* update LomapAtomMapper default settings to established best practices
* fixup tests for relative_alchemical_network_planner following lomap default change
make these tests use the legacy default settings for Lomap, they're just smoke testing and the actual mappings don't matter
* fixup regression tests for command line plan-rbfe
these are different now that the lomap defaults have been changed for 1.0
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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* fixes issue #618
openfe gather will not correctly report DDG hydration values
* cli: add --report raw option to gather
this reports the unit estimates individually
* add doc to cli for gather raw option
* cli: add test for gather raw
* cli: gather, remove dg-raw option
* Update openfecli/commands/gather.py
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* Update environment.yml
* change tyk2 regression to use gather --report ddg
* fixup raw gather test to include MBAR uncertainty label
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Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
