Modernize CMake build system with modular structure and toolchain files by Copilot · Pull Request #48 · hdclark/DICOMautomaton

Copilot · 2026-01-31T03:23:45Z

Summary

This PR modernizes the DICOMautomaton CMake build system by:

Creating modular cmake/ helper modules that encapsulate compiler options, dependency finding, platform checks, and feature definitions into reusable functions
Adding FetchContent fallbacks in DCMADependencies.cmake for Eigen and NLopt when system packages are unavailable
Creating cross-compilation toolchain files for Windows (MXE), macOS (osxcross), ARM64, and musl libc builds
Adding CMakePresets.json for standardized build configurations (debug, release, minimal, full, sanitizers, cross-compile presets)
Improving dependency handling by using QUIET instead of REQUIRED with graceful fallback, allowing builds to succeed with fewer dependencies
Adding DCMA_ prefixed options with backward compatibility for existing build scripts using legacy option names
Adding a dependency configuration summary at configure time for better build visibility

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Co-authored-by: hdclark <934858+hdclark@users.noreply.github.com>

Copilot

Pull request overview

This PR modernizes the CMake build system by introducing a modular structure with separate files for compiler options, dependencies, platform checks, and definitions. It adds comprehensive cross-compilation toolchain files for Windows (MXE), macOS (osxcross), Linux ARM64/ARMv7, and musl-based static builds, along with CMakePresets.json for common build configurations.

Changes:

Introduced modular CMake structure with cmake/DCMA*.cmake files providing reusable functions for compiler options, dependency finding (with FetchContent fallbacks), platform detection, and feature definitions
Added four cross-compilation toolchain files and CMakePresets.json with debug, release, minimal, full, sanitizer, and cross-compile configurations
Updated root CMakeLists.txt to use DCMA_-prefixed options with backward compatibility for legacy names, changed dependency finding from REQUIRED to QUIET with graceful fallback, and added a dependency configuration summary

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
CMakePresets.json	Adds preset configurations for debug, release, minimal, full, sanitizers, static, and cross-compilation builds
cmake/DCMACompilerOptions.cmake	Provides target-based compiler flag functions with GCC/Clang support and sanitizer configurations
cmake/DCMADependencies.cmake	Implements dependency finding with FetchContent fallbacks for Eigen and NLopt
cmake/DCMAPlatformChecks.cmake	Handles ARM detection, stdlib feature checks, CGAL compatibility, and Windows configuration
cmake/DCMADefines.cmake	Manages feature compile definitions and version extraction
cmake/toolchains/mxe-x86_64-w64-mingw32.cmake	Windows cross-compilation via MXE toolchain
cmake/toolchains/macos-x86_64.cmake	macOS cross-compilation via osxcross
cmake/toolchains/linux-musl.cmake	musl libc static build configuration
cmake/toolchains/linux-aarch64.cmake	ARM64/ARMv7 cross-compilation setup
CMakeLists.txt	Adds DCMA_-prefixed options, backward compatibility mapping, graceful dependency fallback, and configuration summary

Copilot · 2026-01-31T03:59:59Z

cmake/DCMACompilerOptions.cmake

+            -pie
+            -fsanitize-memory-track-origins
+        )
+        target_link_options(${target} PRIVATE -fsanitize=memory)


The -pie flag in line 110 is a linker flag, not a compiler flag. It should be passed via target_link_options instead of target_compile_options. The -fPIE flag is correct for compile options, but -pie should be moved to the link options in line 113 along with -fsanitize=memory.

Suggested change

-pie

-fsanitize-memory-track-origins

)

target_link_options(${target} PRIVATE -fsanitize=memory)

-fsanitize-memory-track-origins

)

target_link_options(${target} PRIVATE

-fsanitize=memory

-pie

)

Copilot · 2026-01-31T04:00:00Z

cmake/toolchains/mxe-x86_64-w64-mingw32.cmake

+    set(CMAKE_EXE_LINKER_FLAGS "-static")
+    set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build shared libraries" FORCE)


The linker flag -static is being set globally in CMAKE_EXE_LINKER_FLAGS on line 48, but this may not propagate correctly to all targets. Consider using add_link_options(-static) instead or documenting that users may need to set additional link options for libraries. Additionally, the CACHE FORCE approach on line 49 prevents users from overriding this setting.

Suggested change

set(CMAKE_EXE_LINKER_FLAGS "-static")

set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build shared libraries" FORCE)

# Prefer static linking for executables built with this static MXE toolchain;

# use add_link_options so that the flag propagates correctly to targets.

add_link_options(-static)

# Default to building static libraries, but allow users to override

# BUILD_SHARED_LIBS from the command line or presets.

if(NOT DEFINED BUILD_SHARED_LIBS)

set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build shared libraries")

endif()

Copilot · 2026-01-31T04:00:00Z

cmake/toolchains/linux-musl.cmake

+# Flags for musl compatibility
+set(CMAKE_C_FLAGS_INIT "-static")
+set(CMAKE_CXX_FLAGS_INIT "-static")
+set(CMAKE_EXE_LINKER_FLAGS_INIT "-static")


The static linking flags are set via CMAKE_*_FLAGS_INIT variables (lines 67-69), which are initialization flags. While this is a valid approach, these flags may not apply to all link scenarios (e.g., shared libraries if BUILD_SHARED_LIBS is later changed). Consider using add_link_options(-static) or document that this toolchain is strictly for static executables only.

Suggested change

set(CMAKE_EXE_LINKER_FLAGS_INIT "-static")

add_link_options(-static)

Copilot · 2026-01-31T04:00:00Z

cmake/DCMAPlatformChecks.cmake

+function(dcma_run_all_platform_checks)
+    dcma_detect_arm_architecture()
+    dcma_check_cppstdlib_features()
+    dcma_check_system_features()


The function dcma_check_cgal_compatibility() is defined but not called in dcma_run_all_platform_checks() on line 126. If this function is intended to be part of the platform checks workflow, it should be added to the function. If it's intended to be called separately, consider documenting this or renaming the umbrella function to clarify its scope.

Suggested change

dcma_check_system_features()

dcma_check_system_features()

dcma_check_cgal_compatibility()

Copilot · 2026-01-31T04:00:01Z

CMakePresets.json

+    "version": 6,
+    "cmakeMinimumRequired": {
+        "major": 3,
+        "minor": 21,


The CMakePresets.json file specifies cmakeMinimumRequired as 3.21.0, but the root CMakeLists.txt file requires CMake 3.12.0. This creates an inconsistency where presets require a newer CMake version than the project itself. Consider updating CMakeLists.txt to require CMake 3.21 if presets are intended to be the primary configuration method, or lower the preset requirement to match the project minimum.

Suggested change

"minor": 21,

"minor": 12,

Copilot · 2026-01-31T04:00:01Z

CMakeLists.txt

+if(DEFINED WITH_SFML AND NOT DEFINED DCMA_WITH_SFML_SET)
+    set(DCMA_WITH_SFML ${WITH_SFML})
+endif()
+if(DEFINED WITH_SDL AND NOT DEFINED DCMA_WITH_SDL_SET)
+    set(DCMA_WITH_SDL ${WITH_SDL})
+endif()
+if(DEFINED WITH_WT AND NOT DEFINED DCMA_WITH_WT_SET)
+    set(DCMA_WITH_WT ${WITH_WT})
+endif()
+if(DEFINED WITH_GNU_GSL AND NOT DEFINED DCMA_WITH_GNU_GSL_SET)
+    set(DCMA_WITH_GNU_GSL ${WITH_GNU_GSL})
+endif()
+if(DEFINED WITH_POSTGRES AND NOT DEFINED DCMA_WITH_POSTGRES_SET)
+    set(DCMA_WITH_POSTGRES ${WITH_POSTGRES})
+endif()
+if(DEFINED WITH_JANSSON AND NOT DEFINED DCMA_WITH_JANSSON_SET)
+    set(DCMA_WITH_JANSSON ${WITH_JANSSON})
+endif()
+if(DEFINED WITH_THRIFT AND NOT DEFINED DCMA_WITH_THRIFT_SET)
+    set(DCMA_WITH_THRIFT ${WITH_THRIFT})
+endif()
+if(DEFINED WITH_LTO AND NOT DEFINED DCMA_WITH_LTO_SET)


The backward compatibility mechanism is incomplete. The code checks for variables like DCMA_MEMORY_CONSTRAINED_BUILD_SET, DCMA_WITH_IWYU_SET, etc., but these variables are never set anywhere in the code. This means that if a user provides both the legacy option (e.g., WITH_EIGEN) and the new option (e.g., DCMA_WITH_EIGEN), the legacy option will always override the new one, which is likely not the intended behavior. The condition should either remove the _SET check, or the code should set these sentinel variables when the DCMA_ prefixed options are explicitly provided.

Suggested change

if(DEFINED WITH_SFML AND NOT DEFINED DCMA_WITH_SFML_SET)

set(DCMA_WITH_SFML ${WITH_SFML})

endif()

if(DEFINED WITH_SDL AND NOT DEFINED DCMA_WITH_SDL_SET)

set(DCMA_WITH_SDL ${WITH_SDL})

endif()

if(DEFINED WITH_WT AND NOT DEFINED DCMA_WITH_WT_SET)

set(DCMA_WITH_WT ${WITH_WT})

endif()

if(DEFINED WITH_GNU_GSL AND NOT DEFINED DCMA_WITH_GNU_GSL_SET)

set(DCMA_WITH_GNU_GSL ${WITH_GNU_GSL})

endif()

if(DEFINED WITH_POSTGRES AND NOT DEFINED DCMA_WITH_POSTGRES_SET)

set(DCMA_WITH_POSTGRES ${WITH_POSTGRES})

endif()

if(DEFINED WITH_JANSSON AND NOT DEFINED DCMA_WITH_JANSSON_SET)

set(DCMA_WITH_JANSSON ${WITH_JANSSON})

endif()

if(DEFINED WITH_THRIFT AND NOT DEFINED DCMA_WITH_THRIFT_SET)

set(DCMA_WITH_THRIFT ${WITH_THRIFT})

endif()

if(DEFINED WITH_LTO AND NOT DEFINED DCMA_WITH_LTO_SET)

if(DEFINED WITH_SFML)

set(DCMA_WITH_SFML ${WITH_SFML})

endif()

if(DEFINED WITH_SDL)

set(DCMA_WITH_SDL ${WITH_SDL})

endif()

if(DEFINED WITH_WT)

set(DCMA_WITH_WT ${WITH_WT})

endif()

if(DEFINED WITH_GNU_GSL)

set(DCMA_WITH_GNU_GSL ${WITH_GNU_GSL})

endif()

if(DEFINED WITH_POSTGRES)

set(DCMA_WITH_POSTGRES ${WITH_POSTGRES})

endif()

if(DEFINED WITH_JANSSON)

set(DCMA_WITH_JANSSON ${WITH_JANSSON})

endif()

if(DEFINED WITH_THRIFT)

set(DCMA_WITH_THRIFT ${WITH_THRIFT})

endif()

if(DEFINED WITH_LTO)

Copilot · 2026-01-31T04:00:01Z

CMakeLists.txt

-option(WITH_LTO       "Use link-time optimization when available."              OFF)
+option(DCMA_WITH_LTO       "Use link-time optimization when available."              OFF)

 option(BUILD_SHARED_LIBS "Build shared-object/dynamicly-loaded binaries."       ON)


The word "dynamicly" is misspelled and should be "dynamically".

Suggested change

option(BUILD_SHARED_LIBS "Build shared-object/dynamicly-loaded binaries." ON)

option(BUILD_SHARED_LIBS "Build shared-object/dynamically-loaded binaries." ON)

Copilot · 2026-01-31T04:00:01Z

cmake/DCMACompilerOptions.cmake

+        target_link_libraries(${target} PRIVATE gcov)
+    endif()
+
+    target_compile_definitions(${target} PRIVATE -U_FORTIFY_SOURCE)


The -U_FORTIFY_SOURCE flag is being passed to target_compile_definitions but this is a compiler flag, not a definition. It should be passed to target_compile_options instead. The correct approach would be to use target_compile_options(${target} PRIVATE -U_FORTIFY_SOURCE) or target_compile_definitions(${target} PRIVATE _FORTIFY_SOURCE=0) depending on the intent.

Suggested change

target_compile_definitions(${target} PRIVATE -U_FORTIFY_SOURCE)

target_compile_options(${target} PRIVATE -U_FORTIFY_SOURCE)

hdclark · 2026-01-31T05:28:12Z

@copilot apply changes based on the comments in this thread

…d version consistency Co-authored-by: hdclark <934858+hdclark@users.noreply.github.com>

Copilot · 2026-01-31T05:30:50Z

@copilot apply changes based on the comments in this thread

Applied all 8 review comments in commit ae95c39:

Moved -pie from compile options to link options for MSan
Changed MXE toolchain to use add_link_options(-static) and removed CACHE FORCE for BUILD_SHARED_LIBS
Changed musl toolchain to use add_link_options(-static) for proper propagation
Added dcma_check_cgal_compatibility() to dcma_run_all_platform_checks()
Lowered CMakePresets.json CMake version requirement from 3.21 to 3.12 to match project minimum
Fixed backward compatibility by removing unused _SET suffix checks
Fixed "dynamicly" typo to "dynamically"
Changed -U_FORTIFY_SOURCE to use target_compile_options instead of target_compile_definitions

Initial plan

44e0765

Copilot AI assigned Copilot and hdclark Jan 31, 2026

Copilot started work on behalf of hdclark January 31, 2026 03:24 View session

Copilot AI and others added 2 commits January 31, 2026 03:31

Add modular CMake structure with helper modules and toolchain files

d9e6ee4

Co-authored-by: hdclark <934858+hdclark@users.noreply.github.com>

Add comment documenting existing TCGETADDR variable name typo

e703fad

Co-authored-by: hdclark <934858+hdclark@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Refactor CMakeLists.txt for modern idiomatic usage~~ Modernize CMake build system with modular structure and toolchain files Jan 31, 2026

Copilot AI requested a review from hdclark January 31, 2026 03:36

Copilot finished work on behalf of hdclark January 31, 2026 03:36

hdclark marked this pull request as ready for review January 31, 2026 03:53

Copilot AI review requested due to automatic review settings January 31, 2026 03:53

Copilot started reviewing on behalf of hdclark January 31, 2026 03:54 View session

Copilot AI reviewed Jan 31, 2026

View reviewed changes

Copilot started work on behalf of hdclark January 31, 2026 05:28 View session

Apply review feedback: fix compiler/linker flags, backward compat, an…

ae95c39

…d version consistency Co-authored-by: hdclark <934858+hdclark@users.noreply.github.com>

Copilot finished work on behalf of hdclark January 31, 2026 05:32

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Modernize CMake build system with modular structure and toolchain files#48

Modernize CMake build system with modular structure and toolchain files#48
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		set(CMAKE_EXE_LINKER_FLAGS "-static")
		set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build shared libraries" FORCE)

-    set(CMAKE_EXE_LINKER_FLAGS "-static")
-    set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build shared libraries" FORCE)
+    # Prefer static linking for executables built with this static MXE toolchain;
+    # use add_link_options so that the flag propagates correctly to targets.
+    add_link_options(-static)
+    # Default to building static libraries, but allow users to override
+    # BUILD_SHARED_LIBS from the command line or presets.
+    if(NOT DEFINED BUILD_SHARED_LIBS)
+        set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build shared libraries")
+    endif()

	set(CMAKE_EXE_LINKER_FLAGS_INIT "-static")
	add_link_options(-static)

	dcma_check_system_features()
	dcma_check_system_features()
	dcma_check_cgal_compatibility()

	option(BUILD_SHARED_LIBS "Build shared-object/dynamicly-loaded binaries." ON)
	option(BUILD_SHARED_LIBS "Build shared-object/dynamically-loaded binaries." ON)

	target_compile_definitions(${target} PRIVATE -U_FORTIFY_SOURCE)
	target_compile_options(${target} PRIVATE -U_FORTIFY_SOURCE)

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Copilot AI commented Jan 31, 2026 •

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