anndata 0.12.1__tar.gz → 0.12.3__tar.gz

anndata-0.12.3/.github/dependabot.yml

@@ -0,0 +1,9 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    labels:
+      - no milestone
+      - skip-gpu-ci

{anndata-0.12.1 → anndata-0.12.3}/.github/workflows/benchmark.yml

@@ -11,7 +11,10 @@ env:
 
 defaults:
   run:
-    shell: bash -el {0}
+    # Add `-l` to GitHub’s default bash options to activate mamba environments
+    # https://docs.github.com/en/actions/reference/workflows-and-actions/workflow-syntax#exit-codes-and-error-action-preference
+    # https://github.com/mamba-org/setup-micromamba/#readme
+    shell: bash -elo pipefail {0}
 
 jobs:
   benchmark:
@@ -29,9 +32,10 @@ jobs:
       ASV_DIR: "./benchmarks"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
+          # no blob filter so asv can checkout other commits
 
       - run: git fetch origin main:main
         if: ${{ github.ref_name != 'main' }}
@@ -42,11 +46,10 @@ jobs:
           environment-name: asv
           cache-environment: true
           # Deps documented in https://asv.readthedocs.io/en/latest/installing.html
-          # libmambapy upper bound: https://github.com/airspeed-velocity/asv/issues/1438
           create-args: >-
             python=${{ matrix.python }}
             asv
-            libmambapy<2
+            py_rattler
             conda-build
 
       - name: Cache datasets

anndata-0.12.1/.github/workflows/check-pr-milestoned.yml → anndata-0.12.3/.github/workflows/check-pr.yml

@@ -24,7 +24,7 @@ env:
 
 jobs:
   check-milestone:
-    name: "Triage: Check Milestone"
+    name: "Triage: Check PR title, milestone, and labels"
     runs-on: ubuntu-latest
     steps:
       - name: Check if merging isn’t blocked
@@ -35,3 +35,7 @@ jobs:
         uses: flying-sheep/check@v1
         with:
           success: ${{ github.event.pull_request.milestone != null || contains(env.LABELS, 'no milestone') }}
+      - name: Check if PR title is valid
+        uses: amannn/action-semantic-pull-request@v6
+        env: # Needs repo options: “Squash and merge” with commit message set to “PR title”
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

{anndata-0.12.1 → anndata-0.12.3}/.github/workflows/publish.yml

@@ -11,7 +11,7 @@ jobs:
     permissions:
       id-token: write # to authenticate as Trusted Publisher to pypi.org
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           filter: blob:none

{anndata-0.12.1 → anndata-0.12.3}/.github/workflows/test-cpu.yml

@@ -10,12 +10,7 @@ on:
 env:
   FORCE_COLOR: "1"
 
-defaults:
-  run:
-    shell: bash -el {0}
-
-# Cancel the job if new commits are pushed
-# https://stackoverflow.com/questions/66335225/how-to-cancel-previous-runs-in-the-pr-when-you-push-new-commitsupdate-the-curre
+# Cancel the job if new commits are pushed: https://stackoverflow.com/q/66335225/247482
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
@@ -26,11 +21,11 @@ jobs:
     outputs:
       envs: ${{ steps.get-envs.outputs.envs }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
-      - uses: astral-sh/setup-uv@v5
+      - uses: astral-sh/setup-uv@v6
         with:
           enable-cache: false
       - id: get-envs
@@ -38,9 +33,10 @@ jobs:
           ENVS_JSON=$(NO_COLOR=1 uvx hatch env show --json | jq -c 'to_entries
             | map(
               select(.key | startswith("hatch-test"))
-              | { name: .key, python: .value.python }
+              | { name: .key, python: .value.python, args: (.value."extra-args" // [] | join(" ")) }
             )')
           echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
   test:
     needs: get-environments
     runs-on: ubuntu-latest
@@ -48,51 +44,68 @@ jobs:
       matrix:
         env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
         io_mark: ["zarr_io", "not zarr_io"]
-    env:  # environment variable for use in codecov’s env_vars tagging
+    env:  # environment variables for use in codecov’s env_vars tagging
       ENV_NAME: ${{ matrix.env.name }}
+      IO_MARK: ${{ matrix.io_mark }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           filter: blob:none
 
-      - name: Set up Python ${{ matrix.env.python }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.env.python }}
+      - name: Install system dependencies
+        run: sudo apt install -y hdf5-tools
 
       - name: Install UV
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           enable-cache: true
-          cache-dependency-glob: pyproject.toml
+          python-version: ${{ matrix.env.python }}
 
       - name: Install dependencies
-        run: uvx hatch -v env create ${{ matrix.env.name }}
+        run: |
+          # https://github.com/pallets/click/issues/3066
+          uv tool install --with='click!=8.3.0' hatch
+          hatch -v env create ${{ matrix.env.name }}
 
       - name: Run tests
-        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto --cov --cov-report=xml --junitxml=test-data/test-results.xml -m "${{matrix.io_mark}}"
+        env:
+          COVERAGE_PROCESS_START: ${{ github.workspace }}/pyproject.toml
+        run: |
+          hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto --junitxml=test-data/test-results.xml -m "${{ matrix.io_mark }}" ${{ matrix.env.args }}
+          hatch run ${{ matrix.env.name }}:cov-combine
+          hatch run ${{ matrix.env.name }}:coverage xml
+
+      - name: Upload test results
+        if: ${{ !cancelled() }}
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          env_vars: ENV_NAME,IO_MARK
+          fail_ci_if_error: true
+          file: test-data/test-results.xml
 
       - name: Upload coverage data
         uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          env_vars: ENV_NAME
+          env_vars: ENV_NAME,IO_MARK
           fail_ci_if_error: true
           files: test-data/coverage.xml
 
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           filter: blob:none
 
-      - name: Set up Python 3.13
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.13'
+          python-version: '3.x'
+          cache: pip
 
       - name: Install build tools and requirements
         run: |
@@ -107,11 +120,6 @@ jobs:
           python -m build --sdist --wheel .
           twine check dist/*
 
-      - name: Check runtime version
-        run: |
-          pip install dist/*.whl
-          python -c 'import anndata; print(anndata.__version__)'
-
   check:
     if: always()
     needs:
@@ -120,6 +128,6 @@ jobs:
       - build
     runs-on: ubuntu-latest
     steps:
-        - uses: re-actors/alls-green@release/v1
-          with:
-            jobs: ${{ toJSON(needs) }}
+      - uses: re-actors/alls-green@release/v1
+        with:
+          jobs: ${{ toJSON(needs) }}

{anndata-0.12.1 → anndata-0.12.3}/.github/workflows/test-gpu.yml

@@ -13,10 +13,6 @@ 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:
@@ -48,7 +44,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4 # TODO: upgrade once cirun image supports node 24
         with:
           fetch-depth: 0
           filter: blob:none
@@ -66,28 +62,29 @@ jobs:
           max_version=$(echo "$classifiers" | sort -V | tail -1)
           echo "max_python_version=$max_version" >> $GITHUB_ENV
 
-      - name: Install Python
-        uses: actions/setup-python@v5
-        with:
-          # 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
+        uses: astral-sh/setup-uv@v6
         with:
           enable-cache: true
-          cache-dependency-glob: pyproject.toml
+          python-version: ${{ env.max_python_version }}
 
       - name: Install AnnData
-        run: uv pip install --system -e ".[dev,test,cu12]" -c ci/constraints.txt
+        run: |
+          uv venv
+          uv pip install -e ".[dev,test,cu12]" -c ci/constraints.txt
 
       - name: Env list
-        run: pip list
+        run: uv pip list
 
       - name: Run test
-        run: coverage run -m pytest -m gpu -n auto --cov --cov-report=xml
+        env:
+          COVERAGE_PROCESS_START: ${{ github.workspace }}/pyproject.toml
+        run: |
+          uv run coverage run -m pytest -m gpu -n auto
+          uv run coverage combine
+          uv run coverage xml
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true

{anndata-0.12.1 → anndata-0.12.3}/.pre-commit-config.yaml

@@ -1,8 +1,8 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.4
+    rev: v0.13.0
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: ["--fix"]
       - id: ruff-format
       # The following can be removed once PLR0917 is out of preview

{anndata-0.12.1 → anndata-0.12.3}/.readthedocs.yml

@@ -1,6 +1,6 @@
 version: 2
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
     python: "3.13"
   jobs:

{anndata-0.12.1 → anndata-0.12.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: anndata
-Version: 0.12.1
+Version: 0.12.3
 Summary: Annotated data.
 Project-URL: Documentation, https://anndata.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/anndata
@@ -38,15 +38,14 @@ 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,>=2023.5.1; extra == 'dask'
+Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,!=2025.2.*,!=2025.3.*,!=2025.4.*,!=2025.5.*,!=2025.6.*,!=2025.7.*,!=2025.8.*,>=2023.5.1; extra == 'dask'
 Provides-Extra: dev
-Requires-Dist: hatch-vcs; extra == 'dev'
 Requires-Dist: towncrier>=24.8.0; 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: dask[array]!=2024.8.*,!=2024.9.*,!=2025.2.*,!=2025.3.*,!=2025.4.*,!=2025.5.*,!=2025.6.*,!=2025.7.*,!=2025.8.*,>=2023.5.1; extra == 'doc'
 Requires-Dist: ipython; extra == 'doc'
 Requires-Dist: myst-nb; extra == 'doc'
 Requires-Dist: myst-parser; extra == 'doc'
@@ -64,14 +63,14 @@ 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: dask[array]!=2024.8.*,!=2024.9.*,!=2025.2.*,!=2025.3.*,!=2025.4.*,!=2025.5.*,!=2025.6.*,!=2025.7.*,!=2025.8.*,>=2023.5.1; extra == 'lazy'
 Requires-Dist: requests; extra == 'lazy'
 Requires-Dist: xarray>=2025.06.1; extra == 'lazy'
 Provides-Extra: test
 Requires-Dist: aiohttp; extra == 'test'
 Requires-Dist: awkward>=2.3.2; extra == 'test'
 Requires-Dist: boltons; extra == 'test'
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'test'
+Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,!=2025.2.*,!=2025.3.*,!=2025.4.*,!=2025.5.*,!=2025.6.*,!=2025.7.*,!=2025.8.*,>=2023.5.1; extra == 'test'
 Requires-Dist: dask[distributed]; extra == 'test'
 Requires-Dist: filelock; extra == 'test'
 Requires-Dist: httpx<1.0; extra == 'test'
@@ -93,7 +92,7 @@ Requires-Dist: xarray>=2025.06.1; extra == 'test'
 Provides-Extra: test-min
 Requires-Dist: awkward>=2.3.2; extra == 'test-min'
 Requires-Dist: boltons; extra == 'test-min'
-Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,<2025.2.0,>=2023.5.1; extra == 'test-min'
+Requires-Dist: dask[array]!=2024.8.*,!=2024.9.*,!=2025.2.*,!=2025.3.*,!=2025.4.*,!=2025.5.*,!=2025.6.*,!=2025.7.*,!=2025.8.*,>=2023.5.1; extra == 'test-min'
 Requires-Dist: dask[distributed]; extra == 'test-min'
 Requires-Dist: filelock; extra == 'test-min'
 Requires-Dist: httpx<1.0; extra == 'test-min'

{anndata-0.12.1 → anndata-0.12.3}/benchmarks/asv.conf.json

@@ -36,7 +36,7 @@
     // If missing or the empty string, the tool will be automatically
     // determined by looking for tools on the PATH environment
     // variable.
-    "environment_type": "mamba",
+    "environment_type": "rattler",
     // timeout in seconds for installing any dependencies in environment
     // defaults to 10 min
     //"install_timeout": 600,

{anndata-0.12.1 → anndata-0.12.3}/benchmarks/benchmarks/anndata.py

@@ -13,18 +13,16 @@ class GarbargeCollectionSuite:
     # custom because `memory_profiler` is a line-by-line profiler (also: https://github.com/pythonprofilers/memory_profiler/issues/402)
     def track_peakmem_garbage_collection(self, *_):
         def display_top(snapshot, key_type="lineno"):
-            snapshot = snapshot.filter_traces(
-                (
-                    tracemalloc.Filter(
-                        inclusive=False,
-                        filename_pattern="<frozen importlib._bootstrap>",
-                    ),
-                    tracemalloc.Filter(
-                        inclusive=False,
-                        filename_pattern="<unknown>",
-                    ),
-                )
-            )
+            snapshot = snapshot.filter_traces((
+                tracemalloc.Filter(
+                    inclusive=False,
+                    filename_pattern="<frozen importlib._bootstrap>",
+                ),
+                tracemalloc.Filter(
+                    inclusive=False,
+                    filename_pattern="<unknown>",
+                ),
+            ))
             top_stats = snapshot.statistics(key_type)
             total = sum(stat.size for stat in top_stats)
             return total

{anndata-0.12.1 → anndata-0.12.3}/benchmarks/benchmarks/readwrite.py

@@ -171,9 +171,11 @@ class H5ADWriteSuite:
         self.adata.write_h5ad(self.writepth, compression="gzip")
 
     def track_peakmem_write_compressed(self, *_):
-        return get_peak_mem(
-            (sedate(self.adata.write_h5ad), (self.writepth,), {"compression": "gzip"})
-        )
+        return get_peak_mem((
+            sedate(self.adata.write_h5ad),
+            (self.writepth,),
+            {"compression": "gzip"},
+        ))
 
 
 class H5ADBackedWriteSuite(H5ADWriteSuite):

{anndata-0.12.1 → anndata-0.12.3}/benchmarks/benchmarks/sparse_dataset.py

@@ -21,18 +21,16 @@ def make_alternating_mask(n):
 
 
 class SparseCSRContiguousSlice:
-    _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),
-        }
-    )
+    _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),

{anndata-0.12.1 → anndata-0.12.3}/docs/conf.py

@@ -133,7 +133,8 @@ intersphinx_mapping = dict(
     numpy=("https://numpy.org/doc/stable", None),
     obstore=("https://developmentseed.org/obstore/latest/", None),
     pandas=("https://pandas.pydata.org/pandas-docs/stable", None),
-    python=("https://docs.python.org/3", None),
+    # TODO: switch to `/3` once docs are built with Python 3.14
+    python=("https://docs.python.org/3.13", None),
     scipy=("https://docs.scipy.org/doc/scipy", None),
     sklearn=("https://scikit-learn.org/stable", None),
     xarray=("https://docs.xarray.dev/en/stable", None),

anndata-0.12.3/docs/release-notes/0.12.2.md

@@ -0,0 +1,6 @@
+(v0.12.2)=
+### 0.12.2 {small}`2025-08-11`
+
+### Bug fixes
+
+- Revert accidental change where {attr}`~anndata.AnnData.X` got written to disk when it was `None` {user}`flying-sheep` ({pr}`2054`)

anndata-0.12.3/docs/release-notes/0.12.3.md

@@ -0,0 +1,14 @@
+(v0.12.3)=
+### 0.12.3 {small}`2025-10-16`
+
+#### Miscellaneous changes
+
+- Deprecate `AnnData.*_keys()` methods. {user}`flying-sheep` ({pr}`2102`)
+
+#### Bug fixes
+
+- Deprecate `__version__` and use standard {func}`~importlib.metadata.version` API {user}`flying-sheep` ({pr}`1318`)
+- Allow writing of views of {class}`dask.array.Array` {user}`ilan-gold` ({pr}`2084`)
+- Enable writing of views of {class}`~anndata.AnnData` in backed mode {user}`ilan-gold` ({pr}`2092`)
+- Reallow writing of keys in `h5ad` files with forward slashes instead of erroring.  Now a warning will be raised that the behavior will be disallowed in the future.  To enable the new behavior, use {attr}`anndata.settings.disallow_forward_slash_in_h5ad`. {user}`ilan-gold` ({pr}`2097`)
+- Respect off-axis merge options in {func}`anndata.experimental.concat_on_disk` {user}`ilan-gold` ({pr}`2122`)

{anndata-0.12.1 → anndata-0.12.3}/docs/tutorials/zarr-v3.md

@@ -1,6 +1,6 @@
 # zarr-v3 Guide/Roadmap
 
-`anndata` now uses the much improved {mod}`zarr` v3 package and also allows writing of datasets in the v3 format via {attr}`anndata.settings.zarr_write_format`, with the exception of structured arrays.
+`anndata` now uses the much improved {mod}`zarr` v3 package and also allows writing of datasets in the v3 format via {attr}`anndata.settings.zarr_write_format` via {func}`anndata.io.write_zarr` or {meth}`anndata.AnnData.write_zarr`, with the exception of structured arrays.
 Users should notice a significant performance improvement, especially for cloud data, but also likely for local data as well.
 Here is a quick guide on some of our learnings so far:
 
@@ -48,7 +48,7 @@ import anndata as ad
 from collections.abc import Mapping
 from typing import Any
 
-ad.settings.zarr_write_format = 3 # Absolutely crucial! Sharding is only for the v3 file format!
+g = zarr.open_group(orig_path, mode="a", use_consolidated=False, zarr_version=3) # zarr_version 3 is default but note that sharding only works with v3!
 
 def write_sharded(group: zarr.Group, adata: ad.AnnData):
     def callback(
@@ -94,11 +94,6 @@ The default `zarr-python` v3 codec for the v3 format is no longer `blosc` but `z
 While `zstd` is more widespread, you may find its performance to not meet your old expectations.
 Therefore, we recommend passing in the {class}`zarr.codecs.BloscCodec` to `compressor` on {func}`~anndata.AnnData.write_zarr` if you wish to return to the old behavior.
 
-There is currently a bug with `numcodecs` that prevents data written from other non-numcodecs `zstd` implementations from being read in by the default zarr pipeline (to which the above rust pipeline falls back if it cannot handle a datatype or indexing scheme, like `vlen-string`): {issue}`zarr-developers/numcodecs#424`.
-Thus is may be advisable to use `BloscCodec` with `zarr` v3 file format data if you wish to use the rust-accelerated pipeline until this issue is resolved.
-
-The same issue with `zstd` applies to data that may eventually be written by the GPU `zstd` implementation (see below).
-
 ## Dask
 
 Zarr v3 should be compatible with dask, although the default behavior is to use zarr's chunking for dask's own. With sharding, this behavior may be undesirable as shards can often contain many small chunks, thereby slowing down i/o as dask will need to index into the zarr store for every chunk.  Therefore it may be better to customize this behavior by passing `chunks=my_zarr_array.shards` as an argument to {func}`dask.array.from_zarr` or similar.

{anndata-0.12.1 → anndata-0.12.3}/hatch.toml

@@ -36,6 +36,7 @@ overrides.matrix.deps.python = [
 overrides.matrix.deps.features = [
     { if = [ "stable", "pre" ], value = "test" },
 ]
+overrides.matrix.deps.extra-args = { if = [ "stable", "pre" ], value = [ "--strict-warnings" ] }
 
 [[envs.hatch-test.matrix]]
 deps = [ "stable", "pre", "min" ]

{anndata-0.12.1 → anndata-0.12.3}/pyproject.toml

@@ -57,8 +57,6 @@ Home-page = "https://github.com/scverse/anndata"
 
 [project.optional-dependencies]
 dev = [
-    # runtime dev version generation
-    "hatch-vcs",
     "anndata[dev-doc]",
 ]
 doc = [
@@ -82,7 +80,7 @@ dev-doc = [ "towncrier>=24.8.0" ] # release notes tool
 test-min = [
     "loompy>=3.0.5",
     "pytest>=8.2,<8.3.4",
-    "pytest-cov",
+    "pytest-cov",           # only for VS Code
     "pytest-randomly",
     "pytest-memray",
     "pytest-mock",
@@ -109,7 +107,9 @@ cu11 = [ "cupy-cuda11x" ]
 lazy = [ "xarray>=2025.06.1", "aiohttp", "requests", "anndata[dask]" ]
 # https://github.com/dask/dask/issues/11290
 # https://github.com/dask/dask/issues/11752
-dask = [ "dask[array]>=2023.5.1,!=2024.8.*,!=2024.9.*,<2025.2.0" ]
+dask = [
+    "dask[array]>=2023.5.1,!=2024.8.*,!=2024.9.*,!=2025.2.*,!=2025.3.*,!=2025.4.*,!=2025.5.*,!=2025.6.*,!=2025.7.*,!=2025.8.*",
+]
 
 [tool.hatch.version]
 source = "vcs"
@@ -118,17 +118,15 @@ raw-options.version_scheme = "release-branch-semver"
 packages = [ "src/anndata", "src/testing" ]
 
 [tool.coverage.run]
-data_file = "test-data/coverage"
+data_file = "test-data/raw-coverage"
 source_pkgs = [ "anndata" ]
 omit = [ "src/anndata/_version.py", "**/test_*.py" ]
 concurrency = [ "multiprocessing" ]
-parallel = "true"
-
+parallel = true
 [tool.coverage.xml]
 output = "test-data/coverage.xml"
 [tool.coverage.paths]
 source = [ "./src", "**/site-packages" ]
-
 [tool.coverage.report]
 exclude_also = [
     "if TYPE_CHECKING:",
@@ -146,6 +144,12 @@ addopts = [
 filterwarnings = [
     "ignore::anndata._warnings.OldFormatWarning",
     "ignore::anndata._warnings.ExperimentalFeatureWarning",
+    "ignore:.*first_column_names:FutureWarning:scanpy",                           # scanpy 1.10.x
+    "ignore:Importing read_.* from `anndata` is deprecated:FutureWarning:scanpy",
+    "ignore:`__version__` is deprecated:FutureWarning:scanpy",
+    # https://github.com/matplotlib/matplotlib/pull/30589
+    "ignore:.*'(oneOf|parseString|resetCache|enablePackrat)'.*'(one_of|parse_string|reset_cache|enable_packrat)':DeprecationWarning:matplotlib",
+
 ]
 # When `--strict-warnings` is used, all warnings are treated as errors, except those:
 filterwarnings_when_strict = [
@@ -158,6 +162,8 @@ filterwarnings_when_strict = [
     "default:The codec `vlen-utf8:UserWarning",
     "default:The dtype `StringDType():UserWarning",
     "default:Consolidated metadata is:UserWarning",
+    "default:.*Structured:zarr.core.dtype.common.UnstableSpecificationWarning",
+    "default:.*FixedLengthUTF32:zarr.core.dtype.common.UnstableSpecificationWarning",
 ]
 python_files = "test_*.py"
 testpaths = [
@@ -174,6 +180,7 @@ markers = [ "gpu: mark test to run on GPU", "zarr_io: mark tests that involve za
 src = [ "src" ]
 
 [tool.ruff.format]
+preview = true
 docstring-code-format = true
 
 [tool.ruff.lint]
@@ -247,10 +254,13 @@ single_file = false
 package_dir = "src"
 issue_format = "{{pr}}`{issue}`"
 title_format = "(v{version})=\n### {version} {{small}}`{project_date}`"
-fragment.bugfix.name = "Bug fixes"
-fragment.doc.name = "Documentation"
-fragment.feature.name = "Features"
-fragment.misc.name = "Miscellaneous improvements"
-fragment.performance.name = "Performance"
-fragment.breaking.name = "Breaking changes"
-fragment.dev.name = "Development Process"
+# Valid fragments should be a subset of conventional commit types (except for `breaking`):
+# https://github.com/commitizen/conventional-commit-types/blob/master/index.json
+# style, refactor, test, build, ci: should not go into changelog
+fragment.feat.name = "Features"
+fragment.fix.name = "Bug fixes"
+fragment.docs.name = "Documentation"
+fragment.perf.name = "Performance"
+fragment.chore.name = "Miscellaneous changes"
+fragment.revert.name = "Revert"
+fragment.breaking.name = "Breaking changes"   # add `!` to commit type (e.g. “feature!:”)