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openturns · Nov 2, 2023 · f55063e · f55063e
1 parent 2da5643
commit f55063e
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diff --git a/.ci_support/run_docker_linux.sh b/.ci_support/run_docker_linux.sh
@@ -18,6 +18,6 @@ uid=$1
 gid=$2
 if test -n "${uid}" -a -n "${gid}"
 then
-  sudo cp -r ~/.local/share/*/doc/html /io
+  sudo cp -r ~/.local/share/doc/*/html /io
   sudo chown -R ${uid}:${gid} /io/html
 fi
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,14 +1,14 @@
 cmake_minimum_required (VERSION 3.13)
 
-option ( BUILD_PYTHON                 "Build the python module for the library"                               ON )
-option (USE_SPHINX                    "Use sphinx for documentation"                                          ON)
-option ( BUILD_SHARED_LIBS            "Build shared libraries"                                                ON )
-option ( USE_INTERNAL_LIBSVM          "Use internal LibSVM"                                                   ON )
+option (BUILD_PYTHON                 "Build the python module for the library"                               ON)
+option (USE_SPHINX                   "Use sphinx for documentation"                                          ON)
+option (BUILD_SHARED_LIBS            "Build shared libraries"                                                ON)
+option (USE_EXTERNAL_LIBSVM          "Use internal LibSVM"                                                   OFF)
 
 # By default, build in Release mode. Must appear before project() command
-set( CMAKE_BUILD_TYPE Release CACHE STRING "Build type")
+set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type")
 
-project (OTSVM)
+project (otsvm)
 
 string (TOLOWER ${CMAKE_PROJECT_NAME} PACKAGE_NAME)
 
@@ -34,26 +34,28 @@ if (NOT DEFINED OPENTURNS_PYTHON_MODULE_PATH)
   set (OPENTURNS_PYTHON_MODULE_PATH ${OPENTURNS_PYTHON3_MODULE_PATH})
 endif ()
 
+if (USE_EXTERNAL_LIBSVM)
+  find_package (LibSVM 3.24 REQUIRED)
+endif ()
+
 if (NOT BUILD_SHARED_LIBS)
-  list ( APPEND OTSVM_DEFINITIONS "-DOTSVM_STATIC" )
+  list (APPEND OTSVM_DEFINITIONS "-DOTSVM_STATIC")
 endif ()
-add_definitions ( ${OTSVM_DEFINITIONS} )
+add_definitions (${OTSVM_DEFINITIONS})
 
 if (MSVC)
   # Disable some warnings
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4197 /wd4244 /wd4251 /wd4267 /wd4996")
 endif ()
 
-if (NOT DEFINED CMAKE_INSTALL_LIBDIR)
-  set (CMAKE_INSTALL_LIBDIR lib${LIB_SUFFIX})
-endif ()
+include (GNUInstallDirs)
 
 set (OTSVM_LIBRARY_PATH ${CMAKE_INSTALL_LIBDIR})
-set (OTSVM_INCLUDE_PATH include)
+set (OTSVM_INCLUDE_PATH ${CMAKE_INSTALL_INCLUDEDIR})
 set (OTSVM_SWIG_INCLUDE_DIRS ${OTSVM_INCLUDE_PATH}/${PACKAGE_NAME}/swig)
-set (OTSVM_DATA_PATH share)
-set (OTSVM_CONFIG_CMAKE_PATH ${CMAKE_INSTALL_LIBDIR}/cmake/otsvm)
-set (OTSVM_DOC_PATH share/${PACKAGE_NAME}/doc)
+set (OTSVM_DATA_PATH ${CMAKE_INSTALL_DATAROOTDIR})
+set (OTSVM_CONFIG_CMAKE_PATH ${CMAKE_INSTALL_LIBDIR}/cmake/ottemplate)
+set (OTSVM_DOC_PATH ${CMAKE_INSTALL_DOCDIR})
 
 set (CMAKE_CXX_STANDARD 11)
 

diff --git a/cmake/FindLibSVM.cmake b/cmake/FindLibSVM.cmake
@@ -1,6 +1,6 @@
 # - Find LibSVM
 # LibSVM is a Library for Support Vector Machines
-# available at http://www.csie.ntu.edu.tw/~cjlin/libsvm/
+# available at https://github.com/cjlin1/libsvm
 #
 # The module defines the following variables:
 #  LIBSVM_FOUND - the system has LibSVM
@@ -10,12 +10,11 @@
 #  LIBSVM_LIBRARIES - aditional libraries
 #  LIBSVM_MAJOR_VERSION - major version
 #  LIBSVM_MINOR_VERSION - minor version
-#  LIBSVM_PATCH_VERSION - patch version
 #  LIBSVM_VERSION_STRING - version (ex. 2.9.0)
 #  LIBSVM_ROOT_DIR - root dir (ex. /usr/local)
 
 #=============================================================================
-# Copyright 2010-2013, Julien Schueller
+# Copyright 2010-2023, Julien Schueller
 # All rights reserved.
 # 
 # Redistribution and use in source and binary forms, with or without
@@ -44,7 +43,7 @@
 #=============================================================================
 
 # set LIBSVM_INCLUDE_DIR
-find_path ( LIBSVM_INCLUDE_DIR
+find_path (LIBSVM_INCLUDE_DIR
   NAMES
     svm.h
   PATH_SUFFIXES
@@ -54,43 +53,39 @@ find_path ( LIBSVM_INCLUDE_DIR
 
 
 # set LIBSVM_INCLUDE_DIRS
-if ( LIBSVM_INCLUDE_DIR )
-  set ( LIBSVM_INCLUDE_DIRS ${LIBSVM_INCLUDE_DIR} )
-endif ()
-
+set (LIBSVM_INCLUDE_DIRS ${LIBSVM_INCLUDE_DIR})
 
 # version
-set ( _VERSION_FILE ${LIBSVM_INCLUDE_DIR}/svm.h )
-if ( EXISTS ${_VERSION_FILE} )
+set (_VERSION_FILE ${LIBSVM_INCLUDE_DIR}/svm.h)
+if (EXISTS ${_VERSION_FILE})
   # LIBSVM_VERSION_STRING macro defined in svm.h since version 2.8.9
-  file ( STRINGS ${_VERSION_FILE} _VERSION_STRING REGEX ".*define[ ]+LIBSVM_VERSION[ ]+[0-9]+.*" )
-  if ( _VERSION_STRING )
-    string ( REGEX REPLACE ".*LIBSVM_VERSION[ ]+([0-9]+)" "\\1" _VERSION_NUMBER "${_VERSION_STRING}" )
-    math ( EXPR LIBSVM_MAJOR_VERSION "${_VERSION_NUMBER} / 100" )
-    math ( EXPR LIBSVM_MINOR_VERSION "(${_VERSION_NUMBER} % 100 ) / 10" )
-    math ( EXPR LIBSVM_PATCH_VERSION "${_VERSION_NUMBER} % 10" )
-    set ( LIBSVM_VERSION_STRING "${LIBSVM_MAJOR_VERSION}.${LIBSVM_MINOR_VERSION}.${LIBSVM_PATCH_VERSION}" )
+  file (STRINGS ${_VERSION_FILE} _VERSION_STRING REGEX ".*define[ ]+LIBSVM_VERSION[ ]+[0-9]+.*")
+  if (_VERSION_STRING)
+    string (REGEX REPLACE ".*LIBSVM_VERSION[ ]+([0-9]+)" "\\1" _VERSION_NUMBER "${_VERSION_STRING}")
+    math (EXPR LIBSVM_MAJOR_VERSION "${_VERSION_NUMBER} / 100")
+    math (EXPR LIBSVM_MINOR_VERSION "(${_VERSION_NUMBER} % 100 )")
+    set (LIBSVM_VERSION_STRING "${LIBSVM_MAJOR_VERSION}.${LIBSVM_MINOR_VERSION}")
   endif ()
 endif ()
 
 
 # check version
-set ( _LIBSVM_VERSION_MATCH TRUE )
-if ( LibSVM_FIND_VERSION AND LIBSVM_VERSION_STRING )
-  if ( LibSVM_FIND_VERSION_EXACT )
-    if ( NOT LibSVM_FIND_VERSION VERSION_EQUAL LIBSVM_VERSION_STRING )
-      set ( _LIBSVM_VERSION_MATCH FALSE )
+set (_LIBSVM_VERSION_MATCH TRUE)
+if (LibSVM_FIND_VERSION AND LIBSVM_VERSION_STRING)
+  if (LibSVM_FIND_VERSION_EXACT)
+    if (NOT LibSVM_FIND_VERSION VERSION_EQUAL LIBSVM_VERSION_STRING)
+      set (_LIBSVM_VERSION_MATCH FALSE)
     endif ()
   else ()
-    if ( LIBSVM_VERSION_STRING VERSION_LESS LibSVM_FIND_VERSION )
-      set ( _LIBSVM_VERSION_MATCH FALSE )
+    if (LIBSVM_VERSION_STRING VERSION_LESS LibSVM_FIND_VERSION)
+      set (_LIBSVM_VERSION_MATCH FALSE)
     endif ()
   endif ()
 endif ()
 
 
 # set LIBSVM_LIBRARY
-find_library ( LIBSVM_LIBRARY
+find_library (LIBSVM_LIBRARY
   NAMES
     svm
   DOC
@@ -99,30 +94,26 @@ find_library ( LIBSVM_LIBRARY
 
 
 # set LIBSVM_LIBRARIES
-set ( LIBSVM_LIBRARIES ${LIBSVM_LIBRARY} )
+set (LIBSVM_LIBRARIES ${LIBSVM_LIBRARY})
 
 # link with math library on unix
-if ( UNIX )
-  list ( APPEND LIBSVM_LIBRARIES "-lm" )
+if (UNIX)
+  list (APPEND LIBSVM_LIBRARIES "m")
 endif ()
 
 
 # try to guess root dir from include dir
-if ( LIBSVM_INCLUDE_DIR )
-  string ( REGEX REPLACE "(.*)/include.*" "\\1" LIBSVM_ROOT_DIR ${LIBSVM_INCLUDE_DIR} )
+if (LIBSVM_INCLUDE_DIR)
+  string (REGEX REPLACE "(.*)/include.*" "\\1" LIBSVM_ROOT_DIR ${LIBSVM_INCLUDE_DIR})
 # try to guess root dir from library dir
-elseif ( LIBSVM_LIBRARY )
-  string ( REGEX REPLACE "(.*)/lib[/|32|64].*" "\\1" LIBSVM_ROOT_DIR ${LIBSVM_LIBRARY} )
+elseif (LIBSVM_LIBRARY)
+  string (REGEX REPLACE "(.*)/lib[/|32|64].*" "\\1" LIBSVM_ROOT_DIR ${LIBSVM_LIBRARY})
 endif ()
 
 
 # handle REQUIRED and QUIET options
-include ( FindPackageHandleStandardArgs )
-if ( CMAKE_VERSION VERSION_LESS 2.8.3 )
-  find_package_handle_standard_args ( LibSVM DEFAULT_MSG LIBSVM_LIBRARY LIBSVM_INCLUDE_DIR _LIBSVM_VERSION_MATCH )
-else ()
-  find_package_handle_standard_args ( LibSVM REQUIRED_VARS LIBSVM_LIBRARY LIBSVM_INCLUDE_DIR _LIBSVM_VERSION_MATCH VERSION_VAR LIBSVM_VERSION_STRING )
-endif ()
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (LibSVM REQUIRED_VARS LIBSVM_LIBRARY LIBSVM_INCLUDE_DIR _LIBSVM_VERSION_MATCH VERSION_VAR LIBSVM_VERSION_STRING)
 
 mark_as_advanced (
   LIBSVM_LIBRARY
@@ -133,5 +124,4 @@ mark_as_advanced (
   LIBSVM_VERSION_STRING
   LIBSVM_MAJOR_VERSION
   LIBSVM_MINOR_VERSION
-  LIBSVM_PATCH_VERSION
 )
diff --git a/lib/src/CMakeLists.txt b/lib/src/CMakeLists.txt
@@ -1,6 +1,6 @@
-
-if ( NOT LIBSVM_FOUND )
-  add_subdirectory ( LibSVM )
+if (NOT LIBSVM_FOUND)
+  add_subdirectory (LibSVM)
+  include_directories (${CMAKE_CURRENT_SOURCE_DIR}/LibSVM/otsvm)
 endif ()
 
 ot_add_current_dir_to_include_dirs ()
@@ -54,9 +54,14 @@ endif ()
 if ( NOT DEFINED LIB_SOVERSION ) 
   set ( LIB_SOVERSION 0 )
 endif ()
-set_target_properties ( otsvm PROPERTIES VERSION ${LIB_VERSION} )
-set_target_properties ( otsvm PROPERTIES SOVERSION ${LIB_SOVERSION} )
-target_link_libraries (otsvm ${OPENTURNS_LIBRARY})
+set_target_properties (otsvm PROPERTIES VERSION ${LIB_VERSION})
+set_target_properties (otsvm PROPERTIES SOVERSION ${LIB_SOVERSION})
+target_link_libraries (otsvm PUBLIC ${OPENTURNS_LIBRARY})
+
+if (LIBSVM_FOUND)
+  target_link_libraries (otsvm PRIVATE ${LIBSVM_LIBRARIES})
+  target_include_directories (otsvm PRIVATE ${LIBSVM_INCLUDE_DIRS})
+endif ()
 
 # Add targets to the build-tree export set
 export (TARGETS otsvm FILE ${PROJECT_BINARY_DIR}/OTSVM-Targets.cmake)
@@ -73,3 +78,4 @@ install(TARGETS otsvm
         ARCHIVE DESTINATION ${OTSVM_LIBRARY_PATH}
 )
 
+
diff --git a/lib/src/ExponentialRBF.cxx b/lib/src/ExponentialRBF.cxx
@@ -4,19 +4,18 @@
  *
  *  Copyright 2014-2023 Phimeca
  *
- *  This library is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public
- *  License as published by the Free Software Foundation; either
- *  version 2.1 of the License.
+ *  This library is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
  *
- *  This library is distributed in the hope that it will be useful
+ *  This library is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
  *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this library; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this library.  If not, see <http://www.gnu.org/licenses/>.
  *
  */
 #include "otsvm/ExponentialRBF.hxx"

diff --git a/lib/src/KMeansClustering.cxx b/lib/src/KMeansClustering.cxx
@@ -34,27 +34,27 @@ void KMeansClustering::run()
   UnsignedInteger change = 0;
 
   Indices cluster(size);
-  Sample means(k_ , dimension);
+  Sample means(k_, dimension);
 
   const Point min(inputSample_.getMin());
   const Point max(inputSample_.getMax());
 
-  for (UnsignedInteger i = 0 ; i < dimension ; ++ i)
+  for (UnsignedInteger i = 0; i < dimension; ++ i)
   {
     Uniform uniform(min[i], max[i]);
     for (UnsignedInteger j = 0 ; j < k_; ++ j)
     {
-      means(j , i) = uniform.getRealization()[0];
+      means(j, i) = uniform.getRealization()[0];
     }
   }
 
   while (!change)
   {
-    for (UnsignedInteger i = 0 ; i < size; ++ i)
+    for (UnsignedInteger i = 0; i < size; ++ i)
     {
       Scalar distancemin = ( inputSample_[i] - means[0] ).norm();
 
-      for (UnsignedInteger j = 1 ; j < k_; ++j)
+      for (UnsignedInteger j = 1; j < k_; ++ j)
       {
         const Scalar distance = ( inputSample_[i] - means[j] ).norm();