workbench 0.8.166__tar.gz → 0.8.198__tar.gz

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  1. {workbench-0.8.166 → workbench-0.8.198}/.github/workflows/python-lint.yml +2 -3
  2. workbench-0.8.198/Dockerfile +7 -0
  3. {workbench-0.8.166 → workbench-0.8.198}/LICENSE +1 -1
  4. {workbench-0.8.166 → workbench-0.8.198}/PKG-INFO +24 -2
  5. {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/Dockerfile +1 -1
  6. workbench-0.8.166/aws_setup/aws_account_check.py → workbench-0.8.198/aws_setup/aws_account_setup.py +25 -1
  7. workbench-0.8.198/aws_setup/workbench_compute/README.md +58 -0
  8. workbench-0.8.198/aws_setup/workbench_compute/app.py +64 -0
  9. workbench-0.8.198/aws_setup/workbench_compute/cdk.json +97 -0
  10. {workbench-0.8.166/aws_setup/workbench_core → workbench-0.8.198/aws_setup/workbench_compute}/requirements.txt +1 -2
  11. workbench-0.8.198/aws_setup/workbench_compute/tests/unit/test_workbench_compute_stack.py +17 -0
  12. workbench-0.8.198/aws_setup/workbench_compute/workbench_compute/workbench_compute_stack.py +279 -0
  13. workbench-0.8.198/aws_setup/workbench_core/app.py +75 -0
  14. workbench-0.8.198/aws_setup/workbench_core/requirements.txt +3 -0
  15. {workbench-0.8.166 → workbench-0.8.198}/aws_setup/workbench_core/workbench_core/workbench_core_stack.py +552 -103
  16. {workbench-0.8.166 → workbench-0.8.198}/aws_setup/workbench_dashboard_full/app.py +1 -1
  17. {workbench-0.8.166 → workbench-0.8.198}/aws_setup/workbench_dashboard_lite/app.py +1 -1
  18. {workbench-0.8.166 → workbench-0.8.198}/docs/api_classes/endpoint.md +3 -7
  19. {workbench-0.8.166 → workbench-0.8.198}/docs/api_classes/monitor.md +2 -2
  20. {workbench-0.8.166 → workbench-0.8.198}/docs/api_classes/overview.md +2 -7
  21. {workbench-0.8.166 → workbench-0.8.198}/docs/api_classes/views.md +2 -2
  22. {workbench-0.8.166 → workbench-0.8.198}/docs/aws_setup/core_stack.md +34 -6
  23. {workbench-0.8.166 → workbench-0.8.198}/docs/aws_setup/sso_assume_role.md +22 -4
  24. {workbench-0.8.166 → workbench-0.8.198}/docs/core_classes/views/overview.md +2 -2
  25. {workbench-0.8.166 → workbench-0.8.198}/examples/chem_utils/tautomerize_smiles.py +10 -4
  26. {workbench-0.8.166 → workbench-0.8.198}/examples/endpoint/endpoint_inference.py +3 -7
  27. {workbench-0.8.166 → workbench-0.8.198}/examples/full_ml_pipeline.py +1 -3
  28. workbench-0.8.198/examples/ml_pipelines/list_models.py +11 -0
  29. workbench-0.8.198/examples/ml_pipelines/wine_classifier.py +41 -0
  30. workbench-0.8.198/examples/models/smiles_to_md_v1.py +27 -0
  31. workbench-0.8.166/examples/models/uq/mapie_xgb.py → workbench-0.8.198/examples/models/uq/mapie.py +4 -4
  32. {workbench-0.8.166 → workbench-0.8.198}/examples/monitor/monitor_usage.py +1 -6
  33. {workbench-0.8.166 → workbench-0.8.198}/experiments/chem_info/bulk_sims.py +1 -1
  34. {workbench-0.8.166 → workbench-0.8.198}/experiments/chem_info/knn_sims.py +1 -1
  35. workbench-0.8.198/experiments/chemprop_model.py +492 -0
  36. workbench-0.8.198/experiments/mapie_model.py +477 -0
  37. {workbench-0.8.166 → workbench-0.8.198}/experiments/pytorch_model.py +2 -2
  38. workbench-0.8.198/ml_pipelines/hyper_uq.py +50 -0
  39. {workbench-0.8.166/model_docker_images/pytorch_inference → workbench-0.8.198/model_docker_images/inference}/Dockerfile +5 -2
  40. workbench-0.8.198/model_docker_images/inference/requirements.txt +9 -0
  41. workbench-0.8.198/model_docker_images/ml_pipelines/Dockerfile +38 -0
  42. workbench-0.8.198/model_docker_images/ml_pipelines/ml_pipeline_runner.py +73 -0
  43. workbench-0.8.198/model_docker_images/ml_pipelines/requirements.txt +16 -0
  44. {workbench-0.8.166 → workbench-0.8.198}/model_docker_images/scripts/build_deploy.sh +12 -8
  45. {workbench-0.8.166 → workbench-0.8.198}/model_docker_images/tests/example_model_script.py +2 -2
  46. {workbench-0.8.166 → workbench-0.8.198}/model_docker_images/training/Dockerfile +9 -2
  47. workbench-0.8.198/model_docker_images/training/requirements.txt +7 -0
  48. {workbench-0.8.166 → workbench-0.8.198}/notebooks/Inference_On_Legacy_Models.ipynb +2 -2
  49. {workbench-0.8.166 → workbench-0.8.198}/notebooks/ML_Pipeline_with_Workbench_2.ipynb +1 -1
  50. {workbench-0.8.166 → workbench-0.8.198}/pyproject.toml +5 -1
  51. workbench-0.8.198/scripts/delete_data_capture.py +72 -0
  52. workbench-0.8.166/scripts/endpoint_inference_launch.py → workbench-0.8.198/scripts/endpoint_timing.py +3 -26
  53. workbench-0.8.198/scripts/sagemaker_feature_group_issue.py +61 -0
  54. workbench-0.8.198/scripts/test_feature_set_creation.py +20 -0
  55. {workbench-0.8.166 → workbench-0.8.198}/scripts/tox21/test_tox_heuristic.py +1 -1
  56. workbench-0.8.198/scripts/tox21/tox21_to_df_store.py +186 -0
  57. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/algorithms/dataframe/__init__.py +1 -2
  58. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/algorithms/dataframe/fingerprint_proximity.py +2 -2
  59. workbench-0.8.198/src/workbench/algorithms/dataframe/proximity.py +403 -0
  60. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/algorithms/graph/light/proximity_graph.py +10 -8
  61. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/api/compound.py +1 -1
  62. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/api/endpoint.py +2 -2
  63. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/api/feature_set.py +4 -4
  64. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/api/model.py +15 -14
  65. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/api/monitor.py +1 -16
  66. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/artifacts/artifact.py +11 -3
  67. workbench-0.8.198/src/workbench/core/artifacts/data_capture_core.py +355 -0
  68. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/artifacts/endpoint_core.py +129 -34
  69. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/artifacts/feature_set_core.py +197 -16
  70. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/artifacts/model_core.py +70 -53
  71. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/artifacts/monitor_core.py +33 -249
  72. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/cloud_platform/aws/aws_account_clamp.py +50 -1
  73. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/cloud_platform/aws/aws_meta.py +11 -4
  74. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/cloud_platform/aws/aws_session.py +4 -4
  75. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/transforms/data_to_features/light/molecular_descriptors.py +4 -4
  76. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/transforms/features_to_model/features_to_model.py +12 -7
  77. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/transforms/model_to_endpoint/model_to_endpoint.py +36 -6
  78. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/transforms/pandas_transforms/pandas_to_features.py +27 -0
  79. workbench-0.8.198/src/workbench/core/views/training_view.py +231 -0
  80. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/views/view.py +51 -1
  81. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/views/view_utils.py +4 -4
  82. workbench-0.8.198/src/workbench/model_scripts/__pycache__/script_generation.cpython-312.pyc +0 -0
  83. workbench-0.8.198/src/workbench/model_scripts/__pycache__/script_generation.cpython-313.pyc +0 -0
  84. workbench-0.8.198/src/workbench/model_scripts/custom_models/chem_info/mol_descriptors.py +483 -0
  85. workbench-0.8.198/src/workbench/model_scripts/custom_models/chem_info/mol_standardize.py +450 -0
  86. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/chem_info/molecular_descriptors.py +7 -9
  87. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/proximity/feature_space_proximity.template +3 -5
  88. workbench-0.8.198/src/workbench/model_scripts/custom_models/proximity/proximity.py +403 -0
  89. workbench-0.8.198/src/workbench/model_scripts/custom_models/proximity/requirements.txt +0 -0
  90. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/uq_models/bayesian_ridge.template +7 -8
  91. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/uq_models/ensemble_xgb.template +10 -17
  92. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/uq_models/gaussian_process.template +5 -11
  93. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/uq_models/meta_uq.template +156 -58
  94. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/uq_models/ngboost.template +20 -14
  95. workbench-0.8.198/src/workbench/model_scripts/custom_models/uq_models/proximity.py +403 -0
  96. workbench-0.8.198/src/workbench/model_scripts/custom_models/uq_models/requirements.txt +1 -0
  97. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/ensemble_xgb/ensemble_xgb.template +5 -13
  98. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/pytorch_model/generated_model_script.py +14 -23
  99. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/pytorch_model/pytorch.template +9 -18
  100. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/scikit_learn/scikit_learn.template +4 -9
  101. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/script_generation.py +7 -2
  102. workbench-0.8.198/src/workbench/model_scripts/uq_models/generated_model_script.py +589 -0
  103. workbench-0.8.198/src/workbench/model_scripts/uq_models/mapie.template +589 -0
  104. workbench-0.8.198/src/workbench/model_scripts/uq_models/requirements.txt +1 -0
  105. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/xgb_model/generated_model_script.py +34 -43
  106. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/xgb_model/xgb_model.template +31 -40
  107. workbench-0.8.198/src/workbench/repl/__init__.py +0 -0
  108. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/repl/workbench_shell.py +7 -7
  109. workbench-0.8.198/src/workbench/scripts/lambda_launcher.py +63 -0
  110. workbench-0.8.198/src/workbench/scripts/ml_pipeline_batch.py +137 -0
  111. workbench-0.8.198/src/workbench/scripts/ml_pipeline_sqs.py +186 -0
  112. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/scripts/monitor_cloud_watch.py +20 -100
  113. workbench-0.8.198/src/workbench/utils/__init__.py +0 -0
  114. workbench-0.8.198/src/workbench/utils/chem_utils/__init__.py +0 -0
  115. workbench-0.8.198/src/workbench/utils/chem_utils/fingerprints.py +134 -0
  116. workbench-0.8.198/src/workbench/utils/chem_utils/misc.py +194 -0
  117. workbench-0.8.198/src/workbench/utils/chem_utils/mol_descriptors.py +483 -0
  118. workbench-0.8.198/src/workbench/utils/chem_utils/mol_standardize.py +450 -0
  119. workbench-0.8.198/src/workbench/utils/chem_utils/mol_tagging.py +348 -0
  120. workbench-0.8.198/src/workbench/utils/chem_utils/projections.py +209 -0
  121. workbench-0.8.198/src/workbench/utils/chem_utils/salts.py +256 -0
  122. workbench-0.8.198/src/workbench/utils/chem_utils/sdf.py +292 -0
  123. workbench-0.8.198/src/workbench/utils/chem_utils/toxicity.py +250 -0
  124. workbench-0.8.198/src/workbench/utils/chem_utils/vis.py +253 -0
  125. workbench-0.8.198/src/workbench/utils/cloudwatch_utils.py +137 -0
  126. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/config_manager.py +2 -6
  127. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/endpoint_utils.py +5 -7
  128. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/license_manager.py +2 -6
  129. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/model_utils.py +95 -34
  130. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/monitor_utils.py +44 -62
  131. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/pandas_utils.py +3 -3
  132. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/shap_utils.py +10 -2
  133. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/workbench_sqs.py +1 -1
  134. workbench-0.8.198/src/workbench/utils/xgboost_model_utils.py +626 -0
  135. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/model_plot.py +7 -1
  136. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/plugin_unit_test.py +5 -2
  137. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/plugins/dashboard_status.py +3 -1
  138. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/plugins/generated_compounds.py +1 -1
  139. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/plugins/model_details.py +9 -7
  140. {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/plugins/scatter_plot.py +3 -3
  141. {workbench-0.8.166 → workbench-0.8.198}/src/workbench.egg-info/PKG-INFO +24 -2
  142. {workbench-0.8.166 → workbench-0.8.198}/src/workbench.egg-info/SOURCES.txt +70 -61
  143. {workbench-0.8.166 → workbench-0.8.198}/src/workbench.egg-info/entry_points.txt +3 -0
  144. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_aqsol_uq_artifacts.py +9 -21
  145. workbench-0.8.198/test_artifacts/hyper_testing.py +70 -0
  146. workbench-0.8.198/test_artifacts/hyper_uq_testing.py +54 -0
  147. {workbench-0.8.166 → workbench-0.8.198}/tests/artifacts/endpoint_tests.py +7 -7
  148. {workbench-0.8.166 → workbench-0.8.198}/tests/chem_info/test_tautomerization.py +24 -6
  149. {workbench-0.8.166 → workbench-0.8.198}/tests/pytorch/pytorch_hello.py +2 -2
  150. {workbench-0.8.166 → workbench-0.8.198}/tox.ini +12 -7
  151. workbench-0.8.166/Dockerfile +0 -31
  152. workbench-0.8.166/aws_setup/event_bridge/dynamic_docker/Readme.md +0 -6
  153. workbench-0.8.166/aws_setup/event_bridge/dynamic_docker/app.py +0 -25
  154. workbench-0.8.166/aws_setup/event_bridge/dynamic_docker/lambda/lambda_replace_task.py +0 -56
  155. workbench-0.8.166/aws_setup/event_bridge/dynamic_docker/workbench_image_update_stack.py +0 -59
  156. workbench-0.8.166/aws_setup/workbench_core/app.py +0 -47
  157. workbench-0.8.166/aws_setup/workbench_dashboard_lite/cdk.json +0 -58
  158. workbench-0.8.166/examples/chem_utils/canonicalize_smiles.py +0 -22
  159. workbench-0.8.166/examples/pipelines/abalone_pipeline_v1.json +0 -43
  160. workbench-0.8.166/examples/pipelines/abalone_pipeline_v2.json +0 -45
  161. workbench-0.8.166/examples/pipelines/aqsol_pipeline_v1.json +0 -66
  162. workbench-0.8.166/examples/pipelines/pipeline_details.py +0 -5
  163. workbench-0.8.166/examples/pipelines/pipeline_execute.py +0 -11
  164. workbench-0.8.166/examples/pipelines/pipeline_manager.py +0 -18
  165. workbench-0.8.166/examples/storage/sagemaker_pipelines/all_steps.py +0 -27
  166. workbench-0.8.166/examples/storage/sagemaker_pipelines/hello.py +0 -1
  167. workbench-0.8.166/examples/storage/sagemaker_pipelines/ml_pipeline.py +0 -60
  168. workbench-0.8.166/examples/storage/sagemaker_pipelines/storage/full_pipeline_experiment/data_source.py +0 -27
  169. workbench-0.8.166/examples/storage/sagemaker_pipelines/storage/full_pipeline_experiment/endpoint.py +0 -5
  170. workbench-0.8.166/examples/storage/sagemaker_pipelines/storage/full_pipeline_experiment/feature_set.py +0 -5
  171. workbench-0.8.166/examples/storage/sagemaker_pipelines/storage/full_pipeline_experiment/ml_pipeline.py +0 -65
  172. workbench-0.8.166/examples/storage/sagemaker_pipelines/storage/full_pipeline_experiment/model.py +0 -13
  173. workbench-0.8.166/model_docker_images/inference/requirements.txt +0 -7
  174. workbench-0.8.166/model_docker_images/training/requirements.txt +0 -5
  175. workbench-0.8.166/scripts/endpoint_timing/endpoint_timing.py +0 -86
  176. workbench-0.8.166/scripts/endpoint_timing/endpoint_timing_old.py +0 -139
  177. workbench-0.8.166/scripts/endpoint_timing/timing_plot.py +0 -54
  178. workbench-0.8.166/scripts/model_to_endpoint_debugging.py +0 -124
  179. workbench-0.8.166/scripts/tox21/tox21_to_df_store.py +0 -114
  180. workbench-0.8.166/src/workbench/algorithms/dataframe/proximity.py +0 -384
  181. workbench-0.8.166/src/workbench/core/views/training_view.py +0 -160
  182. workbench-0.8.166/src/workbench/model_scripts/custom_models/chem_info/local_utils.py +0 -769
  183. workbench-0.8.166/src/workbench/model_scripts/custom_models/chem_info/tautomerize.py +0 -83
  184. workbench-0.8.166/src/workbench/model_scripts/custom_models/proximity/generated_model_script.py +0 -138
  185. workbench-0.8.166/src/workbench/model_scripts/custom_models/proximity/proximity.py +0 -384
  186. workbench-0.8.166/src/workbench/model_scripts/custom_models/uq_models/generated_model_script.py +0 -393
  187. workbench-0.8.166/src/workbench/model_scripts/custom_models/uq_models/mapie_xgb.template +0 -203
  188. workbench-0.8.166/src/workbench/model_scripts/custom_models/uq_models/proximity.py +0 -384
  189. workbench-0.8.166/src/workbench/model_scripts/custom_models/uq_models/requirements.txt +0 -3
  190. workbench-0.8.166/src/workbench/model_scripts/ensemble_xgb/generated_model_script.py +0 -279
  191. workbench-0.8.166/src/workbench/model_scripts/quant_regression/quant_regression.template +0 -279
  192. workbench-0.8.166/src/workbench/model_scripts/scikit_learn/generated_model_script.py +0 -307
  193. workbench-0.8.166/src/workbench/model_scripts/xgb_model/requirements.txt +0 -1
  194. workbench-0.8.166/src/workbench/utils/chem_utils.py +0 -1556
  195. workbench-0.8.166/src/workbench/utils/fast_inference.py +0 -167
  196. workbench-0.8.166/src/workbench/utils/resource_utils.py +0 -39
  197. workbench-0.8.166/src/workbench/utils/xgboost_model_utils.py +0 -416
  198. workbench-0.8.166/tests/chem_info/test_canonicalize.py +0 -37
  199. {workbench-0.8.166 → workbench-0.8.198}/.flake8 +0 -0
  200. {workbench-0.8.166 → workbench-0.8.198}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
  201. {workbench-0.8.166 → workbench-0.8.198}/.github/dependabot.yml +0 -0
  202. {workbench-0.8.166 → workbench-0.8.198}/.github/workflows/deploy-docs.yml +0 -0
  203. {workbench-0.8.166 → workbench-0.8.198}/.gitignore +0 -0
  204. {workbench-0.8.166 → workbench-0.8.198}/CONTRIBUTING.md +0 -0
  205. {workbench-0.8.166 → workbench-0.8.198}/Makefile +0 -0
  206. {workbench-0.8.166 → workbench-0.8.198}/README.md +0 -0
  207. {workbench-0.8.166 → workbench-0.8.198}/SECURITY.md +0 -0
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  773. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_aqsol_rt_artifacts.py +0 -0
  774. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_basic_test_artifacts.py +0 -0
  775. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_copy_artifacts.py +0 -0
  776. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_empty_model_group.py +0 -0
  777. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_endpoints_for_timing.py +0 -0
  778. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_graph_artifacts.py +0 -0
  779. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_knn_artifacts.py +0 -0
  780. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_meta_endpoints.py +0 -0
  781. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_pipeline_model.py +0 -0
  782. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_proximity_models.py +0 -0
  783. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_quant_regression_artifacts.py +0 -0
  784. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_realtime_endpoint.py +0 -0
  785. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_training_adjusted_artifacts.py +0 -0
  786. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_wine_artifacts.py +0 -0
  787. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/delete_stress_test_artifacts.py +0 -0
  788. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/delete_test_artifacts.py +0 -0
  789. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/regression_ensemble.py +0 -0
  790. {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/stress_test_aws.py +0 -0
  791. {workbench-0.8.166 → workbench-0.8.198}/tests/README.md +0 -0
  792. {workbench-0.8.166 → workbench-0.8.198}/tests/artifacts/data_source_tests.py +0 -0
  793. {workbench-0.8.166 → workbench-0.8.198}/tests/artifacts/empty_model_group.py +0 -0
  794. {workbench-0.8.166 → workbench-0.8.198}/tests/artifacts/featureset_ingest_boundaries.py +0 -0
  795. {workbench-0.8.166 → workbench-0.8.198}/tests/artifacts/featureset_tests.py +0 -0
  796. {workbench-0.8.166 → workbench-0.8.198}/tests/artifacts/graph_tests.py +0 -0
  797. {workbench-0.8.166 → workbench-0.8.198}/tests/artifacts/model_metrics_tests.py +0 -0
  798. {workbench-0.8.166 → workbench-0.8.198}/tests/artifacts/model_tests.py +0 -0
  799. {workbench-0.8.166 → workbench-0.8.198}/tests/aws_account/aws_account_clamp_tests.py +0 -0
  800. {workbench-0.8.166 → workbench-0.8.198}/tests/cached/cached_artifact_tests.py +0 -0
  801. {workbench-0.8.166 → workbench-0.8.198}/tests/corner_cases/end_to_end.py +0 -0
  802. {workbench-0.8.166 → workbench-0.8.198}/tests/df_store/df_store_tests.py +0 -0
  803. {workbench-0.8.166 → workbench-0.8.198}/tests/lambda/decompress_layers.py +0 -0
  804. {workbench-0.8.166 → workbench-0.8.198}/tests/pandas_tests/test_drift.py +0 -0
  805. {workbench-0.8.166 → workbench-0.8.198}/tests/parameter_store/param_store_tests.py +0 -0
  806. {workbench-0.8.166 → workbench-0.8.198}/tests/plugin_tests/crashing_plugin.py +0 -0
  807. {workbench-0.8.166 → workbench-0.8.198}/tests/requirements-dev.txt +0 -0
  808. {workbench-0.8.166 → workbench-0.8.198}/tests/specific/capital_tests.py +0 -0
  809. {workbench-0.8.166 → workbench-0.8.198}/tests/specific/column_changes.py +0 -0
  810. {workbench-0.8.166 → workbench-0.8.198}/tests/specific/config_manager.py +0 -0
  811. {workbench-0.8.166 → workbench-0.8.198}/tests/specific/deletion_tests.py +0 -0
  812. {workbench-0.8.166 → workbench-0.8.198}/tests/specific/shap_tests.py +0 -0
  813. {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/data_to_data_tests.py +0 -0
  814. {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/data_to_features_tests.py +0 -0
  815. {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/features_to_model_tests.py +0 -0
  816. {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/model_to_endpoint_tests.py +0 -0
  817. {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/pandas_to_data_tests.py +0 -0
  818. {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/pandas_to_features_test.py +0 -0
  819. {workbench-0.8.166 → workbench-0.8.198}/tests/views/view_tests.py +0 -0
  820. {workbench-0.8.166 → workbench-0.8.198}/tests/views/view_tests_complex.py +0 -0
  821. {workbench-0.8.166 → workbench-0.8.198}/tests/web_components/confusion_matrix_test.py +0 -0
  822. {workbench-0.8.166 → workbench-0.8.198}/tests/web_components/correlation_matrix_test.py +0 -0
  823. {workbench-0.8.166 → workbench-0.8.198}/tests/web_components/graph_plot_test.py +0 -0
  824. {workbench-0.8.166 → workbench-0.8.198}/tests/web_components/plugin_interface_test.py +0 -0
  825. {workbench-0.8.166 → workbench-0.8.198}/tests/web_components/scatter_plot_test.py +0 -0
  826. {workbench-0.8.166 → workbench-0.8.198}/ui_testing/assets/custom.css +0 -0
  827. {workbench-0.8.166 → workbench-0.8.198}/ui_testing/table_comparison.py +0 -0
  828. {workbench-0.8.166 → workbench-0.8.198}/ui_testing/theme_switching.py +0 -0
  829. {workbench-0.8.166 → workbench-0.8.198}/ui_testing/theme_switching_2.py +0 -0
@@ -12,9 +12,9 @@ jobs:
12
12
  - uses: actions/checkout@v4
13
13
 
14
14
  - name: Set up Python
15
- uses: actions/setup-python@v4
15
+ uses: actions/setup-python@v5
16
16
  with:
17
- python-version: '3.x'
17
+ python-version: '3.13'
18
18
 
19
19
  - name: Install dependencies
20
20
  run: |
@@ -27,4 +27,3 @@ jobs:
27
27
  - name: Run Flake8 (Linting)
28
28
  run: |
29
29
  flake8 --exclude '*generated*' src/workbench applications tests
30
-
@@ -0,0 +1,7 @@
1
+ FROM python:3.12-slim
2
+
3
+ ARG WORKBENCH_VERSION=
4
+ RUN apt-get update && apt-get upgrade -y && \
5
+ apt-get install -y --no-install-recommends libexpat1 libnghttp2-dev && \
6
+ apt-get clean && rm -rf /var/lib/apt/lists/* && \
7
+ pip install --no-cache-dir workbench${WORKBENCH_VERSION:+==$WORKBENCH_VERSION}
@@ -1,6 +1,6 @@
1
1
  MIT License
2
2
 
3
- Copyright (c) 2021-2024 SuperCowPowers LLC
3
+ Copyright (c) 2021-2026 SuperCowPowers LLC
4
4
 
5
5
  Permission is hereby granted, free of charge, to any person obtaining a copy
6
6
  of this software and associated documentation files (the "Software"), to deal
@@ -1,15 +1,37 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: workbench
3
- Version: 0.8.166
3
+ Version: 0.8.198
4
4
  Summary: Workbench: A Dashboard and Python API for creating and deploying AWS SageMaker Model Pipelines
5
5
  Author-email: SuperCowPowers LLC <support@supercowpowers.com>
6
- License-Expression: MIT
6
+ License: MIT License
7
+
8
+ Copyright (c) 2021-2026 SuperCowPowers LLC
9
+
10
+ Permission is hereby granted, free of charge, to any person obtaining a copy
11
+ of this software and associated documentation files (the "Software"), to deal
12
+ in the Software without restriction, including without limitation the rights
13
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
14
+ copies of the Software, and to permit persons to whom the Software is
15
+ furnished to do so, subject to the following conditions:
16
+
17
+ The above copyright notice and this permission notice shall be included in all
18
+ copies or substantial portions of the Software.
19
+
20
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
21
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
22
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
23
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
24
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
25
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
26
+ SOFTWARE.
27
+
7
28
  Project-URL: Homepage, https://github.com/SuperCowPowers/workbench
8
29
  Keywords: SageMaker,Machine Learning,AWS,Python,Utilities
9
30
  Classifier: Development Status :: 4 - Beta
10
31
  Classifier: Programming Language :: Python :: 3.10
11
32
  Classifier: Programming Language :: Python :: 3.11
12
33
  Classifier: Programming Language :: Python :: 3.12
34
+ Classifier: Programming Language :: Python :: 3.13
13
35
  Classifier: Topic :: Scientific/Engineering
14
36
  Requires-Python: >=3.10
15
37
  Description-Content-Type: text/markdown
@@ -7,7 +7,7 @@ EXPOSE 8000
7
7
  ENV PYTHONHASHSEED=0
8
8
 
9
9
  # Define workbench version
10
- ARG WORKBENCH_VERSION=0.8.165
10
+ ARG WORKBENCH_VERSION=0.8.196
11
11
 
12
12
  # Install system packages and gunicorn in one layer
13
13
  RUN apt-get update && apt-get install -y --no-install-recommends \
@@ -39,12 +39,31 @@ class AWSAccountCheck:
39
39
  self.log.error(f"AccessDeniedException {e}")
40
40
  self.log.error(f"Access denied while trying to create/access the catalog database '{catalog_db}'.")
41
41
  self.log.error("Create the database manually in the AWS Glue Console, or run this command:")
42
- self.log.error('aws glue create-database --database-input \'{"Name": "workbench"}\'')
42
+ self.log.error(f'aws glue create-database --database-input \'{{"Name": "{catalog_db}"}}\'')
43
43
  sys.exit(1)
44
44
  else:
45
45
  self.log.error(f"Unexpected error: {e}")
46
46
  sys.exit(1)
47
47
 
48
+ def ensure_athena_results_bucket(self):
49
+ """Ensure that the Athena results S3 bucket exists"""
50
+ bucket_name = f"aws-athena-query-results-{self.aws_clamp.account_id}-{self.aws_clamp.region}"
51
+ self.log.important(f"Checking if Athena results bucket {bucket_name} exists...")
52
+
53
+ try:
54
+ s3_client = self.aws_clamp.boto3_session.client("s3")
55
+ s3_client.head_bucket(Bucket=bucket_name)
56
+ self.log.info(f"Athena results bucket {bucket_name} already exists")
57
+ except ClientError as e:
58
+ if e.response["Error"]["Code"] == "404":
59
+ self.log.error(f"Athena results bucket {bucket_name} does not exist.")
60
+ self.log.error("Create the bucket manually using this AWS CLI command:")
61
+ self.log.error(f"aws s3 mb s3://{bucket_name}")
62
+ sys.exit(1)
63
+ else:
64
+ self.log.error(f"Error checking bucket {bucket_name}: {e}")
65
+ sys.exit(1)
66
+
48
67
  def check(self):
49
68
  """Check if the AWS Account is set up Correctly"""
50
69
  self.log.info("*** Caller/Base AWS Identity Check ***")
@@ -71,6 +90,11 @@ class AWSAccountCheck:
71
90
  self.ensure_aws_catalog_db(catalog_db)
72
91
  print("\n")
73
92
 
93
+ # Check that the Athena Results Bucket exists
94
+ self.log.info("*** AWS Athena Results Bucket Check ***")
95
+ self.ensure_athena_results_bucket()
96
+ print("\n")
97
+
74
98
  self.log.info("AWS Account Clamp: AOK!")
75
99
 
76
100
 
@@ -0,0 +1,58 @@
1
+
2
+ # Welcome to your CDK Python project!
3
+
4
+ This is a blank project for CDK development with Python.
5
+
6
+ The `cdk.json` file tells the CDK Toolkit how to execute your app.
7
+
8
+ This project is set up like a standard Python project. The initialization
9
+ process also creates a virtualenv within this project, stored under the `.venv`
10
+ directory. To create the virtualenv it assumes that there is a `python3`
11
+ (or `python` for Windows) executable in your path with access to the `venv`
12
+ package. If for any reason the automatic creation of the virtualenv fails,
13
+ you can create the virtualenv manually.
14
+
15
+ To manually create a virtualenv on MacOS and Linux:
16
+
17
+ ```
18
+ $ python3 -m venv .venv
19
+ ```
20
+
21
+ After the init process completes and the virtualenv is created, you can use the following
22
+ step to activate your virtualenv.
23
+
24
+ ```
25
+ $ source .venv/bin/activate
26
+ ```
27
+
28
+ If you are a Windows platform, you would activate the virtualenv like this:
29
+
30
+ ```
31
+ % .venv\Scripts\activate.bat
32
+ ```
33
+
34
+ Once the virtualenv is activated, you can install the required dependencies.
35
+
36
+ ```
37
+ $ pip install -r requirements.txt
38
+ ```
39
+
40
+ At this point you can now synthesize the CloudFormation template for this code.
41
+
42
+ ```
43
+ $ cdk synth
44
+ ```
45
+
46
+ To add additional dependencies, for example other CDK libraries, just add
47
+ them to your `setup.py` file and rerun the `pip install -r requirements.txt`
48
+ command.
49
+
50
+ ## Useful commands
51
+
52
+ * `cdk ls` list all stacks in the app
53
+ * `cdk synth` emits the synthesized CloudFormation template
54
+ * `cdk deploy` deploy this stack to your default AWS account/region
55
+ * `cdk diff` compare deployed stack with current state
56
+ * `cdk docs` open CDK documentation
57
+
58
+ Enjoy!
@@ -0,0 +1,64 @@
1
+ import boto3
2
+ import aws_cdk as cdk
3
+ from aws_cdk import Fn
4
+ from workbench_compute.workbench_compute_stack import WorkbenchComputeStack, WorkbenchComputeStackProps
5
+
6
+ # Initialize Workbench ConfigManager
7
+ try:
8
+ from workbench.utils.config_manager import ConfigManager
9
+
10
+ cm = ConfigManager()
11
+ except ImportError:
12
+ print("Workbench Configuration Manager Not Found...")
13
+ print("Set the WORKBENCH_CONFIG Env var and run again...")
14
+ raise SystemExit(1)
15
+
16
+ # Grab the account and region using boto3
17
+ session = boto3.session.Session()
18
+ aws_account = session.client("sts").get_caller_identity().get("Account")
19
+ aws_region = session.region_name
20
+ print(f"Account: {aws_account}")
21
+ print(f"Region: {aws_region}")
22
+
23
+ # Get configurations needed for compute stack
24
+ workbench_bucket = cm.get_config("WORKBENCH_BUCKET")
25
+ if not workbench_bucket:
26
+ print("Error: WORKBENCH_BUCKET is required but not found in config.")
27
+ exit(1)
28
+
29
+
30
+ # Get the Batch and Lambda Roles from WorkbenchCore stack outputs
31
+ batch_role_arn = Fn.import_value("WorkbenchCore-BatchRoleArn")
32
+ lambda_role_arn = Fn.import_value("WorkbenchCore-LambdaRoleArn")
33
+
34
+ # VPC and subnet configuration (optional)
35
+ existing_vpc_id = cm.get_config("WORKBENCH_VPC_ID")
36
+ subnet_ids = cm.get_config("WORKBENCH_SUBNET_IDS") or []
37
+
38
+ # Log the configuration for transparency
39
+ print("Configuration:")
40
+ print(f" WORKBENCH_BUCKET: {workbench_bucket}")
41
+ print(f" WORKBENCH_BATCH_ROLE_ARN: {batch_role_arn}")
42
+ print(f" WORKBENCH_LAMBDA_ROLE_ARN: {lambda_role_arn}")
43
+ print(f" WORKBENCH_VPC_ID: {existing_vpc_id}")
44
+ print(f" WORKBENCH_SUBNET_IDS: {subnet_ids}")
45
+
46
+ # Our CDK App and Environment
47
+ app = cdk.App()
48
+ env = cdk.Environment(account=aws_account, region=aws_region)
49
+
50
+ # Create the Workbench Compute Stack
51
+ compute_stack = WorkbenchComputeStack(
52
+ app,
53
+ "WorkbenchCompute",
54
+ env=env,
55
+ props=WorkbenchComputeStackProps(
56
+ workbench_bucket=workbench_bucket,
57
+ batch_role_arn=batch_role_arn,
58
+ lambda_role_arn=lambda_role_arn,
59
+ existing_vpc_id=existing_vpc_id,
60
+ subnet_ids=subnet_ids,
61
+ ),
62
+ )
63
+
64
+ app.synth()
@@ -0,0 +1,97 @@
1
+ {
2
+ "app": "python3 app.py",
3
+ "watch": {
4
+ "include": [
5
+ "**"
6
+ ],
7
+ "exclude": [
8
+ "README.md",
9
+ "cdk*.json",
10
+ "requirements*.txt",
11
+ "source.bat",
12
+ "**/__init__.py",
13
+ "**/__pycache__",
14
+ "tests"
15
+ ]
16
+ },
17
+ "context": {
18
+ "@aws-cdk/aws-lambda:recognizeLayerVersion": true,
19
+ "@aws-cdk/core:checkSecretUsage": true,
20
+ "@aws-cdk/core:target-partitions": [
21
+ "aws",
22
+ "aws-cn"
23
+ ],
24
+ "@aws-cdk-containers/ecs-service-extensions:enableDefaultLogDriver": true,
25
+ "@aws-cdk/aws-ec2:uniqueImdsv2TemplateName": true,
26
+ "@aws-cdk/aws-ecs:arnFormatIncludesClusterName": true,
27
+ "@aws-cdk/aws-iam:minimizePolicies": true,
28
+ "@aws-cdk/core:validateSnapshotRemovalPolicy": true,
29
+ "@aws-cdk/aws-codepipeline:crossAccountKeyAliasStackSafeResourceName": true,
30
+ "@aws-cdk/aws-s3:createDefaultLoggingPolicy": true,
31
+ "@aws-cdk/aws-sns-subscriptions:restrictSqsDescryption": true,
32
+ "@aws-cdk/aws-apigateway:disableCloudWatchRole": true,
33
+ "@aws-cdk/core:enablePartitionLiterals": true,
34
+ "@aws-cdk/aws-events:eventsTargetQueueSameAccount": true,
35
+ "@aws-cdk/aws-ecs:disableExplicitDeploymentControllerForCircuitBreaker": true,
36
+ "@aws-cdk/aws-iam:importedRoleStackSafeDefaultPolicyName": true,
37
+ "@aws-cdk/aws-s3:serverAccessLogsUseBucketPolicy": true,
38
+ "@aws-cdk/aws-route53-patters:useCertificate": true,
39
+ "@aws-cdk/customresources:installLatestAwsSdkDefault": false,
40
+ "@aws-cdk/aws-rds:databaseProxyUniqueResourceName": true,
41
+ "@aws-cdk/aws-codedeploy:removeAlarmsFromDeploymentGroup": true,
42
+ "@aws-cdk/aws-apigateway:authorizerChangeDeploymentLogicalId": true,
43
+ "@aws-cdk/aws-ec2:launchTemplateDefaultUserData": true,
44
+ "@aws-cdk/aws-secretsmanager:useAttachedSecretResourcePolicyForSecretTargetAttachments": true,
45
+ "@aws-cdk/aws-redshift:columnId": true,
46
+ "@aws-cdk/aws-stepfunctions-tasks:enableEmrServicePolicyV2": true,
47
+ "@aws-cdk/aws-ec2:restrictDefaultSecurityGroup": true,
48
+ "@aws-cdk/aws-apigateway:requestValidatorUniqueId": true,
49
+ "@aws-cdk/aws-kms:aliasNameRef": true,
50
+ "@aws-cdk/aws-kms:applyImportedAliasPermissionsToPrincipal": true,
51
+ "@aws-cdk/aws-autoscaling:generateLaunchTemplateInsteadOfLaunchConfig": true,
52
+ "@aws-cdk/core:includePrefixInUniqueNameGeneration": true,
53
+ "@aws-cdk/aws-efs:denyAnonymousAccess": true,
54
+ "@aws-cdk/aws-opensearchservice:enableOpensearchMultiAzWithStandby": true,
55
+ "@aws-cdk/aws-lambda-nodejs:useLatestRuntimeVersion": true,
56
+ "@aws-cdk/aws-efs:mountTargetOrderInsensitiveLogicalId": true,
57
+ "@aws-cdk/aws-rds:auroraClusterChangeScopeOfInstanceParameterGroupWithEachParameters": true,
58
+ "@aws-cdk/aws-appsync:useArnForSourceApiAssociationIdentifier": true,
59
+ "@aws-cdk/aws-rds:preventRenderingDeprecatedCredentials": true,
60
+ "@aws-cdk/aws-codepipeline-actions:useNewDefaultBranchForCodeCommitSource": true,
61
+ "@aws-cdk/aws-cloudwatch-actions:changeLambdaPermissionLogicalIdForLambdaAction": true,
62
+ "@aws-cdk/aws-codepipeline:crossAccountKeysDefaultValueToFalse": true,
63
+ "@aws-cdk/aws-codepipeline:defaultPipelineTypeToV2": true,
64
+ "@aws-cdk/aws-kms:reduceCrossAccountRegionPolicyScope": true,
65
+ "@aws-cdk/aws-eks:nodegroupNameAttribute": true,
66
+ "@aws-cdk/aws-ec2:ebsDefaultGp3Volume": true,
67
+ "@aws-cdk/aws-ecs:removeDefaultDeploymentAlarm": true,
68
+ "@aws-cdk/custom-resources:logApiResponseDataPropertyTrueDefault": false,
69
+ "@aws-cdk/aws-s3:keepNotificationInImportedBucket": false,
70
+ "@aws-cdk/core:explicitStackTags": true,
71
+ "@aws-cdk/aws-ecs:enableImdsBlockingDeprecatedFeature": false,
72
+ "@aws-cdk/aws-ecs:disableEcsImdsBlocking": true,
73
+ "@aws-cdk/aws-ecs:reduceEc2FargateCloudWatchPermissions": true,
74
+ "@aws-cdk/aws-dynamodb:resourcePolicyPerReplica": true,
75
+ "@aws-cdk/aws-ec2:ec2SumTImeoutEnabled": true,
76
+ "@aws-cdk/aws-appsync:appSyncGraphQLAPIScopeLambdaPermission": true,
77
+ "@aws-cdk/aws-rds:setCorrectValueForDatabaseInstanceReadReplicaInstanceResourceId": true,
78
+ "@aws-cdk/core:cfnIncludeRejectComplexResourceUpdateCreatePolicyIntrinsics": true,
79
+ "@aws-cdk/aws-lambda-nodejs:sdkV3ExcludeSmithyPackages": true,
80
+ "@aws-cdk/aws-stepfunctions-tasks:fixRunEcsTaskPolicy": true,
81
+ "@aws-cdk/aws-ec2:bastionHostUseAmazonLinux2023ByDefault": true,
82
+ "@aws-cdk/aws-route53-targets:userPoolDomainNameMethodWithoutCustomResource": true,
83
+ "@aws-cdk/aws-elasticloadbalancingV2:albDualstackWithoutPublicIpv4SecurityGroupRulesDefault": true,
84
+ "@aws-cdk/aws-iam:oidcRejectUnauthorizedConnections": true,
85
+ "@aws-cdk/core:enableAdditionalMetadataCollection": true,
86
+ "@aws-cdk/aws-lambda:createNewPoliciesWithAddToRolePolicy": false,
87
+ "@aws-cdk/aws-s3:setUniqueReplicationRoleName": true,
88
+ "@aws-cdk/aws-events:requireEventBusPolicySid": true,
89
+ "@aws-cdk/core:aspectPrioritiesMutating": true,
90
+ "@aws-cdk/aws-dynamodb:retainTableReplica": true,
91
+ "@aws-cdk/aws-stepfunctions:useDistributedMapResultWriterV2": true,
92
+ "@aws-cdk/s3-notifications:addS3TrustKeyPolicyForSnsSubscriptions": true,
93
+ "@aws-cdk/aws-ec2:requirePrivateSubnetsForEgressOnlyInternetGateway": true,
94
+ "@aws-cdk/aws-s3:publicAccessBlockedByDefault": true,
95
+ "@aws-cdk/aws-lambda:useCdkManagedLogGroup": true
96
+ }
97
+ }
@@ -1,3 +1,2 @@
1
- aws-cdk-lib>=2.77.0
1
+ aws-cdk-lib==2.211.0
2
2
  constructs>=10.0.0,<11.0.0
3
- boto3
@@ -0,0 +1,17 @@
1
+ import aws_cdk as core
2
+ import aws_cdk.assertions as assertions
3
+
4
+ from workbench_compute.workbench_compute_stack import WorkbenchComputeStack
5
+
6
+
7
+ # example tests. To run these tests, uncomment this file along with the example
8
+ # resource in workbench_compute/workbench_compute_stack.py
9
+ def test_sqs_queue_created():
10
+ app = core.App()
11
+ stack = WorkbenchComputeStack(app, "workbench-compute")
12
+ template = assertions.Template.from_stack(stack)
13
+
14
+
15
+ # template.has_resource_properties("AWS::SQS::Queue", {
16
+ # "VisibilityTimeout": 300
17
+ # })
@@ -0,0 +1,279 @@
1
+ from aws_cdk import (
2
+ Environment,
3
+ Stack,
4
+ aws_iam as iam,
5
+ aws_ec2 as ec2,
6
+ aws_ecs as ecs,
7
+ aws_ecr as ecr,
8
+ aws_batch as batch,
9
+ aws_sqs as sqs,
10
+ aws_lambda as lambda_,
11
+ aws_lambda_event_sources as lambda_events,
12
+ aws_logs as logs,
13
+ Duration,
14
+ Size,
15
+ )
16
+ from constructs import Construct
17
+ from typing import Any, List, Dict
18
+ from dataclasses import dataclass, field
19
+ from textwrap import dedent
20
+
21
+
22
+ @dataclass
23
+ class WorkbenchComputeStackProps:
24
+ workbench_bucket: str
25
+ batch_role_arn: str
26
+ lambda_role_arn: str
27
+ existing_vpc_id: str = None
28
+ subnet_ids: List[str] = field(default_factory=list) # Optional subnets ids for the Batch compute environment
29
+
30
+
31
+ class WorkbenchComputeStack(Stack):
32
+ def __init__(
33
+ self,
34
+ scope: Construct,
35
+ construct_id: str,
36
+ env: Environment,
37
+ props: WorkbenchComputeStackProps,
38
+ **kwargs: Any,
39
+ ) -> None:
40
+ desc = "Workbench Compute: Defines the compute infrastructure for Workbench including Batch resources."
41
+ super().__init__(scope, construct_id, env=env, description=desc, **kwargs)
42
+
43
+ # Print the environment details
44
+ print("Environment")
45
+ print(env)
46
+
47
+ # Grab our properties
48
+ self.workbench_bucket = props.workbench_bucket
49
+ self.batch_role_arn = props.batch_role_arn
50
+ self.existing_vpc_id = props.existing_vpc_id
51
+ self.subnet_ids = props.subnet_ids
52
+
53
+ # Import the Batch role
54
+ self.workbench_batch_role = iam.Role.from_role_arn(self, "ImportedBatchRole", self.batch_role_arn)
55
+
56
+ # Import the Lambda role
57
+ self.workbench_lambda_role = iam.Role.from_role_arn(self, "ImportedLambdaRole", props.lambda_role_arn)
58
+
59
+ # Create Batch resources first (Lambda will reference them)
60
+ self.batch_compute_environment = self.create_batch_compute_environment()
61
+ self.batch_job_queue = self.create_batch_job_queue()
62
+ self.batch_job_definitions = self.create_batch_job_definitions()
63
+
64
+ # Create ML Pipeline SQS Queue and Lambda (after Batch resources)
65
+ self.ml_pipeline_queue = self.create_ml_pipeline_queue()
66
+ self.batch_trigger_lambda = self.create_batch_trigger_lambda()
67
+
68
+ #####################
69
+ # Batch Compute #
70
+ #####################
71
+ def create_batch_compute_environment(self) -> batch.FargateComputeEnvironment:
72
+ """Create the Batch compute environment with Fargate."""
73
+
74
+ # Check if we have an existing VPC to use
75
+ if self.existing_vpc_id:
76
+ vpc = ec2.Vpc.from_lookup(self, "ImportedVPC", vpc_id=self.existing_vpc_id)
77
+ vpc_subnets = None
78
+
79
+ # Use specific subnets if provided
80
+ if self.subnet_ids:
81
+ vpc_subnets = ec2.SubnetSelection(
82
+ subnets=[
83
+ ec2.Subnet.from_subnet_id(self, f"BatchSubnet{i}", subnet_id)
84
+ for i, subnet_id in enumerate(self.subnet_ids)
85
+ ]
86
+ )
87
+ else:
88
+ raise ValueError(
89
+ 'Please provide the Workbench Config entry: "WORKBENCH_VPC_ID":"vpc-123456789abcdef0". '
90
+ "Default VPC networks cannot pull ECR images for Batch jobs."
91
+ )
92
+
93
+ return batch.FargateComputeEnvironment(
94
+ self,
95
+ "WorkbenchBatchComputeEnvironment",
96
+ compute_environment_name="workbench-compute-env",
97
+ vpc=vpc,
98
+ vpc_subnets=vpc_subnets,
99
+ maxv_cpus=16, # Limit to 16 vCPU to minimize AWS Throttling issues
100
+ )
101
+
102
+ def create_batch_job_queue(self) -> batch.JobQueue:
103
+ """Create the Batch job queue."""
104
+ return batch.JobQueue(
105
+ self,
106
+ "WorkbenchBatchJobQueue",
107
+ job_queue_name="workbench-job-queue",
108
+ compute_environments=[
109
+ batch.OrderedComputeEnvironment(compute_environment=self.batch_compute_environment, order=1)
110
+ ],
111
+ )
112
+
113
+ def create_batch_job_definitions(self) -> Dict[str, batch.EcsJobDefinition]:
114
+ """Create ML pipeline job definitions in small/medium/large tiers."""
115
+
116
+ # Using ECR image for ML pipelines
117
+ ecr_image = ecs.ContainerImage.from_ecr_repository(
118
+ repository=ecr.Repository.from_repository_arn(
119
+ self,
120
+ "MLPipelineRepo",
121
+ repository_arn=f"arn:aws:ecr:{self.region}:507740646243:repository/aws-ml-images/py312-ml-pipelines",
122
+ ),
123
+ tag="0.2",
124
+ )
125
+
126
+ # Job Definition Tiers
127
+ tiers = {
128
+ "small": (2, 4096), # 2 vCPU, 4GB RAM
129
+ "medium": (4, 8192), # 4 vCPU, 8GB RAM
130
+ "large": (8, 16384), # 8 vCPU, 16GB RAM
131
+ }
132
+
133
+ job_definitions = {}
134
+ for size, (cpu, memory_mib) in tiers.items():
135
+ job_definitions[size] = batch.EcsJobDefinition(
136
+ self,
137
+ f"JobDef{size.capitalize()}",
138
+ job_definition_name=f"workbench-batch-{size}",
139
+ container=batch.EcsFargateContainerDefinition(
140
+ self,
141
+ f"Container{size.capitalize()}",
142
+ cpu=cpu,
143
+ memory=Size.mebibytes(memory_mib),
144
+ image=ecr_image,
145
+ job_role=self.workbench_batch_role,
146
+ execution_role=self.workbench_batch_role,
147
+ environment={
148
+ "WORKBENCH_BUCKET": self.workbench_bucket,
149
+ "PYTHONUNBUFFERED": "1",
150
+ },
151
+ ),
152
+ timeout=Duration.hours(3),
153
+ )
154
+ return job_definitions
155
+
156
+ ###########################
157
+ # ML Pipeline SQS Queue #
158
+ ###########################
159
+ def create_ml_pipeline_queue(self) -> sqs.Queue:
160
+ """Create SQS FIFO queue for ML pipeline orchestration with deduplication."""
161
+
162
+ # Dead letter queue for failed messages (also FIFO)
163
+ dlq = sqs.Queue(
164
+ self,
165
+ "MLPipelineDLQ",
166
+ queue_name="workbench-ml-pipeline-dlq.fifo", # Must end with .fifo
167
+ fifo=True,
168
+ retention_period=Duration.days(14),
169
+ )
170
+
171
+ # Main FIFO queue with deduplication
172
+ return sqs.Queue(
173
+ self,
174
+ "MLPipelineQueue",
175
+ queue_name="workbench-ml-pipeline-queue.fifo", # Must end with .fifo
176
+ fifo=True,
177
+ content_based_deduplication=True, # Auto-dedupe based on message content
178
+ visibility_timeout=Duration.minutes(15),
179
+ retention_period=Duration.days(1),
180
+ dead_letter_queue=sqs.DeadLetterQueue(max_receive_count=1, queue=dlq),
181
+ )
182
+
183
+ def create_batch_trigger_lambda(self) -> lambda_.Function:
184
+ """Create Lambda function to process SQS messages and trigger Batch jobs."""
185
+
186
+ # Create a mapping of job definition names to pass to Lambda
187
+ job_def_names = {size: f"workbench-batch-{size}" for size in ["small", "medium", "large"]}
188
+
189
+ batch_trigger_lambda = lambda_.Function(
190
+ self,
191
+ "BatchTriggerLambda",
192
+ function_name="workbench-batch-trigger",
193
+ runtime=lambda_.Runtime.PYTHON_3_12,
194
+ handler="index.lambda_handler",
195
+ code=lambda_.Code.from_inline(self._get_lambda_code()),
196
+ timeout=Duration.minutes(5),
197
+ log_retention=logs.RetentionDays.ONE_WEEK,
198
+ environment={
199
+ "WORKBENCH_BUCKET": self.workbench_bucket,
200
+ "JOB_QUEUE": self.batch_job_queue.job_queue_name,
201
+ "JOB_DEF_SMALL": job_def_names["small"],
202
+ "JOB_DEF_MEDIUM": job_def_names["medium"],
203
+ "JOB_DEF_LARGE": job_def_names["large"],
204
+ },
205
+ role=self.workbench_lambda_role,
206
+ )
207
+
208
+ # Connect SQS to Lambda
209
+ batch_trigger_lambda.add_event_source(
210
+ lambda_events.SqsEventSource(
211
+ self.ml_pipeline_queue, batch_size=1 # One message at a time for precise error handling
212
+ )
213
+ )
214
+ return batch_trigger_lambda
215
+
216
+ @staticmethod
217
+ def _get_lambda_code() -> str:
218
+ """Return the Lambda function code as a string."""
219
+ return dedent(
220
+ '''
221
+ import json
222
+ import boto3
223
+ import os
224
+ from datetime import datetime
225
+ from pathlib import Path
226
+
227
+ batch = boto3.client('batch')
228
+ s3 = boto3.client('s3')
229
+
230
+ WORKBENCH_BUCKET = os.environ['WORKBENCH_BUCKET']
231
+ JOB_QUEUE = os.environ['JOB_QUEUE']
232
+ JOB_DEFINITIONS = {
233
+ 'small': os.environ['JOB_DEF_SMALL'],
234
+ 'medium': os.environ['JOB_DEF_MEDIUM'],
235
+ 'large': os.environ['JOB_DEF_LARGE'],
236
+ }
237
+
238
+ def lambda_handler(event, context):
239
+ """Process SQS messages and submit Batch jobs."""
240
+
241
+ for record in event['Records']:
242
+ try:
243
+ message = json.loads(record['body'])
244
+ script_path = message['script_path'] # s3://bucket/path/to/script.py
245
+ size = message.get('size', 'small')
246
+ extra_env = message.get('environment', {})
247
+
248
+ script_name = Path(script_path).stem
249
+ job_name = f"workbench_{script_name}_{datetime.now():%Y%m%d_%H%M%S}"
250
+
251
+ # Get job definition name from environment variables
252
+ job_def_name = JOB_DEFINITIONS.get(size, JOB_DEFINITIONS['small'])
253
+
254
+ # Build environment variables
255
+ env_vars = [
256
+ {'name': 'ML_PIPELINE_S3_PATH', 'value': script_path},
257
+ {'name': 'WORKBENCH_BUCKET', 'value': WORKBENCH_BUCKET},
258
+ *[{'name': k, 'value': v} for k, v in extra_env.items()]
259
+ ]
260
+
261
+ # Submit Batch job to the queue
262
+ response = batch.submit_job(
263
+ jobName=job_name,
264
+ jobQueue=JOB_QUEUE,
265
+ jobDefinition=job_def_name,
266
+ containerOverrides={
267
+ 'environment': env_vars
268
+ }
269
+ )
270
+
271
+ print(f"Submitted job: {job_name} ({response['jobId']})")
272
+
273
+ except Exception as e:
274
+ print(f"Error processing message: {e}")
275
+ raise # Let SQS retry via DLQ
276
+
277
+ return {'statusCode': 200}
278
+ '''
279
+ ).strip()