* add more checks
* make precommit manual
* apply formatting to pyproject.toml
* add TODO
* remove unneeded, add a few more
* add ruff, but turn everything off
* add openfe known first party
* format highest-level files
* first half of openfe protocols
* second half of openfe protocols
* openfe protocols formatting, with alyssa's fmt skips
* add ruff formatter to precommit
* fmt: off all vendored _rfe_utils code
* addressing review comments
* Disable user supplied host & guest atoms in restraint settings
* disable validator
* Fix some tests
* Store selection indices
* Add partial test
* Update serialized results
* try to make mypy happy
* Update equil_septop_method.py
* update rbfe_results.tar.gz for new settings schema
* re-enable test_gather tests
* devscript for updating rbfe_results.tar.gz
* cli: gather: rework raw gather to work off protocol_result dict
this allows us to later deduplicate and remove the unit_results key from results dicts
* cli: gather: update expected gather results
current raw results are only one replicate, should probably have multiple repeats to test raw output
* cli: gather: use \t escape code in gather raw test
could instead normalise the whitespace to be more permissive...
* Apply suggestions from code review
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* rerun ci
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
