Provide option to specify local dependencies folder

- Developers can now specify an optional local folder containing that
points to the sources of eigen, json for modern c++ and half. This can
be useful in offline environments without network access.

- Dependency handling code is moved into a separate CMake module.

- Half is directly fetched from sourceforge.net

- FetchContent now downloads source repos in PROJECT_SOURCE_DIR/_deps to
avoid downloading repos again for separate build directories.

.gitignore

@@ -35,3 +35,4 @@ build/
 CMakeLists.txt.user
 testing/data/tmp*
 testing/data/*-tmp-*
+_deps/

CMakeLists.txt

@@ -25,6 +25,13 @@ option(MRTRIX_USE_PCH "Use precompiled headers" ON)
 option(MRTRIX_PYTHON_SOFTLINK "Build directory softlink to Python source code rather than copying" ON)
 option(MRTRIX_BUILD_NON_CORE_STATIC "Build MRtrix's non-core code as a static library" OFF)
 
+set(MRTRIX_DEPENDENCIES_DIR "" CACHE PATH
+    "An optional local directory containing thirdparty dependencies:\n \
+    - Eigen3 https://gitlab.com/libeigen/eigen\n \
+    - Json for Modern C++ https://github.com/nlohmann/json\n \
+    - Half https://half.sourceforge.net/\n"
+)
+
 if(MRTRIX_BUILD_TESTS)
     if(CMAKE_VERSION VERSION_GREATER 3.17)
         list(APPEND CMAKE_CTEST_ARGUMENTS "--output-on-failure")
@@ -68,6 +75,7 @@ include(LinkerSetup)
 include(FindFFTW)
 include(CompilerCache)
 include(ECMEnableSanitizers)
+include(Dependencies)
 if(CMAKE_SYSTEM_NAME MATCHES "Darwin")
     include(MacOSBundle)
 endif()

cmake/Dependencies.cmake

@@ -0,0 +1,73 @@
+include(FetchContent)
+
+set(FETCHCONTENT_BASE_DIR ${PROJECT_SOURCE_DIR}/_deps)
+
+message(STATUS "${MRTRIX_DEPENDENCIES_DIR}")
+if(NOT ${MRTRIX_DEPENDENCIES_DIR} STREQUAL "")
+    message(STATUS "Using local dependencies at ${MRTRIX_DEPENDENCIES_DIR}")
+    set(MRTRIX_LOCAL_DEPENDENCIES ON)
+else()
+    set(MRTRIX_LOCAL_DEPENDENCIES OFF)
+endif()
+
+# Eigen
+if(MRTRIX_LOCAL_DEPENDENCIES)
+    FetchContent_Declare(
+        eigen3
+        SOURCE_DIR ${MRTRIX_DEPENDENCIES_DIR}/eigen
+        UPDATE_DISCONNECTED ON
+    )
+else()
+    FetchContent_Declare(
+      eigen3
+      GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
+      GIT_TAG 3.4.0
+      PATCH_COMMAND git apply --ignore-space-change --ignore-whitespace ${PROJECT_SOURCE_DIR}/thirdparty/eigen.patch
+      UPDATE_DISCONNECTED ON
+    )
+endif()
+FetchContent_MakeAvailable(eigen3)
+
+
+# Json for Modern C++
+if(MRTRIX_LOCAL_DEPENDENCIES)
+    FetchContent_Declare(
+        json
+        SOURCE_DIR ${MRTRIX_DEPENDENCIES_DIR}/json
+        UPDATE_DISCONNECTED ON
+    )
+else()
+    FetchContent_Declare(json
+        DOWNLOAD_EXTRACT_TIMESTAMP ON
+        URL https://github.com/nlohmann/json/releases/download/v3.11.3/json.tar.xz
+    )
+endif()
+FetchContent_MakeAvailable(json)
+
+
+# Half-precision floating-point library
+if(MRTRIX_LOCAL_DEPENDENCIES)
+    FetchContent_Declare(
+        half
+        SOURCE_DIR ${MRTRIX_DEPENDENCIES_DIR}/half
+        UPDATE_DISCONNECTED ON
+    )
+else()
+    FetchContent_Declare(
+        half
+        DOWNLOAD_EXTRACT_TIMESTAMP ON
+        URL "https://sourceforge.net/projects/half/files/half/2.1.0/half-2.1.0.zip/download"
+    )
+endif()
+
+FetchContent_MakeAvailable(half)
+
+add_library(half INTERFACE)
+add_library(half::half ALIAS half)
+target_include_directories(half INTERFACE "${half_SOURCE_DIR}/include")
+
+
+# Nifti headers
+add_library(nifti INTERFACE)
+add_library(nifti::nifti ALIAS nifti)
+target_include_directories(nifti INTERFACE "${PROJECT_SOURCE_DIR}/thirdparty/nifti")

core/CMakeLists.txt

@@ -87,6 +87,7 @@ target_link_libraries(mrtrix-core PUBLIC
     ${FFTW_LIBRARIES}
     nlohmann_json::nlohmann_json
     nifti::nifti
+    half::half
 )
 
 target_include_directories(mrtrix-core PUBLIC