Update LfricApps to allow for kernel API changes in Core Science components (Tranche 2)

[Ricky Wong (mo-rickywong)]

PR Summary

Sci/Tech Reviewer:
Code Reviewer:

This is a linked PR, it's primarily to maintain a working test suite after updates to LFRic Core API changes from MetOffice/lfric_core#465. Main aspects of this PR are:

• Plumbing to get the application configuration object config to the correct locations before configuration variables are required, generally before invokes.
• Where APIS use mesh_id, they have been migrated to using the mesh_object_type, in the order (config, mesh, ...) at the beginning of the argument list.
• geometry/topology enumerations are more appropriately accessed from the mesh object in low-level code and not via config%base_mesh. The enumerations are the same for now, and access has been updated when in the vicinity of code being updated in this PR.

As the changes here are to maintain a working test-suite, the LFRic apps repository still contains many routines accessing configuration from module scope and using feigners in the corresponding unit tests. Those remaining instances are out of scope on this PR.

Linked PRs

• linked Remove global scope access of namelist configurations from science component kernels with feigners (tranche 2) lfric_core#465

This PR is blocked

• blocked-by Update LfricApps to allow for kernel API changes in Core Science components (Tranche 1) #654
• blocked-by Changes to apps as a result of decoupling base_mesh_config geology / topology enumerations #757

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

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

• 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)

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 HPC Optimisation 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