workbench 0.8.171__py3-none-any.whl → 0.8.173__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (49) hide show
  1. workbench/algorithms/graph/light/proximity_graph.py +2 -1
  2. workbench/api/compound.py +1 -1
  3. workbench/api/feature_set.py +4 -4
  4. workbench/api/monitor.py +1 -16
  5. workbench/core/artifacts/artifact.py +11 -3
  6. workbench/core/artifacts/data_capture_core.py +315 -0
  7. workbench/core/artifacts/endpoint_core.py +9 -3
  8. workbench/core/artifacts/model_core.py +37 -14
  9. workbench/core/artifacts/monitor_core.py +33 -249
  10. workbench/core/cloud_platform/aws/aws_account_clamp.py +4 -1
  11. workbench/core/transforms/data_to_features/light/molecular_descriptors.py +4 -4
  12. workbench/core/transforms/features_to_model/features_to_model.py +4 -4
  13. workbench/model_scripts/custom_models/chem_info/mol_descriptors.py +471 -0
  14. workbench/model_scripts/custom_models/chem_info/mol_standardize.py +428 -0
  15. workbench/model_scripts/custom_models/chem_info/molecular_descriptors.py +7 -9
  16. workbench/model_scripts/custom_models/uq_models/generated_model_script.py +19 -9
  17. workbench/model_scripts/custom_models/uq_models/mapie.template +502 -0
  18. workbench/model_scripts/custom_models/uq_models/meta_uq.template +8 -5
  19. workbench/model_scripts/custom_models/uq_models/requirements.txt +1 -3
  20. workbench/model_scripts/script_generation.py +5 -0
  21. workbench/model_scripts/xgb_model/generated_model_script.py +5 -5
  22. workbench/repl/workbench_shell.py +3 -3
  23. workbench/utils/chem_utils/__init__.py +0 -0
  24. workbench/utils/chem_utils/fingerprints.py +134 -0
  25. workbench/utils/chem_utils/misc.py +194 -0
  26. workbench/utils/chem_utils/mol_descriptors.py +471 -0
  27. workbench/utils/chem_utils/mol_standardize.py +428 -0
  28. workbench/utils/chem_utils/mol_tagging.py +348 -0
  29. workbench/utils/chem_utils/projections.py +209 -0
  30. workbench/utils/chem_utils/salts.py +256 -0
  31. workbench/utils/chem_utils/sdf.py +292 -0
  32. workbench/utils/chem_utils/toxicity.py +250 -0
  33. workbench/utils/chem_utils/vis.py +253 -0
  34. workbench/utils/model_utils.py +1 -1
  35. workbench/utils/monitor_utils.py +49 -56
  36. workbench/utils/pandas_utils.py +3 -3
  37. workbench/utils/workbench_sqs.py +1 -1
  38. workbench/utils/xgboost_model_utils.py +1 -0
  39. workbench/web_interface/components/plugins/generated_compounds.py +1 -1
  40. {workbench-0.8.171.dist-info → workbench-0.8.173.dist-info}/METADATA +1 -1
  41. {workbench-0.8.171.dist-info → workbench-0.8.173.dist-info}/RECORD +45 -34
  42. workbench/model_scripts/custom_models/chem_info/local_utils.py +0 -769
  43. workbench/model_scripts/custom_models/chem_info/tautomerize.py +0 -83
  44. workbench/model_scripts/custom_models/uq_models/mapie_xgb.template +0 -203
  45. workbench/utils/chem_utils.py +0 -1556
  46. {workbench-0.8.171.dist-info → workbench-0.8.173.dist-info}/WHEEL +0 -0
  47. {workbench-0.8.171.dist-info → workbench-0.8.173.dist-info}/entry_points.txt +0 -0
  48. {workbench-0.8.171.dist-info → workbench-0.8.173.dist-info}/licenses/LICENSE +0 -0
  49. {workbench-0.8.171.dist-info → workbench-0.8.173.dist-info}/top_level.txt +0 -0
@@ -152,7 +152,7 @@ def compare_dataframes(df1: pd.DataFrame, df2: pd.DataFrame, display_columns: li
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  # Check for differences in common columns
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  for column in common_columns:
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- if pd.api.types.is_string_dtype(df1[column]) or pd.api.types.is_string_dtype(df2[column]):
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+ if pd.api.types.is_string_dtype(df1[column]) and pd.api.types.is_string_dtype(df2[column]):
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  # String comparison with NaNs treated as equal
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  differences = ~(df1[column].fillna("") == df2[column].fillna(""))
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  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
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  pd.isna(df1[column]) & pd.isna(df2[column])
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  )
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  else:
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- # Other types (e.g., int) with NaNs treated as equal
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- differences = ~(df1[column].fillna(0) == df2[column].fillna(0))
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+ # Other types (int, Int64, etc.) - compare with NaNs treated as equal
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+ differences = (df1[column] != df2[column]) & ~(pd.isna(df1[column]) & pd.isna(df2[column]))
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  # If differences exist, display them
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  if differences.any():
@@ -12,7 +12,7 @@ class WorkbenchSQS:
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  self.log = logging.getLogger("workbench")
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  self.queue_url = queue_url
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- # Grab a Workbench Session (this allows us to assume the Workbench-ExecutionRole)
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+ # Grab a Workbench Session
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  self.boto3_session = AWSAccountClamp().boto3_session
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  print(self.boto3_session)
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@@ -57,6 +57,7 @@ def xgboost_model_from_s3(model_artifact_uri: str):
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  patterns = [
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  # Direct XGBoost model files
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  os.path.join(tmpdir, "xgboost-model"),
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+ os.path.join(tmpdir, "xgb_model*.json"),
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  os.path.join(tmpdir, "model"),
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  os.path.join(tmpdir, "*.bin"),
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  os.path.join(tmpdir, "**", "*model*.json"),
@@ -5,7 +5,7 @@ import dash_bootstrap_components as dbc
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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
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: workbench
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- Version: 0.8.171
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+ Version: 0.8.173
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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-Expression: MIT
@@ -17,7 +17,7 @@ workbench/algorithms/graph/__init__.py,sha256=Hi2vBi-qw2OPLZnCu5qVTDdorRMOd3wNIt
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  workbench/algorithms/graph/heavy/Readme.md,sha256=QzefnMevGXHBtaP3umzMNn2KEdNQMvJkJNbhkrUw7QE,96
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  workbench/algorithms/graph/light/Readme.md,sha256=8kP_hRrRC6JtKtl5qyTwrV6gdO5rz6uq54c8WW1fTLg,122
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  workbench/algorithms/graph/light/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- workbench/algorithms/graph/light/proximity_graph.py,sha256=2mb1BLMdKX1NZbhNX3OGcpYED2RHJlTh4l7nd_0jAXE,9584
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+ workbench/algorithms/graph/light/proximity_graph.py,sha256=cwPqyswX4l4my8yGyC3LDZ0Jc5ZkVFx3N6W8xFxfzEY,9651
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  workbench/algorithms/spark/Readme.md,sha256=18bPoFISlT3Ls5t1cBGb5N5Z6lOWyJupQkQxab1wcO4,615
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  workbench/algorithms/sql/Readme.md,sha256=fzm4jQ-unJWT-fp5JhIjpApYSAqHUGSiuHE0eNfbF4A,685
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  workbench/algorithms/sql/__init__.py,sha256=TbOZQwCfx6Tjc3pCCLCiM31wpCX26j5MBNQ6yG11EwY,462
@@ -28,15 +28,15 @@ workbench/algorithms/sql/outliers.py,sha256=2hoilOk0gaz9pwrnGEBY2y7M-UqFED3KO_mF
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  workbench/algorithms/sql/sample_rows.py,sha256=SRYoGb24QP_iPvOoW9bGZ95yZuseYDtyoNhilfoLu34,2688
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  workbench/algorithms/sql/value_counts.py,sha256=F-rZoLTTKv1cHYl2_tDlvWDjczy76uLTr3EMHa-WrEk,3340
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  workbench/api/__init__.py,sha256=kvrP70ypDOMdPGj_Eeftdh8J0lu_1qQVne6GXMkD4_E,1027
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- workbench/api/compound.py,sha256=BHd3Qu4Ra45FEuwiowhFfGMI_HKRRB10XMmoS6ljKrM,2541
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+ workbench/api/compound.py,sha256=kf5EaM5qjWwsZutcxqj9IC_MPnDV1uVHDMns9OA_GOo,2545
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  workbench/api/data_source.py,sha256=Ngz36YZWxFfpJbmURhM1LQPYjh5kdpZNGo6_fCRePbA,8321
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  workbench/api/df_store.py,sha256=Wybb3zO-jPpAi2Ns8Ks1-lagvXAaBlRpBZHhnnl3Lms,6131
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  workbench/api/endpoint.py,sha256=RWGqxsCW_pMiENMb_XZlm2ZCldMS4suEBM3F5gT3hYI,3814
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- workbench/api/feature_set.py,sha256=wzNxNjN0K2FaIC7QUIogMnoHqw2vo0iAHYlGk6fWLCw,6649
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+ workbench/api/feature_set.py,sha256=Yxei3tvWR4gSLcdJnNndux07dNeKNu1HKgsChJtHxEM,6633
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  workbench/api/graph_store.py,sha256=LremJyPrQFgsHb7hxsctuCsoxx3p7TKtaY5qALHe6pc,4372
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  workbench/api/meta.py,sha256=1_9989cPvf3hd3tA-83hLijOGNnhwXAF8aZF45adeDQ,8596
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  workbench/api/model.py,sha256=RkFVXnlLcMlzNKRUFr_GCmZ7IQJMyhB2lwMwd22HBBo,4691
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- workbench/api/monitor.py,sha256=kQHSFiVLRWnHekSdatMKR3QbRj1BBNrVXpZgvV83LPM,5027
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+ workbench/api/monitor.py,sha256=Cez89Uac7Tzt47FxkjoX-YDGccEhvBcxw3sZFtw4ud8,4506
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  workbench/api/parameter_store.py,sha256=7BObkuATuP6C5AG_46kCWsmuCwuh1vgMJDBSN0gTkwM,4294
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  workbench/api/pipeline.py,sha256=MSYGrDSXrRB_oQELtAlOwBfxSBTw3REAkHy5XBHau0Y,6261
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  workbench/cached/__init__.py,sha256=wvTyIFvusv2HjU3yop6OSr3js5_-SZuR8nPmlCuZQJ4,525
@@ -48,18 +48,19 @@ workbench/cached/cached_model.py,sha256=iMc_fySUE5qau3feduVXMNb24JY0sBjt1g6WeLLc
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  workbench/cached/cached_pipeline.py,sha256=QOVnEKu5RbIdlNpJUi-0Ebh0_-C68RigSPwKh4dvZTM,1948
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  workbench/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  workbench/core/artifacts/__init__.py,sha256=ps7rA_rbWnDbvWbg4kvu--IKMY8WmbPRyv4Si0xub1Q,965
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- workbench/core/artifacts/artifact.py,sha256=mF1lqQ8EP43zMRSxqPYuWoHRwQTjyWdpW9LewU7utEE,17517
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+ workbench/core/artifacts/artifact.py,sha256=AtTw8wfMd-fi7cHJHsBAXHUk53kRW_6lyBwwsIbHw54,17750
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  workbench/core/artifacts/athena_source.py,sha256=RNmCe7s6uH4gVHpcdJcL84aSbF5Q1ahJBLLGwHYRXEU,26081
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  workbench/core/artifacts/cached_artifact_mixin.py,sha256=ngqFLZ4cQx_TFouXZgXZQsv_7W6XCvxVGXXSfzzaft8,3775
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+ workbench/core/artifacts/data_capture_core.py,sha256=VJL5AcXOx8PxY1Urw0AFm-czqvs55cDiwH_ZTcr2LS0,13207
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  workbench/core/artifacts/data_source_abstract.py,sha256=5IRCzFVK-17cd4NXPMRfx99vQAmQ0WHE5jcm5RfsVTg,10619
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  workbench/core/artifacts/data_source_factory.py,sha256=YL_tA5fsgubbB3dPF6T4tO0rGgz-6oo3ge4i_YXVC-M,2380
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- workbench/core/artifacts/endpoint_core.py,sha256=CtLo_eqONpDvyyYtjRkrrujVVv6cJV-vRQxHef6MYdk,48841
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+ workbench/core/artifacts/endpoint_core.py,sha256=lwgiz0jttW8C4YqcKaA8nf231WI3kol-nLnKcAbFJko,49049
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  workbench/core/artifacts/feature_set_core.py,sha256=055VdSYR09HP4ygAuYvIYtHQ7Ec4XxsZygpgEl5H5jQ,29136
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- workbench/core/artifacts/model_core.py,sha256=U0dSkpZMrsIgbUglVkPwAgN0gji7Oa7glOjqMQJDAzE,50927
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- workbench/core/artifacts/monitor_core.py,sha256=BvJ8gMxZXYZeMzAC25PVTXWiyXKtxD1qK6LqDcIByzs,37657
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+ workbench/core/artifacts/model_core.py,sha256=6d5dV4DGUBgD9E_Gpk0F5x7OEc4oiDKokvA8m42vnK4,51724
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+ workbench/core/artifacts/monitor_core.py,sha256=M307yz7tEzOEHgv-LmtVy9jKjSbM98fHW3ckmNYrwlU,27897
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  workbench/core/cloud_platform/cloud_meta.py,sha256=-g4-LTC3D0PXb3VfaXdLR1ERijKuHdffeMK_zhD-koQ,8809
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  workbench/core/cloud_platform/aws/README.md,sha256=QT5IQXoUHbIA0qQ2wO6_2P2lYjYQFVYuezc22mWY4i8,97
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- workbench/core/cloud_platform/aws/aws_account_clamp.py,sha256=OzFknZXKW7VTvnDGGX4BXKoh0i1gQ7yaEBhkLCyHFSs,6310
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+ workbench/core/cloud_platform/aws/aws_account_clamp.py,sha256=vAVC_HEk1YGSlo5F2bhQlWUxPN2QgRe3ht73O42faWQ,6452
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  workbench/core/cloud_platform/aws/aws_df_store.py,sha256=utRIlTCPwFneHHZ8_Z3Hw3rOJSeryiFA4wBtucxULRQ,15055
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  workbench/core/cloud_platform/aws/aws_graph_store.py,sha256=ytYxQTplUmeWbsPmxyZbf6mO9qyTl60ewlJG8MyfyEY,9414
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  workbench/core/cloud_platform/aws/aws_meta.py,sha256=eY9Pn6pl2yAyseACFb2nitR-0vLwG4i8CSEXe8Iaswc,34778
@@ -96,12 +97,12 @@ workbench/core/transforms/data_to_features/heavy/glue/Readme.md,sha256=TuyCatWfo
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  workbench/core/transforms/data_to_features/heavy/storage/data_to_features_heavy_old.py,sha256=tIfmnUjUAYpJhyHjHmM2D6jIt1pN7SabBqS8exV6f40,6438
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  workbench/core/transforms/data_to_features/light/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  workbench/core/transforms/data_to_features/light/data_to_features_light.py,sha256=CvybCeWom6CMkVJEf3gyD3MWCgntTUtWtRIF6v9Q_iU,3592
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- workbench/core/transforms/data_to_features/light/molecular_descriptors.py,sha256=lxbK8EO4GdBs56mNNjf6GuE9ciNcVUolqcmlVT-0HsE,2460
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+ workbench/core/transforms/data_to_features/light/molecular_descriptors.py,sha256=dOAJsei8-JYoPMzhKQjQVHex7Vx_KexQGQXOQSezq7w,2436
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  workbench/core/transforms/features_to_features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  workbench/core/transforms/features_to_features/heavy/emr/Readme.md,sha256=YtQgCEQeKe0CQXQkhzMTYq9xOtCsCYb5P5LW2BmRKWQ,68
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  workbench/core/transforms/features_to_model/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- workbench/core/transforms/features_to_model/features_to_model.py,sha256=gwqdQZJUIfZv1M7uGhzzBxUwRS0thJE_o_H2IUsBT40,19789
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+ workbench/core/transforms/features_to_model/features_to_model.py,sha256=ALGH5UmCdMYv4Fs2ebh6qMlwzt34xYkVSMpn4YfPbaA,19773
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  workbench/core/transforms/model_to_endpoint/model_to_endpoint.py,sha256=TIYXvuK0s383PwJ4iS6fCRhuif6oIxsoWb4CpMGJjY4,6358
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  workbench/core/transforms/pandas_transforms/__init__.py,sha256=xL4MT8-fZ1SFqDbTLc8XyxjupHtB1YR6Ej0AC2nwd7I,894
@@ -121,13 +122,13 @@ workbench/core/views/training_view.py,sha256=mUkv1oVhDG-896RdLNKxCg0j0yvudEcPnvL
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  workbench/core/views/storage/mdq_view.py,sha256=qf_ep1KwaXOIfO930laEwNIiCYP7VNOqjE3VdHfopRE,5195
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- workbench/model_scripts/script_generation.py,sha256=VVgRxvJsbpn6Uw6KpDAZe8oMtmg0l_fTImxDiUFJEes,7722
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+ workbench/model_scripts/script_generation.py,sha256=dL23XYwEsHIStc7i53DtF_47FqOrI9gq0kQAT6sNpZ8,7923
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  workbench/model_scripts/custom_models/chem_info/Readme.md,sha256=mH1lxJ4Pb7F5nBnVXaiuxpi8zS_yjUw_LBJepVKXhlA,574
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- workbench/model_scripts/custom_models/chem_info/local_utils.py,sha256=Rsz_VRoA3O3-VoitmN8o5OymstsF433QgdSRHc-iZ24,29071
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- workbench/model_scripts/custom_models/chem_info/molecular_descriptors.py,sha256=E8SK4oOHaYnYx4ycQJ6R7yg799kjtbipM3KEc8SPArQ,3011
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+ workbench/model_scripts/custom_models/chem_info/mol_descriptors.py,sha256=N07kGqyLd9DE9S23WfPqXGO5NMQzNxe0jtl1RgtC4yY,18315
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+ workbench/model_scripts/custom_models/chem_info/mol_standardize.py,sha256=-BMtNzZSbXFnfoxFESHdfg7yjXO83JVecpIEsj39eDM,17145
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+ workbench/model_scripts/custom_models/chem_info/molecular_descriptors.py,sha256=xljMjdfh4Idi4v1Afq1zZxvF1SDa7pDOLSAhvGBEj88,2891
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  workbench/model_scripts/custom_models/chem_info/requirements.txt,sha256=7HBUzvNiM8lOir-UfQabXYlUp3gxdGJ42u18EuSMGjc,39
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- workbench/model_scripts/custom_models/chem_info/tautomerize.py,sha256=KAxTAqtTql4_FvnrAyYRgaJEmtAx399HXA_iw_awa08,3125
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  workbench/model_scripts/custom_models/meta_endpoints/example.py,sha256=hzOAuLhIGB8vei-555ruNxpsE1GhuByHGjGB0zw8GSs,1726
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  workbench/model_scripts/custom_models/network_security/Readme.md,sha256=Z2gtiu0hLHvEJ1x-_oFq3qJZcsK81sceBAGAGltpqQ8,222
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@@ -139,12 +140,12 @@ workbench/model_scripts/custom_models/uq_models/Readme.md,sha256=UVpL-lvtTrLqwBe
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  workbench/model_scripts/custom_models/uq_models/bayesian_ridge.template,sha256=U4LIlpp8Rbu3apyzPR7-55lvlutpTsCro_PUvQ5pklY,6457
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  workbench/model_scripts/custom_models/uq_models/ensemble_xgb.template,sha256=0IJnSBACQ556ldEiPqR7yPCOOLJs1hQhHmPBvB2d9tY,13491
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  workbench/model_scripts/custom_models/uq_models/gaussian_process.template,sha256=QbDUfkiPCwJ-c-4Twgu4utZuYZaAyeW_3T1IP-_tutw,6683
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- workbench/model_scripts/custom_models/uq_models/generated_model_script.py,sha256=QsMivNf77m4XfrV9aYTB7K3vI-InwegD7gyLZFNQmF4,17170
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+ workbench/utils/xgboost_model_utils.py,sha256=iiDJH0O81aO6aOTwgssqQygvTgjE7lRDRzLJ_fI3RVs,15554
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+ workbench/utils/chem_utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ workbench/utils/chem_utils/mol_standardize.py,sha256=-BMtNzZSbXFnfoxFESHdfg7yjXO83JVecpIEsj39eDM,17145
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+ workbench/utils/chem_utils/mol_tagging.py,sha256=8Bt6gHvyN8B2jvVuz12JgYMHVLDkCLnEPAfqkyMEoMc,9995
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+ workbench/utils/chem_utils/salts.py,sha256=ZzFb6Z71Z_kMjVF-PKwHx0fn9pN9rPMj-oEY8Nt5JWA,9095
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+ workbench/utils/chem_utils/sdf.py,sha256=wucyMtnmdg6onBa5N_sX6ONDE4PThJokImFxCBk22RI,10319
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+ workbench/utils/chem_utils/toxicity.py,sha256=OmVvR05XjP8rLteQ0gjlC5tRh3WitjoahPnSLPhbUXQ,10195
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+ workbench/web_interface/components/plugins/generated_compounds.py,sha256=A6JGlkl7buZUugPK21YgufVFDRoGlHJowaqf8PAmz_s,8056
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