[MRG+1] Deprecate ridge_alpha param on SparsePCA.transform() (scikit-learn#8137)

naoyak · raghavrv · commit 81f5b3e7d0f4 · 2017-01-05T19:37:46.000+01:00
diff --git a/sklearn/decomposition/sparse_pca.py b/sklearn/decomposition/sparse_pca.py
@@ -2,6 +2,8 @@
 # Author: Vlad Niculae, Gael Varoquaux, Alexandre Gramfort
 # License: BSD 3 clause
 
+import warnings
+
 import numpy as np
 
 from ..utils import check_random_state, check_array
@@ -130,7 +132,7 @@ def fit(self, X, y=None):
         self.error_ = E
         return self
 
-    def transform(self, X, ridge_alpha=None):
+    def transform(self, X, ridge_alpha='deprecated'):
         """Least Squares projection of the data onto the sparse components.
 
         To avoid instability issues in case the system is under-determined,
@@ -150,6 +152,10 @@ def transform(self, X, ridge_alpha=None):
             Amount of ridge shrinkage to apply in order to improve
             conditioning.
 
+            .. deprecated:: 0.19
+               This parameter will be removed in 0.21.
+               Specify ``ridge_alpha`` in the ``SparsePCA`` constructor.
+
         Returns
         -------
         X_new array, shape (n_samples, n_components)
@@ -158,7 +164,15 @@ def transform(self, X, ridge_alpha=None):
         check_is_fitted(self, 'components_')
 
         X = check_array(X)
-        ridge_alpha = self.ridge_alpha if ridge_alpha is None else ridge_alpha
+        if ridge_alpha != 'deprecated':
+            warnings.warn("The ridge_alpha parameter on transform() is "
+                          "deprecated since 0.19 and will be removed in 0.21. "
+                          "Specify ridge_alpha in the SparsePCA constructor.",
+                          DeprecationWarning)
+            if ridge_alpha is None:
+                ridge_alpha = self.ridge_alpha
+        else:
+            ridge_alpha = self.ridge_alpha
         U = ridge_regression(self.components_.T, X.T, ridge_alpha,
                              solver='cholesky')
         s = np.sqrt((U ** 2).sum(axis=0))
diff --git a/sklearn/decomposition/tests/test_sparse_pca.py b/sklearn/decomposition/tests/test_sparse_pca.py
@@ -11,6 +11,7 @@
 from sklearn.utils.testing import SkipTest
 from sklearn.utils.testing import assert_true
 from sklearn.utils.testing import assert_false
+from sklearn.utils.testing import assert_warns_message
 from sklearn.utils.testing import if_safe_multiprocessing_with_blas
 
 from sklearn.decomposition import SparsePCA, MiniBatchSparsePCA
@@ -70,6 +71,13 @@ def test_fit_transform():
     spca_lasso.fit(Y)
     assert_array_almost_equal(spca_lasso.components_, spca_lars.components_)
 
+    # Test that deprecated ridge_alpha parameter throws warning
+    warning_msg = "The ridge_alpha parameter on transform()"
+    assert_warns_message(DeprecationWarning, warning_msg, spca_lars.transform,
+                         Y, ridge_alpha=0.01)
+    assert_warns_message(DeprecationWarning, warning_msg, spca_lars.transform,
+                         Y, ridge_alpha=None)
+
 
 @if_safe_multiprocessing_with_blas
 def test_fit_transform_parallel():
