address pio issues

[jedwards4b]

Description

Updates build process for netcdf/4.9.3 in a backward compatible manner.
Adds logic to make sure that typename netcdf4p is not combined with format 64bit_data.

• Closes pio_typename=netcdf4p is not compatible with pio_netcdf_format=64bit_data #4924
• Closes pio updates and improved logic #4923

Checklist

• My code follows the style guidelines of this project (black formatting)
• I have performed a self-review of my own code
• My changes generate no new warnings
• I have added tests that exercise my feature/fix and existing tests continue to pass
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding additions and changes to the documentation

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 31.32%. Comparing base (800e2d7) to head (20ffc33).
⚠️ Report is 24 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #4925      +/-   ##
==========================================
- Coverage   31.38%   31.32%   -0.07%     
==========================================
  Files         264      264              
  Lines       38869    38967      +98     
  Branches     8260     8280      +20     
==========================================
+ Hits        12199    12206       +7     
- Misses      25430    25521      +91     
  Partials     1240     1240              

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[Copilot]

Pull request overview

This PR updates the CIME build process to support netcdf/4.9.3 in a backward-compatible manner and adds validation to prevent incompatible PIO configuration combinations (specifically, preventing the use of netcdf4p typename with 64bit_data format).

Changes:

• Updated CMake cache string detection in buildlib.pio for netcdf 4.9.3 compatibility
• Added validation in env_run.py to check PIO_TYPENAME and PIO_NETCDF_FORMAT compatibility when setting values
• Added validation in preview_namelists.py to verify compatibility before creating namelists

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 8 comments.

File	Description
CIME/build_scripts/buildlib.pio	Updates expect_string and netcdf4_string to match netcdf 4.9.3 CMake output format, adds backward compatibility check for old expect_string format
CIME/XML/env_run.py	Adds import for zip_longest, implements validation logic in set_value() to prevent incompatible PIO_TYPENAME and PIO_NETCDF_FORMAT combinations
CIME/case/preview_namelists.py	Adds validation check during namelist creation to catch incompatible PIO configurations

Comments suppressed due to low confidence (1)

CIME/build_scripts/buildlib.pio:212

• The netcdf4_string was changed from "NetCDF_C_HAS_PARALLEL:BOOL=TRUE" to "HAVE_NETCDF_PAR:INTERNAL=1" for netcdf 4.9.3 compatibility. However, unlike expect_string which has backward compatibility logic (line 207-208), there's no fallback check for the old netcdf4_string pattern. This could cause netcdf4_parallel_found to remain False when using older versions of netcdf, preventing netcdf4p and netcdf4c from being added to valid_values. Consider adding a similar elif check for "NetCDF_C_HAS_PARALLEL:BOOL=TRUE" to maintain backward compatibility.

        netcdf4_string = "HAVE_NETCDF_PAR:INTERNAL=1"

    # make sure case pio_typename valid_values is set correctly
    expect_string_found = False
    pnetcdf_found = False
    netcdf4_parallel_found = False

    cache_file = open(os.path.join(pio_dir, "CMakeCache.txt"), "r")
    for line in cache_file:
        if re.search(expect_string, line):
            expect_string_found = True
        elif re.search("NetCDF_C_LIBRARY-ADVANCED", line):
            expect_string_found = True
        if re.search(pnetcdf_string, line):
            pnetcdf_found = True
        if re.search(netcdf4_string, line):
            netcdf4_parallel_found = True

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[Copilot]

If get_value() returns None (which can happen if the entry is not found), this will create a list containing None [None]. Later when the validation tries to check "64bit_data" in pio_netcdf_format (line 105), it will raise a TypeError because the in operator cannot be used with None. Consider adding a check to handle the case where get_value returns None, or provide a default value.

[Copilot]

The new validation logic for incompatible PIO_TYPENAME and PIO_NETCDF_FORMAT combinations lacks test coverage. Given that this repo has comprehensive automated testing (as seen in the CIME/tests directory), consider adding unit tests to verify that:

1. The validation correctly prevents setting netcdf4p/netcdf4c with 64bit_data format
2. The validation works for both component-specific and general PIO settings
3. Edge cases like None values or empty lists are handled properly
4. The validation allows valid combinations to pass through

[Copilot]

This code will raise an IndexError if either pio_netcdf_formats or pio_typenames is an empty list, since it tries to access [-1] index. This could happen if get_values() returns an empty list when the variable is not found or has no values. Consider adding a check to ensure the lists are not empty before accessing the last element, or handle the case where no values are found.

Suggested change

	# If either list is empty, we cannot perform a meaningful compatibility
	# check. In that case, skip the check and proceed with setting the value.
	if not pio_netcdf_formats or not pio_typenames:
	return EnvBase.set_value(self, vid, value, subgroup, ignore_type)