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ci: write zarr 3 format with supported anndata versions #3959

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Merged
flying-sheep merged 2 commits into from
Jan 29, 2026
Merged

ci: write zarr 3 format with supported anndata versions #3959

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bddc2d9
fix: write zarr 3 format on supported platforms
flying-sheep Jan 29, 2026
2553102
Sphinx 9
flying-sheep Jan 29, 2026
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6 changes: 5 additions & 1 deletion hatch.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,11 @@ dependency-groups = [ "dev" ]

[envs.docs]
dependency-groups = [ "doc" ]
extra-dependencies = [ "pandas>=3" ]
# MyST-NB 1.3.0 spams the doc build logs making debugging hard, so use https://github.com/executablebooks/MyST-NB/pull/704
extra-dependencies = [
"pandas>=3",
"myst-nb @ git+https://github.com/executablebooks/MyST-NB.git@91273a686c66fd0383466c80eede61b208d7e426",
]
scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
scripts.open = "python3 -m webbrowser -t docs/_build/html/index.html"
scripts.clean = "git clean -fdX -- {args:docs}"
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4 changes: 3 additions & 1 deletion pyproject.toml
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Expand Up @@ -111,7 +111,7 @@ test = [
"scanpy[plotting]",
]
doc = [
"sphinx>=8.2.3",
"sphinx>=9.1.0",
"sphinx-book-theme>=1.1.0",
"scanpydoc>=0.16.1",
"sphinx-autodoc-typehints>=1.25.2",
Expand Down Expand Up @@ -198,6 +198,8 @@ filterwarnings = [
"ignore:.*'(parseAll)'.*'(parse_all)':DeprecationWarning",
# igraph vs leidenalg warning
"ignore:The `igraph` implementation of leiden clustering:UserWarning",
# everybody uses this zarr 3 feature, including us, XArray, lots of data out there …
"ignore:Consolidated metadata is currently not part:UserWarning",
]

[tool.coverage.run]
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5 changes: 5 additions & 0 deletions src/testing/scanpy/_pytest/__init__.py
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Expand Up @@ -8,6 +8,7 @@
from typing import TYPE_CHECKING

import pytest
from packaging.version import Version

from .fixtures import * # noqa: F403
from .marks import needs
Expand All @@ -28,17 +29,21 @@ def original_settings(
) -> Generator[Mapping[str, object], None, None]:
"""Switch to agg backend, reset settings, and close all figures at teardown."""
# make sure seaborn is imported and did its thing
import anndata as ad
import seaborn as sns # noqa: F401
from matplotlib import pyplot as plt
from matplotlib.testing import setup

import scanpy as sc
from scanpy._compat import pkg_version

global _original_settings # noqa: PLW0603
if _original_settings is None:
_original_settings = MappingProxyType(sc.settings.__dict__.copy())

setup()
if pkg_version("anndata") >= Version("0.12"):
ad.settings.zarr_write_format = 3 # default in anndata 0.13, warns otherwise
sc.settings.logfile = sys.stderr
sc.settings.verbosity = "hint"
sc.settings.autoshow = True
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