Fix safe_copy(..., preserve_meta=False)

[samsrabin]

Description

This changes safe_copy(..., preserve_meta=False) to use shutil.copyfile instead of shutil.copy when safe_copy is called on a file directly. This fixes the bug where preserve_meta=False incorrectly preserved permissions.

The first set of test runs will fail because I'm pushing without the bugfix. Once those tests are complete, I'll push the fix and they should pass.

I added the tests in a new file, but they could be moved to test_unit_utils.py instead.

• Closes safe_copy(..., preserve_meta=False) does preserve perms #4937.

Checklist

• My code follows the style guidelines of this project (black formatting)
• I have performed a self-review of my own code
• My changes generate no new warnings
• I have added tests that exercise my feature/fix and existing tests continue to pass
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding additions and changes to the documentation

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 28.35%. Comparing base (fc2de6d) to head (4524f13).
⚠️ Report is 67 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #4938      +/-   ##
==========================================
- Coverage   31.37%   28.35%   -3.03%     
==========================================
  Files         264      262       -2     
  Lines       38899    38362     -537     
  Branches     8260     8116     -144     
==========================================
- Hits        12204    10876    -1328     
- Misses      25457    26245     +788     
- Partials     1238     1241       +3     

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[jedwards4b]

Thank you!

[samsrabin]

Hmm... not sure what that failing CESM system test is about.

[samsrabin]

Very strange; it works on Derecho. Resubmitting.

[samsrabin]

That did it! All tests have now passed.

[samsrabin]

In my testing on Izumi, all CTSM baseline files now have at least rw-r--r--. Unfortunately they're not all group-writable, but I can file that as a separate issue.

[Copilot]

Pull request overview

Fixes safe_copy(..., preserve_meta=False) so that direct file copies do not accidentally preserve permissions (allowing SharedArea’s umask behavior to take effect as intended).

Changes:

• Switch direct file copy behavior for preserve_meta=False from shutil.copy to shutil.copyfile (avoid copying mode bits).
• Add a new unit test module covering safe_copy behavior across preserve_meta settings and within/outside SharedArea.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 5 comments.

File	Description
CIME/utils.py	Updates safe_copy to avoid preserving permissions when preserve_meta=False for new direct-file copies.
CIME/tests/test_unit_safe_copy.py	Adds unit tests intended to catch permission/umask regressions and validate SharedArea interactions.

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[samsrabin]

@rljacob Could you request a Claude re-review?

[Copilot]

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 5 comments.

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[samsrabin]

@jedwards4b @rljacob I think this is ready to go!