Move shellouts

[Pierre Siddall (Pierre-siddall)]

PR Summary

Code Reviewer: Erica Neininger (@ericaneininger)

This PR aims to unify shell out commands across MOCI so that they all have the same semantics. The changes involved include adding a separate library to handle shell operations and replacing current shell operations with a newly implemented exec_subprocess function and subsequently also deprecates legacy shell out commands to be redirected to use exec_subprocess in mocilib .

closes #12
closes #23

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 undertanding and enhance the
  readability of the code
• My changes generate no new warnings

Testing

• I have tested this change locally, using the Moci rose-stem suite
• If any tests fail (rose-stem or CI) the reason is understood and
  acceptable (eg. kgo changes)
• I have added tests to cover new functionality as appropriate (eg. system
  tests, unit tests, etc.)

Test Suite Results - moci - test-mocilib/run2

Suite Information

Item	Value
Suite Name	test-mocilib/run2
Suite User	pierre.siddall
Workflow Start	2026-03-18T13:31:20
Groups Run	all

Dependency	Reference	Main Like
moci	Pierre-siddall/moci@move-shellouts	False
SimSys_Scripts	MetOffice/SimSys_Scripts@main	True

Task Information

✅ succeeded tasks - 116

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

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

[Pierre Siddall (Pierre-siddall)]

Erica Neininger (@ericaneininger) hopefully this should be ready to go on now, let me know if there's anything else that is needed.

[Erica Neininger (ericaneininger)]

Just a couple of typos and copyright dates to fix please.

[Erica Neininger (ericaneininger)]

There are a couple of print statements in this file. For consistency, please can we stick to if verbose: sys.stdout.write(...) for info or sys.stderr.write(...) for error messages.

If these prints statements are simply debug statements (this one in particular!) for your own testing then the should be removed.

[Pierre Siddall (Pierre-siddall)]

Good point I forgot that debug message was there

[Pierre Siddall (Pierre-siddall)]

I'm hoping that is fixed now, apologies for not removing those debug messages as agreed.

[Erica Neininger (ericaneininger)]

Thanks for the changes. Happy to approve