workbench 0.8.168__py3-none-any.whl → 0.8.193__py3-none-any.whl

workbench/utils/model_utils.py

@@ -3,6 +3,7 @@
 import logging
 import pandas as pd
 import numpy as np
+from scipy.stats import spearmanr
 import importlib.resources
 from pathlib import Path
 import os
@@ -92,6 +93,31 @@ def get_custom_script_path(package: str, script_name: str) -> Path:
     return script_path
 
 
+def proximity_model_local(model: "Model"):
+    """Create a Proximity Model for this Model
+
+    Args:
+        model (Model): The Model/FeatureSet used to create the proximity model
+
+    Returns:
+        Proximity: The proximity model
+    """
+    from workbench.algorithms.dataframe.proximity import Proximity  # noqa: F401 (avoid circular import)
+    from workbench.api import Model, FeatureSet  # noqa: F401 (avoid circular import)
+
+    # Get Feature and Target Columns from the existing given Model
+    features = model.features()
+    target = model.target()
+
+    # Backtrack our FeatureSet to get the ID column
+    fs = FeatureSet(model.get_input())
+    id_column = fs.id_column
+
+    # Create the Proximity Model from our Training Data
+    df = model.training_view().pull_dataframe()
+    return Proximity(df, id_column, features, target, track_columns=features)
+
+
 def proximity_model(model: "Model", prox_model_name: str, track_columns: list = None) -> "Model":
     """Create a proximity model based on the given model
 
@@ -140,7 +166,7 @@ def uq_model(model: "Model", uq_model_name: str, train_all_data: bool = False) -
     from workbench.api import Model, ModelType, FeatureSet  # noqa: F401 (avoid circular import)
 
     # Get the custom script path for the UQ model
-    script_path = get_custom_script_path("uq_models", "meta_uq.template")
+    script_path = get_custom_script_path("uq_models", "mapie.template")
 
     # Get Feature and Target Columns from the existing given Model
     features = model.features()
@@ -162,6 +188,20 @@ def uq_model(model: "Model", uq_model_name: str, train_all_data: bool = False) -
     return uq_model
 
 
+def safe_extract_tarfile(tar_path: str, extract_path: str) -> None:
+    """
+    Extract a tarball safely, using data filter if available.
+
+    The filter parameter was backported to Python 3.8+, 3.9+, 3.10.13+, 3.11+
+    as a security patch, but may not be present in older patch versions.
+    """
+    with tarfile.open(tar_path, "r:gz") as tar:
+        if hasattr(tarfile, "data_filter"):
+            tar.extractall(path=extract_path, filter="data")
+        else:
+            tar.extractall(path=extract_path)
+
+
 def load_category_mappings_from_s3(model_artifact_uri: str) -> Optional[dict]:
     """
     Download and extract category mappings from a model artifact in S3.
@@ -180,8 +220,7 @@ def load_category_mappings_from_s3(model_artifact_uri: str) -> Optional[dict]:
         wr.s3.download(path=model_artifact_uri, local_file=local_tar_path)
 
         # Extract tarball
-        with tarfile.open(local_tar_path, "r:gz") as tar:
-            tar.extractall(path=tmpdir, filter="data")
+        safe_extract_tarfile(local_tar_path, tmpdir)
 
         # Look for category mappings in base directory only
         mappings_path = os.path.join(tmpdir, "category_mappings.json")
@@ -220,28 +259,41 @@ def uq_metrics(df: pd.DataFrame, target_col: str) -> Dict[str, Any]:
     # --- Coverage and Interval Width ---
     if "q_025" in df.columns and "q_975" in df.columns:
         lower_95, upper_95 = df["q_025"], df["q_975"]
+        lower_90, upper_90 = df["q_05"], df["q_95"]
+        lower_80, upper_80 = df["q_10"], df["q_90"]
+        lower_68 = df.get("q_16", df["q_10"])  # fallback to 80% interval
+        upper_68 = df.get("q_84", df["q_90"])  # fallback to 80% interval
         lower_50, upper_50 = df["q_25"], df["q_75"]
     elif "prediction_std" in df.columns:
         lower_95 = df["prediction"] - 1.96 * df["prediction_std"]
         upper_95 = df["prediction"] + 1.96 * df["prediction_std"]
+        lower_90 = df["prediction"] - 1.645 * df["prediction_std"]
+        upper_90 = df["prediction"] + 1.645 * df["prediction_std"]
+        lower_80 = df["prediction"] - 1.282 * df["prediction_std"]
+        upper_80 = df["prediction"] + 1.282 * df["prediction_std"]
+        lower_68 = df["prediction"] - 1.0 * df["prediction_std"]
+        upper_68 = df["prediction"] + 1.0 * df["prediction_std"]
         lower_50 = df["prediction"] - 0.674 * df["prediction_std"]
         upper_50 = df["prediction"] + 0.674 * df["prediction_std"]
     else:
         raise ValueError(
             "Either quantile columns (q_025, q_975, q_25, q_75) or 'prediction_std' column must be present."
         )
+    median_std = df["prediction_std"].median()
     coverage_95 = np.mean((df[target_col] >= lower_95) & (df[target_col] <= upper_95))
-    coverage_50 = np.mean((df[target_col] >= lower_50) & (df[target_col] <= upper_50))
-    avg_width_95 = np.mean(upper_95 - lower_95)
-    avg_width_50 = np.mean(upper_50 - lower_50)
+    coverage_90 = np.mean((df[target_col] >= lower_90) & (df[target_col] <= upper_90))
+    coverage_80 = np.mean((df[target_col] >= lower_80) & (df[target_col] <= upper_80))
+    coverage_68 = np.mean((df[target_col] >= lower_68) & (df[target_col] <= upper_68))
+    median_width_95 = np.median(upper_95 - lower_95)
+    median_width_90 = np.median(upper_90 - lower_90)
+    median_width_80 = np.median(upper_80 - lower_80)
+    median_width_50 = np.median(upper_50 - lower_50)
+    median_width_68 = np.median(upper_68 - lower_68)
 
     # --- CRPS (measures calibration + sharpness) ---
-    if "prediction_std" in df.columns:
-        z = (df[target_col] - df["prediction"]) / df["prediction_std"]
-        crps = df["prediction_std"] * (z * (2 * norm.cdf(z) - 1) + 2 * norm.pdf(z) - 1 / np.sqrt(np.pi))
-        mean_crps = np.mean(crps)
-    else:
-        mean_crps = np.nan
+    z = (df[target_col] - df["prediction"]) / df["prediction_std"]
+    crps = df["prediction_std"] * (z * (2 * norm.cdf(z) - 1) + 2 * norm.pdf(z) - 1 / np.sqrt(np.pi))
+    mean_crps = np.mean(crps)
 
     # --- Interval Score @ 95% (penalizes miscoverage) ---
     alpha_95 = 0.05
@@ -252,31 +304,43 @@ def uq_metrics(df: pd.DataFrame, target_col: str) -> Dict[str, Any]:
     )
     mean_is_95 = np.mean(is_95)
 
-    # --- Adaptive Calibration (correlation between errors and uncertainty) ---
+    # --- Interval to Error Correlation ---
     abs_residuals = np.abs(df[target_col] - df["prediction"])
-    width_95 = upper_95 - lower_95
-    adaptive_calibration = np.corrcoef(abs_residuals, width_95)[0, 1]
+    width_68 = upper_68 - lower_68
+
+    # Spearman correlation for robustness
+    interval_to_error_corr = spearmanr(width_68, abs_residuals)[0]
 
     # Collect results
     results = {
+        "coverage_68": coverage_68,
+        "coverage_80": coverage_80,
+        "coverage_90": coverage_90,
         "coverage_95": coverage_95,
-        "coverage_50": coverage_50,
-        "avg_width_95": avg_width_95,
-        "avg_width_50": avg_width_50,
-        "crps": mean_crps,
-        "interval_score_95": mean_is_95,
-        "adaptive_calibration": adaptive_calibration,
+        "median_std": median_std,
+        "median_width_50": median_width_50,
+        "median_width_68": median_width_68,
+        "median_width_80": median_width_80,
+        "median_width_90": median_width_90,
+        "median_width_95": median_width_95,
+        "interval_to_error_corr": interval_to_error_corr,
         "n_samples": len(df),
     }
 
     print("\n=== UQ Metrics ===")
+    print(f"Coverage @ 68%: {coverage_68:.3f} (target: 0.68)")
+    print(f"Coverage @ 80%: {coverage_80:.3f} (target: 0.80)")
+    print(f"Coverage @ 90%: {coverage_90:.3f} (target: 0.90)")
     print(f"Coverage @ 95%: {coverage_95:.3f} (target: 0.95)")
-    print(f"Coverage @ 50%: {coverage_50:.3f} (target: 0.50)")
-    print(f"Average 95% Width: {avg_width_95:.3f}")
-    print(f"Average 50% Width: {avg_width_50:.3f}")
+    print(f"Median Prediction StdDev: {median_std:.3f}")
+    print(f"Median 50% Width: {median_width_50:.3f}")
+    print(f"Median 68% Width: {median_width_68:.3f}")
+    print(f"Median 80% Width: {median_width_80:.3f}")
+    print(f"Median 90% Width: {median_width_90:.3f}")
+    print(f"Median 95% Width: {median_width_95:.3f}")
     print(f"CRPS: {mean_crps:.3f} (lower is better)")
     print(f"Interval Score 95%: {mean_is_95:.3f} (lower is better)")
-    print(f"Adaptive Calibration: {adaptive_calibration:.3f} (higher is better, target: >0.5)")
+    print(f"Interval/Error Corr: {interval_to_error_corr:.3f} (higher is better, target: >0.5)")
     print(f"Samples: {len(df)}")
     return results
 
@@ -313,9 +377,3 @@ if __name__ == "__main__":
     df = end.auto_inference(capture=True)
     results = uq_metrics(df, target_col="solubility")
     print(results)
-
-    # Test the uq_metrics function
-    end = Endpoint("aqsol-uq-100")
-    df = end.auto_inference(capture=True)
-    results = uq_metrics(df, target_col="solubility")
-    print(results)

workbench/utils/monitor_utils.py

@@ -14,7 +14,7 @@ from workbench.utils.s3_utils import read_content_from_s3
 log = logging.getLogger("workbench")
 
 
-def pull_data_capture(data_capture_path, max_files=1) -> Union[pd.DataFrame, None]:
+def pull_data_capture_for_testing(data_capture_path, max_files=1) -> Union[pd.DataFrame, None]:
     """
     Read and process captured data from S3.
 
@@ -26,7 +26,12 @@ def pull_data_capture(data_capture_path, max_files=1) -> Union[pd.DataFrame, Non
 
     Returns:
         Union[pd.DataFrame, None]: A dataframe of the captured data (or None if no data is found).
+
+    Notes:
+        This method is really only for testing and debugging.
     """
+    log.important("This method is for testing and debugging only.")
+
     # List files in the specified S3 path
     files = wr.s3.list_objects(data_capture_path)
     if not files:
@@ -64,59 +69,53 @@ def pull_data_capture(data_capture_path, max_files=1) -> Union[pd.DataFrame, Non
 def process_data_capture(df: pd.DataFrame) -> tuple[pd.DataFrame, pd.DataFrame]:
     """
     Process the captured data DataFrame to extract input and output data.
-    Continues processing even if individual files are malformed.
+    Handles cases where input or output might not be captured.
+
     Args:
         df (DataFrame): DataFrame with captured data.
     Returns:
         tuple[DataFrame, DataFrame]: Input and output DataFrames.
     """
+
+    def parse_endpoint_data(data: dict) -> pd.DataFrame:
+        """Parse endpoint data based on encoding type."""
+        encoding = data["encoding"].upper()
+
+        if encoding == "CSV":
+            return pd.read_csv(StringIO(data["data"]))
+        elif encoding == "JSON":
+            json_data = json.loads(data["data"])
+            if isinstance(json_data, dict):
+                return pd.DataFrame({k: [v] if not isinstance(v, list) else v for k, v in json_data.items()})
+            else:
+                return pd.DataFrame(json_data)
+        else:
+            return None  # Unknown encoding
+
     input_dfs = []
     output_dfs = []
 
-    for idx, row in df.iterrows():
+    # Use itertuples() instead of iterrows() for better performance
+    for row in df.itertuples(index=True):
         try:
-            capture_data = row["captureData"]
-
-            # Check if this capture has the required fields (all or nothing)
-            if "endpointInput" not in capture_data:
-                log.warning(f"Row {idx}: No endpointInput found in capture data.")
-                continue
-
-            if "endpointOutput" not in capture_data:
-                log.critical(
-                    f"Row {idx}: No endpointOutput found in capture data. DataCapture needs to include Output capture!"
-                )
-                continue
-
-            # Process input data
-            input_data = capture_data["endpointInput"]
-            if input_data["encoding"].upper() == "CSV":
-                input_df = pd.read_csv(StringIO(input_data["data"]))
-            elif input_data["encoding"].upper() == "JSON":
-                json_data = json.loads(input_data["data"])
-                if isinstance(json_data, dict):
-                    input_df = pd.DataFrame({k: [v] if not isinstance(v, list) else v for k, v in json_data.items()})
-                else:
-                    input_df = pd.DataFrame(json_data)
-
-            # Process output data
-            output_data = capture_data["endpointOutput"]
-            if output_data["encoding"].upper() == "CSV":
-                output_df = pd.read_csv(StringIO(output_data["data"]))
-            elif output_data["encoding"].upper() == "JSON":
-                json_data = json.loads(output_data["data"])
-                if isinstance(json_data, dict):
-                    output_df = pd.DataFrame({k: [v] if not isinstance(v, list) else v for k, v in json_data.items()})
-                else:
-                    output_df = pd.DataFrame(json_data)
-
-            # If we get here, both processed successfully
-            input_dfs.append(input_df)
-            output_dfs.append(output_df)
+            capture_data = row.captureData
+
+            # Process input data if present
+            if "endpointInput" in capture_data:
+                input_df = parse_endpoint_data(capture_data["endpointInput"])
+                if input_df is not None:
+                    input_dfs.append(input_df)
+
+            # Process output data if present
+            if "endpointOutput" in capture_data:
+                output_df = parse_endpoint_data(capture_data["endpointOutput"])
+                if output_df is not None:
+                    output_dfs.append(output_df)
 
         except Exception as e:
-            log.error(f"Row {idx}: Failed to process row: {e}")
+            log.debug(f"Row {row.Index}: Failed to process row: {e}")
             continue
+
     # Combine and return results
     return (
         pd.concat(input_dfs, ignore_index=True) if input_dfs else pd.DataFrame(),
@@ -178,23 +177,6 @@ def parse_monitoring_results(results_json: str) -> Dict[str, Any]:
         return {"error": str(e)}
 
 
-"""TEMP
-                # If the status is "CompletedWithViolations", we grab the lastest
-                # violation file and add it to the result
-                if status == "CompletedWithViolations":
-                    violation_file = f"{self.monitoring_path}/
-                    {last_run['CreationTime'].strftime('%Y/%m/%d')}/constraint_violations.json"
-                    if wr.s3.does_object_exist(violation_file):
-                        violations_json = read_content_from_s3(violation_file)
-                        violations = parse_monitoring_results(violations_json)
-                        result["violations"] = violations.get("constraint_violations", [])
-                        result["violation_count"] = len(result["violations"])
-                    else:
-                        result["violations"] = []
-                        result["violation_count"] = 0
-"""
-
-
 def preprocessing_script(feature_list: list[str]) -> str:
     """
     A preprocessing script for monitoring jobs.
@@ -245,8 +227,8 @@ if __name__ == "__main__":
     from workbench.api.monitor import Monitor
 
     # Test pulling data capture
-    mon = Monitor("caco2-pappab-class-0")
-    df = pull_data_capture(mon.data_capture_path)
+    mon = Monitor("abalone-regression-rt")
+    df = pull_data_capture_for_testing(mon.data_capture_path)
     print("Data Capture:")
     print(df.head())
 
@@ -262,4 +244,4 @@ if __name__ == "__main__":
     # Test preprocessing script
     script = preprocessing_script(["feature1", "feature2", "feature3"])
     print("\nPreprocessing Script:")
-    print(script)
+    # print(script)

workbench/utils/pandas_utils.py

@@ -152,7 +152,7 @@ def compare_dataframes(df1: pd.DataFrame, df2: pd.DataFrame, display_columns: li
 
     # Check for differences in common columns
     for column in common_columns:
-        if pd.api.types.is_string_dtype(df1[column]) or pd.api.types.is_string_dtype(df2[column]):
+        if pd.api.types.is_string_dtype(df1[column]) and pd.api.types.is_string_dtype(df2[column]):
             # String comparison with NaNs treated as equal
             differences = ~(df1[column].fillna("") == df2[column].fillna(""))
         elif pd.api.types.is_float_dtype(df1[column]) or pd.api.types.is_float_dtype(df2[column]):
@@ -161,8 +161,8 @@ def compare_dataframes(df1: pd.DataFrame, df2: pd.DataFrame, display_columns: li
                 pd.isna(df1[column]) & pd.isna(df2[column])
             )
         else:
-            # Other types (e.g., int) with NaNs treated as equal
-            differences = ~(df1[column].fillna(0) == df2[column].fillna(0))
+            # Other types (int, Int64, etc.) - compare with NaNs treated as equal
+            differences = (df1[column] != df2[column]) & ~(pd.isna(df1[column]) & pd.isna(df2[column]))
 
         # If differences exist, display them
         if differences.any():

workbench/utils/shap_utils.py

@@ -212,6 +212,14 @@ def _calculate_shap_values(workbench_model, sample_df: pd.DataFrame = None):
         log.error("No XGBoost model found in the artifact.")
         return None, None, None, None
 
+    # Get the booster (SHAP requires the booster, not the sklearn wrapper)
+    if hasattr(xgb_model, "get_booster"):
+        # Full sklearn model - extract the booster
+        booster = xgb_model.get_booster()
+    else:
+        # Already a booster
+        booster = xgb_model
+
     # Load category mappings if available
     category_mappings = load_category_mappings_from_s3(model_artifact_uri)
 
@@ -229,8 +237,8 @@ def _calculate_shap_values(workbench_model, sample_df: pd.DataFrame = None):
     # Create a DMatrix with categorical support
     dmatrix = xgb.DMatrix(X, enable_categorical=True)
 
-    # Use XGBoost's built-in SHAP calculation
-    shap_values = xgb_model.predict(dmatrix, pred_contribs=True, strict_shape=True)
+    # Use XGBoost's built-in SHAP calculation (booster method, not sklearn)
+    shap_values = booster.predict(dmatrix, pred_contribs=True, strict_shape=True)
     features_with_bias = features + ["bias"]
 
     # Now we need to subset the columns based on top 10 SHAP values

workbench/utils/workbench_sqs.py

@@ -12,7 +12,7 @@ class WorkbenchSQS:
         self.log = logging.getLogger("workbench")
         self.queue_url = queue_url
 
-        # Grab a Workbench Session (this allows us to assume the Workbench-ExecutionRole)
+        # Grab a Workbench Session
         self.boto3_session = AWSAccountClamp().boto3_session
         print(self.boto3_session)