Add skeleton fab script

[hiker]

PR Summary

Sci/Tech Reviewer: @MatthewHambley
Code Reviewer: @t00sa

Adds a first Fab build script for Skeleton. To keep this change minimal, it's command line only (i.e. no cylc integration, which can come later).

• closes Add Fab build script for Skeleton apps #240

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 Core rose-stem suite
• If required (e.g. API changes) I have also run the LFRic Apps test suite using this branch
• 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 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

[hiker]

This PR only adds a command-line build system using Fab for the Skeleton apps. It is not at all integrated into cylc or any other test suite. Tests have been added to the infrastructure/build/fab scripts which cover the newly added infrastructure files there.

Some unit tests are based on some AI input to setup the frame work, but have been manually tweaked to ensure code coverage.

Documentation is in form of a README in the above directory, please let me know if you want me to add more elsewhere.

[MatthewHambley]

I note that a lot of requests made in the original review on SRS have not been addressed so for convenience I have repeated them here.

[hiker]

I note that a lot of requests made in the original review on SRS have not been addressed so for convenience I have repeated them here.

I note that all my comments and questions to your original reviews (as originally agreed a few months ago on MetOffice/lfric-baf#83) have not been addressed so for convenience I will repeat them here.

It will take me a while to get through all your comments, but I will start adding comments now, so ideally we can discuss some of the issue and reach an agreement while I still work on other comments.

[hiker]

I believe I have all issues addressed. The main remaining issue seems to be the usage of the .py suffix, which might require a meeting to sort this out?

[MatthewHambley]

I'm hopeful this will be the last round.

[hiker]

I can't reply to your comment about precision, so I'll copy your comment here and hope for the best :)

There are a number of precision bubbles for different science sections and each of these has a default. These are things like R_TRAN and R_SOLVER. There is then the catch-all bubble for everything else, which is unhelpfully called R_DEF. So, in fact this "default" value is only a default for itself. This is what I'd forgotten.

Yes, R_DEF is 'everything else`.

So the question then becomes - how do we handle this at the command line.

I think the solution is to use different terminology which better describes what's happening. I like the -precision = form for command-line arguments but suggest "other" for the catch-all. Obviously the preprocessor macro will still be R_DEF because to use otherwise would require a substantial change to the source code.

My problem is that this does not follow standard argparse format, i.e. would require additional work on adding help text, verification of bubble name etc. What about just --precision-BUBBLENAME WORD_SIZE (which would also accept --precision-BUBBLENAME=WORD_SIZE

So we would then have (say) --precision-other=32, which would set R_DEF internally (the rest remain the way it is).

And then I remove the handling of a floating point default value that I have added (i.e. --precision-default) entirely?

Do I understand this correctly?

I'm not entirely happy with "other" but it should make it clear that this is not a default to the other precision bubbles, but a specific value for unspecified bubbles.

I might not agree with that (I would think lfric developer know what R_DEF is, but might get confused by precision-other) , but I will try to address this in the help message for this option.

[hiker]

I'm hopeful this will be the last round.

Could you just clarify if my understanding of your precision is correct? So that I can implement it the right way from the start? Thanks

[hiker]

I haven't received an answer to my question, I try a 're-request review', to confirm what I am expected to be doing.

[MatthewHambley]

Your proposed CLI form for precision bubbles seems workable so we'll go with that.

And remember, I'm an LFRic developer and got confused over what R_DEF means so I think it's entirely possible that others, or fresh starters, may as well.

[hiker]

Your proposed CLI form for precision bubbles seems workable so we'll go with that.

And remember, I'm an LFRic developer and got confused over what R_DEF means so I think it's entirely possible that others, or fresh starters, may as well.

OK, I have removed the code to support a default, and added --precision_other as command line option for RDEF.

[MatthewHambley]

This change represents an initial implementation on which we can build.