fix: ci's and scanpy 1.13 plot compat - #1253
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## main #1253 +/- ##
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- Coverage 77.24% 77.21% -0.04%
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Files 63 63
Lines 9378 9396 +18
Branches 1579 1579
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+ Hits 7244 7255 +11
- Misses 1532 1539 +7
Partials 602 602
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August 5, 2026 10:24
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This pull request improves compatibility with recent Scanpy releases, refactors how plotting palettes are imported, and reorganizes experimental plotting tests. It also adjusts test execution in pre-release environments to avoid failures due to external dependencies.
Scanpy compatibility and palette import refactor:
src/squidpy/_compat.pyto use the newscanpy.plotting.legacymodule when available, including fallback logic for older versions. Thedefault_paletteis now also imported via_compat.pyand re-exported for use elsewhere.src/squidpy/im/_container.pyto importdefault_palettefromsquidpy._compatinstead of directly from Scanpy, ensuring consistent palette usage regardless of Scanpy version.Test organization and execution:
tests/experimental/test_stain_normalize.pyto a new file,tests/experimental/plotting/test_stain_normalize.py, and updated imports accordingly. [1] [2] [3] [4]hatch.tomlto skip running the experimental plotting tests in pre-release environments, preventing unrelated failures due to upstream changes inspatialdata-plot.