Add CMake support

.gitignore

@@ -1 +1,3 @@
 obj/
+tools/*.svg
+build/

CMakeLists.txt

@@ -0,0 +1,23 @@
+cmake_minimum_required(VERSION 3.0.0)
+project(BioSim4 VERSION 0.2.0)
+
+include(CTest)
+enable_testing()
+
+add_subdirectory(src)
+
+
+install(FILES ./biosim4.ini DESTINATION ./)
+install(DIRECTORY ./tools/ DESTINATION tools)
+install (DIRECTORY DESTINATION "logs" DIRECTORY_PERMISSIONS 
+    OWNER_WRITE OWNER_READ OWNER_EXECUTE
+    GROUP_READ GROUP_READ GROUP_EXECUTE
+    GROUP_READ WORLD_READ WORLD_EXECUTE)
+install (DIRECTORY DESTINATION "images" DIRECTORY_PERMISSIONS 
+    OWNER_WRITE OWNER_READ OWNER_EXECUTE
+    GROUP_READ GROUP_READ GROUP_EXECUTE
+    GROUP_READ WORLD_READ WORLD_EXECUTE)
+
+set(CPACK_PROJECT_NAME ${PROJECT_NAME})
+set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
+include(CPack)

Makefile

@@ -17,7 +17,7 @@ RESINC =
 LIBDIR = 
 ARCH = `arch`
 LIB = /usr/lib/$(ARCH)-linux-gnu/libopencv_core.so /usr/lib/$(ARCH)-linux-gnu/libopencv_video.so /usr/lib/$(ARCH)-linux-gnu/libopencv_videoio.so
-LDFLAGS = -lX11 -lpthread  -lgomp
+LDFLAGS = -lpthread  -lgomp
 
 INC_DEBUG = $(INC)
 CFLAGS_DEBUG = $(CFLAGS) -g -fopenmp

README.md

@@ -213,16 +213,24 @@ cimg-dev is replaced with version 2.8.4 or later.
 <a name="Compiling"></a>
 ### Compiling
 
-Two (and a half) ways to compile:
+You have several options:
 
-* The file named "biosim4.cbp" is a configuration file for the Code::Blocks IDE version 20.03.
+#### Code::Blocks project file
 
-* A Makefile is provided which
-was created from biosim4.cbp with cbp2make, but is not tested. A default "make" will generate a debug and a
-release version.
+The file named "biosim4.cbp" is a configuration file for the Code::Blocks IDE version 20.03.
 
+#### Makefile
 
-* A Dockerfile is provided which leverages the aforementioned Makefile.
+A Makefile is provided which was created from biosim4.cbp with cbp2make. Possible make commands include:
+
+* "make" with no arguments makes release and debug versions in ./bin/Release and ./bin/Debug
+* "make release" makes a release version in ./bin/Release
+* "make debug" makes a debug version in ./bin/Debug
+* "make clean" removes the intermediate build files
+
+#### Docker
+
+A Dockerfile is provided which leverages the aforementioned Makefile.
 
 To build a Docker environment in which you can compile the program:
 
@@ -237,6 +245,42 @@ docker run --rm -ti -v `pwd`:/app --name biosim biosim4 make
 ```
 When you exit the container, the files compiled in your container files will persist in `./bin`.
 
+#### CMake
+
+A `CMakeList.txt` file is provided to allow development, build, test, installation and packaging with the CMake tool chain and all IDE's that support CMake. 
+
+To build with cmake you need to install cmake. Once installed use the procedure below:
+
+```sh
+mkdir build
+cd build
+cmake ../
+cmake --build ./
+```
+
+To make a test installation and run the program:
+
+```sh
+mkdir build
+cd build
+cmake ../
+cmake --build ./
+mkdir test_install
+cmake --install ./ --prefix ./test_install
+cd test_install
+./bin/biosim4
+```
+
+To make a release package:
+
+```sh
+mkdir build
+cd build
+cmake ../
+cmake --build ./
+cpack ./
+```
+
 <a name="Bugs"></a>
 ## Bugs
 --------------------

src/CMakeLists.txt

@@ -0,0 +1,31 @@
+
+FILE(GLOB MyCppSources ./*.cpp)
+FILE(GLOB MyCppheaders ./*.h)
+
+# TODO move the unit test to test build and include in test mechanims of cmake
+#list(REMOVE_ITEM MyCppSources "./unitTestBasicTypes.cpp")
+#list(REMOVE_ITEM MyCppSources "./unitTestConnectNeuralNetWiringFromGenome.cpp")
+#list(REMOVE_ITEM MyCppSources "./unitTestGridVisitNeighborhood.cpp")
+
+find_package(OpenCV REQUIRED)
+
+include_directories( ${OpenCV_INCLUDE_DIRS} )
+
+SET(GCC_COVERAGE_COMPILE_FLAGS "-O3 -Wall -fexceptions -fopenmp")
+SET(GCC_COVERAGE_LINK_FLAGS    "-lpthread -O3 -lz -lgomp")
+
+SET(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} ${GCC_COVERAGE_COMPILE_FLAGS}")
+SET(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} ${GCC_COVERAGE_LINK_FLAGS}")
+set( CMAKE_VERBOSE_MAKEFILE on )
+
+add_executable(biosim4 ${MyCppSources} ${MyCppheaders})
+target_link_libraries( biosim4 PUBLIC ${OpenCV_LIBS} )
+
+
+install(TARGETS biosim4 DESTINATION bin)
+
+set(CPACK_PROJECT_NAME ${PROJECT_NAME})
+set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
+include(CPack)
+
+

src/imageWriter.cpp

@@ -10,6 +10,7 @@
 #include "simulator.h"
 #include "imageWriter.h"
 #define cimg_use_opencv 1
+#define cimg_display 0
 #include "CImg.h"
 
 namespace BS {