Fix pypi flag behavior

[PaulKMueller]

Motivation

The default behavior by clap is to set arguments with action = ArgAction::SetTrue to Some(value).
While sensible in some contexts, this breaks some of our checks.

Changes

The osi and ignore-pypi flags now need to be specified like so:
--ignore-pypi false

[pavelzw]

can you bump the version here to 0.4.0?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 88.58%. Comparing base (9e4f0c3) to head (eeacaa2).
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #37      +/-   ##
==========================================
+ Coverage   84.25%   88.58%   +4.33%     
==========================================
  Files          12       12              
  Lines         508      508              
==========================================
+ Hits          428      450      +22     
+ Misses         80       58      -22     

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