workbench 0.8.162__py3-none-any.whl → 0.8.202__py3-none-any.whl

workbench/algorithms/graph/light/proximity_graph.py

@@ -4,7 +4,7 @@ from typing import Union
 import logging
 
 # Workbench Imports
-from workbench.algorithms.dataframe import Proximity, ProximityType
+from workbench.algorithms.dataframe import Proximity
 from workbench.api.graph_store import GraphStore
 
 # Set up logging
@@ -50,12 +50,13 @@ class ProximityGraph:
         self._nx_graph.add_nodes_from(node_df.set_index(id_column, drop=False).to_dict("index").items())
 
         # Determine edge weights based on proximity type
-        if prox.proximity_type == ProximityType.SIMILARITY:
-            all_neighbors_df["weight"] = all_neighbors_df["similarity"]
-        elif prox.proximity_type == ProximityType.DISTANCE:
-            # Normalize and invert distance
-            max_distance = all_neighbors_df["distance"].max()
-            all_neighbors_df["weight"] = 1.0 - all_neighbors_df["distance"] / max_distance
+        # if prox.proximity_type == ProximityType.SIMILARITY:
+        #     all_neighbors_df["weight"] = all_neighbors_df["similarity"]
+        # elif prox.proximity_type == ProximityType.DISTANCE:
+
+        # Normalize and invert distance
+        max_distance = all_neighbors_df["distance"].max()
+        all_neighbors_df["weight"] = 1.0 - all_neighbors_df["distance"] / max_distance
 
         # Add edges to the graph
         log.info("Adding edges to the graph...")
@@ -135,7 +136,8 @@ if __name__ == "__main__":
     from workbench.algorithms.dataframe.fingerprint_proximity import FingerprintProximity
     from workbench.web_interface.components.plugins.graph_plot import GraphPlot
     from workbench.api import DFStore
-    from workbench.utils.chem_utils import compute_morgan_fingerprints, project_fingerprints
+    from workbench.utils.chem_utils.fingerprints import compute_morgan_fingerprints
+    from workbench.utils.chem_utils.projections import project_fingerprints
     from workbench.utils.graph_utils import connected_sample, graph_layout
 
     def show_graph(graph, id_column):

workbench/api/__init__.py

@@ -14,7 +14,7 @@ These class provide high-level APIs for the Workbench package, offering easy acc
 
 from .data_source import DataSource
 from .feature_set import FeatureSet
-from .model import Model, ModelType
+from .model import Model, ModelType, ModelFramework
 from .endpoint import Endpoint
 from .meta import Meta
 from .parameter_store import ParameterStore
@@ -25,6 +25,7 @@ __all__ = [
     "FeatureSet",
     "Model",
     "ModelType",
+    "ModelFramework",
     "Endpoint",
     "Meta",
     "ParameterStore",

workbench/api/compound.py

@@ -3,7 +3,7 @@ import logging
 from typing import List
 
 # Workbench Imports
-from workbench.utils.chem_utils import svg_from_smiles
+from workbench.utils.chem_utils.vis import svg_from_smiles
 
 
 @dataclass

workbench/api/endpoint.py

@@ -70,6 +70,17 @@ class Endpoint(EndpointCore):
         """
         return super().fast_inference(eval_df, threads=threads)
 
+    def cross_fold_inference(self, nfolds: int = 5) -> pd.DataFrame:
+        """Run cross-fold inference (only works for XGBoost models)
+
+        Args:
+            nfolds (int): The number of folds to use for cross-validation (default: 5)
+
+        Returns:
+            pd.DataFrame: A DataFrame with cross fold predictions
+        """
+        return super().cross_fold_inference(nfolds)
+
 
 if __name__ == "__main__":
     """Exercise the Endpoint Class"""

workbench/api/feature_set.py

@@ -12,7 +12,7 @@ import pandas as pd
 from workbench.core.artifacts.artifact import Artifact
 from workbench.core.artifacts.feature_set_core import FeatureSetCore
 from workbench.core.transforms.features_to_model.features_to_model import FeaturesToModel
-from workbench.api.model import Model, ModelType
+from workbench.api.model import Model, ModelType, ModelFramework
 
 
 class FeatureSet(FeatureSetCore):
@@ -79,6 +79,7 @@ class FeatureSet(FeatureSetCore):
         self,
         name: str,
         model_type: ModelType,
+        model_framework: ModelFramework = ModelFramework.XGBOOST,
         tags: list = None,
         description: str = None,
         feature_list: list = None,
@@ -87,8 +88,8 @@ class FeatureSet(FeatureSetCore):
         model_import_str: str = None,
         custom_script: Union[str, Path] = None,
         custom_args: dict = None,
-        training_image: str = "xgb_training",
-        inference_image: str = "xgb_inference",
+        training_image: str = "training",
+        inference_image: str = "inference",
         inference_arch: str = "x86_64",
         **kwargs,
     ) -> Union[Model, None]:
@@ -98,15 +99,16 @@ class FeatureSet(FeatureSetCore):
 
             name (str): The name of the Model to create
             model_type (ModelType): The type of model to create (See workbench.model.ModelType)
+            model_framework (ModelFramework, optional): The framework to use for the model (default: XGBOOST)
             tags (list, optional): Set the tags for the model.  If not given tags will be generated.
             description (str, optional): Set the description for the model. If not give a description is generated.
             feature_list (list, optional): Set the feature list for the model. If not given a feature list is generated.
             target_column (str, optional): The target column for the model (use None for unsupervised model)
-            model_class (str, optional): Model class to use (e.g. "KMeans", "PyTorch", default: None)
+            model_class (str, optional): Model class to use (e.g. "KMeans", default: None)
             model_import_str (str, optional): The import for the model (e.g. "from sklearn.cluster import KMeans")
             custom_script (str, optional): The custom script to use for the model (default: None)
-            training_image (str, optional): The training image to use (default: "xgb_training")
-            inference_image (str, optional): The inference image to use (default: "xgb_inference")
+            training_image (str, optional): The training image to use (default: "training")
+            inference_image (str, optional): The inference image to use (default: "inference")
             inference_arch (str, optional): The architecture to use for inference (default: "x86_64")
             kwargs (dict, optional): Additional keyword arguments to pass to the model
 
@@ -128,8 +130,8 @@ class FeatureSet(FeatureSetCore):
         # Create the Model Tags
         tags = [name] if tags is None else tags
 
-        # If the model_class is PyTorch, ensure we set the training and inference images
-        if model_class and model_class.lower() == "pytorch":
+        # If the model framework is PyTorch or ChemProp, ensure we set the training and inference images
+        if model_framework in (ModelFramework.PYTORCH_TABULAR, ModelFramework.CHEMPROP):
             training_image = "pytorch_training"
             inference_image = "pytorch_inference"
 
@@ -138,6 +140,7 @@ class FeatureSet(FeatureSetCore):
             feature_name=self.name,
             model_name=name,
             model_type=model_type,
+            model_framework=model_framework,
             model_class=model_class,
             model_import_str=model_import_str,
             custom_script=custom_script,

workbench/api/meta.py

@@ -113,13 +113,16 @@ class Meta(CloudMeta):
         """
         return super().models(details=details)
 
-    def endpoints(self) -> pd.DataFrame:
+    def endpoints(self, details: bool = False) -> pd.DataFrame:
         """Get a summary of the Endpoints deployed in the Cloud Platform
 
+        Args:
+            details (bool, optional): Include detailed information. Defaults to False.
+
         Returns:
             pd.DataFrame: A summary of the Endpoints in the Cloud Platform
         """
-        return super().endpoints()
+        return super().endpoints(details=details)
 
     def pipelines(self) -> pd.DataFrame:
         """Get a summary of the ML Pipelines deployed in the Cloud Platform

workbench/api/model.py

@@ -7,10 +7,10 @@ Dashboard UI, which provides additional model details and performance metrics
 
 # Workbench Imports
 from workbench.core.artifacts.artifact import Artifact
-from workbench.core.artifacts.model_core import ModelCore, ModelType  # noqa: F401
+from workbench.core.artifacts.model_core import ModelCore, ModelType, ModelFramework  # noqa: F401
 from workbench.core.transforms.model_to_endpoint.model_to_endpoint import ModelToEndpoint
 from workbench.api.endpoint import Endpoint
-from workbench.utils.model_utils import proximity_model, uq_model
+from workbench.utils.model_utils import proximity_model_local, uq_model
 
 
 class Model(ModelCore):
@@ -40,6 +40,7 @@ class Model(ModelCore):
         mem_size: int = 2048,
         max_concurrency: int = 5,
         instance: str = "ml.t2.medium",
+        data_capture: bool = False,
     ) -> Endpoint:
         """Create an Endpoint from the Model.
 
@@ -50,6 +51,7 @@ class Model(ModelCore):
             mem_size (int): The memory size for the Endpoint in MB (default: 2048)
             max_concurrency (int): The maximum concurrency for the Endpoint (default: 5)
             instance (str): The instance type to use for Realtime(serverless=False) Endpoints (default: "ml.t2.medium")
+            data_capture (bool): Enable data capture for the Endpoint (default: False)
 
         Returns:
             Endpoint: The Endpoint created from the Model
@@ -73,6 +75,7 @@ class Model(ModelCore):
         model_to_endpoint.transform(
             mem_size=mem_size,
             max_concurrency=max_concurrency,
+            data_capture=data_capture,
         )
 
         # Set the Endpoint Owner and Return the Endpoint
@@ -80,19 +83,13 @@ class Model(ModelCore):
         end.set_owner(self.get_owner())
         return end
 
-    def prox_model(self, prox_model_name: str = None, track_columns: list = None) -> "Model":
-        """Create a Proximity Model for this Model
-
-        Args:
-            prox_model_name (str, optional): Name of the Proximity Model (if not specified, a name will be generated)
-            track_columns (list, optional): List of columns to track in the Proximity Model.
+    def prox_model(self):
+        """Create a local Proximity Model for this Model
 
         Returns:
-            Model: The Proximity Model
+           Proximity: A local Proximity Model
         """
-        if prox_model_name is None:
-            prox_model_name = self.model_name + "-prox"
-        return proximity_model(self, prox_model_name, track_columns=track_columns)
+        return proximity_model_local(self)
 
     def uq_model(self, uq_model_name: str = None, train_all_data: bool = False) -> "Model":
         """Create a Uncertainty Quantification Model for this Model
@@ -118,6 +115,10 @@ if __name__ == "__main__":
     pprint(my_model.summary())
     pprint(my_model.details())
 
-    # Create an Endpoint from the Model
-    my_endpoint = my_model.to_endpoint()
-    pprint(my_endpoint.summary())
+    # Create an Endpoint from the Model (commented out for now)
+    # my_endpoint = my_model.to_endpoint()
+    # pprint(my_endpoint.summary())
+
+    # Create a local Proximity Model for this Model
+    prox_model = my_model.prox_model()
+    print(prox_model.neighbors(3398))

workbench/api/monitor.py

@@ -15,7 +15,7 @@ class Monitor(MonitorCore):
 
     Common Usage:
        ```
-       mon = Endpoint(name).get_monitor()  # Pull from endpoint OR
+       mon = Endpoint(name).monitor()  # Pull from endpoint OR
        mon = Monitor(name)                 # Create using Endpoint Name
        mon.summary()
        mon.details()
@@ -29,7 +29,6 @@ class Monitor(MonitorCore):
        baseline_df = mon.get_baseline()
        constraints_df = mon.get_constraints()
        stats_df = mon.get_statistics()
-       input_df, output_df = mon.get_captured_data()
        ```
     """
 
@@ -81,15 +80,6 @@ class Monitor(MonitorCore):
         """
         super().create_monitoring_schedule(schedule)
 
-    def get_captured_data(self) -> (pd.DataFrame, pd.DataFrame):
-        """
-        Get the latest data capture input and output from S3.
-
-        Returns:
-            DataFrame (input), DataFrame(output): Flattened and processed DataFrames for input and output data.
-        """
-        return super().get_captured_data()
-
     def get_baseline(self) -> Union[pd.DataFrame, None]:
         """Code to get the baseline CSV from the S3 baseline directory
 
@@ -155,8 +145,3 @@ if __name__ == "__main__":
 
     print("\nStatistics...")
     print(mm.get_statistics())
-
-    # Get the latest data capture
-    input_df, output_df = mm.get_captured_data()
-    print(input_df.head())
-    print(output_df.head())

workbench/core/artifacts/__init__.py

@@ -15,7 +15,16 @@ from .artifact import Artifact
 from .athena_source import AthenaSource
 from .data_source_abstract import DataSourceAbstract
 from .feature_set_core import FeatureSetCore
-from .model_core import ModelCore, ModelType
+from .model_core import ModelCore, ModelType, ModelFramework
 from .endpoint_core import EndpointCore
 
-__all__ = ["Artifact", "AthenaSource", "DataSourceAbstract", "FeatureSetCore", "ModelCore", "ModelType", "EndpointCore"]
+__all__ = [
+    "Artifact",
+    "AthenaSource",
+    "DataSourceAbstract",
+    "FeatureSetCore",
+    "ModelCore",
+    "ModelType",
+    "ModelFramework",
+    "EndpointCore",
+]

workbench/core/artifacts/artifact.py

@@ -236,6 +236,12 @@ class Artifact(ABC):
             This functionality will work for FeatureSets, Models, and Endpoints
             but not for DataSources. The DataSource class overrides this method.
         """
+
+        # Check for ReadOnly Role
+        if self.aws_account_clamp.read_only:
+            self.log.info("Cannot add metadata with a ReadOnly Permissions...")
+            return
+
         # Sanity check
         aws_arn = self.arn()
         if aws_arn is None:
@@ -444,10 +450,12 @@ class Artifact(ABC):
 
 if __name__ == "__main__":
     """Exercise the Artifact Class"""
-    from workbench.api.data_source import DataSource
-    from workbench.api.feature_set import FeatureSet
+    from workbench.api import DataSource, FeatureSet, Endpoint
+
+    # Grab an Endpoint (which is a subclass of Artifact)
+    end = Endpoint("wine-classification")
 
-    # Create a DataSource (which is a subclass of Artifact)
+    # Grab a DataSource (which is a subclass of Artifact)
     data_source = DataSource("test_data")
 
     # Just some random tests