Update Apps to work with purge of intermediate configuration object api on lfric core

[mo-rickywong]

PR Summary

This is a technical infrastructure change, it does not change science or the overall structure of applications. SciTech is N/A though code owners may wish to check their relevant code areas in case they have comments/objections.

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

NOTE: @ukmo-juan-castillo added to review changes in a Code Owner capacity only

MetOffice/lfric_core#262 Removes instances of usage of the intermediate api to access namelist configurations from lfric_core. This however means that some routines in lfric_core have their argument lists changed, this may impact some applications in lfric_apps.

This PR only changes what is required to work with the linked MetOffice/lfric_core#262. Further PRs to remove usage of the Intermediate api from Lfric_apps will follow.

Linked PRs

• Purge Intermediate Api access to configuration object from in favor of new config_type object lfric_core#262

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)

trac.log

Testing was done with developer group and lfric_atm_extra as some iau is not exercised in the main developer group.

Test Suite Results - lfric_apps - AppsIntermediateApiPurge/run4

Suite Information: lfric_atm_extra group

Item	Value
Suite Name	AppsIntermediateApiPurge/run4
Suite User	ricky.wong
Workflow Start	2026-02-03T10:08:00
Groups Run	lfric_atm_extra

Dependency	Reference	Main Like
casim	MetOffice/casim@2025.12.1	True
jules	MetOffice/jules@69aaf4d	True
lfric_apps	mo-rickywong/lfric_apps@AppsIntermediateApiPurge	False
lfric_core	mo-rickywong/lfric_core@IntermediateApiPurge	True
moci	MetOffice/moci@2025.12.1	True
SimSys_Scripts	MetOffice/SimSys_Scripts@2025.12.1	True
socrates	MetOffice/socrates@2025.12.1	True
socrates-spectral	MetOffice/socrates-spectral@2025.12.1	True
ukca	MetOffice/ukca@2025.12.1	True

Task Information

✅ succeeded tasks - 173

Test Suite Results - lfric_apps - AppsIntermediateApiPurge/run5

Suite Information: Developer group

Item	Value
Suite Name	AppsIntermediateApiPurge/run5
Suite User	ricky.wong
Workflow Start	2026-02-03T10:08:51
Groups Run	developer

Dependency	Reference	Main Like
casim	MetOffice/casim@2025.12.1	True
jules	MetOffice/jules@69aaf4d	True
lfric_apps	mo-rickywong/lfric_apps@AppsIntermediateApiPurge	False
lfric_core	mo-rickywong/lfric_core@IntermediateApiPurge	True
moci	MetOffice/moci@2025.12.1	True
SimSys_Scripts	MetOffice/SimSys_Scripts@2025.12.1	True
socrates	MetOffice/socrates@2025.12.1	True
socrates-spectral	MetOffice/socrates-spectral@2025.12.1	True
ukca	MetOffice/ukca@2025.12.1	True

Task Information

✅ succeeded tasks - 1106

Security Considerations

• I have reviewed my changes for potential security issues
• Sensitive data is properly handled (if applicable)
• Authentication and authorisation are properly implemented (if applicable)

Performance Impact

N/A

• Performance of the code has been considered and, if applicable, suitable performance measurements have been conducted

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)

No AI was used on this PR developerment

Documentation

N/A

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

PSyclone Approval

N/A

• 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

N/A : Code owners may wish to review / comment

• 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

[jennyhickson]

While this is a non-scientific change its still too large for only one review, please can you organise a SciTech reviewer as well?

[ss421]

This change will need to have a linked PR in lfric-jedi. We can create a PR for this and test it. Since we have an issue with the change in MetOffice/lfric_core#175 I think its worth waiting for a fix before doing the test although it will likely just work with this change if I understand this correctly.

Ive added this PR to the list or required updates documented in: https://github.com/JCSDA-internal/lfric-jedi/pull/1206

@DanStoneMO - could you take a look at this please? Thanks.

[mo-rickywong]

This change will need to have a linked PR in lfric-jedi. We can create a PR for this and test it. Since we have an issue with the change in MetOffice/lfric_core#175 I think its worth waiting for a fix before doing the test although it will likely just work with this change if I understand this correctly.

Ive added this PR to the list or required updates documented in: https://github.com/JCSDA-internal/lfric-jedi/pull/1206

@DanStoneMO - could you take a look at this please? Thanks.

The lfric-jedi link is not reachable, can you reference the linked PR when available.

[ukmo-juan-castillo]

From the lfric2lfric perspective, everything looks in order when looking at the code in lfric_core. I run the lfric2lfric checks myself successfully. The only comment I have is that, in the follow-up ticket, the lfric2lfric init_mesh subroutine version should be updated so that it has the same parameters as the lfric_core init_mesh subroutine.

Thank you, though strictly that comment is not relevant to this PR, but should be made on the follow-up PR
(@mo-rickywong )

[ukmo-juan-castillo]

From the lfric2lfric perspective, everything looks in order when looking at the code in lfric_core. I run the lfric2lfric checks myself successfully. The only comment I have is that, in the follow-up ticket, the lfric2lfric init_mesh subroutine version should be updated so that it has the same parameters as the lfric_core init_mesh subroutine.

Thank you, though strictly that comment is not relevant to this PR, but should be made on the follow-up PR
(@mo-rickywong )

[ss421]

This change will need to have a linked PR in lfric-jedi. We can create a PR for this and test it. Since we have an issue with the change in MetOffice/lfric_core#175 I think its worth waiting for a fix before doing the test although it will likely just work with this change if I understand this correctly.
Ive added this PR to the list or required updates documented in: JCSDA-internal/lfric-jedi#1206
@DanStoneMO - could you take a look at this please? Thanks.

The lfric-jedi link is not reachable, can you reference the linked PR when available.

@DanStoneMO has a branch but the tests are failing at runtime, see for example: ctest_jjtests_hofx_atms__spice_gnu_debug . I think this is the same issue we have already seen and was fixed via: MetOffice/lfric_core#264. It seems the lfric_core branch does not include that change.

Would it be possible to merge upto the head of main?

[iboutle]

This change appears to affect far more than expected, i.e. there are KGO changes and all sorts going on here - I'm not sure if something has gone wrong with the branch or the diff, but is it possible to show a clean diff of the changes just in this PR?

[github-actions]

⚠️ Hello @mo-rickywong!

Your CLA signature was found on the base branch, but you appear to have modified the CONTRIBUTORS.md file in this PR.

Please do not edit the CONTRIBUTORS.md file. If you have already signed the CLA, revert changes to the file and your signature will be picked up.

[mo-rickywong]

This change appears to affect far more than expected, i.e. there are KGO changes and all sorts going on here - I'm not sure if something has gone wrong with the branch or the diff, but is it possible to show a clean diff of the changes just in this PR?

I tried to bring this up to date as JEDI what to take account of a the jedi fix. Though the merge changed lots of unexepcted stuff. I've reverted the change as bringing it up-to-date should change much

[thomasmelvin]

These changes look fine but (without knowing the details) I am a bit confused by routines having both a config and configuration passed in which are very similar name so it's not really obvious what the difference is. Could one set be renamed? or will it be changed in the future?