Using out-of-date scikit.learn
jmmcd opened this issue · 3 comments
jmmcd commented
It looks like scikit-learn has changed a lot since FFX was written. I had to edit core.py to import as follows:
from sklearn.linear_model import ElasticNet
After fixing that, it imported ok. When I ran the sample code in Readme.md, I got an error concerning args in ElasticNet.fit() (pasted below) -- I tried fiddling with the args, but then I got a different error, and I don't really know those modules, so I stopped fiddling.
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-1-5756048b6a36> in <module>()
8 test_y = np.array( [3.03,0.9113,1.823])
9
---> 10 models = ffx.run(train_X, train_y, test_X, test_y, ["predictor_a", "predictor_b"])
11 for model in models:
12 yhat = model.simulate(test_X)
/Users/jmmcd/Documents/dev/anaconda/lib/python2.7/site-packages/ffx/api.pyc in run(train_X, train_y, test_X, test_y, varnames, verbose)
2
3 def run(train_X, train_y, test_X, test_y, varnames=None, verbose=False):
----> 4 return core.MultiFFXModelFactory().build(train_X, train_y, test_X, test_y, varnames, verbose)
/Users/jmmcd/Documents/dev/anaconda/lib/python2.7/site-packages/ffx/core.py in build(self, train_X, train_y, test_X, test_y, varnames, verbose)
441 ss = FFXBuildStrategy(approach)
442
--> 443 next_models = FFXModelFactory().build(train_X, train_y, ss, varnames, verbose)
444
445 #set test_nmse on each model
/Users/jmmcd/Documents/dev/anaconda/lib/python2.7/site-packages/ffx/core.py in build(self, X, y, ss, varnames, verbose)
582 target_train_nmse = 0.01
583 models = self._basesToModels(
--> 584 ss, varnames, order1_bases, X, y, max_num_bases, target_train_nmse, verbose)
585 if models is None: #fit failed.
586 model = ConstantModel(y[0], 0)
/Users/jmmcd/Documents/dev/anaconda/lib/python2.7/site-packages/ffx/core.py in _basesToModels(self, ss, varnames, bases, X, y, max_num_bases, target_train_nmse, verbose)
681 #compute models.
682 models = self._pathwiseLearn(ss, varnames, bases, X, regress_X, y,
--> 683 max_num_bases, target_train_nmse, verbose)
684 return models
685
/Users/jmmcd/Documents/dev/anaconda/lib/python2.7/site-packages/ffx/core.py in _pathwiseLearn(self, ss, varnames, bases, X_orig, X_orig_regress, y_orig, max_num_bases, target_nmse, verbose, **fit_params)
727 try:
728 clf.fit(X_unbiased, y_unbiased, coef_init=cur_unbiased_coefs,
--> 729 max_iter=max_iter, **fit_params)
730 except TimeoutError:
731 print ' Regularized update failed. Returning None'
/Users/jmmcd/Documents/dev/anaconda/lib/python2.7/site-packages/ffx/core.py in new_f(*args, **kwargs)
839 signal.alarm(seconds_before_timeout)
840 try:
--> 841 result = f(*args, **kwargs)
842 finally:
843 signal.signal(signal.SIGALRM, old)
/Users/jmmcd/Documents/dev/anaconda/lib/python2.7/site-packages/ffx/core.py in fit(self, *args, **kwargs)
851 @timeout(MAX_TIME_REGULARIZE_UPDATE) #if this freezes, then exit with a TimeoutError
852 def fit(self, *args, **kwargs):
--> 853 return ElasticNet.fit(self, *args, **kwargs)
854
855 #========================================================================================
TypeError: fit() got an unexpected keyword argument 'precompute'
/Users/jmmcd/Documents/dev/anaconda/lib/python2.7/site-packages/sklearn/linear_model/coordinate_descent.py:137: DeprecationWarning: rho was renamed to l1_ratio and will be removed in 0.15
"in 0.15", DeprecationWarning)
keyvan-m-sadeghi commented
Having the same issue. @natekupp are you planning to update the pip version any time soon?
keyvan-m-sadeghi commented