new folder structure

CMakeLists.txt

@@ -31,51 +31,55 @@ if(AARE_BUILD_TESTS)
     add_subdirectory(tests)
 endif()
 
-
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 find_package(fmt 6 REQUIRED)
 
 
-set(CMAKE_BUILD_TYPE "Debug")
+# set(CMAKE_BUILD_TYPE "Debug")
 
-if (CMAKE_BUILD_TYPE STREQUAL "Debug")
-    set(OPTIMIZATION_FLAGS "-Og -ggdb3 -D_GLIBCXX_DEBUG -D_GLIBCXX_DEBUG_PEDANTIC")
-else()
-    set(OPTIMIZATION_FLAGS "-O3")
-endif()
-set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+# if (CMAKE_BUILD_TYPE STREQUAL "Debug")
+#     set(OPTIMIZATION_FLAGS "-Og -ggdb3 -D_GLIBCXX_DEBUG -D_GLIBCXX_DEBUG_PEDANTIC")
+# else()
+#     set(OPTIMIZATION_FLAGS "-O3")
+# endif()
 
 
 
 
-set(OPTIONAL_FLAGS "")
-if(DISABLE_WARNINGS)
-    set(OPTIONAL_FLAGS "${OPTIONAL_FLAGS} -Wall -Wextra -pedantic -Wno-unused-parameter -Wshadow -Wformat=2 -Wold-style-cast -Wnon-virtual-dtor  -Wfloat-equal -Wconversion -Wlogical-op -Wshift-overflow=2 -Woverloaded-virtual -Winline")
-endif()
 
-if(USE_SANITIZER)
-    set(OPTIONAL_FLAGS "${OPTIONAL_FLAGS} -fdiagnostics-parseable-fixits -fdiagnostics-generate-patch -fdiagnostics-show-template-tree -fsanitize=address,undefined,pointer-compare -fno-sanitize-recover -D_FORTIFY_SOURCE=2 -fstack-protector -fno-omit-frame-pointer ")
-endif()
+# set(OPTIONAL_FLAGS "")
+# if(DISABLE_WARNINGS)
+#     set(OPTIONAL_FLAGS "${OPTIONAL_FLAGS} -Wall -Wextra -pedantic -Wno-unused-parameter -Wshadow -Wformat=2 -Wold-style-cast -Wnon-virtual-dtor  -Wfloat-equal -Wconversion -Wlogical-op -Wshift-overflow=2 -Woverloaded-virtual -Winline")
+# endif()
 
+# if(USE_SANITIZER)
+#     set(OPTIONAL_FLAGS "${OPTIONAL_FLAGS} -fdiagnostics-parseable-fixits -fdiagnostics-generate-patch -fdiagnostics-show-template-tree -fsanitize=address,undefined,pointer-compare -fno-sanitize-recover -D_FORTIFY_SOURCE=2 -fstack-protector -fno-omit-frame-pointer ")
+# endif()
 
 
-set(SUPPRESSED_WARNINGS "-Wno-return-type")
 
-set(CMAKE_CXX_FLAGS  "${OPTIMIZATION_FLAGS} ${SUPPRESSED_WARNINGS}")
+# set(SUPPRESSED_WARNINGS "-Wno-return-type")
+
+# set(CMAKE_CXX_FLAGS  "${OPTIMIZATION_FLAGS} ${SUPPRESSED_WARNINGS}")
+
+# if(USE_PYTHON)
+# set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -fPIC")
+# endif(USE_PYTHON)
+
 
-if(USE_PYTHON)
-set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -fPIC")
-endif(USE_PYTHON)
 
 
+# include_directories(include)
+# add_subdirectory(src)
 
+add_subdirectory(core)
+add_subdirectory(file_io)
 
-include_directories(include)
-add_subdirectory(src)
 
 
 add_library(aare INTERFACE) 
-target_link_libraries(aare INTERFACE common core file_io)
+target_link_libraries(aare INTERFACE core file_io)
 
 
 add_subdirectory(examples)

README.md

@@ -4,5 +4,13 @@ Data analysis library for PSI hybrid detectors
 
 
 
+## Folder structure 
+
+| Folder   | subfolder     | Content                             |
+|----------|---------------|-------------------------------------|
+| include/ |  aare/        | top level header/s                  |
+| core/    |    include/   | public headers for core             |
+|          | src/          | source files and non public headers |
+
 ## file_io class diagram
 ![file_io class diagram](./extra/uml/out/file_io/ClassDiagram.png)

core/CMakeLists.txt

@@ -0,0 +1,23 @@
+
+
+set(SourceFiles
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.cpp
+)
+
+add_library(core STATIC ${SourceFiles})
+target_include_directories(core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
+target_link_libraries(core PUBLIC fmt::fmt)
+set_property(TARGET core PROPERTY POSITION_INDEPENDENT_CODE ON)
+
+if(AARE_BUILD_TESTS)
+    set(TestSources
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.test.cpp
+        )
+    target_sources(tests PRIVATE ${TestSources} )
+
+    #Work around to remove, this is not the way to do it =) 
+    # target_include_directories(tests PRIVATE ${CMAKE_SOURCE_DIR}/include/common)
+    target_link_libraries(tests PRIVATE core)
+
+endif()

include/core/Frame.hpp → core/include/aare/Frame.hpp

@@ -4,7 +4,7 @@
 #include <cstdint>
 #include <bits/unique_ptr.h>
 #include <vector>
-#include "common/defs.hpp"
+#include "aare/defs.hpp"
 
 
 

src/core/Frame.cpp → core/src/Frame.cpp

@@ -1,4 +1,4 @@
-#include "core/Frame.hpp"
+#include "aare/Frame.hpp"
 #include <iostream>
 
 template <typename DataType>

src/common/defs.cpp → core/src/defs.cpp

@@ -1,4 +1,4 @@
-#include "common/defs.hpp"
+#include "aare/defs.hpp"
 
 template <> std::string toString(DetectorType type) {
     switch (type) {

src/common/defs.test.cpp → core/src/defs.test.cpp

@@ -1,6 +1,6 @@
 #include <catch2/catch_test_macros.hpp>
 #include <string>
-#include "defs.hpp"
+#include "aare/defs.hpp"
 TEST_CASE("Enum to string conversion"){
     //By the way I don't think the enum string conversions should be in the defs.hpp file
     //but let's use this to show a test

examples/main.cpp

@@ -1,6 +1,6 @@
 // Your First C++ Program
 #include <iostream>
-#include "file_io/FileHandler.hpp"
+#include "aare/FileHandler.hpp"
 
 using JFileHandler = FileHandler<DetectorType::Jungfrau,uint16_t>;
 using JFile = File<DetectorType::Jungfrau,uint16_t>;

file_io/CMakeLists.txt

@@ -0,0 +1,28 @@
+
+
+set(SourceFiles
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/File.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/FileFactory.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/helpers.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/JsonFile.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/JsonFileFactory.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/SubFile.cpp
+)
+
+add_library(file_io STATIC ${SourceFiles})
+target_include_directories(file_io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
+target_link_libraries(file_io  PUBLIC fmt::fmt core nlohmann_json::nlohmann_json)
+set_property(TARGET file_io PROPERTY POSITION_INDEPENDENT_CODE ON)
+
+
+# if(AARE_BUILD_TESTS)
+#     set(TestSources
+#             ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.test.cpp
+#         )
+#     target_sources(tests PRIVATE ${TestSources} )
+
+#     #Work around to remove, this is not the way to do it =) 
+#     # target_include_directories(tests PRIVATE ${CMAKE_SOURCE_DIR}/include/common)
+#     target_link_libraries(tests PRIVATE file_io)
+
+# endif()

include/file_io/File.hpp → file_io/include/aare/File.hpp

@@ -1,8 +1,9 @@
 #pragma once
 
-#include "common/defs.hpp"
-#include "core/Frame.hpp"
+#include "aare/defs.hpp"
+#include "aare/Frame.hpp"
 #include "SubFile.hpp"
+
 #include <filesystem>
 #include <fmt/core.h>
 #include <iostream>

include/file_io/FileFactory.hpp → file_io/include/aare/FileFactory.hpp

@@ -1,6 +1,7 @@
 #pragma once
 #include <filesystem>
-#include "file_io/File.hpp"
+#include "aare/File.hpp"
+
 template <DetectorType detector,typename DataType>
 class FileFactory{
     // Class that will be used to create File objects

include/file_io/FileHandler.hpp → file_io/include/aare/FileHandler.hpp

@@ -1,6 +1,7 @@
 #include <filesystem>
-#include "file_io/FileFactory.hpp"
-#include "file_io/File.hpp"
+#include "aare/FileFactory.hpp"
+#include "aare/File.hpp"
+
 template <DetectorType detector,typename DataType>
 class FileHandler{
     private:

include/file_io/JsonFile.hpp → file_io/include/aare/JsonFile.hpp

@@ -1,7 +1,7 @@
 #pragma once
-#include "file_io/File.hpp"
-#include "core/Frame.hpp"
-#include "common/defs.hpp"
+#include "aare/File.hpp"
+#include "aare/Frame.hpp"
+#include "aare/defs.hpp"
 template <DetectorType detector, typename DataType>
 class JsonFile : public File<detector, DataType> {
 

include/file_io/JsonFileFactory.hpp → file_io/include/aare/JsonFileFactory.hpp

@@ -1,4 +1,4 @@
-#include "file_io/FileFactory.hpp"
+#include "aare/FileFactory.hpp"
 template <DetectorType detector,typename DataType>
 class JsonFileFactory: public FileFactory<detector,DataType>
 {

include/file_io/RawFileFactory.hpp → file_io/include/aare/RawFileFactory.hpp

@@ -1,4 +1,4 @@
-#include "file_io/File.hpp"
+#include "aare/File.hpp"
 #include <filesystem>
 template<DetectorType detector,typename DataType>  
 class RawFileFactory{

include/file_io/SubFile.hpp → file_io/include/aare/SubFile.hpp

@@ -1,5 +1,5 @@
 #pragma once
-#include "common/defs.hpp"
+#include "aare/defs.hpp"
 #include <cstdint>
 #include <filesystem>
 #include <variant>

include/file_io/helpers.hpp → file_io/include/aare/helpers.hpp

@@ -1,6 +1,6 @@
 #pragma once
 
-#include "file_io/File.hpp"
+#include "aare/File.hpp"
 #include <filesystem>
 #include <fmt/core.h>
 

src/file_io/file/File.cpp → file_io/src/File.cpp

@@ -1,4 +1,5 @@
-#include "file_io/File.hpp"
+#include "aare/File.hpp"
+
 template <DetectorType detector, typename DataType>
 File<detector,DataType>::~File<detector,DataType>() {
     for (auto& subfile : subfiles) {

src/file_io/file_factory/FileFactory.cpp → file_io/src/FileFactory.cpp

@@ -1,6 +1,6 @@
-#include "file_io/FileFactory.hpp"
-#include "file_io/File.hpp"
-#include "file_io/JsonFileFactory.hpp"
+#include "aare/FileFactory.hpp"
+#include "aare/File.hpp"
+#include "aare/JsonFileFactory.hpp"
 #include <iostream>
 
 template <DetectorType detector, typename DataType>

src/file_io/file/JsonFile.cpp → file_io/src/JsonFile.cpp

@@ -1,4 +1,4 @@
-#include "file_io/JsonFile.hpp"
+#include "aare/JsonFile.hpp"
 #include <typeinfo>
 
 template <DetectorType detector, typename DataType>

src/file_io/file_factory/JsonFileFactory.cpp → file_io/src/JsonFileFactory.cpp

@@ -1,8 +1,8 @@
-#include "file_io/JsonFileFactory.hpp"
-#include "file_io/JsonFile.hpp"
-#include "file_io/SubFile.hpp"
-#include "common/defs.hpp"
-#include "file_io/helpers.hpp"
+#include "aare/JsonFileFactory.hpp"
+#include "aare/JsonFile.hpp"
+#include "aare/SubFile.hpp"
+#include "aare/defs.hpp"
+#include "aare/helpers.hpp"
 #include <fstream>
 #include <iostream>
 #include <nlohmann/json.hpp>

src/file_io/file/SubFile.cpp → file_io/src/SubFile.cpp

@@ -1,4 +1,4 @@
-#include "file_io/SubFile.hpp"
+#include "aare/SubFile.hpp"
 #include <iostream>
 // #include <filesystem>
 

src/file_io/helpers.cpp → file_io/src/helpers.cpp

@@ -1,4 +1,4 @@
-#include "file_io/helpers.hpp"
+#include "aare/helpers.hpp"
 
 
 bool is_master_file(std::filesystem::path fpath) {

include/aare/aare.hpp

@@ -0,0 +1 @@
+//This is the top level header to include and what most users will use

python/CMakeLists.txt

@@ -1 +1,4 @@
 pybind11_add_module(_aare src/bindings.cpp)
+set_target_properties(_aare PROPERTIES
+    LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
+)

python/src/bindings.cpp

@@ -3,9 +3,9 @@
 #include <pybind11/pybind11.h>
 #include <string>
 
-#include "common/defs.hpp"
-#include "core/Frame.hpp"
-#include "file_io/FileHandler.hpp"
+#include "aare/defs.hpp"
+#include "aare/Frame.hpp"
+#include "aare/FileHandler.hpp"
 
 namespace py = pybind11;