Run notebooks in CI

[selmanozleyen]

Closes #993

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 66.67%. Comparing base (d8b8f91) to head (77c7eca).
⚠️ Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1013      +/-   ##
==========================================
+ Coverage   66.63%   66.67%   +0.03%     
==========================================
  Files          40       40              
  Lines        6060     6067       +7     
  Branches     1015     1015              
==========================================
+ Hits         4038     4045       +7     
  Misses       1662     1662              
  Partials      360      360              

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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