Enable reading for cyclic data files using temporal controller

[EdHone]

PR Summary

Sci/Tech Reviewer: @harry-shepherd
Code Reviewer: @mo-lucy-gordon

This PR enables the handling of cyclic data files(files which we start reading again from the beginning once we reach the end) by the new lfric-xios temporal controller. The contents of this PR are:

• a simple switch within the source code to enable reading cyclic data
• new functionality to perform an additional "initial" read of data where necessary (when our first model step is not perfectly aligned with a file datapoint)
  • two new integration tests (NonSync) which exercise this functionality
• several integrations tests which exercise the reading of cyclic data
• new test capability to generate plots to check the validity of the tests

• closes Cyclic file reading with lfric_xios temporal controller #230

Code Quality Checklist

(Some checks are automatically carried out via the CI pipeline)

• 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

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)

Some plots from the LFRic-XIOS integration tests which show that the data is being correctly digested

trac.log

Test Suite Results - lfric_core - lfric_core-230-cyclic-read/run4

Suite Information

Item	Value
Suite Name	lfric_core-230-cyclic-read/run4
Suite User	edward.hone
Workflow Start	2026-01-26T13:26:17
Groups Run	developer

Dependency	Reference	Main Like
lfric_core	EdHone/lfric_core@230-cyclic-read	False
SimSys_Scripts	MetOffice/SimSys_Scripts@2025.12.1	True

Task Information

✅ succeeded tasks - 372

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
  tooscollabdevteam@metoffice.gov.uk

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

[harry-shepherd]

Just a couple of trivial changes

[EdHone]

Thanks @harry-shepherd - all comments addressed in the latest commit

[EdHone]

I noticed something is wrong - the initial data is being read in for the timestep before the one it needs to be reading, as can be seen in the second plot above - reverting to draft to fix

[EdHone]

Issue fixed - back out of draft

[EdHone]

Requesting another sci -tech review from @harry-shepherd: The new plot above shows that we are getting the correct initial data now, when compared to the plot before

[mo-lucy-gordon]

Overall the code looks good but there were a few style issues when I checked the python files with flake8 tool and there a few comments in the code requesting minor changes.

[mo-lucy-gordon]

Please could you edit copyright to look like: https://metoffice.github.io/lfric_core/how_to_contribute/coding_standards/python_coding_standards.html#copyright

[mo-lucy-gordon]

Please could you edit copyright to look like: https://metoffice.github.io/lfric_core/how_to_contribute/coding_standards/python_coding_standards.html#copyright

[mo-lucy-gordon]

I can't see a corresponding deallocate for this so please could you add one?