Update docs with changes to Transmute

[MetBenjaminWent]

PR Summary

Linked issue: #25

A few issues and PRs to apps and core have adjusted slightly how transmute functions.
To improve the docs and bring them in line with its current usage with the make build system, we need to update a few sections.

See #49, #246 and MetOffice/lfric_core#271

Sci/Tech Reviewer: @oakleybrunt
Code Reviewer: @mo-lucy-gordon

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

Test Suite Results - lfric_apps - update_transmute_docs/run1

Suite Information

Item	Value
Suite Name	update_transmute_docs/run1
Suite User	benjamin.went
Workflow Start	2026-02-12T16:20:28
Groups Run	developer

Dependency	Reference	Main Like
casim	MetOffice/[email protected]	True
jules	MetOffice/jules@69aaf4d	True
lfric_apps	MetBenjaminWent/lfric_apps@update_transmute_docs	False
lfric_core	MetOffice/lfric_core@a9ea959	True
moci	MetOffice/[email protected]	True
SimSys_Scripts	MetOffice/[email protected]	True
socrates	MetOffice/[email protected]	True
socrates-spectral	MetOffice/[email protected]	True
ukca	MetOffice/[email protected]	True

Task Information

❌ failed tasks - 3

Task	State
generate_weights_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam-lbc_azspice_weightgen_script	failed
generate_weights_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam_azspice_weightgen_script	failed
run_gungho_model_robert-moist-smag-BiP100x8-10x10_azspice_gnu_fast-debug-64bit	failed

✅ succeeded tasks - 1096

⌛ waiting tasks - 4

Task	State
run_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam-lbc_azspice_gnu_fast-debug-64bit	waiting
run_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam-lbc_ex1a_cce_fast-debug-64bit	waiting
run_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam_azspice_gnu_fast-debug-64bit	waiting
run_lfric2lfric_oasis_clim_gal9_C12-ral_seuk_C16_lam_ex1a_cce_fast-debug-64bit	waiting

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 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

[oakleybrunt]

Thanks Ben, I think this is really good information that is important to record. I have suggested some tweaks to the wording in places to improve calrity, though may have missed some key information. Feel free to add/take away from my suggestions as you see fit.

[oakleybrunt]

Suggested change

	``PSYCLONE_PASS_NO_SCRIPT`` has been implemented primarily for the ``TRANSMUTE_INCLUDE_METHOD``
	``specify_include``, however can be expanded to either.
	It controls whether files are to be passed to PSyclone, but not to have a script applied to them.
	This can be useful to remove existing clauses from a file, but not add anything back.
	files to be affected this way should only be added to this list, as they will be filtered out of
	``PSYCLONE_PHYSICS_FILES`` anyway.
	``PSYCLONE_PASS_NO_SCRIPT`` specifies files to be passed to PSyclone without any associated transformation scripts.
	The primary use case is to remove existing clauses from a file without modifying the Fortran source.
	Any files included in ``PSYCLONE_PASS_NO_SCRIPT`` are filtered out of the ``PSYCLONE_PHYSICS_FILES`` list.
	No transformation scripts will be applied to files in this list regardless of the ``TRANSMUTE_INCLUDE_METHOD``.

[MetBenjaminWent]

Currently I'm not sure specify_exclude actually works for PSYCLONE_PASS_NO_SCRIPT.

I've implemented a very minimum viable product currently, whilst FAB/BAF or simular is being developed. I think I wanted to highlight this here somewhat that the intended use is with specify_include at this time.

[oakleybrunt]

Thanks, I wasn't aware of that. Can I suggest modifying the wording to reflect this? Currently, the phrase "can be expanded to either" suggests to me that users can use PSYCLONE_PASS_NO_SCRIPT with specify_exclude. Maybe this is clearer?

Suggested change

	``PSYCLONE_PASS_NO_SCRIPT`` has been implemented primarily for the ``TRANSMUTE_INCLUDE_METHOD``
	``specify_include``, however can be expanded to either.
	It controls whether files are to be passed to PSyclone, but not to have a script applied to them.
	This can be useful to remove existing clauses from a file, but not add anything back.
	files to be affected this way should only be added to this list, as they will be filtered out of
	``PSYCLONE_PHYSICS_FILES`` anyway.
	``PSYCLONE_PASS_NO_SCRIPT`` has been implemented for the ``TRANSMUTE_INCLUDE_METHOD``
	``specify_include``. Use of this variable for the ``specify_exclude`` method is not mature,
	though work is planned (see [GitHub issue number here]).
	This variable specifies files to be passed to PSyclone without applying any transformations.
	This can be useful to remove existing clauses from a file without modifying the Fortran source.
	Any files included in ``PSYCLONE_PASS_NO_SCRIPT`` are filtered out of the ``PSYCLONE_PHYSICS_FILES`` list.

[mo-lucy-gordon]

• I agree that the wording would be a little clearer if it were changed to something like Oakley's suggestions for lines 128 and 130 specifically:

  • "This variable specifies files to be passed to PSyclone without applying any transformations.
    and
  • "Any files included in PSYCLONE_PASS_NO_SCRIPT are filtered out of the PSYCLONE_PHYSICS_FILES list." .

  And then you could leave in your other lines to just reflect what is currently possible?

• Maybe you could also change line 126 to "however this could be expanded to exclude in the future" ?

[MetBenjaminWent]

@oakleybrunt, thanks for the SR, I've implemented the changes which are viable, though I've not accepted one as the trunk functionality is a little underbaked currently (Given FAB coming and requests from Chris to keep my implementations need only), I wanted the docs to reflect what is currently possible.
Regarding the example, hopefully they come to us to implement it, otherwise emulating the compiler (CCE for example) overrides would be the best place to start. (I also haven't added it due to the above as well).

[mo-lucy-gordon]

Overall this looks good but I also left a comment about suggested wording changes