Modernize CMake to use target-scoped constructs (minimum 3.22)

[Copilot]

Replaces deprecated directory-scoped CMake commands with modern target-scoped equivalents across the entire build system.

Minimum version & project

• Bump cmake_minimum_required from 3.10 to 3.22
• Add LANGUAGES C CXX to project()

Target-scoped build properties

• add_definitions() → target_compile_definitions() on library targets
• include_directories() → target_include_directories() with PUBLIC visibility for transitive propagation
• link_libraries() → per-target target_link_libraries() in testdir, ezminc/tests, ezminc/examples

# Before (directory-scoped, affects all targets)
add_definitions(-DHAVE_CONFIG_H)
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/libcommon)
link_libraries(${LIBMINC_LIBRARIES})

# After (target-scoped, propagates via PUBLIC)
target_compile_definitions(${LIBMINC_LIBRARY} PUBLIC HAVE_CONFIG_H)
target_include_directories(${LIBMINC_LIBRARY} PUBLIC ${MINC_INCLUDE_DIRS})
target_link_libraries(volume_test ${LIBMINC_LIBRARIES})

Other modernizations

• Manual -fPIC flag injection → CMAKE_POSITION_INDEPENDENT_CODE
• set(CMAKE_MODULE_PATH ...) → list(APPEND CMAKE_MODULE_PATH ...)
• FindNETCDF.cmake / FindNIFTI.cmake: replace manual found-logic with find_package_handle_standard_args, drop hardcoded search paths
• UseLIBMINC.cmake.in: remove deprecated include_directories() and link_directories()

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[Copilot]

Pull request overview

This PR modernizes the libminc build system by replacing directory-scoped CMake settings with target-scoped properties and updating several custom find modules, aligned with a new minimum CMake version (3.22).

Changes:

• Replaces directory-scoped link_libraries() usage in tests/examples with per-target target_link_libraries().
• Introduces target-scoped include paths and compile definitions for core targets (e.g., minc2, minc_io).
• Modernizes FindNETCDF.cmake / FindNIFTI.cmake to use find_package_handle_standard_args() and simplifies CMAKE_MODULE_PATH handling.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
CMakeLists.txt	Bumps CMake minimum, switches to target-scoped include dirs/compile defs, enables PIC via CMAKE_POSITION_INDEPENDENT_CODE.
testdir/CMakeLists.txt	Replaces directory-wide linking with explicit per-test target linking.
ezminc/CMakeLists.txt	Makes minc_io include paths/compile defs target-scoped.
ezminc/tests/CMakeLists.txt	Switches to per-target linking for test executables.
ezminc/examples/CMakeLists.txt	Switches to per-target linking for example executables.
cmake-modules/FindNETCDF.cmake	Uses FindPackageHandleStandardArgs for standardized discovery reporting.
cmake-modules/FindNIFTI.cmake	Uses FindPackageHandleStandardArgs for standardized discovery reporting.
UseLIBMINC.cmake.in	Removes legacy include/link directory side effects and adds guidance comments.

Comments suppressed due to low confidence (2)

CMakeLists.txt:490

• When building the static library variant (LIBMINC_BUILD_SHARED_LIBS), MINC1 support currently only adds NETCDF include/link settings to the shared target. The static target (${LIBMINC_LIBRARY_STATIC}) may fail to compile (missing netcdf headers) and/or link (missing netcdf lib) when LIBMINC_MINC1_SUPPORT is ON. Apply NETCDF include dirs and NETCDF_LIBRARY to the static target as well, and ensure the NETCDF link is attached to the static target (not the shared one) inside the UNIX/LIBMINC_BUILD_SHARED_LIBS block.

  if(LIBMINC_BUILD_SHARED_LIBS)
    add_library(${LIBMINC_LIBRARY_STATIC} STATIC ${minc_LIB_SRCS} ${minc_HEADERS} ${volume_io_LIB_SRCS} ${volume_io_HEADERS} )
    target_include_directories(${LIBMINC_LIBRARY_STATIC} PUBLIC ${MINC_INCLUDE_DIRS} ${HDF5_INCLUDE_DIRS})
    target_compile_definitions(${LIBMINC_LIBRARY_STATIC} PUBLIC ${MINC_COMPILE_DEFINITIONS})
    target_link_libraries(${LIBMINC_LIBRARY_STATIC} ${HDF5_LIBRARY} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY} ${RT_LIBRARY} m ${CMAKE_DL_LIBS} )
    if(LIBMINC_MINC1_SUPPORT)
      target_link_libraries(${LIBMINC_LIBRARY} ${NETCDF_LIBRARY})
    endif()

UseLIBMINC.cmake.in:17

• UseLIBMINC.cmake.in no longer applies LIBMINC_INCLUDE_DIRS/LIBMINC_LIBRARY_DIRS to consumers (include_directories/link_directories were removed), but the installed package does not appear to install an EXPORT file / imported targets either. This makes the advertised “backward-compatible variable-based configuration” effectively non-functional for downstream projects that still do include(${LIBMINC_USE_FILE}) and link via ${LIBMINC_LIBRARIES}/${EZMINC_LIBRARIES}. Either restore the legacy include/link directory setup here, or complete the migration by installing/exporting targets and updating the config/use-file to rely on them.

# Usage: Downstream projects should prefer using target_link_libraries()
# with the imported LIBMINC targets. This file provides backward-compatible
# variable-based configuration.

# Legacy include/link directory variables for projects not using
# target-based dependencies directly:
# LIBMINC_INCLUDE_DIRS, LIBMINC_LIBRARY_DIRS, LIBMINC_LIBRARIES

if(HAVE_MINC1)
  add_definitions( -DHAVE_MINC1=1)
endif()

if(HAVE_MINC2)
  set(MINC2 "1")
  add_definitions( -DMINC2=1 -DHAVE_MINC2=1)
endif()

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[vfonov]

@gdevenyi what is this?

[vfonov]

i was working on my own changes in https://github.com/BIC-MNI/libminc/tree/modernize_cmake

[gdevenyi]

i was working on my own changes in modernize_cmake

Sorry I didn't see that. I am indeed also trying to modernize the cmake because it won't build on the newest versions of cmake. I'll leave this here for you to cherry-pick any changes, but I will otherwise defer to your branch.

[gdevenyi]

Already fixed.