replace SimpleNamespace configs with typed dataclasses and enums. update pyproject.toml to pin pandas to 2.* (pandas 3.* introduced breaking changes). update uv.lock to use latest iddata commit

Author: matthewcornell

CHANGELOG.md

@@ -7,6 +7,30 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.3.0]
+
+### Added
+- Concrete configuration dataclasses: `ModelConfig`, `RunConfig` (abstract bases), `SARIXModelConfig`, `SARIXRunConfig`, `GBQRModelConfig`, `GBQRRunConfig`
+- `SARIXFourierModelConfig` dataclass with `fourier_K` and `fourier_pooling` fields
+- Wave feature fields on `GBQRModelConfig` (`use_directional_waves`, `wave_directions`, etc.), disabled by default
+- Enum types: `DataSource`, `Disease`, `PowerTransform`, `PoolingStrategy`
+- Docstrings for `ModelConfig` and `RunConfig` base classes
+- All config types exported from `idmodels.__init__`
+
+### Changed
+- **Breaking**: `model_config.sources` now expects `list[DataSource]` instead of `list[str]`
+- **Breaking**: `model_config.power_transform` now expects `PowerTransform` instead of `str`
+- **Breaking**: `model_config.disease` now expects `Disease` instead of `str`
+- Source validation in `sarix.py` and `gbqr.py` uses `DataSource` enums and set operations instead of `np.isin` with string arrays
+- All tests use concrete config dataclasses instead of `SimpleNamespace`
+- Updated `directional_wave_features.md` examples to use config dataclasses
+
+### Removed
+- `SimpleNamespace` usage throughout tests and documentation
+- `model_class` field from model configurations (implied by the dataclass type)
+- `num_bags` from `GBQRRunConfig` test helper (it is a `GBQRModelConfig` field)
+- `save_feat_importance` from `SARIXRunConfig` test helper (not a SARIX field)
+
 ## [1.1.0] - 2025-12-08
 
 ### Added
@@ -71,7 +95,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 - Updated to latest iddata API
 
-[Unreleased]: https://github.com/reichlab/idmodels/compare/v1.1.0...HEAD
+[Unreleased]: https://github.com/reichlab/idmodels/compare/v1.3.0...HEAD
+[1.3.0]: https://github.com/reichlab/idmodels/compare/v1.1.0...v1.3.0
 [1.1.0]: https://github.com/reichlab/idmodels/compare/v1.0.0...v1.1.0
 [1.0.0]: https://github.com/reichlab/idmodels/compare/v0.1.0...v1.0.0
 [0.1.0]: https://github.com/reichlab/idmodels/compare/v0.0.1...v0.1.0

docs/directional_wave_features.md

@@ -43,10 +43,13 @@ For each location and time point, the following features are generated:
 Directional wave features are **disabled by default** for backwards compatibility. To enable them, add the following parameters to your `model_config`:
 
 ```python
-from types import SimpleNamespace
+from idmodels.config import DataSource, GBQRModelConfig, PowerTransform
 
-model_config = SimpleNamespace(
-    # ... existing parameters ...
+model_config = GBQRModelConfig(
+    model_name = "gbqr_with_waves",
+    sources = [DataSource.NHSN],
+    fit_locations_separately = False,
+    power_transform = PowerTransform.FOURTH_ROOT,
 
     # Directional wave features (disabled by default)
     use_directional_waves = True,  # Set to True to enable
@@ -111,8 +114,8 @@ model_config = SimpleNamespace(
 
 ### Minimal Configuration (4 cardinal directions)
 ```python
-model_config = SimpleNamespace(
-    # ... other params ...
+model_config = GBQRModelConfig(
+    # ... required base params ...
     use_directional_waves = True,
     wave_directions = ['N', 'S', 'E', 'W']
 )
@@ -121,8 +124,8 @@ Generates: 4 base + 4 aggregate + (4+1)×2 lags = **14 features**
 
 ### Standard Configuration (8 directions)
 ```python
-model_config = SimpleNamespace(
-    # ... other params ...
+model_config = GBQRModelConfig(
+    # ... required base params ...
     use_directional_waves = True,
     wave_directions = ['N', 'NE', 'E', 'SE', 'S', 'SW', 'W', 'NW'],
     wave_temporal_lags = [1, 2]
@@ -132,8 +135,8 @@ Generates: 8 base + 1 aggregate + (8+1)×2 lags = **27 features**
 
 ### Maximum Information (all options)
 ```python
-model_config = SimpleNamespace(
-    # ... other params ...
+model_config = GBQRModelConfig(
+    # ... required base params ...
     use_directional_waves = True,
     wave_directions = ['N', 'NE', 'E', 'SE', 'S', 'SW', 'W', 'NW'],
     wave_temporal_lags = [1, 2],
@@ -147,8 +150,8 @@ Generates: 8 base + 1 aggregate + (8+1)×2 lags + (8+1) velocity = **36 features
 ### Hypothesis-Driven (specific directions)
 ```python
 # If you suspect disease spreads along NE-SW axis
-model_config = SimpleNamespace(
-    # ... other params ...
+model_config = GBQRModelConfig(
+    # ... required base params ...
     use_directional_waves = True,
     wave_directions = ['NE', 'SW'],
     wave_temporal_lags = [1, 2, 3],  # Longer lags for slower spread
@@ -240,22 +243,21 @@ The implementation includes validation that warns about:
 ## Example: Complete GBQR Configuration
 
 ```python
-from types import SimpleNamespace
+import datetime
+from pathlib import Path
+from idmodels.config import DataSource, Disease, GBQRModelConfig, GBQRRunConfig, PowerTransform
 from idmodels.gbqr import GBQRModel
 
 # Model configuration with directional wave features
-model_config = SimpleNamespace(
-    model_class = "gbqr",
+model_config = GBQRModelConfig(
     model_name = "gbqr_with_waves",
-
-    # Standard GBQR parameters
+    sources = [DataSource.NHSN],
+    fit_locations_separately = False,
+    power_transform = PowerTransform.FOURTH_ROOT,
     incl_level_feats = True,
     num_bags = 10,
     bag_frac_samples = 0.7,
     reporting_adj = False,
-    sources = ["nhsn"],
-    fit_locations_separately = False,
-    power_transform = "4rt",
 
     # Directional wave features
     use_directional_waves = True,
@@ -267,16 +269,17 @@ model_config = SimpleNamespace(
 )
 
 # Run configuration
-run_config = SimpleNamespace(
-    disease = "flu",
+run_config = GBQRRunConfig(
+    disease = Disease.FLU,
     ref_date = datetime.date(2024, 1, 6),
-    output_root = "output/",
-    artifact_store_root = "artifacts/",
-    save_feat_importance = True,
-    locations = None,  # All locations
+    output_root = Path("output/"),
+    artifact_store_root = Path("artifacts/"),
     max_horizon = 4,
+    states = ["US", "01", "06", "13", "36", "48"],
+    hsas = [],
     q_levels = [0.025, 0.10, 0.25, 0.50, 0.75, 0.90, 0.975],
-    q_labels = ["0.025", "0.1", "0.25", "0.5", "0.75", "0.9", "0.975"]
+    q_labels = ["0.025", "0.1", "0.25", "0.5", "0.75", "0.9", "0.975"],
+    save_feat_importance = True
 )
 
 # Run model

pyproject.toml

@@ -14,8 +14,8 @@ dependencies = [
     "iddata @ git+https://github.com/reichlab/iddata",
     "lightgbm",
     "numpy",
-    "pandas",
-    "sarix @ git+https://github.com/reichlab/sarix",
+    "pandas~=2.0",  # pandas 3.0 breaks compatibility; remove cap once validated
+    "sarix @ git+https://github.com/reichlab/sarix?rev=35eea2379a9790e0457b1aed41d13509e5d5056f",
     "scikit-learn",
     "tqdm",
     "timeseriesutils @ git+https://github.com/reichlab/timeseriesutils"

src/idmodels/__init__.py

@@ -1,2 +1,11 @@
-__version__ = "1.2.0"
+from idmodels.config import (DataSource, Disease, GBQRModelConfig, GBQRRunConfig, PoolingStrategy, PowerTransform,
+                             SARIXFourierModelConfig, SARIXModelConfig, SARIXRunConfig)
+from idmodels.gbqr import GBQRModel
+from idmodels.sarix import SARIXFourierModel, SARIXModel
 
+
+__all__ = ['DataSource', 'Disease', 'GBQRModel', 'GBQRModelConfig', 'GBQRRunConfig', 'PoolingStrategy',
+           'PowerTransform', 'SARIXFourierModel', 'SARIXFourierModelConfig', 'SARIXModel', 'SARIXModelConfig',
+           'SARIXRunConfig']
+
+__version__ = '1.3.0'

src/idmodels/config.py

@@ -0,0 +1,114 @@
+import datetime
+from abc import ABC
+from dataclasses import dataclass, field
+from enum import Enum
+from pathlib import Path
+
+
+class DataSource(str, Enum):
+    NHSN = "nhsn"
+    NSSP = "nssp"
+    FLUSURVNET = "flusurvnet"
+    ILINET = "ilinet"
+
+
+class Disease(str, Enum):
+    FLU = "flu"
+    COVID = "covid"
+
+
+class PowerTransform(str, Enum):
+    FOURTH_ROOT = "4rt"
+
+
+class PoolingStrategy(str, Enum):
+    NONE = "none"
+    SHARED = "shared"
+
+
+@dataclass
+class ModelConfig(ABC):
+    """
+    Abstract base for model configuration.
+
+    Holds settings that describe *what* model to run and how it processes data (sources, transforms, pooling).
+    Not instantiated directly - use :class:`SARIXModelConfig` or :class:`GBQRModelConfig`.
+    """
+
+    model_name: str
+    sources: list[DataSource]
+    fit_locations_separately: bool
+    power_transform: PowerTransform
+
+    def __post_init__(self):
+        if type(self) is ModelConfig:
+            raise TypeError("ModelConfig is abstract - use SARIXModelConfig or GBQRModelConfig")
+
+
+@dataclass
+class RunConfig(ABC):
+    """
+    Abstract base for run configuration.
+
+    Holds settings that describe a single execution: which disease, which locations, output paths, quantile levels, etc.
+    Not instantiated directly - use :class:`SARIXRunConfig` or :class:`GBQRRunConfig`.
+    """
+
+    disease: Disease
+    ref_date: datetime.date
+    output_root: Path
+    artifact_store_root: Path | None
+    max_horizon: int
+    states: list[str]
+    hsas: list[str]
+    q_levels: list[float]
+    q_labels: list[str]
+
+    def __post_init__(self):
+        if type(self) is RunConfig:
+            raise TypeError("RunConfig is abstract - use SARIXRunConfig or GBQRRunConfig")
+
+
+@dataclass
+class SARIXModelConfig(ModelConfig):
+    p: int = 0
+    P: int = 0
+    d: int = 0
+    D: int = 0
+    season_period: int = 1
+    theta_pooling: PoolingStrategy = PoolingStrategy.NONE
+    sigma_pooling: PoolingStrategy = PoolingStrategy.NONE
+    x: list = field(default_factory=list)
+
+
+@dataclass
+class SARIXFourierModelConfig(SARIXModelConfig):
+    fourier_K: int = 1
+    fourier_pooling: PoolingStrategy = PoolingStrategy.NONE
+
+
+@dataclass
+class GBQRModelConfig(ModelConfig):
+    incl_level_feats: bool = True
+    num_bags: int = 100
+    bag_frac_samples: float = 0.7
+    reporting_adj: bool = False
+    # directional wave features (disabled by default)
+    use_directional_waves: bool = False
+    wave_directions: list[str] = field(default_factory=lambda: ["N", "NE", "E", "SE", "S", "SW", "W", "NW"])
+    wave_temporal_lags: list[int] = field(default_factory=lambda: [1, 2])
+    wave_max_distance_km: float = 1000.0
+    wave_include_velocity: bool = False
+    wave_include_aggregate: bool = True
+
+
+@dataclass
+class SARIXRunConfig(RunConfig):
+    num_warmup: int = 2000
+    num_samples: int = 2000
+    num_chains: int = 1
+
+
+@dataclass
+class GBQRRunConfig(RunConfig):
+    save_feat_importance: bool = False

src/idmodels/gbqr.py

@@ -6,6 +6,7 @@
 from iddata.loader import DiseaseDataLoader
 from tqdm.autonotebook import tqdm
 
+from idmodels.config import DataSource, Disease, PowerTransform
 from idmodels.preprocess import create_directional_wave_features, create_features_and_targets
 from idmodels.utils import build_save_path
 
@@ -31,22 +32,22 @@ def run(self, run_config):
             ilinet_kwargs = {"scale_to_positive": False}
             flusurvnet_kwargs = {"burden_adj": False}
 
-        valid_sources = ["flusurvnet", "nhsn", "ilinet", "nssp"]
-        if not np.isin(np.array(self.model_config.sources), valid_sources).all():
+        valid_sources = {DataSource.FLUSURVNET, DataSource.NHSN, DataSource.ILINET, DataSource.NSSP}
+        if not set(self.model_config.sources) <= valid_sources:
           raise ValueError("For GBQR, the only supported data sources are 'nhsn', 'flusurvnet', 'ilinet', or 'nssp'.")
-        
+
         # Check if both nhsn and nssp data are included as sources
-        if all(src in self.model_config.sources for src in ["nhsn", "nssp"]):
+        if (DataSource.NHSN in self.model_config.sources) and (DataSource.NSSP in self.model_config.sources):
             raise ValueError("Only one of 'nhsn' or 'nssp' may be selected as a data source.")
-        
+
         fdl = DiseaseDataLoader()
-        if "nhsn" in self.model_config.sources:
+        if DataSource.NHSN in self.model_config.sources:
             df = fdl.load_data(nhsn_kwargs={"as_of": run_config.ref_date, "disease": run_config.disease},
                                ilinet_kwargs=ilinet_kwargs,
                                flusurvnet_kwargs=flusurvnet_kwargs,
                                sources=self.model_config.sources,
                                power_transform=self.model_config.power_transform)
-        elif "nssp" in self.model_config.sources:
+        elif DataSource.NSSP in self.model_config.sources:
             df = fdl.load_data(nssp_kwargs={"as_of": run_config.ref_date, "disease": run_config.disease},
                                ilinet_kwargs=ilinet_kwargs,
                                flusurvnet_kwargs=flusurvnet_kwargs,
@@ -62,20 +63,20 @@ def run(self, run_config):
         df["unique_id"] = df["agg_level"] + df["location"]
 
         # augment data with features and target values
-        if run_config.disease == "flu":
+        if run_config.disease == Disease.FLU:
             init_feats = ["inc_trans_cs", "season_week", "log_pop"]
-        elif run_config.disease == "covid":
+        elif run_config.disease == Disease.COVID:
             init_feats = ["inc_trans_cs", "log_pop"]
 
         # Create directional wave features if enabled
-        if hasattr(self.model_config, "use_directional_waves") and self.model_config.use_directional_waves:
+        if self.model_config.use_directional_waves:
             wave_config = {
                 "enabled": True,
-                "directions": getattr(self.model_config, "wave_directions", ["N", "NE", "E", "SE", "S", "SW", "W", "NW"]),
-                "temporal_lags": getattr(self.model_config, "wave_temporal_lags", [1, 2]),
-                "max_distance_km": getattr(self.model_config, "wave_max_distance_km", 1000),
-                "include_velocity": getattr(self.model_config, "wave_include_velocity", False),
-                "include_aggregate": getattr(self.model_config, "wave_include_aggregate", True)
+                "directions": self.model_config.wave_directions,
+                "temporal_lags": self.model_config.wave_temporal_lags,
+                "max_distance_km": self.model_config.wave_max_distance_km,
+                "include_velocity": self.model_config.wave_include_velocity,
+                "include_aggregate": self.model_config.wave_include_aggregate,
             }
             df, wave_feat_names = create_directional_wave_features(df, wave_config)
             init_feats = init_feats + wave_feat_names
@@ -87,7 +88,7 @@ def run(self, run_config):
             curr_feat_names=init_feats)
 
         # keep only rows that are in-season
-        if run_config.disease == "flu":
+        if run_config.disease == Disease.FLU:
             df = df.query("season_week >= 5 and season_week <= 45")
 
         # "test set" df used to generate look-ahead predictions
@@ -176,12 +177,10 @@ def _train_gbq_and_predict(self, run_config,
         # build data frame with predictions on the original scale
         preds_df["inc_trans_cs_target_hat"] = preds_df["inc_trans_cs"] + preds_df["delta_hat"]
         preds_df["inc_trans_target_hat"] = (preds_df["inc_trans_cs_target_hat"] + preds_df["inc_trans_center_factor"]) * (preds_df["inc_trans_scale_factor"] + 0.01)
-        if self.model_config.power_transform == "4rt":
+        if self.model_config.power_transform == PowerTransform.FOURTH_ROOT:
             inv_power = 4
-        elif self.model_config.power_transform is None:
-            inv_power = 1
         else:
-            raise ValueError('unsupported power_transform: must be "4rt" or None')
+            raise ValueError(f"unsupported power_transform: {self.model_config.power_transform!r}")
 
         preds_df["value"] = (np.maximum(preds_df["inc_trans_target_hat"], 0.0) ** inv_power - 0.01 - 0.75**4)