Merge branch 'developing' into fix-ext-binding

CMakeLists.txt

@@ -0,0 +1,86 @@
+# 
+cmake_minimum_required(VERSION 3.6)
+
+# set the project name and version
+project(IOHexperimenter VERSION 1.0)
+SET(EXECUTABLE_OUTPUT_PATH "build/Cpp/")
+
+# add the executable
+add_executable(IOHprofiler_run_experiment build/Cpp/IOHprofiler_run_experiment.cpp)
+add_executable(IOHprofiler_run_problem build/Cpp/IOHprofiler_run_problem.cpp)
+add_executable(IOHprofiler_run_suite build/Cpp/IOHprofiler_run_suite.cpp)
+
+# specify the C++ standard
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+
+# specify the CXX FLAGS
+set(CMAKE_CXX_FLAGS "-g -std=c++11 -Wall -Wno-unused-variable -Wno-sign-compare -Wno-unused-function -O2")
+
+# set source file directorys and prepare for adding libraries.
+SET(PROBLEMS_BBOB_DIR "src/Problems/BBOB")
+FILE (GLOB PROBLEMS_BBOB_SRC "${PROBLEMS_BBOB_DIR}/*.cpp" "${PROBLEMS_BBOB_DIR}/*.hpp"  "${PROBLEMS_BBOB_DIR}/*.h")
+
+SET(PROBLEMS_BBOB_COMMON_DIR "src/Problems/BBOB/bbob_common_used_functions")
+FILE (GLOB PROBLEMS_BBOB_COMMON_SRC "${PROBLEMS_BBOB_COMMON_DIR}/*.cpp" "${PROBLEMS_BBOB_COMMON_DIR}/*.hpp" "${PROBLEMS_BBOB_COMMON_DIR}/*.h")
+
+SET(PROBLEMS_COMMON_DIR "src/Problems/common_used_functions")
+FILE (GLOB PROBLEMS_COMMON_SRC "${PROBLEMS_COMMON_DIR}/*.cpp" "${PROBLEMS_COMMON_DIR}/*.hpp" "${PROBLEMS_COMMON_DIR}/*.h")
+
+SET(PROBLEMS_PBO_DIR "src/Problems/PBO")
+FILE (GLOB PROBLEMS_PBO_SRC "${PROBLEMS_PBO_DIR}/*.cpp" "${PROBLEMS_PBO_DIR}/*.hpp" "${PROBLEMS_PBO_DIR}/*.h")
+
+SET(PROBLEMS_WMODEL_DIR "src/Problems/WModel")
+FILE (GLOB PROBLEMS_WMODEL_SRC "${PROBLEMS_WMODEL_DIR}/*.cpp" "${PROBLEMS_WMODEL_DIR}/*.hpp" "${PROBLEMS_WMODEL_DIR}/*.h")
+
+SET(SUITES_DIR "src/Suites")
+FILE (GLOB SUITES_SRC "${SUITES_DIR}/*.cpp" "${SUITES_DIR}/*.hpp" "${SUITES_DIR}/*.h")
+
+SET(TEMPLATE_DIR "src/Template")
+FILE (GLOB TEMPLATE_SRC "${TEMPLATE_DIR}/*.cpp" "${TEMPLATE_DIR}/*.hpp" "${TEMPLATE_DIR}/*.h")
+
+SET(TEMPLATE_EXPERIMENTS_DIR "src/Template/Experiments")
+FILE (GLOB TEMPLATE_EXPERIMENTS_SRC "${TEMPLATE_EXPERIMENTS_DIR}/*.cpp" "${TEMPLATE_EXPERIMENTS_DIR}/*.hpp" "${TEMPLATE_EXPERIMENTS_DIR}/*.h")
+
+SET(TEMPLATE_LOGGERS_DIR "src/Template/Loggers")
+FILE (GLOB TEMPLATE_LOGGERS_SRC "${TEMPLATE_LOGGERS_DIR}/*.cpp" "${TEMPLATE_LOGGERS_DIR}/*.hpp" "${TEMPLATE_LOGGERS_DIR}/*.h")
+
+SET(IOHEXPERIMENTER_SRC 
+  "${PROBLEMS_COMMON_SRC}"
+	"${PROBLEMS_BBOB_SRC}"
+	"${PROBLEMS_BBOB_COMMON_SRC}"
+	"${PROBLEMS_PBO_SRC}"
+  "${PROBLEMS_WMODEL_SRC}"
+  "${SUITES_SRC}"
+	"${TEMPLATE_SRC}"
+  "${TEMPLATE_EXPERIMENTS_SRC}"
+	"${TEMPLATE_LOGGERS_SRC}"
+)
+
+SET(IOHEXPERIMENTER_DIR 
+  "${PROBLEMS_COMMON_DIR}"
+  "${PROBLEMS_BBOB_DIR}"
+  "${PROBLEMS_BBOB_COMMON_DIR}"
+  "${PROBLEMS_PBO_DIR}"
+  "${PROBLEMS_WMODEL_DIR}"
+  "${SUITES_DIR}"
+  "${TEMPLATE_DIR}"
+  "${TEMPLATE_EXPERIMENTS_DIR}"
+  "${TEMPLATE_LOGGERS_DIR}"
+)
+
+# add the binary tree to the search path for include files
+# so that we will find header files of IOHexperimenter.
+include_directories(${IOHEXPERIMENTER_DIR})
+
+# add the IOH library
+add_library(IOH ${IOHEXPERIMENTER_SRC})
+
+# link the IOH library to executable files.
+target_link_libraries(IOHprofiler_run_experiment IOH)
+target_link_libraries(IOHprofiler_run_problem IOH)
+target_link_libraries(IOHprofiler_run_suite IOH)
+
+# install. set name of the installed library as 'IOH'.
+install (TARGETS IOH DESTINATION lib)
+install (FILES ${IOHEXPERIMENTER_SRC} DESTINATION include)

README.md

@@ -16,29 +16,34 @@ This is the __benchmarking platform__ for <b>I</b>terative <b>O</b>ptimization <
 
 <b>IOHexperimenter</b> is <i>built on</i>:
 
-* `C++` (tested on `gcc 5.4.0`)
-* `boost.filesystem` library for logging files.
+* `C++`
 
 <b>IOHexperimenter</b> is available for:
 
 * `C++`
 * `R` package [https://github.com/IOHprofiler/IOHexperimenter/tree/R](https://github.com/IOHprofiler/IOHexperimenter/tree/R)
-* `Python` interface (soon to come)
+* `Python` interface
 * `Java` interface (soon to come)
 
 ## Using IOHexperimenter
 
 ### Running Experiments
 
-The __IOHexperimenter__ has been built on `C++` and tested on complier `gcc 5.4.0`. To use the logging of `csv` output files, `boost.filesystem` library is required (To install boost library, please visit [https://www.boost.org](https://www.boost.org)).
+The __IOHexperimenter__ has been built on `C++`.
 
 #### Using IOHexperimenter in C++
 
-If you are using the tool for the first time, please download or clone this branch and run `make` at the root directory of the project. After running `make` to compile,
-* object files will be generated in `build/c/obj`
-* three exectuable files will be generated in `build/c/bin`
+[Cmake](https://cmake.org) is used to build this project, please make sure you have it installed.
+
+If you are using the tool for the first time, please download or clone this branch, and run `cmake .` and `make install` at the directory where the project locates.
+* If you want to set up the install directory, please run `cmake -DCMAKE_INSTALL_PREFIX=your/path .` before installation.
+* three exectuable files will be generated in `build/Cpp` for test.
+
+After installation, you can compile your project as follow (with linking IOH library):
+```
+g++ $CMPL_FLAGS -o IOHprofiler_run_experiment IOHprofiler_run_experiment.cpp -lIOH
+```
 
-Afterwards, you can use the folder `build/c` and use the `Makefile` therein for your experiments.
 For more details of how to use the `C++` version, please visit [this page](/build/Cpp).
 
 #### Using IOHexperimenter in R

build/Cpp/IOHprofiler_run_experiment.cpp

@@ -1,4 +1,4 @@
-#include "src/IOHprofiler_experimenter.hpp"
+#include <IOHprofiler_experimenter.hpp>
 
 IOHprofiler_random random_generator(1);
 static int budget_scale = 100;
@@ -37,7 +37,7 @@ void evolutionary_algorithm(std::shared_ptr<IOHprofiler_problem<int> > problem,
   *mutation_rate = 1.0/problem->IOHprofiler_get_number_of_variables();
   int budget = budget_scale * problem->IOHprofiler_get_number_of_variables() * problem->IOHprofiler_get_number_of_variables();
 
-  std::vector<std::shared_ptr<double>> parameters;
+  std::vector<std::shared_ptr<double> > parameters;
   parameters.push_back(std::shared_ptr<double>(mutation_rate));
   std::vector<std::string> parameters_name;
   parameters_name.push_back("mutation_rate");

build/Cpp/IOHprofiler_run_problem.cpp

@@ -1,7 +1,7 @@
 
-#include "src/f_one_max.hpp"
-#include "src/f_w_model_one_max.hpp"
-#include "src/IOHprofiler_csv_logger.h"
+#include <f_one_max.hpp>
+#include <f_w_model_one_max.hpp>
+#include <IOHprofiler_csv_logger.h>
 
 
 std::vector<int> Initialization(int dimension) {
@@ -62,7 +62,7 @@ void _run_w_model() {
   /// Set problem_id as 1
   w_model_om.IOHprofiler_set_problem_id(1);
   /// Set dimension.
-  w_model_om.Initilize_problem(dimension);
+  w_model_om.IOHprofiler_set_number_of_variables(dimension);
   int restart_flag = 0;
   while (restart_flag < 10) {
     /// reset_problem must be called before testing the same problem class repeatedly.
@@ -118,7 +118,7 @@ void _run_problem() {
   /// Allocate the problem to be tested.
   OneMax om;
   int dimension = 1000;
-  om.Initilize_problem(dimension);
+  om.IOHprofiler_set_number_of_variables(dimension);
 
   /// If no logger is added, there will be not any output files, but users
   /// can still get fitness values.

build/Cpp/IOHprofiler_run_suite.cpp

@@ -1,5 +1,5 @@
-#include "src/IOHprofiler_PBO_suite.hpp"
-#include "src/IOHprofiler_csv_logger.h"
+#include <IOHprofiler_PBO_suite.hpp>
+#include <IOHprofiler_csv_logger.h>
 
 std::vector<int> Initialization(int dimension) {
   std::vector<int> x;