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
@@ -1,277 +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/__init__.py
6
-
7
- """
8
- GenAI module for unified access to multiple AI providers.
9
-
10
- This module provides a consistent interface for interacting with various
11
- AI providers (OpenAI, Anthropic, Google, etc.) with built-in cost tracking,
12
- chat history management, and error handling.
13
- """
14
-
15
- from typing import List, Dict, Any, Optional, Union
16
- import logging
17
-
18
- from .provider_factory import Provider, create_provider, GenAI as GenAIFactory
19
- from .auth_manager import AuthManager
20
- from .chat_history import ChatHistory
21
- from .cost_tracker import CostTracker
22
- from .response_handler import ResponseHandler
23
- from .base_provider import BaseProvider, CompletionResponse
24
-
25
- # Import legacy providers for backward compatibility
26
- from .anthropic import Anthropic
27
- from .openai import OpenAI
28
- from .google import Google
29
- from .groq import Groq
30
- from .deepseek import DeepSeek
31
- from .llama import Llama
32
- from .perplexity import Perplexity
33
- from .genai_factory import genai_factory
34
-
35
- logger = logging.getLogger(__name__)
36
-
37
-
38
- class GenAI:
39
- """
40
- Unified interface for multiple AI providers.
41
-
42
- This class provides a consistent API for interacting with various AI providers
43
- while handling authentication, chat history, cost tracking, and response processing.
44
-
45
- Args:
46
- provider: Provider name (e.g., 'openai', 'anthropic', 'google')
47
- api_key: Optional API key (if not provided, will use environment variable)
48
- model: Model name (if not provided, will use provider's default)
49
- system_prompt: Optional system prompt to prepend to conversations
50
- **kwargs: Additional provider-specific configuration
51
-
52
- Example:
53
- >>> from scitex.ai.genai import GenAI
54
- >>>
55
- >>> # Basic usage
56
- >>> ai = GenAI(provider="openai")
57
- >>> response = ai.complete("What is the capital of France?")
58
- >>> print(response)
59
- "The capital of France is Paris."
60
- >>>
61
- >>> # With specific model and system prompt
62
- >>> ai = GenAI(
63
- ... provider="anthropic",
64
- ... model="claude-3-opus-20240229",
65
- ... system_prompt="You are a helpful geography expert."
66
- ... )
67
- >>> response = ai.complete("Tell me about Paris.")
68
- >>>
69
- >>> # Check costs
70
- >>> print(ai.get_cost_summary())
71
- "Total cost: $0.015 | Requests: 2 | Tokens: 1,234"
72
- """
73
-
74
- def __init__(
75
- self,
76
- provider: Union[str, Provider],
77
- api_key: Optional[str] = None,
78
- model: Optional[str] = None,
79
- system_prompt: Optional[str] = None,
80
- **kwargs
81
- ):
82
- """Initialize GenAI with specified provider."""
83
- # Store provider name
84
- if isinstance(provider, str):
85
- self.provider_name = provider.lower()
86
- else:
87
- self.provider_name = provider.value
88
-
89
- # Initialize components
90
- self.auth_manager = AuthManager(api_key, self.provider_name)
91
- self.chat_history = ChatHistory(n_keep=-1) # Keep all messages by default
92
- self.response_handler = ResponseHandler()
93
-
94
- # Get API key from auth manager if not provided
95
- if api_key is None:
96
- api_key = self.auth_manager.api_key
97
-
98
- # Create provider instance
99
- self.provider = create_provider(
100
- provider=self.provider_name, api_key=api_key, model=model, **kwargs
101
- )
102
-
103
- # Initialize cost tracker with provider and model
104
- # Note: provider instance may have a model attribute set during initialization
105
- actual_model = getattr(self.provider, "model", None) or model or "unknown"
106
- self.cost_tracker = CostTracker(provider=self.provider_name, model=actual_model)
107
-
108
- # Add system prompt if provided
109
- if system_prompt:
110
- self.chat_history.add_message("system", system_prompt)
111
-
112
- logger.info(f"Initialized GenAI with provider: {self.provider_name}")
113
-
114
- def complete(
115
- self, prompt: str, images: Optional[List[str]] = None, **kwargs
116
- ) -> str:
117
- """
118
- Generate a completion for the given prompt.
119
-
120
- Args:
121
- prompt: The input prompt
122
- images: Optional list of image URLs or base64 strings
123
- **kwargs: Additional provider-specific parameters
124
-
125
- Returns:
126
- The generated response text
127
-
128
- Raises:
129
- ValueError: If the provider doesn't support images but images are provided
130
- Exception: Provider-specific exceptions
131
- """
132
- # Add user message to history
133
- self.chat_history.add_message("user", prompt, images)
134
-
135
- # Get messages for API call
136
- messages = [msg.to_dict() for msg in self.chat_history.get_messages()]
137
-
138
- # Call provider
139
- try:
140
- response: CompletionResponse = self.provider.complete(
141
- messages=messages, **kwargs
142
- )
143
- except Exception as e:
144
- logger.error(f"Provider {self.provider_name} failed: {str(e)}")
145
- raise
146
-
147
- # Process response - CompletionResponse has a content attribute
148
- content = response.content
149
-
150
- # Add assistant message to history
151
- self.chat_history.add_message("assistant", content)
152
-
153
- # Track costs - CompletionResponse has input_tokens and output_tokens
154
- self.cost_tracker.update(
155
- input_tokens=response.input_tokens, output_tokens=response.output_tokens
156
- )
157
-
158
- return content
159
-
160
- def complete_async(self, prompt: str, images: Optional[List[str]] = None, **kwargs):
161
- """
162
- Async version of complete method.
163
-
164
- Args:
165
- prompt: The input prompt
166
- images: Optional list of image URLs or base64 strings
167
- **kwargs: Additional provider-specific parameters
168
-
169
- Returns:
170
- Awaitable that resolves to the generated response text
171
- """
172
- raise NotImplementedError("Async completion not yet implemented")
173
-
174
- def stream(self, prompt: str, images: Optional[List[str]] = None, **kwargs):
175
- """
176
- Stream completions for the given prompt.
177
-
178
- Args:
179
- prompt: The input prompt
180
- images: Optional list of image URLs or base64 strings
181
- **kwargs: Additional provider-specific parameters
182
-
183
- Yields:
184
- Chunks of the generated response
185
- """
186
- raise NotImplementedError("Streaming not yet implemented")
187
-
188
- def clear_history(self):
189
- """Clear the chat history."""
190
- self.chat_history.clear()
191
- logger.info("Chat history cleared")
192
-
193
- def get_history(self) -> List[Dict[str, str]]:
194
- """Get the current chat history."""
195
- return self.chat_history.messages
196
-
197
- def get_cost_summary(self) -> str:
198
- """Get a summary of costs incurred."""
199
- return self.cost_tracker.get_summary()
200
-
201
- def get_detailed_costs(self) -> Dict[str, Any]:
202
- """Get detailed cost breakdown."""
203
- return {
204
- "total_cost": self.cost_tracker.total_cost,
205
- "total_prompt_tokens": self.cost_tracker.total_prompt_tokens,
206
- "total_completion_tokens": self.cost_tracker.total_completion_tokens,
207
- "request_count": self.cost_tracker.request_count,
208
- "cost_by_model": self.cost_tracker.cost_by_model,
209
- }
210
-
211
- def reset_costs(self):
212
- """Reset cost tracking."""
213
- self.cost_tracker.reset()
214
- logger.info("Cost tracking reset")
215
-
216
- def __repr__(self) -> str:
217
- """String representation of GenAI instance."""
218
- return (
219
- f"GenAI(provider='{self.provider_name}', "
220
- f"model='{self.provider.model}', "
221
- f"requests={self.cost_tracker.request_count})"
222
- )
223
-
224
-
225
- # Convenience function for one-off completions
226
- def complete(
227
- prompt: str,
228
- provider: Union[str, Provider] = "openai",
229
- model: Optional[str] = None,
230
- api_key: Optional[str] = None,
231
- **kwargs
232
- ) -> str:
233
- """
234
- Convenience function for one-off completions without managing state.
235
-
236
- Args:
237
- prompt: The input prompt
238
- provider: Provider name or enum
239
- model: Optional model name
240
- api_key: Optional API key
241
- **kwargs: Additional parameters
242
-
243
- Returns:
244
- The generated response text
245
-
246
- Example:
247
- >>> from scitex.ai.genai import complete
248
- >>> response = complete("What is 2+2?", provider="anthropic")
249
- >>> print(response)
250
- "2 + 2 = 4"
251
- """
252
- genai = GenAI(provider=provider, model=model, api_key=api_key)
253
- return genai.complete(prompt, **kwargs)
254
-
255
-
256
- # Export public API
257
- __all__ = [
258
- # New API
259
- "GenAI",
260
- "GenAIFactory",
261
- "complete",
262
- "Provider",
263
- "create_provider",
264
- "AuthManager",
265
- "ChatHistory",
266
- "CostTracker",
267
- "ResponseHandler",
268
- # Legacy API for backward compatibility
269
- "genai_factory",
270
- "Anthropic",
271
- "OpenAI",
272
- "Google",
273
- "Groq",
274
- "DeepSeek",
275
- "Llama",
276
- "Perplexity",
277
- ]
@@ -1,320 +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/anthropic_provider.py
6
-
7
- """
8
- Anthropic provider implementation for GenAI.
9
- """
10
-
11
- from typing import List, Dict, Any, Optional, Generator
12
- import logging
13
-
14
- from .base_provider import BaseProvider, CompletionResponse
15
-
16
- logger = logging.getLogger(__name__)
17
-
18
-
19
- class AnthropicProvider(BaseProvider):
20
- """
21
- Anthropic provider implementation.
22
-
23
- Supports Claude 3 models (Opus, Sonnet, Haiku).
24
- """
25
-
26
- SUPPORTED_MODELS = [
27
- "claude-3-opus-20240229",
28
- "claude-3-sonnet-20240229",
29
- "claude-3-haiku-20240307",
30
- "claude-2.1",
31
- "claude-2.0",
32
- "claude-instant-1.2",
33
- ]
34
-
35
- DEFAULT_MODEL = "claude-3-sonnet-20240229"
36
-
37
- def __init__(self, config):
38
- """Initialize Anthropic provider."""
39
- self.config = config
40
- self.api_key = config.api_key
41
- self.model = config.model or self.DEFAULT_MODEL
42
- self.kwargs = config.kwargs or {}
43
-
44
- # Import Anthropic client
45
- try:
46
- from anthropic import Anthropic as AnthropicClient
47
-
48
- self.client = AnthropicClient(api_key=api_key)
49
- except ImportError:
50
- raise ImportError(
51
- "Anthropic package not installed. Install with: pip install anthropic"
52
- )
53
-
54
- def complete(self, messages: List[Dict[str, Any]], **kwargs) -> CompletionResponse:
55
- """
56
- Generate completion using Anthropic API.
57
-
58
- Args:
59
- messages: List of message dictionaries
60
- **kwargs: Additional parameters (max_tokens, temperature, etc.)
61
-
62
- Returns:
63
- CompletionResponse with generated text and usage info
64
- """
65
- # Validate messages
66
- if not self.validate_messages(messages):
67
- raise ValueError("Invalid message format")
68
-
69
- # Format messages for Anthropic
70
- formatted_messages = self.format_messages(messages)
71
-
72
- # Extract system message if present
73
- system_message = None
74
- user_messages = []
75
-
76
- for msg in formatted_messages:
77
- if msg["role"] == "system":
78
- system_message = msg["content"]
79
- else:
80
- user_messages.append(msg)
81
-
82
- # Prepare API parameters
83
- api_params = {
84
- "model": self.model,
85
- "messages": user_messages,
86
- "max_tokens": kwargs.get("max_tokens", 4096),
87
- }
88
-
89
- # Add system message if present
90
- if system_message:
91
- api_params["system"] = system_message
92
-
93
- # Add optional parameters
94
- for param in ["temperature", "top_p", "top_k", "stop_sequences"]:
95
- if param in kwargs:
96
- api_params[param] = kwargs[param]
97
-
98
- try:
99
- # Make API call
100
- response = self.client.messages.create(**api_params)
101
-
102
- # Extract content
103
- content = response.content[0].text if response.content else ""
104
-
105
- # Extract usage
106
- usage = {
107
- "prompt_tokens": response.usage.input_tokens,
108
- "completion_tokens": response.usage.output_tokens,
109
- "total_tokens": response.usage.input_tokens
110
- + response.usage.output_tokens,
111
- }
112
-
113
- return CompletionResponse(content=content, usage=usage)
114
-
115
- except Exception as e:
116
- logger.error(f"Anthropic API error: {str(e)}")
117
- raise
118
-
119
- def format_messages(self, messages: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
120
- """
121
- Format messages for Anthropic API.
122
-
123
- Anthropic expects messages in the format::
124
-
125
- [
126
- {"role": "user", "content": "..."},
127
- {"role": "assistant", "content": "..."}
128
- ]
129
-
130
- System messages are passed separately.
131
-
132
- For images, the content should be a list::
133
-
134
- {
135
- "role": "user",
136
- "content": [
137
- {"type": "text", "text": "What's in this image?"},
138
- {"type": "image", "source": {"type": "base64", "media_type": "image/jpeg", "data": "..."}}
139
- ]
140
- }
141
- """
142
- formatted_messages = []
143
-
144
- for msg in messages:
145
- role = msg["role"]
146
- content = msg["content"]
147
- images = msg.get("images", [])
148
-
149
- if images and self.model.startswith("claude-3"):
150
- # Format with images (only Claude 3 supports images)
151
- content_parts = [{"type": "text", "text": content}]
152
-
153
- for img in images:
154
- if img.startswith("data:"):
155
- # Extract base64 data
156
- header, data = img.split(",", 1)
157
- media_type = header.split(":")[1].split(";")[0]
158
-
159
- content_parts.append(
160
- {
161
- "type": "image",
162
- "source": {
163
- "type": "base64",
164
- "media_type": media_type,
165
- "data": data,
166
- },
167
- }
168
- )
169
- else:
170
- # URL images not directly supported, would need to download first
171
- logger.warning("URL images not directly supported by Anthropic")
172
-
173
- formatted_messages.append({"role": role, "content": content_parts})
174
- else:
175
- # Regular text message
176
- formatted_messages.append({"role": role, "content": content})
177
-
178
- return formatted_messages
179
-
180
- def validate_messages(self, messages: List[Dict[str, Any]]) -> bool:
181
- """Validate message format."""
182
- if not messages:
183
- return False
184
-
185
- for msg in messages:
186
- if not isinstance(msg, dict):
187
- return False
188
- if "role" not in msg or "content" not in msg:
189
- return False
190
- if msg["role"] not in ["system", "user", "assistant"]:
191
- return False
192
-
193
- return True
194
-
195
- def stream(
196
- self, messages: List[Dict[str, Any]], **kwargs
197
- ) -> Generator[str, None, CompletionResponse]:
198
- """Generate a streaming completion.
199
-
200
- Args:
201
- messages: List of messages in standard format
202
- **kwargs: Additional parameters
203
-
204
- Yields:
205
- Text chunks during streaming
206
-
207
- Returns:
208
- Final CompletionResponse when complete
209
- """
210
- # Validate messages
211
- if not self.validate_messages(messages):
212
- raise ValueError("Invalid message format")
213
-
214
- # Format messages for Anthropic
215
- formatted_messages = self.format_messages(messages)
216
-
217
- # Extract system message if present
218
- system_message = None
219
- user_messages = []
220
-
221
- for msg in formatted_messages:
222
- if msg["role"] == "system":
223
- system_message = msg["content"]
224
- else:
225
- user_messages.append(msg)
226
-
227
- # Prepare API parameters
228
- api_params = {
229
- "model": self.model,
230
- "messages": user_messages,
231
- "max_tokens": kwargs.get("max_tokens", 4096),
232
- "stream": True,
233
- }
234
-
235
- # Add system message if present
236
- if system_message:
237
- api_params["system"] = system_message
238
-
239
- # Add optional parameters
240
- for param in ["temperature", "top_p", "top_k", "stop_sequences"]:
241
- if param in kwargs:
242
- api_params[param] = kwargs[param]
243
-
244
- try:
245
- # Make streaming API call
246
- full_content = ""
247
- prompt_tokens = 0
248
- completion_tokens = 0
249
-
250
- with self.client.messages.stream(**api_params) as stream:
251
- for text in stream.text_stream:
252
- full_content += text
253
- yield text
254
-
255
- # Get final message with usage info
256
- message = stream.get_final_message()
257
- if hasattr(message, "usage"):
258
- prompt_tokens = message.usage.input_tokens
259
- completion_tokens = message.usage.output_tokens
260
-
261
- # Return final response
262
- return CompletionResponse(
263
- content=full_content,
264
- usage={
265
- "prompt_tokens": prompt_tokens,
266
- "completion_tokens": completion_tokens,
267
- "total_tokens": prompt_tokens + completion_tokens,
268
- },
269
- )
270
-
271
- except Exception as e:
272
- logger.error(f"Anthropic streaming error: {str(e)}")
273
- raise
274
-
275
- def count_tokens(self, text: str) -> int:
276
- """Count tokens in the given text.
277
-
278
- Args:
279
- text: Text to count tokens for
280
-
281
- Returns:
282
- Number of tokens
283
- """
284
- try:
285
- # Anthropic uses its own tokenizer
286
- return self.client.count_tokens(text)
287
- except Exception:
288
- # Fallback: rough estimate (Claude tends to use fewer tokens than GPT)
289
- return len(text.split()) * 3 // 4
290
-
291
- @property
292
- def supports_images(self) -> bool:
293
- """Check if this provider/model supports image inputs."""
294
- # Only Claude 3 models support images
295
- return self.model.startswith("claude-3")
296
-
297
- @property
298
- def supports_streaming(self) -> bool:
299
- """Check if this provider/model supports streaming."""
300
- return True # All Anthropic models support streaming
301
-
302
- @property
303
- def max_context_length(self) -> int:
304
- """Get maximum context length for this model."""
305
- context_lengths = {
306
- "claude-3-opus-20240229": 200000,
307
- "claude-3-sonnet-20240229": 200000,
308
- "claude-3-haiku-20240307": 200000,
309
- "claude-2.1": 200000,
310
- "claude-2.0": 100000,
311
- "claude-instant-1.2": 100000,
312
- }
313
- return context_lengths.get(self.model, 100000)
314
-
315
-
316
- # Auto-register when module is imported
317
- from .base_provider import Provider
318
- from .provider_factory import register_provider
319
-
320
- register_provider(Provider.ANTHROPIC.value, AnthropicProvider)
@@ -1,109 +0,0 @@
1
- #!/usr/bin/env python3
2
- """Refactored Anthropic provider using component architecture."""
3
-
4
- from typing import List, Dict, Any, Generator
5
- import anthropic
6
-
7
- from .provider_base import ProviderBase, ProviderConfig
8
-
9
-
10
- class AnthropicProvider(ProviderBase):
11
- """Anthropic (Claude) provider implementation."""
12
-
13
- def _init_client(self) -> anthropic.Anthropic:
14
- """Initialize Anthropic client."""
15
- client_config = self.auth.get_client_config()
16
- return anthropic.Anthropic(**client_config)
17
-
18
- def _api_call(self, messages: List[Dict[str, Any]]) -> Any:
19
- """Make a non-streaming API call to Anthropic."""
20
- # Extract system prompt if present
21
- system_prompt = None
22
- filtered_messages = []
23
-
24
- for msg in messages:
25
- if msg["role"] == "system":
26
- system_prompt = msg["content"]
27
- else:
28
- filtered_messages.append(msg)
29
-
30
- # Make API call
31
- response = self.client.messages.create(
32
- model=self.config.model,
33
- messages=filtered_messages,
34
- max_tokens=self.config.max_tokens,
35
- temperature=self.config.temperature,
36
- system=system_prompt or self.config.system_prompt,
37
- stream=False,
38
- )
39
-
40
- return response
41
-
42
- def _api_stream(self, messages: List[Dict[str, Any]]) -> Generator[Any, None, None]:
43
- """Make a streaming API call to Anthropic."""
44
- # Extract system prompt
45
- system_prompt = None
46
- filtered_messages = []
47
-
48
- for msg in messages:
49
- if msg["role"] == "system":
50
- system_prompt = msg["content"]
51
- else:
52
- filtered_messages.append(msg)
53
-
54
- # Make streaming API call
55
- stream = self.client.messages.create(
56
- model=self.config.model,
57
- messages=filtered_messages,
58
- max_tokens=self.config.max_tokens,
59
- temperature=self.config.temperature,
60
- system=system_prompt or self.config.system_prompt,
61
- stream=True,
62
- )
63
-
64
- for chunk in stream:
65
- yield chunk
66
-
67
- def _extract_token_counts(self, response: Any) -> tuple[int, int]:
68
- """Extract token counts from Anthropic response."""
69
- input_tokens = getattr(response.usage, "input_tokens", 0)
70
- output_tokens = getattr(response.usage, "output_tokens", 0)
71
- return input_tokens, output_tokens
72
-
73
- def count_tokens(self, text: str) -> int:
74
- """Count tokens using Anthropic's tokenizer."""
75
- # Anthropic doesn't provide a public tokenizer
76
- # Use approximation for now
77
- # Claude's tokenization is roughly 1 token per 3.5 characters
78
- return len(text) // 3
79
-
80
-
81
- # Example usage:
82
- if __name__ == "__main__":
83
- # Create configuration
84
- config = ProviderConfig(
85
- provider="anthropic",
86
- model="claude-3-opus-20240229",
87
- system_prompt="You are a helpful assistant.",
88
- temperature=0.7,
89
- max_tokens=1024,
90
- )
91
-
92
- # Create provider instance
93
- claude = AnthropicProvider(config)
94
-
95
- # Use it
96
- messages = [{"role": "user", "content": "Hello, how are you?"}]
97
-
98
- # Non-streaming
99
- response = claude.complete(messages)
100
- print(response.content)
101
- print(f"Tokens: {response.input_tokens} in, {response.output_tokens} out")
102
-
103
- # Streaming
104
- print("\nStreaming response:")
105
- for chunk in claude.stream(messages):
106
- print(chunk, end="", flush=True)
107
-
108
- # Get cost summary
109
- print("\n\n" + claude.get_cost_summary())