#127 - restructure

.gitignore

@@ -1,6 +1,6 @@
 _*.so
 bin/
-build/
+build
 
 # All hidden files except for gitignore
 .*
@@ -40,12 +40,12 @@ doc/tex/**/*.blg
 
 
 # Doxygen generated files
-doc_cpp/
-!doc_cpp/mainpage.dox
+lib/doc/*
+!lib/doc/mainpage.dox
 
 # XCode Project
 XCode/
 
 # Build directory for C++ tests
 cpp_test_build/
-tick/cmake-build-debug
+lib/cmake-build-debug

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "tick/third_party/cereal"]
-	path = tick/third_party/cereal
+[submodule "lib/third_party/cereal"]
+	path = lib/third_party/cereal
 	url = https://github.com/USCiLab/cereal.git

tick/CMakeLists.txt → lib/CMakeLists.txt

@@ -20,16 +20,7 @@ if (${BLAS_FOUND})
 endif()
 
 include_directories(
-        ${CMAKE_CURRENT_SOURCE_DIR}/base/src
-        ${CMAKE_CURRENT_SOURCE_DIR}/base/array/src
-        ${CMAKE_CURRENT_SOURCE_DIR}/base/array_test/src
-        ${CMAKE_CURRENT_SOURCE_DIR}/random/src
-        ${CMAKE_CURRENT_SOURCE_DIR}/simulation/src
-        ${CMAKE_CURRENT_SOURCE_DIR}/optim/model/src
-        ${CMAKE_CURRENT_SOURCE_DIR}/optim/prox/src
-        ${CMAKE_CURRENT_SOURCE_DIR}/optim/solver/src
-        ${CMAKE_CURRENT_SOURCE_DIR}/inference/src
-        ${CMAKE_CURRENT_SOURCE_DIR}/preprocessing/src
+        ${CMAKE_CURRENT_SOURCE_DIR}/include
 )
 
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/third_party/cereal/include)
@@ -51,16 +42,17 @@ if (${TICK_REBUILD_LIBS})
     set(TICK_LIB_SOLVER     tick_solver)
 endif()
 
-add_subdirectory(base/src)
-add_subdirectory(base/array/src)
-add_subdirectory(base/array_test/src)
-add_subdirectory(random/src)
-add_subdirectory(simulation/src)
-add_subdirectory(optim/model/src)
-add_subdirectory(optim/prox/src)
-add_subdirectory(optim/solver/src)
-add_subdirectory(inference/src)
-add_subdirectory(preprocessing/src)
+
+add_subdirectory(src/cpp/base)
+add_subdirectory(src/cpp/array)
+add_subdirectory(src/cpp/array_test)
+add_subdirectory(src/cpp/random)
+add_subdirectory(src/cpp/simulation)
+add_subdirectory(src/cpp/optim/model)
+add_subdirectory(src/cpp/optim/prox)
+add_subdirectory(src/cpp/optim/solver)
+add_subdirectory(src/cpp/inference)
+add_subdirectory(src/cpp/preprocessing)
 
 find_package(GTest)
 
@@ -81,7 +73,7 @@ if (${GTEST_FOUND})
         ${TICK_BLAS_LIBRARIES})
 
     if(APPLE)
-        set(TICK_INSTALL_RPATH "${CMAKE_CURRENT_SOURCE_DIR}/base/build;${CMAKE_CURRENT_SOURCE_DIR}/base/array/build;${CMAKE_CURRENT_SOURCE_DIR}/optim/model/build;${CMAKE_CURRENT_SOURCE_DIR}/random/build;${CMAKE_CURRENT_SOURCE_DIR}/optim/prox/build;${CMAKE_CURRENT_SOURCE_DIR}/optim/solver/build;${CMAKE_CURRENT_SOURCE_DIR}/simulation/build")
+        set(TICK_INSTALL_RPATH "${CMAKE_CURRENT_SOURCE_DIR}/../tick/base/build;${CMAKE_CURRENT_SOURCE_DIR}/../tick/array/build;${CMAKE_CURRENT_SOURCE_DIR}/../tick/optim/model/build;${CMAKE_CURRENT_SOURCE_DIR}/../tick/random/build;${CMAKE_CURRENT_SOURCE_DIR}/../tick/optim/prox/build;${CMAKE_CURRENT_SOURCE_DIR}/../tick/optim/solver/build;${CMAKE_CURRENT_SOURCE_DIR}/../tick/simulation/build")
 
         set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
         set(CMAKE_INSTALL_RPATH "${TICK_INSTALL_RPATH}")
@@ -93,19 +85,19 @@ if (${GTEST_FOUND})
         set(TICK_TEST_LIBS ${TICK_TEST_LIBS} -lrt -ldl -lutil)
     endif(APPLE)
 
-    add_subdirectory(base/tests/src)
-    add_subdirectory(base/array/tests/src)
-    add_subdirectory(optim/model/tests/src)
-    add_subdirectory(optim/solver/tests/src)
-    add_subdirectory(simulation/tests/src)
+    add_subdirectory(src/cpp-test/base)
+    add_subdirectory(src/cpp-test/array)
+    add_subdirectory(src/cpp-test/optim/model)
+    add_subdirectory(src/cpp-test/optim/solver)
+    add_subdirectory(src/cpp-test/simulation)
 
     add_custom_target(check
-            COMMAND base/tests/src/tick_test_base
-            COMMAND base/array/tests/src/tick_test_array
-            COMMAND base/array/tests/src/tick_test_varray
-            COMMAND optim/model/tests/src/tick_test_model
-            COMMAND simulation/tests/src/tick_test_hawkes
-            COMMAND optim/solver/tests/src/tick_test_solver
+            COMMAND src/cpp-test/base/tick_test_base
+            COMMAND src/cpp-test/array/tick_test_array
+            COMMAND src/cpp-test/array/tick_test_varray
+            COMMAND src/cpp-test/optim/model/tick_test_model
+            COMMAND src/cpp-test/simulation/tick_test_hawkes
+            COMMAND src/cpp-test/optim/solver/tick_test_solver
             )
 else()
     message(STATUS "Testing in C++ NOT enabled")

Doxyfile → lib/Doxyfile

@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = ./doc_cpp
+OUTPUT_DIRECTORY       = ./doc
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and
@@ -758,11 +758,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  =   ./tick/base/src ./tick/base/utils/src \
-                           ./tick/base/array/src DOC_C/mainpage.dox \
-                           ./tick/simulation/src ./tick/optim/model/src \
-                           ./tick/random/src \
-                           ./tick/simulation/src/hawkes_kernels
+INPUT                  =   ./doc/mainpage.dox ./include/tick
 
 
 # This tag can be used to specify the character encoding of the source files
@@ -789,7 +785,7 @@ FILE_PATTERNS          =
 # be searched for input files as well.
 # The default value is: NO.
 
-RECURSIVE              = NO
+RECURSIVE              = YES
 
 # The EXCLUDE tag can be used to specify files and/or directories that should be
 # excluded from the INPUT source files. This way you can easily exclude a

tick/base/array/src/alloc.h → lib/include/tick/array/alloc.h

@@ -5,7 +5,7 @@
 
 /** @file */
 
-#include "debug.h"
+#include "tick/base/debug.h"
 
 #if defined(PYTHON_LINK)
 

tick/base/array/src/array.h → lib/include/tick/array/array.h

@@ -5,7 +5,7 @@
 
 /** @file */
 
-#include "defs.h"
+#include "tick/base/defs.h"
 #include "alloc.h"
 
 #include <iostream>

tick/base/array/src/array2d.h → lib/include/tick/array/array2d.h

@@ -5,7 +5,7 @@
 
 /** @file */
 
-#include "defs.h"
+#include "tick/base/defs.h"
 #include "alloc.h"
 #include "basearray2d.h"
 

tick/base/array/src/sarray.h → lib/include/tick/array/sarray.h

@@ -5,7 +5,7 @@
 
 /** @file */
 
-#include "defs.h"
+#include "tick/base/defs.h"
 
 #include <memory>
 #include "array.h"

tick/base/array/src/sparsearray.h → lib/include/tick/array/sparsearray.h

@@ -5,7 +5,7 @@
 
 /** @file */
 
-#include "defs.h"
+#include "tick/base/defs.h"
 #include "alloc.h"
 
 //////////////////////////////////////////////////////////////////////////////////////////////////

tick/base/array/src/vector_operations.h → lib/include/tick/array/vector_operations.h

@@ -5,7 +5,7 @@
 
 #include <numeric>
 
-#include "defs.h"
+#include "tick/base/defs.h"
 #include "promote.h"
 
 namespace tick {

tick/base/array_test/src/array_test.h → lib/include/tick/array_test/array_test.h

@@ -3,7 +3,7 @@
 
 // License: BSD 3 clause
 
-#include "base.h"
+#include "tick/base/base.h"
 
 //
 // Simple tests on ArrayDouble

tick/base/array_test/src/performance_test.h → lib/include/tick/array_test/performance_test.h

@@ -8,7 +8,7 @@
 // License: BSD 3 clause
 
 #include "timer.h"
-#include "base.h"
+#include "tick/base/base.h"
 
 
 extern void test_element_access();

tick/base/array_test/src/sbasearray_container.h → lib/include/tick/array_test/sbasearray_container.h

@@ -11,7 +11,7 @@
 
 // License: BSD 3 clause
 
-#include "base.h"
+#include "tick/base/base.h"
 
 extern void test_sbasearray_container_new(SBaseArrayDoublePtr a);
 extern void test_sbasearray_container_clear();

tick/base/array_test/src/timer.h → lib/include/tick/array_test/timer.h

@@ -11,7 +11,7 @@
 
 // License: BSD 3 clause
 
-#include "defs.h"
+#include "tick/base/defs.h"
 
 #include <iostream>
 #include <sstream>

tick/base/array_test/src/typemap_test.h → lib/include/tick/array_test/typemap_test.h

@@ -8,7 +8,7 @@
 // License: BSD 3 clause
 
 
-#include "base.h"
+#include "tick/base/base.h"
 
 /// @brief Test ArrayDouble Typemap
 

tick/base/array_test/src/varraycontainer.h → lib/include/tick/array_test/varraycontainer.h

@@ -7,8 +7,8 @@
 
 // License: BSD 3 clause
 
-#include "varray.h"
-#include "array.h"
+#include "tick/array/varray.h"
+#include "tick/array/array.h"
 #include "array_test.h"
 
 // Test classes in order to see if a varray is correctly deallocated

lib/include/tick/base/base.h

@@ -0,0 +1,38 @@
+//
+//  base.h
+//  TICK
+//
+//  Created by bacry on 21/12/2015.
+//  Copyright (c) 2015 bacry. All rights reserved.
+//
+
+#ifndef TICK_BASE_SRC_BASE_H_
+#define TICK_BASE_SRC_BASE_H_
+
+// License: BSD 3 clause
+
+#include "defs.h"
+#include "debug.h"
+
+#include "interruption.h"
+#include "time_func.h"
+#include "parallel/parallel.h"
+#include "math/t2exp.h"
+#include "math/normal_distribution.h"
+
+#include "tick/array/array.h"
+#include "tick/array/array2d.h"
+#include "tick/array/sparsearray.h"
+#include "tick/array/sparsearray2d.h"
+#include "tick/array/sarray.h"
+#include "tick/array/sarray2d.h"
+#include "tick/array/ssparsearray.h"
+#include "tick/array/dot.h"
+#include "tick/array/view.h"
+#include "tick/array/view2d.h"
+#include "tick/array/ssparsearray2d.h"
+#include "tick/array/sbasearray.h"
+#include "tick/array/sbasearray2d.h"
+#include "tick/array/varray.h"
+
+#endif  // TICK_BASE_SRC_BASE_H_

tick/base/src/math/normal_distribution.h → lib/include/tick/base/math/normal_distribution.h

@@ -7,7 +7,7 @@
 
 // License: BSD 3 clause
 
-#include "array.h"
+#include "tick/array/array.h"
 
 extern double standard_normal_cdf(double x);