fix: package-type fixer to avoid duplicated empty section

[wey-gu]

close: #2577

Pull Request Checklist

• A news fragment is added in news/ describing what is new.
• Test cases added for changed code.

Describe what you have changed in this PR.

This seems to be a tomlkit issue, the workaround(instead of fixing upstream) here is to pop the parent section and write back the whole.

[frostming]

thanks for the fix. I will review it tomorrow

[frostming]

Though a bit ugly, modifying a TOML while keeping the styles and orders are hard.

[wey-gu]

Opps, sorry for my silly typo

[wey-gu]

I will test it locally and maybe put the lock file in the test project.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (348b79c) 84.76% compared to head (15e3a2b) 84.79%.
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2578      +/-   ##
==========================================
+ Coverage   84.76%   84.79%   +0.02%     
==========================================
  Files         104      104              
  Lines       10387    10387              
  Branches     2272     2272              
==========================================
+ Hits         8805     8808       +3     
+ Misses       1106     1105       -1     
+ Partials      476      474       -2     

Flag	Coverage Δ
unittests	84.58% <ø> (+0.02%)	⬆️

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