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Change hydrogen on hydrogen mapping default to True #69

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Following the review of the default filters in #59, this PR changes the default value for map_hydrogens_on_hydrogens_only to True this should have no change on the performance when using the hybrid topology protocol from OpenFE as these mappings were removed silently as they involve bond constraints.

@jthorton jthorton self-assigned this Nov 22, 2024
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codecov bot commented Nov 22, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.24%. Comparing base (8ebfea7) to head (a764bd4).

Additional details and impacted files
@@            Coverage Diff             @@
##             main      #69      +/-   ##
==========================================
+ Coverage   96.60%   97.24%   +0.64%     
==========================================
  Files          13       13              
  Lines         618      618              
==========================================
+ Hits          597      601       +4     
+ Misses         21       17       -4     

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