Use git to download Eigen library

Also, upgrade Eigen library to 3.3.*

.github/workflows/analysis.yml

@@ -53,7 +53,7 @@ jobs:
             REPORT_PR_CHANGES_ONLY: false
         run: |
             analysis_file="analysis.txt"
-            cppcheck_params="--enable=warning --check-level=exhaustive --inline-suppr --suppress=internalError --suppress=internalAstError --suppress=*:*third-party/eigen3/*"
+            cppcheck_params="--enable=warning --check-level=exhaustive --inline-suppr --suppress=internalError --suppress=internalAstError --suppress=*:*third-party/eigen/*"
             cppcheck -j4 $cppcheck_params --project=$(pwd)/build/compile_commands.json --output-file=$analysis_file
             # Since cppcheck does not support OpenCL and CUDA, we need to check these files separately
             find $(pwd)/reg-lib/cl/. -name "*.cl" -print0 | while IFS= read -r -d '' file; do cppcheck "$file" $cppcheck_params --language=c++ 2>> $analysis_file; done

CMakeLists.txt

@@ -134,7 +134,7 @@ include_directories(${CMAKE_SOURCE_DIR}/reg-lib/cpu)
 include_directories(${CMAKE_SOURCE_DIR}/reg-io)
 include_directories(${CMAKE_SOURCE_DIR}/third-party)
 include_directories(${CMAKE_BINARY_DIR})
-include_directories(${CMAKE_BINARY_DIR}/third-party/eigen3)
+include_directories(${CMAKE_BINARY_DIR}/third-party/eigen)
 #-----------------------------------------------------------------------------
 if(USE_OPENCL)
   # Find the OpenCL package

niftyreg_build_version.txt

@@ -1 +1 @@
-415
+416

third-party/CMakeLists.txt

@@ -1,24 +1,17 @@
 #-----------------------------------------------------------------------------
-# Eigen version 3.3.3 - 67e894c6cd8f
-if(NOT EXISTS ${CMAKE_BINARY_DIR}/third-party/eigen3)
+# Eigen version 3.3.*
+if(NOT EXISTS ${CMAKE_BINARY_DIR}/third-party/eigen)
+  message(STATUS "Cloning Eigen...")
   execute_process(
-    COMMAND ${CMAKE_COMMAND} -E tar x ${CMAKE_SOURCE_DIR}/third-party/eigen_3.3.3.tar.gz
+    COMMAND git clone -q -b 3.3 https://gitlab.com/libeigen/eigen.git
     WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/third-party
+    RESULT_VARIABLE result
   )
-  execute_process(
-    COMMAND ${CMAKE_COMMAND} -E rename
-    ${CMAKE_BINARY_DIR}/third-party/eigen-eigen-67e894c6cd8f
-    ${CMAKE_BINARY_DIR}/third-party/eigen3
-  )
-  message(STATUS "Eigen3 files are copied in ${CMAKE_BINARY_DIR}/third-party/eigen3")
-endif(NOT EXISTS ${CMAKE_BINARY_DIR}/third-party/eigen3)
-#-----------------------------------------------------------------------------
-if(MSVC)
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj" )
-	set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} /bigobj" )
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /EHsc /wd4127 /wd4505 /wd4714")
-	string(REGEX REPLACE "/W[0-9]" "/W4" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
-endif()
+  if(result)
+    message(FATAL_ERROR "Failed to clone Eigen!")
+  endif(result)
+  message(STATUS "Eigen is cloned into ${CMAKE_BINARY_DIR}/third-party/eigen")
+endif(NOT EXISTS ${CMAKE_BINARY_DIR}/third-party/eigen)
 #-----------------------------------------------------------------------------
 if(OPENMP_FOUND)
 	if(USE_OPENMP)