Merge remote-tracking branch 'origin/dev' into new_peaks_cmds

Conflicts: core/file/nifti_utils.h python/mrtrix3/commands/peakscheck
MRtrix3 · Sep 17, 2024 · 68aa74b · 68aa74b
2 parents 81d10ef + 39d61f8
commit 68aa74b
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -119,3 +119,13 @@ cd8a6f1c2d0debcf3a6de185f8b92fc0be3e1401
 #Author: MRtrixBot <[email protected]>
 #Date:   Fri, 5 Apr 2024 14:06:00 +0100
 #    Replace include guards with #pragma once
+
+9b3de4d4defc3c7572bcd3ab9f214b72ce91abf3
+#Author: MRtrixBot <[email protected]>
+#Date:   Sun Jun 9 20:33:33 2024 +1000
+#    population_template: Split source code between files
+
+10c49930a63e6a2b0ce7d25d3f6d8dde290b2719
+#Author: MRtrixBot <[email protected]>
+#Date:   Mon, 19 Aug 2024 16:18:12 +0100
+#    Remove core/file/json.h and core/half.hpp
diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml
@@ -25,7 +25,7 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build python3-distutils python3-numpy
+         sudo apt-get install clang qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-distutils python3-numpy
 
     - name: Run sccache-cache
       uses: mozilla-actions/[email protected]
@@ -86,7 +86,7 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install g++-9 qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build python3-numpy
+         sudo apt-get install g++-9 qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-numpy
 
     - name: Run sccache-cache
       uses: mozilla-actions/[email protected]
@@ -208,10 +208,8 @@ jobs:
             ${{env.MINGW_PACKAGE_PREFIX}}-bc
             ${{env.MINGW_PACKAGE_PREFIX}}-cmake
             ${{env.MINGW_PACKAGE_PREFIX}}-diffutils
-            ${{env.MINGW_PACKAGE_PREFIX}}-eigen3
             ${{env.MINGW_PACKAGE_PREFIX}}-fftw
             ${{env.MINGW_PACKAGE_PREFIX}}-gcc
-            ${{env.MINGW_PACKAGE_PREFIX}}-libtiff
             ${{env.MINGW_PACKAGE_PREFIX}}-ninja
             ${{env.MINGW_PACKAGE_PREFIX}}-pkg-config
             ${{env.MINGW_PACKAGE_PREFIX}}-qt6-base
@@ -268,7 +266,6 @@ jobs:
 
     - name: pylint
       run: |
-         echo "__version__ = 'pylint testing' #pylint: disable=unused-variable" > ./python/lib/mrtrix3/_version.py
          ./run_pylint || { cat pylint.log; false; }
 
     - name: check copyright headers
@@ -284,5 +281,4 @@ jobs:
         extensions: 'h,cpp'
         clangFormatVersion: 16
         # Ignore third party headers
-        exclude: './core/file/json.h ./core/file/nifti1.h ./core/file/nifti2.h'
-
+        exclude: './thirdparty ./_deps'
diff --git a/.github/workflows/clang-tidy.yml b/.github/workflows/clang-tidy.yml
@@ -17,7 +17,7 @@ jobs:
     - uses: ZedThree/[email protected]
       id: review
       with:
-        apt_packages: g++,qt6-base-dev,libqt6opengl6-dev,libglvnd-dev,libeigen3-dev,zlib1g-dev,libfftw3-dev,ninja-build
+        apt_packages: g++,qt6-base-dev,libqt6opengl6-dev,libglvnd-dev,zlib1g-dev,libfftw3-dev,ninja-build
         config_file: .clang-tidy
 
     - uses: ZedThree/clang-tidy-review/[email protected]

diff --git a/.gitignore b/.gitignore
@@ -32,4 +32,6 @@
 .check_syntax.tmp
 .check_syntax2.tmp
 build/
-CMakeLists.txt.user
+CMakeLists.txt.user
+testing/data/tmp*
+testing/data/*-tmp-*
diff --git a/.gitmodules b/.gitmodules
@@ -1,8 +0,0 @@
-[submodule "testing/data"]
-	path = testing/binaries/data
-	url = https://github.com/MRtrix3/test_data
-	ignore = dirty
-[submodule "testing/script_data"]
-	path = testing/scripts/data
-	url = https://github.com/MRtrix3/script_test_data.git
-	ignore = dirty

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,7 +1,14 @@
 cmake_minimum_required(VERSION 3.16 FATAL_ERROR)
 
+set(CMAKE_OSX_DEPLOYMENT_TARGET 11.00 CACHE STRING "")
 project(mrtrix3 LANGUAGES CXX VERSION 3.0.4)
 
+if(NOT CMAKE_GENERATOR STREQUAL "Ninja")
+    message(WARNING "It is recommended to use the Ninja generator to build MRtrix3. "
+                    "To use it, run cmake with -G Ninja or set the CMAKE_GENERATOR "
+                    "environment variable to Ninja.")
+endif()
+
 include(GNUInstallDirs)
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
@@ -15,6 +22,17 @@ option(MRTRIX_STL_DEBUGGING "Enable STL debug mode" OFF)
 option(MRTRIX_BUILD_TESTS "Build tests executables" OFF)
 option(MRTRIX_STRIP_CONDA "Strip ananconda/mininconda from PATH to avoid conflicts" ON)
 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)
+option(MRTRIX_USE_LLD "Use lld as the linker" OFF)
+
+set(MRTRIX_DEPENDENCIES_DIR "" CACHE PATH
+    "An optional local directory containing all thirdparty dependencies:\n \
+    - Eigen3 https://gitlab.com/libeigen/eigen (version 3.4.0 in .tar.gz format)\n \
+    - Json for Modern C++ https://github.com/nlohmann/json (version 3.11.3 in .tar.xz format)\n \
+    - Half https://half.sourceforge.net/ (version 2.1.0 in zip format)\n \
+    - NIfTI C headers https://nifti.nimh.nih.gov/pub/dist/src/nifti2/ (nifti1.h and nifti2.h stored in nifti/ subdirectory)\n"
+)
 
 if(MRTRIX_BUILD_TESTS)
     if(CMAKE_VERSION VERSION_GREATER 3.17)
@@ -59,6 +77,10 @@ include(LinkerSetup)
 include(FindFFTW)
 include(CompilerCache)
 include(ECMEnableSanitizers)
+include(Dependencies)
+if(CMAKE_SYSTEM_NAME MATCHES "Darwin")
+    include(MacOSBundle)
+endif()
 
 use_compiler_cache()
 
@@ -69,30 +91,35 @@ if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git AND NOT EXISTS ${CMAKE_CURRENT_SOURCE
         "and then run `pre-commit install` from the ${CMAKE_CURRENT_SOURCE_DIR} directory.")
 endif()
 
-
-add_compile_definitions(
+add_library(mrtrix-common INTERFACE)
+add_library(mrtrix::common ALIAS mrtrix-common)
+target_compile_definitions(mrtrix-common INTERFACE
     MRTRIX_BUILD_TYPE="${CMAKE_BUILD_TYPE}"
     $<$<PLATFORM_ID:Windows>:MRTRIX_WINDOWS>
     $<$<PLATFORM_ID:Darwin>:MRTRIX_MACOSX>
     $<$<PLATFORM_ID:FreeBSD>:MRTRIX_FREEBSD>
 )
 
-if(MRTRIX_STL_DEBUGGING AND $<NOT:$<CONFIG:Debug>>)
-    if(MSVC)
-        add_compile_definitions(_ITERATOR_DEBUG_LEVEL=1)
-    elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
-        add_compile_options(_LIBCPP_DEBUG)
-    elseif(CMAKE_CXX_COMPILER_ID MATCHES "GNU")
-        add_compile_options(_GLIBCXX_DEBUG _GLIBCXX_DEBUG_PEDANTIC)
-    endif()
+if(MRTRIX_STL_DEBUGGING AND NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
+    message(STATUS "Enabling STL debug mode")
+    target_compile_definitions(mrtrix-common INTERFACE
+        $<$<CXX_COMPILER_ID:MSVC>:_ITERATOR_DEBUG_LEVEL=1>
+        $<$<CXX_COMPILER_ID:GNU>:_GLIBCXX_DEBUG _GLIBCXX_DEBUG_PEDANTIC>
+        $<$<CXX_COMPILER_ID:Clang>:_LIBCPP_DEBUG=1>
+    )
 endif()
 
 if(MRTRIX_WARNINGS_AS_ERRORS)
-    if (MSVC)
-        add_compile_options(/WX)
-    else()
-        add_compile_options(-Werror)
-    endif()
+    message(STATUS "Enabling warnings as errors")
+    target_compile_options(mrtrix-common INTERFACE
+        $<$<CXX_COMPILER_ID:MSVC>:/WX>
+        $<$<CXX_COMPILER_ID:GNU,Clang>:-Werror>
+    )
+endif()
+
+# Allow compilation of big object of files in debug mode on MINGW
+if(MINGW AND CMAKE_BUILD_TYPE MATCHES "Debug")
+    target_compile_options(mrtrix-common INTERFACE -Wa,-mbig-obj)
 endif()
 
 

diff --git a/clang-format-all b/clang-format-all
@@ -1,4 +1,4 @@
-#!/usr/env/python3
+#!/usr/bin/env python3
 
 # Copyright (c) 2008-2024 the MRtrix3 contributors.
 #

diff --git a/cmake/BashTests.cmake b/cmake/BashTests.cmake
@@ -6,7 +6,7 @@ function(add_bash_test)
         message(FATAL_ERROR "bash not found")
     endif()
 
-    set(singleValueArgs FILE_PATH PREFIX WORKING_DIRECTORY)
+    set(singleValueArgs FILE_PATH PREFIX WORKING_DIRECTORY ENVIRONMENT)
     set(multiValueArgs EXEC_DIRECTORIES LABELS)
     cmake_parse_arguments(
         ARG
@@ -20,6 +20,7 @@ function(add_bash_test)
     set(prefix ${ARG_PREFIX})
     set(working_directory ${ARG_WORKING_DIRECTORY})
     set(exec_directories ${ARG_EXEC_DIRECTORIES})
+    set(environment ${ARG_ENVIRONMENT})
     set(labels ${ARG_LABELS})
 
     # Regenerate tests when the test script changes
@@ -47,11 +48,11 @@ function(add_bash_test)
     )
     set_tests_properties(${test_name}
         PROPERTIES
-        ENVIRONMENT "PATH=${exec_directories}"
+        ENVIRONMENT "PATH=${exec_directories};${environment}"
     )
     if(labels)
         set_tests_properties(${test_name} PROPERTIES LABELS "${labels}")
     endif()
 
-    message(VERBOSE "Add bash tests commands for ${test_name}: ${line}")
+    message(VERBOSE "Added bash test command ${test_name}")
 endfunction()
diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
@@ -0,0 +1,92 @@
+include(FetchContent)
+
+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
+# We avoid configuring the Eigen library via FetchContent_MakeAvaiable
+# to avoid the verbosity of Eigen's CMake configuration output.
+if(MRTRIX_LOCAL_DEPENDENCIES)
+    set(eigen_url ${MRTRIX_DEPENDENCIES_DIR}/eigen-3.4.0.tar.gz)
+else()
+    set(eigen_url "https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz")
+endif()
+
+FetchContent_Declare(
+    eigen3
+    DOWNLOAD_EXTRACT_TIMESTAMP ON
+    URL ${eigen_url}
+)
+FetchContent_GetProperties(Eigen3)
+if(NOT eigen3_POPULATED)
+    FetchContent_Populate(Eigen3)
+    add_library(Eigen3 INTERFACE)
+    add_library(Eigen3::Eigen ALIAS Eigen3)
+    target_include_directories(Eigen3 INTERFACE "${eigen3_SOURCE_DIR}")
+endif()
+
+# Json for Modern C++
+if(MRTRIX_LOCAL_DEPENDENCIES)
+    set(json_url ${MRTRIX_DEPENDENCIES_DIR}/json.tar.xz)
+else()
+    set(json_url "https://github.com/nlohmann/json/releases/download/v3.11.3/json.tar.xz")
+endif()
+FetchContent_Declare(
+    json
+    DOWNLOAD_EXTRACT_TIMESTAMP ON
+    URL ${json_url}
+)
+FetchContent_MakeAvailable(json)
+
+
+# Half-precision floating-point library
+if(MRTRIX_LOCAL_DEPENDENCIES)
+    set(half_url ${MRTRIX_DEPENDENCIES_DIR}/half-2.1.0.zip)
+else()
+    set(half_url "https://sourceforge.net/projects/half/files/half/2.1.0/half-2.1.0.zip/download")
+endif()
+FetchContent_Declare(
+    half
+    DOWNLOAD_EXTRACT_TIMESTAMP ON
+    URL ${half_url}
+)
+FetchContent_MakeAvailable(half)
+
+add_library(half INTERFACE)
+add_library(half::half ALIAS half)
+target_include_directories(half INTERFACE "${half_SOURCE_DIR}/include")
+
+
+# Nifti headers
+add_library(nifti INTERFACE)
+add_library(nifti::nifti ALIAS nifti)
+
+if(MRTRIX_LOCAL_DEPENDENCIES)
+    target_include_directories(nifti INTERFACE "${MRTRIX_DEPENDENCIES_DIR}/nifti")
+else()
+    include(ExternalProject)
+    ExternalProject_Add(
+        nifti1
+        PREFIX nifti
+        URL "https://raw.githubusercontent.com/NIFTI-Imaging/nifti_clib/master/nifti2/nifti1.h"
+        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+        DOWNLOAD_NO_EXTRACT ON
+        DOWNLOAD_NO_PROGRESS ON
+        LOG_DOWNLOAD ON
+    )
+    ExternalProject_Add(
+        nifti2
+        PREFIX nifti
+        URL "https://raw.githubusercontent.com/NIFTI-Imaging/nifti_clib/master/nifti2/nifti2.h"
+        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+        DOWNLOAD_NO_EXTRACT ON
+        DOWNLOAD_NO_PROGRESS ON
+        LOG_DOWNLOAD ON
+    )
+    target_include_directories(nifti INTERFACE "${CMAKE_CURRENT_BINARY_DIR}/nifti/src/")
+endif()
+
diff --git a/cmake/FindFFTW.cmake b/cmake/FindFFTW.cmake
@@ -54,22 +54,6 @@ if( FFTW_ROOT )
     NO_DEFAULT_PATH
   )
 
-  find_library(
-    FFTWF_LIB
-    NAMES "fftw3f"
-    PATHS ${FFTW_ROOT}
-    PATH_SUFFIXES "lib" "lib64"
-    NO_DEFAULT_PATH
-  )
-
-  find_library(
-    FFTWL_LIB
-    NAMES "fftw3l"
-    PATHS ${FFTW_ROOT}
-    PATH_SUFFIXES "lib" "lib64"
-    NO_DEFAULT_PATH
-  )
-
   #find includes
   find_path(
     FFTW_INCLUDES
@@ -87,19 +71,6 @@ else()
     PATHS ${PKG_FFTW_LIBRARY_DIRS} ${LIB_INSTALL_DIR}
   )
 
-  find_library(
-    FFTWF_LIB
-    NAMES "fftw3f"
-    PATHS ${PKG_FFTW_LIBRARY_DIRS} ${LIB_INSTALL_DIR}
-  )
-
-
-  find_library(
-    FFTWL_LIB
-    NAMES "fftw3l"
-    PATHS ${PKG_FFTW_LIBRARY_DIRS} ${LIB_INSTALL_DIR}
-  )
-
   find_path(
     FFTW_INCLUDES
     NAMES "fftw3.h"
@@ -108,17 +79,13 @@ else()
 
 endif()
 
-set(FFTW_LIBRARIES ${FFTW_LIB} ${FFTWF_LIB})
-
-if(FFTWL_LIB)
-  set(FFTW_LIBRARIES ${FFTW_LIBRARIES} ${FFTWL_LIB})
-endif()
+set(FFTW_LIBRARIES ${FFTW_LIB})
 
 set( CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_FIND_LIBRARY_SUFFIXES_SAV} )
 
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(FFTW DEFAULT_MSG
                                   FFTW_INCLUDES FFTW_LIBRARIES)
 
-mark_as_advanced(FFTW_INCLUDES FFTW_LIBRARIES FFTW_LIB FFTWF_LIB FFTWL_LIB)
+mark_as_advanced(FFTW_INCLUDES FFTW_LIBRARIES FFTW_LIB)