update cmake build

[jedwards4b]

Brings minimum cmake version to 3.10 and removes some obsolete functions.

[Copilot]

Pull request overview

This PR modernizes the CMake build system by updating the minimum required CMake version from 3.5.2 to 3.10 and adopting newer CMake conventions. The update removes obsolete functions and replaces them with modern alternatives, while also improving dependency management for NetCDF and PnetCDF libraries.

Changes:

• Updated minimum CMake version requirement from 3.5.2 to 3.10 across all CMakeLists.txt files
• Replaced uppercase CMake commands (e.g., ADD_DEFINITIONS, SET) with lowercase equivalents (e.g., add_definitions, set)
• Replaced deprecated find_package modules for NetCDF and PnetCDF with pkg-config and direct configuration script detection
• Added explicit library directory linking via link_directories() for NetCDF and PnetCDF dependencies

Reviewed changes

Copilot reviewed 20 out of 20 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
CMakeLists.txt	Updated minimum version, modernized commands, replaced FindNetCDF/FindPnetCDF with pkg-config and pnetcdf-config detection
src/clib/CMakeLists.txt	Updated minimum version, fixed PnetCDF library variable reference
src/flib/CMakeLists.txt	Updated minimum version, added NetCDF variable propagation from cache
src/gptl/CMakeLists.txt	Updated minimum version, modernized formatting with consistent spacing
src/CMakeLists.txt	Added blank lines for improved readability
tests/*/CMakeLists.txt	Added link_directories for NetCDF and PnetCDF library paths
examples/*/CMakeLists.txt	Modernized commands to lowercase, added NetCDF library directory linking
cmake/FindNetCDF.cmake	Removed obsolete custom find module
cmake/FindPnetCDF.cmake	Removed obsolete custom find module
cmake/LibFind.cmake	Fixed find_package_handle_standard_args to use main package name
doc/CMakeLists.txt	Modernized commands to lowercase

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[Copilot]

NetCDF C detection code is duplicated (lines 67-75 and 333-341). This duplicate check should be removed and the first detection block should be used consistently throughout the file.

[Copilot]

The REQUIRED keyword for find_program causes a CMake fatal error if pnetcdf-config is not found, but there's no informative error message guiding users on how to resolve this. Consider adding a custom error message or making it conditional based on WITH_PNETCDF option.

Suggested change

	find_program(PNETCDF_CONFIG pnetcdf-config REQUIRED)
	find_program(PNETCDF_CONFIG pnetcdf-config)
	if(NOT PNETCDF_CONFIG)
	message(FATAL_ERROR
	"Could not find 'pnetcdf-config' in your PATH.\n"
	"Please install PnetCDF (which provides the 'pnetcdf-config' tool) "
	"or disable PnetCDF support by configuring with -DWITH_PNETCDF=OFF."
	)
	endif()

[Copilot]

Variable naming inconsistency: PnetCDF_C_INCLUDE_DIRS and PnetCDF_C_LIBRARIES use component-style naming (with C), but are being set from PNETCDF_INCLUDEDIR and PNETCDF_LIBS which don't include the C component. This creates confusion about which variables represent what. Consider using consistent naming throughout.

[Copilot]

Variable naming inconsistency: line 491 sets HAVE_PAR_FILTERS but line 493 also sets HAVE_PAR_FILTERS, while line 590 checks HAVE_PAR_FILTERS and sets PIO_HAS_PAR_FILTERS. This dual naming convention (HAVE_PAR_FILTERS vs PIO_HAS_PAR_FILTERS) should be unified for clarity.