Copy overwrite changes

[james-bruten-mo]

PR Summary

Sci/Tech Reviewer:
Code Reviewer: @t00sa

This merges changes from MetOffice/lfric_apps#162 into this repo as they may be of use here in the future.

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

• This change has been tested appropriately (please describe)

Tested by running with the Apps rose-stem suite

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)

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)

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
• Code quality standards have been met
• Tests are adequate and have passed
• Security considerations have been addressed
• Performance impact is acceptable

[yaswant]

Will this (assigning Path to an empty string) not raise a type mismatch? Perhaps you meant mirror_loc: Path = Path("")?

[yaswant]

I see you are reverting this back to original. But please note that run_command() will not always have a value so I added if result and result.returncode (sorry if I messed up your original logic.

Alternatively, you should probably use try/except:

try:
    result = runc_command(...)
    if result.returncode:
        ...
except Exception:
    result = None  # or you chose how to handle it

[james-bruten-mo]

Not intended - didn't merge the file correctly