workbench 0.8.182__py3-none-any.whl → 0.8.183__py3-none-any.whl

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Files changed (8) hide show
  1. workbench/model_scripts/custom_models/proximity/generated_model_script.py +5 -7
  2. workbench/scripts/ml_pipeline_sqs.py +14 -4
  3. {workbench-0.8.182.dist-info → workbench-0.8.183.dist-info}/METADATA +1 -1
  4. {workbench-0.8.182.dist-info → workbench-0.8.183.dist-info}/RECORD +8 -8
  5. {workbench-0.8.182.dist-info → workbench-0.8.183.dist-info}/WHEEL +0 -0
  6. {workbench-0.8.182.dist-info → workbench-0.8.183.dist-info}/entry_points.txt +0 -0
  7. {workbench-0.8.182.dist-info → workbench-0.8.183.dist-info}/licenses/LICENSE +0 -0
  8. {workbench-0.8.182.dist-info → workbench-0.8.183.dist-info}/top_level.txt +0 -0
workbench/model_scripts/custom_models/proximity/generated_model_script.py CHANGED
@@ -6,9 +6,9 @@
6
6
  # Template Placeholders
7
7
  TEMPLATE_PARAMS = {
8
8
  "id_column": "udm_mol_bat_id",
9
- "features": ['bcut2d_logplow', 'numradicalelectrons', 'smr_vsa5', 'fr_lactam', 'fr_morpholine', 'fr_aldehyde', 'slogp_vsa1', 'fr_amidine', 'bpol', 'fr_ester', 'fr_azo', 'kappa3', 'peoe_vsa5', 'fr_ketone_topliss', 'vsa_estate9', 'estate_vsa9', 'bcut2d_mrhi', 'fr_ndealkylation1', 'numrotatablebonds', 'minestateindex', 'fr_quatn', 'peoe_vsa3', 'fr_epoxide', 'fr_aniline', 'minpartialcharge', 'fr_nitroso', 'fpdensitymorgan2', 'fr_oxime', 'fr_sulfone', 'smr_vsa1', 'kappa1', 'fr_pyridine', 'numaromaticrings', 'vsa_estate6', 'molmr', 'estate_vsa1', 'fr_dihydropyridine', 'vsa_estate10', 'fr_alkyl_halide', 'chi2n', 'fr_thiocyan', 'fpdensitymorgan1', 'fr_unbrch_alkane', 'slogp_vsa9', 'chi4n', 'fr_nitro_arom', 'fr_al_oh', 'fr_furan', 'fr_c_s', 'peoe_vsa8', 'peoe_vsa14', 'numheteroatoms', 'fr_ndealkylation2', 'maxabspartialcharge', 'vsa_estate2', 'peoe_vsa7', 'apol', 'numhacceptors', 'fr_tetrazole', 'vsa_estate1', 'peoe_vsa9', 'naromatom', 'bcut2d_chghi', 'fr_sh', 'fr_halogen', 'slogp_vsa4', 'fr_benzodiazepine', 'molwt', 'fr_isocyan', 'fr_prisulfonamd', 'maxabsestateindex', 'minabsestateindex', 'peoe_vsa11', 'slogp_vsa12', 'estate_vsa5', 'numaliphaticcarbocycles', 'bcut2d_mwlow', 'slogp_vsa7', 'fr_allylic_oxid', 'fr_methoxy', 'fr_nh0', 'fr_coo2', 'fr_phenol', 'nacid', 'nbase', 'chi3v', 'fr_ar_nh', 'fr_nitrile', 'fr_imidazole', 'fr_urea', 'bcut2d_mrlow', 'chi1', 'smr_vsa6', 'fr_aryl_methyl', 'narombond', 'fr_alkyl_carbamate', 'fr_piperzine', 'exactmolwt', 'qed', 'chi0n', 'fr_sulfonamd', 'fr_thiazole', 'numvalenceelectrons', 'fr_phos_acid', 'peoe_vsa12', 'fr_nh1', 'fr_hdrzine', 'fr_c_o_nocoo', 'fr_lactone', 'estate_vsa6', 'bcut2d_logphi', 'vsa_estate7', 'peoe_vsa13', 'numsaturatedcarbocycles', 'fr_nitro', 'fr_phenol_noorthohbond', 'rotratio', 'fr_barbitur', 'fr_isothiocyan', 'balabanj', 'fr_arn', 'fr_imine', 'maxpartialcharge', 'fr_sulfide', 'slogp_vsa11', 'fr_hoccn', 'fr_n_o', 'peoe_vsa1', 'slogp_vsa6', 'heavyatommolwt', 'fractioncsp3', 'estate_vsa8', 'peoe_vsa10', 'numaliphaticrings', 'fr_thiophene', 'maxestateindex', 'smr_vsa10', 'labuteasa', 'smr_vsa2', 'fpdensitymorgan3', 'smr_vsa9', 'slogp_vsa10', 'numaromaticheterocycles', 'fr_nh2', 'fr_diazo', 'chi3n', 'fr_ar_coo', 'slogp_vsa5', 'fr_bicyclic', 'fr_amide', 'estate_vsa10', 'fr_guanido', 'chi1n', 'numsaturatedrings', 'fr_piperdine', 'fr_term_acetylene', 'estate_vsa4', 'slogp_vsa3', 'fr_coo', 'fr_ether', 'estate_vsa7', 'bcut2d_chglo', 'fr_oxazole', 'peoe_vsa6', 'hallkieralpha', 'peoe_vsa2', 'chi2v', 'nocount', 'vsa_estate5', 'fr_nhpyrrole', 'fr_al_coo', 'bertzct', 'estate_vsa11', 'minabspartialcharge', 'slogp_vsa8', 'fr_imide', 'kappa2', 'numaliphaticheterocycles', 'numsaturatedheterocycles', 'fr_hdrzone', 'smr_vsa4', 'fr_ar_n', 'nrot', 'smr_vsa8', 'slogp_vsa2', 'chi4v', 'fr_phos_ester', 'fr_para_hydroxylation', 'smr_vsa3', 'nhohcount', 'estate_vsa2', 'mollogp', 'tpsa', 'fr_azide', 'peoe_vsa4', 'numhdonors', 'fr_al_oh_notert', 'fr_c_o', 'chi0', 'fr_nitro_arom_nonortho', 'vsa_estate3', 'fr_benzene', 'fr_ketone', 'vsa_estate8', 'smr_vsa7', 'fr_ar_oh', 'fr_priamide', 'ringcount', 'estate_vsa3', 'numaromaticcarbocycles', 'bcut2d_mwhi', 'chi1v', 'heavyatomcount', 'vsa_estate4', 'chi0v'],
10
- "target": "udm_asy_res_value",
11
- "track_columns": None
9
+ "features": ['chi2v', 'fr_sulfone', 'chi1v', 'bcut2d_logplow', 'fr_piperzine', 'kappa3', 'smr_vsa1', 'slogp_vsa5', 'fr_ketone_topliss', 'fr_sulfonamd', 'fr_imine', 'fr_benzene', 'fr_ester', 'chi2n', 'labuteasa', 'peoe_vsa2', 'smr_vsa6', 'bcut2d_chglo', 'fr_sh', 'peoe_vsa1', 'fr_allylic_oxid', 'chi4n', 'fr_ar_oh', 'fr_nh0', 'fr_term_acetylene', 'slogp_vsa7', 'slogp_vsa4', 'estate_vsa1', 'vsa_estate4', 'numbridgeheadatoms', 'numheterocycles', 'fr_ketone', 'fr_morpholine', 'fr_guanido', 'estate_vsa2', 'numheteroatoms', 'fr_nitro_arom_nonortho', 'fr_piperdine', 'nocount', 'numspiroatoms', 'fr_aniline', 'fr_thiophene', 'slogp_vsa10', 'fr_amide', 'slogp_vsa2', 'fr_epoxide', 'vsa_estate7', 'fr_ar_coo', 'fr_imidazole', 'fr_nitrile', 'fr_oxazole', 'numsaturatedrings', 'fr_pyridine', 'fr_hoccn', 'fr_ndealkylation1', 'numaliphaticheterocycles', 'fr_phenol', 'maxpartialcharge', 'vsa_estate5', 'peoe_vsa13', 'minpartialcharge', 'qed', 'fr_al_oh', 'slogp_vsa11', 'chi0n', 'fr_bicyclic', 'peoe_vsa12', 'fpdensitymorgan1', 'fr_oxime', 'molwt', 'fr_dihydropyridine', 'smr_vsa5', 'peoe_vsa5', 'fr_nitro', 'hallkieralpha', 'heavyatommolwt', 'fr_alkyl_halide', 'peoe_vsa8', 'fr_nhpyrrole', 'fr_isocyan', 'bcut2d_chghi', 'fr_lactam', 'peoe_vsa11', 'smr_vsa9', 'tpsa', 'chi4v', 'slogp_vsa1', 'phi', 'bcut2d_logphi', 'avgipc', 'estate_vsa11', 'fr_coo', 'bcut2d_mwhi', 'numunspecifiedatomstereocenters', 'vsa_estate10', 'estate_vsa8', 'numvalenceelectrons', 'fr_nh2', 'fr_lactone', 'vsa_estate1', 'estate_vsa4', 'numatomstereocenters', 'vsa_estate8', 'fr_para_hydroxylation', 'peoe_vsa3', 'fr_thiazole', 'peoe_vsa10', 'fr_ndealkylation2', 'slogp_vsa12', 'peoe_vsa9', 'maxestateindex', 'fr_quatn', 'smr_vsa7', 'minestateindex', 'numaromaticheterocycles', 'numrotatablebonds', 'fr_ar_nh', 'fr_ether', 'exactmolwt', 'fr_phenol_noorthohbond', 'slogp_vsa3', 'fr_ar_n', 'sps', 'fr_c_o_nocoo', 'bertzct', 'peoe_vsa7', 'slogp_vsa8', 'numradicalelectrons', 'molmr', 'fr_tetrazole', 'numsaturatedcarbocycles', 'bcut2d_mrhi', 'kappa1', 'numamidebonds', 'fpdensitymorgan2', 'smr_vsa8', 'chi1n', 'estate_vsa6', 'fr_barbitur', 'fr_diazo', 'kappa2', 'chi0', 'bcut2d_mrlow', 'balabanj', 'peoe_vsa4', 'numhacceptors', 'fr_sulfide', 'chi3n', 'smr_vsa2', 'fr_al_oh_notert', 'fr_benzodiazepine', 'fr_phos_ester', 'fr_aldehyde', 'fr_coo2', 'estate_vsa5', 'fr_prisulfonamd', 'numaromaticcarbocycles', 'fr_unbrch_alkane', 'fr_urea', 'fr_nitroso', 'smr_vsa10', 'fr_c_s', 'smr_vsa3', 'fr_methoxy', 'maxabspartialcharge', 'slogp_vsa9', 'heavyatomcount', 'fr_azide', 'chi3v', 'smr_vsa4', 'mollogp', 'chi0v', 'fr_aryl_methyl', 'fr_nh1', 'fpdensitymorgan3', 'fr_furan', 'fr_hdrzine', 'fr_arn', 'numaromaticrings', 'vsa_estate3', 'fr_azo', 'fr_halogen', 'estate_vsa9', 'fr_hdrzone', 'numhdonors', 'fr_alkyl_carbamate', 'fr_isothiocyan', 'minabspartialcharge', 'fr_al_coo', 'ringcount', 'chi1', 'estate_vsa7', 'fr_nitro_arom', 'vsa_estate9', 'minabsestateindex', 'maxabsestateindex', 'vsa_estate6', 'estate_vsa10', 'estate_vsa3', 'fr_n_o', 'fr_amidine', 'fr_thiocyan', 'fr_phos_acid', 'fr_c_o', 'fr_imide', 'numaliphaticrings', 'peoe_vsa6', 'vsa_estate2', 'nhohcount', 'numsaturatedheterocycles', 'slogp_vsa6', 'peoe_vsa14', 'fractioncsp3', 'bcut2d_mwlow', 'numaliphaticcarbocycles', 'fr_priamide', 'nacid', 'nbase', 'naromatom', 'narombond', 'sz', 'sm', 'sv', 'sse', 'spe', 'sare', 'sp', 'si', 'mz', 'mm', 'mv', 'mse', 'mpe', 'mare', 'mp', 'mi', 'xch_3d', 'xch_4d', 'xch_5d', 'xch_6d', 'xch_7d', 'xch_3dv', 'xch_4dv', 'xch_5dv', 'xch_6dv', 'xch_7dv', 'xc_3d', 'xc_4d', 'xc_5d', 'xc_6d', 'xc_3dv', 'xc_4dv', 'xc_5dv', 'xc_6dv', 'xpc_4d', 'xpc_5d', 'xpc_6d', 'xpc_4dv', 'xpc_5dv', 'xpc_6dv', 'xp_0d', 'xp_1d', 'xp_2d', 'xp_3d', 'xp_4d', 'xp_5d', 'xp_6d', 'xp_7d', 'axp_0d', 'axp_1d', 'axp_2d', 'axp_3d', 'axp_4d', 'axp_5d', 'axp_6d', 'axp_7d', 'xp_0dv', 'xp_1dv', 'xp_2dv', 'xp_3dv', 'xp_4dv', 'xp_5dv', 'xp_6dv', 'xp_7dv', 'axp_0dv', 'axp_1dv', 'axp_2dv', 'axp_3dv', 'axp_4dv', 'axp_5dv', 'axp_6dv', 'axp_7dv', 'c1sp1', 'c2sp1', 'c1sp2', 'c2sp2', 'c3sp2', 'c1sp3', 'c2sp3', 'c3sp3', 'c4sp3', 'hybratio', 'fcsp3', 'num_stereocenters', 'num_unspecified_stereocenters', 'num_defined_stereocenters', 'num_r_centers', 'num_s_centers', 'num_stereobonds', 'num_e_bonds', 'num_z_bonds', 'stereo_complexity', 'frac_defined_stereo'],
10
+ "target": "udm_asy_res_free_percent",
11
+ "track_columns": None,
12
12
  }
13
13
 
14
14
  from io import StringIO
@@ -73,10 +73,7 @@ if __name__ == "__main__":
73
73
  args = parser.parse_args()
74
74
 
75
75
  # Load training data from the specified directory
76
- training_files = [
77
- os.path.join(args.train, file)
78
- for file in os.listdir(args.train) if file.endswith(".csv")
79
- ]
76
+ training_files = [os.path.join(args.train, file) for file in os.listdir(args.train) if file.endswith(".csv")]
80
77
  all_df = pd.concat([pd.read_csv(file, engine="python") for file in training_files])
81
78
 
82
79
  # Check if the DataFrame is empty
@@ -88,6 +85,7 @@ if __name__ == "__main__":
88
85
  # Now serialize the model
89
86
  model.serialize(args.model_dir)
90
87
 
88
+
91
89
  # Model loading and prediction functions
92
90
  def model_fn(model_dir):
93
91
 
workbench/scripts/ml_pipeline_sqs.py CHANGED
@@ -13,13 +13,14 @@ cm = ConfigManager()
13
13
  workbench_bucket = cm.get_config("WORKBENCH_BUCKET")
14
14
 
15
15
 
16
- def submit_to_sqs(script_path: str, size: str = "small", realtime: bool = False) -> None:
16
+ def submit_to_sqs(script_path: str, size: str = "small", realtime: bool = False, recreate: bool = False) -> None:
17
17
  """
18
18
  Upload script to S3 and submit message to SQS queue for processing.
19
19
  Args:
20
20
  script_path: Local path to the ML pipeline script
21
21
  size: Job size tier - "small" (default), "medium", or "large"
22
22
  realtime: If True, sets serverless=False for real-time processing (default: False, meaning serverless=True)
23
+ recreate: If True, sets RECREATE=True in environment (default: False)
23
24
  """
24
25
  print(f"\n{'=' * 60}")
25
26
  print("🚀 SUBMITTING ML PIPELINE JOB")
@@ -35,6 +36,7 @@ def submit_to_sqs(script_path: str, size: str = "small", realtime: bool = False)
35
36
  print(f"📄 Script: {script_file.name}")
36
37
  print(f"📏 Size tier: {size}")
37
38
  print(f"⚡ Mode: {'Real-time' if realtime else 'Serverless'} (serverless={'False' if realtime else 'True'})")
39
+ print(f"🔄 Recreate: {recreate}")
38
40
  print(f"🪣 Bucket: {workbench_bucket}")
39
41
  sqs = AWSAccountClamp().boto3_session.client("sqs")
40
42
  script_name = script_file.name
@@ -91,8 +93,10 @@ def submit_to_sqs(script_path: str, size: str = "small", realtime: bool = False)
91
93
  # Prepare message
92
94
  message = {"script_path": s3_path, "size": size}
93
95
 
94
- # Set serverless environment variable (defaults to True, False if --realtime)
96
+ # Set environment variables
95
97
  message["environment"] = {"SERVERLESS": "False" if realtime else "True"}
98
+ if recreate:
99
+ message["environment"]["RECREATE"] = "True"
96
100
 
97
101
  print("\n📨 Sending message to SQS...")
98
102
 
@@ -117,6 +121,7 @@ def submit_to_sqs(script_path: str, size: str = "small", realtime: bool = False)
117
121
  print(f"📄 Script: {script_name}")
118
122
  print(f"📏 Size: {size}")
119
123
  print(f"⚡ Mode: {'Real-time' if realtime else 'Serverless'} (SERVERLESS={'False' if realtime else 'True'})")
124
+ print(f"🔄 Recreate: {recreate}")
120
125
  print(f"🆔 Message ID: {message_id}")
121
126
  print("\n🔍 MONITORING LOCATIONS:")
122
127
  print(f" • SQS Queue: AWS Console → SQS → {queue_name}")
@@ -136,11 +141,16 @@ def main():
136
141
  parser.add_argument(
137
142
  "--realtime",
138
143
  action="store_true",
139
- help="Run in real-time mode (sets serverless=False). Default is serverless mode (serverless=True)",
144
+ help="Create realtime endpoints (default is serverless)",
145
+ )
146
+ parser.add_argument(
147
+ "--recreate",
148
+ action="store_true",
149
+ help="Set RECREATE=True (will force recreation of resources)",
140
150
  )
141
151
  args = parser.parse_args()
142
152
  try:
143
- submit_to_sqs(args.script_file, args.size, realtime=args.realtime)
153
+ submit_to_sqs(args.script_file, args.size, realtime=args.realtime, recreate=args.recreate)
144
154
  except Exception as e:
145
155
  print(f"\n❌ ERROR: {e}")
146
156
  log.error(f"Error: {e}")
{workbench-0.8.182.dist-info → workbench-0.8.183.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: workbench
3
- Version: 0.8.182
3
+ Version: 0.8.183
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
6
  License-Expression: MIT
{workbench-0.8.182.dist-info → workbench-0.8.183.dist-info}/RECORD RENAMED
@@ -133,7 +133,7 @@ workbench/model_scripts/custom_models/meta_endpoints/example.py,sha256=hzOAuLhIG
133
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  workbench/model_scripts/custom_models/network_security/Readme.md,sha256=Z2gtiu0hLHvEJ1x-_oFq3qJZcsK81sceBAGAGltpqQ8,222
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  workbench/model_scripts/custom_models/proximity/Readme.md,sha256=RlMFAJZgAT2mCgDk-UwR_R0Y_NbCqeI5-8DUsxsbpWQ,289
135
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  workbench/model_scripts/custom_models/proximity/feature_space_proximity.template,sha256=eOllmqB20BWtTiV53dgpIqXKtgSbPFDW_zf8PvM3oF0,4813
136
- workbench/model_scripts/custom_models/proximity/generated_model_script.py,sha256=RdbKbXtrSNYQJvB-oLcRHpJ6w0TM7zbmMfuocHb7GM0,7967
136
+ workbench/model_scripts/custom_models/proximity/generated_model_script.py,sha256=Zk170ztSM_rNSxgbY6ofb5NaqkEdQdhYg0UZprYqRyk,9056
137
137
  workbench/model_scripts/custom_models/proximity/proximity.py,sha256=zqmNlX70LnWXr5fdtFFQppSNTLjlOciQVrjGr-g9jRE,13716
138
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  workbench/model_scripts/custom_models/proximity/requirements.txt,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
139
139
  workbench/model_scripts/custom_models/uq_models/Readme.md,sha256=UVpL-lvtTrLqwBeQFinLhd_uNrEw4JUlggIdUSDrd-w,188
@@ -169,7 +169,7 @@ workbench/resources/signature_verify_pub.pem,sha256=V3-u-3_z2PH-805ybkKvzDOBwAbv
169
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  workbench/scripts/check_double_bond_stereo.py,sha256=p5hnL54Weq77ES0HCELq9JeoM-PyUGkvVSeWYF2dKyo,7776
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  workbench/scripts/glue_launcher.py,sha256=bIKQvfGxpAhzbeNvTnHfRW_5kQhY-169_868ZnCejJk,10692
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  workbench/scripts/ml_pipeline_batch.py,sha256=1T5JnLlUJR7bwAGBLHmLPOuj1xFRqVIQX8PsuDhHy8o,4907
172
- workbench/scripts/ml_pipeline_sqs.py,sha256=COewJcFYuv5Pa_l0q0PA4ZZb-AQ_7opKJP4JTEKBQ2c,5847
172
+ workbench/scripts/ml_pipeline_sqs.py,sha256=s1861q4zuvV-aSOhwy8xW1xid9yDVNGioDHxba80Qpg,6185
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  workbench/scripts/monitor_cloud_watch.py,sha256=s7MY4bsHts0nup9G0lWESCvgJZ9Mw1Eo-c8aKRgLjMw,9235
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  workbench/scripts/redis_expire.py,sha256=DxI_RKSNlrW2BsJZXcsSbaWGBgPZdPhtzHjV9SUtElE,1120
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  workbench/scripts/redis_report.py,sha256=iaJSuGPyLCs6e0TMcZDoT0YyJ43xJ1u74YD8FLnnUg4,990
@@ -287,9 +287,9 @@ workbench/web_interface/page_views/main_page.py,sha256=X4-KyGTKLAdxR-Zk2niuLJB2Y
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  workbench/web_interface/page_views/models_page_view.py,sha256=M0bdC7bAzLyIaE2jviY12FF4abdMFZmg6sFuOY_LaGI,2650
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  workbench/web_interface/page_views/page_view.py,sha256=Gh6YnpOGlUejx-bHZAf5pzqoQ1H1R0OSwOpGhOBO06w,455
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  workbench/web_interface/page_views/pipelines_page_view.py,sha256=v2pxrIbsHBcYiblfius3JK766NZ7ciD2yPx0t3E5IJo,2656
290
- workbench-0.8.182.dist-info/licenses/LICENSE,sha256=z4QMMPlLJkZjU8VOKqJkZiQZCEZ--saIU2Z8-p3aVc0,1080
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- workbench-0.8.182.dist-info/METADATA,sha256=mNhjFYFQS3MP33Z2CCAI2ydB_BPSpTxlvSAQiwTQdy8,9210
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- workbench-0.8.182.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- workbench-0.8.182.dist-info/entry_points.txt,sha256=zPFPruY9uayk8-wsKrhfnIyIB6jvZOW_ibyllEIsLWo,356
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- workbench-0.8.182.dist-info/top_level.txt,sha256=Dhy72zTxaA_o_yRkPZx5zw-fwumnjGaeGf0hBN3jc_w,10
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- workbench-0.8.182.dist-info/RECORD,,
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+ workbench-0.8.183.dist-info/licenses/LICENSE,sha256=z4QMMPlLJkZjU8VOKqJkZiQZCEZ--saIU2Z8-p3aVc0,1080
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+ workbench-0.8.183.dist-info/METADATA,sha256=-awjVDp5bJexow_nWLET9GLfph_LRFcouLnPIDgeoAA,9210
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+ workbench-0.8.183.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ workbench-0.8.183.dist-info/entry_points.txt,sha256=zPFPruY9uayk8-wsKrhfnIyIB6jvZOW_ibyllEIsLWo,356
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+ workbench-0.8.183.dist-info/top_level.txt,sha256=Dhy72zTxaA_o_yRkPZx5zw-fwumnjGaeGf0hBN3jc_w,10
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+ workbench-0.8.183.dist-info/RECORD,,