{
  "$defs": {
    "CrossValidationConfig": {
      "description": "Configs for splitting a dataset into cross-validation folds.",
      "properties": {
        "seed": {
          "default": 42,
          "description": "Seed for the random number generator.",
          "title": "Seed",
          "type": "integer"
        },
        "folds": {
          "default": 5,
          "description": "Number of folds to split the dataset into.",
          "title": "Folds",
          "type": "integer"
        }
      },
      "title": "CrossValidationConfig",
      "type": "object"
    },
    "DataConfig": {
      "description": "Where to load lymphatic progression data from and how to feed it into a model.",
      "properties": {
        "source": {
          "anyOf": [
            {
              "format": "file-path",
              "type": "string"
            },
            {
              "$ref": "#/$defs/LyDataset"
            }
          ],
          "description": "Either a path to a CSV file or a config that specifies how and where to fetch the data from.",
          "title": "Source"
        },
        "side": {
          "anyOf": [
            {
              "enum": [
                "ipsi",
                "contra"
              ],
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Side of the neck to load data for. Only for Unilateral models.",
          "title": "Side"
        },
        "mapping": {
          "additionalProperties": {
            "anyOf": [
              {
                "type": "integer"
              },
              {
                "type": "string"
              }
            ]
          },
          "description": "Optional mapping of numeric T-stages to model T-stages.",
          "title": "Mapping",
          "type": "object"
        }
      },
      "required": [
        "source"
      ],
      "title": "DataConfig",
      "type": "object"
    },
    "DiagnosisConfig": {
      "description": "Defines an ipsi- and contralateral diagnosis pattern.",
      "properties": {
        "ipsi": {
          "additionalProperties": {
            "additionalProperties": {
              "anyOf": [
                {
                  "enum": [
                    false,
                    0,
                    "healthy",
                    true,
                    1,
                    "involved",
                    "micro",
                    "macro",
                    "notmacro"
                  ]
                },
                {
                  "type": "null"
                }
              ]
            },
            "type": "object"
          },
          "default": {},
          "description": "Observed diagnoses by different modalities on the ipsi neck.",
          "examples": [
            {
              "CT": {
                "II": true,
                "III": false
              }
            }
          ],
          "title": "Ipsi",
          "type": "object"
        },
        "contra": {
          "additionalProperties": {
            "additionalProperties": {
              "anyOf": [
                {
                  "enum": [
                    false,
                    0,
                    "healthy",
                    true,
                    1,
                    "involved",
                    "micro",
                    "macro",
                    "notmacro"
                  ]
                },
                {
                  "type": "null"
                }
              ]
            },
            "type": "object"
          },
          "default": {},
          "description": "Observed diagnoses by different modalities on the contra neck.",
          "title": "Contra",
          "type": "object"
        }
      },
      "title": "DiagnosisConfig",
      "type": "object"
    },
    "DistributionConfig": {
      "description": "Configuration defining a distribution over diagnose times.",
      "properties": {
        "kind": {
          "default": "frozen",
          "description": "Parametric distributions may be updated.",
          "enum": [
            "frozen",
            "parametric"
          ],
          "title": "Kind",
          "type": "string"
        },
        "func": {
          "const": "binomial",
          "default": "binomial",
          "description": "Name of predefined function to use as distribution.",
          "title": "Func",
          "type": "string"
        },
        "params": {
          "additionalProperties": {
            "anyOf": [
              {
                "type": "integer"
              },
              {
                "type": "number"
              }
            ]
          },
          "default": {},
          "description": "Parameters to pass to the predefined function.",
          "title": "Params",
          "type": "object"
        }
      },
      "title": "DistributionConfig",
      "type": "object"
    },
    "GraphConfig": {
      "description": "Specifies how the tumor(s) and LNLs are connected in a DAG.",
      "properties": {
        "tumor": {
          "additionalProperties": {
            "items": {
              "type": "string"
            },
            "type": "array"
          },
          "description": "Define the name of the tumor(s) and which LNLs it/they drain to.",
          "title": "Tumor",
          "type": "object"
        },
        "lnl": {
          "additionalProperties": {
            "items": {
              "type": "string"
            },
            "type": "array"
          },
          "description": "Define the name of the LNL(s) and which LNLs it/they drain to.",
          "title": "Lnl",
          "type": "object"
        }
      },
      "required": [
        "tumor",
        "lnl"
      ],
      "title": "GraphConfig",
      "type": "object"
    },
    "InvolvementConfig": {
      "description": "Config that defines an ipsi- and contralateral involvement pattern.",
      "properties": {
        "ipsi": {
          "additionalProperties": {
            "anyOf": [
              {
                "enum": [
                  false,
                  0,
                  "healthy",
                  true,
                  1,
                  "involved",
                  "micro",
                  "macro",
                  "notmacro"
                ]
              },
              {
                "type": "null"
              }
            ]
          },
          "default": {},
          "description": "Involvement pattern for the ipsilateral side of the neck.",
          "examples": [
            {
              "II": true,
              "III": false
            }
          ],
          "title": "Ipsi",
          "type": "object"
        },
        "contra": {
          "additionalProperties": {
            "anyOf": [
              {
                "enum": [
                  false,
                  0,
                  "healthy",
                  true,
                  1,
                  "involved",
                  "micro",
                  "macro",
                  "notmacro"
                ]
              },
              {
                "type": "null"
              }
            ]
          },
          "default": {},
          "description": "Involvement pattern for the contralateral side of the neck.",
          "title": "Contra",
          "type": "object"
        }
      },
      "title": "InvolvementConfig",
      "type": "object"
    },
    "LyDataset": {
      "description": "Specification of a dataset.",
      "properties": {
        "year": {
          "description": "Release year of dataset.",
          "exclusiveMinimum": 0,
          "maximum": 2025,
          "title": "Year",
          "type": "integer"
        },
        "institution": {
          "description": "Institution's short code. E.g., University Hospital Zurich: `usz`.",
          "minLength": 1,
          "title": "Institution",
          "type": "string"
        },
        "subsite": {
          "description": "Tumor subsite(s) patients in this dataset were diagnosed with.",
          "minLength": 1,
          "title": "Subsite",
          "type": "string"
        },
        "repo_name": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": "lycosystem/lydata",
          "description": "GitHub `repository/owner`.",
          "title": "Repo Name"
        },
        "ref": {
          "anyOf": [
            {
              "minLength": 1,
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": "main",
          "description": "Branch/tag/commit of the repo.",
          "title": "Ref"
        },
        "local_dataset_dir": {
          "anyOf": [
            {
              "format": "directory-path",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Path to directory containing all the dataset subdirectories. So, e.g. if `path_on_disk` is `~/datasets` and the dataset is `2023-clb-multisite`, then the CSV file is expected to be at `~/datasets/2023-clb-multisite/data.csv`.",
          "title": "Local Dataset Dir"
        }
      },
      "required": [
        "year",
        "institution",
        "subsite"
      ],
      "title": "LyDataset",
      "type": "object"
    },
    "ModalityConfig": {
      "description": "Define a diagnostic or pathological modality.",
      "properties": {
        "spec": {
          "description": "Specificity of the modality.",
          "maximum": 1.0,
          "minimum": 0.5,
          "title": "Spec",
          "type": "number"
        },
        "sens": {
          "description": "Sensitivity of the modality.",
          "maximum": 1.0,
          "minimum": 0.5,
          "title": "Sens",
          "type": "number"
        },
        "kind": {
          "default": "clinical",
          "description": "Clinical modalities cannot detect microscopic disease.",
          "enum": [
            "clinical",
            "pathological"
          ],
          "title": "Kind",
          "type": "string"
        }
      },
      "required": [
        "spec",
        "sens"
      ],
      "title": "ModalityConfig",
      "type": "object"
    },
    "ModelConfig": {
      "description": "Define which of the ``lymph`` models to use and how to set them up.",
      "properties": {
        "external_file": {
          "anyOf": [
            {
              "format": "file-path",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Path to a Python file that defines a model.",
          "title": "External File"
        },
        "class_name": {
          "default": "Unilateral",
          "description": "Name of the model class to use.",
          "enum": [
            "Unilateral",
            "Bilateral",
            "Midline"
          ],
          "title": "Class Name",
          "type": "string"
        },
        "constructor": {
          "default": "binary",
          "description": "Trinary models differentiate btw. micro- and macroscopic disease.",
          "enum": [
            "binary",
            "trinary"
          ],
          "title": "Constructor",
          "type": "string"
        },
        "max_time": {
          "default": 10,
          "description": "Max. number of time-steps to evolve the model over.",
          "title": "Max Time",
          "type": "integer"
        },
        "named_params": {
          "default": null,
          "description": "Subset of valid model parameters a sampler may provide in the form of a dictionary to the model instead of as an array. Or, after sampling, with this list, one may safely recover which parameter corresponds to which index in the sample.",
          "items": {
            "type": "string"
          },
          "title": "Named Params",
          "type": "array"
        },
        "kwargs": {
          "default": {},
          "description": "Additional keyword arguments to pass to the model constructor.",
          "title": "Kwargs",
          "type": "object"
        }
      },
      "title": "ModelConfig",
      "type": "object"
    },
    "SamplingConfig": {
      "description": "Settings to configure the MCMC sampling.",
      "properties": {
        "storage_file": {
          "description": "Path to HDF5 file store results or load last state.",
          "format": "path",
          "title": "Storage File",
          "type": "string"
        },
        "history_file": {
          "anyOf": [
            {
              "format": "path",
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Path to store the burn-in metrics (as CSV file).",
          "title": "History File"
        },
        "dataset": {
          "default": "mcmc",
          "description": "Name of the dataset in the HDF5 file.",
          "title": "Dataset",
          "type": "string"
        },
        "cores": {
          "anyOf": [
            {
              "exclusiveMinimum": 0,
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": 16,
          "description": "Number of cores to use for parallel sampling. If `None`, no parallel processing is used.",
          "title": "Cores"
        },
        "seed": {
          "default": 42,
          "description": "Seed for the random number generator.",
          "title": "Seed",
          "type": "integer"
        },
        "walkers_per_dim": {
          "default": 20,
          "description": "Number of walkers per parameter space dimension.",
          "title": "Walkers Per Dim",
          "type": "integer"
        },
        "check_interval": {
          "default": 50,
          "description": "Check for convergence each time after this many steps.",
          "title": "Check Interval",
          "type": "integer"
        },
        "trust_factor": {
          "default": 50.0,
          "description": "Trust the autocorrelation time only when it's smaller than this factor times the length of the chain.",
          "title": "Trust Factor",
          "type": "number"
        },
        "relative_thresh": {
          "default": 0.05,
          "description": "Relative threshold for convergence.",
          "title": "Relative Thresh",
          "type": "number"
        },
        "burnin_steps": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Number of burn-in steps to take. If None, burn-in runs until convergence.",
          "title": "Burnin Steps"
        },
        "num_steps": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": 100,
          "description": "Number of steps to take in the MCMC sampling.",
          "title": "Num Steps"
        },
        "thin_by": {
          "default": 10,
          "description": "How many samples to draw before for saving one.",
          "title": "Thin By",
          "type": "integer"
        },
        "inverse_temp": {
          "default": 1.0,
          "description": "Inverse temperature for thermodynamic integration. Note that this is not yet fully implemented.",
          "title": "Inverse Temp",
          "type": "number"
        }
      },
      "required": [
        "storage_file"
      ],
      "title": "SamplingConfig",
      "type": "object"
    },
    "ScenarioConfig": {
      "description": "Define a scenario for which e.g. prevalences and risks may be computed.",
      "properties": {
        "t_stages": {
          "description": "List of T-stages to marginalize over in the scenario.",
          "examples": [
            [
              "early"
            ],
            [
              3,
              4
            ]
          ],
          "items": {
            "anyOf": [
              {
                "type": "integer"
              },
              {
                "type": "string"
              }
            ]
          },
          "title": "T Stages",
          "type": "array"
        },
        "t_stages_dist": {
          "default": [
            1.0
          ],
          "description": "Distribution over T-stages to use for marginalization.",
          "examples": [
            [
              1.0
            ],
            [
              0.6,
              0.4
            ]
          ],
          "items": {
            "type": "number"
          },
          "title": "T Stages Dist",
          "type": "array"
        },
        "midext": {
          "anyOf": [
            {
              "type": "boolean"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Whether the patient's tumor extends over the midline.",
          "title": "Midext"
        },
        "mode": {
          "default": "HMM",
          "description": "Which underlying model architecture to use.",
          "enum": [
            "HMM",
            "BN"
          ],
          "title": "Mode",
          "type": "string"
        },
        "involvement": {
          "$ref": "#/$defs/InvolvementConfig",
          "default": {
            "ipsi": {},
            "contra": {}
          }
        },
        "diagnosis": {
          "$ref": "#/$defs/DiagnosisConfig",
          "default": {
            "ipsi": {},
            "contra": {}
          }
        }
      },
      "required": [
        "t_stages"
      ],
      "title": "ScenarioConfig",
      "type": "object"
    },
    "ScheduleConfig": {
      "description": "Configuration for generating a schedule of inverse temperatures.",
      "properties": {
        "method": {
          "default": "power",
          "description": "Method to generate the inverse temperature schedule.",
          "enum": [
            "geometric",
            "linear",
            "power"
          ],
          "title": "Method",
          "type": "string"
        },
        "num": {
          "default": 32,
          "description": "Number of inverse temperatures in the schedule.",
          "title": "Num",
          "type": "integer"
        },
        "power": {
          "default": 4.0,
          "description": "If a power schedule is chosen, use this as power.",
          "title": "Power",
          "type": "number"
        },
        "values": {
          "anyOf": [
            {
              "items": {
                "type": "number"
              },
              "type": "array"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "List of inverse temperatures to use instead of generating a schedule. If a list is provided, the other parameters are ignored.",
          "title": "Values"
        }
      },
      "title": "ScheduleConfig",
      "type": "object"
    }
  },
  "description": "Settings for generating a JSON schema for lyscripts configuration files.",
  "properties": {
    "version": {
      "description": "For future compatibility reasons, every config file must have a `version: 1` field at the top level.",
      "maximum": 1,
      "minimum": 1,
      "title": "Version",
      "type": "integer"
    },
    "cross_validation": {
      "$ref": "#/$defs/CrossValidationConfig",
      "default": null
    },
    "data": {
      "$ref": "#/$defs/DataConfig",
      "default": null
    },
    "diagnosis": {
      "$ref": "#/$defs/DiagnosisConfig",
      "default": null
    },
    "distributions": {
      "additionalProperties": {
        "$ref": "#/$defs/DistributionConfig"
      },
      "default": {},
      "title": "Distributions",
      "type": "object"
    },
    "graph": {
      "$ref": "#/$defs/GraphConfig",
      "default": null
    },
    "involvement": {
      "$ref": "#/$defs/InvolvementConfig",
      "default": null
    },
    "modalities": {
      "additionalProperties": {
        "$ref": "#/$defs/ModalityConfig"
      },
      "default": {},
      "title": "Modalities",
      "type": "object"
    },
    "model": {
      "$ref": "#/$defs/ModelConfig",
      "default": null
    },
    "sampling": {
      "$ref": "#/$defs/SamplingConfig",
      "default": null
    },
    "scenarios": {
      "default": [],
      "items": {
        "$ref": "#/$defs/ScenarioConfig"
      },
      "title": "Scenarios",
      "type": "array"
    },
    "schedule": {
      "$ref": "#/$defs/ScheduleConfig",
      "default": null
    }
  },
  "required": [
    "version"
  ],
  "title": "SchemaSettings",
  "type": "object"
}