* 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>
* 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
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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* [skip ci]
draft of yaml format for CI
* adds yaml reader for cli options input
fixes#580
* change plan_rXfe_network_main functions to expect list of mappers
* move settings yaml parsing to be parameter
* add YAML_OPTIONS as parameter
* add YAML_OPTIONS to plan_rbfe_network
currently does nothing
* cli: add interpretation of settings yaml
* cli: enable settings yaml reading in plan_rbfe_network
* cli: some extra documentation on load_yaml
* cli: fix tests to account for normalisation
* cli: add test for custom rbfe yaml usage
* cli: update plan_rhfe to allow yaml options
* cli: use v1/2 compatible Pydantic
* cli: fixup pydantic v1/2 compat
* remove draft yaml idea
* cli: centralise parsing of yaml options and defaults
* add pyyaml to deps
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Co-authored-by: Irfan Alibay <IAlibay@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>
* improve error message
* Add --allow-partial to gather
* use it for the other call as well
* ignore coverage on line that should never happen
* Make it possible to do both RHFE and RBFE
