`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                                                                 |

Bắt đầu bằng cách chạy notebook_spatial_query.ipynb từ spaitaldata-notebooks và tái hiện ValueError do pl.show() phát sinh. Truy tìm sự không khớp giữa các trục của biểu đồ và các panel, sau đó xác minh rằng notebook hoàn tất thành công trong khi vẫn duy trì khả năng tương thích ngược khi có thể.