Simplify config module

src/troute-config/troute/config/bmi_parameters.py

@@ -2,7 +2,7 @@
 from typing import Optional, List
 
 
-class BMIParameters(BaseModel, extra='forbid'):
+class BMIParameters(BaseModel):
     flowpath_columns: Optional[List[str]] = Field(
         default_factory=lambda: [
             'id',

src/troute-config/troute/config/compute_parameters.py

@@ -22,7 +22,7 @@
 ComputeKernel = Literal["V02-structured", "diffusive", "diffusice_cnt"]
 
 
-class ComputeParameters(BaseModel, extra='forbid'):
+class ComputeParameters(BaseModel):
     parallel_compute_method: ParallelComputeMethod = "by-network"
     compute_kernel: ComputeKernel = "V02-structured"
     assume_short_ts: bool = False
@@ -44,7 +44,7 @@ class ComputeParameters(BaseModel, extra='forbid'):
 
 # TODO: determine how to handle context specific required fields
 # TODO: consider other ways to handle wrf hydro fields (i.e. subclass)
-class RestartParameters(BaseModel, extra='forbid'):
+class RestartParameters(BaseModel):
     # NOTE: this is technically optional as it can be derived from the
     # `wrf_hydro_channel_restart_file` if the `start_datetime` is not provided.
     start_datetime: Optional[datetime] = None
@@ -77,9 +77,9 @@ class RestartParameters(BaseModel, extra='forbid'):
 
 
 # TODO: determine how to handle context specific required fields
-class HybridParameters(BaseModel, extra='forbid'):
+class HybridParameters(BaseModel):
     # NOTE: required for hybrid simulations
-    run_hybrid_routing: bool
+    run_hybrid_routing: bool = False
     # NOTE: required for hybrid simulations
     diffusive_domain: Optional[FilePath] = None
 
@@ -97,15 +97,15 @@ class HybridParameters(BaseModel, extra='forbid'):
     coastal_boundary_domain: Optional[FilePath] = None
 
 
-class QLateralForcingSet(BaseModel, extra='forbid'):
+class QLateralForcingSet(BaseModel):
     nts: "QLateralFiles"
 
 
-class QLateralFiles(BaseModel, extra='forbid'):
+class QLateralFiles(BaseModel):
     qlat_files: List[FilePath]
 
 
-class StreamflowDA(BaseModel, extra='forbid'):
+class StreamflowDA(BaseModel):
     # NOTE: mandatory for streamflow DA, defaults to False
     streamflow_nudging: bool = False
     # NOTE: mandatory for streamflow DA on NHDNetwork.
@@ -140,15 +140,15 @@ class ReservoirPersistenceDA(BaseModel, extra='ignore'):
     crosswalk_usace_lakeID_field: str = "usace_lake_id"
 
 
-class ReservoirRfcParameters(BaseModel, extra='forbid'):
+class ReservoirRfcParameters(BaseModel):
     reservoir_rfc_forecasts: bool = False
-    reservoir_rfc_forecasts_time_series_path: Optional[FilePath] = None
+    reservoir_rfc_forecasts_time_series_path: Optional[DirectoryPath] = None
     reservoir_rfc_forecasts_lookback_hours: int = 28
     reservoir_rfc_forecasts_offset_hours: int = 28
     reservoir_rfc_forecast_persist_days: int = 11
 
 
-class ReservoirDA(BaseModel, extra='forbid'):
+class ReservoirDA(BaseModel):
     reservoir_persistence_da: Optional[ReservoirPersistenceDA] = None
     reservoir_rfc_da: Optional[ReservoirRfcParameters] = None
     reservoir_parameter_file: Optional[FilePath] = None
@@ -162,15 +162,15 @@ class DataAssimilationParameters(BaseModel, extra='ignore'):
     # NOTE: required for canada reservoir DA
     canada_timeslices_folder: Optional[DirectoryPath] = None
     # NOTE: required for LakeOntario reservoir DA
-    LakeOntario_outflow: Optional[DirectoryPath] = None
+    LakeOntario_outflow: Optional[FilePath] = None
     # NOTE: required for reservoir DA - suggested value 24 (1 days)
     timeslice_lookback_hours: int = 24
 
     interpolation_limit_min: int = 59
 
     wrf_hydro_lastobs_lead_time_relative_to_simulation_start_time: int = 0
     wrf_lastobs_type: str = "obs-based"
-    streamflow_da: StreamflowDA
+    streamflow_da: StreamflowDA = None
     # NOTE: this appears to be optional. See nwm_routing/input.py ~:439
     reservoir_da: Optional[ReservoirDA] = None
 
@@ -183,7 +183,7 @@ class DataAssimilationParameters(BaseModel, extra='ignore'):
     )(coerce_none_to_default)
 
 
-class ForcingParameters(BaseModel, extra='forbid'):
+class ForcingParameters(BaseModel):
     qts_subdivisions: int = 12
     dt: int = 300
     # TODO: see note about potentially throwing in v3_doc.yaml

src/troute-config/troute/config/config.py

@@ -13,8 +13,12 @@
 from .bmi_parameters import BMIParameters
 from ._utils import use_strict
 
+class LoggingParameters(BaseModel):
+    showtiming: Optional[bool] = None
+    log_level: Optional[str] = None
+    log_directory: Optional[str] = None  
 
-class Config(BaseModel, extra='forbid'):
+class Config(BaseModel):
     log_parameters: LoggingParameters = Field(default_factory=LoggingParameters)
     # TODO: not sure if default is None or {}. see nhd_io.read_config_file ~:100
     network_topology_parameters: Optional[NetworkTopologyParameters] = None
@@ -105,83 +109,92 @@ def check_coastal_domain(cls, values):
 
     @root_validator(skip_on_failure=True)
     def check_gage_segID_crosswalk_file(cls, values):
-        streamflow_DA = values['compute_parameters'].data_assimilation_parameters.streamflow_da
-        streamflow_nudging = streamflow_DA.streamflow_nudging
-        network_type = values['network_topology_parameters'].supernetwork_parameters.network_type
-        if streamflow_nudging and network_type=='NHDNetwork':
-            assert streamflow_DA.gage_segID_crosswalk_file, 'Streamflow nuding is enabled on NHDNetwork, but gage_segID_crosswalk_file is missing.'
+        da_parameters = values['compute_parameters'].data_assimilation_parameters
+        if da_parameters:
+            streamflow_DA = da_parameters.streamflow_da
+            if streamflow_DA:
+                streamflow_nudging = streamflow_DA.streamflow_nudging
+                network_type = values['network_topology_parameters'].supernetwork_parameters.network_type
+                if streamflow_nudging and network_type=='NHDNetwork':
+                    assert streamflow_DA.gage_segID_crosswalk_file, 'Streamflow nuding is enabled on NHDNetwork, but gage_segID_crosswalk_file is missing.'
 
         return values
 
     @root_validator(skip_on_failure=True)
     def check_rfc_parameters(cls, values):
-        reservoir_da = values['compute_parameters'].data_assimilation_parameters.reservoir_da
-        if reservoir_da:
-            reservoir_rfc_da = reservoir_da.reservoir_rfc_da
-            reservoir_rfc_forecasts = False
-            if reservoir_rfc_da:
-                reservoir_rfc_forecasts = reservoir_rfc_da.reservoir_rfc_forecasts
-                reservoir_rfc_forecasts_time_series_path = reservoir_rfc_da.reservoir_rfc_forecasts_time_series_path
-            if reservoir_rfc_forecasts:
-                error_message = ''
-                network_type = values['network_topology_parameters'].supernetwork_parameters.network_type
-                reservoir_parameter_file = reservoir_da.reservoir_parameter_file
-                if not reservoir_parameter_file and network_type=='NHDNetwork':
-                    error_message += ' Reservoir_parameter_file is missing (and network type is NHDNetwork).'
-                if not reservoir_rfc_forecasts_time_series_path:
-                    error_message  += ' RFC timeseries path is missing.'
-                else:
-                    if not os.path.exists(reservoir_rfc_forecasts_time_series_path):
-                        error_message += ' reservoir_rfc_forecasts_time_series_path provided does not exist. '                    
-                assert not error_message, 'RFC forecast is enabled, but:' + error_message
+        da_parameters = values['compute_parameters'].data_assimilation_parameters
+        if da_parameters:
+            reservoir_da = da_parameters.reservoir_da
+            if reservoir_da:
+                reservoir_rfc_da = reservoir_da.reservoir_rfc_da
+                reservoir_rfc_forecasts = False
+                if reservoir_rfc_da:
+                    reservoir_rfc_forecasts = reservoir_rfc_da.reservoir_rfc_forecasts
+                    reservoir_rfc_forecasts_time_series_path = reservoir_rfc_da.reservoir_rfc_forecasts_time_series_path
+                if reservoir_rfc_forecasts:
+                    error_message = ''
+                    network_type = values['network_topology_parameters'].supernetwork_parameters.network_type
+                    reservoir_parameter_file = reservoir_da.reservoir_parameter_file
+                    if not reservoir_parameter_file and network_type=='NHDNetwork':
+                        error_message += ' Reservoir_parameter_file is missing (and network type is NHDNetwork).'
+                    if not reservoir_rfc_forecasts_time_series_path:
+                        error_message  += ' RFC timeseries path is missing.'
+                    else:
+                        if not os.path.exists(reservoir_rfc_forecasts_time_series_path):
+                            error_message += ' reservoir_rfc_forecasts_time_series_path provided does not exist. '                    
+                    assert not error_message, 'RFC forecast is enabled, but:' + error_message
 
         return values
 
     @root_validator(skip_on_failure=True)
     def check_usgs_reservoir_da_parameters(cls, values):
-        reservoir_da = values['compute_parameters'].data_assimilation_parameters.reservoir_da
-        if reservoir_da:
-            reservoir_persistence_da = reservoir_da.reservoir_persistence_da
-            reservoir_persistence_usgs = False
-            if reservoir_persistence_da:
-                reservoir_persistence_usgs = reservoir_persistence_da.reservoir_persistence_usgs
-                usgs_timeslices_folder = values['compute_parameters'].data_assimilation_parameters.usgs_timeslices_folder
-            if reservoir_persistence_usgs:
-                error_message = ''
-                network_type = values['network_topology_parameters'].supernetwork_parameters.network_type
-                reservoir_parameter_file = reservoir_da.reservoir_parameter_file
-                if not reservoir_parameter_file and network_type=='NHDNetwork':
-                    error_message += ' Reservoir_parameter_file is missing (and network type is NHDNetwork).'
-                if not usgs_timeslices_folder:
-                    error_message  += ' USGS_timeslices_folder is missing.'
-                else:
-                    if not os.path.exists(usgs_timeslices_folder):
-                        error_message += ' USGS_timeslices_folder path provided does not exist. '
-                assert not error_message, 'USGS reservoir DA is enabled, but:' + error_message
+        da_parameters = values['compute_parameters'].data_assimilation_parameters
+        if da_parameters:
+            reservoir_da = da_parameters.reservoir_da
+            if reservoir_da:
+                reservoir_persistence_da = reservoir_da.reservoir_persistence_da
+                reservoir_persistence_usgs = False
+                if reservoir_persistence_da:
+                    reservoir_persistence_usgs = reservoir_persistence_da.reservoir_persistence_usgs
+                    usgs_timeslices_folder = values['compute_parameters'].data_assimilation_parameters.usgs_timeslices_folder
+                if reservoir_persistence_usgs:
+                    error_message = ''
+                    network_type = values['network_topology_parameters'].supernetwork_parameters.network_type
+                    reservoir_parameter_file = reservoir_da.reservoir_parameter_file
+                    if not reservoir_parameter_file and network_type=='NHDNetwork':
+                        error_message += ' Reservoir_parameter_file is missing (and network type is NHDNetwork).'
+                    if not usgs_timeslices_folder:
+                        error_message  += ' USGS_timeslices_folder is missing.'
+                    else:
+                        if not os.path.exists(usgs_timeslices_folder):
+                            error_message += ' USGS_timeslices_folder path provided does not exist. '
+                    assert not error_message, 'USGS reservoir DA is enabled, but:' + error_message
 
         return values
 
     @root_validator(skip_on_failure=True)
     def check_usace_reservoir_da_parameters(cls, values):
-        reservoir_da = values['compute_parameters'].data_assimilation_parameters.reservoir_da
-        if reservoir_da:
-            reservoir_persistence_da = reservoir_da.reservoir_persistence_da
-            reservoir_persistence_usace = False
-            if reservoir_persistence_da:
-                reservoir_persistence_usace = reservoir_persistence_da.reservoir_persistence_usace
-                usace_timeslices_folder = values['compute_parameters'].data_assimilation_parameters.usace_timeslices_folder
-            if reservoir_persistence_usace:
-                error_message = ''
-                network_type = values['network_topology_parameters'].supernetwork_parameters.network_type
-                reservoir_parameter_file = reservoir_da.reservoir_parameter_file
-                if not reservoir_parameter_file and network_type=='NHDNetwork':
-                    error_message += ' Reservoir_parameter_file is missing (and network type is NHDNetwork).'
-                if not usace_timeslices_folder:
-                    error_message  += ' USACE_timeslices_folder is missing.'
-                else:
-                    if not os.path.exists(usace_timeslices_folder):
-                        error_message += ' USACE_timeslices_folder path provided does not exist. '                    
-                assert not error_message, 'USACE reservoir DA is enabled, but:' + error_message
+        da_parameters = values['compute_parameters'].data_assimilation_parameters
+        if da_parameters:
+            reservoir_da = da_parameters.reservoir_da
+            if reservoir_da:
+                reservoir_persistence_da = reservoir_da.reservoir_persistence_da
+                reservoir_persistence_usace = False
+                if reservoir_persistence_da:
+                    reservoir_persistence_usace = reservoir_persistence_da.reservoir_persistence_usace
+                    usace_timeslices_folder = values['compute_parameters'].data_assimilation_parameters.usace_timeslices_folder
+                if reservoir_persistence_usace:
+                    error_message = ''
+                    network_type = values['network_topology_parameters'].supernetwork_parameters.network_type
+                    reservoir_parameter_file = reservoir_da.reservoir_parameter_file
+                    if not reservoir_parameter_file and network_type=='NHDNetwork':
+                        error_message += ' Reservoir_parameter_file is missing (and network type is NHDNetwork).'
+                    if not usace_timeslices_folder:
+                        error_message  += ' USACE_timeslices_folder is missing.'
+                    else:
+                        if not os.path.exists(usace_timeslices_folder):
+                            error_message += ' USACE_timeslices_folder path provided does not exist. '                    
+                    assert not error_message, 'USACE reservoir DA is enabled, but:' + error_message
 
         return values
 

src/troute-config/troute/config/logging_parameters.py

@@ -5,7 +5,7 @@
 LogLevel = Literal["CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG", "NOTSET"]
 
 
-class LoggingParameters(BaseModel, extra='forbid'):
+class LoggingParameters(BaseModel):
     log_level: LogLevel = "DEBUG"
     """
     Python logging level. Can either be a string or an integer from the list below optional,

src/troute-config/troute/config/network_topology_parameters.py

@@ -6,7 +6,7 @@
 from .types import FilePath, DirectoryPath
 
 
-class NetworkTopologyParameters(BaseModel, extra='forbid'):
+class NetworkTopologyParameters(BaseModel):
     # TODO: default {}. see nhd_io.read_config_file ~:100
     preprocessing_parameters: "PreprocessingParameters" = Field(default_factory=dict)
     # TODO: not sure if default {}. see nhd_io.read_config_file ~:100
@@ -19,7 +19,7 @@ class NetworkTopologyParameters(BaseModel, extra='forbid'):
 
 # TODO: This is an old parameter but probably worth keeping moving forward. However, it is
 # not implemented in V4 at the moment (Aug 11, 2023). Need to add this functionality to t-route.
-class PreprocessingParameters(BaseModel, extra='forbid'):
+class PreprocessingParameters(BaseModel):
     preprocess_only: bool = False
     # NOTE: required if preprocess_only = True
     # TODO: determine if str type
@@ -31,10 +31,10 @@ class PreprocessingParameters(BaseModel, extra='forbid'):
     preprocess_source_file: Optional[FilePath] = None
 
 
-class SupernetworkParameters(BaseModel, extra='forbid'):
+class SupernetworkParameters(BaseModel):
     title_string: Optional[str] = None
     # TODO: hopefully places in the code can be changed so this is a `Path` instead of a `str`
-    geo_file_path: str
+    geo_file_path: FilePath
     network_type: Literal["HYFeaturesNetwork", "NHDNetwork"] = "HYFeaturesNetwork"
     flowpath_edge_list: Optional[str] = None
     mask_file_path: Optional[FilePath] = None
@@ -55,51 +55,7 @@ class SupernetworkParameters(BaseModel, extra='forbid'):
         ]
     )
     synthetic_wb_id_offset: float = 9.99e11
-    duplicate_wb_segments: Optional[List[int]] = Field(
-        default_factory=lambda: [
-            717696,
-            1311881,
-            3133581,
-            1010832,
-            1023120,
-            1813525,
-            1531545,
-            1304859,
-            1320604,
-            1233435,
-            11816,
-            1312051,
-            2723765,
-            2613174,
-            846266,
-            1304891,
-            1233595,
-            1996602,
-            2822462,
-            2384576,
-            1021504,
-            2360642,
-            1326659,
-            1826754,
-            572364,
-            1336910,
-            1332558,
-            1023054,
-            3133527,
-            3053788,
-            3101661,
-            2043487,
-            3056866,
-            1296744,
-            1233515,
-            2045165,
-            1230577,
-            1010164,
-            1031669,
-            1291638,
-            1637751,
-        ]
-    )
+
     terminal_code: int = 0
     # TODO: It would be nice if this were a literal / str
     driver_string: Union[str, Literal["NetCDF"]] = "NetCDF"
@@ -150,7 +106,7 @@ def get_columns(cls, columns: dict, values: Dict[str, Any]) -> dict:
         return default_columns
 
 
-class Columns(BaseModel, extra='forbid'):
+class Columns(BaseModel):
     # string, unique segment identifier
     key: str 
     # string, unique identifier of downstream segment
@@ -185,14 +141,14 @@ class Columns(BaseModel, extra='forbid'):
     mainstem: Optional[str]
 
 
-class WaterbodyParameters(BaseModel, extra='forbid'):
+class WaterbodyParameters(BaseModel):
     # NOTE: required, True for simulations with waterbodies.
     break_network_at_waterbodies: bool = False
     level_pool: Optional["LevelPool"] = None
     waterbody_null_code: int = -9999
 
 
-class LevelPool(BaseModel, extra='forbid'):
+class LevelPool(BaseModel):
     # string, filepath to waterbody parameter file (LAKEPARM.nc)
     level_pool_waterbody_parameter_file_path: Optional[FilePath] = None
     level_pool_waterbody_id: Union[str, Literal["lake_id"]] = "lake_id"