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@LucaMarconato LucaMarconato commented Aug 11, 2025

  • adding _latest_run_notebook.ipynb to gitignore to make integration testing more ergonomic (so the latest error is readily available to debug)
  • making the squidpy notebook faster (by querying the data on a smaller crop and discarding points)
  • re-rendered alignment_using_landmarks.ipynb notebook and copied utils code to use affine transformations into alignment_utils.py
  • napari_rois.ipynb and densenet.ipynb now use alignment_utils.py
  • densenet.py now work on the downloadable visium.zarr and xenium.zarr data, without the need to run other notebooks before. Also the plots are improved.
  • added a notice that the xenium_and_visium will not be tested anymore in the data CI (execution time too long, it slows development turnaround times).

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LucaMarconato and others added 17 commits August 12, 2025 14:01
@LucaMarconato LucaMarconato changed the title faster squidpy notebook Easier to execute notebooks Aug 13, 2025
@LucaMarconato LucaMarconato marked this pull request as ready for review August 13, 2025 14:56
@LucaMarconato LucaMarconato merged commit bb6959b into main Aug 14, 2025
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@LucaMarconato LucaMarconato deleted the fix/notebooks branch August 14, 2025 17:42
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