scitex 2.0.0__py2.py3-none-any.whl → 2.1.0__py2.py3-none-any.whl

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Files changed (704) hide show
  1. scitex/__init__.py +53 -15
  2. scitex/__main__.py +72 -26
  3. scitex/__version__.py +1 -1
  4. scitex/_sh.py +145 -23
  5. scitex/ai/__init__.py +30 -16
  6. scitex/ai/_gen_ai/_Anthropic.py +5 -7
  7. scitex/ai/_gen_ai/_BaseGenAI.py +2 -2
  8. scitex/ai/_gen_ai/_DeepSeek.py +10 -2
  9. scitex/ai/_gen_ai/_Google.py +2 -2
  10. scitex/ai/_gen_ai/_Llama.py +2 -2
  11. scitex/ai/_gen_ai/_OpenAI.py +2 -2
  12. scitex/ai/_gen_ai/_PARAMS.py +51 -65
  13. scitex/ai/_gen_ai/_Perplexity.py +2 -2
  14. scitex/ai/_gen_ai/__init__.py +25 -14
  15. scitex/ai/_gen_ai/_format_output_func.py +4 -4
  16. scitex/ai/classification/{classifier_server.py → Classifier.py} +5 -5
  17. scitex/ai/classification/CrossValidationExperiment.py +374 -0
  18. scitex/ai/classification/__init__.py +43 -4
  19. scitex/ai/classification/reporters/_BaseClassificationReporter.py +281 -0
  20. scitex/ai/classification/reporters/_ClassificationReporter.py +773 -0
  21. scitex/ai/classification/reporters/_MultiClassificationReporter.py +406 -0
  22. scitex/ai/classification/reporters/_SingleClassificationReporter.py +1834 -0
  23. scitex/ai/classification/reporters/__init__.py +11 -0
  24. scitex/ai/classification/reporters/reporter_utils/_Plotter.py +1028 -0
  25. scitex/ai/classification/reporters/reporter_utils/__init__.py +80 -0
  26. scitex/ai/classification/reporters/reporter_utils/aggregation.py +457 -0
  27. scitex/ai/classification/reporters/reporter_utils/data_models.py +313 -0
  28. scitex/ai/classification/reporters/reporter_utils/reporting.py +1056 -0
  29. scitex/ai/classification/reporters/reporter_utils/storage.py +221 -0
  30. scitex/ai/classification/reporters/reporter_utils/validation.py +395 -0
  31. scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +568 -0
  32. scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +688 -0
  33. scitex/ai/classification/timeseries/_TimeSeriesMetadata.py +139 -0
  34. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +1716 -0
  35. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +1685 -0
  36. scitex/ai/classification/timeseries/_TimeSeriesStrategy.py +84 -0
  37. scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +610 -0
  38. scitex/ai/classification/timeseries/__init__.py +39 -0
  39. scitex/ai/classification/timeseries/_normalize_timestamp.py +436 -0
  40. scitex/ai/clustering/_umap.py +2 -2
  41. scitex/ai/feature_extraction/vit.py +1 -0
  42. scitex/ai/feature_selection/__init__.py +30 -0
  43. scitex/ai/feature_selection/feature_selection.py +364 -0
  44. scitex/ai/loss/multi_task_loss.py +1 -1
  45. scitex/ai/metrics/__init__.py +51 -4
  46. scitex/ai/metrics/_calc_bacc.py +61 -0
  47. scitex/ai/metrics/_calc_bacc_from_conf_mat.py +38 -0
  48. scitex/ai/metrics/_calc_clf_report.py +78 -0
  49. scitex/ai/metrics/_calc_conf_mat.py +93 -0
  50. scitex/ai/metrics/_calc_feature_importance.py +183 -0
  51. scitex/ai/metrics/_calc_mcc.py +61 -0
  52. scitex/ai/metrics/_calc_pre_rec_auc.py +116 -0
  53. scitex/ai/metrics/_calc_roc_auc.py +110 -0
  54. scitex/ai/metrics/_calc_seizure_prediction_metrics.py +490 -0
  55. scitex/ai/metrics/{silhoute_score_block.py → _calc_silhouette_score.py} +15 -8
  56. scitex/ai/metrics/_normalize_labels.py +83 -0
  57. scitex/ai/plt/__init__.py +47 -8
  58. scitex/ai/plt/{_conf_mat.py → _plot_conf_mat.py} +158 -87
  59. scitex/ai/plt/_plot_feature_importance.py +323 -0
  60. scitex/ai/plt/_plot_learning_curve.py +345 -0
  61. scitex/ai/plt/_plot_optuna_study.py +225 -0
  62. scitex/ai/plt/_plot_pre_rec_curve.py +290 -0
  63. scitex/ai/plt/_plot_roc_curve.py +255 -0
  64. scitex/ai/training/{learning_curve_logger.py → _LearningCurveLogger.py} +197 -213
  65. scitex/ai/training/__init__.py +2 -2
  66. scitex/ai/utils/grid_search.py +3 -3
  67. scitex/benchmark/__init__.py +52 -0
  68. scitex/benchmark/benchmark.py +400 -0
  69. scitex/benchmark/monitor.py +370 -0
  70. scitex/benchmark/profiler.py +297 -0
  71. scitex/browser/__init__.py +48 -0
  72. scitex/browser/automation/CookieHandler.py +216 -0
  73. scitex/browser/automation/__init__.py +7 -0
  74. scitex/browser/collaboration/__init__.py +55 -0
  75. scitex/browser/collaboration/auth_helpers.py +94 -0
  76. scitex/browser/collaboration/collaborative_agent.py +136 -0
  77. scitex/browser/collaboration/credential_manager.py +188 -0
  78. scitex/browser/collaboration/interactive_panel.py +400 -0
  79. scitex/browser/collaboration/persistent_browser.py +170 -0
  80. scitex/browser/collaboration/shared_session.py +383 -0
  81. scitex/browser/collaboration/standard_interactions.py +246 -0
  82. scitex/browser/collaboration/visual_feedback.py +181 -0
  83. scitex/browser/core/BrowserMixin.py +326 -0
  84. scitex/browser/core/ChromeProfileManager.py +446 -0
  85. scitex/browser/core/__init__.py +9 -0
  86. scitex/browser/debugging/__init__.py +18 -0
  87. scitex/browser/debugging/_browser_logger.py +657 -0
  88. scitex/browser/debugging/_highlight_element.py +143 -0
  89. scitex/browser/debugging/_show_grid.py +154 -0
  90. scitex/browser/interaction/__init__.py +24 -0
  91. scitex/browser/interaction/click_center.py +149 -0
  92. scitex/browser/interaction/click_with_fallbacks.py +206 -0
  93. scitex/browser/interaction/close_popups.py +498 -0
  94. scitex/browser/interaction/fill_with_fallbacks.py +209 -0
  95. scitex/browser/pdf/__init__.py +14 -0
  96. scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +200 -0
  97. scitex/browser/pdf/detect_chrome_pdf_viewer.py +198 -0
  98. scitex/browser/remote/CaptchaHandler.py +434 -0
  99. scitex/browser/remote/ZenRowsAPIClient.py +347 -0
  100. scitex/browser/remote/ZenRowsBrowserManager.py +570 -0
  101. scitex/browser/remote/__init__.py +11 -0
  102. scitex/browser/stealth/HumanBehavior.py +344 -0
  103. scitex/browser/stealth/StealthManager.py +1008 -0
  104. scitex/browser/stealth/__init__.py +9 -0
  105. scitex/browser/template.py +122 -0
  106. scitex/capture/__init__.py +110 -0
  107. scitex/capture/__main__.py +25 -0
  108. scitex/capture/capture.py +848 -0
  109. scitex/capture/cli.py +233 -0
  110. scitex/capture/gif.py +344 -0
  111. scitex/capture/mcp_server.py +961 -0
  112. scitex/capture/session.py +70 -0
  113. scitex/capture/utils.py +705 -0
  114. scitex/cli/__init__.py +17 -0
  115. scitex/cli/cloud.py +447 -0
  116. scitex/cli/main.py +42 -0
  117. scitex/cli/scholar.py +280 -0
  118. scitex/context/_suppress_output.py +5 -3
  119. scitex/db/__init__.py +30 -3
  120. scitex/db/__main__.py +75 -0
  121. scitex/db/_check_health.py +381 -0
  122. scitex/db/_delete_duplicates.py +25 -386
  123. scitex/db/_inspect.py +335 -114
  124. scitex/db/_inspect_optimized.py +301 -0
  125. scitex/db/{_PostgreSQL.py → _postgresql/_PostgreSQL.py} +3 -3
  126. scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_BackupMixin.py +1 -1
  127. scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_BatchMixin.py +1 -1
  128. scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_BlobMixin.py +1 -1
  129. scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_ConnectionMixin.py +1 -1
  130. scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_MaintenanceMixin.py +1 -1
  131. scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_QueryMixin.py +1 -1
  132. scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_SchemaMixin.py +1 -1
  133. scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_TransactionMixin.py +1 -1
  134. scitex/db/_postgresql/__init__.py +6 -0
  135. scitex/db/_sqlite3/_SQLite3.py +210 -0
  136. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin.py +581 -0
  137. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin_v01-need-_hash-col.py +517 -0
  138. scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_BatchMixin.py +1 -1
  139. scitex/db/_sqlite3/_SQLite3Mixins/_BlobMixin.py +281 -0
  140. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin.py +548 -0
  141. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +583 -0
  142. scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_ConnectionMixin.py +29 -13
  143. scitex/db/_sqlite3/_SQLite3Mixins/_GitMixin.py +583 -0
  144. scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_ImportExportMixin.py +1 -1
  145. scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_IndexMixin.py +1 -1
  146. scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_MaintenanceMixin.py +2 -1
  147. scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_QueryMixin.py +37 -10
  148. scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_RowMixin.py +46 -6
  149. scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_TableMixin.py +56 -10
  150. scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_TransactionMixin.py +1 -1
  151. scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/__init__.py +14 -2
  152. scitex/db/_sqlite3/__init__.py +7 -0
  153. scitex/db/_sqlite3/_delete_duplicates.py +274 -0
  154. scitex/decorators/__init__.py +2 -0
  155. scitex/decorators/_cache_disk.py +13 -5
  156. scitex/decorators/_cache_disk_async.py +49 -0
  157. scitex/decorators/_deprecated.py +175 -10
  158. scitex/decorators/_timeout.py +1 -1
  159. scitex/dev/_analyze_code_flow.py +2 -2
  160. scitex/dict/_DotDict.py +73 -15
  161. scitex/dict/_DotDict_v01-not-handling-recursive-instantiations.py +442 -0
  162. scitex/dict/_DotDict_v02-not-serializing-Path-object.py +446 -0
  163. scitex/dict/__init__.py +2 -0
  164. scitex/dict/_flatten.py +27 -0
  165. scitex/dsp/_crop.py +2 -2
  166. scitex/dsp/_demo_sig.py +2 -2
  167. scitex/dsp/_detect_ripples.py +2 -2
  168. scitex/dsp/_hilbert.py +2 -2
  169. scitex/dsp/_listen.py +6 -6
  170. scitex/dsp/_modulation_index.py +2 -2
  171. scitex/dsp/_pac.py +1 -1
  172. scitex/dsp/_psd.py +2 -2
  173. scitex/dsp/_resample.py +2 -1
  174. scitex/dsp/_time.py +3 -2
  175. scitex/dsp/_wavelet.py +3 -2
  176. scitex/dsp/add_noise.py +2 -2
  177. scitex/dsp/example.py +1 -0
  178. scitex/dsp/filt.py +10 -9
  179. scitex/dsp/template.py +3 -2
  180. scitex/dsp/utils/_differential_bandpass_filters.py +1 -1
  181. scitex/dsp/utils/pac.py +2 -2
  182. scitex/dt/_normalize_timestamp.py +432 -0
  183. scitex/errors.py +572 -0
  184. scitex/gen/_DimHandler.py +2 -2
  185. scitex/gen/__init__.py +37 -7
  186. scitex/gen/_deprecated_close.py +80 -0
  187. scitex/gen/_deprecated_start.py +26 -0
  188. scitex/gen/_detect_environment.py +152 -0
  189. scitex/gen/_detect_notebook_path.py +169 -0
  190. scitex/gen/_embed.py +6 -2
  191. scitex/gen/_get_notebook_path.py +257 -0
  192. scitex/gen/_less.py +1 -1
  193. scitex/gen/_list_packages.py +2 -2
  194. scitex/gen/_norm.py +44 -9
  195. scitex/gen/_norm_cache.py +269 -0
  196. scitex/gen/_src.py +3 -5
  197. scitex/gen/_title_case.py +3 -3
  198. scitex/io/__init__.py +28 -6
  199. scitex/io/_glob.py +13 -7
  200. scitex/io/_load.py +108 -21
  201. scitex/io/_load_cache.py +303 -0
  202. scitex/io/_load_configs.py +40 -15
  203. scitex/io/{_H5Explorer.py → _load_modules/_H5Explorer.py} +80 -17
  204. scitex/io/_load_modules/_ZarrExplorer.py +114 -0
  205. scitex/io/_load_modules/_bibtex.py +207 -0
  206. scitex/io/_load_modules/_hdf5.py +53 -178
  207. scitex/io/_load_modules/_json.py +5 -3
  208. scitex/io/_load_modules/_pdf.py +871 -16
  209. scitex/io/_load_modules/_sqlite3.py +15 -0
  210. scitex/io/_load_modules/_txt.py +41 -12
  211. scitex/io/_load_modules/_yaml.py +4 -3
  212. scitex/io/_load_modules/_zarr.py +126 -0
  213. scitex/io/_save.py +429 -171
  214. scitex/io/_save_modules/__init__.py +6 -0
  215. scitex/io/_save_modules/_bibtex.py +194 -0
  216. scitex/io/_save_modules/_csv.py +8 -4
  217. scitex/io/_save_modules/_excel.py +174 -15
  218. scitex/io/_save_modules/_hdf5.py +251 -226
  219. scitex/io/_save_modules/_image.py +1 -3
  220. scitex/io/_save_modules/_json.py +49 -4
  221. scitex/io/_save_modules/_listed_dfs_as_csv.py +1 -3
  222. scitex/io/_save_modules/_listed_scalars_as_csv.py +1 -3
  223. scitex/io/_save_modules/_tex.py +277 -0
  224. scitex/io/_save_modules/_yaml.py +42 -3
  225. scitex/io/_save_modules/_zarr.py +160 -0
  226. scitex/io/utils/__init__.py +20 -0
  227. scitex/io/utils/h5_to_zarr.py +616 -0
  228. scitex/linalg/_geometric_median.py +6 -2
  229. scitex/{gen/_tee.py → logging/_Tee.py} +43 -84
  230. scitex/logging/__init__.py +122 -0
  231. scitex/logging/_config.py +158 -0
  232. scitex/logging/_context.py +103 -0
  233. scitex/logging/_formatters.py +128 -0
  234. scitex/logging/_handlers.py +64 -0
  235. scitex/logging/_levels.py +35 -0
  236. scitex/logging/_logger.py +163 -0
  237. scitex/logging/_print_capture.py +95 -0
  238. scitex/ml/__init__.py +69 -0
  239. scitex/{ai/genai/anthropic.py → ml/_gen_ai/_Anthropic.py} +13 -19
  240. scitex/{ai/genai/base_genai.py → ml/_gen_ai/_BaseGenAI.py} +5 -5
  241. scitex/{ai/genai/deepseek.py → ml/_gen_ai/_DeepSeek.py} +11 -16
  242. scitex/{ai/genai/google.py → ml/_gen_ai/_Google.py} +7 -15
  243. scitex/{ai/genai/groq.py → ml/_gen_ai/_Groq.py} +1 -8
  244. scitex/{ai/genai/llama.py → ml/_gen_ai/_Llama.py} +3 -16
  245. scitex/{ai/genai/openai.py → ml/_gen_ai/_OpenAI.py} +3 -3
  246. scitex/{ai/genai/params.py → ml/_gen_ai/_PARAMS.py} +51 -65
  247. scitex/{ai/genai/perplexity.py → ml/_gen_ai/_Perplexity.py} +3 -14
  248. scitex/ml/_gen_ai/__init__.py +43 -0
  249. scitex/{ai/genai/calc_cost.py → ml/_gen_ai/_calc_cost.py} +1 -1
  250. scitex/{ai/genai/format_output_func.py → ml/_gen_ai/_format_output_func.py} +4 -4
  251. scitex/{ai/genai/genai_factory.py → ml/_gen_ai/_genai_factory.py} +8 -8
  252. scitex/ml/activation/__init__.py +8 -0
  253. scitex/ml/activation/_define.py +11 -0
  254. scitex/{ai/classifier_server.py → ml/classification/Classifier.py} +5 -5
  255. scitex/ml/classification/CrossValidationExperiment.py +374 -0
  256. scitex/ml/classification/__init__.py +46 -0
  257. scitex/ml/classification/reporters/_BaseClassificationReporter.py +281 -0
  258. scitex/ml/classification/reporters/_ClassificationReporter.py +773 -0
  259. scitex/ml/classification/reporters/_MultiClassificationReporter.py +406 -0
  260. scitex/ml/classification/reporters/_SingleClassificationReporter.py +1834 -0
  261. scitex/ml/classification/reporters/__init__.py +11 -0
  262. scitex/ml/classification/reporters/reporter_utils/_Plotter.py +1028 -0
  263. scitex/ml/classification/reporters/reporter_utils/__init__.py +80 -0
  264. scitex/ml/classification/reporters/reporter_utils/aggregation.py +457 -0
  265. scitex/ml/classification/reporters/reporter_utils/data_models.py +313 -0
  266. scitex/ml/classification/reporters/reporter_utils/reporting.py +1056 -0
  267. scitex/ml/classification/reporters/reporter_utils/storage.py +221 -0
  268. scitex/ml/classification/reporters/reporter_utils/validation.py +395 -0
  269. scitex/ml/classification/timeseries/_TimeSeriesBlockingSplit.py +568 -0
  270. scitex/ml/classification/timeseries/_TimeSeriesCalendarSplit.py +688 -0
  271. scitex/ml/classification/timeseries/_TimeSeriesMetadata.py +139 -0
  272. scitex/ml/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +1716 -0
  273. scitex/ml/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +1685 -0
  274. scitex/ml/classification/timeseries/_TimeSeriesStrategy.py +84 -0
  275. scitex/ml/classification/timeseries/_TimeSeriesStratifiedSplit.py +610 -0
  276. scitex/ml/classification/timeseries/__init__.py +39 -0
  277. scitex/ml/classification/timeseries/_normalize_timestamp.py +436 -0
  278. scitex/ml/clustering/__init__.py +11 -0
  279. scitex/ml/clustering/_pca.py +115 -0
  280. scitex/ml/clustering/_umap.py +376 -0
  281. scitex/ml/feature_extraction/__init__.py +56 -0
  282. scitex/ml/feature_extraction/vit.py +149 -0
  283. scitex/ml/feature_selection/__init__.py +30 -0
  284. scitex/ml/feature_selection/feature_selection.py +364 -0
  285. scitex/ml/loss/_L1L2Losses.py +34 -0
  286. scitex/ml/loss/__init__.py +12 -0
  287. scitex/ml/loss/multi_task_loss.py +47 -0
  288. scitex/ml/metrics/__init__.py +56 -0
  289. scitex/ml/metrics/_calc_bacc.py +61 -0
  290. scitex/ml/metrics/_calc_bacc_from_conf_mat.py +38 -0
  291. scitex/ml/metrics/_calc_clf_report.py +78 -0
  292. scitex/ml/metrics/_calc_conf_mat.py +93 -0
  293. scitex/ml/metrics/_calc_feature_importance.py +183 -0
  294. scitex/ml/metrics/_calc_mcc.py +61 -0
  295. scitex/ml/metrics/_calc_pre_rec_auc.py +116 -0
  296. scitex/ml/metrics/_calc_roc_auc.py +110 -0
  297. scitex/ml/metrics/_calc_seizure_prediction_metrics.py +490 -0
  298. scitex/ml/metrics/_calc_silhouette_score.py +503 -0
  299. scitex/ml/metrics/_normalize_labels.py +83 -0
  300. scitex/ml/optim/Ranger_Deep_Learning_Optimizer/__init__.py +0 -0
  301. scitex/ml/optim/Ranger_Deep_Learning_Optimizer/ranger/__init__.py +3 -0
  302. scitex/ml/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger.py +207 -0
  303. scitex/ml/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger2020.py +238 -0
  304. scitex/ml/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger913A.py +215 -0
  305. scitex/ml/optim/Ranger_Deep_Learning_Optimizer/ranger/rangerqh.py +184 -0
  306. scitex/ml/optim/Ranger_Deep_Learning_Optimizer/setup.py +24 -0
  307. scitex/ml/optim/__init__.py +13 -0
  308. scitex/ml/optim/_get_set.py +31 -0
  309. scitex/ml/optim/_optimizers.py +71 -0
  310. scitex/ml/plt/__init__.py +60 -0
  311. scitex/ml/plt/_plot_conf_mat.py +663 -0
  312. scitex/ml/plt/_plot_feature_importance.py +323 -0
  313. scitex/ml/plt/_plot_learning_curve.py +345 -0
  314. scitex/ml/plt/_plot_optuna_study.py +225 -0
  315. scitex/ml/plt/_plot_pre_rec_curve.py +290 -0
  316. scitex/ml/plt/_plot_roc_curve.py +255 -0
  317. scitex/ml/sk/__init__.py +11 -0
  318. scitex/ml/sk/_clf.py +58 -0
  319. scitex/ml/sk/_to_sktime.py +100 -0
  320. scitex/ml/sklearn/__init__.py +26 -0
  321. scitex/ml/sklearn/clf.py +58 -0
  322. scitex/ml/sklearn/to_sktime.py +100 -0
  323. scitex/{ai/training/early_stopping.py → ml/training/_EarlyStopping.py} +1 -2
  324. scitex/{ai → ml/training}/_LearningCurveLogger.py +198 -242
  325. scitex/ml/training/__init__.py +7 -0
  326. scitex/ml/utils/__init__.py +22 -0
  327. scitex/ml/utils/_check_params.py +50 -0
  328. scitex/ml/utils/_default_dataset.py +46 -0
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  331. scitex/ml/utils/_merge_labels.py +22 -0
  332. scitex/ml/utils/_sliding_window_data_augmentation.py +11 -0
  333. scitex/ml/utils/_under_sample.py +51 -0
  334. scitex/ml/utils/_verify_n_gpus.py +16 -0
  335. scitex/ml/utils/grid_search.py +148 -0
  336. scitex/nn/_BNet.py +15 -9
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  338. scitex/nn/_ModulationIndex.py +2 -2
  339. scitex/nn/_PAC.py +1 -1
  340. scitex/nn/_Spectrogram.py +12 -3
  341. scitex/nn/__init__.py +9 -10
  342. scitex/path/__init__.py +18 -0
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  344. scitex/path/_find.py +9 -4
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  351. scitex/plt/_subplots/_AxisWrapper.py +7 -3
  352. scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +47 -13
  353. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +160 -2
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  357. scitex/plt/_subplots/_FigWrapper.py +62 -6
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  360. scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +81 -0
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  365. scitex/plt/_subplots/_export_as_csv_formatters/_format_errorbar.py +35 -18
  366. scitex/plt/_subplots/_export_as_csv_formatters/_format_eventplot.py +1 -3
  367. scitex/plt/_subplots/_export_as_csv_formatters/_format_fill.py +1 -3
  368. scitex/plt/_subplots/_export_as_csv_formatters/_format_fill_between.py +1 -3
  369. scitex/plt/_subplots/_export_as_csv_formatters/_format_hist.py +1 -3
  370. scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow.py +1 -3
  371. scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow2d.py +1 -3
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  373. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_box.py +1 -3
  374. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_conf_mat.py +1 -3
  375. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_ecdf.py +1 -3
  376. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_fillv.py +1 -3
  377. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_heatmap.py +1 -3
  378. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_image.py +1 -3
  379. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_joyplot.py +1 -3
  380. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_kde.py +1 -3
  381. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_line.py +1 -3
  382. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_mean_ci.py +1 -3
  383. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_mean_std.py +1 -3
  384. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_median_iqr.py +1 -3
  385. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_raster.py +1 -3
  386. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_rectangle.py +1 -3
  387. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter.py +35 -0
  388. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter_hist.py +1 -3
  389. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_shaded_line.py +1 -3
  390. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_violin.py +1 -3
  391. scitex/plt/_subplots/_export_as_csv_formatters/_format_scatter.py +6 -4
  392. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_barplot.py +1 -3
  393. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_boxplot.py +1 -3
  394. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_heatmap.py +1 -3
  395. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_histplot.py +1 -3
  396. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_jointplot.py +1 -3
  397. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_kdeplot.py +1 -3
  398. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_lineplot.py +1 -3
  399. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_pairplot.py +1 -3
  400. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_scatterplot.py +1 -3
  401. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_stripplot.py +1 -3
  402. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_swarmplot.py +1 -3
  403. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_violinplot.py +1 -3
  404. scitex/plt/_subplots/_export_as_csv_formatters/_format_text.py +60 -0
  405. scitex/plt/_subplots/_export_as_csv_formatters/_format_violin.py +1 -3
  406. scitex/plt/_subplots/_export_as_csv_formatters/_format_violinplot.py +1 -3
  407. scitex/plt/_subplots/_export_as_csv_formatters/test_formatters.py +1 -3
  408. scitex/plt/_subplots/_export_as_csv_formatters.py +56 -59
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  411. scitex/plt/ax/_style/_rotate_labels_v01.py +248 -0
  412. scitex/plt/ax/_style/_set_meta.py +11 -4
  413. scitex/plt/ax/_style/_set_supxyt.py +3 -3
  414. scitex/plt/ax/_style/_set_xyt.py +3 -3
  415. scitex/plt/ax/_style/_share_axes.py +2 -2
  416. scitex/plt/color/__init__.py +4 -4
  417. scitex/plt/color/{_get_colors_from_cmap.py → _get_colors_from_conf_matap.py} +7 -7
  418. scitex/plt/utils/_configure_mpl.py +99 -86
  419. scitex/plt/utils/_histogram_utils.py +1 -3
  420. scitex/plt/utils/_is_valid_axis.py +1 -3
  421. scitex/plt/utils/_scitex_config.py +1 -0
  422. scitex/repro/__init__.py +75 -0
  423. scitex/{reproduce → repro}/_gen_ID.py +1 -1
  424. scitex/{reproduce → repro}/_gen_timestamp.py +1 -1
  425. scitex/repro_rng/_RandomStateManager.py +590 -0
  426. scitex/repro_rng/_RandomStateManager_v01-no-verbose-options.py +414 -0
  427. scitex/repro_rng/__init__.py +39 -0
  428. scitex/reproduce/__init__.py +25 -13
  429. scitex/reproduce/_hash_array.py +22 -0
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  431. scitex/resource/_get_specs.py +2 -2
  432. scitex/resource/_log_processor_usages.py +2 -2
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  434. scitex/rng/_RandomStateManager_v01-no-verbose-options.py +414 -0
  435. scitex/rng/__init__.py +39 -0
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  437. scitex/scholar/__main__.py +319 -0
  438. scitex/scholar/auth/ScholarAuthManager.py +308 -0
  439. scitex/scholar/auth/__init__.py +12 -0
  440. scitex/scholar/auth/core/AuthenticationGateway.py +473 -0
  441. scitex/scholar/auth/core/BrowserAuthenticator.py +386 -0
  442. scitex/scholar/auth/core/StrategyResolver.py +309 -0
  443. scitex/scholar/auth/core/__init__.py +16 -0
  444. scitex/scholar/auth/gateway/_OpenURLLinkFinder.py +120 -0
  445. scitex/scholar/auth/gateway/_OpenURLResolver.py +209 -0
  446. scitex/scholar/auth/gateway/__init__.py +38 -0
  447. scitex/scholar/auth/gateway/_resolve_functions.py +101 -0
  448. scitex/scholar/auth/providers/BaseAuthenticator.py +166 -0
  449. scitex/scholar/auth/providers/EZProxyAuthenticator.py +484 -0
  450. scitex/scholar/auth/providers/OpenAthensAuthenticator.py +619 -0
  451. scitex/scholar/auth/providers/ShibbolethAuthenticator.py +686 -0
  452. scitex/scholar/auth/providers/__init__.py +18 -0
  453. scitex/scholar/auth/session/AuthCacheManager.py +189 -0
  454. scitex/scholar/auth/session/SessionManager.py +159 -0
  455. scitex/scholar/auth/session/__init__.py +11 -0
  456. scitex/scholar/auth/sso/BaseSSOAutomator.py +373 -0
  457. scitex/scholar/auth/sso/OpenAthensSSOAutomator.py +378 -0
  458. scitex/scholar/auth/sso/SSOAutomator.py +180 -0
  459. scitex/scholar/auth/sso/UniversityOfMelbourneSSOAutomator.py +380 -0
  460. scitex/scholar/auth/sso/__init__.py +15 -0
  461. scitex/scholar/browser/ScholarBrowserManager.py +705 -0
  462. scitex/scholar/browser/__init__.py +38 -0
  463. scitex/scholar/browser/utils/__init__.py +13 -0
  464. scitex/scholar/browser/utils/click_and_wait.py +205 -0
  465. scitex/scholar/browser/utils/close_unwanted_pages.py +140 -0
  466. scitex/scholar/browser/utils/wait_redirects.py +732 -0
  467. scitex/scholar/config/PublisherRules.py +132 -0
  468. scitex/scholar/config/ScholarConfig.py +126 -0
  469. scitex/scholar/config/__init__.py +17 -0
  470. scitex/scholar/core/Paper.py +627 -0
  471. scitex/scholar/core/Papers.py +722 -0
  472. scitex/scholar/core/Scholar.py +1975 -0
  473. scitex/scholar/core/__init__.py +9 -0
  474. scitex/scholar/impact_factor/ImpactFactorEngine.py +204 -0
  475. scitex/scholar/impact_factor/__init__.py +20 -0
  476. scitex/scholar/impact_factor/estimation/ImpactFactorEstimationEngine.py +0 -0
  477. scitex/scholar/impact_factor/estimation/__init__.py +40 -0
  478. scitex/scholar/impact_factor/estimation/build_database.py +0 -0
  479. scitex/scholar/impact_factor/estimation/core/__init__.py +28 -0
  480. scitex/scholar/impact_factor/estimation/core/cache_manager.py +523 -0
  481. scitex/scholar/impact_factor/estimation/core/calculator.py +355 -0
  482. scitex/scholar/impact_factor/estimation/core/journal_matcher.py +428 -0
  483. scitex/scholar/integration/__init__.py +59 -0
  484. scitex/scholar/integration/base.py +502 -0
  485. scitex/scholar/integration/mendeley/__init__.py +22 -0
  486. scitex/scholar/integration/mendeley/exporter.py +166 -0
  487. scitex/scholar/integration/mendeley/importer.py +236 -0
  488. scitex/scholar/integration/mendeley/linker.py +79 -0
  489. scitex/scholar/integration/mendeley/mapper.py +212 -0
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  493. scitex/scholar/integration/zotero/importer.py +372 -0
  494. scitex/scholar/integration/zotero/linker.py +415 -0
  495. scitex/scholar/integration/zotero/mapper.py +286 -0
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  498. scitex/scholar/metadata_engines/individual/ArXivEngine.py +397 -0
  499. scitex/scholar/metadata_engines/individual/CrossRefEngine.py +274 -0
  500. scitex/scholar/metadata_engines/individual/CrossRefLocalEngine.py +263 -0
  501. scitex/scholar/metadata_engines/individual/OpenAlexEngine.py +350 -0
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  503. scitex/scholar/metadata_engines/individual/SemanticScholarEngine.py +438 -0
  504. scitex/scholar/metadata_engines/individual/URLDOIEngine.py +410 -0
  505. scitex/scholar/metadata_engines/individual/_BaseDOIEngine.py +487 -0
  506. scitex/scholar/metadata_engines/individual/__init__.py +7 -0
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  510. scitex/scholar/metadata_engines/utils/_metadata2bibtex.py +103 -0
  511. scitex/scholar/metadata_engines/utils/_standardize_metadata.py +376 -0
  512. scitex/scholar/pdf_download/ScholarPDFDownloader.py +579 -0
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  522. scitex/scholar/pipelines/ScholarPipelineSingle.py +767 -0
  523. scitex/scholar/pipelines/__init__.py +49 -0
  524. scitex/scholar/storage/BibTeXHandler.py +1018 -0
  525. scitex/scholar/storage/PaperIO.py +468 -0
  526. scitex/scholar/storage/ScholarLibrary.py +182 -0
  527. scitex/scholar/storage/_DeduplicationManager.py +548 -0
  528. scitex/scholar/storage/_LibraryCacheManager.py +724 -0
  529. scitex/scholar/storage/_LibraryManager.py +1835 -0
  530. scitex/scholar/storage/__init__.py +28 -0
  531. scitex/scholar/url_finder/ScholarURLFinder.py +379 -0
  532. scitex/scholar/url_finder/__init__.py +7 -0
  533. scitex/scholar/url_finder/strategies/__init__.py +33 -0
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  535. scitex/scholar/url_finder/strategies/find_pdf_urls_by_dropdown.py +67 -0
  536. scitex/scholar/url_finder/strategies/find_pdf_urls_by_href.py +204 -0
  537. scitex/scholar/url_finder/strategies/find_pdf_urls_by_navigation.py +256 -0
  538. scitex/scholar/url_finder/strategies/find_pdf_urls_by_publisher_patterns.py +165 -0
  539. scitex/scholar/url_finder/strategies/find_pdf_urls_by_zotero_translators.py +163 -0
  540. scitex/scholar/url_finder/strategies/find_supplementary_urls_by_href.py +70 -0
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  543. scitex/scholar/utils/bibtex/_parse_bibtex.py +71 -0
  544. scitex/scholar/utils/cleanup/__init__.py +8 -0
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  546. scitex/scholar/utils/cleanup/cleanup_old_extractions.py +117 -0
  547. scitex/scholar/utils/text/_TextNormalizer.py +407 -0
  548. scitex/scholar/utils/text/__init__.py +9 -0
  549. scitex/scholar/zotero/__init__.py +38 -0
  550. scitex/session/__init__.py +51 -0
  551. scitex/session/_lifecycle.py +736 -0
  552. scitex/session/_manager.py +102 -0
  553. scitex/session/template.py +122 -0
  554. scitex/stats/__init__.py +30 -26
  555. scitex/stats/correct/__init__.py +21 -0
  556. scitex/stats/correct/_correct_bonferroni.py +551 -0
  557. scitex/stats/correct/_correct_fdr.py +634 -0
  558. scitex/stats/correct/_correct_holm.py +548 -0
  559. scitex/stats/correct/_correct_sidak.py +499 -0
  560. scitex/stats/descriptive/__init__.py +85 -0
  561. scitex/stats/descriptive/_circular.py +540 -0
  562. scitex/stats/descriptive/_describe.py +219 -0
  563. scitex/stats/descriptive/_nan.py +518 -0
  564. scitex/stats/descriptive/_real.py +189 -0
  565. scitex/stats/effect_sizes/__init__.py +41 -0
  566. scitex/stats/effect_sizes/_cliffs_delta.py +325 -0
  567. scitex/stats/effect_sizes/_cohens_d.py +342 -0
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  569. scitex/stats/effect_sizes/_eta_squared.py +302 -0
  570. scitex/stats/effect_sizes/_prob_superiority.py +296 -0
  571. scitex/stats/posthoc/__init__.py +19 -0
  572. scitex/stats/posthoc/_dunnett.py +463 -0
  573. scitex/stats/posthoc/_games_howell.py +383 -0
  574. scitex/stats/posthoc/_tukey_hsd.py +367 -0
  575. scitex/stats/power/__init__.py +19 -0
  576. scitex/stats/power/_power.py +433 -0
  577. scitex/stats/template.py +119 -0
  578. scitex/stats/utils/__init__.py +62 -0
  579. scitex/stats/utils/_effect_size.py +985 -0
  580. scitex/stats/utils/_formatters.py +270 -0
  581. scitex/stats/utils/_normalizers.py +927 -0
  582. scitex/stats/utils/_power.py +433 -0
  583. scitex/stats_v01/_EffectSizeCalculator.py +488 -0
  584. scitex/stats_v01/_StatisticalValidator.py +411 -0
  585. scitex/stats_v01/__init__.py +60 -0
  586. scitex/stats_v01/_additional_tests.py +415 -0
  587. scitex/{stats → stats_v01}/_p2stars.py +19 -5
  588. scitex/stats_v01/_two_sample_tests.py +141 -0
  589. scitex/stats_v01/desc/__init__.py +83 -0
  590. scitex/stats_v01/desc/_circular.py +540 -0
  591. scitex/stats_v01/desc/_describe.py +219 -0
  592. scitex/stats_v01/desc/_nan.py +518 -0
  593. scitex/{stats/desc/_nan.py → stats_v01/desc/_nan_v01-20250920_145731.py} +23 -12
  594. scitex/stats_v01/desc/_real.py +189 -0
  595. scitex/stats_v01/tests/__corr_test_optimized.py +221 -0
  596. scitex/stats_v01/tests/_corr_test_optimized.py +179 -0
  597. scitex/str/__init__.py +1 -3
  598. scitex/str/_clean_path.py +6 -2
  599. scitex/str/_latex_fallback.py +267 -160
  600. scitex/str/_parse.py +44 -36
  601. scitex/str/_printc.py +1 -3
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  605. scitex/template/create_research.py +80 -0
  606. scitex/template/create_singularity.py +80 -0
  607. scitex/units.py +291 -0
  608. scitex/utils/_compress_hdf5.py +14 -3
  609. scitex/utils/_email.py +21 -2
  610. scitex/utils/_grid.py +6 -4
  611. scitex/utils/_notify.py +13 -10
  612. scitex/utils/_verify_scitex_format.py +589 -0
  613. scitex/utils/_verify_scitex_format_v01.py +370 -0
  614. scitex/utils/template.py +122 -0
  615. scitex/web/_search_pubmed.py +62 -16
  616. scitex-2.1.0.dist-info/LICENSE +21 -0
  617. scitex-2.1.0.dist-info/METADATA +677 -0
  618. scitex-2.1.0.dist-info/RECORD +919 -0
  619. {scitex-2.0.0.dist-info → scitex-2.1.0.dist-info}/WHEEL +1 -1
  620. scitex-2.1.0.dist-info/entry_points.txt +3 -0
  621. scitex/ai/__Classifiers.py +0 -101
  622. scitex/ai/classification/classification_reporter.py +0 -1137
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  624. scitex/ai/classification_reporter.py +0 -1161
  625. scitex/ai/genai/__init__.py +0 -277
  626. scitex/ai/genai/anthropic_provider.py +0 -320
  627. scitex/ai/genai/anthropic_refactored.py +0 -109
  628. scitex/ai/genai/auth_manager.py +0 -200
  629. scitex/ai/genai/base_provider.py +0 -291
  630. scitex/ai/genai/chat_history.py +0 -307
  631. scitex/ai/genai/cost_tracker.py +0 -276
  632. scitex/ai/genai/deepseek_provider.py +0 -251
  633. scitex/ai/genai/google_provider.py +0 -228
  634. scitex/ai/genai/groq_provider.py +0 -248
  635. scitex/ai/genai/image_processor.py +0 -250
  636. scitex/ai/genai/llama_provider.py +0 -214
  637. scitex/ai/genai/mock_provider.py +0 -127
  638. scitex/ai/genai/model_registry.py +0 -304
  639. scitex/ai/genai/openai_provider.py +0 -293
  640. scitex/ai/genai/perplexity_provider.py +0 -205
  641. scitex/ai/genai/provider_base.py +0 -302
  642. scitex/ai/genai/provider_factory.py +0 -370
  643. scitex/ai/genai/response_handler.py +0 -235
  644. scitex/ai/layer/_Pass.py +0 -21
  645. scitex/ai/layer/__init__.py +0 -10
  646. scitex/ai/layer/_switch.py +0 -8
  647. scitex/ai/metrics/_bACC.py +0 -51
  648. scitex/ai/plt/_learning_curve.py +0 -194
  649. scitex/ai/plt/_optuna_study.py +0 -111
  650. scitex/ai/plt/aucs/__init__.py +0 -2
  651. scitex/ai/plt/aucs/example.py +0 -60
  652. scitex/ai/plt/aucs/pre_rec_auc.py +0 -223
  653. scitex/ai/plt/aucs/roc_auc.py +0 -246
  654. scitex/ai/sampling/undersample.py +0 -29
  655. scitex/db/_SQLite3.py +0 -2136
  656. scitex/db/_SQLite3Mixins/_BlobMixin.py +0 -229
  657. scitex/gen/_close.py +0 -222
  658. scitex/gen/_start.py +0 -451
  659. scitex/general/__init__.py +0 -5
  660. scitex/io/_load_modules/_db.py +0 -24
  661. scitex/life/__init__.py +0 -10
  662. scitex/life/_monitor_rain.py +0 -49
  663. scitex/reproduce/_fix_seeds.py +0 -45
  664. scitex/res/__init__.py +0 -5
  665. scitex/scholar/_local_search.py +0 -454
  666. scitex/scholar/_paper.py +0 -244
  667. scitex/scholar/_pdf_downloader.py +0 -325
  668. scitex/scholar/_search.py +0 -393
  669. scitex/scholar/_vector_search.py +0 -370
  670. scitex/scholar/_web_sources.py +0 -457
  671. scitex/stats/desc/__init__.py +0 -40
  672. scitex-2.0.0.dist-info/METADATA +0 -307
  673. scitex-2.0.0.dist-info/RECORD +0 -572
  674. scitex-2.0.0.dist-info/licenses/LICENSE +0 -7
  675. /scitex/ai/{act → activation}/__init__.py +0 -0
  676. /scitex/ai/{act → activation}/_define.py +0 -0
  677. /scitex/ai/{early_stopping.py → training/_EarlyStopping.py} +0 -0
  678. /scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_ImportExportMixin.py +0 -0
  679. /scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_IndexMixin.py +0 -0
  680. /scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_RowMixin.py +0 -0
  681. /scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_TableMixin.py +0 -0
  682. /scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/__init__.py +0 -0
  683. /scitex/{stats → stats_v01}/_calc_partial_corr.py +0 -0
  684. /scitex/{stats → stats_v01}/_corr_test_multi.py +0 -0
  685. /scitex/{stats → stats_v01}/_corr_test_wrapper.py +0 -0
  686. /scitex/{stats → stats_v01}/_describe_wrapper.py +0 -0
  687. /scitex/{stats → stats_v01}/_multiple_corrections.py +0 -0
  688. /scitex/{stats → stats_v01}/_nan_stats.py +0 -0
  689. /scitex/{stats → stats_v01}/_p2stars_wrapper.py +0 -0
  690. /scitex/{stats → stats_v01}/_statistical_tests.py +0 -0
  691. /scitex/{stats/desc/_describe.py → stats_v01/desc/_describe_v01-20250920_145731.py} +0 -0
  692. /scitex/{stats/desc/_real.py → stats_v01/desc/_real_v01-20250920_145731.py} +0 -0
  693. /scitex/{stats → stats_v01}/multiple/__init__.py +0 -0
  694. /scitex/{stats → stats_v01}/multiple/_bonferroni_correction.py +0 -0
  695. /scitex/{stats → stats_v01}/multiple/_fdr_correction.py +0 -0
  696. /scitex/{stats → stats_v01}/multiple/_multicompair.py +0 -0
  697. /scitex/{stats → stats_v01}/tests/__corr_test.py +0 -0
  698. /scitex/{stats → stats_v01}/tests/__corr_test_multi.py +0 -0
  699. /scitex/{stats → stats_v01}/tests/__corr_test_single.py +0 -0
  700. /scitex/{stats → stats_v01}/tests/__init__.py +0 -0
  701. /scitex/{stats → stats_v01}/tests/_brunner_munzel_test.py +0 -0
  702. /scitex/{stats → stats_v01}/tests/_nocorrelation_test.py +0 -0
  703. /scitex/{stats → stats_v01}/tests/_smirnov_grubbs.py +0 -0
  704. {scitex-2.0.0.dist-info → scitex-2.1.0.dist-info}/top_level.txt +0 -0
@@ -1,248 +0,0 @@
1
- #!/usr/bin/env python3
2
- # -*- coding: utf-8 -*-
3
- # Time-stamp: "2024-11-25 12:00:00"
4
- # Author: Yusuke Watanabe (ywatanabe@alumni.u-tokyo.ac.jp)
5
- # scitex/src/scitex/ai/genai/groq_provider.py
6
-
7
- """
8
- Groq provider implementation for GenAI.
9
-
10
- Provides access to Groq's API with models like Llama, Mixtral, etc.
11
- """
12
-
13
- from typing import List, Dict, Any, Optional, Generator
14
- import logging
15
- import os
16
-
17
- from .base_provider import BaseProvider, CompletionResponse, Provider
18
- from .provider_factory import register_provider
19
-
20
- logger = logging.getLogger(__name__)
21
-
22
-
23
- class GroqProvider(BaseProvider):
24
- """
25
- Groq provider implementation.
26
-
27
- Supports Llama 3, Mixtral, and other models available through Groq.
28
- """
29
-
30
- SUPPORTED_MODELS = [
31
- "llama3-8b-8192",
32
- "llama3-70b-8192",
33
- "llama2-70b-4096",
34
- "mixtral-8x7b-32768",
35
- "gemma-7b-it",
36
- ]
37
-
38
- DEFAULT_MODEL = "llama3-8b-8192"
39
-
40
- def __init__(self, config):
41
- """Initialize Groq provider."""
42
- self.config = config
43
- self.api_key = config.api_key or os.getenv("GROQ_API_KEY")
44
- self.model = config.model or self.DEFAULT_MODEL
45
- self.kwargs = config.kwargs or {}
46
-
47
- if not self.api_key:
48
- raise ValueError("GROQ_API_KEY not provided and not found in environment")
49
-
50
- # Import Groq client
51
- try:
52
- from groq import Groq as GroqClient
53
-
54
- self.client = GroqClient(api_key=self.api_key)
55
- except ImportError:
56
- raise ImportError(
57
- "Groq package not installed. Install with: pip install groq"
58
- )
59
-
60
- def complete(self, messages: List[Dict[str, Any]], **kwargs) -> CompletionResponse:
61
- """
62
- Generate completion using Groq API.
63
-
64
- Args:
65
- messages: List of message dictionaries
66
- **kwargs: Additional parameters (temperature, max_tokens, etc.)
67
-
68
- Returns:
69
- CompletionResponse with generated text and usage info
70
- """
71
- # Validate messages
72
- if not self.validate_messages(messages):
73
- raise ValueError("Invalid message format")
74
-
75
- # Format messages for Groq (same as OpenAI format)
76
- formatted_messages = self.format_messages(messages)
77
-
78
- # Prepare API parameters
79
- api_params = {
80
- "model": self.model,
81
- "messages": formatted_messages,
82
- "stream": False,
83
- }
84
-
85
- # Add optional parameters
86
- for param in ["temperature", "max_tokens", "top_p", "stop", "seed"]:
87
- if param in kwargs:
88
- api_params[param] = kwargs[param]
89
-
90
- # Groq has a max token limit of 8000
91
- if "max_tokens" in api_params:
92
- api_params["max_tokens"] = min(api_params["max_tokens"], 8000)
93
-
94
- try:
95
- # Make API call
96
- response = self.client.chat.completions.create(**api_params)
97
-
98
- # Extract content and usage
99
- content = response.choices[0].message.content
100
- usage = response.usage
101
-
102
- return CompletionResponse(
103
- content=content,
104
- input_tokens=usage.prompt_tokens,
105
- output_tokens=usage.completion_tokens,
106
- finish_reason=response.choices[0].finish_reason,
107
- provider_response=response,
108
- )
109
-
110
- except Exception as e:
111
- logger.error(f"Groq API error: {str(e)}")
112
- raise
113
-
114
- def format_messages(self, messages: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
115
- """
116
- Format messages for Groq API.
117
-
118
- Groq uses the same message format as OpenAI.
119
- """
120
- formatted_messages = []
121
-
122
- for msg in messages:
123
- formatted_msg = {"role": msg["role"], "content": msg["content"]}
124
- formatted_messages.append(formatted_msg)
125
-
126
- return formatted_messages
127
-
128
- def validate_messages(self, messages: List[Dict[str, Any]]) -> bool:
129
- """Validate message format."""
130
- if not messages:
131
- return False
132
-
133
- for msg in messages:
134
- if not isinstance(msg, dict):
135
- return False
136
- if "role" not in msg or "content" not in msg:
137
- return False
138
- if msg["role"] not in ["system", "user", "assistant"]:
139
- return False
140
-
141
- return True
142
-
143
- def stream(
144
- self, messages: List[Dict[str, Any]], **kwargs
145
- ) -> Generator[str, None, CompletionResponse]:
146
- """Generate a streaming completion.
147
-
148
- Args:
149
- messages: List of messages in standard format
150
- **kwargs: Additional parameters
151
-
152
- Yields:
153
- Text chunks during streaming
154
-
155
- Returns:
156
- Final CompletionResponse when complete
157
- """
158
- # Validate messages
159
- if not self.validate_messages(messages):
160
- raise ValueError("Invalid message format")
161
-
162
- # Format messages for Groq
163
- formatted_messages = self.format_messages(messages)
164
-
165
- # Prepare API parameters
166
- api_params = {
167
- "model": self.model,
168
- "messages": formatted_messages,
169
- "stream": True,
170
- }
171
-
172
- # Add optional parameters
173
- for param in ["temperature", "max_tokens", "top_p", "stop", "seed"]:
174
- if param in kwargs:
175
- api_params[param] = kwargs[param]
176
-
177
- # Groq has a max token limit of 8000
178
- if "max_tokens" in api_params:
179
- api_params["max_tokens"] = min(api_params["max_tokens"], 8000)
180
-
181
- try:
182
- # Make streaming API call
183
- stream = self.client.chat.completions.create(**api_params)
184
-
185
- # Track content
186
- full_content = ""
187
-
188
- for chunk in stream:
189
- if chunk.choices[0].delta.content:
190
- content = chunk.choices[0].delta.content
191
- full_content += content
192
- yield content
193
-
194
- # Estimate tokens for streaming (Groq doesn't provide usage in stream)
195
- input_tokens = self.count_tokens(str(formatted_messages))
196
- output_tokens = self.count_tokens(full_content)
197
-
198
- # Return final response
199
- return CompletionResponse(
200
- content=full_content,
201
- input_tokens=input_tokens,
202
- output_tokens=output_tokens,
203
- finish_reason="stop",
204
- )
205
-
206
- except Exception as e:
207
- logger.error(f"Groq streaming error: {str(e)}")
208
- raise
209
-
210
- def count_tokens(self, text: str) -> int:
211
- """Count tokens in the given text.
212
-
213
- Args:
214
- text: Text to count tokens for
215
-
216
- Returns:
217
- Number of tokens (estimated)
218
- """
219
- # Groq doesn't provide a token counter, so estimate
220
- # Llama tokenization is roughly similar to GPT
221
- return len(text.split()) * 4 // 3
222
-
223
- @property
224
- def supports_images(self) -> bool:
225
- """Check if this provider/model supports image inputs."""
226
- # Groq doesn't currently support multimodal inputs
227
- return False
228
-
229
- @property
230
- def supports_streaming(self) -> bool:
231
- """Check if this provider/model supports streaming."""
232
- return True
233
-
234
- @property
235
- def max_context_length(self) -> int:
236
- """Get maximum context length for this model."""
237
- context_lengths = {
238
- "llama3-8b-8192": 8192,
239
- "llama3-70b-8192": 8192,
240
- "llama2-70b-4096": 4096,
241
- "mixtral-8x7b-32768": 32768,
242
- "gemma-7b-it": 8192,
243
- }
244
- return context_lengths.get(self.model, 8192)
245
-
246
-
247
- # Auto-register when module is imported
248
- register_provider(Provider.GROQ.value, GroqProvider)
@@ -1,250 +0,0 @@
1
- #!/usr/bin/env python3
2
- # -*- coding: utf-8 -*-
3
- # Time-stamp: "2025-05-31 10:25:00"
4
- # Author: ywatanabe
5
- # File: ./src/scitex/ai/genai/image_processor.py
6
-
7
- """
8
- Handles image processing for multimodal AI inputs.
9
-
10
- This module provides image processing functionality including:
11
- - Image resizing to fit token limits
12
- - Base64 encoding for API transmission
13
- - Multiple format support (file path, bytes, PIL Image)
14
- - Format validation
15
- """
16
-
17
- import base64
18
- import io
19
- from typing import Union, Tuple, Optional
20
- from PIL import Image
21
-
22
-
23
- class ImageProcessor:
24
- """Processes images for multimodal AI inputs.
25
-
26
- Example
27
- -------
28
- >>> processor = ImageProcessor()
29
- >>> # Process image from file
30
- >>> base64_str = processor.process_image("path/to/image.jpg", max_size=512)
31
- >>> print(base64_str[:50])
32
- /9j/4AAQSkZJRgABAQEASABIAAD/2wBDAAgGBgcGBQgHBw...
33
-
34
- >>> # Process PIL Image
35
- >>> from PIL import Image
36
- >>> img = Image.new('RGB', (100, 100), color='red')
37
- >>> base64_str = processor.process_image(img)
38
- """
39
-
40
- def __init__(self):
41
- """Initialize image processor."""
42
- self.supported_formats = {".jpg", ".jpeg", ".png", ".gif", ".bmp", ".webp"}
43
-
44
- def process_image(
45
- self, image: Union[str, bytes, Image.Image], max_size: int = 512
46
- ) -> str:
47
- """Process an image for API transmission.
48
-
49
- Parameters
50
- ----------
51
- image : Union[str, bytes, Image.Image]
52
- Image as file path, bytes, or PIL Image
53
- max_size : int
54
- Maximum dimension (width or height) in pixels
55
-
56
- Returns
57
- -------
58
- str
59
- Base64 encoded image string
60
- """
61
- # Convert to PIL Image
62
- pil_image = self._to_pil_image(image)
63
-
64
- # Resize if needed
65
- if max(pil_image.size) > max_size:
66
- pil_image = self.resize_image(pil_image, max_size)
67
-
68
- # Convert to base64
69
- return self.to_base64(pil_image)
70
-
71
- def _to_pil_image(self, image: Union[str, bytes, Image.Image]) -> Image.Image:
72
- """Convert various image formats to PIL Image.
73
-
74
- Parameters
75
- ----------
76
- image : Union[str, bytes, Image.Image]
77
- Input image in various formats
78
-
79
- Returns
80
- -------
81
- Image.Image
82
- PIL Image object
83
- """
84
- if isinstance(image, Image.Image):
85
- return image
86
-
87
- if isinstance(image, str):
88
- # Check if it's a base64 string
89
- if image.startswith("data:image"):
90
- # Extract base64 data from data URL
91
- base64_data = image.split(",")[1]
92
- image_bytes = base64.b64decode(base64_data)
93
- return Image.open(io.BytesIO(image_bytes))
94
- else:
95
- # Assume it's a file path
96
- try:
97
- return Image.open(image)
98
- except Exception as e:
99
- # Maybe it's already base64 encoded
100
- try:
101
- image_bytes = base64.b64decode(image)
102
- return Image.open(io.BytesIO(image_bytes))
103
- except:
104
- raise ValueError(f"Could not load image from string: {e}")
105
-
106
- if isinstance(image, bytes):
107
- return Image.open(io.BytesIO(image))
108
-
109
- raise ValueError(f"Unsupported image type: {type(image)}")
110
-
111
- def resize_image(self, image: Image.Image, max_size: int) -> Image.Image:
112
- """Resize image to fit within max_size while maintaining aspect ratio.
113
-
114
- Parameters
115
- ----------
116
- image : Image.Image
117
- PIL Image to resize
118
- max_size : int
119
- Maximum dimension in pixels
120
-
121
- Returns
122
- -------
123
- Image.Image
124
- Resized PIL Image
125
- """
126
- # Calculate new dimensions
127
- width, height = image.size
128
- aspect_ratio = width / height
129
-
130
- if width > height:
131
- new_width = max_size
132
- new_height = int(max_size / aspect_ratio)
133
- else:
134
- new_height = max_size
135
- new_width = int(max_size * aspect_ratio)
136
-
137
- # Use high-quality resampling
138
- return image.resize((new_width, new_height), Image.Resampling.LANCZOS)
139
-
140
- def to_base64(self, image: Image.Image, format: str = "JPEG") -> str:
141
- """Convert PIL Image to base64 string.
142
-
143
- Parameters
144
- ----------
145
- image : Image.Image
146
- PIL Image to encode
147
- format : str
148
- Output format (JPEG, PNG, etc.)
149
-
150
- Returns
151
- -------
152
- str
153
- Base64 encoded image string
154
- """
155
- # Convert RGBA to RGB if saving as JPEG
156
- if format.upper() == "JPEG" and image.mode in ("RGBA", "LA", "P"):
157
- # Create a white background
158
- background = Image.new("RGB", image.size, (255, 255, 255))
159
- if image.mode == "P":
160
- image = image.convert("RGBA")
161
- background.paste(
162
- image, mask=image.split()[-1] if image.mode == "RGBA" else None
163
- )
164
- image = background
165
-
166
- # Save to bytes buffer
167
- buffer = io.BytesIO()
168
- image.save(
169
- buffer, format=format, quality=95 if format.upper() == "JPEG" else None
170
- )
171
-
172
- # Encode to base64
173
- return base64.b64encode(buffer.getvalue()).decode("utf-8")
174
-
175
- def get_image_info(self, image: Union[str, bytes, Image.Image]) -> dict:
176
- """Get information about an image.
177
-
178
- Parameters
179
- ----------
180
- image : Union[str, bytes, Image.Image]
181
- Image to analyze
182
-
183
- Returns
184
- -------
185
- dict
186
- Image information including size, mode, format
187
- """
188
- pil_image = self._to_pil_image(image)
189
-
190
- return {
191
- "width": pil_image.width,
192
- "height": pil_image.height,
193
- "mode": pil_image.mode,
194
- "format": pil_image.format,
195
- "size_mb": self._estimate_size_mb(pil_image),
196
- }
197
-
198
- def _estimate_size_mb(self, image: Image.Image) -> float:
199
- """Estimate image size in megabytes.
200
-
201
- Parameters
202
- ----------
203
- image : Image.Image
204
- PIL Image
205
-
206
- Returns
207
- -------
208
- float
209
- Estimated size in MB
210
- """
211
- # Rough estimate based on dimensions and mode
212
- bytes_per_pixel = len(image.mode) # Rough estimate
213
- total_bytes = image.width * image.height * bytes_per_pixel
214
- return total_bytes / (1024 * 1024)
215
-
216
- def validate_image(self, image_path: str) -> bool:
217
- """Validate if a file is a supported image format.
218
-
219
- Parameters
220
- ----------
221
- image_path : str
222
- Path to image file
223
-
224
- Returns
225
- -------
226
- bool
227
- True if valid image format
228
- """
229
- if not isinstance(image_path, str):
230
- return False
231
-
232
- # Check file extension
233
- ext = image_path.lower().split(".")[-1]
234
- if f".{ext}" not in self.supported_formats:
235
- return False
236
-
237
- # Try to open the image
238
- try:
239
- img = Image.open(image_path)
240
- img.verify()
241
- return True
242
- except:
243
- return False
244
-
245
- def __repr__(self) -> str:
246
- """String representation of ImageProcessor."""
247
- return f"ImageProcessor(supported_formats={self.supported_formats})"
248
-
249
-
250
- # EOF
@@ -1,214 +0,0 @@
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- #!/usr/bin/env python3
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- # -*- coding: utf-8 -*-
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- # Time-stamp: "2024-11-13 20:25:55 (ywatanabe)"
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- # File: ./scitex_repo/src/scitex/ai/genai/llama_provider.py
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-
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- """Llama provider implementation using the new component-based architecture.
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-
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- This module provides integration with local Llama models through the official Llama library.
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- It supports loading and running Llama models locally with full control over model parameters.
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- """
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-
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- import os
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- from typing import Dict, List, Iterator, Optional, Any
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-
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- try:
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- from llama import Llama as _Llama
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- from llama import Dialog
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- except ImportError:
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- _Llama = None
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- Dialog = None
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- print(
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- "Warning: llama package not installed. "
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- "Install with the official Meta Llama repository instructions."
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- )
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-
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- from .base_provider import BaseProvider, ProviderConfig
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-
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-
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- class LlamaProvider(BaseProvider):
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- """Llama provider implementation for local model inference."""
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-
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- SUPPORTED_MODELS = [
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- "Meta-Llama-3-8B",
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- "Meta-Llama-3-70B",
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- "Meta-Llama-3.1-8B",
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- "Meta-Llama-3.1-70B",
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- "Meta-Llama-3.1-405B",
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- "Llama-2-7b",
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- "Llama-2-13b",
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- "Llama-2-70b",
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- ]
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-
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- DEFAULT_MODEL = "Meta-Llama-3-8B"
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-
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- def __init__(self, config: ProviderConfig):
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- """Initialize Llama provider.
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-
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- Args:
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- config: Provider configuration
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- """
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- self.config = config
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- self.model_name = config.model or self.DEFAULT_MODEL
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-
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- # Llama-specific configuration
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- self.ckpt_dir = getattr(config, "ckpt_dir", None) or f"{self.model_name}/"
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- self.tokenizer_path = (
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- getattr(config, "tokenizer_path", None)
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- or f"{self.model_name}/tokenizer.model"
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- )
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- self.max_seq_len = getattr(config, "max_seq_len", 32_768)
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- self.max_batch_size = getattr(config, "max_batch_size", 4)
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- self.max_gen_len = config.max_tokens
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-
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- # Configure environment variables for distributed inference
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- self._setup_environment()
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-
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- # Initialize the Llama model
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- if _Llama is None:
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- raise ImportError(
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- "Llama package is not installed. Please install it from the official Meta repository."
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- )
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-
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- try:
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- self.generator = _Llama.build(
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- ckpt_dir=self.ckpt_dir,
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- tokenizer_path=self.tokenizer_path,
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- max_seq_len=self.max_seq_len,
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- max_batch_size=self.max_batch_size,
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- )
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- except Exception as e:
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- raise RuntimeError(f"Failed to load Llama model: {str(e)}")
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-
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- def _setup_environment(self):
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- """Set up environment variables for distributed inference."""
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- env_vars = {
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- "MASTER_ADDR": os.getenv("MASTER_ADDR", "localhost"),
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- "MASTER_PORT": os.getenv("MASTER_PORT", "12355"),
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- "WORLD_SIZE": os.getenv("WORLD_SIZE", "1"),
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- "RANK": os.getenv("RANK", "0"),
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- }
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-
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- for key, value in env_vars.items():
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- os.environ[key] = value
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-
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- def validate_messages(self, messages: List[Dict[str, Any]]) -> None:
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- """Validate message format.
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-
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- Args:
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- messages: List of message dictionaries
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-
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- Raises:
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- ValueError: If messages are invalid
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- """
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- if not messages:
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- raise ValueError("Messages cannot be empty")
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-
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- for msg in messages:
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- if "role" not in msg:
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- raise ValueError(f"Missing role in message: {msg}")
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- if "content" not in msg:
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- raise ValueError(f"Missing content in message: {msg}")
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- if msg["role"] not in ["system", "user", "assistant"]:
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- raise ValueError(f"Invalid role: {msg['role']}")
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-
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- def format_messages(self, messages: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
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- """Format messages for Llama API.
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-
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- Args:
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- messages: List of message dictionaries
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-
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- Returns:
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- Formatted messages for Llama
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- """
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- formatted = []
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-
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- # Add system prompt if configured
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- if self.config.system_prompt:
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- formatted.append({"role": "system", "content": self.config.system_prompt})
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-
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- # Add user messages
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- formatted.extend(messages)
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-
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- return formatted
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-
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- def complete(self, messages: List[Dict[str, Any]], **kwargs) -> Dict[str, Any]:
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- """Generate a completion.
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-
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- Args:
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- messages: List of message dictionaries
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- **kwargs: Additional parameters for the API
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-
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- Returns:
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- Completion response dictionary
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- """
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- self.validate_messages(messages)
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- formatted_messages = self.format_messages(messages)
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-
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- # Convert to Llama Dialog format
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- dialogs: List[Dialog] = [formatted_messages]
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-
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- # Merge config parameters with kwargs
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- params = {
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- "max_gen_len": self.max_gen_len,
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- "temperature": self.config.temperature or 1.0,
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- "top_p": kwargs.get("top_p", 0.9),
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- }
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-
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- try:
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- results = self.generator.chat_completion(dialogs, **params)
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-
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- result = results[0]
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- content = result["generation"]["content"]
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-
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- # Estimate token counts (Llama doesn't provide exact counts)
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- prompt_tokens = len(
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- " ".join(msg["content"] for msg in formatted_messages).split()
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- )
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- completion_tokens = len(content.split())
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-
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- return {
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- "content": content,
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- "model": self.model_name,
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- "usage": {
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- "prompt_tokens": prompt_tokens,
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- "completion_tokens": completion_tokens,
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- "total_tokens": prompt_tokens + completion_tokens,
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- },
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- "finish_reason": "stop",
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- }
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- except Exception as e:
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- raise RuntimeError(f"Llama inference error: {str(e)}")
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-
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- def stream(
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- self, messages: List[Dict[str, Any]], **kwargs
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- ) -> Iterator[Dict[str, Any]]:
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- """Stream a completion.
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-
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- Note: Llama doesn't have native streaming support, so this simulates streaming
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- by yielding characters one at a time.
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-
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- Args:
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- messages: List of message dictionaries
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- **kwargs: Additional parameters for the API
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-
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- Yields:
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- Chunks of the completion
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- """
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- # Get the full response
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- response = self.complete(messages, **kwargs)
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- content = response["content"]
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-
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- # Simulate streaming by yielding characters
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- for i, char in enumerate(content):
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- yield {
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- "content": char,
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- "model": self.model_name,
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- }
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-
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- # Yield final chunk with usage info
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- yield {
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- "content": "",
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- "usage": response["usage"],
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- "finish_reason": "stop",
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- }