[mlpack] 02/13: forward port quilt patches, augment spelling patch
Barak A. Pearlmutter
barak+git at pearlmutter.net
Mon Jan 18 16:07:53 UTC 2016
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bap pushed a commit to branch master
in repository mlpack.
commit d6a7bb775d1b18b01841a99cc3ced76abe6c4fc7
Author: Barak A. Pearlmutter <barak+git at pearlmutter.net>
Date: Thu Jan 7 23:37:44 2016 +0100
forward port quilt patches, augment spelling patch
---
debian/patches/0001-build-Doxygen.patch | 4 +-
debian/patches/0002-spelling.patch | 200 +++++++++++++++-------------
debian/patches/0003-Doxygen-timestamp.patch | 2 +-
3 files changed, 112 insertions(+), 94 deletions(-)
diff --git a/debian/patches/0001-build-Doxygen.patch b/debian/patches/0001-build-Doxygen.patch
index c375ecb..289719c 100644
--- a/debian/patches/0001-build-Doxygen.patch
+++ b/debian/patches/0001-build-Doxygen.patch
@@ -11,10 +11,10 @@ to the debian/rules override_dh_auto_build target.
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 881f7d6..bc05880 100644
+index 0cf2e32..91deb22 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -268,7 +268,7 @@ if (DOXYGEN_FOUND)
+@@ -303,7 +303,7 @@ if (DOXYGEN_FOUND)
)
# Generate documentation.
diff --git a/debian/patches/0002-spelling.patch b/debian/patches/0002-spelling.patch
index 84b2e41..81ddbad 100644
--- a/debian/patches/0002-spelling.patch
+++ b/debian/patches/0002-spelling.patch
@@ -3,68 +3,64 @@ Date: Sun, 17 Aug 2014 09:03:13 +0200
Subject: spelling
---
- doc/tutorials/amf/amf.txt | 6 +++---
- src/mlpack/core/kernels/example_kernel.hpp | 2 +-
- src/mlpack/core/tree/ballbound_impl.hpp | 2 +-
- src/mlpack/core/tree/cosine_tree/cosine_tree.cpp | 2 +-
- src/mlpack/methods/amf/init_rules/random_acol_init.hpp | 2 +-
- src/mlpack/methods/amf/init_rules/random_init.hpp | 4 ++--
- .../amf/termination_policies/simple_tolerance_termination.hpp | 2 +-
- src/mlpack/methods/lsh/lsh_search.hpp | 4 ++--
- src/mlpack/methods/neighbor_search/neighbor_search.hpp | 2 +-
- src/mlpack/methods/rann/ra_search.hpp | 2 +-
- .../methods/sparse_autoencoder/sparse_autoencoder_function.hpp | 2 +-
- src/mlpack/tests/cosine_tree_test.cpp | 2 +-
- 12 files changed, 16 insertions(+), 16 deletions(-)
+ doc/tutorials/amf/amf.txt | 8 ++++----
+ src/mlpack/core/tree/ballbound_impl.hpp | 2 +-
+ src/mlpack/core/tree/cosine_tree/cosine_tree.cpp | 2 +-
+ src/mlpack/methods/amf/init_rules/average_init.hpp | 4 ++--
+ src/mlpack/methods/amf/init_rules/random_acol_init.hpp | 2 +-
+ src/mlpack/methods/amf/init_rules/random_init.hpp | 4 ++--
+ .../amf/termination_policies/simple_tolerance_termination.hpp | 2 +-
+ .../amf/termination_policies/validation_RMSE_termination.hpp | 2 +-
+ src/mlpack/methods/lsh/lsh_search.hpp | 4 ++--
+ .../methods/softmax_regression/softmax_regression_function.cpp | 2 +-
+ .../methods/sparse_autoencoder/sparse_autoencoder_function.hpp | 2 +-
+ src/mlpack/tests/cosine_tree_test.cpp | 2 +-
+ 12 files changed, 18 insertions(+), 18 deletions(-)
diff --git a/doc/tutorials/amf/amf.txt b/doc/tutorials/amf/amf.txt
-index 6b4bf9a..ea5d4c3 100644
+index abb4c03..bc4f8ed 100644
--- a/doc/tutorials/amf/amf.txt
+++ b/doc/tutorials/amf/amf.txt
@@ -72,14 +72,14 @@ the threshold or the number of iterations goes beyond the threshold, positive
- termination signal is passed to AMF.
+ termination signal is passed to AMF.
- In SimpleToleranceTermination, termination criterion is met when increase in
--residue value drops below the given tolerance. To accomodate spikes, certain
-+residue value drops below the given tolerance. To accommodate spikes, certain
- number of successive residue drops are accepted. Secondary termination criterion
- terminates algorithm when iteration count goes beyond the threshold.
+ In SimpleToleranceTermination, termination criterion is met when increase in
+-residue value drops below the given tolerance. To accomodate spikes, certain
++residue value drops below the given tolerance. To accommodate spikes, certain
+ number of successive residue drops are accepted. Secondary termination criterion
+ terminates algorithm when iteration count goes beyond the threshold.
- ValidationRMSETermination divids the data into 2 sets, training set and
- validation set. Entries of validation set are nullifed in the input matrix.
- Termination criterion is met when increase in validation set RMSe value drops
--below the given tolerance. To accomodate spikes certain number of successive
-+below the given tolerance. To accommodate spikes certain number of successive
- validation RMSE drops are accepted. This upper imit on successive drops can be
- adjusted with reverseStepCount. Secondary termination criterion terminates
+ ValidationRMSETermination divids the data into 2 sets, training set and
+ validation set. Entries of validation set are nullifed in the input matrix.
+ Termination criterion is met when increase in validation set RMSe value drops
+-below the given tolerance. To accomodate spikes certain number of successive
++below the given tolerance. To accommodate spikes certain number of successive
+ validation RMSE drops are accepted. This upper imit on successive drops can be
+ adjusted with reverseStepCount. Secondary termination criterion terminates
algorithm when iteration count goes above the threshold. Though this termination
+@@ -101,7 +101,7 @@ The AMF class comes with 2 initialization policies
+
+ RandomInitialization initializes matrices W and H with random uniform distribution
+ while RandomAcolInitialization initializes the W matrix by averaging p randomly
+-chosen columns of V. In case of RandomAcolIntialization, p is a template parameter.
++chosen columns of V. In case of RandomAcolInitialization, p is a template parameter.
+
+ To implement their own initialization policy, users need to define the following
+ function in their class.
@@ -160,7 +160,7 @@ int main()
}
@endcode
--NMFALSFactorizer uses SimpleResidueTermination which is most prefered with
-+NMFALSFactorizer uses SimpleResidueTermination which is most preferred with
+-NMFALSFactorizer uses SimpleResidueTermination which is most prefered with
++NMFALSFactorizer uses SimpleResidueTermination which is most preferred with
Non-Negative Matrix factorizers. Initialization of W and H in NMFALSFactorizer
- is random. The Apply function returns the residue obtained by comparing the
+ is random. The Apply function returns the residue obtained by comparing the
constructed matrix W * H with the original matrix V.
-diff --git a/src/mlpack/core/kernels/example_kernel.hpp b/src/mlpack/core/kernels/example_kernel.hpp
-index fe3794e..0c7e3ec 100644
---- a/src/mlpack/core/kernels/example_kernel.hpp
-+++ b/src/mlpack/core/kernels/example_kernel.hpp
-@@ -111,7 +111,7 @@ class ExampleKernel
- /**
- * Returns a string for the kernel object; in this case, with only the memory
- * address for the kernel. If your kernel has any members, your ToString()
-- * method should include those as neccessary as well.
-+ * method should include those as necessary as well.
- **/
- std::string ToString() const
- {
diff --git a/src/mlpack/core/tree/ballbound_impl.hpp b/src/mlpack/core/tree/ballbound_impl.hpp
-index 64e222b..9dcf872 100644
+index 78bf2f1..97226e1 100644
--- a/src/mlpack/core/tree/ballbound_impl.hpp
+++ b/src/mlpack/core/tree/ballbound_impl.hpp
-@@ -248,7 +248,7 @@ BallBound<VecType, TMetricType>::operator|=(const MatType& data)
+@@ -271,7 +271,7 @@ BallBound<VecType, TMetricType>::operator|=(const MatType& data)
if (dist > radius)
{
// Move towards the new point and increase the radius just enough to
@@ -74,10 +70,10 @@ index 64e222b..9dcf872 100644
center += ((dist - radius) / (2 * dist)) * diff;
radius = 0.5 * (dist + radius);
diff --git a/src/mlpack/core/tree/cosine_tree/cosine_tree.cpp b/src/mlpack/core/tree/cosine_tree/cosine_tree.cpp
-index 006bad6..15fc02d 100644
+index 7343c4b..3b23226 100644
--- a/src/mlpack/core/tree/cosine_tree/cosine_tree.cpp
+++ b/src/mlpack/core/tree/cosine_tree/cosine_tree.cpp
-@@ -334,7 +334,7 @@ void CosineTree::ColumnSamplesLS(std::vector<size_t>& sampledIndices,
+@@ -340,7 +340,7 @@ void CosineTree::ColumnSamplesLS(std::vector<size_t>& sampledIndices,
cDistribution(i+1) = cDistribution(i) + l2NormsSquared(i) / frobNormSquared;
}
@@ -86,35 +82,57 @@ index 006bad6..15fc02d 100644
sampledIndices.resize(numSamples);
probabilities.zeros(numSamples);
+diff --git a/src/mlpack/methods/amf/init_rules/average_init.hpp b/src/mlpack/methods/amf/init_rules/average_init.hpp
+index 49fbe07..15d08c6 100644
+--- a/src/mlpack/methods/amf/init_rules/average_init.hpp
++++ b/src/mlpack/methods/amf/init_rules/average_init.hpp
+@@ -2,7 +2,7 @@
+ * @file averge_init.hpp
+ * @author Sumedh Ghaisas
+ *
+- * Intialization rule for Alternating Matrix Factorization.
++ * Initialization rule for Alternating Matrix Factorization.
+ *
+ * This file is part of mlpack 2.0.0.
+ *
+@@ -76,7 +76,7 @@ class AverageInitialization
+
+ avgV = sqrt(((avgV / (n * m)) - min) / r);
+
+- // Intialize to random values.
++ // Initialize to random values.
+ W.randu(n, r);
+ H.randu(r, m);
+
diff --git a/src/mlpack/methods/amf/init_rules/random_acol_init.hpp b/src/mlpack/methods/amf/init_rules/random_acol_init.hpp
-index 36352a1..2ec97be 100644
+index 5362481..5b87dbf 100644
--- a/src/mlpack/methods/amf/init_rules/random_acol_init.hpp
+++ b/src/mlpack/methods/amf/init_rules/random_acol_init.hpp
@@ -2,7 +2,7 @@
* @file random_acol_init.hpp
* @author Mohan Rajendran
*
-- * Intialization rule for Alternating Matrix Factorization.
+- * Intialization rule for Alternating Matrix Factorization.
+ * Initialization rule for Alternating Matrix Factorization.
*
- * This file is part of mlpack 1.0.12.
+ * This file is part of mlpack 2.0.0.
*
diff --git a/src/mlpack/methods/amf/init_rules/random_init.hpp b/src/mlpack/methods/amf/init_rules/random_init.hpp
-index 993897e..aa94101 100644
+index a0a64db..f6655eb 100644
--- a/src/mlpack/methods/amf/init_rules/random_init.hpp
+++ b/src/mlpack/methods/amf/init_rules/random_init.hpp
@@ -2,7 +2,7 @@
* @file random_init.hpp
* @author Mohan Rajendran
*
-- * Intialization rule for Non-Negative Matrix Factorization (NMF). This simple
-+ * Initialization rule for Non-Negative Matrix Factorization (NMF). This simple
+- * Intialization rule for alternating matrix forization (AMF). This simple
++ * Initialization rule for alternating matrix forization (AMF). This simple
* initialization is performed by assigning a random matrix to W and H.
*
- * This file is part of mlpack 1.0.12.
-@@ -36,7 +36,7 @@ class RandomInitialization
- size_t n = V.n_rows;
- size_t m = V.n_cols;
+ * This file is part of mlpack 2.0.0.
+@@ -56,7 +56,7 @@ class RandomInitialization
+ const size_t n = V.n_rows;
+ const size_t m = V.n_cols;
- // Intialize to random values.
+ // Initialize to random values.
@@ -122,10 +140,10 @@ index 993897e..aa94101 100644
H.randu(r, m);
}
diff --git a/src/mlpack/methods/amf/termination_policies/simple_tolerance_termination.hpp b/src/mlpack/methods/amf/termination_policies/simple_tolerance_termination.hpp
-index db74af3..58de3d7 100644
+index 509d06d..0920e9b 100644
--- a/src/mlpack/methods/amf/termination_policies/simple_tolerance_termination.hpp
+++ b/src/mlpack/methods/amf/termination_policies/simple_tolerance_termination.hpp
-@@ -22,7 +22,7 @@ namespace amf {
+@@ -30,7 +30,7 @@ namespace amf {
/**
* This class implements residue tolerance termination policy. Termination
* criterion is met when increase in residue value drops below the given tolerance.
@@ -134,11 +152,24 @@ index db74af3..58de3d7 100644
* This upper imit on successive drops can be adjusted with reverseStepCount.
* Secondary termination criterion terminates algorithm when iteration count
* goes above the threshold.
+diff --git a/src/mlpack/methods/amf/termination_policies/validation_RMSE_termination.hpp b/src/mlpack/methods/amf/termination_policies/validation_RMSE_termination.hpp
+index 80c5bf9..1ad1853 100644
+--- a/src/mlpack/methods/amf/termination_policies/validation_RMSE_termination.hpp
++++ b/src/mlpack/methods/amf/termination_policies/validation_RMSE_termination.hpp
+@@ -34,7 +34,7 @@ namespace amf
+ * The input data matrix is divided into 2 sets, training set and validation set.
+ * Entries of validation set are nullifed in the input matrix. Termination
+ * criterion is met when increase in validation set RMSe value drops below the
+- * given tolerance. To accomodate spikes certain number of successive validation
++ * given tolerance. To accommodate spikes certain number of successive validation
+ * RMSE drops are accepted. This upper imit on successive drops can be adjusted
+ * with reverseStepCount. Secondary termination criterion terminates algorithm
+ * when iteration count goes above the threshold.
diff --git a/src/mlpack/methods/lsh/lsh_search.hpp b/src/mlpack/methods/lsh/lsh_search.hpp
-index 0c51593..88e7e80 100644
+index 0a7b550..ea5728b 100644
--- a/src/mlpack/methods/lsh/lsh_search.hpp
+++ b/src/mlpack/methods/lsh/lsh_search.hpp
-@@ -144,8 +144,8 @@ class LSHSearch
+@@ -200,8 +200,8 @@ class LSHSearch
* standard hash.
*
* This function does not have any parameters and relies on parameters which
@@ -149,37 +180,24 @@ index 0c51593..88e7e80 100644
*/
void BuildHash();
-diff --git a/src/mlpack/methods/neighbor_search/neighbor_search.hpp b/src/mlpack/methods/neighbor_search/neighbor_search.hpp
-index fa16c02..a2964a9 100644
---- a/src/mlpack/methods/neighbor_search/neighbor_search.hpp
-+++ b/src/mlpack/methods/neighbor_search/neighbor_search.hpp
-@@ -64,7 +64,7 @@ class NeighborSearch
- *
- * This method will copy the matrices to internal copies, which are rearranged
- * during tree-building. You can avoid this extra copy by pre-constructing
-- * the trees and passing them using a diferent constructor.
-+ * the trees and passing them using a different constructor.
- *
- * @param referenceSet Set of reference points.
- * @param querySet Set of query points.
-diff --git a/src/mlpack/methods/rann/ra_search.hpp b/src/mlpack/methods/rann/ra_search.hpp
-index c7a06e4..9106cce 100644
---- a/src/mlpack/methods/rann/ra_search.hpp
-+++ b/src/mlpack/methods/rann/ra_search.hpp
-@@ -72,7 +72,7 @@ class RASearch
- *
- * This method will copy the matrices to internal copies, which are rearranged
- * during tree-building. You can avoid this extra copy by pre-constructing
-- * the trees and passing them using a diferent constructor.
-+ * the trees and passing them using a different constructor.
- *
- * @param referenceSet Set of reference points.
- * @param querySet Set of query points.
+diff --git a/src/mlpack/methods/softmax_regression/softmax_regression_function.cpp b/src/mlpack/methods/softmax_regression/softmax_regression_function.cpp
+index 005dd2a..fe473c6 100644
+--- a/src/mlpack/methods/softmax_regression/softmax_regression_function.cpp
++++ b/src/mlpack/methods/softmax_regression/softmax_regression_function.cpp
+@@ -35,7 +35,7 @@ SoftmaxRegressionFunction::SoftmaxRegressionFunction(
+ lambda(lambda),
+ fitIntercept(fitIntercept)
+ {
+- // Intialize the parameters to suitable values.
++ // Initialize the parameters to suitable values.
+ initialPoint = InitializeWeights();
+
+ // Calculate the label matrix.
diff --git a/src/mlpack/methods/sparse_autoencoder/sparse_autoencoder_function.hpp b/src/mlpack/methods/sparse_autoencoder/sparse_autoencoder_function.hpp
-index 6b4a135..f93a2f7 100644
+index f3fe967..8dae8f5 100644
--- a/src/mlpack/methods/sparse_autoencoder/sparse_autoencoder_function.hpp
+++ b/src/mlpack/methods/sparse_autoencoder/sparse_autoencoder_function.hpp
-@@ -149,7 +149,7 @@ class SparseAutoencoderFunction
+@@ -157,7 +157,7 @@ class SparseAutoencoderFunction
private:
//! The matrix of data points.
const arma::mat& data;
@@ -189,10 +207,10 @@ index 6b4a135..f93a2f7 100644
//! Size of the visible layer.
size_t visibleSize;
diff --git a/src/mlpack/tests/cosine_tree_test.cpp b/src/mlpack/tests/cosine_tree_test.cpp
-index 9248951..3c17a3f 100644
+index 2da2465..1e5eda9 100644
--- a/src/mlpack/tests/cosine_tree_test.cpp
+++ b/src/mlpack/tests/cosine_tree_test.cpp
-@@ -55,7 +55,7 @@ BOOST_AUTO_TEST_CASE(CosineTreeNoSplit)
+@@ -63,7 +63,7 @@ BOOST_AUTO_TEST_CASE(CosineTreeNoSplit)
*/
BOOST_AUTO_TEST_CASE(CosineNodeCosineSplit)
{
diff --git a/debian/patches/0003-Doxygen-timestamp.patch b/debian/patches/0003-Doxygen-timestamp.patch
index a2d582a..ea8712f 100644
--- a/debian/patches/0003-Doxygen-timestamp.patch
+++ b/debian/patches/0003-Doxygen-timestamp.patch
@@ -10,7 +10,7 @@ https://wiki.debian.org/ReproducibleBuilds/TimestampsInDocumentationGeneratedByD
1 file changed, 5 insertions(+)
diff --git a/Doxyfile b/Doxyfile
-index b2b23a9..78a59e6 100644
+index 9b96e99..6a7b79b 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -71,6 +71,11 @@ SHOW_USED_FILES = YES
--
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