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Adds YAML input to CLI planning tools (#583)
* [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 --------- Co-authored-by: Irfan Alibay <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,179 @@ | ||
| # This code is part of OpenFE and is licensed under the MIT license. | ||
| # For details, see https://github.com/OpenFreeEnergy/openfe | ||
| """Pydantic models for the definition of advanced CLI options | ||
| """ | ||
| import click | ||
| from collections import namedtuple | ||
| try: | ||
| # todo; once we're fully v2, we can use ConfigDict not nested class | ||
| from pydantic.v1 import BaseModel # , ConfigDict | ||
| except ImportError: | ||
| from pydantic import BaseModel | ||
| from plugcli.params import Option | ||
| from typing import Any, Optional | ||
| import yaml | ||
| import warnings | ||
|
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| PlanNetworkOptions = namedtuple('PlanNetworkOptions', | ||
| ['mapper', 'scorer', | ||
| 'ligand_network_planner', 'solvent']) | ||
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| class MapperSelection(BaseModel): | ||
| # model_config = ConfigDict(extra='allow', str_to_lower=True) | ||
| class Config: | ||
| extra = 'allow' | ||
| anystr_lower = True | ||
|
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| method: Optional[str] = None | ||
| settings: dict[str, Any] = {} | ||
|
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| class NetworkSelection(BaseModel): | ||
| # model_config = ConfigDict(extra='allow', str_to_lower=True) | ||
| class Config: | ||
| extra = 'allow' | ||
| anystr_lower = True | ||
|
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| method: Optional[str] = None | ||
| settings: dict[str, Any] = {} | ||
|
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|
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| class CliYaml(BaseModel): | ||
| # model_config = ConfigDict(extra='allow') | ||
| class Config: | ||
| extra = 'allow' | ||
|
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| mapper: Optional[MapperSelection] = None | ||
| network: Optional[NetworkSelection] = None | ||
|
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|
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| def parse_yaml_planner_options(contents: str) -> CliYaml: | ||
| """Parse and minimally validate a user provided yaml | ||
| Parameters | ||
| ---------- | ||
| contents : str | ||
| raw yaml formatted input to parse | ||
| Returns | ||
| ------- | ||
| options : CliOptions | ||
| will have keys for mapper and network topology choices | ||
| Raises | ||
| ------ | ||
| ValueError | ||
| for any malformed inputs | ||
| """ | ||
| raw = yaml.safe_load(contents) | ||
|
|
||
| if False: | ||
| # todo: warnings about extra fields we don't expect? | ||
| expected = {'mapper', 'network'} | ||
| for field in raw: | ||
| if field in expected: | ||
| continue | ||
| warnings.warn(f"Ignoring unexpected section: '{field}'") | ||
|
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| return CliYaml(**raw) | ||
|
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| def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOptions: | ||
| """Load cli options from yaml file path and resolve these to objects | ||
| Parameters | ||
| ---------- | ||
| path : str | ||
| path to the yaml file | ||
| context | ||
| unused | ||
| Returns | ||
| ------- | ||
| PlanNetworkOptions : namedtuple | ||
| a namedtuple with fields 'mapper', 'scorer', 'network_planning_algorithm', | ||
| and 'solvent' fields. | ||
| these fields each hold appropriate objects ready for use | ||
| """ | ||
| from gufe import SolventComponent | ||
| from openfe.setup.ligand_network_planning import ( | ||
| generate_radial_network, | ||
| generate_minimal_spanning_network, | ||
| generate_maximal_network, | ||
| generate_minimal_redundant_network, | ||
| ) | ||
| from openfe.setup import ( | ||
| LomapAtomMapper, | ||
| ) | ||
| from openfe.setup.atom_mapping.lomap_scorers import ( | ||
| default_lomap_score, | ||
| ) | ||
| from functools import partial | ||
|
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| if path is not None: | ||
| with open(path, 'r') as f: | ||
| raw = f.read() | ||
|
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| # convert raw yaml to normalised pydantic model | ||
| opt = parse_yaml_planner_options(raw) | ||
| else: | ||
| opt = None | ||
|
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| # convert normalised inputs to objects | ||
| if opt and opt.mapper: | ||
| mapper_choices = { | ||
| 'lomap': LomapAtomMapper, | ||
| 'lomapatommapper': LomapAtomMapper, | ||
| } | ||
|
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| try: | ||
| cls = mapper_choices[opt.mapper.method] | ||
| except KeyError: | ||
| raise KeyError(f"Bad mapper choice: '{opt.mapper.method}'") | ||
| mapper_obj = cls(**opt.mapper.settings) | ||
| else: | ||
| mapper_obj = LomapAtomMapper(time=20, threed=True, element_change=False, | ||
| max3d=1) | ||
|
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| # todo: choice of scorer goes here | ||
| mapping_scorer = default_lomap_score | ||
|
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| if opt and opt.network: | ||
| network_choices = { | ||
| 'generate_radial_network': generate_radial_network, | ||
| 'radial': generate_radial_network, | ||
| 'generate_minimal_spanning_network': generate_minimal_spanning_network, | ||
| 'mst': generate_minimal_spanning_network, | ||
| 'generate_minimal_redundant_network': generate_minimal_redundant_network, | ||
| 'generate_maximal_network': generate_maximal_network, | ||
| } | ||
|
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| try: | ||
| func = network_choices[opt.network.method] | ||
| except KeyError: | ||
| raise KeyError(f"Bad network algorithm choice: '{opt.network.method}'") | ||
|
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| ligand_network_planner = partial(func, **opt.network.settings) | ||
| else: | ||
| ligand_network_planner = generate_minimal_spanning_network | ||
|
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| # todo: choice of solvent goes here | ||
| solvent = SolventComponent() | ||
|
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| return PlanNetworkOptions( | ||
| mapper_obj, | ||
| mapping_scorer, | ||
| ligand_network_planner, | ||
| solvent, | ||
| ) | ||
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| YAML_OPTIONS = Option( | ||
| '-s', "--settings", "yaml_settings", | ||
| type=click.Path(exists=True, dir_okay=False), | ||
| help="Path to planning settings yaml file.", | ||
| getter=load_yaml_planner_options, | ||
| ) |
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