Use ExtendOverwriteDefault for all multi-value options

[victorlin]

Description of proposed changes

This is largely a follow-up to #1445 which in hindsight was not done properly. See commits for details.

Related issue(s)

#1707

89fbda2 closes #1706 (no longer necessary)

Checklist

• Automated checks pass
• Check if you need to add a changelog message
• Check if you need to add tests
• Check if you need to update docs
• Post-merge: follow up on Improve help text of CLI options that use extend and ExtendOverwriteDefault actions #1654 (comment)

[codecov]

Codecov Report

Attention: Patch coverage is 95.69892% with 4 lines in your changes missing coverage. Please review.

Project coverage is 72.90%. Comparing base (1843a9b) to head (28e6e8c).
Report is 9 commits behind head on master.

Files with missing lines	Patch %	Lines
augur/argparse_.py	86.66%	1 Missing and 1 partial ⚠️
augur/export_v2.py	85.71%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1709      +/-   ##
==========================================
+ Coverage   72.72%   72.90%   +0.17%     
==========================================
  Files          79       79              
  Lines        8287     8299      +12     
  Branches     1697     1694       -3     
==========================================
+ Hits         6027     6050      +23     
+ Misses       1972     1961      -11     
  Partials      288      288              

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[tsibley]

Ideally, there should be a way to enforce that if nargs="+"/"*" is used, it must be paired with ExtendOverwriteDefault. A note in the dev docs doesn't seem useful enough, but I'm not sure how to do enforce automatically in PR checks.

I'll contribute a test file for this shortly.

[tsibley]

See 8f6f145.

[victorlin]

Amazing!

=================================== FAILURES ===================================
_ test_ExtendOverwriteDefault[augur curate transform-strain-name --backup-fields] _
tests/test_argparse_linting.py:26: in test_ExtendOverwriteDefault
    assert isinstance(action, ExtendOverwriteDefault)
E   assert False
E    +  where False = isinstance(_StoreAction(option_strings=['--backup-fields'], dest='backup_fields', nargs='*', const=None, default=[], type=None, choices=None, required=False, help="List of backup fields to use as strain name if the value in 'strain' does not match the strain regex pattern. If multiple fields are provided, will use the first field that has a non-empty string.", metavar=None), ExtendOverwriteDefault)
        action     = _StoreAction(option_strings=['--backup-fields'], dest='backup_fields', nargs='*', const=None, default=[], type=None, choices=None, required=False, help="List of backup fields to use as strain name if the value in 'strain' does not match the strain regex pattern. If multiple fields are provided, will use the first field that has a non-empty string.", metavar=None)

[joverlee521]

Thanks @victorlin! Sorry for the inconsistent usage of ExtendOverwriteDefault 🙏