workbench 0.8.162__py3-none-any.whl → 0.8.202__py3-none-any.whl
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- workbench/algorithms/dataframe/__init__.py +1 -2
- workbench/algorithms/dataframe/fingerprint_proximity.py +2 -2
- workbench/algorithms/dataframe/proximity.py +261 -235
- workbench/algorithms/graph/light/proximity_graph.py +10 -8
- workbench/api/__init__.py +2 -1
- workbench/api/compound.py +1 -1
- workbench/api/endpoint.py +11 -0
- workbench/api/feature_set.py +11 -8
- workbench/api/meta.py +5 -2
- workbench/api/model.py +16 -15
- workbench/api/monitor.py +1 -16
- workbench/core/artifacts/__init__.py +11 -2
- workbench/core/artifacts/artifact.py +11 -3
- workbench/core/artifacts/data_capture_core.py +355 -0
- workbench/core/artifacts/endpoint_core.py +256 -118
- workbench/core/artifacts/feature_set_core.py +265 -16
- workbench/core/artifacts/model_core.py +107 -60
- workbench/core/artifacts/monitor_core.py +33 -248
- workbench/core/cloud_platform/aws/aws_account_clamp.py +50 -1
- workbench/core/cloud_platform/aws/aws_meta.py +12 -5
- workbench/core/cloud_platform/aws/aws_parameter_store.py +18 -2
- workbench/core/cloud_platform/aws/aws_session.py +4 -4
- workbench/core/transforms/data_to_features/light/molecular_descriptors.py +4 -4
- workbench/core/transforms/features_to_model/features_to_model.py +42 -32
- workbench/core/transforms/model_to_endpoint/model_to_endpoint.py +36 -6
- workbench/core/transforms/pandas_transforms/pandas_to_features.py +27 -0
- workbench/core/views/training_view.py +113 -42
- workbench/core/views/view.py +53 -3
- workbench/core/views/view_utils.py +4 -4
- workbench/model_scripts/chemprop/chemprop.template +852 -0
- workbench/model_scripts/chemprop/generated_model_script.py +852 -0
- workbench/model_scripts/chemprop/requirements.txt +11 -0
- workbench/model_scripts/custom_models/chem_info/fingerprints.py +134 -0
- workbench/model_scripts/custom_models/chem_info/mol_descriptors.py +483 -0
- workbench/model_scripts/custom_models/chem_info/mol_standardize.py +450 -0
- workbench/model_scripts/custom_models/chem_info/molecular_descriptors.py +7 -9
- workbench/model_scripts/custom_models/chem_info/morgan_fingerprints.py +1 -1
- workbench/model_scripts/custom_models/proximity/feature_space_proximity.template +3 -5
- workbench/model_scripts/custom_models/proximity/proximity.py +261 -235
- workbench/model_scripts/custom_models/uq_models/bayesian_ridge.template +7 -8
- workbench/model_scripts/custom_models/uq_models/ensemble_xgb.template +20 -21
- workbench/model_scripts/custom_models/uq_models/gaussian_process.template +5 -11
- workbench/model_scripts/custom_models/uq_models/meta_uq.template +166 -62
- workbench/model_scripts/custom_models/uq_models/ngboost.template +30 -18
- workbench/model_scripts/custom_models/uq_models/proximity.py +261 -235
- workbench/model_scripts/custom_models/uq_models/requirements.txt +1 -3
- workbench/model_scripts/ensemble_xgb/ensemble_xgb.template +15 -17
- workbench/model_scripts/pytorch_model/generated_model_script.py +373 -190
- workbench/model_scripts/pytorch_model/pytorch.template +370 -187
- workbench/model_scripts/scikit_learn/generated_model_script.py +7 -12
- workbench/model_scripts/scikit_learn/scikit_learn.template +4 -9
- workbench/model_scripts/script_generation.py +17 -9
- workbench/model_scripts/uq_models/generated_model_script.py +605 -0
- workbench/model_scripts/uq_models/mapie.template +605 -0
- workbench/model_scripts/uq_models/requirements.txt +1 -0
- workbench/model_scripts/xgb_model/generated_model_script.py +37 -46
- workbench/model_scripts/xgb_model/xgb_model.template +44 -46
- workbench/repl/workbench_shell.py +28 -14
- workbench/scripts/endpoint_test.py +162 -0
- workbench/scripts/lambda_test.py +73 -0
- workbench/scripts/ml_pipeline_batch.py +137 -0
- workbench/scripts/ml_pipeline_sqs.py +186 -0
- workbench/scripts/monitor_cloud_watch.py +20 -100
- workbench/utils/aws_utils.py +4 -3
- workbench/utils/chem_utils/__init__.py +0 -0
- workbench/utils/chem_utils/fingerprints.py +134 -0
- workbench/utils/chem_utils/misc.py +194 -0
- workbench/utils/chem_utils/mol_descriptors.py +483 -0
- workbench/utils/chem_utils/mol_standardize.py +450 -0
- workbench/utils/chem_utils/mol_tagging.py +348 -0
- workbench/utils/chem_utils/projections.py +209 -0
- workbench/utils/chem_utils/salts.py +256 -0
- workbench/utils/chem_utils/sdf.py +292 -0
- workbench/utils/chem_utils/toxicity.py +250 -0
- workbench/utils/chem_utils/vis.py +253 -0
- workbench/utils/chemprop_utils.py +760 -0
- workbench/utils/cloudwatch_handler.py +1 -1
- workbench/utils/cloudwatch_utils.py +137 -0
- workbench/utils/config_manager.py +3 -7
- workbench/utils/endpoint_utils.py +5 -7
- workbench/utils/license_manager.py +2 -6
- workbench/utils/model_utils.py +95 -34
- workbench/utils/monitor_utils.py +44 -62
- workbench/utils/pandas_utils.py +3 -3
- workbench/utils/pytorch_utils.py +526 -0
- workbench/utils/shap_utils.py +10 -2
- workbench/utils/workbench_logging.py +0 -3
- workbench/utils/workbench_sqs.py +1 -1
- workbench/utils/xgboost_model_utils.py +371 -156
- workbench/web_interface/components/model_plot.py +7 -1
- workbench/web_interface/components/plugin_unit_test.py +5 -2
- workbench/web_interface/components/plugins/dashboard_status.py +3 -1
- workbench/web_interface/components/plugins/generated_compounds.py +1 -1
- workbench/web_interface/components/plugins/model_details.py +9 -7
- workbench/web_interface/components/plugins/scatter_plot.py +3 -3
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/METADATA +27 -6
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/RECORD +101 -85
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/entry_points.txt +4 -0
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/licenses/LICENSE +1 -1
- workbench/model_scripts/custom_models/chem_info/local_utils.py +0 -769
- workbench/model_scripts/custom_models/chem_info/tautomerize.py +0 -83
- workbench/model_scripts/custom_models/proximity/generated_model_script.py +0 -138
- workbench/model_scripts/custom_models/uq_models/generated_model_script.py +0 -393
- workbench/model_scripts/custom_models/uq_models/mapie_xgb.template +0 -203
- workbench/model_scripts/ensemble_xgb/generated_model_script.py +0 -279
- workbench/model_scripts/quant_regression/quant_regression.template +0 -279
- workbench/model_scripts/quant_regression/requirements.txt +0 -1
- workbench/utils/chem_utils.py +0 -1556
- workbench/utils/execution_environment.py +0 -211
- workbench/utils/fast_inference.py +0 -167
- workbench/utils/resource_utils.py +0 -39
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/WHEEL +0 -0
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/top_level.txt +0 -0
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@@ -39,7 +39,13 @@ class ModelPlot(ComponentInterface):
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# Calculate the distance from the diagonal for each point
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target = model.target()
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df["error"] = abs(df["prediction"] - df[target])
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return ScatterPlot().update_properties(
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return ScatterPlot().update_properties(
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df,
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color="error",
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regression_line=True,
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x=target,
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y="prediction",
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)[0]
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else:
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return self.display_text(f"Model Type: {model.model_type}\n\n Awesome Plot Coming Soon!")
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@@ -156,10 +156,13 @@ class PluginUnitTest:
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"""Run the Dash server for the plugin, handling common errors gracefully."""
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while self.is_port_in_use(self.port):
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log.info(f"Port {self.port} is in use. Trying the next one...")
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self.port += 1
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self.port += 1
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log.info(f"Starting Dash server on port {self.port}...")
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try:
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self.app.run(debug=True, use_reloader=False, port=self.port)
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except KeyboardInterrupt:
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log.info("Shutting down Dash server...")
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@staticmethod
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def is_port_in_use(port):
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details = "**Redis:** 🔴 Failed to Connect<br>"
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# Fill in the license details
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redis_host = config_info.get("REDIS_HOST", "NOT SET")
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redis_port = config_info.get("REDIS_PORT", "NOT SET")
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details += f"**Redis Server:** {redis_host}:{redis_port}<br>"
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details += f"**Workbench S3 Bucket:** {config_info['WORKBENCH_BUCKET']}<br>"
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details += f"**Plugin Path:** {config_info.get('WORKBENCH_PLUGINS', 'unknown')}<br>"
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details += f"**Themes Path:** {config_info.get('WORKBENCH_THEMES', 'unknown')}<br>"
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# Workbench Imports
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from workbench.api.compound import Compound
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from workbench.utils.chem_utils import svg_from_smiles
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from workbench.utils.chem_utils.vis import svg_from_smiles
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from workbench.web_interface.components.plugin_interface import PluginInterface, PluginPage, PluginInputType
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from workbench.utils.theme_manager import ThemeManager
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from workbench.utils.ai_summary import AISummary
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html.H5(children="Inference Metrics", style={"marginTop": "20px"}),
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dcc.Dropdown(id=f"{self.component_id}-dropdown", className="dropdown"),
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dcc.Markdown(id=f"{self.component_id}-metrics"),
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dcc.Markdown(id=f"{self.component_id}-cross-metrics", dangerously_allow_html=True),
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],
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)
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(f"{self.component_id}-dropdown", "options"),
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(f"{self.component_id}-dropdown", "value"),
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(f"{self.component_id}-cross-metrics", "children"),
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self.signals = [(f"{self.component_id}-dropdown", "value")]
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return [header, details, inference_runs, default_run, metrics]
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def cross_metrics(self) -> str:
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# Get cross fold metrics if they exist
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# Note: Currently not used since we show cross fold metrics in the dropdown
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cross_fold_data = self.params.get(f"/workbench/models/{model_name}/inference/cross_fold", warn=False)
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return [], None
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#
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# Default inference run (full_cross_fold if it exists, then auto_inference, then first)
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if "full_cross_fold" in inference_runs:
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default_inference_run = "full_cross_fold"
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elif "auto_inference" in inference_runs:
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default_inference_run = "auto_inference"
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default_inference_run = inference_runs[0]
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# Return the options for the dropdown and the selected value
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self.df = self.df.drop(columns=aws_cols, errors="ignore")
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self.hover_columns = kwargs.get("hover_columns", sorted(self.df.columns.tolist()[:15]))
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).run()
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Metadata-Version: 2.4
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Name: workbench
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Version: 0.8.
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Version: 0.8.202
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Summary: Workbench: A Dashboard and Python API for creating and deploying AWS SageMaker Model Pipelines
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Author-email: SuperCowPowers LLC <support@supercowpowers.com>
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License
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License: MIT License
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Copyright (c) 2021-2026 SuperCowPowers LLC
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Project-URL: Homepage, https://github.com/SuperCowPowers/workbench
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Keywords: SageMaker,Machine Learning,AWS,Python,Utilities
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Classifier: Development Status :: 4 - Beta
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Classifier: Topic :: Scientific/Engineering
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Requires-Python: >=3.10
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Description-Content-Type: text/markdown
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@@ -168,7 +190,6 @@ Using Workbench will minimize the time and manpower needed to incorporate AWS ML
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```
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pip install workbench # Installs Workbench with Core Dependencies
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