workbench 0.8.189__tar.gz → 0.8.210__tar.gz

{workbench-0.8.189 → workbench-0.8.210}/.github/workflows/python-lint.yml

@@ -12,9 +12,9 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.x'
+        python-version: '3.13'
 
     - name: Install dependencies
       run: |
@@ -27,4 +27,3 @@ jobs:
     - name: Run Flake8 (Linting)
       run: |
         flake8 --exclude '*generated*' src/workbench applications tests
-

{workbench-0.8.189 → workbench-0.8.210}/.gitignore

@@ -149,5 +149,5 @@ workbench_lambda_layer_output/
 # Some test datasets
 test_evaluation_data.csv
 
-# This is a copied file
-src/workbench/model_scripts/custom_models/chem_info/chem_utils.py
+# PyTorch checkpoint/tmp directories
+.pt_tmp/ 

{workbench-0.8.189 → workbench-0.8.210}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021-2024 SuperCowPowers LLC
+Copyright (c) 2021-2026 SuperCowPowers LLC
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{workbench-0.8.189 → workbench-0.8.210}/PKG-INFO

@@ -1,9 +1,30 @@
 Metadata-Version: 2.4
 Name: workbench
-Version: 0.8.189
+Version: 0.8.210
 Summary: Workbench: A Dashboard and Python API for creating and deploying AWS SageMaker Model Pipelines
 Author-email: SuperCowPowers LLC <support@supercowpowers.com>
-License-Expression: MIT
+License: MIT License
+        
+        Copyright (c) 2021-2026 SuperCowPowers LLC
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
 Project-URL: Homepage, https://github.com/SuperCowPowers/workbench
 Keywords: SageMaker,Machine Learning,AWS,Python,Utilities
 Classifier: Development Status :: 4 - Beta
@@ -21,7 +42,7 @@ Requires-Dist: redis>=5.0.1
 Requires-Dist: numpy>=1.26.4
 Requires-Dist: pandas>=2.2.1
 Requires-Dist: awswrangler>=3.4.0
-Requires-Dist: sagemaker>=2.143
+Requires-Dist: sagemaker<3.0,>=2.143
 Requires-Dist: cryptography>=44.0.2
 Requires-Dist: ipython>=8.37.0
 Requires-Dist: pyreadline3; sys_platform == "win32"
@@ -31,7 +52,7 @@ Requires-Dist: joblib>=1.3.2
 Requires-Dist: requests>=2.26.0
 Requires-Dist: rdkit>=2024.9.5
 Requires-Dist: mordredcommunity>=2.0.6
-Requires-Dist: workbench-bridges>=0.1.10
+Requires-Dist: workbench-bridges>=0.1.16
 Provides-Extra: ui
 Requires-Dist: plotly>=6.0.0; extra == "ui"
 Requires-Dist: dash>3.0.0; extra == "ui"

{workbench-0.8.189 → workbench-0.8.210}/applications/aws_dashboard/Dockerfile

@@ -7,7 +7,7 @@ EXPOSE 8000
 ENV PYTHONHASHSEED=0
 
 # Define workbench version
-ARG WORKBENCH_VERSION=0.8.165
+ARG WORKBENCH_VERSION=0.8.208
 
 # Install system packages and gunicorn in one layer
 RUN apt-get update && apt-get install -y --no-install-recommends \

{workbench-0.8.189 → workbench-0.8.210}/applications/compound_explorer/requirements.txt

@@ -4,7 +4,7 @@ redis >= 5.0.1
 numpy >= 1.26.4
 pandas >= 2.2.1
 awswrangler >= 3.4.0
-sagemaker >= 2.143
+sagemaker >= 2.143, < 3.0
 cryptography>=44.0.2
 ipython>=8.17.2
 xgboost>=3.0.3

{workbench-0.8.189 → workbench-0.8.210}/aws_setup/aws_identity_check.py

@@ -1,6 +1,5 @@
 """Just a Utility Script that allows people to check which AWS Identity is active"""
 
-import os
 import sys
 import logging
 

{workbench-0.8.189 → workbench-0.8.210}/aws_setup/workbench_compute/workbench_compute/workbench_compute_stack.py

@@ -120,7 +120,7 @@ class WorkbenchComputeStack(Stack):
                 "MLPipelineRepo",
                 repository_arn=f"arn:aws:ecr:{self.region}:507740646243:repository/aws-ml-images/py312-ml-pipelines",
             ),
-            tag="0.1",
+            tag="0.2",
         )
 
         # Job Definition Tiers

{workbench-0.8.189 → workbench-0.8.210}/aws_setup/workbench_dashboard_full/app.py

@@ -12,7 +12,7 @@ print(f"Account: {aws_account}")
 print(f"Region: {aws_region}")
 
 # When you want a different docker image change this line
-dashboard_image = "public.ecr.aws/m6i5k1r2/workbench_dashboard:v0_8_165_amd64"
+dashboard_image = "public.ecr.aws/m6i5k1r2/workbench_dashboard:v0_8_208_amd64"
 
 # Workbench Configuration
 try:

{workbench-0.8.189 → workbench-0.8.210}/aws_setup/workbench_dashboard_full/workbench_dashboard_full/workbench_dashboard_stack.py

@@ -8,7 +8,6 @@ from aws_cdk import (
     aws_elasticache as elasticache,
     aws_logs as logs,
 )
-from aws_cdk.aws_ec2 import Subnet
 from aws_cdk.aws_certificatemanager import Certificate
 from aws_cdk.aws_ecs_patterns import ApplicationLoadBalancedFargateService
 from constructs import Construct

{workbench-0.8.189 → workbench-0.8.210}/aws_setup/workbench_dashboard_lite/app.py

@@ -1,4 +1,3 @@
-import os
 import boto3
 import aws_cdk as cdk
 from pprint import pprint
@@ -13,7 +12,7 @@ print(f"Account: {aws_account}")
 print(f"Region: {aws_region}")
 
 # When you want a different docker image change this line
-dashboard_image = "public.ecr.aws/m6i5k1r2/workbench_dashboard:v0_8_165_amd64"
+dashboard_image = "public.ecr.aws/m6i5k1r2/workbench_dashboard:v0_8_208_amd64"
 
 # Workbench Configuration
 try:

{workbench-0.8.189 → workbench-0.8.210}/docs/api_classes/meta.md

@@ -86,7 +86,7 @@ wine-classification
 	Description: Wine Classification Model
 	Tags: wine::classification
 	Performance Metrics:
-		[{'wine_class': 'TypeA', 'precision': 1.0, 'recall': 1.0, 'fscore': 1.0, 'roc_auc': 1.0, 'support': 12}, {'wine_class': 'TypeB', 'precision': 1.0, 'recall': 1.0, 'fscore': 1.0, 'roc_auc': 1.0, 'support': 14}, {'wine_class': 'TypeC', 'precision': 1.0, 'recall': 1.0, 'fscore': 1.0, 'roc_auc': 1.0, 'support': 9}]
+		[{'wine_class': 'TypeA', 'precision': 1.0, 'recall': 1.0, 'f1': 1.0, 'roc_auc': 1.0, 'support': 12}, {'wine_class': 'TypeB', 'precision': 1.0, 'recall': 1.0, 'f1': 1.0, 'roc_auc': 1.0, 'support': 14}, {'wine_class': 'TypeC', 'precision': 1.0, 'recall': 1.0, 'f1': 1.0, 'roc_auc': 1.0, 'support': 9}]
 
 abalone-regression
 	ARN: arn:aws:sagemaker:us-west-2:507740646243:model-package-group/abalone-regression

{workbench-0.8.189 → workbench-0.8.210}/docs/cached/cached_meta.md

@@ -86,7 +86,7 @@ wine-classification
 	Description: Wine Classification Model
 	Tags: wine::classification
 	Performance Metrics:
-		[{'wine_class': 'TypeA', 'precision': 1.0, 'recall': 1.0, 'fscore': 1.0, 'roc_auc': 1.0, 'support': 12}, {'wine_class': 'TypeB', 'precision': 1.0, 'recall': 1.0, 'fscore': 1.0, 'roc_auc': 1.0, 'support': 14}, {'wine_class': 'TypeC', 'precision': 1.0, 'recall': 1.0, 'fscore': 1.0, 'roc_auc': 1.0, 'support': 9}]
+		[{'wine_class': 'TypeA', 'precision': 1.0, 'recall': 1.0, 'f1': 1.0, 'roc_auc': 1.0, 'support': 12}, {'wine_class': 'TypeB', 'precision': 1.0, 'recall': 1.0, 'f1': 1.0, 'roc_auc': 1.0, 'support': 14}, {'wine_class': 'TypeC', 'precision': 1.0, 'recall': 1.0, 'f1': 1.0, 'roc_auc': 1.0, 'support': 9}]
 
 abalone-regression
 	ARN: arn:aws:sagemaker:us-west-2:507740646243:model-package-group/abalone-regression

{workbench-0.8.189 → workbench-0.8.210}/examples/glue_jobs/glue_example_1.py

@@ -13,7 +13,7 @@ cm = ConfigManager()
 cm.set_config("WORKBENCH_BUCKET", glue_args["workbench-bucket"])
 
 # Important Note: This import needs to happen after the WORKBENCH_BUCKET is set
-from workbench.api import DataSource
+from workbench.api import DataSource  # noqa: E402
 
 # Grab a test DataSource
 ds = DataSource("abalone_data")

{workbench-0.8.189 → workbench-0.8.210}/examples/glue_jobs/glue_example_2.py

@@ -13,7 +13,7 @@ cm = ConfigManager()
 cm.set_config("WORKBENCH_BUCKET", glue_args["workbench-bucket"])
 
 # Important Note: This import needs to happen after the WORKBENCH_BUCKET is set
-from workbench.api import Meta
+from workbench.api import Meta  # noqa: E402
 
 # List all the models in AWS
 meta = Meta()

{workbench-0.8.189 → workbench-0.8.210}/examples/glue_jobs/glue_example_3.py

@@ -13,7 +13,7 @@ cm = ConfigManager()
 cm.set_config("WORKBENCH_BUCKET", glue_args["workbench-bucket"])
 
 # Important Note: This import needs to happen after the WORKBENCH_BUCKET is set
-from workbench.api import Endpoint
+from workbench.api import Endpoint  # noqa: E402
 
 # Run Inference on a particular model (using its endpoint)
 end = Endpoint("abalone-regression")

{workbench-0.8.189 → workbench-0.8.210}/examples/ml_pipelines/list_models.py

@@ -1,4 +1,3 @@
-import time
 import logging
 from workbench.api import Meta
 

{workbench-0.8.189 → workbench-0.8.210}/examples/ml_pipelines/wine_classifier.py

@@ -10,7 +10,7 @@ Endpoints:
     - wine-classification-end
 """
 
-from workbench.api import DataSource, FeatureSet, Model, ModelType, Endpoint
+from workbench.api import DataSource, FeatureSet, Model, ModelType
 
 
 if __name__ == "__main__":

workbench-0.8.210/examples/models/chemprop.py

@@ -0,0 +1,69 @@
+from workbench.api import FeatureSet, Model, ModelType, ModelFramework, Endpoint
+
+# Recreate Flag in case you want to recreate the artifacts
+recreate = True
+
+# =============================================================================
+# Single-Target Chemprop Regression Model
+# =============================================================================
+if recreate or not Model("open-admet-chemprop-logd").exists():
+    feature_set = FeatureSet("open_admet_all")
+    m = feature_set.to_model(
+        name="open-admet-chemprop-logd",
+        model_type=ModelType.REGRESSOR,
+        model_framework=ModelFramework.CHEMPROP,
+        target_column="logd",  # Single target (string)
+        feature_list=["smiles"],
+        description="Single-target Chemprop Regression Model for LogD",
+        tags=["chemprop", "open_admet"],
+        hyperparameters={"max_epochs": 400, "hidden_dim": 300, "depth": 3, "n_folds": 5},
+    )
+    m.set_owner("BW")
+
+# Create an Endpoint for the Regression Model
+if recreate or not Endpoint("open-admet-chemprop-logd").exists():
+    m = Model("open-admet-chemprop-logd")
+    end = m.to_endpoint(tags=["chemprop", "open_admet"])
+    end.set_owner("BW")
+    end.auto_inference(capture=True)
+    end.cross_fold_inference()
+
+# =============================================================================
+# Multi-Target Chemprop Regression Model (Open ADMET)
+# =============================================================================
+# This example shows how to train a multi-task model predicting all 9 ADMET endpoints
+# from the Open ADMET challenge: logd, ksol, hlm_clint, mlm_clint, caco_2_papp_a_b,
+# caco_2_efflux, mppb, mbpb, mgmb
+
+ADMET_TARGETS = [
+    "logd",
+    "ksol",
+    "hlm_clint",
+    "mlm_clint",
+    "caco_2_papp_a_b",
+    "caco_2_efflux",
+    "mppb",
+    "mbpb",
+    "mgmb",
+]
+
+if recreate or not Model("open-admet-chemprop-mt").exists():
+    feature_set = FeatureSet("open_admet_all")
+    m = feature_set.to_model(
+        name="open-admet-chemprop-mt",
+        model_type=ModelType.REGRESSOR,
+        model_framework=ModelFramework.CHEMPROP,
+        target_column=ADMET_TARGETS,  # Multi-task: list of 9 targets
+        feature_list=["smiles"],
+        description="Multi-task ChemProp model for 9 ADMET endpoints",
+        tags=["chemprop", "open_admet", "multitask"],
+    )
+    m.set_owner("BW")
+
+# Create an Endpoint for the Multi-Task Regression Model
+if recreate or not Endpoint("open-admet-chemprop-mt").exists():
+    m = Model("open-admet-chemprop-mt")
+    end = m.to_endpoint(tags=["chemprop", "open_admet", "multitask"])
+    end.set_owner("BW")
+    end.auto_inference(capture=True)
+    end.cross_fold_inference()

{workbench-0.8.189 → workbench-0.8.210}/examples/models/pytorch.py

@@ -1,4 +1,4 @@
-from workbench.api import FeatureSet, Model, ModelType, Endpoint
+from workbench.api import FeatureSet, Model, ModelType, ModelFramework, Endpoint
 
 # Grab a FeatureSet
 my_features = FeatureSet("aqsol_features")
@@ -7,20 +7,20 @@ feature_list = model.features()
 target = model.target()
 
 # Recreate Flag in case you want to recreate the artifacts
-recreate = True
+recreate = False
 
 # PyTorch Regression Model
 if recreate or not Model("aqsol-pytorch-reg").exists():
     feature_set = FeatureSet("aqsol_features")
     m = feature_set.to_model(
         name="aqsol-pytorch-reg",
-        model_type=ModelType.REGRESSOR,
-        model_class="PyTorch",
+        model_type=ModelType.UQ_REGRESSOR,
+        model_framework=ModelFramework.PYTORCH_TABULAR,
         feature_list=feature_list,
         target_column=target,
         description="PyTorch Regression Model for AQSol",
         tags=["pytorch", "molecular descriptors"],
-        hyperparameters={"training_config": {"max_epochs": 150}, "model_config": {"layers": "128-64-32"}},
+        hyperparameters={"max_epochs": 150, "layers": "128-64-32"},
     )
     m.set_owner("BW")
 
@@ -39,12 +39,12 @@ if recreate or not Model("aqsol-pytorch-class").exists():
     m = feature_set.to_model(
         name="aqsol-pytorch-class",
         model_type=ModelType.CLASSIFIER,
-        model_class="PyTorch",
+        model_framework=ModelFramework.PYTORCH_TABULAR,
         feature_list=feature_list,
         target_column="solubility_class",
         description="PyTorch Classification Model for AQSol",
         tags=["pytorch", "molecular descriptors"],
-        hyperparameters={"training_config": {"max_epochs": 150}, "model_config": {"layers": "256-128-64"}},
+        hyperparameters={"max_epochs": 150, "layers": "256-128-64"},
     )
     m.set_owner("BW")
     m.set_class_labels(["low", "medium", "high"])

{workbench-0.8.189 → workbench-0.8.210}/examples/models/smiles_to_md_v1.py

@@ -1,7 +1,7 @@
 """Create the SMILES to Standardize + Tautomer + Molecular Descriptors + Stereo Model and Endpoint"""
 
 # Workbench Imports
-from workbench.api import FeatureSet, ModelType, Model
+from workbench.api import FeatureSet, ModelType
 from workbench.utils.model_utils import get_custom_script_path
 
 # fs_name = "aqsol_features"

{workbench-0.8.189 → workbench-0.8.210}/examples/models/uq/bayesian_ridge.py

@@ -19,7 +19,7 @@ my_model = fs.to_model(
     model_type=ModelType.REGRESSOR,
     feature_list=features,
     target_column=target,
-    description=f"Bayesian Ridge Model for AQSol",
+    description="Bayesian Ridge Model for AQSol",
     tags=["aqsol", "bayesian", "regression"],
     custom_script=script_path,
 )

{workbench-0.8.189 → workbench-0.8.210}/examples/models/uq/gaussian_process.py

@@ -23,7 +23,7 @@ my_model = fs.to_model(
     model_type=ModelType.REGRESSOR,
     feature_list=features,
     target_column=target,
-    description=f"GaussianProcessRegressor Model for AQSol",
+    description="GaussianProcessRegressor Model for AQSol",
     tags=["aqsol", "gaussian", "regression"],
     custom_script=script_path,
 )

{workbench-0.8.189 → workbench-0.8.210}/examples/models/uq/meta_uq.py

@@ -23,7 +23,7 @@ my_model = fs.to_model(
     model_type=ModelType.UQ_REGRESSOR,
     feature_list=features,
     target_column=target,
-    description=f"Meta UQ Model for AQSol",
+    description="Meta UQ Model for AQSol",
     tags=["aqsol", "meta-uq", "regression"],
     custom_script=script_path,
     custom_args={"id_column": "id", "track_columns": "solubility"},

{workbench-0.8.189 → workbench-0.8.210}/examples/models/uq/ngboost.py

@@ -23,7 +23,7 @@ my_model = fs.to_model(
     model_type=ModelType.UQ_REGRESSOR,
     feature_list=features,
     target_column=target,
-    description=f"NGBoost Model for AQSol",
+    description="NGBoost Model for AQSol",
     tags=["aqsol", "ngboost", "regression"],
     custom_script=script_path,
 )

{workbench-0.8.189 → workbench-0.8.210}/examples/models/uq/quant_xgb.py

@@ -1,5 +1,5 @@
 from workbench.api.feature_set import FeatureSet
-from workbench.api.model import Model, ModelType, Endpoint
+from workbench.api.model import Model, ModelType
 
 # Grab our existing AQSol Regression Model
 model = Model("aqsol-regression")

workbench-0.8.210/examples/models/xgb_model.py

@@ -0,0 +1,76 @@
+from workbench.api import FeatureSet, Model, ModelType, Endpoint
+
+# Grab a FeatureSet
+my_features = FeatureSet("aqsol_features")
+model = Model("aqsol-regression")
+feature_list = [
+    "molwt",
+    "mollogp",
+    "molmr",
+    "heavyatomcount",
+    "numhacceptors",
+    "numhdonors",
+    "numheteroatoms",
+    "numrotatablebonds",
+    "numvalenceelectrons",
+    "numaromaticrings",
+    "numsaturatedrings",
+    "numaliphaticrings",
+    "ringcount",
+    "tpsa",
+    "labuteasa",
+    "balabanj",
+    "bertzct",
+]
+target = "solubility"
+
+# Recreate Flag in case you want to recreate the artifacts
+recreate = True
+
+# XGBoost Regression Model
+if recreate or not Model("aqsol-regression").exists():
+    feature_set = FeatureSet("aqsol_features")
+    m = feature_set.to_model(
+        name="aqsol-regression",
+        model_type=ModelType.UQ_REGRESSOR,
+        feature_list=feature_list,
+        target_column=target,
+        description="XGBoost Regression Model for AQSol",
+        tags=["xgboost", "molecular descriptors"],
+        hyperparameters={"n_estimators": 200, "max_depth": 6},
+    )
+    m.set_owner("BW")
+
+# Create an Endpoint for the Regression Model
+if recreate or not Endpoint("aqsol-regression").exists():
+    m = Model("aqsol-regression")
+    end = m.to_endpoint(tags=["xgboost", "molecular descriptors"])
+    end.set_owner("BW")
+
+    # Run inference on the endpoint
+    end.auto_inference(capture=True)
+    end.cross_fold_inference()
+
+# XGBoost Classification Model
+if recreate or not Model("aqsol-class").exists():
+    feature_set = FeatureSet("aqsol_features")
+    m = feature_set.to_model(
+        name="aqsol-class",
+        model_type=ModelType.CLASSIFIER,
+        feature_list=feature_list,
+        target_column="solubility_class",
+        description="XGBoost Classification Model for AQSol",
+        tags=["xgboost", "molecular descriptors"],
+    )
+    m.set_owner("BW")
+    m.set_class_labels(["low", "medium", "high"])
+
+# Create an Endpoint for the Classification Model
+if recreate or not Endpoint("aqsol-class").exists():
+    m = Model("aqsol-class")
+    end = m.to_endpoint(tags=["xgboost", "molecular descriptors"])
+    end.set_owner("BW")
+
+    # Run inference on the endpoint
+    end.auto_inference(capture=True)
+    end.cross_fold_inference()

{workbench-0.8.189/scripts/admin → workbench-0.8.210/experiments}/db_scan_test.py

@@ -1,6 +1,6 @@
 import pandas as pd
 from sklearn.preprocessing import StandardScaler
-from sklearn.cluster import DBSCAN, HDBSCAN
+from sklearn.cluster import HDBSCAN
 from sklearn.cluster import MeanShift
 
 # Workbench Imports
@@ -16,7 +16,7 @@ def run_dbscan(df: pd.DataFrame, feature_list: list, eps: float = 0.5, min_sampl
         df (pd.DataFrame): The input DataFrame.
         feature_list (list): The list of features to use for clustering.
         eps (float): The maximum distance between two samples for them to be considered as in the same neighborhood.
-        min_samples (int): The number of samples (or total weight) in a neighborhood for a point to be considered a core point.
+        min_samples (int): The samples (or total weight) in a neighborhood for a point to be considered a core point.
 
     Returns:
         pd.Series: Cluster labels assigned by DBSCAN.

{workbench-0.8.189 → workbench-0.8.210}/experiments/rocauc_testing.py

@@ -57,5 +57,5 @@ for i, label in enumerate(class_labels):
     print(f"  Precision: {precision[i]:.2f}")
     print(f"  Recall: {recall[i]:.2f}")
     print(f"  F1-Score: {fscore[i]:.2f}")
-    print(f"  ROC AUC (per class): { roc_auc_per_class[i]}")
+    print(f"  ROC AUC (per class): {roc_auc_per_class[i]}")
     print(f"  Averaged ROC AUC (OVR): {roc_auc_all_in_one}")

{workbench-0.8.189 → workbench-0.8.210}/glue_jobs/example_glue_job.py

@@ -12,7 +12,8 @@ glue_args = get_resolved_options(sys.argv)
 cm = ConfigManager()
 cm.set_config("WORKBENCH_BUCKET", glue_args["workbench-bucket"])
 
-from workbench.api import DataSource
+# Important Note: This import needs to happen after the WORKBENCH_BUCKET is set
+from workbench.api import DataSource  # noqa: E402
 
 # Grab a test DataSource
 ds = DataSource("abalone_data")

workbench-0.8.189/test_artifacts/hyper_uq_testing.py → workbench-0.8.210/ml_pipelines/hyper_uq.py

@@ -1,7 +1,6 @@
 from pprint import pprint
 from workbench.api.feature_set import FeatureSet
 from workbench.api.model import Model, ModelType
-from workbench.utils.model_utils import get_custom_script_path
 
 hyperparameters = {
     "n_estimators": 200,  # Number of trees
@@ -23,14 +22,11 @@ my_features = FeatureSet("aqsol_features")
 # Grab our AQSol Regression Model
 model = Model("aqsol-regression")
 
-# Get the custom script path for the proximity model
-script_path = get_custom_script_path("uq_models", "mapie.template")
-
 # Get Feature and Target Columns from the existing given Model
 features = model.features()
 target = model.target()
 
-# Create the Mapie Model from our FeatureSet
+# Create the UQ Model from our FeatureSet
 fs = FeatureSet(model.get_input())
 my_model = fs.to_model(
     name="aqsol-uq-hyper",
@@ -39,7 +35,6 @@ my_model = fs.to_model(
     target_column=target,
     description="Mapie + XGB Model",
     tags=["aqsol", "mapie", "regression"],
-    custom_script=script_path,
     hyperparameters=hyperparameters,
 )
 # Print the details of the created model

workbench-0.8.210/model_docker_images/inference/requirements.txt

@@ -0,0 +1,9 @@
+fastapi==0.121.0       # FastAPI for serving the model
+uvicorn==0.34.0        # ASGI server for running FastAPI
+scikit-learn==1.7.2
+xgboost==3.1.1
+lightgbm==4.6.0
+ngboost==0.5.6
+pandas==2.3.3
+awswrangler==3.14.0
+joblib==1.5.2

{workbench-0.8.189 → workbench-0.8.210}/model_docker_images/ml_pipelines/Dockerfile

@@ -29,7 +29,7 @@ COPY --from=builder /usr/local/lib/python3.12/site-packages /usr/local/lib/pytho
 COPY --from=builder /usr/local/bin /usr/local/bin
 
 # Install workbench only
-RUN pip install --no-cache-dir workbench==0.8.188
+RUN pip install --no-cache-dir workbench==0.8.208
 
 # Add the script runner
 COPY ml_pipeline_runner.py /app/ml_pipeline_runner.py

workbench-0.8.210/model_docker_images/ml_pipelines/requirements.txt

@@ -0,0 +1,16 @@
+# This file is used to install the required packages for the ML Pipeline Docker image.
+--index-url https://download.pytorch.org/whl/cpu
+--extra-index-url https://pypi.org/simple/
+pandas==2.3.3
+awswrangler==3.14.0
+torch==2.9.1
+pytorch-tabular==1.1.1
+requests==2.32.5
+joblib==1.5.2
+boto3==1.40.72
+botocore==1.40.72
+redis==7.0.1
+scikit-learn==1.7.2
+xgboost==3.1.1
+rdkit==2025.9.1
+mordredcommunity==2.0.6

workbench-0.8.210/model_docker_images/pytorch_inference/requirements.txt

@@ -0,0 +1,14 @@
+# This file is used to install the required packages for the PyTorch Inference Docker image.
+# Using PyTorch CUDA 13.0 index (smaller than default PyPI, works on CPU and GPU instances)
+--index-url https://download.pytorch.org/whl/cu130
+--extra-index-url https://pypi.org/simple/
+torch==2.9.1
+pandas==2.3.3
+awswrangler==3.14.0
+pytorch-tabular==1.1.1
+requests==2.32.5  # Needed by PyTorch-Tabular
+joblib==1.5.2
+fastapi==0.122.0  # FastAPI for serving the model
+uvicorn==0.38.0   # ASGI server for running FastAPI
+chemprop==2.2.1   # Message Passing Neural Networks for molecular property prediction
+rdkit==2025.9.1   # Cheminformatics toolkit for SMILES processing

workbench-0.8.210/model_docker_images/pytorch_training/Dockerfile

@@ -0,0 +1,25 @@
+# Lightweight CUDA base image with Python 3.12 support
+# Uses runtime image (not devel) to minimize size while supporting GPU inference/training
+FROM nvidia/cuda:13.0.0-runtime-ubuntu24.04
+
+# Install pip and build tools (Python 3.12 is included in Ubuntu 24.04)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    python3-pip \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy requirements file
+COPY requirements.txt /tmp/
+
+# Install dependencies
+RUN pip install --no-cache-dir --break-system-packages -r /tmp/requirements.txt
+
+# Copy the SageMaker entrypoint script
+COPY sagemaker_entrypoint.py /opt/program/
+WORKDIR /opt/program
+
+# Make the entrypoint executable
+RUN chmod +x /opt/program/sagemaker_entrypoint.py
+
+# Set the entrypoint
+ENTRYPOINT ["/opt/program/sagemaker_entrypoint.py"]

workbench-0.8.210/model_docker_images/pytorch_training/requirements.txt

@@ -0,0 +1,12 @@
+# This file is used to install the required packages for the PyTorch Training Docker image.
+# Using PyTorch CUDA 13.0 index (matches our Base Training image)
+--index-url https://download.pytorch.org/whl/cu130
+--extra-index-url https://pypi.org/simple/
+torch==2.9.1
+pandas==2.3.3
+awswrangler==3.14.0
+pytorch-tabular==1.1.1
+requests==2.32.5  # Needed by PyTorch-Tabular
+joblib==1.5.2
+chemprop==2.2.1   # Message Passing Neural Networks for molecular property prediction
+rdkit==2025.9.1   # Cheminformatics toolkit for SMILES processing