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slevang avatar slevang commented on June 24, 2024 1

Looks like the whole serialize/deserialize pathway doesn't quite work with Datasets. That's an issue since .compute() now relies on temporarily converting to a DataTree to compute everything at once. I'll try to look at getting this properly supported in the next few days. In the meantime your example works fine on the DataArray:

t2m = xr.tutorial.open_dataset("air_temperature")
# fails
xe.models.EOF(n_modes=10).fit(t2m, "time").compute()
# succeeds
xe.models.EOF(n_modes=10).fit(t2m.air, "time").compute()

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nicrie avatar nicrie commented on June 24, 2024

Hey, thanks a lot for the kind words @malmans2 , and sorry for the late reply, these past few days have been pretty hectic.

I really like the idea of automatically synchronizing the documentation and the code! I've tried to integrate both suggestions, but I'm stuck with the implementation.

Notebook & nbstripout
[to the PR]
Cleaning the notebook output with nbstripout using a pre-commit hook works. However, I don't understand how to instruct ReadTheDocs to execute the notebook itself. It seems that ReadTheDocs doesn't do this automatically and thus fails when building the documentation. @malmans2 do you have any experience with this or know the relevant part in the ReadTheDocs documentation?

README & doctest
[to the PR]
I've started rewriting the README for doctest. Strangely, the examples for Varimax Rotation fail$^{**}$ with doctest, even though pytest shows no problem. I honestly can't make heads or tails of the error message. The origin seems to be the serialize method, here's the relevant part of the doctest error message:

Error Message 
=================================== FAILURES ===================================
_____________________________ [doctest] README.md ______________________________
072 >>> scores = eof.scores()  # PCs (temporal patterns)
073 
074 ```
075 
076 **Varimax-rotated EOF analysis**
077 Initiate and fit an `EOFRotator` class to the model to obtain a varimax-rotated EOF analysis
078 
079 ```python
080 >>> rotator = xe.models.EOFRotator(n_modes=3)
081 >>> rotator.fit(eof) # doctest: +ELLIPSIS
UNEXPECTED EXCEPTION: KeyError('Could not find node at mean_')
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/doctest.py", line 1350, in __run
  exec(compile(example.source, filename, "single",
File "<doctest README.md[10]>", line 1, in <module>
File "/home/runner/work/xeofs/xeofs/xeofs/models/eof_rotator.py", line 116, in fit
  self.compute()
File "/home/runner/work/xeofs/xeofs/xeofs/models/_base_model.py", line 380, in compute
  self._deserialize_attrs(dt)
File "/home/runner/work/xeofs/xeofs/xeofs/models/_base_model.py", line 456, in _deserialize_attrs
  deserialized_obj = getattr(self, key).deserialize(dt[key])
File "/home/runner/work/xeofs/xeofs/xeofs/preprocessing/preprocessor.py", line 412, in deserialize
  deserialized = preprocessor.transformer_types()[name].deserialize(
File "/home/runner/work/xeofs/xeofs/xeofs/preprocessing/transformer.py", line 162, in deserialize
  return cls._deserialize(dt)
File "/home/runner/work/xeofs/xeofs/xeofs/preprocessing/transformer.py", line 177, in _deserialize
  data = transformer._deserialize_data_node(key, dt[key])
File "/home/runner/work/xeofs/xeofs/.venv/lib/python3.10/site-packages/datatree/datatree.py", line 876, in __getitem__
  return self._get_item(path)
File "/home/runner/work/xeofs/xeofs/.venv/lib/python3.10/site-packages/datatree/treenode.py", line 448, in _get_item
  raise KeyError(f"Could not find node at {path}")
KeyError: 'Could not find node at mean_'
/home/runner/work/xeofs/xeofs/README.md:81: UnexpectedException

@slevang, as a budding xarray-datatree expert, any idea why doctest is hitting a snag here, even though pytest runs through without a hitch?

Alternatively, I think we could also omit the Quickstart in the README and directly refer to Documentation > Quickstart, since both are essentially redundant.

$^{**}$ Additionally, pytest raises a lot of warnings which I think originate from the test modules in xeofs themselves, not the actual code.

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nicrie avatar nicrie commented on June 24, 2024

Thanks again for the quick fix @slevang.
Closing, fixed by #135 and #136

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