Change hydrogen on hydrogen mapping default to True

[jthorton]

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.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.15%. Comparing base (4532c95) to head (76c4c9c).

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #69      +/-   ##
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+ Coverage   97.53%   98.15%   +0.61%     
==========================================
  Files          13       13              
  Lines         649      649              
==========================================
+ Hits          633      637       +4     
+ Misses         16       12       -4     

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[jthorton]

@IAlibay, you mentioned changing the defaults in openfe as well, but openfe exports the mapper again.

[IAlibay]

@jthorton admittedly I've not put a ton of thought into this, so I could be completely off the mark, what I'm thinking of is we could:

a) ensure that the default settings for the mapper in the CLI has our best practice defaults: https://github.com/OpenFreeEnergy/openfe/blob/be3433c031b3c7e5c0444a4ecbbfdc233f82b4de/openfecli/parameters/plan_network_options.py#L127
b) make sure that any documentation (assuming we have any) that directs the use of Kartograf, tells users to use the right filter options.

[IAlibay]

I'm going to put a block on this pending internal discussions - at least I suggest we skip on this for v1.1.0 and target a v1.2.0 (or maybe even just jump straight to a v2.0!)