config

Schema for the YAML config files passed to metabolike setup.

The main sections are config.Neo4jConfig and config.MetacycConfig.

MetacycConfig

Bases: BaseModel

Config schema for parsing MetaCyc data files into a graph.

Valid keys include sbml, reactions, atom_mapping, pathways, compounds, publications, and classes. All values should be paths to local files. Only the sbml key is required.

Neo4jConfig

Bases: BaseModel

Config schema for connecting to a Neo4j instance.

See db.neo4j.Neo4jClient for details. Valid keys are uri, user, password, and database.