Merge pull request #11 from slsdetectorgroup/project_structure

Project structure

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.12)
-set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD 17) #TODO! Global or per target?
 project(aare 
     VERSION 0.1
     DESCRIPTION "Data processing library for PSI detectors"
@@ -10,81 +10,76 @@ project(aare
 cmake_policy(SET CMP0135 NEW)
 cmake_policy(SET CMP0079 NEW)
 
-
 include(GNUInstallDirs)
-
 include(FetchContent)
 
 
-option(USE_SANITIZER "Sanitizers for debugging" ON)
-option(DISABLE_WARNINGS "Disbale compilation warnings" OFF)
-option(USE_PYTHON "Build python bindings" ON)
-option(AARE_BUILD_TESTS "Build tests" OFF)
+option(AARE_USE_SANITIZER "Sanitizers for debugging" ON)
+option(AARE_PYTHON_BINDINGS "Build python bindings" ON)
+option(AARE_TESTS "Build tests" OFF)
+option(AARE_EXAMPLES "Build examples" OFF)
 
+#TODO! Should this be on the top level or move it down to the component
+#that needs it? 
 FetchContent_Declare(json
     GIT_REPOSITORY https://github.com/nlohmann/json
     GIT_TAG v3.11.3
 )
 FetchContent_MakeAvailable(json)
 
-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")
+# 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(SUPPRESSED_WARNINGS "-Wno-return-type")
+
+# set(CMAKE_CXX_FLAGS  "${OPTIMIZATION_FLAGS} ${SUPPRESSED_WARNINGS}")
+
+
+if(AARE_BUILD_TESTS)
+    add_subdirectory(tests)
 endif()
-set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
-
-
-
-
-set(OPTIONAL_FLAGS "")
-if(DISABLE_WARNINGS)
-    set(OPTIONAL_FLAGS "${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} ${SUPPRESSED_WARNINGS}")
-
-if(USE_PYTHON)
-set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -fPIC")
-endif(USE_PYTHON)
-
-
-
-
-include_directories(include)
-add_subdirectory(src)
+add_subdirectory(core)
+add_subdirectory(file_io)
 
 
+#Overall target to link to when using the library
 add_library(aare INTERFACE) 
-target_link_libraries(aare INTERFACE common core file_io)
-
+target_link_libraries(aare INTERFACE core file_io)
+target_include_directories(aare INTERFACE 
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+    $<INSTALL_INTERFACE:include>
+)
 
 add_subdirectory(examples)
 target_link_libraries(example PUBLIC aare)
 
 
-if(USE_PYTHON)
-    find_package (Python 3.11 COMPONENTS Interpreter Development)
-    find_package(pybind11 2.11 REQUIRED)
+if(AARE_PYTHON_BINDINGS)
     add_subdirectory(python)
-    target_link_libraries(_aare PRIVATE aare nlohmann_json::nlohmann_json fmt::fmt)
 endif()

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()

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"
 
 
 

core/src/Frame.cpp

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

core/src/defs.cpp

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

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()

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>

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

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:

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> {
 

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>
 {

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{

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>

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>
 

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) {

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>

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>

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>

file_io/src/SubFile.cpp

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

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 +1,8 @@
+
+find_package (Python 3.11 COMPONENTS Interpreter Development)
+find_package(pybind11 2.11 REQUIRED)
 pybind11_add_module(_aare src/bindings.cpp)
+set_target_properties(_aare PROPERTIES
+    LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
+)
+target_link_libraries(_aare PRIVATE aare)

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;
 

src/.gitignore

@@ -1 +0,0 @@
-

src/CMakeLists.txt

@@ -1,4 +0,0 @@
-add_subdirectory(file_io)
-add_subdirectory(core)
-add_subdirectory(processing)
-add_subdirectory(common)

src/common/CMakeLists.txt

@@ -1,16 +0,0 @@
-add_library(common "${CMAKE_CURRENT_SOURCE_DIR}/defs.cpp")
-
-target_link_libraries(common PUBLIC fmt::fmt)
-
-
-if(AARE_BUILD_TESTS)
-    set(TestSources
-            ${CMAKE_CURRENT_SOURCE_DIR}/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 common)
-
-endif()

src/core/CMakeLists.txt

@@ -1,10 +0,0 @@
-# target_include_directories(aare PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
-
-# target_sources(aare PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/Frame.cpp")
-
-
-add_library(core "${CMAKE_CURRENT_SOURCE_DIR}/Frame.cpp")
-
-target_link_libraries(core PUBLIC common)
-
-

src/file_io/CMakeLists.txt

@@ -1,16 +0,0 @@
-
-set(FILE_IO_SOURCES "file/File.cpp"
-                    "file/JsonFile.cpp"
-                    "file/SubFile.cpp"
-                    "file_factory/FileFactory.cpp"
-                    "file_factory/JsonFileFactory.cpp"
-                    "helpers.cpp"
-                    )
-# append ${CMAKE_CURRENT_SOURCE_DIR} to the list of sources using for loop
-foreach(FILE_IO_SOURCE ${FILE_IO_SOURCES})
-    list(APPEND FILE_IO_SOURCES_WITH_PATH "${CMAKE_CURRENT_SOURCE_DIR}/${FILE_IO_SOURCE}")
-endforeach()
-
-add_library(file_io ${FILE_IO_SOURCES_WITH_PATH})
-
-target_link_libraries(file_io common fmt::fmt core nlohmann_json::nlohmann_json)

tests/.gitignore

@@ -1 +0,0 @@
-