Speed up permission updates

[andrewdnolan]

This PR speeds up the file permission updating by removing nested for loops and added the ability to parallelize the file permission departures over threads.

Checklist

• User's Guide has been updated if needed
• Developer's Guide has been updated if needed
• API documentation lists any new or modified class, method, or function
• Documentation builds cleanly and changes look as expected
• Tests pass and new features are covered by tests
• PR description includes a summary and any relevant issue references
• Testing comment, if appropriate, in the PR documents testing used to verify the changes

[xylar]

Looks good!

[xylar]

Feel free to merge when you're ready.

[andrewdnolan]

Testing:

Setting up the test directory:

$ mkdir mache_testing
$ cp -r /lcrc/soft/climate/e3sm-unified/e3sm_unified_1_12_0rc1 mache_testing/
$ python -c 'from mache.permissions import update_permissions; update_permissions("mache_testing/spack", "cels", show_progress=True, group_writable=True, other_readable=False)

Updating file permissions for: mache_testing/e3sm_unified_1_12_0rc1
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████| 534374/534374 [04:17<00:00, 2075.54item/s]

I intentionally changed the group_writable and other_readable value from what e3sm-unified uses, to make sure actual changes were being applied. This branch finished in 4 min 17 sec, whereas it took over 2 hour using the old version to deploy on chrysalis yesterday.