`pl.show()` leading to `ValueError` due to mismatch between number of axes and number of panels

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Blocking a release. To reproduce please run notebook_spatial_query.ipynb from spaitaldata-notebooks.

Some notebooks started throwing some ValueError due to a mismatch between the number of axes and the number of panels in the plot. If possible, I would try to be backward compatible.

INFO - SpatialData object, with associated Zarr store: /Users/macbook/embl/projects/basel/spatialdata-integration-testing/dependencies/spatialdata-sandbox/visium/data.zarr
INFO - ├── Images
INFO - │     ├── 'ST8059048_hires_image': DataArray[cyx] (3, 2000, 1969)
INFO - │     ├── 'ST8059048_lowres_image': DataArray[cyx] (3, 600, 591)
INFO - │     ├── 'ST8059050_hires_image': DataArray[cyx] (3, 2000, 1968)
INFO - │     └── 'ST8059050_lowres_image': DataArray[cyx] (3, 600, 590)
INFO - ├── Shapes
INFO - │     ├── 'ST8059048': GeoDataFrame shape: (2987, 2) (2D shapes)
INFO - │     └── 'ST8059050': GeoDataFrame shape: (3497, 2) (2D shapes)
INFO - └── Tables
INFO -       └── 'table': AnnData (6484, 31053)
INFO - with coordinate systems:
INFO -     ▸ 'ST8059048', with elements:
INFO -         ST8059048_hires_image (Images), ST8059048 (Shapes)
INFO -     ▸ 'ST8059048_downscaled_lowres', with elements:
INFO -         ST8059048_lowres_image (Images), ST8059048 (Shapes)
INFO -     ▸ 'ST8059050', with elements:
INFO -         ST8059050_hires_image (Images), ST8059050 (Shapes)
INFO -     ▸ 'ST8059050_downscaled_lowres', with elements:
INFO -         ST8059050_lowres_image (Images), ST8059050 (Shapes)
INFO - 
INFO - Ending Cell 3------------------------------------------
INFO - Executing Cell 4---------------------------------------
INFO - Ending Cell 4------------------------------------------
INFO - Executing Cell 5---------------------------------------
INFO - /Users/macbook/embl/projects/basel/spatialdata-integration-testing/dependencies/spatialdata/src/spatialdata/_core/spatialdata.py:170: UserWarning: The table is annotating 'ST8059050', which is not present in the SpatialData object.
INFO -   self.validate_table_in_spatialdata(v)
INFO - /Users/macbook/embl/projects/basel/spatialdata-integration-testing/dependencies/spatialdata/src/spatialdata/_core/spatialdata.py:170: UserWarning: The table is annotating 'ST8059050', which is not present in the SpatialData object.
INFO -   self.validate_table_in_spatialdata(v)

Again, session_info2 seems to be uninformative. Please let me know if you can't reproduce and I will dig deeper.

Versions

| Dependency                    | Version |
| ----------------------------- | ------- |
| sphinxcontrib-devhelp         | 2.0.0   |
| sphinxcontrib-htmlhelp        | 2.1.0   |
| sphinxcontrib-serializinghtml | 2.0.0   |
| session-info2                 | 0.3     |
| sphinxcontrib-qthelp          | 2.0.0   |
| sphinxcontrib-bibtex          | 2.6.5   |
| sphinxcontrib-jsmath          | 1.0.1   |
| sphinxcontrib-applehelp       | 2.0.0   |
| setuptools                    | 80.9.0  |

| Component | Info                                                                             |
| --------- | -------------------------------------------------------------------------------- |
| Python    | 3.13.0 | packaged by conda-forge | (main, Nov 27 2024, 19:18:26) [Clang 18.1.8 ] |
| OS        | macOS-26.5.1-arm64-arm-64bit-Mach-O                                              |
| Updated   | 2026-07-02 17:52                                                                 |

Commencez par exécuter notebook_spatial_query.ipynb depuis spaitaldata-notebooks et reproduisez le ValueError levé par pl.show(). Analysez le décalage entre les axes du graphique et les panneaux, puis vérifiez que le notebook s’exécute jusqu’au bout tout en préservant autant que possible la rétrocompatibilité.