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filter: Deprecate --output and -o #1622

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@victorlin victorlin commented Sep 4, 2024

Description of proposed changes

--output and -o are aliases to --output-sequences. They will be removed to avoid confusion with other output options.

Related issue(s)

Closes #1607

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

This makes it easier to search for usage, since `args.output` also
matches other output options.
Planning for upcoming deprecation.
- Put options in a new argument group for deprecated options
- Add entry to DEPRECATED.md
- Add test to ensure deprecated options still work
@victorlin victorlin self-assigned this Sep 4, 2024
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codecov bot commented Sep 4, 2024

Codecov Report

Attention: Patch coverage is 85.71429% with 3 lines in your changes missing coverage. Please review.

Project coverage is 71.06%. Comparing base (e1a30ba) to head (e700ea3).

Files with missing lines Patch % Lines
augur/filter/io.py 0.00% 1 Missing and 1 partial ⚠️
augur/filter/_run.py 75.00% 0 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1622      +/-   ##
==========================================
+ Coverage   71.03%   71.06%   +0.03%     
==========================================
  Files          79       79              
  Lines        8258     8268      +10     
  Branches     2005     2007       +2     
==========================================
+ Hits         5866     5876      +10     
  Misses       2101     2101              
  Partials      291      291              

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filter: Prefer "output sequences" over "output"?
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