Run notebooks in CI

[selmanozleyen]

Closes #993

[codecov-commenter]

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✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 24.29%. Comparing base (d8b8f91) to head (fd6f9a4).
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Additional details and impacted files

@@             Coverage Diff             @@
##             main    #1013       +/-   ##
===========================================
- Coverage   66.63%   24.29%   -42.35%     
===========================================
  Files          40       41        +1     
  Lines        6060     6060               
  Branches     1015     1012        -3     
===========================================
- Hits         4038     1472     -2566     
- Misses       1662     4571     +2909     
+ Partials      360       17      -343     

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[selmanozleyen]

Hi,

I added all the notebooks except the tutorials as they required plenty of external modules. Only one notebook (squidpy/docs/notebooks/examples/image/compute_crops.ipynb) failed because of trying to use a deprecated function. So I created an issue for it: scverse/squidpy_notebooks#147

This is the error log

------------------
crop_corner.interactive(adata_crop)
------------------

----- stderr -----
/tmp/ipykernel_2900/2108321461.py:1: DeprecationWarning: Call to deprecated function interactive (The squidpy napari plugin is deprecated, please use https://github.com/scverse/napari-spatialdata).
  crop_corner.interactive(adata_crop)
------------------

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[8], line 1
----> 1 crop_corner.interactive(adata_crop)

File ~/work/squidpy/squidpy/src/squidpy/_utils.py:313, in deprecated.<locals>.decorator.<locals>.new_func1(*args, **kwargs)
    307 warnings.warn(
    308     fmt1.format(name=func1.__name__, reason=reason),
    309     category=DeprecationWarning,
    310     stacklevel=2,
    311 )
    312 warnings.simplefilter("default", DeprecationWarning)
--> 313 return func1(*args, **kwargs)

File ~/work/squidpy/squidpy/src/squidpy/im/_container.py:1136, in ImageContainer.interactive(self, adata, spatial_key, library_key, library_id, cmap, palette, blending, symbol, key_added)
   1079 @d.get_sections(base="_interactive", sections=["Parameters"])
   1080 @d.dedent
   1081 @deprecated(
   (...)   1094     key_added: str = "shapes",
   1095 ) -> Interactive:  # type: ignore[type-var]
   1096     """
   1097     Launch :mod:`napari` viewer.
   1098 
   (...)   1134     :meth:`squidpy.pl.Interactive.screenshot`.
   1135     """
-> 1136     from squidpy.pl import Interactive  # type: ignore[attr-defined]
   1138     return Interactive(  # type: ignore[no-any-return]
   1139         img=self,
   1140         adata=adata,
   (...)   1148         symbol=symbol,
   1149     ).show()

ImportError: cannot import name 'Interactive' from 'squidpy.pl' (/home/runner/work/squidpy/squidpy/src/squidpy/pl/__init__.py)

Failed to run /home/runner/work/squidpy/squidpy/docs/notebooks/examples/image/compute_crops.ipynb

[flying-sheep]

@LucaMarconato wants to look into how to do this with caching, see also scverse/cookiecutter-scverse#40

PS: shell scripting is the devil, if you add shell scripts, also add CI that runs shellcheck on them and fails if shellcheck complains. Or just don’t use shell scripts, Python is a very nice scripting language that you already know much better 😉

[LucaMarconato]

@selmanozleyen how long do they take to run? Around 15 minutes?

[selmanozleyen]

@LucaMarconato yes they take around 15 for the selected notebooks

[ilan-gold]

For reproducibility, should we have a check for whether the notebooks change? This would basically turn the notebooks into tests-for-stability, but could be a nice check. @timtreis or @LucaMarconato have you guys ever received feedback about stability?

[selmanozleyen]

we could have expected and output folders to compare but we'd have to update expected when we expect/want the output to change. Similar to plot unit tests. I think this is doable but would fit better as a separate issue imo