Merge pull request #1190 from sbrodehl/dev-cmake-project

cmake project

src/mlpack/bindings/cli/CMakeLists.txt

@@ -23,6 +23,7 @@ set(SOURCES
   print_doc_functions_impl.hpp
   print_help.hpp
   print_help.cpp
+  set_param.hpp
   string_type_param.hpp
   string_type_param_impl.hpp
 )

src/mlpack/bindings/tests/CMakeLists.txt

@@ -2,6 +2,7 @@
 # Anything not in this list will not be compiled into mlpack.
 set(SOURCES
   test_option.hpp
+  ignore_check.hpp
   get_param.hpp
   get_printable_param.hpp
   get_printable_param_impl.hpp

src/mlpack/core/arma_extend/CMakeLists.txt

@@ -3,6 +3,7 @@
 set(SOURCES
   arma_extend.hpp
   fn_ccov.hpp
+  fn_inplace_reshape.hpp
   glue_ccov_meat.hpp
   glue_ccov_proto.hpp
   hdf5_misc.hpp

src/mlpack/core/data/CMakeLists.txt

@@ -19,6 +19,7 @@ set(SOURCES
   normalize_labels_impl.hpp
   save.hpp
   save_impl.hpp
+  serialization_template_version.hpp
   split_data.hpp
   imputer.hpp
   binarize.hpp

src/mlpack/core/data/map_policies/CMakeLists.txt

@@ -3,6 +3,7 @@
 set(SOURCES
   increment_policy.hpp
   missing_policy.hpp
+  datatype.hpp
 )
 
 # Add directory name to sources.

src/mlpack/core/math/CMakeLists.txt

@@ -7,6 +7,7 @@ set(SOURCES
   lin_alg.hpp
   lin_alg_impl.hpp
   lin_alg.cpp
+  make_alias.hpp
   random.hpp
   random.cpp
   random_basis.hpp
@@ -14,6 +15,7 @@ set(SOURCES
   range.hpp
   range_impl.hpp
   round.hpp
+  shuffle_data.hpp
 )
 
 # add directory name to sources

src/mlpack/core/math/range_serialization.cpp

@@ -1,13 +0,0 @@
-/**
- * @file range_serialization.cpp
- * @author Ryan Curtin
- *
- * Instantiation of Serialize() operators for math::Range.
- */
-#include <limits>
-#include "range_serialization.hpp"
-
-using namespace mlpack;
-using namespace mlpack::math;
-
-MLPACK_SERIALIZATION_INSTANTIATE(Range);

src/mlpack/core/math/range_serialization.hpp

@@ -1,28 +0,0 @@
-/**
- * @file range_serialization.hpp
- * @author Ryan Curtin
- *
- * Implementations of Serialize() for math::Range.
- */
-#ifndef MLPACK_CORE_MATH_RANGE_SERIALIZATION_HPP
-#define MLPACK_CORE_MATH_RANGE_SERIALIZATION_HPP
-
-#include "range.hpp"
-#include <mlpack/core/data/serialization.hpp>
-
-namespace mlpack {
-namespace math {
-
-//! Serialize the range.
-template<typename T>
-template<typename Archive>
-void RangeType<T>::Serialize(Archive& ar, const unsigned int /* version */)
-{
-  ar & data::CreateNVP(hi, "hi");
-  ar & data::CreateNVP(lo, "lo");
-}
-
-} // namespace math
-} // namespace mlpack
-
-#endif

src/mlpack/core/optimizers/CMakeLists.txt

@@ -12,10 +12,13 @@ set(DIRS
   lbfgs
   line_search
   proximal
+  parallel_sgd
   rmsprop
   sa
+  scd
   sdp
   sgd
+  sgdr
   smorms3
   spalera_sgd
 )

src/mlpack/core/optimizers/parallel_sgd/CMakeLists.txt

@@ -1,4 +1,6 @@
 set(SOURCES
+  decay_policies/constant_step.hpp
+  decay_policies/exponential_backoff.hpp
   parallel_sgd.hpp
   parallel_sgd_impl.hpp
   sparse_test_function.hpp

src/mlpack/core/optimizers/parallel_sgd/decay_policies/CMakeLists.txt

@@ -1,11 +0,0 @@
-set(SOURCES
-  constant_step.hpp
-  exponential_backoff.hpp
-)
-
-set(DIR_SRCS)
-foreach(file ${SOURCES})
-  set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file})
-endforeach()
-
-set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)

src/mlpack/core/optimizers/scd/CMakeLists.txt

@@ -1,4 +1,7 @@
 set(SOURCES
+  descent_policies/cyclic_descent.hpp
+  descent_policies/greedy_descent.hpp
+  descent_policies/random_descent.hpp
   scd.hpp
   scd_impl.hpp
 )

src/mlpack/core/optimizers/sgd/update_policies/CMakeLists.txt

@@ -1,11 +0,0 @@
-set(SOURCES
-  vanilla_update.hpp
-  momentum_update.hpp
-)
-
-set(DIR_SRCS)
-foreach(file ${SOURCES})
-  set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file})
-endforeach()
-
-set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)

src/mlpack/core/tree/CMakeLists.txt

@@ -33,6 +33,7 @@ set(SOURCES
   cellbound_impl.hpp
   cosine_tree/cosine_tree.hpp
   cosine_tree/cosine_tree.cpp
+  cover_tree.hpp
   cover_tree/cover_tree.hpp
   cover_tree/cover_tree_impl.hpp
   cover_tree/first_point_is_root.hpp
@@ -74,6 +75,8 @@ set(SOURCES
   rectangle_tree/r_star_tree_descent_heuristic_impl.hpp
   rectangle_tree/r_star_tree_split.hpp
   rectangle_tree/r_star_tree_split_impl.hpp
+  rectangle_tree/traits.hpp
+  rectangle_tree/typedef.hpp
   rectangle_tree/x_tree_split.hpp
   rectangle_tree/x_tree_split_impl.hpp
   rectangle_tree/x_tree_auxiliary_information.hpp

src/mlpack/core/util/CMakeLists.txt

@@ -1,6 +1,7 @@
 # Define the files we need to compile.
 # Anything not in this list will not be compiled into mlpack.
 set(SOURCES
+  arma_traits.hpp
   arma_config.hpp
   arma_config_check.hpp
   backtrace.hpp
@@ -17,6 +18,7 @@ set(SOURCES
   log.cpp
   mlpack_main.hpp
   nulloutstream.hpp
+  param.hpp
   param_checks.hpp
   param_checks_impl.hpp
   param_data.hpp

src/mlpack/core/util/param_data_impl.hpp

@@ -1,127 +0,0 @@
-/**
- * @file param_data_impl.hpp
- * @author Ryan Curtin
- *
- * Implementation of utility functions for ParamData structures.
- */
-#ifndef MLPACK_CORE_UTIL_PARAM_DATA_IMPL_HPP
-#define MLPACK_CORE_UTIL_PARAM_DATA_IMPL_HPP
-
-#include "param_data.hpp"
-#include <mlpack/core/data/load.hpp>
-
-namespace mlpack {
-namespace util {
-
-//! This overload is called when nothing special needs to happen to the name of
-//! the parameter.
-template<typename T>
-std::string MapParameterName(
-    const std::string& identifier,
-    const typename boost::disable_if<arma::is_arma_type<T>>::type* /* junk */,
-    const typename boost::disable_if<data::HasSerialize<T>>::type* /* junk */,
-    const typename boost::disable_if<std::is_same<T,
-        std::tuple<mlpack::data::DatasetInfo, arma::mat>>>::type* /* junk */)
-{
-  return identifier;
-}
-
-//! This is called for matrices, DatasetInfo objects, and serializable objects,
-//! which have a different boost name.
-template<typename T>
-std::string MapParameterName(
-    const std::string& identifier,
-    const typename boost::enable_if_c<
-        arma::is_arma_type<T>::value ||
-        std::is_same<T, std::tuple<mlpack::data::DatasetInfo,
-                                   arma::mat>>::value ||
-        data::HasSerialize<T>::value>::type* /* junk */)
-{
-  return identifier + "_file";
-}
-
-//! This overload is called when T == ParameterType<T>::value.
-template<typename T>
-T& HandleParameter(
-    typename ParameterType<T>::type& value,
-    ParamData& /* d */,
-    const typename boost::disable_if<arma::is_arma_type<T>>::type* /* junk */,
-    const typename boost::disable_if<data::HasSerialize<T>>::type* /* junk */,
-    const typename boost::disable_if<std::is_same<T,
-        std::tuple<mlpack::data::DatasetInfo, arma::mat>>>::type* /* junk */)
-{
-  return value;
-}
-
-//! This overload is called for matrices, which return a different type.
-template<typename T>
-T& HandleParameter(
-    typename ParameterType<T>::type& value,
-    ParamData& d,
-    const typename boost::enable_if<arma::is_arma_type<T>>::type* /* junk */)
-{
-  // If the matrix is an input matrix, we have to load the matrix.  'value'
-  // contains the filename.  It's possible we could load empty matrices many
-  // times, but I am not bothered by that---it shouldn't be something that
-  // happens.
-  T& matrix = *boost::any_cast<T>(&d.mappedValue);
-  if (d.input && !d.loaded)
-  {
-    // call correct data::Load() function
-    if (arma::is_Row<T>::value || arma::is_Col<T>::value)
-      data::Load(value, matrix, true);
-    else
-      data::Load(value, matrix, true, !d.noTranspose);
-    d.loaded = true;
-  }
-
-  return matrix;
-}
-
-//! This must be overloaded for matrices and dataset info objects.
-template<typename T>
-T& HandleParameter(
-    typename util::ParameterType<T>::type& value,
-    util::ParamData& d,
-    const typename boost::enable_if<std::is_same<T,
-        std::tuple<mlpack::data::DatasetInfo, arma::mat>>>::type* /* junk */)
-{
-  // If this is an input parameter, we need to load both the matrix and the
-  // dataset info.
-  std::tuple<mlpack::data::DatasetInfo, arma::mat>& tuple =
-      *boost::any_cast<std::tuple<mlpack::data::DatasetInfo,
-      arma::mat>>(&d.mappedValue);
-  if (d.input && !d.loaded)
-  {
-    data::Load(value, std::get<1>(tuple), std::get<0>(tuple), true,
-        !d.noTranspose);
-    d.loaded = true;
-  }
-
-  return tuple;
-}
-
-//! This is called for serializable mlpack objects, which have a different boost
-//! name.
-template<typename T>
-T& HandleParameter(
-    typename ParameterType<T>::type& value,
-    ParamData& d,
-    const typename boost::enable_if<data::HasSerialize<T>>::type* /* junk */)
-{
-  // If the model is an input model, we have to load it from file.  'value'
-  // contains the filename.
-  T& model = *boost::any_cast<T>(&d.mappedValue);
-  if (d.input && !d.loaded)
-  {
-    data::Load(value, "model", model, true);
-    d.loaded = true;
-  }
-
-  return model;
-}
-
-} // namespace util
-} // namespace mlpack
-
-#endif

src/mlpack/methods/CMakeLists.txt

@@ -21,11 +21,11 @@ endmacro ()
 
 # Recurse into each method mlpack provides.
 set(DIRS
-  preprocess
+  # mvu # Note: this implementation of MVU does not work.  See #189.
   adaboost
-  approx_kfn
   amf
   ann
+  approx_kfn
   block_krylov_svd
   cf
   dbscan
@@ -39,33 +39,33 @@ set(DIRS
   hoeffding_trees
   kernel_pca
   kmeans
-  mean_shift
   lars
   linear_regression
   local_coordinate_coding
   logistic_regression
   lsh
-#  mvu
   matrix_completion
+  mean_shift
   naive_bayes
   nca
   neighbor_search
   nmf
-#  lmf
+  nystroem_method
   pca
   perceptron
+  preprocess
   quic_svd
   radical
-  randomized_svd
   random_forest
+  randomized_svd
   range_search
   rann
-#  rmva
   regularized_svd
+  reinforcement_learning
   softmax_regression
   sparse_autoencoder
   sparse_coding
-  nystroem_method
+  sparse_svm
 )
 
 foreach(dir ${DIRS})

src/mlpack/methods/amf/CMakeLists.txt

@@ -5,6 +5,10 @@ set(SOURCES
   amf_impl.hpp
 )
 
+add_subdirectory(update_rules)
+add_subdirectory(init_rules)
+add_subdirectory(termination_policies)
+
 # Add directory name to sources.
 set(DIR_SRCS)
 foreach(file ${SOURCES})
@@ -13,7 +17,3 @@ endforeach()
 # Append sources (with directory name) to list of all mlpack sources (used at
 # the parent scope).
 set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)
-
-add_subdirectory(update_rules)
-add_subdirectory(init_rules)
-add_subdirectory(termination_policies)

src/mlpack/methods/ann/CMakeLists.txt

@@ -7,6 +7,13 @@ set(SOURCES
   rnn_impl.hpp
 )
 
+add_subdirectory(visitor)
+add_subdirectory(activation_functions)
+add_subdirectory(init_rules)
+add_subdirectory(layer)
+add_subdirectory(convolution_rules)
+add_subdirectory(augmented)
+
 # Add directory name to sources.
 set(DIR_SRCS)
 foreach(file ${SOURCES})
@@ -15,10 +22,3 @@ endforeach()
 # Append sources (with directory name) to list of all mlpack sources (used at
 # the parent scope).
 set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)
-
-add_subdirectory(visitor)
-add_subdirectory(activation_functions)
-add_subdirectory(init_rules)
-add_subdirectory(layer)
-add_subdirectory(convolution_rules)
-add_subdirectory(augmented)

src/mlpack/methods/ann/augmented/tasks/CMakeLists.txt

@@ -2,9 +2,13 @@
 # Anything not in this list will not be compiled into mlpack.
 set(SOURCES
   add.hpp
+  add_impl.hpp
   copy.hpp
+  copy_impl.hpp
   score.hpp
+  score_impl.hpp
   sort.hpp
+  sort_impl.hpp
 )
 
 # Add directory name to sources.

src/mlpack/methods/ann/layer/CMakeLists.txt

@@ -69,7 +69,7 @@ set(SOURCES
   select_impl.hpp
   sequential.hpp
   sequential_impl.hpp
-  vr_class_reward_impl.hpp
+  vr_class_reward.hpp
   vr_class_reward_impl.hpp
 )
 

src/mlpack/methods/fastmks/CMakeLists.txt

@@ -8,6 +8,7 @@ set(SOURCES
   fastmks_model.cpp
   fastmks_rules.hpp
   fastmks_rules_impl.hpp
+  fastmks_stat.hpp
 )
 
 # Add directory name to sources.

src/mlpack/methods/hmm/CMakeLists.txt

@@ -6,6 +6,8 @@ set(SOURCES
   hmm_model.hpp
   hmm_regression.hpp
   hmm_regression_impl.hpp
+  hmm_util.hpp
+  hmm_util_impl.hpp
 )
 
 # Add directory name to sources.

src/mlpack/methods/kernel_pca/CMakeLists.txt

@@ -5,6 +5,8 @@ set(SOURCES
   kernel_pca_impl.hpp
 )
 
+add_subdirectory(kernel_rules)
+
 # Add directory name to sources.
 set(DIR_SRCS)
 foreach(file ${SOURCES})
@@ -14,7 +16,5 @@ endforeach()
 # the parent scope).
 set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)
 
-add_subdirectory(kernel_rules)
-
 add_cli_executable(kernel_pca)
 add_python_binding(kernel_pca)

src/mlpack/methods/pca/CMakeLists.txt

@@ -7,6 +7,8 @@ set(SOURCES
 #  pca_nomain.cpp
 )
 
+add_subdirectory(decomposition_policies)
+
 # Add directory name to sources.
 set(DIR_SRCS)
 foreach(file ${SOURCES})
@@ -16,7 +18,5 @@ endforeach()
 # the parent scope).
 set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)
 
-add_subdirectory(decomposition_policies)
-
 add_cli_executable(pca)
 add_python_binding(pca)

src/mlpack/methods/perceptron/CMakeLists.txt

@@ -7,6 +7,9 @@ set(SOURCES
   perceptron_impl.hpp
 )
 
+add_subdirectory(initialization_methods)
+add_subdirectory(learning_policies)
+
 # Add directory name to sources.
 set(DIR_SRCS)
 foreach(file ${SOURCES})
@@ -16,8 +19,5 @@ endforeach()
 # the parent scope).
 set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)
 
-add_subdirectory(initialization_methods)
-add_subdirectory(learning_policies)
-
 add_cli_executable(perceptron)
 add_python_binding(perceptron)

src/mlpack/methods/reinforcement_learning/CMakeLists.txt

@@ -8,6 +8,11 @@ set(SOURCES
   training_config.hpp
 )
 
+add_subdirectory(environment)
+add_subdirectory(policy)
+add_subdirectory(replay)
+add_subdirectory(worker)
+
 # Add directory name to sources.
 set(DIR_SRCS)
 foreach(file ${SOURCES})
@@ -16,7 +21,3 @@ endforeach()
 # Append sources (with directory name) to list of all mlpack sources (used at
 # the parent scope).
 set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)
-
-add_subdirectory(environment)
-add_subdirectory(estimator)
-add_subdirectory(policy)

src/mlpack/tests/CMakeLists.txt

@@ -1,27 +1,27 @@
 # mlpack test executable.
 add_executable(mlpack_test
   activation_functions_test.cpp
-  adaboost_test.cpp
-  adam_test.cpp
   ada_delta_test.cpp
   ada_grad_test.cpp
+  adaboost_test.cpp
+  adam_test.cpp
   akfn_test.cpp
   aknn_test.cpp
   ann_layer_test.cpp
-  armadillo_svd_test.cpp
   arma_extend_test.cpp
+  armadillo_svd_test.cpp
   async_learning_test.cpp
   aug_lagrangian_test.cpp
   augmented_rnns_tasks_test.cpp
   binarize_test.cpp
   block_krylov_svd_test.cpp
   cf_test.cpp
+  cli_binding_test.cpp
   cli_test.cpp
   cmaes_test.cpp
-  cli_binding_test.cpp
   cne_test.cpp
-  convolutional_network_test.cpp
   convolution_test.cpp
+  convolutional_network_test.cpp
   cosine_tree_test.cpp
   cv_test.cpp
   dbscan_test.cpp
@@ -55,14 +55,22 @@ add_executable(mlpack_test
   lars_test.cpp
   lbfgs_test.cpp
   lin_alg_test.cpp
-  linear_regression_test.cpp
   line_search_test.cpp
+  linear_regression_test.cpp
   load_save_test.cpp
   local_coordinate_coding_test.cpp
-  logistic_regression_test.cpp
   log_test.cpp
+  logistic_regression_test.cpp
   lrsdp_test.cpp
   lsh_test.cpp
+  main_tests/decision_tree_test.cpp
+  main_tests/emst_test.cpp
+  main_tests/linear_regression_test.cpp
+  main_tests/pca_test.cpp
+  main_tests/preprocess_binarize_test.cpp
+  main_tests/preprocess_imputer_test.cpp
+  main_tests/preprocess_split_test.cpp
+  main_tests/test_helper.hpp
   math_test.cpp
   matrix_completion_test.cpp
   maximal_inputs_test.cpp
@@ -79,9 +87,9 @@ add_executable(mlpack_test
   parallel_sgd_test.cpp
   pca_test.cpp
   perceptron_test.cpp
-  python_binding_test.cpp
   prefixedoutstream_test.cpp
   proximal_test.cpp
+  python_binding_test.cpp
   q_learning_test.cpp
   qdafn_test.cpp
   quic_svd_test.cpp
@@ -98,12 +106,12 @@ add_executable(mlpack_test
   sa_test.cpp
   scd_test.cpp
   sdp_primal_dual_test.cpp
-  serialization.hpp
   serialization.cpp
+  serialization.hpp
   serialization_test.cpp
-  sgdr_test.cpp
-  sgd_test.cpp
   sfinae_test.cpp
+  sgd_test.cpp
+  sgdr_test.cpp
   smorms3_test.cpp
   snapshot_ensembles.cpp
   softmax_regression_test.cpp
@@ -116,20 +124,13 @@ add_executable(mlpack_test
   svd_batch_test.cpp
   svd_incremental_test.cpp
   termination_policy_test.cpp
+  test_tools.hpp
   timer_test.cpp
   tree_test.cpp
   tree_traits_test.cpp
   ub_tree_test.cpp
   union_find_test.cpp
   vantage_point_tree_test.cpp
-  main_tests/test_helper.hpp
-  main_tests/emst_test.cpp
-  main_tests/decision_tree_test.cpp
-  main_tests/linear_regression_test.cpp
-  main_tests/pca_test.cpp
-  main_tests/preprocess_binarize_test.cpp
-  main_tests/preprocess_imputer_test.cpp
-  main_tests/preprocess_split_test.cpp
 )
 
 # Link dependencies of test executable.

src/mlpack/tests/svd_batch_test.cpp

@@ -14,7 +14,7 @@
 #include <mlpack/methods/amf/update_rules/svd_batch_learning.hpp>
 #include <mlpack/methods/amf/init_rules/random_init.hpp>
 #include <mlpack/methods/amf/init_rules/average_init.hpp>
-#include <mlpack/methods/amf/termination_policies/validation_RMSE_termination.hpp>
+#include <mlpack/methods/amf/termination_policies/validation_rmse_termination.hpp>
 #include <mlpack/methods/amf/termination_policies/simple_tolerance_termination.hpp>
 
 #include <boost/test/unit_test.hpp>

src/mlpack/tests/svd_incremental_test.cpp

@@ -18,7 +18,7 @@
 #include <mlpack/methods/amf/termination_policies/incomplete_incremental_termination.hpp>
 #include <mlpack/methods/amf/termination_policies/complete_incremental_termination.hpp>
 #include <mlpack/methods/amf/termination_policies/simple_tolerance_termination.hpp>
-#include <mlpack/methods/amf/termination_policies/validation_RMSE_termination.hpp>
+#include <mlpack/methods/amf/termination_policies/validation_rmse_termination.hpp>
 
 #include <boost/test/unit_test.hpp>
 #include "test_tools.hpp"