Test reproducibility notebooks

[kevinyamauchi]

We should do a test of our paper reproducibility notebooks to make sure our latest API changes didn't break anything:

• Xenium+Visium
  • 00_xenium_and_visium.ipynb
  • 01_xenium_and_visium.ipynb
• lundeberg.ipynb
• nsclc_cosmx.ipynb (small notebook)

[kevinyamauchi]

@LucaMarconato , can you please link the notebooks here

[melonora]

I will list opened issues regarding notebooks here

[melonora]

00_xenium_and_visium.ipynb

• issue: Nested sandbox.zarr in 00_xenium_and_visium.ipynb spatialdata-notebooks#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-notebooks#38
  • no fix yet
• issue: Image not in visium data spatialdata-notebooks#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-notebooks#38
  • no fix yet

[LucaMarconato]

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

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.

[melonora]

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:)

[LucaMarconato]

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.

[melonora]

ok, I can also pull and then update when you are done

[LucaMarconato]

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