anndata 0.11.4__tar.gz → 0.12.0rc1__tar.gz

{anndata-0.11.4 → anndata-0.12.0rc1}/.github/ISSUE_TEMPLATE/bug-report.yml

@@ -53,10 +53,18 @@ body:
       description: |
         Which version of anndata and other related software you used.
 
-        Please install `session-info`, run the following command, then paste the results into the text box below.
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button,
+        then paste the results into the text box below.
 
         ```python
-        >>> import anndata, session_info; session_info.show(html=False, dependencies=True)
+        In[1]: import anndata, session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
         ```
       render: python
     validations:

{anndata-0.11.4 → anndata-0.12.0rc1}/.github/workflows/test-cpu.yml

@@ -27,14 +27,14 @@ jobs:
     strategy:
       matrix:
         include:
-          - python-version: '3.12'
+          - python-version: '3.13'
             test-type: coverage
-          - python-version: '3.10'
+          - python-version: '3.11'
             test-type: standard
-          - python-version: '3.12'
+          - python-version: '3.13'
             dependencies-version: pre-release
             test-type: strict-warning
-          - python-version: '3.10'
+          - python-version: '3.11'
             dependencies-version: minimum
             test-type: coverage
     steps:
@@ -56,19 +56,18 @@ jobs:
 
       - name: Install dependencies
         if: matrix.dependencies-version == null
-        run: uv pip install --system --compile "anndata[dev,test] @ ." -c ci/constraints.txt
+        run: uv pip install --system --compile "anndata[dev,test-full] @ ." -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 @ ."
 
       - name: Install dependencies release candidates
         if: matrix.dependencies-version == 'pre-release'
-        run: uv pip install -v --system --compile --pre "anndata[dev,test] @ ." -c ci/constraints.txt
+        run: uv pip install -v --system --compile --pre "anndata[dev,test-full] @ ." -c ci/constraints.txt
 
       - name: Display installed versions
         run: uv pip list
@@ -100,10 +99,10 @@ jobs:
           fetch-depth: 0
           filter: blob:none
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Install build tools and requirements
         run: |

{anndata-0.11.4 → anndata-0.12.0rc1}/.github/workflows/test-gpu.yml

@@ -69,7 +69,8 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ env.max_python_version }}
+          # https://github.com/cupy/cupy/issues/8651 cupy does not support python3.13 yet
+          python-version: "3.12"
 
       - name: Install UV
         uses: astral-sh/setup-uv@v5

{anndata-0.11.4 → anndata-0.12.0rc1}/.gitignore

@@ -7,6 +7,7 @@ __pycache__/
 /*cache/
 /node_modules/
 /data/
+/venv/
 
 # Distribution / packaging
 /dist/

{anndata-0.11.4 → anndata-0.12.0rc1}/.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.2
+    rev: v0.11.4
     hooks:
       - id: ruff
         args: ["--fix"]

{anndata-0.11.4 → anndata-0.12.0rc1}/.readthedocs.yml

@@ -2,7 +2,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.12"
+    python: "3.13"
   jobs:
     post_checkout:
       # unshallow so version can be derived from tag

{anndata-0.11.4 → anndata-0.12.0rc1}/LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2025, scverse
+Copyright (c) 2025, scverse®
 Copyright (c) 2017-2018, P. Angerer, F. Alexander Wolf, Theis Lab
 All rights reserved.
 

{anndata-0.11.4 → anndata-0.12.0rc1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: anndata
-Version: 0.11.4
+Version: 0.12.0rc1
 Summary: Annotated data.
 Project-URL: Documentation, https://anndata.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/anndata
@@ -18,30 +18,31 @@ Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Requires-Dist: array-api-compat!=1.5,>1.4
-Requires-Dist: exceptiongroup; python_version < '3.11'
-Requires-Dist: h5py>=3.7
+Requires-Dist: h5py>=3.8
+Requires-Dist: legacy-api-wrap
 Requires-Dist: natsort
-Requires-Dist: numpy>=1.23
+Requires-Dist: numpy>=1.25
 Requires-Dist: packaging>=24.2
-Requires-Dist: pandas!=2.1.0rc0,!=2.1.2,>=1.4
-Requires-Dist: scipy>1.8
+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
 Provides-Extra: cu11
 Requires-Dist: cupy-cuda11x; extra == 'cu11'
 Provides-Extra: cu12
 Requires-Dist: cupy-cuda12x; extra == 'cu12'
 Provides-Extra: dask
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2022.09.2; 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: boltons; extra == 'dev'
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2022.09.2; 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'
@@ -51,20 +52,20 @@ Requires-Dist: loompy>=3.0.5; extra == 'dev'
 Requires-Dist: matplotlib; extra == 'dev'
 Requires-Dist: openpyxl; extra == 'dev'
 Requires-Dist: pyarrow; extra == 'dev'
-Requires-Dist: pytest-cov>=2.10; 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: scanpy>=1.9.8; 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: zarr<3; extra == 'dev'
 Provides-Extra: dev-doc
 Requires-Dist: towncrier>=24.8.0; extra == 'dev-doc'
 Provides-Extra: doc
 Requires-Dist: awkward>=2.3; extra == 'doc'
+Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'doc'
 Requires-Dist: ipython; extra == 'doc'
 Requires-Dist: myst-nb; extra == 'doc'
 Requires-Dist: myst-parser; extra == 'doc'
@@ -79,13 +80,17 @@ Requires-Dist: sphinx-toolbox>=3.8.0; extra == 'doc'
 Requires-Dist: sphinx>=8.2.1; extra == 'doc'
 Requires-Dist: sphinxext-opengraph; extra == 'doc'
 Requires-Dist: towncrier>=24.8.0; extra == 'doc'
-Requires-Dist: zarr<3; extra == 'doc'
 Provides-Extra: gpu
 Requires-Dist: cupy; extra == 'gpu'
+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'
 Provides-Extra: test
 Requires-Dist: awkward>=2.3; extra == 'test'
 Requires-Dist: boltons; extra == 'test'
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2022.09.2; 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'
@@ -94,18 +99,40 @@ Requires-Dist: loompy>=3.0.5; extra == 'test'
 Requires-Dist: matplotlib; extra == 'test'
 Requires-Dist: openpyxl; extra == 'test'
 Requires-Dist: pyarrow; extra == 'test'
-Requires-Dist: pytest-cov>=2.10; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
 Requires-Dist: pytest-memray; extra == 'test'
 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: scanpy>=1.9.8; extra == 'test'
+Requires-Dist: scanpy>=1.10; extra == 'test'
 Requires-Dist: scikit-learn; extra == 'test'
-Requires-Dist: zarr<3; 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'
 Description-Content-Type: text/markdown
 
-[![Build Status](https://dev.azure.com/scverse/anndata/_apis/build/status/scverse.anndata?branchName=main)](https://dev.azure.com/scverse/anndata/_build)
+[![Tests](https://github.com/scverse/anndata/actions/workflows/test-cpu.yml/badge.svg)](https://github.com/scverse/anndata/actions)
 [![Conda](https://img.shields.io/conda/vn/conda-forge/anndata.svg)](https://anaconda.org/conda-forge/anndata)
 [![Coverage](https://codecov.io/gh/scverse/anndata/branch/main/graph/badge.svg?token=IN1mJN1Wi8)](https://codecov.io/gh/scverse/anndata)
 [![Docs](https://readthedocs.com/projects/icb-anndata/badge/?version=latest)](https://anndata.readthedocs.io)

{anndata-0.11.4 → anndata-0.12.0rc1}/README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://dev.azure.com/scverse/anndata/_apis/build/status/scverse.anndata?branchName=main)](https://dev.azure.com/scverse/anndata/_build)
+[![Tests](https://github.com/scverse/anndata/actions/workflows/test-cpu.yml/badge.svg)](https://github.com/scverse/anndata/actions)
 [![Conda](https://img.shields.io/conda/vn/conda-forge/anndata.svg)](https://anaconda.org/conda-forge/anndata)
 [![Coverage](https://codecov.io/gh/scverse/anndata/branch/main/graph/badge.svg?token=IN1mJN1Wi8)](https://codecov.io/gh/scverse/anndata)
 [![Docs](https://readthedocs.com/projects/icb-anndata/badge/?version=latest)](https://anndata.readthedocs.io)

{anndata-0.11.4 → anndata-0.12.0rc1}/benchmarks/asv.conf.json

@@ -2,22 +2,17 @@
     // The version of the config file format.  Do not change, unless
     // you know what you are doing.
     "version": 1,
-
     // The name of the project being benchmarked
     "project": "anndata",
-
     // The project's homepage
     "project_url": "https://anndata.readthedocs.io/",
-
     // The URL or local path of the source code repository for the
     // project being benchmarked
     "repo": "../../anndata",
-
     // The Python project's subdirectory in your repo.  If missing or
     // the empty string, the project is assumed to be located at the root
     // of the repository.
     // "repo_subdir": "",
-
     // Customizable commands for building, installing, and
     // uninstalling the project. See asv.conf.json documentation.
     //
@@ -27,40 +22,32 @@
         "python -m pip install build",
         "python -m build --wheel -o {build_cache_dir} {build_dir}",
     ],
-
     // List of branches to benchmark. If not provided, defaults to "master"
     // (for git) or "default" (for mercurial).
     "branches": ["main"], // for git
     // "branches": ["default"],    // for mercurial
-
     // The DVCS being used.  If not set, it will be automatically
     // determined from "repo" by looking at the protocol in the URL
     // (if remote), or by looking for special directories, such as
     // ".git" (if local).
     "dvcs": "git",
-
     // The tool to use to create environments.  May be "conda",
     // "virtualenv" or other value depending on the plugins in use.
     // If missing or the empty string, the tool will be automatically
     // determined by looking for tools on the PATH environment
     // variable.
     "environment_type": "mamba",
-
     // timeout in seconds for installing any dependencies in environment
     // defaults to 10 min
     //"install_timeout": 600,
-
     // the base URL to show a commit for the project.
     "show_commit_url": "https://github.com/theislab/anndata/commit/",
-
     // The Pythons you'd like to test against.  If not provided, defaults
     // to the current version of Python used to run `asv`.
     // "pythons": ["2.7", "3.6"],
-
     // The list of conda channel names to be searched for benchmark
     // dependency packages in the specified order
     "conda_channels": ["conda-forge", "defaults"],
-
     // The matrix of dependencies to test.  Each key is the name of a
     // package (in PyPI) and the values are version numbers.  An empty
     // list or empty string indicates to just test against the default
@@ -79,14 +66,13 @@
         "natsort": [""],
         "pandas": [""],
         "memory_profiler": [""],
-        "zarr": ["2.18.4"],
+        "zarr": [""],
         "pytoml": [""],
         "pytest": [""],
         "pooch": [""],
         // "scanpy": [""],
         // "psutil": [""]
     },
-
     // Combinations of libraries/python versions can be excluded/included
     // from the set to test. Each entry is a dictionary containing additional
     // key-value pairs to include/exclude.
@@ -119,31 +105,24 @@
     //     // additional env if run on windows+conda
     //     {"platform": "win32", "environment_type": "mamba", "python": "2.7", "libpython": ""},
     // ],
-
     // The directory (relative to the current directory) that benchmarks are
     // stored in.  If not provided, defaults to "benchmarks"
     // "benchmark_dir": "benchmarks",
-
     // The directory (relative to the current directory) to cache the Python
     // environments in.  If not provided, defaults to "env"
     "env_dir": ".asv/env",
-
     // The directory (relative to the current directory) that raw benchmark
     // results are stored in.  If not provided, defaults to "results".
     "results_dir": ".asv/results",
-
     // The directory (relative to the current directory) that the html tree
     // should be written to.  If not provided, defaults to "html".
     "html_dir": ".asv/html",
-
     // The number of characters to retain in the commit hashes.
     // "hash_length": 8,
-
     // `asv` will cache results of the recent builds in each
     // environment, making them faster to install next time.  This is
     // the number of builds to keep, per environment.
     // "build_cache_size": 2,
-
     // The commits after which the regression search in `asv publish`
     // should start looking for regressions. Dictionary whose keys are
     // regexps matching to benchmark names, and values corresponding to
@@ -156,7 +135,6 @@
     //    "some_benchmark": "352cdf",  // Consider regressions only after this commit
     //    "another_benchmark": null,   // Skip regression detection altogether
     // },
-
     // The thresholds for relative change in results, after which `asv
     // publish` starts reporting regressions. Dictionary of the same
     // form as in ``regressions_first_commits``, with values

{anndata-0.11.4 → anndata-0.12.0rc1}/benchmarks/benchmarks/anndata.py

@@ -15,8 +15,14 @@ class GarbargeCollectionSuite:
         def display_top(snapshot, key_type="lineno"):
             snapshot = snapshot.filter_traces(
                 (
-                    tracemalloc.Filter(False, "<frozen importlib._bootstrap>"),
-                    tracemalloc.Filter(False, "<unknown>"),
+                    tracemalloc.Filter(
+                        inclusive=False,
+                        filename_pattern="<frozen importlib._bootstrap>",
+                    ),
+                    tracemalloc.Filter(
+                        inclusive=False,
+                        filename_pattern="<unknown>",
+                    ),
                 )
             )
             top_stats = snapshot.statistics(key_type)

{anndata-0.11.4 → anndata-0.12.0rc1}/ci/scripts/min-deps.py

@@ -10,17 +10,13 @@ from __future__ import annotations
 
 import argparse
 import sys
+import tomllib
 from collections import deque
 from contextlib import ExitStack
 from functools import cached_property
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-if sys.version_info >= (3, 11):
-    import tomllib
-else:
-    import tomli as tomllib
-
 from packaging.requirements import Requirement
 from packaging.version import Version
 
@@ -39,6 +35,8 @@ def min_dep(req: Requirement) -> Requirement:
 
     >>> min_dep(Requirement("numpy>=1.0"))
     <Requirement('numpy==1.0.*')>
+    >>> min_dep(Requirement("numpy<3.0"))
+    <Requirement('numpy<3.0')>
     """
     req_name = req.name
     if req.extras:
@@ -48,8 +46,8 @@ def min_dep(req: Requirement) -> Requirement:
         spec for spec in req.specifier if spec.operator in {"==", "~=", ">=", ">"}
     ]
     if not filter_specs:
-        return Requirement(req_name)
-
+        # TODO: handle markers
+        return Requirement(f"{req_name}{req.specifier}")
     min_version = Version("0.0.0.a1")
     for spec in filter_specs:
         if spec.operator in {">", ">=", "~="}:

{anndata-0.11.4 → anndata-0.12.0rc1}/docs/api.md

@@ -13,6 +13,8 @@ The central class:
    AnnData
 ```
 
+(combining-api)=
+
 ## Combining
 
 Combining {class}`AnnData` objects.
@@ -25,6 +27,8 @@ See also the section on concatenation.
    concat
 ```
 
+(reading-api)=
+
 ## Reading
 
 Reading anndata’s native formats `.h5ad` and `zarr`.
@@ -66,6 +70,8 @@ You might have more success by assembling the {class}`AnnData` object yourself f
    io.read_umi_tools
 ```
 
+(writing-api)=
+
 ## Writing
 
 Writing a complete {class}`AnnData` object to disk in anndata’s native formats `.h5ad` and `zarr`.
@@ -146,7 +152,8 @@ Low level methods for reading and writing elements of an {class}`AnnData` object
 .. autosummary::
    :toctree: generated/
 
-   experimental.read_elem_as_dask
+   experimental.read_elem_lazy
+   experimental.read_lazy
 ```
 
 Utilities for customizing the IO process:
@@ -171,8 +178,34 @@ Types used by the former:
    experimental.ReadCallback
    experimental.WriteCallback
    experimental.StorageType
+   experimental.backed._lazy_arrays.MaskedArray
+   experimental.backed._lazy_arrays.CategoricalArray
+   experimental.backed._xarray.Dataset2D
+```
+
+(extensions-api)=
+
+## Extensions
+
+```{eval-rst}
+.. autosummary::
+   :toctree: generated/
+
+   register_anndata_namespace
+
 ```
 
+Types used by the former:
+
+```{eval-rst}
+.. autosummary::
+   :toctree: generated/
+
+   types.ExtensionNamespace
+```
+
+(errors-api)=
+
 ## Errors and warnings
 
 ```{eval-rst}
@@ -182,6 +215,8 @@ Types used by the former:
    ImplicitModificationWarning
 ```
 
+(settings-api)=
+
 ## Settings
 
 ```{eval-rst}
@@ -192,6 +227,8 @@ Types used by the former:
    settings.override
 ```
 
+(types-api)=
+
 ## Custom Types/Classes for Readable/Writeable Elements
 
 ```{eval-rst}

{anndata-0.11.4 → anndata-0.12.0rc1}/docs/conf.py

@@ -75,9 +75,10 @@ nb_execution_mode = "off"
 # Generate the API documentation when building
 autosummary_generate = True
 autodoc_member_order = "bysource"
+autodoc_mock_imports = ["torch"]
+# autodoc_default_flags = ['members']
 issues_github_path = "scverse/anndata"
 rtd_links_prefix = PurePosixPath("src")
-# autodoc_default_flags = ['members']
 napoleon_google_docstring = False
 napoleon_numpy_docstring = True
 napoleon_include_init_with_doc = False
@@ -112,9 +113,14 @@ 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),
     xarray=("https://docs.xarray.dev/en/stable", None),
-    zarr=("https://zarr.readthedocs.io/en/v2.18.4/", None),
+    obstore=("https://developmentseed.org/obstore/latest/", None),
+    kvikio=("https://docs.rapids.ai/api/kvikio/stable/", None),
+    zarrs=("https://zarrs-python.readthedocs.io/en/stable/", None),
 )
+
 qualname_overrides = {
     "h5py._hl.group.Group": "h5py.Group",
     "h5py._hl.files.File": "h5py.File",
@@ -129,7 +135,11 @@ qualname_overrides = {
     "anndata._types.WriteCallback": "anndata.experimental.WriteCallback",
     "anndata._types.Read": "anndata.experimental.Read",
     "anndata._types.Write": "anndata.experimental.Write",
-    "zarr._storage.store.BaseStore": "zarr.storage.MemoryStore",
+    "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
+    "zarr.core.buffer.core.Buffer": "zarr.registry.Registry",
+    "zarr.storage._common.StorePath": "zarr.storage.StorePath",
     "anndata.compat.DaskArray": "dask.array.Array",
     "anndata.compat.CupyArray": "cupy.ndarray",
     "anndata.compat.CupySparseMatrix": "cupyx.scipy.sparse.spmatrix",
@@ -139,6 +149,7 @@ qualname_overrides = {
     "pandas.DataFrame.loc": ("py:attr", "pandas.DataFrame.loc"),
     # should be fixed soon: https://github.com/tox-dev/sphinx-autodoc-typehints/pull/516
     "types.EllipsisType": ("py:data", "types.EllipsisType"),
+    "pathlib._local.Path": "pathlib.Path",
 }
 autodoc_type_aliases = dict(
     NDArray=":data:`~numpy.typing.NDArray`",

{anndata-0.11.4 → anndata-0.12.0rc1}/docs/extensions/no_skip_abc_members.py

@@ -16,7 +16,7 @@ def autodoc_skip_member(
     what: Literal["module", "class", "exception", "function", "method", "attribute"],
     name: str,
     obj: object,
-    skip: bool,
+    skip: bool,  # noqa: FBT001
     options: Options,
 ):
     if what == "method" and getattr(obj, "__isabstractmethod__", False):

{anndata-0.11.4 → anndata-0.12.0rc1}/docs/fileformat-prose.md

@@ -91,7 +91,7 @@ Using this information, we're able to dispatch onto readers for the different el
 ## Dense arrays
 
 Dense numeric arrays have the most simple representation on disk,
-as they have native equivalents in H5py {doc}`h5py:high/dataset` and Zarr {ref}`Arrays <zarr:tutorial_create>`.
+as they have native equivalents in H5py {doc}`h5py:high/dataset` and Zarr {doc}`Arrays <zarr:user-guide/arrays>`.
 We can see an example of this with dimensionality reductions stored in the `obsm` group:
 
 `````{tab-set}

{anndata-0.11.4 → anndata-0.12.0rc1}/docs/release-notes/0.11.0.md

@@ -40,7 +40,7 @@ Release candidates:
 - {guilabel}`rc1` Allow `axis` parameter of e.g. {func}`anndata.concat` to accept `'obs'` and `'var'` {user}`flying-sheep` ({pr}`1244`)
 - {guilabel}`rc1` Add `settings` object with methods for altering internally-used options, like checking for uniqueness on `obs`' index {user}`ilan-gold` ({pr}`1270`)
 - {guilabel}`rc1` Add {attr}`~anndata.settings.remove_unused_categories` option to {attr}`anndata.settings` to override current behavior {user}`ilan-gold` ({pr}`1340`)
-- {guilabel}`rc1` Add {func}`~anndata.experimental.read_elem_as_dask` function to handle i/o with sparse and dense arrays {user}`ilan-gold` ({pr}`1469`)
+- {guilabel}`rc1` Add `~anndata.experimental.read_elem_as_dask` function to handle i/o with sparse and dense arrays {user}`ilan-gold` ({pr}`1469`)
 - {guilabel}`rc1` Add ability to convert strings to categoricals on write in {meth}`~anndata.AnnData.write_h5ad` and {meth}`~anndata.AnnData.write_zarr` via `convert_strings_to_categoricals` parameter {user}` falexwolf` ({pr}`1474`)
 - {guilabel}`rc1` Add {attr}`~anndata.settings.check_uniqueness` option to {attr}`anndata.settings` to override current behavior {user}`ilan-gold` ({pr}`1507`)
 - {guilabel}`rc1` Add functionality to write from GPU {class}`dask.array.Array` to disk {user}`ilan-gold` ({pr}`1550`)

{anndata-0.11.4 → anndata-0.12.0rc1}/docs/release-notes/0.11.1.md

@@ -4,5 +4,5 @@
 ### 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 {func}`~anndata.experimental.read_elem_as_dask` {user}`ilan-gold` ({pr}`1743`)
+- Fix chunking with -1 in `chunks` argument of `~anndata.experimental.read_elem_as_dask` {user}`ilan-gold` ({pr}`1743`)
 - Fix `cupy<0.13` imports in non-gpu environments {user}`ilan-gold` ({pr}`1754`)

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

@@ -0,0 +1,4 @@
+(v0.12.0rc1)=
+### 0.12.0rc1 {small}`2025-04-09`
+
+No significant changes.

{anndata-0.11.4 → anndata-0.12.0rc1}/docs/tutorials/index.md

@@ -14,4 +14,6 @@ notebooks/anncollection-annloader
 notebooks/anndata_dask_array
 notebooks/awkward-arrays
 notebooks/{read,write}_dispatched
+notebooks/read_lazy
+zarr-v3
 ```