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 31.51%. Comparing base (fc2de6d) to head (7e7893e).
⚠️ Report is 11 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #4938      +/-   ##
==========================================
+ Coverage   31.37%   31.51%   +0.13%     
==========================================
  Files         264      264              
  Lines       38899    38869      -30     
  Branches     8260     8254       -6     
==========================================
+ Hits        12204    12248      +44     
+ Misses      25457    25384      -73     
+ Partials     1238     1237       -1     

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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.