From e629d08cd401d9c0970134db3b36b6f7b4d5904f Mon Sep 17 00:00:00 2001
From: Gael Varoquaux <gael.varoquaux@normalesup.org>
Date: Sun, 6 May 2012 16:07:22 +0200
Subject: [PATCH] FIX: handle deprecation with estimator API
An estimator's init cannot include any logic
---
examples/manifold/plot_swissroll.py | 3 ++-
sklearn/manifold/isomap.py | 13 ++++++++++---
sklearn/manifold/locally_linear.py | 21 +++++++++++++++------
3 files changed, 27 insertions(+), 10 deletions(-)
diff --git a/examples/manifold/plot_swissroll.py b/examples/manifold/plot_swissroll.py
index 92d4bf4022..71dfd1c868 100644
--- a/examples/manifold/plot_swissroll.py
+++ b/examples/manifold/plot_swissroll.py
@@ -25,7 +25,8 @@ from sklearn import manifold, datasets
X, color = datasets.samples_generator.make_swiss_roll(n_samples=1500)
print "Computing LLE embedding"
-X_r, err = manifold.locally_linear_embedding(X, n_neighbors=12, out_dim=2)
+X_r, err = manifold.locally_linear_embedding(X, n_neighbors=12,
+ n_components=2)
print "Done. Reconstruction error: %g" % err
#----------------------------------------------------------------------
diff --git a/sklearn/manifold/isomap.py b/sklearn/manifold/isomap.py
index dff954215f..9cb9e225e9 100644
--- a/sklearn/manifold/isomap.py
+++ b/sklearn/manifold/isomap.py
@@ -80,10 +80,11 @@ class Isomap(BaseEstimator):
tol=0, max_iter=None, path_method='auto',
neighbors_algorithm='auto', out_dim=None):
- if not out_dim is None:
+ if out_dim:
warnings.warn("Parameter ``out_dim`` was renamed to "
- "``n_components`` and is now deprecated.", DeprecationWarning)
- n_components = n_components
+ "``n_components`` and is now deprecated.", DeprecationWarning,
+ stacklevel=2)
+ self.out_dim = out_dim
self.n_neighbors = n_neighbors
self.n_components = n_components
self.eigen_solver = eigen_solver
@@ -95,6 +96,12 @@ class Isomap(BaseEstimator):
algorithm=neighbors_algorithm)
def _fit_transform(self, X):
+ if self.out_dim:
+ warnings.warn("Parameter ``out_dim`` was renamed to "
+ "``n_components`` and is now deprecated.", DeprecationWarning,
+ stacklevel=3)
+ self.n_components = self.out_dim
+ self.out_dim = None
self.nbrs_.fit(X)
self.training_data_ = self.nbrs_._fit_X
self.kernel_pca_ = KernelPCA(n_components=self.n_components,
diff --git a/sklearn/manifold/locally_linear.py b/sklearn/manifold/locally_linear.py
index b9529670f4..ebda42af17 100644
--- a/sklearn/manifold/locally_linear.py
+++ b/sklearn/manifold/locally_linear.py
@@ -272,10 +272,11 @@ def locally_linear_embedding(
if method not in ('standard', 'hessian', 'modified', 'ltsa'):
raise ValueError("unrecognized method '%s'" % method)
- if not out_dim is None:
+ if out_dim:
warnings.warn("Parameter ``out_dim`` was renamed to ``n_components`` "
- "and is now deprecated.", DeprecationWarning)
- n_components = n_components
+ "and is now deprecated.", DeprecationWarning,
+ stacklevel=2)
+ n_components = out_dim
nbrs = NearestNeighbors(n_neighbors=n_neighbors + 1)
nbrs.fit(X)
@@ -594,10 +595,11 @@ class LocallyLinearEmbedding(BaseEstimator):
hessian_tol=1E-4, modified_tol=1E-12, neighbors_algorithm='auto',
random_state=None, out_dim=None):
- if not out_dim is None:
+ if out_dim:
warnings.warn("Parameter ``out_dim`` was renamed to "
- "``n_components`` and is now deprecated.", DeprecationWarning)
- n_components = n_components
+ "``n_components`` and is now deprecated.", DeprecationWarning,
+ stacklevel=2)
+ self.out_dim = out_dim
self.n_neighbors = n_neighbors
self.n_components = n_components
@@ -613,6 +615,13 @@ class LocallyLinearEmbedding(BaseEstimator):
algorithm=neighbors_algorithm)
def _fit_transform(self, X):
+ if self.out_dim:
+ warnings.warn("Parameter ``out_dim`` was renamed to "
+ "``n_components`` and is now deprecated.", DeprecationWarning,
+ stacklevel=3)
+ self.n_components = self.out_dim
+ self.out_dim = None
+
self.random_state = check_random_state(self.random_state)
self.nbrs_.fit(X)
self.embedding_, self.reconstruction_error_ = \
--
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