0, 1000),
-        "0:9000": slice(0, 9000),
-        ":9000:-1": slice(None, 9000, -1),
-        "::-2": slice(None, None, 2),
-        "array": np.array([0, 5000, 9999]),
-        "arange": np.arange(0, 1000),
-        "first": 0,
-        "alternating": make_alternating_mask(10),
-    }
+    _slices = MappingProxyType(
+        {
+            "0:1000": slice(0, 1000),
+            "0:9000": slice(0, 9000),
+            ":9000:-1": slice(None, 9000, -1),
+            "::-2": slice(None, None, 2),
+            "array": np.array([0, 5000, 9999]),
+            "arange": np.arange(0, 1000),
+            "first": 0,
+            "alternating": make_alternating_mask(10),
+        }
+    )
     params = (
         [
             (10_000, 10_000),
@@ -34,7 +38,7 @@ class SparseCSRContiguousSlice:
         ],
         _slices.keys(),
     )
-    param_names = ["shape", "slice"]
+    param_names = ("shape", "slice")
 
     def setup(self, shape: tuple[int, int], slice: str):
         X = sparse.random(

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/benchmarks/benchmarks/utils.py

@@ -93,22 +93,6 @@ def gen_indexer(adata, dim, index_kind, ratio):
     return tuple(subset)
 
 
-def take_view(adata, *, dim, index_kind, ratio=0.5, nviews=100):
-    subset = gen_indexer(adata, dim, index_kind, ratio)
-    views = []
-    for i in range(nviews):
-        views.append(adata[subset])
-
-
-def take_repeated_view(adata, *, dim, index_kind, ratio=0.9, nviews=10):
-    v = adata
-    views = []
-    for i in range(nviews):
-        subset = gen_indexer(v, dim, index_kind, ratio)
-        v = v[subset]
-        views.append(v)
-
-
 def gen_adata(n_obs, n_var, attr_set):
     if "X-csr" in attr_set:
         X = sparse.random(n_obs, n_var, density=0.1, format="csr")

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/ci/scripts/min-deps.py

@@ -34,7 +34,7 @@ def min_dep(req: Requirement) -> Requirement:
     -------
 
     >>> min_dep(Requirement("numpy>=1.0"))
-    <Requirement('numpy==1.0.*')>
+    <Requirement('numpy==1.0')>
     >>> min_dep(Requirement("numpy<3.0"))
     <Requirement('numpy<3.0')>
     """
@@ -55,7 +55,7 @@ def min_dep(req: Requirement) -> Requirement:
         elif spec.operator == "==":
             min_version = Version(spec.version)
 
-    return Requirement(f"{req_name}=={min_version}.*")
+    return Requirement(f"{req_name}=={min_version}")
 
 
 def extract_min_deps(
@@ -64,6 +64,7 @@ def extract_min_deps(
     dependencies = deque(dependencies)  # We'll be mutating this
     project_name = pyproject["project"]["name"]
 
+    deps = {}
     while len(dependencies) > 0:
         req = dependencies.pop()
 
@@ -76,7 +77,11 @@ def extract_min_deps(
                 extra_deps = pyproject["project"]["optional-dependencies"][extra]
                 dependencies += map(Requirement, extra_deps)
         else:
-            yield min_dep(req)
+            if req.name in deps:
+                req.specifier &= deps[req.name].specifier
+                req.extras |= deps[req.name].extras
+            deps[req.name] = min_dep(req)
+    yield from deps.values()
 
 
 class Args(argparse.Namespace):
@@ -100,6 +105,7 @@ class Args(argparse.Namespace):
             prog="min-deps",
             description=cls.__doc__,
             usage="pip install `python min-deps.py pyproject.toml`",
+            allow_abbrev=False,
         )
         parser.add_argument(
             "_path",

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/docs/api.md

@@ -180,7 +180,7 @@ Types used by the former:
    experimental.StorageType
    experimental.backed._lazy_arrays.MaskedArray
    experimental.backed._lazy_arrays.CategoricalArray
-   experimental.backed._xarray.Dataset2D
+   _core.xarray.Dataset2D
 ```
 
 (extensions-api)=

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/docs/conf.py

@@ -56,7 +56,6 @@ extensions = [
     "sphinx_autodoc_typehints",  # needs to be after napoleon
     "sphinx_issues",
     "sphinx_design",
-    "sphinx_search.extension",
     "sphinxext.opengraph",
     "scanpydoc",  # needs to be before linkcode
     "sphinx.ext.linkcode",
@@ -113,8 +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),
@@ -128,7 +126,7 @@ qualname_overrides = {
     "anndata._core.anndata.AnnData": "anndata.AnnData",
     **{
         f"anndata._core.aligned_mapping.{cls}{kind}": "collections.abc.Mapping"
-        for cls in "Layers AxisArrays PairwiseArrays".split()
+        for cls in ["Layers", "AxisArrays", "PairwiseArrays"]
         for kind in ["", "View"]
     },
     "anndata._types.ReadCallback": "anndata.experimental.ReadCallback",
@@ -143,6 +141,7 @@ qualname_overrides = {
     "anndata.compat.DaskArray": "dask.array.Array",
     "anndata.compat.CupyArray": "cupy.ndarray",
     "anndata.compat.CupySparseMatrix": "cupyx.scipy.sparse.spmatrix",
+    "anndata.compat.XDataArray": "xarray.DataArray",
     "awkward.highlevel.Array": "ak.Array",
     "numpy.int64": ("py:attr", "numpy.int64"),
     "pandas.DataFrame.iloc": ("py:attr", "pandas.DataFrame.iloc"),

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/docs/extensions/no_skip_abc_members.py

@@ -11,7 +11,7 @@ if TYPE_CHECKING:
     from sphinx.ext.autodoc import Options
 
 
-def autodoc_skip_member(
+def autodoc_skip_member(  # noqa: PLR0917
     app: Sphinx,
     what: Literal["module", "class", "exception", "function", "method", "attribute"],
     name: str,

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/docs/release-notes/0.11.1.md

@@ -1,7 +1,7 @@
 (v0.11.1)=
 ### 0.11.1 {small}`2024-11-12`
 
-### Bug fixes
+#### Bug fixes
 
 - Remove upper pin on `dask` and exclude versions broken with sparse indexing {user}`ilan-gold` ({pr}`1725`)
 - Fix chunking with -1 in `chunks` argument of `~anndata.experimental.read_elem_as_dask` {user}`ilan-gold` ({pr}`1743`)

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/docs/release-notes/0.11.2.md

@@ -1,7 +1,7 @@
 (v0.11.2)=
 ### 0.11.2 {small}`2025-01-07`
 
-### Bug fixes
+#### Bug fixes
 
 - Cache accesses to the `data` and `indices` arrays in {class}`~anndata.abc.CSRDataset` and {class}`~anndata.abc.CSCDataset` {user}`ilan-gold` ({pr}`1744`)
 - Error out on floating point indices that are not actually integers {user}`ilan-gold` ({pr}`1746`)

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/docs/release-notes/0.11.3.md

@@ -1,6 +1,6 @@
 (v0.11.3)=
 ### 0.11.3 {small}`2025-01-10`
 
-### Bug fixes
+#### Bug fixes
 
 - Upper bound `zarr` at runtime {user}`ilan-gold` ({pr}`1819`)

{anndata-0.12.0rc1 → anndata-0.12.0rc3}/docs/release-notes/0.11.4.md

@@ -1,7 +1,7 @@
 (v0.11.4)=
 ### 0.11.4 {small}`2025-03-26`
 
-### Bug fixes
+#### Bug fixes
 
 - Raise {class}`~anndata.ImplicitModificationWarning` when setting `X` on a view. {user}`ilan-gold` ({pr}`1853`)
 - Bound `dask` due to {issue}`dask/dask#11752` {user}`ilan-gold` ({pr}`1859`)
@@ -9,6 +9,6 @@
 - Add `convert_strings_to_categoricals` parameter also to {meth}`~anndata.AnnData.write_h5ad` and {meth}`~anndata.AnnData.write_zarr` as intended {user}`flying-sheep` ({pr}`1914`)
 - Allow initialization of {class}`anndata.AnnData` objects without `X` (since they could be constructed previously by deleting `X`) {user}`ilan-gold` ({pr}`1941`)
 
-### Development Process
+#### Development Process
 
 - Fix version number inference in development environments (CI and local) {user}`flying-sheep` ({pr}`1831`)

anndata-0.12.0rc3/docs/release-notes/0.12.0rc1.md

@@ -0,0 +1,26 @@
+(v0.12.0rc1)=
+### 0.12.0rc1 {small}`2025-04-09`
+
+#### Breaking changes
+
+- Remove `anndata.read` {user}`ilan-gold` ({pr}`1766`)
+- 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`)
+- Disallow declaration of {class}`~anndata.AnnData` with non-`cs{r,c}` sparse data-structures {user}`ilan-gold` ({pr}`1829`)
+- Upgrade all `DeprecationWarning`s to `FutureWarning`s {user}`ilan-gold` ({pr}`1874`)
+
+#### Bug fixes
+
+- Disallow writing of {class}`~anndata._core.xarray.Dataset2D` objects {user}`ilan-gold` ({pr}`1887`)
+- 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`)
+- Don't use {func}`asyncio.run` internally for any operations {user}`ilan-gold` ({pr}`1933`)
+- Disallow forward slashes in keys for writing {user}`ilan-gold` ({pr}`1940`)
+
+#### Features
+
+- {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`)
+- 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`)
+- Support {mod}`zarr` version 3 python package {user}`ilan-gold` ({pr}`1726`)
+- Adopt the Scientific Python [deprecation schedule](https://scientific-python.org/specs/spec-0000/) {user}`ilan-gold` ({pr}`1768`)
+- Allow {mod}`zarr` v3 writing of data {user}`ilan-gold` ({pr}`1892`)
+- {func}`anndata.register_anndata_namespace` functionality for adding custom functionality to an {class}`~anndata.AnnData` object {user}`srivarra` ({pr}`1870`)

anndata-0.12.0rc3/docs/release-notes/0.12.0rc2.md

@@ -0,0 +1,14 @@
+(v0.12.0rc2)=
+### 0.12.0rc2 {small}`2025-05-15`
+
+#### 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
+
+- Allow xarray Datasets to be used for obs/var/obsm/varm. {user}`ilia-kats` ({pr}`1966`)
+
+#### 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-0.12.0rc1 → anndata-0.12.0rc3}/hatch.toml

@@ -15,7 +15,7 @@ scripts.clean = "git restore --source=HEAD --staged --worktree -- docs/release-n
 
 [envs.hatch-test]
 default-args = [  ]
-features = [ "dev", "test" ]
+features = [ "dev", "test-min" ]
 extra-dependencies = [ "ipykernel" ]
 env-vars.UV_CONSTRAINT = "ci/constraints.txt"
 overrides.matrix.deps.env-vars = [
@@ -29,6 +29,9 @@ overrides.matrix.deps.python = [
     { if = [ "min" ], value = "3.11" },
     { if = [ "stable", "pre" ], value = "3.13" },
 ]
+overrides.matrix.deps.features = [
+    { if = [ "stable", "pre" ], value = "test" },
+]
 
 [[envs.hatch-test.matrix]]
 deps = [ "stable", "pre", "min" ]