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
@@ -0,0 +1,414 @@
1
+ #!/usr/bin/env python3
2
+ # -*- coding: utf-8 -*-
3
+ # Timestamp: "2025-09-14 09:51:10 (ywatanabe)"
4
+ # File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/rng/_RandomStateManager.py
5
+ # ----------------------------------------
6
+ from __future__ import annotations
7
+ import os
8
+ __FILE__ = __file__
9
+ __DIR__ = os.path.dirname(__FILE__)
10
+ # ----------------------------------------
11
+
12
+ """
13
+ Clean, simple RandomStateManager for scientific reproducibility.
14
+
15
+ Main API:
16
+ rng = RandomStateManager(seed=42) # Create instance
17
+ gen = rng("name") # Get named generator
18
+ rng.verify(obj, "name") # Verify reproducibility
19
+ """
20
+
21
+ import hashlib
22
+ import json
23
+ import pickle
24
+ from contextlib import contextmanager
25
+ from pathlib import Path
26
+ from typing import Any
27
+
28
+ # Global singleton instance
29
+ _GLOBAL_INSTANCE = None
30
+
31
+
32
+ class RandomStateManager:
33
+ """
34
+ Simple, robust random state manager for scientific computing.
35
+
36
+ Examples
37
+ --------
38
+ >>> import scitex as stx
39
+ >>>
40
+ >>> # Method 1: Direct usage
41
+ >>> rng = stx.rng.RandomStateManager(seed=42)
42
+ >>> data = rng("data").random(100)
43
+ >>>
44
+ >>> # Method 2: From session.start
45
+ >>> CONFIG, stdout, stderr, plt, CC, rng = stx.session.start(seed=42)
46
+ >>> model = rng("model").normal(size=(10, 10))
47
+ >>>
48
+ >>> # Verify reproducibility
49
+ >>> rng.verify(data, "my_data")
50
+ """
51
+
52
+ def __init__(self, seed: int = 42, verbose=True):
53
+ """Initialize with automatic module detection."""
54
+ self.seed = seed
55
+ self.verbose = verbose
56
+ self._generators = {}
57
+ self._cache_dir = Path.home() / ".scitex" / "rng"
58
+ self._cache_dir.mkdir(parents=True, exist_ok=True)
59
+
60
+ if verbose:
61
+ print(f"RandomStateManager initialized with seed {seed}")
62
+
63
+ # Auto-fix all available seeds
64
+ self._auto_fix_seeds(verbose=verbose)
65
+
66
+ def _auto_fix_seeds(self, verbose=True):
67
+ """Automatically detect and fix ALL available random modules."""
68
+ # OS environment
69
+ os.environ["PYTHONHASHSEED"] = str(self.seed)
70
+ os.environ["CUBLAS_WORKSPACE_CONFIG"] = ":4096:8"
71
+
72
+ fixed_modules = []
73
+
74
+ # Python random
75
+ try:
76
+ import random
77
+
78
+ random.seed(self.seed)
79
+ fixed_modules.append("random")
80
+ except ImportError:
81
+ pass
82
+
83
+ # NumPy
84
+ try:
85
+ import numpy as np
86
+
87
+ np.random.seed(self.seed)
88
+ # Also set default_rng for new API
89
+ self._np = np
90
+ self._np_default_rng = np.random.default_rng(self.seed)
91
+ fixed_modules.append("np")
92
+ except ImportError:
93
+ self._np = None
94
+
95
+ # PyTorch
96
+ try:
97
+ import torch
98
+
99
+ torch.manual_seed(self.seed)
100
+ if torch.cuda.is_available():
101
+ torch.cuda.manual_seed_all(self.seed)
102
+ torch.backends.cudnn.deterministic = True
103
+ torch.backends.cudnn.benchmark = False
104
+ fixed_modules.append("torch")
105
+ except ImportError:
106
+ pass
107
+
108
+ # TensorFlow
109
+ try:
110
+ import tensorflow as tf
111
+
112
+ tf.random.set_seed(self.seed)
113
+ fixed_modules.append("tensorflow")
114
+ except ImportError:
115
+ pass
116
+
117
+ # JAX
118
+ try:
119
+ import jax
120
+
121
+ self._jax_key = jax.random.PRNGKey(self.seed)
122
+ fixed_modules.append("jax")
123
+ except ImportError:
124
+ pass
125
+
126
+ if verbose or self.verbose:
127
+ print(f"Fixed random seeds for {fixed_modules}")
128
+
129
+ def __call__(self, name: str, verbose=False):
130
+ """
131
+ Get or create a named random generator.
132
+
133
+ Parameters
134
+ ----------
135
+ name : str
136
+ Generator name (e.g., "data", "model", "augment")
137
+
138
+ Returns
139
+ -------
140
+ numpy.random.Generator
141
+ Independent random generator
142
+
143
+ Examples
144
+ --------
145
+ >>> rng = RandomStateManager(42)
146
+ >>> data_gen = rng("data")
147
+ >>> values = data_gen.random(100)
148
+ """
149
+ if self._np is None:
150
+ raise ImportError("NumPy required for random generators")
151
+
152
+ if name not in self._generators:
153
+ # Create deterministic seed from name
154
+ name_hash = int(hashlib.md5(name.encode()).hexdigest()[:8], 16)
155
+ seed = (self.seed + name_hash) % (2**32)
156
+ self._generators[name] = self._np.random.default_rng(seed)
157
+
158
+ return self._generators[name]
159
+
160
+ def verify(self, obj: Any, name: str = None) -> bool:
161
+ """
162
+ Verify object matches cached hash (detects broken reproducibility).
163
+
164
+ First call: caches the object's hash
165
+ Later calls: verifies object matches cached hash
166
+
167
+ Parameters
168
+ ----------
169
+ obj : Any
170
+ Object to verify (array, tensor, data, model weights, etc.)
171
+ Supports: numpy arrays, torch tensors, tf tensors, jax arrays,
172
+ lists, dicts, pandas dataframes, and basic types
173
+ name : str, optional
174
+ Cache name. Auto-generated if not provided.
175
+
176
+ Returns
177
+ -------
178
+ bool
179
+ True if matches cache (or first call), False if different
180
+
181
+ Examples
182
+ --------
183
+ >>> data = generate_data()
184
+ >>> rng.verify(data, "train_data") # First run: caches
185
+ >>> # Next run:
186
+ >>> rng.verify(data, "train_data") # Verifies match
187
+ """
188
+ import numpy as np
189
+
190
+ # Auto-generate name if needed
191
+ if name is None:
192
+ import inspect
193
+
194
+ frame = inspect.currentframe().f_back
195
+ filename = Path(frame.f_code.co_filename).stem
196
+ lineno = frame.f_lineno
197
+ name = f"{filename}_L{lineno}"
198
+
199
+ # Sanitize name
200
+ safe_name = "".join(
201
+ c if c.isalnum() or c in "-_" else "_" for c in name
202
+ )
203
+ cache_file = self._cache_dir / f"{safe_name}.json"
204
+
205
+ # Compute hash based on object type
206
+ obj_hash = self._compute_hash(obj)
207
+
208
+ # Check cache
209
+ if cache_file.exists():
210
+ with open(cache_file, "r") as f:
211
+ cached = json.load(f)
212
+
213
+ matches = cached["hash"] == obj_hash
214
+ if not matches:
215
+ print(f"⚠️ Reproducibility broken for '{name}'!")
216
+ print(f" Expected: {cached['hash'][:16]}...")
217
+ print(f" Got: {obj_hash[:16]}...")
218
+ return matches
219
+ else:
220
+ # First call - cache it
221
+ with open(cache_file, "w") as f:
222
+ json.dump(
223
+ {"name": name, "hash": obj_hash, "seed": self.seed}, f
224
+ )
225
+ return True
226
+
227
+ def _compute_hash(self, obj: Any) -> str:
228
+ """
229
+ Compute hash for various object types.
230
+
231
+ Supports:
232
+ - NumPy arrays
233
+ - PyTorch tensors
234
+ - TensorFlow tensors
235
+ - JAX arrays
236
+ - Pandas DataFrames/Series
237
+ - Lists, tuples, dicts
238
+ - Basic types (int, float, str, bool)
239
+ """
240
+ import numpy as np
241
+
242
+ # NumPy array
243
+ if isinstance(obj, np.ndarray):
244
+ return hashlib.sha256(obj.tobytes()).hexdigest()[:32]
245
+
246
+ # PyTorch tensor
247
+ try:
248
+ import torch
249
+
250
+ if isinstance(obj, torch.Tensor):
251
+ # Move to CPU and convert to numpy for consistent hashing
252
+ obj_np = obj.detach().cpu().numpy()
253
+ return hashlib.sha256(obj_np.tobytes()).hexdigest()[:32]
254
+ except ImportError:
255
+ pass
256
+
257
+ # TensorFlow tensor
258
+ try:
259
+ import tensorflow as tf
260
+
261
+ if isinstance(obj, (tf.Tensor, tf.Variable)):
262
+ obj_np = obj.numpy()
263
+ return hashlib.sha256(obj_np.tobytes()).hexdigest()[:32]
264
+ except ImportError:
265
+ pass
266
+
267
+ # JAX array
268
+ try:
269
+ import jax.numpy as jnp
270
+
271
+ if isinstance(obj, jnp.ndarray):
272
+ obj_np = np.array(obj)
273
+ return hashlib.sha256(obj_np.tobytes()).hexdigest()[:32]
274
+ except ImportError:
275
+ pass
276
+
277
+ # Pandas DataFrame/Series
278
+ try:
279
+ import pandas as pd
280
+
281
+ if isinstance(obj, (pd.DataFrame, pd.Series)):
282
+ # Use pandas string representation for hashing
283
+ obj_str = obj.to_json(orient="split", date_format="iso")
284
+ return hashlib.sha256(obj_str.encode()).hexdigest()[:32]
285
+ except ImportError:
286
+ pass
287
+
288
+ # Lists and tuples - convert to numpy array if numeric
289
+ if isinstance(obj, (list, tuple)):
290
+ try:
291
+ obj_np = np.array(obj)
292
+ if obj_np.dtype != object: # Numeric array
293
+ return hashlib.sha256(obj_np.tobytes()).hexdigest()[:32]
294
+ except:
295
+ pass
296
+ # Fall through to string representation
297
+
298
+ # Dictionaries - serialize to JSON
299
+ if isinstance(obj, dict):
300
+ try:
301
+ obj_str = json.dumps(obj, sort_keys=True, default=str)
302
+ return hashlib.sha256(obj_str.encode()).hexdigest()[:32]
303
+ except:
304
+ pass
305
+
306
+ # Default: convert to string
307
+ obj_str = str(obj)
308
+ return hashlib.sha256(obj_str.encode()).hexdigest()[:32]
309
+
310
+ def checkpoint(self, name: str = "checkpoint"):
311
+ """Save current state of all generators."""
312
+ checkpoint_file = self._cache_dir / f"{name}.pkl"
313
+ state = {
314
+ "seed": self.seed,
315
+ "generators": {
316
+ k: v.bit_generator.state for k, v in self._generators.items()
317
+ },
318
+ }
319
+ with open(checkpoint_file, "wb") as f:
320
+ pickle.dump(state, f)
321
+ return checkpoint_file
322
+
323
+ def restore(self, checkpoint):
324
+ """Restore from checkpoint."""
325
+ if isinstance(checkpoint, str):
326
+ checkpoint = Path(checkpoint)
327
+
328
+ with open(checkpoint, "rb") as f:
329
+ state = pickle.load(f)
330
+
331
+ self.seed = state["seed"]
332
+ self._auto_fix_seeds()
333
+
334
+ # Restore generator states
335
+ for name, gen_state in state["generators"].items():
336
+ gen = self(name)
337
+ gen.bit_generator.state = gen_state
338
+
339
+ @contextmanager
340
+ def temporary_seed(self, seed: int):
341
+ """Context manager for temporary seed change."""
342
+ import random
343
+
344
+ import numpy as np
345
+
346
+ # Save current states
347
+ old_random_state = random.getstate()
348
+ old_np_state = np.random.get_state() if self._np else None
349
+
350
+ # Set temporary seed
351
+ random.seed(seed)
352
+ if self._np:
353
+ np.random.seed(seed)
354
+
355
+ try:
356
+ yield
357
+ finally:
358
+ # Restore states
359
+ random.setstate(old_random_state)
360
+ if self._np and old_np_state:
361
+ np.random.set_state(old_np_state)
362
+
363
+ def get_generator(self, name: str):
364
+ """Alias for __call__ for compatibility."""
365
+ return self(name)
366
+
367
+
368
+ def get() -> RandomStateManager:
369
+ """
370
+ Get or create the global RandomStateManager instance.
371
+
372
+ Returns
373
+ -------
374
+ RandomStateManager
375
+ Global instance
376
+
377
+ Examples
378
+ --------
379
+ >>> import scitex as stx
380
+ >>> rng = stx.rng.get()
381
+ >>> data = rng("data").random(100)
382
+ """
383
+ global _GLOBAL_INSTANCE
384
+
385
+ if _GLOBAL_INSTANCE is None:
386
+ _GLOBAL_INSTANCE = RandomStateManager(42)
387
+
388
+ return _GLOBAL_INSTANCE
389
+
390
+
391
+ def reset(seed: int = 42) -> RandomStateManager:
392
+ """
393
+ Reset global RandomStateManager with new seed.
394
+
395
+ Parameters
396
+ ----------
397
+ seed : int
398
+ New seed value
399
+
400
+ Returns
401
+ -------
402
+ RandomStateManager
403
+ New global instance
404
+
405
+ Examples
406
+ --------
407
+ >>> import scitex as stx
408
+ >>> rng = stx.rng.reset(seed=123)
409
+ """
410
+ global _GLOBAL_INSTANCE
411
+ _GLOBAL_INSTANCE = RandomStateManager(seed)
412
+ return _GLOBAL_INSTANCE
413
+
414
+ # EOF
scitex/rng/__init__.py ADDED
@@ -0,0 +1,39 @@
1
+ #!/usr/bin/env python3
2
+ """
3
+ SciTeX RNG Module - Simple Random State Management.
4
+
5
+ Main API:
6
+ rng = stx.rng.RandomStateManager(seed=42) # Create instance
7
+ rng = stx.rng.get() # Get global instance
8
+ rng = stx.rng.reset(seed=123) # Reset global
9
+
10
+ gen = rng("name") # Get named generator
11
+ rng.verify(obj, "name") # Verify reproducibility
12
+
13
+ Examples
14
+ --------
15
+ >>> import scitex as stx
16
+
17
+ >>> # Direct usage
18
+ >>> rng = stx.rng.RandomStateManager(seed=42)
19
+ >>> data = rng("data").random(100)
20
+
21
+ >>> # Global instance
22
+ >>> rng = stx.rng.get()
23
+ >>> model = rng("model").normal(size=(10, 10))
24
+
25
+ >>> # From session.start
26
+ >>> CONFIG, stdout, stderr, plt, CC, rng = stx.session.start(seed=42)
27
+ >>> augment = rng("augment").random(50)
28
+
29
+ >>> # Verify reproducibility
30
+ >>> rng.verify(data, "my_data")
31
+ """
32
+
33
+ from ._RandomStateManager import RandomStateManager, get, reset
34
+
35
+ __all__ = [
36
+ "RandomStateManager",
37
+ "get",
38
+ "reset",
39
+ ]