[BUG] AttributeError: can't set attribute in "Introduction to SINDy" ipynb

[theo-brown]

I copied the code from examples/2_introduction_to_sindy.ipynb into a Python script. When I ran the code, I encountered an AttributeError when fitting the model.

Reproducing code example:

import numpy as np
import pysindy as ps

t = np.linspace(0, 1, 100)
x = 3 * np.exp(-2 * t)
y = 0.5 * np.exp(t)
X = np.stack((x, y), axis=-1)

differentiation_method = ps.FiniteDifference(order=2)
feature_library = ps.PolynomialLibrary(degree=3)
optimizer = ps.STLSQ(threshold=0.2)

model = ps.SINDy(differentiation_method=differentiation_method,
                 feature_library=feature_library,
                 optimizer=optimizer,
                 feature_names=["x", "y"])
model.fit(X, t=t)

Error message:

Traceback (most recent call last):
  File "..../example_2.py", line 18, in <module>
    model.fit(X, t=t)
  File "..../venv/lib/python3.9/site-packages/pysindy/pysindy.py", line 292, in fit
    self.model.fit(x, x_dot)
  File "..../venv/lib/python3.9/site-packages/sklearn/pipeline.py", line 390, in fit
    Xt = self._fit(X, y, **fit_params_steps)
  File "..../venv/lib/python3.9/site-packages/sklearn/pipeline.py", line 348, in _fit
    X, fitted_transformer = fit_transform_one_cached(
  File "..../venv/lib/python3.9/site-packages/joblib/memory.py", line 349, in __call__
    return self.func(*args, **kwargs)
  File "..../venv/lib/python3.9/site-packages/sklearn/pipeline.py", line 891, in _fit_transform_one
    res = transformer.fit_transform(X, y, **fit_params)
  File "..../venv/lib/python3.9/site-packages/sklearn/base.py", line 847, in fit_transform
    return self.fit(X, y, **fit_params).transform(X)
  File "..../venv/lib/python3.9/site-packages/pysindy/feature_library/polynomial_library.py", line 170, in fit
    self.n_input_features_ = n_features
AttributeError: can't set attribute

PySINDy/Python version information:

>>> import sys, pysindy; print(pysindy.__version__, sys.version)
1.4.3 3.9.6 (default, Sep 25 2021, 20:17:33) 
[GCC 9.3.0]

[akaptano]

Hi Theo,

Thanks for your interest. See Issues #124 #125 #129. We will fix this bug with a major release in the next few weeks.

[theo-brown]

Ah, got you! Sorry, I didn't search closed issues for this - maybe leave one open until the bug is fixed?

[akaptano]

Agreed, #124 is still open but maybe not very descriptive... I'll see if I can edit the title

[hasnainalik]

I still get the error. Any idea about solving it?

`---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Input In [4], in <cell line: 2>()
1 model = ps.SINDy(feature_names=["x", "y"])
----> 2 model.fit(X, t=t)

File ~/anaconda3/envs/drl/lib/python3.9/site-packages/pysindy/pysindy.py:292, in SINDy.fit(self, x, t, x_dot, u, multiple_trajectories, unbias, quiet)
289 warnings.filterwarnings(action, category=LinAlgWarning)
290 warnings.filterwarnings(action, category=UserWarning)
--> 292 self.model.fit(x, x_dot)
294 self.n_input_features_ = self.model.steps[0][1].n_input_features_
295 self.n_output_features_ = self.model.steps[0][1].n_output_features_

File ~/anaconda3/envs/drl/lib/python3.9/site-packages/sklearn/pipeline.py:378, in Pipeline.fit(self, X, y, **fit_params)
352 """Fit the model.
353
354 Fit all the transformers one after the other and transform the
(...)
375 Pipeline with fitted steps.
376 """
377 fit_params_steps = self._check_fit_params(**fit_params)
--> 378 Xt = self._fit(X, y, **fit_params_steps)
379 with _print_elapsed_time("Pipeline", self._log_message(len(self.steps) - 1)):
380 if self._final_estimator != "passthrough":

File ~/anaconda3/envs/drl/lib/python3.9/site-packages/sklearn/pipeline.py:336, in Pipeline._fit(self, X, y, **fit_params_steps)
334 cloned_transformer = clone(transformer)
335 # Fit or load from cache the current transformer
--> 336 X, fitted_transformer = fit_transform_one_cached(
337 cloned_transformer,
338 X,
339 y,
340 None,
341 message_clsname="Pipeline",
342 message=self._log_message(step_idx),
343 **fit_params_steps[name],
344 )
345 # Replace the transformer of the step with the fitted
346 # transformer. This is necessary when loading the transformer
347 # from the cache.
348 self.steps[step_idx] = (name, fitted_transformer)

File ~/anaconda3/envs/drl/lib/python3.9/site-packages/joblib/memory.py:349, in NotMemorizedFunc.call(self, *args, **kwargs)
348 def call(self, *args, **kwargs):
--> 349 return self.func(*args, **kwargs)

File ~/anaconda3/envs/drl/lib/python3.9/site-packages/sklearn/pipeline.py:870, in _fit_transform_one(transformer, X, y, weight, message_clsname, message, **fit_params)
868 with _print_elapsed_time(message_clsname, message):
869 if hasattr(transformer, "fit_transform"):
--> 870 res = transformer.fit_transform(X, y, **fit_params)
871 else:
872 res = transformer.fit(X, y, **fit_params).transform(X)

File ~/anaconda3/envs/drl/lib/python3.9/site-packages/sklearn/base.py:870, in TransformerMixin.fit_transform(self, X, y, **fit_params)
867 return self.fit(X, **fit_params).transform(X)
868 else:
869 # fit method of arity 2 (supervised transformation)
--> 870 return self.fit(X, y, **fit_params).transform(X)

File ~/anaconda3/envs/drl/lib/python3.9/site-packages/pysindy/feature_library/polynomial_library.py:170, in PolynomialLibrary.fit(self, x, y)
162 n_samples, n_features = check_array(x, accept_sparse=True).shape
163 combinations = self.combinations(
164 n_features,
165 self.degree,
(...)
168 self.include_bias,
169 )
--> 170 self.n_input_features = n_features
171 self.n_output_features_ = sum(1 for _ in combinations)
172 return self

AttributeError: can't set attribute

`

[akaptano]

What are your versions of pysindy and scikit-learn?

[hasnainalik]

What are your versions of pysindy and scikit-learn?

pysindy = 1.3.0
scikit-learn = 1.1.1
Operating system = Ubuntu 20.04.4 LTS

[akaptano]

It has been solved on newer versions of PySINDy.