Remove all usage of namelist collection object modeldb%configuration from LFRic Apps (Full Purge)

[mo-rickywong]

PR Summary

Sci/Tech Reviewer: @allynt
Code Reviewer: @MetBenjaminWent

Technical change as part of migration to new API for accessing namelists from modeldb%config. Code Owners may still comment.

This PR removes the initialisation and usage of the <namelist_collection_type> configuration object. Instances where it was used have been switched to using the <config_type> object

Linked PRs

• linked https://github.com/JCSDA-internal/lfric-jedi/pull/1232

Blocking PRs

• is blocked-by Modify LFRic Apps files that call native/coordinate Jacobian files #184
• is blocked-by Update Apps to work with purge of intermediate configuration object api on lfric core #208

Code Quality Checklist

• I have performed a self-review of my own code
• My code follows the project's style guidelines
• Comments have been included that aid understanding and enhance the readability of the code
• My changes generate no new warnings
• All automated checks in the CI pipeline have completed successfully

Testing

• I have tested this change locally, using the LFRic Apps rose-stem suite
• If any tests fail (rose-stem or CI) the reason is understood and acceptable (e.g. kgo changes)
• I have added tests to cover new functionality as appropriate (e.g. system tests, unit tests, etc.)
• Any new tests have been assigned an appropriate amount of compute resource and have been allocated to an appropriate testing group (i.e. the developer tests are for jobs which use a small amount of compute resource and complete in a matter of minutes)

Test Suite Results - lfric_apps - AppsIntermediateApiFullPurge/run1

Suite Information

Item	Value
Suite Name	AppsIntermediateApiFullPurge/run1
Suite User	ricky.wong
Workflow Start	2026-03-11T08:24:06
Groups Run	developer

Dependency	Reference	Main Like
casim	MetOffice/casim@2026.03.2	True
jules	MetOffice/jules@2026.03.2	True
lfric_apps	MetOffice/lfric_apps@AppsIntermediateApiFullPurge	False
lfric_core	MetOffice/lfric_core@6c47d43	True
moci	MetOffice/moci@2026.03.2	True
SimSys_Scripts	MetOffice/SimSys_Scripts@2026.03.2	True
socrates	MetOffice/socrates@2026.03.2	True
socrates-spectral	MetOffice/socrates-spectral@2026.03.2	True
ukca	MetOffice/ukca@2026.03.2	True

Task Information

✅ succeeded tasks - 1164

Security Considerations

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• Sensitive data is properly handled (if applicable)
• Authentication and authorisation are properly implemented (if applicable)

Performance Impact

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AI Assistance and Attribution

• Some of the content of this change has been produced with the assistance of Generative AI tool name (e.g., Met Office Github Copilot Enterprise, Github Copilot Personal, ChatGPT GPT-4, etc) and I have followed the Simulation Systems AI policy (including attribution labels)

Documentation

• Where appropriate I have updated documentation related to this change and confirmed that it builds correctly

PSyclone Approval

• If you have edited any PSyclone-related code (e.g. PSyKAl-lite, Kernel interface, optimisation scripts, LFRic data structure code) then please contact the TCD Team

Sci/Tech Review

• I understand this area of code and the changes being added
• The proposed changes correspond to the pull request description
• Documentation is sufficient (do documentation papers need updating)
• Sufficient testing has been completed

(Please alert the code reviewer via a tag when you have approved the SR)

Code Review

• All dependencies have been resolved
• Related Issues have been properly linked and addressed
• CLA compliance has been confirmed
• Code quality standards have been met
• Tests are adequate and have passed
• Documentation is complete and accurate
• Security considerations have been addressed
• Performance impact is acceptable

[DanStoneMO]

I expect a linked LFRic-JEDI PR will be needed. I will update once I've been able to test.

[DanStoneMO]

Is there meant to be a linked PR for lfric-core? I've been trying to replicate the changes for lfric-jedi, but the init_config function from lfric's driver_config_mod still requires the configuration object.

[mo-rickywong]

Is there meant to be a linked PR for lfric-core? I've been trying to replicate the changes for lfric-jedi, but the init_config function from lfric's driver_config_mod still requires the configuration object.

It shouldn't do, This branch points to the lfric_core revision at head of main at present:

lfric_core:
    source: git@github.com:MetOffice/lfric_core.git
    ref: 6c47d4320a1ebc2d2d1a5223d047e44423aee622

Which has both the configuration and config arguments as optional for now.

When the old configuration <namelist_collection_type> is not in use it will be removed

[DanStoneMO]

ah okay. I was trying to pass config as a positional argument, so it was being confused for configuration. cheers

[thomasmelvin]

Looks good to me

[DanStoneMO]

Got the JEDI-side changes working now. The PR for them is now live at: https://github.com/JCSDA-internal/lfric-jedi/pull/1232

[allynt]

LGTM