Test reproducibility notebooks #121

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1. kevinyamauchi

   assigned

   melonora

   on Jun 22, 2023
2. kevinyamauchi commented on Jun 22, 2023

   

   kevinyamauchi

   on Jun 22, 2023

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   @LucaMarconato , can you please link the notebooks here

   👍React with 👍1Reacted by LucaMarconato
3. melonora commented on Jun 26, 2023

   

   melonora

   on Jun 26, 2023

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   I will list opened issues regarding notebooks here
4. melonora commented on Jun 26, 2023

   

   melonora

   on Jun 26, 2023

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   00_xenium_and_visium.ipynb

   • issue: Nested sandbox.zarr in 00_xenium_and_visium.ipynb spatialdata-tutorials#36
     • No fix yet. Fixed.
   • issue: Xenium IO AssertionError spatialdata-io#63
     • fix: Coerce cell id to str spatialdata-io#64
   • issue: Multiple spatialdata objects in napari not supported spatialdata-tutorials#38
     • no fix yet
   • issue: Image not in visium data spatialdata-tutorials#37
     • no fix yet, there is a discrepancy between obtaining data through scripts in spatialdata-sandbox and obtaining it through the link. Obtaining through the link gets you the correct dataset with full_image, while spatialdata-sandbox does not contain it. Fixed.

   Potential issue, using os.path is not generalizable to all platforms. Consider using Path. Same for unzipping in spatialdata-io, consider shutil.unpack_archive. Also many imports are not used.

   01_xenium_and_visium.ipynb

   • issue: Multiple spatialdata objects in napari not supported spatialdata-tutorials#38
     • no fix yet

   👍React with 👍2Reacted by Kevin Yamauchi and LucaMarconato
5. LucaMarconato commented on Jun 28, 2023

   

   LucaMarconato

   on Jun 28, 2023

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   Thanks @melonora. Now some issues are fixed.

   Furthermore I have created this extra low priority issue from your last comment:

   • issue: Replace os.path with Path and "unzip" with shutil.unpack_archive spatialdata-tutorials#40

   Re the import, let's just remove them when we see them. I was coding with jupyterlab so unused import where not automatically marked as such, but now I am using VS Code, so I will spot them if I open that notebook.
6. melonora commented on Jun 28, 2023

   

   melonora

   on Jun 28, 2023

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   Thanks @melonora. Now some issues are fixed.

   Furthermore I have created this extra low priority issue from your last comment:

   * issue: [Replace `os.path` with `Path` and "unzip" with `shutil.unpack_archive` spatialdata-notebooks#40](https://github.com/scverse/spatialdata-notebooks/issues/40)
   

   Re the import, let's just remove them when we see them. I was coding with jupyterlab so unused import where not automatically marked as such, but now I am using VS Code, so I will spot them if I open that notebook.

   I can push the notebooks later. Kinda had to change it already because of testing on windows. I am on travel at the moment and it was the only laptop on which I could test:)
7. LucaMarconato commented on Jun 28, 2023

   

   LucaMarconato

   on Jun 28, 2023

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   Thanks. Please be aware that the notebooks will need to be merged as I have slightly updated them meanwhile. VS Code has a nice interface for diffs between notebooks.
8. melonora commented on Jun 28, 2023

   

   melonora

   on Jun 28, 2023

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   ok, I can also pull and then update when you are done
9. LucaMarconato commented on Nov 8, 2023

   

   LucaMarconato

   on Nov 8, 2023

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   Added in the data CI. If something breaks and we need to fix it I get email notifications.
10. LucaMarconato

    closed this as completedon Nov 8, 2023