anndata 0.11.3__tar.gz → 0.11.4__tar.gz

{anndata-0.11.3 → anndata-0.11.4}/.github/workflows/benchmark.yml

@@ -6,12 +6,16 @@ on:
   pull_request:
     branches: [main]
 
+env:
+  FORCE_COLOR: "1"
+
+defaults:
+  run:
+    shell: bash -el {0}
+
 jobs:
   benchmark:
     runs-on: ${{ matrix.os }}
-    defaults:
-      run:
-        shell: bash -el {0} # -e to fail on error, -l for mamba
 
     strategy:
       fail-fast: false

{anndata-0.11.3 → anndata-0.11.4}/.github/workflows/codespell.yml

@@ -16,7 +16,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Codespell
-        uses: codespell-project/actions-codespell@v2
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: blob:none
+      - uses: codespell-project/actions-codespell@v2

{anndata-0.11.3 → anndata-0.11.4}/.github/workflows/publish.yml

@@ -12,6 +12,9 @@ jobs:
       id-token: write # to authenticate as Trusted Publisher to pypi.org
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: blob:none
       - uses: actions/setup-python@v5
         with:
           python-version: "3.x"

anndata-0.11.4/.github/workflows/test-cpu.yml

@@ -0,0 +1,124 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - "[0-9]+.[0-9]+.x"
+  pull_request:
+
+env:
+  PYTEST_ADDOPTS: "-v --color=yes"
+  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:
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - python-version: '3.12'
+            test-type: coverage
+          - python-version: '3.10'
+            test-type: standard
+          - python-version: '3.12'
+            dependencies-version: pre-release
+            test-type: strict-warning
+          - python-version: '3.10'
+            dependencies-version: minimum
+            test-type: coverage
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: blob:none
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install UV
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+
+      - name: Install dependencies
+        if: matrix.dependencies-version == null
+        run: uv pip install --system --compile "anndata[dev,test] @ ." -c ci/constraints.txt
+
+      - name: Install minimum dependencies
+        if: matrix.dependencies-version == 'minimum'
+        run: |
+          uv pip install --system --compile tomli packaging
+
+          deps=$(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
+
+      - name: Display installed versions
+        run: uv pip list
+
+      - name: Run Pytest
+        if: matrix.test-type == 'standard'
+        run: pytest -n auto
+
+      - name: Run Pytest (coverage)
+        if: matrix.test-type == 'coverage'
+        run: coverage run -m pytest -n auto --cov --cov-report=xml
+
+      - name: Run Pytest (treat warnings as errors)
+        if: matrix.test-type == 'strict-warning'
+        run: pytest --strict-warnings -n auto
+
+      - uses: codecov/codecov-action@v4
+        if: matrix.test-type == 'coverage'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          files: test-data/coverage.xml
+
+  check-build:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: blob:none
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - 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__)'

{anndata-0.11.3 → anndata-0.11.4}/.github/workflows/test-gpu.yml

@@ -9,6 +9,14 @@ on:
       - opened
       - synchronize
 
+env:
+  PYTEST_ADDOPTS: "-v --color=yes"
+  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:
@@ -39,14 +47,11 @@ jobs:
     # At time of writing, a typical run takes about 5 minutes
     timeout-minutes: 30
 
-    defaults:
-      run:
-        shell: bash -el {0}
-
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          filter: blob:none
 
       - name: Nvidia SMI sanity check
         run: nvidia-smi
@@ -67,9 +72,10 @@ jobs:
           python-version: ${{ env.max_python_version }}
 
       - name: Install UV
-        uses: hynek/setup-cached-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
-          cache-dependency-path: pyproject.toml
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
 
       - name: Install AnnData
         run: uv pip install --system -e ".[dev,test,cu12]" -c ci/constraints.txt
@@ -78,13 +84,13 @@ jobs:
         run: pip list
 
       - name: Run test
-        run: pytest -m gpu --cov --cov-report=xml --cov-context=test
+        run: coverage run -m pytest -m gpu -n auto --cov --cov-report=xml
 
       - uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
-          verbose: true
+          files: test-data/coverage.xml
 
       - name: Remove 'run-gpu-ci' Label
         if: always()

{anndata-0.11.3 → anndata-0.11.4}/.gitignore

@@ -11,7 +11,6 @@ __pycache__/
 # Distribution / packaging
 /dist/
 /ci/min-deps.txt
-/src/anndata/_version.py
 /requirements*.lock
 /.python-version
 
@@ -28,7 +27,6 @@ __pycache__/
 
 # IDEs
 /.idea/
-/.vscode/
 
 # Benchmark
 .asv

{anndata-0.11.3 → anndata-0.11.4}/.pre-commit-config.yaml

@@ -1,18 +1,18 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.11.2
     hooks:
       - id: ruff
-        types_or: [python, pyi, jupyter]
         args: ["--fix"]
       - id: ruff-format
-        types_or: [python, pyi, jupyter]
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v1.9.4
     hooks:
-      - id: prettier
-        exclude_types:
-          - markdown
+      - id: biome-format
+  - repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
+    hooks:
+      - id: taplo-format
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
@@ -27,7 +27,7 @@ repos:
       - id: no-commit-to-branch
         args: ["--branch=main"]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         additional_dependencies:

anndata-0.11.4/.taplo.toml

@@ -0,0 +1,5 @@
+[formatting]
+array_auto_collapse = false
+column_width = 120
+compact_arrays = false
+indent_string = '    '

anndata-0.11.4/.vscode/launch.json

@@ -0,0 +1,26 @@
+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Docs",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": { "PYTEST_ADDOPTS": "--color=yes" },
+            "presentation": { "hidden": true },
+        },
+    ],
+}

anndata-0.11.4/.vscode/settings.json

@@ -0,0 +1,27 @@
+{
+    "[python][toml][json][jsonc]": {
+        "editor.formatOnSave": true,
+        "editor.codeActionsOnSave": {
+            "source.organizeImports": "explicit",
+            "source.fixAll": "explicit",
+        },
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+    },
+    "[toml]": {
+        "editor.defaultFormatter": "tamasfe.even-better-toml",
+    },
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestEnabled": true,
+    "python.testing.pytestArgs": [
+        "--color=yes",
+        "-vv",
+        "--strict-warnings",
+        //"-nauto",
+    ],
+    "python.terminal.activateEnvironment": true,
+}

{anndata-0.11.3 → anndata-0.11.4}/LICENSE

@@ -1,6 +1,7 @@
 BSD 3-Clause License
 
-Copyright (c) 2017-2018 P. Angerer, F. Alexander Wolf, Theis Lab
+Copyright (c) 2025, scverse
+Copyright (c) 2017-2018, P. Angerer, F. Alexander Wolf, Theis Lab
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

{anndata-0.11.3 → anndata-0.11.4}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: anndata
-Version: 0.11.3
+Version: 0.11.4
 Summary: Annotated data.
 Project-URL: Documentation, https://anndata.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/anndata
 Project-URL: Home-page, https://github.com/scverse/anndata
 Author: Philipp Angerer, Alex Wolf, Isaac Virshup, Sergei Rybakov
-Maintainer-email: Isaac Virshup <ivirshup@gmail.com>, Philipp Angerer <philipp.angerer@helmholtz-munich.de>, Alex Wolf <f.alex.wolf@gmx.de>
+Maintainer-email: Isaac Virshup <ivirshup@gmail.com>, Philipp Angerer <philipp.angerer@helmholtz-munich.de>, Ilan Gold <ilan.gold@helmholtz-munich.de>
 License-Expression: BSD-3-Clause
 License-File: LICENSE
 Classifier: Environment :: Console
@@ -29,7 +29,7 @@ Requires-Dist: exceptiongroup; python_version < '3.11'
 Requires-Dist: h5py>=3.7
 Requires-Dist: natsort
 Requires-Dist: numpy>=1.23
-Requires-Dist: packaging>=20.0
+Requires-Dist: packaging>=24.2
 Requires-Dist: pandas!=2.1.0rc0,!=2.1.2,>=1.4
 Requires-Dist: scipy>1.8
 Provides-Extra: cu11
@@ -37,29 +37,46 @@ 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.*,>=2022.09.2; extra == 'dask'
+Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2022.09.2; extra == 'dask'
 Provides-Extra: dev
-Requires-Dist: pytest-xdist; extra == 'dev'
-Requires-Dist: setuptools-scm; 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[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: pyarrow; extra == 'dev'
+Requires-Dist: pytest-cov>=2.10; 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: 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: dev-test
-Requires-Dist: pytest-xdist; extra == 'dev-test'
 Provides-Extra: doc
 Requires-Dist: awkward>=2.3; extra == 'doc'
 Requires-Dist: ipython; extra == 'doc'
+Requires-Dist: myst-nb; extra == 'doc'
 Requires-Dist: myst-parser; extra == 'doc'
-Requires-Dist: nbsphinx; extra == 'doc'
 Requires-Dist: readthedocs-sphinx-search; extra == 'doc'
-Requires-Dist: scanpydoc[theme,typehints]>=0.14.1; extra == 'doc'
+Requires-Dist: scanpydoc[theme,typehints]>=0.15.1; 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-toolbox>=3.8.0; extra == 'doc'
-Requires-Dist: sphinx>=7.4.6; 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'
@@ -68,8 +85,9 @@ Requires-Dist: cupy; extra == 'gpu'
 Provides-Extra: test
 Requires-Dist: awkward>=2.3; extra == 'test'
 Requires-Dist: boltons; extra == 'test'
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,>=2022.09.2; extra == 'test'
+Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2022.09.2; extra == 'test'
 Requires-Dist: dask[distributed]; extra == 'test'
+Requires-Dist: filelock; extra == 'test'
 Requires-Dist: httpx; extra == 'test'
 Requires-Dist: joblib; extra == 'test'
 Requires-Dist: loompy>=3.0.5; extra == 'test'
@@ -79,6 +97,8 @@ Requires-Dist: pyarrow; extra == 'test'
 Requires-Dist: pytest-cov>=2.10; 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: scikit-learn; extra == 'test'
@@ -112,16 +132,17 @@ anndata is a Python package for handling annotated data matrices in memory and o
 
 [//]: # (numfocus-fiscal-sponsor-attribution)
 
-anndata is part of the scverse project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
-Please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
-
+anndata is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
+If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
 
+<div align="center">
 <a href="https://numfocus.org/project/scverse">
   <img
     src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
     width="200"
   >
 </a>
+</div>
 
 ## Public API
 

{anndata-0.11.3 → anndata-0.11.4}/README.md

@@ -25,16 +25,17 @@ anndata is a Python package for handling annotated data matrices in memory and o
 
 [//]: # (numfocus-fiscal-sponsor-attribution)
 
-anndata is part of the scverse project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
-Please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
-
+anndata is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
+If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
 
+<div align="center">
 <a href="https://numfocus.org/project/scverse">
   <img
     src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
     width="200"
   >
 </a>
+</div>
 
 ## Public API
 

{anndata-0.11.3 → anndata-0.11.4}/benchmarks/benchmarks/utils.py

@@ -63,9 +63,8 @@ def gen_indexer(adata, dim, index_kind, ratio):
     index_kinds = {"slice", "intarray", "boolarray", "strarray"}
 
     if index_kind not in index_kinds:
-        raise ValueError(
-            f"Argument 'index_kind' must be one of {index_kinds}. Was {index_kind}."
-        )
+        msg = f"Argument 'index_kind' must be one of {index_kinds}. Was {index_kind}."
+        raise ValueError(msg)
 
     axis = dimnames.index(dim)
     subset = [slice(None), slice(None)]

anndata-0.11.4/biome.jsonc

@@ -0,0 +1,18 @@
+{
+    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "include": ["./.vscode/*.json", "**/*.jsonc", "**/asv.conf.json"],
+            "json": {
+                "formatter": {
+                    "trailingCommas": "all",
+                },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}

{anndata-0.11.3 → anndata-0.11.4}/ci/scripts/min-deps.py

@@ -71,7 +71,9 @@ def extract_min_deps(
 
         # If we are referring to other optional dependency lists, resolve them
         if req.name == project_name:
-            assert req.extras, f"Project included itself as dependency, without specifying extras: {req}"
+            assert req.extras, (
+                f"Project included itself as dependency, without specifying extras: {req}"
+            )
             for extra in req.extras:
                 extra_deps = pyproject["project"]["optional-dependencies"][extra]
                 dependencies += map(Requirement, extra_deps)

{anndata-0.11.3 → anndata-0.11.4}/docs/api.md

@@ -69,13 +69,28 @@ You might have more success by assembling the {class}`AnnData` object yourself f
 ## Writing
 
 Writing a complete {class}`AnnData` object to disk in anndata’s native formats `.h5ad` and `zarr`.
+(These functions are also exported as {func}`io.write_h5ad` and {func}`io.write_zarr`.)
 
 ```{eval-rst}
 .. autosummary::
    :toctree: generated/
 
-   AnnData.write
+   AnnData.write_h5ad
    AnnData.write_zarr
+
+
+..
+    .. autosummary::
+       :toctree: generated/
+
+       io.write_h5ad
+       io.write_zarr
+
+.. toctree::
+   :hidden:
+
+   generated/anndata.io.write_h5ad
+   generated/anndata.io.write_zarr
 ```
 
 Writing individual portions ({attr}`~AnnData.obs`, {attr}`~AnnData.varm` etc.) of the {class}`AnnData` object.