Add initial mypy configuration and CI integration

[the-mr-dave]

Description

This PR adds mypy type checking to libEnsemble using an intentionally permissive initial configuration.
It establishes a baseline that can be tightened incrementally without impacting CI stability.

Related issue: #1633

Changes

• Add an initial mypy configuration to pyproject.toml
• Add mypy as a CI check
• Restrict type checking scope to libensemble/utils
• Exclude utility modules that are not yet mypy-compliant
• Refactor libensemble/utils/misc.py to satisfy mypy

CI Impact

• mypy is executed with a restricted scope and permissive settings
• No existing CI checks are modified, relaxed, or made less strict

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.29%. Comparing base (0f2ee07) to head (2bd8cab).
⚠️ Report is 13 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #1655   +/-   ##
========================================
  Coverage    78.29%   78.29%           
========================================
  Files           76       76           
  Lines         7580     7580           
  Branches      1119     1119           
========================================
  Hits          5935     5935           
  Misses        1460     1460           
  Partials       185      185           

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[the-mr-dave]

Hi maintainers,

when you have time, I’d appreciate any feedback on this PR.
Thanks.

[jlnav]

Hello,

Thank you for the mypy implementation and fixes. The configuration and CI implementation look good.

However, I'm surprised changes to output_directory.py were included even though it's excluded by mypy's checks. Did you find a bug? If so, how did you come across it?

[the-mr-dave]

Hello,

Thank you for the mypy implementation and fixes. The configuration and CI implementation look good.

However, I'm surprised changes to output_directory.py were included even though it's excluded by mypy's checks. Did you find a bug? If so, how did you come across it?

Thanks a lot for the quick review.
I accidentally pushed the changes for output_directory.py. The changes are only for mypy, but the file was not fully refactored. I would remove the changes out of this PR. And tackle it in the next PR.