moved anglecalibration stuff to own repository still keep some changes

CMakeLists.txt

@@ -62,7 +62,6 @@ option(AARE_FETCH_CATCH "Use FetchContent to download catch2" ON)
 option(AARE_FETCH_JSON "Use FetchContent to download nlohmann::json" ON)
 option(AARE_FETCH_ZMQ "Use FetchContent to download libzmq" ON)
 option(AARE_FETCH_LMFIT "Use FetchContent to download lmfit" ON)
-option(AARE_FETCH_HDF5 "Use FetchContent to download hdf5-devel" OFF)
 
 
 #Convenience option to use system libraries only (no FetchContent)
@@ -74,7 +73,6 @@ if(AARE_SYSTEM_LIBRARIES)
     set(AARE_FETCH_CATCH OFF CACHE BOOL "Disabled FetchContent for catch2" FORCE)
     set(AARE_FETCH_JSON OFF CACHE BOOL "Disabled FetchContent for nlohmann::json" FORCE)
     set(AARE_FETCH_ZMQ OFF CACHE BOOL "Disabled FetchContent for libzmq" FORCE)
-    set(AARE_FETCH_HDF5 OFF CACHE BOOL "Disabled FetchContent for hdf5" FORCE)
     # Still fetch lmfit when setting AARE_SYSTEM_LIBRARIES since this is not available
     # on conda-forge
 endif()
@@ -221,23 +219,6 @@ else()
     find_package(nlohmann_json 3.11.3 REQUIRED)
 endif()
 
-if(AARE_FETCH_HDF5)
-    message(FATAL_ERROR "Fetching HDF5 via FetchContent is not supported here. Please install it via your system. 
-    For Ubuntu: sudo apt install libhdf5-dev
-    For Red Hat: sudo dnf install hdf5-devel
-    For MacOS: brew install hdf5")
-else()
-    find_package(HDF5 QUIET COMPONENTS CXX)
-    if (HDF5_FOUND)
-        message(STATUS "Found HDF5: ${HDF5_INCLUDE_DIRS}")
-    else()
-        message(FATAL_ERROR "HDF5 was NOT found! Please install it via your system  
-            For Ubuntu: sudo apt install libhdf5-dev
-            For Red Hat: sudo dnf install hdf5-devel
-            For MacOS: brew install hdf5")
-    endif()
-endif()
-
 include(GNUInstallDirs)
 
 # If conda build, always set lib dir to 'lib'
@@ -359,7 +340,6 @@ endif()
 ###------------------------------------------------------------------------------------------
 
 set(PUBLICHEADERS
-    include/aare/AngleCalibration.hpp
     include/aare/ArrayExpr.hpp
     include/aare/CalculateEta.hpp
     include/aare/Cluster.hpp
@@ -367,7 +347,6 @@ set(PUBLICHEADERS
     include/aare/ClusterFile.hpp
     include/aare/CtbRawFile.hpp
     include/aare/ClusterVector.hpp
-    include/aare/CustomFiles.hpp
     include/aare/decode.hpp
     include/aare/defs.hpp
     include/aare/Dtype.hpp
@@ -375,14 +354,10 @@ set(PUBLICHEADERS
     include/aare/Fit.hpp
     include/aare/FileInterface.hpp
     include/aare/FilePtr.hpp
-    include/aare/FlatField.hpp
     include/aare/Frame.hpp
     include/aare/GainMap.hpp
     include/aare/geo_helpers.hpp
-    include/aare/Hdf5FileReader.hpp
     include/aare/JungfrauDataFile.hpp
-    include/aare/MythenDetectorSpecifications.hpp
-    include/aare/MythenFileReader.hpp
     include/aare/NDArray.hpp
     include/aare/NDView.hpp
     include/aare/NumpyFile.hpp
@@ -398,9 +373,7 @@ set(PUBLICHEADERS
 
 
 set(SourceFiles
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/AngleCalibration.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/CtbRawFile.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/CustomFiles.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.cpp
@@ -417,7 +390,6 @@ set(SourceFiles
     ${CMAKE_CURRENT_SOURCE_DIR}/src/RawFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/RawSubFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/RawMasterFile.cpp
-
     ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/task.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/ifstream_helpers.cpp
 )
@@ -436,13 +408,11 @@ target_link_libraries(
     PUBLIC 
     fmt::fmt 
     nlohmann_json::nlohmann_json 
-    HDF5::HDF5
     ${STD_FS_LIB} # from helpers.cmake
     PRIVATE 
     aare_compiler_flags 
     Threads::Threads
     $<BUILD_INTERFACE:lmfit>
-
 )
 
 set_target_properties(aare_core PROPERTIES
@@ -457,14 +427,12 @@ endif()
 if(AARE_TESTS)
     set(TestSources
             ${CMAKE_CURRENT_SOURCE_DIR}/src/algorithm.test.cpp
-            ${CMAKE_CURRENT_SOURCE_DIR}/src/AngleCalibration.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/geo_helpers.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/RawMasterFile.test.cpp
-            ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5FileReader.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NDArray.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NDView.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFinder.test.cpp
@@ -475,7 +443,6 @@ if(AARE_TESTS)
             ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFinderMT.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/Pedestal.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/JungfrauDataFile.test.cpp
-            ${CMAKE_CURRENT_SOURCE_DIR}/src/MythenFileReader.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyHelpers.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/RawFile.test.cpp