anndata 0.11.4__tar.gz → 0.12.0rc2__tar.gz

{anndata-0.11.4 → anndata-0.12.0rc2}/.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-0.12.0rc2/.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-0.12.0rc2/.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-0.11.4 → anndata-0.12.0rc2}/.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 -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] @ ." -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
@@ -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-0.12.0rc2}/.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-0.12.0rc2}/.gitignore

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

{anndata-0.11.4 → anndata-0.12.0rc2}/.pre-commit-config.yaml

@@ -1,10 +1,14 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.2
+    rev: v0.11.4
     hooks:
       - 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-0.11.4 → anndata-0.12.0rc2}/.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-0.12.0rc2}/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-0.12.0rc2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: anndata
-Version: 0.11.4
+Version: 0.12.0rc2
 Summary: Annotated data.
 Project-URL: Documentation, https://anndata.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/anndata
@@ -18,30 +18,32 @@ 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-Dist: array-api-compat!=1.5,>1.4
-Requires-Dist: exceptiongroup; python_version < '3.11'
-Requires-Dist: h5py>=3.7
+Requires-Python: >=3.11
+Requires-Dist: array-api-compat>=1.7.1
+Requires-Dist: h5py>=3.8
+Requires-Dist: legacy-api-wrap
 Requires-Dist: natsort
-Requires-Dist: numpy>=1.23
+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,<3.0.7,>=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: 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,>=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'
@@ -50,42 +52,49 @@ 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>=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: 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: zarr<3; 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
 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'
-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'
 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>=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,>=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'
@@ -93,19 +102,41 @@ 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>=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: requests; extra == 'test'
+Requires-Dist: scanpy>=1.10; extra == 'test'
 Requires-Dist: scikit-learn; extra == 'test'
-Requires-Dist: zarr<3; extra == 'test'
+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
 
-[![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-0.12.0rc2}/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-0.12.0rc2}/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-0.12.0rc2}/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-0.12.0rc2}/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-0.11.4 → anndata-0.12.0rc2}/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-0.11.4 → anndata-0.12.0rc2}/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-0.11.4 → anndata-0.12.0rc2}/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
 
@@ -38,7 +34,9 @@ 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')>
     """
     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 {">", ">=", "~="}:
@@ -57,7 +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(
@@ -66,6 +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()
 
@@ -78,7 +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):
@@ -102,6 +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",