* add pandas construction
* removing csv writer
* replicating original behavior
* add rich table
* split into function
* make names clearer
* adding adjustments from rebase
* put it in a box
* adding tsv flag
* update tests to use tsv flag
* add smoke test for pretty print
* adding file creation test
* adding news item
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* switch to assert_click_success to make debugging easier
* fixing tests to look for logger.INFO instead of warnings (due to gufe change)
* updating expected output due to gufe changes
* updating expected transformations
* remove easy prefix, passing 2fe7741b9448
* define _settings_cls, tests pass against g3c6d5f9
* update string match for partial charge logging
* 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
---------
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
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
