spatialdata 0.7.2__tar.gz → 0.7.3__tar.gz

{spatialdata-0.7.2 → spatialdata-0.7.3}/.github/workflows/release.yaml

@@ -9,9 +9,9 @@ jobs:
         runs-on: ubuntu-latest
         if: startsWith(github.ref, 'refs/tags/v')
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v6
             - name: Set up Python 3.12
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v6
               with:
                   python-version: "3.12"
                   cache: pip

{spatialdata-0.7.2 → spatialdata-0.7.3}/.github/workflows/test.yaml

@@ -13,18 +13,18 @@ jobs:
         runs-on: ${{ matrix.os }}
         defaults:
             run:
-                shell: bash -e {0}
+                shell: bash  # bash also on windows
 
         strategy:
             fail-fast: false
             matrix:
                 include:
-                    - {os: windows-latest, python: "3.11", dask-version: "2025.2.0", name: "Dask 2025.2.0"}
-                    - {os: windows-latest, python: "3.13", dask-version: "latest", name: "Dask latest"}
-                    - {os: ubuntu-latest, python: "3.11", dask-version: "latest", name: "Dask latest"}
-                    - {os: ubuntu-latest, python: "3.13", dask-version: "latest", name: "Dask latest"}
-                    - {os: macos-latest, python: "3.11", dask-version: "latest", name: "Dask latest"}
-                    - {os: macos-latest, python: "3.13", prerelease: "allow", name: "Python 3.13 (pre-release)"}
+                    - {os: windows-latest, python: "3.11", dask-version: "2025.12.0", name: "min dask"}
+                    - {os: windows-latest, python: "3.14", dask-version: "latest"}
+                    - {os: ubuntu-latest, python: "3.11", dask-version: "latest"}
+                    - {os: ubuntu-latest, python: "3.14", dask-version: "latest"}
+                    - {os: macos-latest, python: "3.11", dask-version: "latest"}
+                    - {os: macos-latest, python: "3.14", prerelease: "allow", name: "prerelease"}
         env:
             OS: ${{ matrix.os }}
             PYTHON: ${{ matrix.python }}
@@ -32,8 +32,8 @@ jobs:
             PRERELEASE: ${{ matrix.prerelease }}
 
         steps:
-            - uses: actions/checkout@v2
-            - uses: astral-sh/setup-uv@v5
+            - uses: actions/checkout@v6
+            - uses: astral-sh/setup-uv@v7
               id: setup-uv
               with:
                   version: "latest"
@@ -41,29 +41,27 @@ jobs:
             - name: Install dependencies
               run: |
                   if [[ "${PRERELEASE}" == "allow" ]]; then
-                    uv sync --extra test
-                    : # uv sync --extra test --prerelease ${PRERELEASE}
-                    uv pip install git+https://github.com/scverse/anndata.git
-                    uv pip install --prerelease allow pandas
-                  else
-                    uv sync --extra test
+                    sed -i '' 's/requires-python.*//' pyproject.toml # otherwise uv complains that anndata requires python>=3.12 and we only do >=3.11 😱
+                    uv add git+https://github.com/scverse/anndata.git
+                    uv add pandas>=3.dev0
                   fi
                   if [[ -n "${DASK_VERSION}" ]]; then
                     if [[ "${DASK_VERSION}" == "latest" ]]; then
-                      uv pip install --upgrade dask
+                      uv add dask
                     else
-                      uv pip install dask==${DASK_VERSION}
+                      uv add dask==${DASK_VERSION}
                     fi
                   fi
+                  uv sync --group=test
             - name: Test
               env:
                   MPLBACKEND: agg
                   PLATFORM: ${{ matrix.os }}
                   DISPLAY: :42
               run: |
-                  uv run pytest --cov --color=yes --cov-report=xml
+                  uv run pytest --cov --color=yes --cov-report=xml -n auto --dist worksteal
             - name: Upload coverage to Codecov
-              uses: codecov/codecov-action@v4
+              uses: codecov/codecov-action@v5
               with:
                   name: coverage
                   verbose: true

{spatialdata-0.7.2 → spatialdata-0.7.3}/.pre-commit-config.yaml

@@ -9,18 +9,18 @@ ci:
     skip: []
 repos:
     - repo: https://github.com/rbubley/mirrors-prettier
-      rev: v3.8.1
+      rev: v3.8.3
       hooks:
           - id: prettier
             exclude: ^.github/workflows/test.yaml
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.19.1
+      rev: v1.20.2
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.14.14
+      rev: v0.15.12
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

spatialdata-0.7.3/.readthedocs.yaml

@@ -0,0 +1,23 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+    os: ubuntu-24.04
+    tools:
+        python: "3.13"
+    jobs:
+        post_checkout:
+            # unshallow so version can be derived from tag
+            - git fetch --unshallow || true
+        create_environment:
+            - asdf plugin add uv
+            - asdf install uv latest
+            - asdf global uv latest
+        build:
+            html:
+                - uv sync --group=docs --extra=torch
+                - uv run make --directory=docs html
+                - mv docs/_build $READTHEDOCS_OUTPUT
+submodules:
+    include:
+        - "docs/tutorials/notebooks"
+    recursive: true

{spatialdata-0.7.2 → spatialdata-0.7.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: spatialdata
-Version: 0.7.2
+Version: 0.7.3
 Summary: Spatial data format.
 Project-URL: Documentation, https://spatialdata.scverse.org/en/latest
 Project-URL: Source, https://github.com/scverse/spatialdata.git
@@ -42,7 +42,7 @@ Requires-Dist: anndata>=0.9.1
 Requires-Dist: annsel>=0.1.2
 Requires-Dist: click
 Requires-Dist: dask-image
-Requires-Dist: dask<2026.1.2,>=2025.2.0
+Requires-Dist: dask<2026.1.2,>=2025.12.0
 Requires-Dist: datashader
 Requires-Dist: distributed<2026.1.2
 Requires-Dist: fsspec[http,s3]
@@ -51,7 +51,7 @@ Requires-Dist: multiscale-spatial-image==2.0.3
 Requires-Dist: networkx
 Requires-Dist: numba>=0.55.0
 Requires-Dist: numpy
-Requires-Dist: ome-zarr>=0.12.2
+Requires-Dist: ome-zarr>=0.14.0
 Requires-Dist: pandas
 Requires-Dist: pooch
 Requires-Dist: pyarrow
@@ -66,32 +66,10 @@ Requires-Dist: universal-pathlib>=0.2.6
 Requires-Dist: xarray-spatial>=0.3.5
 Requires-Dist: xarray>=2024.10.0
 Requires-Dist: zarr>=3.0.0
-Provides-Extra: benchmark
-Requires-Dist: asv; extra == 'benchmark'
-Requires-Dist: memray; extra == 'benchmark'
-Provides-Extra: dev
-Requires-Dist: bump2version; extra == 'dev'
-Requires-Dist: sentry-prevent-cli; extra == 'dev'
-Provides-Extra: docs
-Requires-Dist: ipython>=8.6.0; extra == 'docs'
-Requires-Dist: myst-nb; extra == 'docs'
-Requires-Dist: sphinx-autobuild; extra == 'docs'
-Requires-Dist: sphinx-autodoc-typehints; extra == 'docs'
-Requires-Dist: sphinx-book-theme>=1.0.0; extra == 'docs'
-Requires-Dist: sphinx-copybutton; extra == 'docs'
-Requires-Dist: sphinx-design; extra == 'docs'
-Requires-Dist: sphinx-pytest; extra == 'docs'
-Requires-Dist: sphinx>=4.5; extra == 'docs'
-Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'docs'
 Provides-Extra: extra
 Requires-Dist: napari-spatialdata[all]; extra == 'extra'
 Requires-Dist: spatialdata-io; extra == 'extra'
 Requires-Dist: spatialdata-plot; extra == 'extra'
-Provides-Extra: test
-Requires-Dist: pytest; extra == 'test'
-Requires-Dist: pytest-cov; extra == 'test'
-Requires-Dist: pytest-mock; extra == 'test'
-Requires-Dist: torch; extra == 'test'
 Provides-Extra: torch
 Requires-Dist: torch; extra == 'torch'
 Description-Content-Type: text/markdown

spatialdata-0.7.3/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.7.3'
+__version_tuple__ = version_tuple = (0, 7, 3)
+
+__commit_id__ = commit_id = None

{spatialdata-0.7.2 → spatialdata-0.7.3}/benchmarks/README.md

@@ -14,25 +14,63 @@ pip install -e '.[docs,test,benchmark]'
 
 ## Usage
 
-Running all the benchmarks is usually not needed. You run the benchmark using `asv run`. See the [asv documentation](https://asv.readthedocs.io/en/stable/commands.html#asv-run) for interesting arguments, like selecting the benchmarks you're interested in by providing a regex pattern `-b` or `--bench` that links to a function or class method e.g. the option `-b timeraw_import_inspect` selects the function `timeraw_import_inspect` in `benchmarks/spatialdata_benchmark.py`. You can run the benchmark in your current environment with `--python=same`. Some example benchmarks:
+Running all the benchmarks is usually not needed. You run the benchmark using `asv run`. See the [asv documentation](https://asv.readthedocs.io/en/stable/commands.html#asv-run) for interesting arguments, like selecting the benchmarks you're interested in by providing a regex pattern `-b` or `--bench` that links to a function or class method. You can run the benchmark in your current environment with `--python=same`. Some example benchmarks:
 
-Importing the SpatialData library can take around 4 seconds:
+### Import time benchmarks
+
+Import benchmarks live in `benchmarks/benchmark_imports.py`. Each `timeraw_*` function returns a Python code snippet that asv runs in a fresh interpreter (cold import, empty module cache):
+
+Run all import benchmarks in your current environment:
 
 ```
-PYTHONWARNINGS="ignore" asv run --python=same --show-stderr -b timeraw_import_inspect
-Couldn't load asv.plugins._mamba_helpers because
-No module named 'conda'
-· Discovering benchmarks
-· Running 1 total benchmarks (1 commits * 1 environments * 1 benchmarks)
-[ 0.00%] ·· Benchmarking existing-py_opt_homebrew_Caskroom_mambaforge_base_envs_spatialdata2_bin_python3.12
-[50.00%] ··· Running (spatialdata_benchmark.timeraw_import_inspect--).
-[100.00%] ··· spatialdata_benchmark.timeraw_import_inspect                                                                            3.65±0.2s
+asv run --python=same --show-stderr -b timeraw
+```
+
+Or a single one:
+
+```
+asv run --python=same --show-stderr -b timeraw_import_spatialdata
+```
+
+### Comparing the current branch against `main`
+
+The simplest way is `asv continuous`, which builds both commits, runs the benchmarks, and prints the comparison in one shot:
+
+```bash
+asv continuous --show-stderr -v -b timeraw main faster-import
 ```
 
+Replace `faster-import` with any branch name or commit hash. The `-v` flag prints per-sample timings; drop it for a shorter summary.
+
+Alternatively, collect results separately and compare afterwards:
+
+```bash
+# 1. Collect results for the tip of main and the tip of your branch
+asv run --show-stderr -b timeraw main
+asv run --show-stderr -b timeraw HEAD
+
+# 2. Print a side-by-side comparison
+asv compare main HEAD
+```
+
+Both approaches build isolated environments from scratch. If you prefer to skip the rebuild and reuse your current environment (faster, less accurate):
+
+```bash
+asv run --python=same --show-stderr -b timeraw HEAD
+
+git stash && git checkout main
+asv run --python=same --show-stderr -b timeraw HEAD
+git checkout - && git stash pop
+
+asv compare main HEAD
+```
+
+### Querying benchmarks
+
 Querying using a bounding box without a spatial index is highly impacted by large amounts of points (transcripts), more than table rows (cells).
 
 ```
-$ PYTHONWARNINGS="ignore" asv run --python=same --show-stderr -b time_query_bounding_box
+$ asv run --python=same --show-stderr -b time_query_bounding_box
 
 [100.00%] ··· ======== ============ ============= ============= ==============
               --                filter_table / n_transcripts_per_cell

spatialdata-0.7.3/benchmarks/benchmark_imports.py

@@ -0,0 +1,56 @@
+"""Benchmarks for import times of the spatialdata package and its submodules.
+
+Each ``timeraw_*`` function returns a snippet of Python code that asv runs in
+a fresh interpreter, so the measured time reflects a cold import with an empty
+module cache.
+"""
+
+from collections.abc import Callable
+from typing import Any
+
+
+def _timeraw(func: Any) -> Any:
+    """Set asv benchmark attributes for a cold-import timeraw function."""
+    func.repeat = 5  # number of independent subprocess measurements
+    func.number = 1  # must be 1: second import in same process hits module cache
+    return func
+
+
+@_timeraw
+def timeraw_import_spatialdata() -> str:
+    """Time a bare ``import spatialdata``."""
+    return """
+    import spatialdata
+    """
+
+
+@_timeraw
+def timeraw_import_SpatialData() -> str:
+    """Time importing the top-level ``SpatialData`` class."""
+    return """
+    from spatialdata import SpatialData
+    """
+
+
+@_timeraw
+def timeraw_import_read_zarr() -> str:
+    """Time importing ``read_zarr`` from the top-level namespace."""
+    return """
+    from spatialdata import read_zarr
+    """
+
+
+@_timeraw
+def timeraw_import_models_elements() -> str:
+    """Time importing the main element model classes."""
+    return """
+    from spatialdata.models import Image2DModel, Labels2DModel, PointsModel, ShapesModel, TableModel
+    """
+
+
+@_timeraw
+def timeraw_import_transformations() -> str:
+    """Time importing the ``spatialdata.transformations`` submodule."""
+    return """
+    from spatialdata.transformations import Affine, Scale, Translation, Sequence
+    """

{spatialdata-0.7.2 → spatialdata-0.7.3}/benchmarks/spatialdata_benchmark.py

@@ -20,13 +20,6 @@ class MemorySpatialData:
         return sdata
 
 
-def timeraw_import_inspect():
-    """Time the import of the spatialdata module."""
-    return """
-    import spatialdata
-    """
-
-
 class TimeMapRaster:
     """Time the."""
 

{spatialdata-0.7.2 → spatialdata-0.7.3}/docs/conf.py

@@ -4,6 +4,8 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+from __future__ import annotations
+
 # -- Path setup --------------------------------------------------------------
 import sys
 from datetime import datetime

{spatialdata-0.7.2 → spatialdata-0.7.3}/docs/extensions/typed_returns.py

@@ -1,5 +1,7 @@
 # code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
 # with some minor adjustment
+from __future__ import annotations
+
 import re
 
 from sphinx.application import Sphinx

{spatialdata-0.7.2 → spatialdata-0.7.3}/docs/index.md

@@ -14,6 +14,23 @@ SpatialData is a data framework that comprises a FAIR storage format and a colle
 
 Please see our publication {cite}`marconatoSpatialDataOpenUniversal2024` for citation and to learn more.
 
+:::{note}
+With dask >= 2025.2.0, users can get an error as described in [#1077](https://github.com/scverse/spatialdata/issues/1064). While we tried implementing fixes in SpatialData, it can be that
+users perform operations on the `Points` data themselves and get this error. In order to prevent it, users can use a context manager we created.
+
+```python
+from spatialdata import disable_dask_tune_optimization
+import contextlib
+...
+
+with disable_dask_tune_optimization() if data.npartitions > 1 else contextlib.nullcontext():
+    <your operation on points dask dataframe>
+```
+
+This will disable dask graph optimization if the dataframe has more than 1 partition and otherwise keep it enabled. This solves
+the problem discussed in this [dask issue](https://github.com/dask/dask/issues/12193). We are looking into an upstream fix.
+:::
+
 [//]: # "numfocus-fiscal-sponsor-attribution"
 
 spatialdata 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/).

{spatialdata-0.7.2 → spatialdata-0.7.3}/pyproject.toml

@@ -26,7 +26,7 @@ dependencies = [
     "annsel>=0.1.2",
     "click",
     "dask-image",
-    "dask>=2025.2.0,<2026.1.2",
+    "dask>=2025.12.0,<2026.1.2",
     "distributed<2026.1.2",
     "datashader",
     "fsspec[s3,http]",
@@ -35,7 +35,7 @@ dependencies = [
     "networkx",
     "numba>=0.55.0",
     "numpy",
-    "ome_zarr>=0.12.2",
+    "ome_zarr>=0.14.0",
     "pandas",
     "pooch",
     "pyarrow",
@@ -51,16 +51,25 @@ dependencies = [
     "xarray-spatial>=0.3.5",
     "zarr>=3.0.0",
 ]
-
 [project.optional-dependencies]
+torch = [
+    "torch"
+]
+extra  = [
+    "napari-spatialdata[all]",
+    "spatialdata-plot",
+    "spatialdata-io",
+]
+
+[dependency-groups]
 dev = [
     "bump2version",
-    "sentry-prevent-cli",
 ]
 test = [
     "pytest",
     "pytest-cov",
     "pytest-mock",
+    "pytest-xdist",
     "torch",
 ]
 docs = [
@@ -79,14 +88,7 @@ docs = [
 benchmark = [
     "asv",
     "memray",
-]
-torch = [
-    "torch"
-]
-extra  = [
-    "napari-spatialdata[all]",
-    "spatialdata-plot",
-    "spatialdata-io",
+    "profimp",
 ]
 
 [tool.coverage.run]
@@ -95,23 +97,25 @@ omit = [
     "**/test_*.py",
 ]
 
-[tool.pytest.ini_options]
+[tool.pytest]
 testpaths = ["tests"]
-xfail_strict = true
+strict = true
 addopts = [
-#    "-Werror",  # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
     "--import-mode=importlib",  # allow using test files with same name
     "-s",  # print output from tests
+    "-p no:napari",  # napari registers a pytest plugin via its entry point; disable it here since spatialdata tests don't need it
 ]
 # These are all markers coming from xarray, dask or anndata. Added here to silence warnings.
 markers = [
     "slow: marks tests as slow (deselect with '-m \"not slow\"')",
     "gpu: run test on GPU using CuPY.",
+    "array_api: used by anndata.tests.helpers, not us",
     "skip_with_pyarrow_strings: skipwhen pyarrow string conversion is turned on",
 ]
 # info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
 filterwarnings = [
-    #     "ignore:.*U.*mode is deprecated:DeprecationWarning",
+    # "error",  # if 3rd party libs raise DeprecationWarnings, TODO: filter them individually below
+    # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
 [tool.jupytext]
@@ -183,6 +187,9 @@ select = [
 ]
 unfixable = ["B", "C4", "UP", "BLE", "T20", "RET"]
 
+[tool.ruff.lint.isort]
+required-imports = ["from __future__ import annotations"]
+
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"