scikit-learn · qinhanmin2014 · Oct 28, 2019 · Oct 21, 2019 · Oct 21, 2019 · Oct 21, 2019
diff --git a/.gitignore b/.gitignore
@@ -130,6 +130,20 @@ sklearn/svm/libsvm.py
 sklearn/svm/libsvm_sparse.py
 sklearn/svm/liblinear.py
 
+sklearn/decomposition/base.py
+sklearn/decomposition/dict_learning.py
+sklearn/decomposition/cdnmf_fast.py
+sklearn/decomposition/factor_analysis.py
+sklearn/decomposition/fastica_.py
+sklearn/decomposition/incremental_pca.py
+sklearn/decomposition/kernel_pca.py
+sklearn/decomposition/nmf.py
+sklearn/decomposition/online_lda.py
+sklearn/decomposition/online_lda_fast.py
+sklearn/decomposition/pca.py
+sklearn/decomposition/sparse_pca.py
+sklearn/decomposition/truncated_svd.py
+
 sklearn/gaussian_process/gpr.py
 sklearn/gaussian_process/gpc.py
 

diff --git a/benchmarks/bench_plot_nmf.py b/benchmarks/bench_plot_nmf.py
@@ -18,10 +18,10 @@
 
 from sklearn.utils.testing import ignore_warnings
 from sklearn.feature_extraction.text import TfidfVectorizer
-from sklearn.decomposition.nmf import NMF
-from sklearn.decomposition.nmf import _initialize_nmf
-from sklearn.decomposition.nmf import _beta_divergence
-from sklearn.decomposition.nmf import _check_init
+from sklearn.decomposition import NMF
+from sklearn.decomposition._nmf import _initialize_nmf
+from sklearn.decomposition._nmf import _beta_divergence
+from sklearn.decomposition._nmf import _check_init
 from sklearn.exceptions import ConvergenceWarning
 from sklearn.utils.extmath import safe_sparse_dot, squared_norm
 from sklearn.utils import check_array

diff --git a/doc/developers/performance.rst b/doc/developers/performance.rst
@@ -200,7 +200,8 @@ Now restart IPython and let us use this new toy::
 
   In [1]: from sklearn.datasets import load_digits
 
-  In [2]: from sklearn.decomposition.nmf import _nls_subproblem, NMF
+  In [2]: from sklearn.decomposition import NMF
+    ... : from sklearn.decomposition._nmf import _nls_subproblem
 
   In [3]: X, _ = load_digits(return_X_y=True)
 

diff --git a/examples/decomposition/plot_beta_divergence.py b/examples/decomposition/plot_beta_divergence.py
@@ -8,7 +8,7 @@
 """
 import numpy as np
 import matplotlib.pyplot as plt
-from sklearn.decomposition.nmf import _beta_divergence
+from sklearn.decomposition._nmf import _beta_divergence
 
 print(__doc__)
 

diff --git a/sklearn/_build_utils/deprecated_modules.py b/sklearn/_build_utils/deprecated_modules.py
@@ -86,6 +86,31 @@
      'set_verbosity_wrap'),
     ('_liblinear', 'sklearn.svm.liblinear', 'sklearn.svm', 'train_wrap'),
 
+    ('_base', 'sklearn.decomposition.base', 'sklearn.decomposition',
+     'BaseEstimator'),
+    ('_dict_learning', 'sklearn.decomposition.dict_learning',
+     'sklearn.decomposition', 'MiniBatchDictionaryLearning'),
+    ('_cdnmf_fast', 'sklearn.decomposition.cdnmf_fast',
+     'sklearn.decomposition', '__dict__'),
+    ('_factor_analysis', 'sklearn.decomposition.factor_analysis',
+     'sklearn.decomposition', 'FactorAnalysis'),
+    ('_fastica', 'sklearn.decomposition.fastica_', 'sklearn.decomposition',
+     'FastICA'),
+    ('_incremental_pca', 'sklearn.decomposition.incremental_pca',
+     'sklearn.decomposition', 'IncrementalPCA'),
+    ('_kernel_pca', 'sklearn.decomposition.kernel_pca',
+     'sklearn.decomposition', 'KernelPCA'),
+    ('_nmf', 'sklearn.decomposition.nmf', 'sklearn.decomposition', 'NMF'),
+    ('_online_lda', 'sklearn.decomposition.online_lda',
+     'sklearn.decomposition', 'LatentDirichletAllocation'),
+    ('_online_lda_fast', 'sklearn.decomposition.online_lda_fast',
+     'sklearn.decomposition', 'mean_change'),
+    ('_pca', 'sklearn.decomposition.pca', 'sklearn.decomposition', 'PCA'),
+    ('_sparse_pca', 'sklearn.decomposition.sparse_pca',
+     'sklearn.decomposition', 'SparsePCA'),
+    ('_truncated_svd', 'sklearn.decomposition.truncated_svd',
+     'sklearn.decomposition', 'TruncatedSVD'),
+
     ('_gpr', 'sklearn.gaussian_process.gpr', 'sklearn.gaussian_process',
      'GaussianProcessRegressor'),
     ('_gpc', 'sklearn.gaussian_process.gpc', 'sklearn.gaussian_process',

diff --git a/sklearn/decomposition/__init__.py b/sklearn/decomposition/__init__.py
@@ -4,19 +4,19 @@
 this module can be regarded as dimensionality reduction techniques.
 """
 
-from .nmf import NMF, non_negative_factorization
-from .pca import PCA
-from .incremental_pca import IncrementalPCA
-from .kernel_pca import KernelPCA
-from .sparse_pca import SparsePCA, MiniBatchSparsePCA
-from .truncated_svd import TruncatedSVD
-from .fastica_ import FastICA, fastica
-from .dict_learning import (dict_learning, dict_learning_online, sparse_encode,
-                            DictionaryLearning, MiniBatchDictionaryLearning,
-                            SparseCoder)
-from .factor_analysis import FactorAnalysis
+from ._nmf import NMF, non_negative_factorization
+from ._pca import PCA
+from ._incremental_pca import IncrementalPCA
+from ._kernel_pca import KernelPCA
+from ._sparse_pca import SparsePCA, MiniBatchSparsePCA
+from ._truncated_svd import TruncatedSVD
+from ._fastica import FastICA, fastica
+from ._dict_learning import (dict_learning, dict_learning_online,
+                             sparse_encode, DictionaryLearning,
+                             MiniBatchDictionaryLearning, SparseCoder)
+from ._factor_analysis import FactorAnalysis
 from ..utils.extmath import randomized_svd
-from .online_lda import LatentDirichletAllocation
+from ._online_lda import LatentDirichletAllocation
 
 __all__ = ['DictionaryLearning',
            'FastICA',

diff --git a/sklearn/decomposition/base.py → sklearn/decomposition/_base.py b/sklearn/decomposition/base.py → sklearn/decomposition/_base.py
diff --git a/sklearn/decomposition/cdnmf_fast.pyx → sklearn/decomposition/_cdnmf_fast.pyx b/sklearn/decomposition/cdnmf_fast.pyx → sklearn/decomposition/_cdnmf_fast.pyx
diff --git a/sklearn/decomposition/dict_learning.py → sklearn/decomposition/_dict_learning.py b/sklearn/decomposition/dict_learning.py → sklearn/decomposition/_dict_learning.py
diff --git a/sklearn/decomposition/factor_analysis.py → sklearn/decomposition/_factor_analysis.py b/sklearn/decomposition/factor_analysis.py → sklearn/decomposition/_factor_analysis.py
diff --git a/sklearn/decomposition/fastica_.py → sklearn/decomposition/_fastica.py b/sklearn/decomposition/fastica_.py → sklearn/decomposition/_fastica.py
diff --git a/sklearn/decomposition/incremental_pca.py → sklearn/decomposition/_incremental_pca.py b/sklearn/decomposition/incremental_pca.py → sklearn/decomposition/_incremental_pca.py
@@ -7,7 +7,7 @@
 import numpy as np
 from scipy import linalg, sparse
 
-from .base import _BasePCA
+from ._base import _BasePCA
 from ..utils import check_array, gen_batches
 from ..utils.extmath import svd_flip, _incremental_mean_and_var
 

diff --git a/sklearn/decomposition/kernel_pca.py → sklearn/decomposition/_kernel_pca.py b/sklearn/decomposition/kernel_pca.py → sklearn/decomposition/_kernel_pca.py
diff --git a/sklearn/decomposition/nmf.py → sklearn/decomposition/_nmf.py b/sklearn/decomposition/nmf.py → sklearn/decomposition/_nmf.py
@@ -13,7 +13,7 @@
 import warnings
 from math import sqrt
 
-from .cdnmf_fast import _update_cdnmf_fast
+from ._cdnmf_fast import _update_cdnmf_fast
 from ..base import BaseEstimator, TransformerMixin
 from ..exceptions import ConvergenceWarning
 from ..utils import check_random_state, check_array

diff --git a/sklearn/decomposition/online_lda.py → sklearn/decomposition/_online_lda.py b/sklearn/decomposition/online_lda.py → sklearn/decomposition/_online_lda.py
@@ -23,8 +23,8 @@
 from ..utils.validation import check_non_negative
 from ..utils.validation import check_is_fitted
 
-from ._online_lda import (mean_change, _dirichlet_expectation_1d,
-                          _dirichlet_expectation_2d)
+from ._online_lda_fast import (mean_change, _dirichlet_expectation_1d,
+                               _dirichlet_expectation_2d)
 
 EPS = np.finfo(np.float).eps
 

diff --git a/sklearn/decomposition/_online_lda.pyx → sklearn/decomposition/_online_lda_fast.pyx b/sklearn/decomposition/_online_lda.pyx → sklearn/decomposition/_online_lda_fast.pyx
diff --git a/sklearn/decomposition/pca.py → sklearn/decomposition/_pca.py b/sklearn/decomposition/pca.py → sklearn/decomposition/_pca.py
@@ -19,7 +19,7 @@
 from scipy.sparse import issparse
 from scipy.sparse.linalg import svds
 
-from .base import _BasePCA
+from ._base import _BasePCA
 from ..utils import check_random_state
 from ..utils import check_array
 from ..utils.extmath import fast_logdet, randomized_svd, svd_flip

diff --git a/sklearn/decomposition/sparse_pca.py → sklearn/decomposition/_sparse_pca.py b/sklearn/decomposition/sparse_pca.py → sklearn/decomposition/_sparse_pca.py
@@ -10,7 +10,7 @@
 from ..utils.validation import check_is_fitted
 from ..linear_model import ridge_regression
 from ..base import BaseEstimator, TransformerMixin
-from .dict_learning import dict_learning, dict_learning_online
+from ._dict_learning import dict_learning, dict_learning_online
 
 
 # FIXME: remove in 0.24

diff --git a/sklearn/decomposition/truncated_svd.py → sklearn/decomposition/_truncated_svd.py b/sklearn/decomposition/truncated_svd.py → sklearn/decomposition/_truncated_svd.py
diff --git a/sklearn/decomposition/setup.py b/sklearn/decomposition/setup.py
@@ -10,13 +10,13 @@ def configuration(parent_package="", top_path=None):
     if os.name == 'posix':
         libraries.append('m')
 
-    config.add_extension("_online_lda",
-                         sources=["_online_lda.pyx"],
+    config.add_extension("_online_lda_fast",
+                         sources=["_online_lda_fast.pyx"],
                          include_dirs=[numpy.get_include()],
                          libraries=libraries)
 
-    config.add_extension('cdnmf_fast',
-                         sources=['cdnmf_fast.pyx'],
+    config.add_extension('_cdnmf_fast',
+                         sources=['_cdnmf_fast.pyx'],
                          include_dirs=[numpy.get_include()],
                          libraries=libraries)
 

diff --git a/sklearn/decomposition/tests/test_fastica.py b/sklearn/decomposition/tests/test_fastica.py
@@ -13,7 +13,7 @@
 from sklearn.utils.testing import assert_warns
 
 from sklearn.decomposition import FastICA, fastica, PCA
-from sklearn.decomposition.fastica_ import _gs_decorrelation
+from sklearn.decomposition._fastica import _gs_decorrelation
 from sklearn.exceptions import ConvergenceWarning
 
 

diff --git a/sklearn/decomposition/tests/test_nmf.py b/sklearn/decomposition/tests/test_nmf.py
@@ -4,7 +4,7 @@
 
 from scipy import linalg
 from sklearn.decomposition import NMF, non_negative_factorization
-from sklearn.decomposition import nmf   # For testing internals
+from sklearn.decomposition import _nmf as nmf  # For testing internals
 from scipy.sparse import csc_matrix
 
 import pytest

diff --git a/sklearn/decomposition/tests/test_pca.py b/sklearn/decomposition/tests/test_pca.py
@@ -7,8 +7,8 @@
 
 from sklearn import datasets
 from sklearn.decomposition import PCA
-from sklearn.decomposition.pca import _assess_dimension_
-from sklearn.decomposition.pca import _infer_dimension_
+from sklearn.decomposition._pca import _assess_dimension_
+from sklearn.decomposition._pca import _infer_dimension_
 
 iris = datasets.load_iris()
 PCA_SOLVERS = ['full', 'arpack', 'randomized', 'auto']