Add Serializable object and drop Wrapped classes

refactor R installation

examples/meta/generator/translate.py

@@ -178,8 +178,8 @@ def injectVarsStoring(self, statementList, programName, varsToStore):
         """ Injects statements at the end of the program that perform variable
             storing
         """
-        storage = "__sg_storage"
-        storageFile = "__sg_storage_file"
+        storage = "sg_storage"
+        storageFile = "sg_storage_file"
 
         # TODO: handle directories
         storageFilename = {
@@ -188,7 +188,7 @@ def injectVarsStoring(self, statementList, programName, varsToStore):
         # 'w'
         storageFilemode = {"Expr": {"CharLiteral": 'w'}}
         storageComment = {"Comment": " Serialize output for integration testing (automatically generated)"}
-        storageInit = {"Init": [{"ObjectType": "WrappedObjectArray"},
+        storageInit = {"Init": [{"ObjectType": "DynamicObjectArray"},
                                 {"Identifier": storage},
                                 {"ArgumentList": []}]}
         storageFileInit = {
@@ -214,16 +214,20 @@ def injectVarsStoring(self, statementList, programName, varsToStore):
             # i.e. one key
             # python2/3 compatible key accessing
             sgType = vartypeAST[list(vartypeAST.keys())[0]]
-
             assert sgType in getBasicTypesToStore() or sgType in getSGTypesToStore()
-            if sgType in getBasicTypesToStore():
-                methodNameSuffix = sgType
-            elif sgType in getSGTypesToStore():
-                methodNameSuffix = getSGTypeToStoreMethodName(sgType)
-
+
+            if "cpp" in self.targetDict["FileExtension"]:
+                methodNameSuffix = "<%s>" % self.targetDict["Type"][sgType]
+            else:
+                if sgType in getBasicTypesToStore():
+                    methodNameSuffix = sgType
+                elif sgType in getSGTypesToStore():
+                    methodNameSuffix = getSGTypeToStoreMethodName(sgType)
+                methodNameSuffix = "_%s" % methodNameSuffix
+
             methodCall = {
                 "MethodCall": [{"Identifier": storage},
-                               {"Identifier": "append_wrapped_%s" % methodNameSuffix},
+                               {"Identifier": "append_element%s" % methodNameSuffix},
                                {"ArgumentList": [varnameIdentifierExpr,
                                                  varnameExpr]}]
             }

src/interfaces/r/CMakeLists.txt

@@ -11,6 +11,28 @@ ENDIF()
 GENERATE_INTERFACE_TARGET(r ${CMAKE_CURRENT_SOURCE_DIR} ${R_LIBRARIES})
 set_target_properties(interface_r PROPERTIES PREFIX "")
 
+EXECUTE_PROCESS(COMMAND ${R_EXECUTABLE} --slave -e "with(R.version, cat(sprintf('%s.%s', major, minor)))"
+	OUTPUT_VARIABLE R_VERSION
+	OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+EXECUTE_PROCESS(COMMAND ${R_EXECUTABLE} --slave -e "cat(R.version\\$platform)"
+	OUTPUT_VARIABLE PLATFORM
+	OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+EXECUTE_PROCESS(COMMAND ${R_EXECUTABLE} --slave -e "cat(.Platform\\$OS.type)"
+	OUTPUT_VARIABLE OSTYPE
+	OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} -c "from time import gmtime, strftime; print(strftime("%Y-%m-%d %H:%M:%S", gmtime()))"
+	OUTPUT_VARIABLE DATE
+	OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/DESCRIPTION.in ${CMAKE_CURRENT_BINARY_DIR}/DESCRIPTION @ONLY)
+
 ADD_CUSTOM_COMMAND(TARGET interface_r
 	POST_BUILD
 	COMMAND echo 'wd="${CMAKE_CURRENT_BINARY_DIR}" \; setwd( wd ) \; f="shogun.R" \; fdata="shogun.RData" \; source( f ) \; save( list=ls( all=TRUE ) , file=fdata , compress=TRUE ) \; q( save="no" ) \;' | ${R_EXECUTABLE} --silent --no-save
@@ -26,6 +48,10 @@ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/shogun.RData
 	DESTINATION ${R_COMPONENT_LIB_PATH}/shogun/R
 	COMPONENT r)
 
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/DESCRIPTION ${CMAKE_CURRENT_BINARY_DIR}/NAMESPACE
+	DESTINATION ${R_COMPONENT_LIB_PATH}/shogun
+	COMPONENT r)
+
 install(CODE "FILE(MAKE_DIRECTORY \$ENV{DESTDIR}/${R_COMPONENT_LIB_PATH}/shogun/Meta)")
 
 install(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/r-install.sh \$ENV{DESTDIR}/${R_COMPONENT_LIB_PATH} shogun so saveRDS WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})")

src/interfaces/r/DESCRIPTION.in

@@ -0,0 +1,26 @@
+Package: shogun
+Version: @VERSION@
+Date: @DATE@
+Title: The SHOGUN Machine Learning Toolbox
+Author: Shogun Team
+Maintainer: Shogun Team <shogun-team@shogun-toolbox.org>
+Depends: R (>= 2.10.0)
+Suggests:
+Description: SHOGUN - is a new machine learning toolbox with focus on large
+        scale kernel methods and especially on Support Vector Machines (SVM) with focus
+        to bioinformatics. It provides a generic SVM object interfacing to several
+        different SVM implementations. Each of the SVMs can be combined with a variety
+        of the many kernels implemented. It can deal with weighted linear combination
+        of a number of sub-kernels, each of which not necessarily working on the same
+        domain, where  an optimal sub-kernel weighting can be learned using Multiple
+        Kernel Learning.  Apart from SVM 2-class classification and regression
+        problems, a number of linear methods like Linear Discriminant Analysis (LDA),
+        Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to
+        train hidden markov models are implemented. The input feature-objects can be
+        dense, sparse or strings and of type int/short/double/char and can be converted
+        into different feature types. Chains of preprocessors (e.g.  substracting the
+        mean) can be attached to each feature object allowing for on-the-fly
+        pre-processing.
+License: GPL Version 3 or later.
+URL: http://www.shogun-toolbox.org
+Built: @R_VERSION@; @PLATFORM@; @OSTYPE@;

src/interfaces/r/NAMESPACE

@@ -0,0 +1 @@
+useDynLib(shogun, .registration = TRUE)

src/interfaces/r/r-install.sh

@@ -9,35 +9,6 @@ DATE="`date '+%Y-%m-%d %H:%M:%S'`"
 PKGFILE="$1/$2/Meta/package.rds"
 SAVERDS="$4"
 
-cat >"$1/$2/DESCRIPTION" <<EOF
-Package: $2
-Version: $VERSION
-Date: $DATE
-Title: The SHOGUN Machine Learning Toolbox
-Author: Shogun Team
-Maintainer: Shogun Team <shogun-team@shogun-toolbox.org>
-Depends: R (>= 2.10.0)
-Suggests:
-Description: SHOGUN - is a new machine learning toolbox with focus on large
-        scale kernel methods and especially on Support Vector Machines (SVM) with focus
-        to bioinformatics. It provides a generic SVM object interfacing to several
-        different SVM implementations. Each of the SVMs can be combined with a variety
-        of the many kernels implemented. It can deal with weighted linear combination
-        of a number of sub-kernels, each of which not necessarily working on the same
-        domain, where  an optimal sub-kernel weighting can be learned using Multiple
-        Kernel Learning.  Apart from SVM 2-class classification and regression
-        problems, a number of linear methods like Linear Discriminant Analysis (LDA),
-        Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to
-        train hidden markov models are implemented. The input feature-objects can be
-        dense, sparse or strings and of type int/short/double/char and can be converted
-        into different feature types. Chains of preprocessors (e.g.  substracting the
-        mean) can be attached to each feature object allowing for on-the-fly
-        pre-processing.
-License: GPL Version 3 or later.
-URL: http://www.shogun-toolbox.org
-Built: $RVERSION; $PLATFORM; $OSTYPE;
-EOF
-
 echo "x=structure(list(DESCRIPTION = c(Package='$2',\
 		Version=\"$VERSION\",\
 		Date=\"$DATE\",\
@@ -58,10 +29,6 @@ echo "x=structure(list(DESCRIPTION = c(Package='$2',\
 # R-MODULAR
 echo "Installing modular shogun interface for R"
 
-cat >"$1/$2/NAMESPACE" <<EOF
-useDynLib(shogun, .registration = TRUE)
-EOF
-
 cat >"$1/$2/R/$2" <<EOF
 .packageName <- "$2"
 #$2 <- function(...) .External("$2",...,PACKAGE="$2")

src/interfaces/swig/Library.i

@@ -22,7 +22,6 @@
 %rename(Hash) CHash;
 %rename(StructuredData) CStructuredData;
 %rename(DynamicObjectArray) CDynamicObjectArray;
-%rename(WrappedObjectArray) CWrappedObjectArray;
 %rename(Tokenizer) CTokenizer;
 %rename(DelimiterTokenizer) CDelimiterTokenizer;
 %rename(NGramTokenizer) CNGramTokenizer;
@@ -399,7 +398,17 @@ namespace shogun
 %include <shogun/lib/StructuredDataTypes.h>
 %include <shogun/lib/StructuredData.h>
 %include <shogun/lib/DynamicObjectArray.h>
-%include <shogun/lib/WrappedObjectArray.h>
+namespace shogun
+{
+    /* Specialize DynamicObjectArray::append_element function */
+    %template(append_element_real) CDynamicObjectArray::append_element<float64_t>;
+    %template(append_element_float) CDynamicObjectArray::append_element<float32_t>;
+    %template(append_element_int) CDynamicObjectArray::append_element<int32_t>;
+    %template(append_element_real_vector) CDynamicObjectArray::append_element<SGVector<float64_t>>;
+    %template(append_element_float_vector) CDynamicObjectArray::append_element<SGVector<float32_t>>;
+    %template(append_element_real_matrix) CDynamicObjectArray::append_element<SGMatrix<float64_t>>;
+    %template(append_element_float_matrix) CDynamicObjectArray::append_element<SGMatrix<float32_t>>;
+}
 %include <shogun/lib/IndexBlock.h>
 %include <shogun/lib/IndexBlockRelation.h>
 %include <shogun/lib/IndexBlockGroup.h>

src/interfaces/swig/Library_includes.i

@@ -21,7 +21,6 @@
 #include <shogun/lib/StructuredDataTypes.h>
 #include <shogun/lib/StructuredData.h>
 #include <shogun/lib/DynamicObjectArray.h>
-#include <shogun/lib/WrappedObjectArray.h>
 #include <shogun/lib/IndexBlock.h>
 #include <shogun/lib/IndexBlockRelation.h>
 #include <shogun/lib/IndexBlockGroup.h>

src/shogun/lib/WrappedSGMatrix.h → src/shogun/io/Serializable.h

@@ -2,7 +2,7 @@
  * -*- coding: utf-8 -*-
  * vim: set fileencoding=utf-8
  *
- * Copyright (c) 2016, Shogun-Toolbox e.V. <shogun-team@shogun-toolbox.org>
+ * Copyright (c) 2017, Shogun-Toolbox e.V. <shogun-team@shogun-toolbox.org>
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -31,81 +31,70 @@
  * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
  * POSSIBILITY OF SUCH DAMAGE.
  *
- * Authors: Heiko Strathmann
  */
-#ifdef USE_META_INTEGRATION_TESTS
-#ifndef WRAPPED_SGMATRIX_H__
-#define WRAPPED_SGMATRIX_H__
+#ifndef SHOGUN_SERIALIZABLE_H__
+#define SHOGUN_SERIALIZABLE_H__
 
 #include <shogun/base/SGObject.h>
-#include <shogun/lib/SGString.h>
-#include <shogun/lib/SGMatrix.h>
-
 
 namespace shogun
 {
 
-/** @brief Simple wrapper class that allows to store any Shogun SGMatrix<T>
- * in a CSGObject, and therefore to make it serializable. Using a template
- * argument that is not a Shogun parameter will cause a compile error when
- * trying to register the passed value as a parameter in the constructors.
+template<typename T>
+struct extract_value_type
+{
+	typedef T value_type;
+};
+
+template<template<typename, typename ...> class X, typename T, typename ...Args>
+struct extract_value_type<X<T, Args...>>
+{
+	typedef T value_type;
+};
+
+/** @brief A trait that makes a none SGObject SG-serializable
+ * This only works with classes derived of SGReferencedData (SGVector, SGMatrix etc)
+ * and fundamental types (std::is_arithmetic)
  */
-template<class T> class CWrappedSGMatrix: public CSGObject
+template<class T> class CSerializable: public CSGObject
 {
 public:
 	/** Default constructor. Do not use. */
-	CWrappedSGMatrix() : CSGObject()
+	CSerializable() : CSGObject()
 	{
-		set_generic<T>();
-		register_params();
+		init();
 	}
 
 	/** Constructor.
-	 * @param value Value to wrap as CSGObject.
+	 * @param value Value to serialize as CSGObject.
 	 * @param value_name Name under which value is registered.
 	*/
-	CWrappedSGMatrix(SGMatrix<T> value, const char* value_name="")
+	CSerializable(T value, const char* value_name="")
 	{
-		set_generic<T>();
-		register_params();
+		init();
 		m_value = value;
 		m_value_name = value_name;
 	}
 
 	/** @return name of the CSGObject, without C prefix */
-	virtual const char* get_name() const { return "WrappedSGMatrix"; }
+	virtual const char* get_name() const { return "Serializable"; }
 
 private:
-	void register_params()
+	void init()
 	{
-	    m_value_name = "Unnamed";
-	    m_value = SGMatrix<T>();
-	    
-		SG_ADD(&m_value, "value", "Wrapped value", MS_NOT_AVAILABLE);
+		set_generic<typename extract_value_type<T>::value_type>();
+		m_value_name = "Unnamed";
+
+		SG_ADD(&m_value, "value", "Serialized value", MS_NOT_AVAILABLE);
 	}
 
 protected:
-	/** Wrapped value. */
-	SGMatrix<T> m_value;
+	/** Serialized value. */
+	T m_value;
 
-	/** Name of wrapped value */
+	/** Name of serialized value */
 	const char* m_value_name;
 };
 
-template class CWrappedSGMatrix<bool>;
-template class CWrappedSGMatrix<char>;
-template class CWrappedSGMatrix<int8_t>;
-template class CWrappedSGMatrix<uint8_t>;
-template class CWrappedSGMatrix<int16_t>;
-template class CWrappedSGMatrix<uint16_t>;
-template class CWrappedSGMatrix<int32_t>;
-template class CWrappedSGMatrix<uint32_t>;
-template class CWrappedSGMatrix<int64_t>;
-template class CWrappedSGMatrix<uint64_t>;
-template class CWrappedSGMatrix<float32_t>;
-template class CWrappedSGMatrix<float64_t>;
-template class CWrappedSGMatrix<floatmax_t>;
-
 };
-#endif // WRAPPED_SGMATRIX_H__
-#endif // USE_META_INTEGRATION_TESTS
+#endif // SHOGUN_SERIALIZABLE_H_

src/shogun/lib/DynamicObjectArray.h

@@ -17,6 +17,7 @@
 #include <shogun/base/SGObject.h>
 #include <shogun/base/DynArray.h>
 #include <shogun/base/Parameter.h>
+#include <shogun/io/Serializable.h>
 
 namespace shogun
 {
@@ -277,6 +278,17 @@ class CDynamicObjectArray : public CSGObject
 			return success;
 		}
 
+		template <typename T>
+		inline bool append_element(typename std::enable_if<!std::is_base_of<CSGObject, std::remove_pointer<T>>::value, T>::type e, const char* name="")
+		{
+			auto serializedElement = new CSerializable<T>(e, name);
+			bool success = m_array.append_element(serializedElement);
+			if (success)
+				SG_REF(serializedElement);
+
+			return success;
+		}
+
 		/** append array element to the end of array
 		 *
 		 * @param e element to append