292 fab pfunit

[Joerg Henrichs (hiker)]

PR Summary

Sci/Tech Reviewer:
Code Reviewer: Matthew Hambley (@MatthewHambley)

As discussed, this PR adds a mixin class that enables building of PFUnit-tests. It adds support to the skeleton app.

• is blocked-by Add skeleton fab script #246
• closes Support pfunit testing with Fab #292

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

All N/A - this change does not integrate with cylc yet. Local builds have been successful.

• 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)

Building skeleton with (and without) testing is now possible.

trac.log

N/A

Security Considerations

• I have reviewed my changes for potential security issues
• [N/A] Sensitive data is properly handled (if applicable)
• [N/A] 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

• [N/A] 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

• [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

• 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

[Joerg Henrichs (hiker)]

I've modified this PR to assume that the pfunit tool will be provided by Fab, and that Fab supports external declarations. While updating Fab's FabBase class based on the code reviews in lfric_core and um (fab ticket #544), the 'root_symbol' usage was renamed to root_symbols, which is also included here (the old names are deprecated, but still available).

Additionally, I discovered that the testing of the LFRicBase class in #240 was totally broken (luckily only the tests were not updated, the class itself was fine), I've fixed all the failing tests as well.

I also noticed that lfric does not compile without openmp (some psykal lite files contain omp calls without sentinels, so it will cause compile time and/or linking errors. I have added a test to abort early if a user tries to disable OpenMP (ideally, we would want to just disable this command line flag, which is handled in FabBase - but afaik argparse does not provide an official way of removing command line options 😢

[Joerg Henrichs (hiker)]

Matthew Hambley (@MatthewHambley), Sam Clarke-Green (@t00sa) - ready for a first review. Though it might be preferable to first handle the three required Fab updates (in case that they will require a change in the implementation, which could affect this PR):

• 559 support external declarations fab#561 (pfunit uses an external declaration)
• #552 Added pfunit tool and tests. fab#562 (providing the pfunit tool)
• Fab for lfric fab#564 (update to root_symbol(s), and providing public symbols for some otherwise private attributes)

[Matthew Hambley (MatthewHambley)]

Only a couple of minor issues.

[Matthew Hambley (MatthewHambley)]

This comment doesn't seem to reflect the preceding line. Is it left over from earlier development?

[Joerg Henrichs (hiker)]

Oops, indeed.

[Matthew Hambley (MatthewHambley)]

I think the plural "apps" is confusing here due to common reference to the "apps repository," which this isn't directly related to. The singular app_dir would seem to make sense, since there's only one of it.

This name crops up all over the place but hopefully a search and replace will fix it.

[Joerg Henrichs (hiker)]

I've renamed it everywhere.

[Joerg Henrichs (hiker)]

Ready for next review.