* 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>
* [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>
* use gufe.SmallMoleculeComponent in place of LigandMolecule
* thought this would fix the serialization test but it doesn't :(
* fix network serialization
Co-authored-by: David W.H. Swenson <david.swenson@omsf.io>
* API renames
To try thinking bigger and be more future proof, label everything currently designed for Ligands as for ligands. i.e.
- Molecule -> LigandMolecule
- AtomMapper -> LigandAtomMapper
- AtomMapping -> LigandAtomMapping
- Network -> LigandNetwork
* fixup
* revert change to Network name
* fixup fixtures to use AddHs
* update pep8 and mypy
* missed one
Co-authored-by: IAlibay <ialibay@mdanalysis.org>
Co-authored-by: David W.H. Swenson <david.swenson@omsf.io>
* Initial skeleton for the CLI
Currently requires the OPS CLI to be installed as well; next steps:
1. Add parameter core classes to infrastructure
2. Fully separate infrastructure into its own package
* switch to using plugcli
* tests for CLI
* helps if you add the tests...
* pep8 and deps cleanup
* add test_plugins
* Start of CLI atommapping report
* Add tests for parameters
* Almost-working atommapping command
* add hack to work-around lomap issue
* fix test
* pep8; docstrings; add header comments
* Add tests for commands/atommapping
* docstrings
* add init to command to stop circular import error
* remove init and it still works?
Co-authored-by: richard <richard@nextmovesoftware.com>
