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

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
  329. scitex/ml/utils/_format_samples_for_sktime.py +26 -0
  330. scitex/ml/utils/_label_encoder.py +134 -0
  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
  337. scitex/nn/_Filters.py +2 -2
  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
  343. scitex/path/_clean.py +4 -0
  344. scitex/path/_find.py +9 -4
  345. scitex/path/_symlink.py +348 -0
  346. scitex/path/_version.py +4 -3
  347. scitex/pd/__init__.py +2 -0
  348. scitex/pd/_get_unique.py +99 -0
  349. scitex/plt/__init__.py +114 -5
  350. scitex/plt/_subplots/_AxesWrapper.py +1 -3
  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
  354. scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +26 -4
  355. scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +322 -0
  356. scitex/plt/_subplots/_AxisWrapperMixins/__init__.py +1 -0
  357. scitex/plt/_subplots/_FigWrapper.py +62 -6
  358. scitex/plt/_subplots/_export_as_csv.py +43 -27
  359. scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +5 -4
  360. scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +81 -0
  361. scitex/plt/_subplots/_export_as_csv_formatters/_format_bar.py +1 -3
  362. scitex/plt/_subplots/_export_as_csv_formatters/_format_barh.py +20 -5
  363. scitex/plt/_subplots/_export_as_csv_formatters/_format_boxplot.py +1 -3
  364. scitex/plt/_subplots/_export_as_csv_formatters/_format_contour.py +1 -3
  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
  372. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot.py +15 -3
  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
  409. scitex/plt/ax/_style/_hide_spines.py +1 -3
  410. scitex/plt/ax/_style/_rotate_labels.py +180 -76
  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
  430. scitex/resource/_get_processor_usages.py +4 -4
  431. scitex/resource/_get_specs.py +2 -2
  432. scitex/resource/_log_processor_usages.py +2 -2
  433. scitex/rng/_RandomStateManager.py +590 -0
  434. scitex/rng/_RandomStateManager_v01-no-verbose-options.py +414 -0
  435. scitex/rng/__init__.py +39 -0
  436. scitex/scholar/__init__.py +309 -19
  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
  490. scitex/scholar/integration/zotero/__init__.py +27 -0
  491. scitex/scholar/integration/zotero/__main__.py +264 -0
  492. scitex/scholar/integration/zotero/exporter.py +351 -0
  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
  496. scitex/scholar/metadata_engines/ScholarEngine.py +588 -0
  497. scitex/scholar/metadata_engines/__init__.py +21 -0
  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
  502. scitex/scholar/metadata_engines/individual/PubMedEngine.py +329 -0
  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
  507. scitex/scholar/metadata_engines/utils/_PubMedConverter.py +469 -0
  508. scitex/scholar/metadata_engines/utils/_URLDOIExtractor.py +283 -0
  509. scitex/scholar/metadata_engines/utils/__init__.py +30 -0
  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
  513. scitex/scholar/pdf_download/__init__.py +5 -0
  514. scitex/scholar/pdf_download/strategies/__init__.py +38 -0
  515. scitex/scholar/pdf_download/strategies/chrome_pdf_viewer.py +376 -0
  516. scitex/scholar/pdf_download/strategies/direct_download.py +131 -0
  517. scitex/scholar/pdf_download/strategies/manual_download_fallback.py +167 -0
  518. scitex/scholar/pdf_download/strategies/manual_download_utils.py +996 -0
  519. scitex/scholar/pdf_download/strategies/response_body.py +207 -0
  520. scitex/scholar/pipelines/ScholarPipelineBibTeX.py +364 -0
  521. scitex/scholar/pipelines/ScholarPipelineParallel.py +478 -0
  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
  534. scitex/scholar/url_finder/strategies/find_pdf_urls_by_direct_links.py +261 -0
  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
  541. scitex/scholar/utils/__init__.py +22 -0
  542. scitex/scholar/utils/bibtex/__init__.py +9 -0
  543. scitex/scholar/utils/bibtex/_parse_bibtex.py +71 -0
  544. scitex/scholar/utils/cleanup/__init__.py +8 -0
  545. scitex/scholar/utils/cleanup/_cleanup_scholar_processes.py +96 -0
  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
  568. scitex/stats/effect_sizes/_epsilon_squared.py +315 -0
  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
  602. scitex/template/__init__.py +87 -0
  603. scitex/template/_create_project.py +267 -0
  604. scitex/template/create_pip_project.py +80 -0
  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
  623. scitex/ai/classification/classifiers.py +0 -101
  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 +1,523 @@
1
+ #!/usr/bin/env python3
2
+ # -*- coding: utf-8 -*-
3
+ # Timestamp: "2025-08-22 18:01:49 (ywatanabe)"
4
+ # File: /home/ywatanabe/proj/SciTeX-Code/src/scitex/scholar/externals/impact_factor/src/impact_factor/core/cache_manager.py
5
+ # ----------------------------------------
6
+ from __future__ import annotations
7
+ import os
8
+ __FILE__ = (
9
+ "./impact_factor/core/cache_manager.py"
10
+ )
11
+ __DIR__ = os.path.dirname(__FILE__)
12
+ # ----------------------------------------
13
+ import json
14
+ import pickle
15
+ import hashlib
16
+ import time
17
+ from pathlib import Path
18
+ from typing import Any, Dict, List, Optional, Union
19
+ from datetime import datetime, timedelta
20
+
21
+ from scitex.logging import getLogger
22
+
23
+ logger = getLogger(__name__)
24
+
25
+
26
+ class CacheManager:
27
+ """
28
+ Efficient caching system for impact factor calculations and API responses
29
+
30
+ Features:
31
+ - JSON and pickle serialization support
32
+ - Configurable expiration times
33
+ - Cache size management
34
+ - Thread-safe operations
35
+ - Hierarchical cache organization
36
+ - Cache statistics and monitoring
37
+ """
38
+
39
+ def __init__(
40
+ self,
41
+ cache_dir: Optional[str] = None,
42
+ default_ttl: int = 3600 * 24 * 7, # 7 days
43
+ max_cache_size_mb: int = 100,
44
+ cleanup_on_start: bool = True
45
+ ):
46
+ """
47
+ Initialize cache manager
48
+
49
+ Args:
50
+ cache_dir: Directory for cache storage (default: ~/.scitex/impact_factor_cache)
51
+ default_ttl: Default time-to-live in seconds
52
+ max_cache_size_mb: Maximum cache size in MB
53
+ cleanup_on_start: Whether to cleanup expired entries on initialization
54
+ """
55
+ if cache_dir is None:
56
+ cache_dir = Path.home() / ".scitex" / "impact_factor_cache"
57
+
58
+ self.cache_dir = Path(cache_dir)
59
+ self.cache_dir.mkdir(parents=True, exist_ok=True)
60
+
61
+ self.default_ttl = default_ttl
62
+ self.max_cache_size_bytes = max_cache_size_mb * 1024 * 1024
63
+
64
+ # Create subdirectories for different data types
65
+ self.subdirs = {
66
+ 'api_responses': self.cache_dir / 'api_responses',
67
+ 'impact_factors': self.cache_dir / 'impact_factors',
68
+ 'journal_data': self.cache_dir / 'journal_data',
69
+ 'search_results': self.cache_dir / 'search_results'
70
+ }
71
+
72
+ for subdir in self.subdirs.values():
73
+ subdir.mkdir(exist_ok=True)
74
+
75
+ # Metadata file for cache tracking
76
+ self.metadata_file = self.cache_dir / 'cache_metadata.json'
77
+ self.metadata = self._load_metadata()
78
+
79
+ if cleanup_on_start:
80
+ self.cleanup_expired()
81
+
82
+ logger.info(f"Cache manager initialized at: {self.cache_dir}")
83
+
84
+ def _load_metadata(self) -> Dict:
85
+ """Load cache metadata from file"""
86
+ if self.metadata_file.exists():
87
+ try:
88
+ with open(self.metadata_file, 'r') as f:
89
+ return json.load(f)
90
+ except Exception as e:
91
+ logger.warning(f"Failed to load cache metadata: {e}")
92
+
93
+ return {
94
+ 'entries': {},
95
+ 'created_at': datetime.now().isoformat(),
96
+ 'last_cleanup': None,
97
+ 'statistics': {
98
+ 'total_gets': 0,
99
+ 'cache_hits': 0,
100
+ 'cache_misses': 0,
101
+ 'total_sets': 0
102
+ }
103
+ }
104
+
105
+ def _save_metadata(self):
106
+ """Save cache metadata to file"""
107
+ try:
108
+ with open(self.metadata_file, 'w') as f:
109
+ json.dump(self.metadata, f, indent=2)
110
+ except Exception as e:
111
+ logger.error(f"Failed to save cache metadata: {e}")
112
+
113
+ def _get_cache_key(self, key: str) -> str:
114
+ """Generate a safe cache key hash"""
115
+ return hashlib.md5(key.encode()).hexdigest()
116
+
117
+ def _get_cache_path(self, cache_key: str, cache_type: str = 'api_responses') -> Path:
118
+ """Get full path for cache file"""
119
+ subdir = self.subdirs.get(cache_type, self.subdirs['api_responses'])
120
+ return subdir / f"{cache_key}.cache"
121
+
122
+ def set(
123
+ self,
124
+ key: str,
125
+ value: Any,
126
+ ttl: Optional[int] = None,
127
+ cache_type: str = 'api_responses',
128
+ use_pickle: bool = False
129
+ ) -> bool:
130
+ """
131
+ Store value in cache
132
+
133
+ Args:
134
+ key: Cache key
135
+ value: Value to cache
136
+ ttl: Time-to-live in seconds (None = default)
137
+ cache_type: Type of cache (api_responses, impact_factors, etc.)
138
+ use_pickle: Whether to use pickle serialization
139
+
140
+ Returns:
141
+ True if successful, False otherwise
142
+ """
143
+ try:
144
+ if ttl is None:
145
+ ttl = self.default_ttl
146
+
147
+ cache_key = self._get_cache_key(key)
148
+ cache_path = self._get_cache_path(cache_key, cache_type)
149
+
150
+ # Prepare cache entry
151
+ cache_entry = {
152
+ 'key': key,
153
+ 'value': value,
154
+ 'created_at': datetime.now().isoformat(),
155
+ 'expires_at': (datetime.now() + timedelta(seconds=ttl)).isoformat(),
156
+ 'ttl': ttl,
157
+ 'cache_type': cache_type,
158
+ 'serialization': 'pickle' if use_pickle else 'json'
159
+ }
160
+
161
+ # Serialize and save
162
+ if use_pickle:
163
+ with open(cache_path, 'wb') as f:
164
+ pickle.dump(cache_entry, f)
165
+ else:
166
+ with open(cache_path, 'w') as f:
167
+ json.dump(cache_entry, f, indent=2, default=str)
168
+
169
+ # Update metadata
170
+ self.metadata['entries'][cache_key] = {
171
+ 'key': key,
172
+ 'cache_type': cache_type,
173
+ 'created_at': cache_entry['created_at'],
174
+ 'expires_at': cache_entry['expires_at'],
175
+ 'file_path': str(cache_path),
176
+ 'serialization': cache_entry['serialization']
177
+ }
178
+ self.metadata['statistics']['total_sets'] += 1
179
+ self._save_metadata()
180
+
181
+ logger.debug(f"Cached key '{key}' in {cache_type}")
182
+ return True
183
+
184
+ except Exception as e:
185
+ logger.error(f"Failed to cache key '{key}': {e}")
186
+ return False
187
+
188
+ def get(self, key: str, cache_type: str = 'api_responses') -> Optional[Any]:
189
+ """
190
+ Retrieve value from cache
191
+
192
+ Args:
193
+ key: Cache key
194
+ cache_type: Type of cache
195
+
196
+ Returns:
197
+ Cached value or None if not found/expired
198
+ """
199
+ try:
200
+ cache_key = self._get_cache_key(key)
201
+ cache_path = self._get_cache_path(cache_key, cache_type)
202
+
203
+ # Update statistics
204
+ self.metadata['statistics']['total_gets'] += 1
205
+
206
+ # Check if file exists
207
+ if not cache_path.exists():
208
+ self.metadata['statistics']['cache_misses'] += 1
209
+ self._save_metadata()
210
+ logger.debug(f"Cache miss: key '{key}' not found")
211
+ return None
212
+
213
+ # Load cache entry
214
+ metadata_entry = self.metadata['entries'].get(cache_key)
215
+ if not metadata_entry:
216
+ self.metadata['statistics']['cache_misses'] += 1
217
+ self._save_metadata()
218
+ logger.debug(f"Cache miss: metadata for key '{key}' not found")
219
+ return None
220
+
221
+ # Check expiration
222
+ expires_at = datetime.fromisoformat(metadata_entry['expires_at'])
223
+ if datetime.now() > expires_at:
224
+ self.metadata['statistics']['cache_misses'] += 1
225
+ self._save_metadata()
226
+ logger.debug(f"Cache miss: key '{key}' expired")
227
+ # Clean up expired entry
228
+ self._remove_cache_entry(cache_key)
229
+ return None
230
+
231
+ # Load and return value
232
+ if metadata_entry['serialization'] == 'pickle':
233
+ with open(cache_path, 'rb') as f:
234
+ cache_entry = pickle.load(f)
235
+ else:
236
+ with open(cache_path, 'r') as f:
237
+ cache_entry = json.load(f)
238
+
239
+ self.metadata['statistics']['cache_hits'] += 1
240
+ self._save_metadata()
241
+
242
+ logger.debug(f"Cache hit: key '{key}' retrieved from {cache_type}")
243
+ return cache_entry['value']
244
+
245
+ except Exception as e:
246
+ logger.error(f"Failed to retrieve cache key '{key}': {e}")
247
+ self.metadata['statistics']['cache_misses'] += 1
248
+ self._save_metadata()
249
+ return None
250
+
251
+ def delete(self, key: str, cache_type: str = 'api_responses') -> bool:
252
+ """Delete a specific cache entry"""
253
+ try:
254
+ cache_key = self._get_cache_key(key)
255
+ return self._remove_cache_entry(cache_key)
256
+ except Exception as e:
257
+ logger.error(f"Failed to delete cache key '{key}': {e}")
258
+ return False
259
+
260
+ def _remove_cache_entry(self, cache_key: str) -> bool:
261
+ """Remove cache entry by cache key"""
262
+ try:
263
+ metadata_entry = self.metadata['entries'].get(cache_key)
264
+ if metadata_entry:
265
+ # Remove file
266
+ cache_path = Path(metadata_entry['file_path'])
267
+ if cache_path.exists():
268
+ cache_path.unlink()
269
+
270
+ # Remove from metadata
271
+ del self.metadata['entries'][cache_key]
272
+ self._save_metadata()
273
+
274
+ return True
275
+ return False
276
+ except Exception as e:
277
+ logger.error(f"Failed to remove cache entry {cache_key}: {e}")
278
+ return False
279
+
280
+ def cleanup_expired(self) -> int:
281
+ """Remove all expired cache entries"""
282
+ logger.info("Starting cache cleanup of expired entries")
283
+
284
+ removed_count = 0
285
+ current_time = datetime.now()
286
+
287
+ # Create a copy of keys to avoid dictionary modification during iteration
288
+ cache_keys = list(self.metadata['entries'].keys())
289
+
290
+ for cache_key in cache_keys:
291
+ entry = self.metadata['entries'][cache_key]
292
+ expires_at = datetime.fromisoformat(entry['expires_at'])
293
+
294
+ if current_time > expires_at:
295
+ if self._remove_cache_entry(cache_key):
296
+ removed_count += 1
297
+
298
+ self.metadata['last_cleanup'] = current_time.isoformat()
299
+ self._save_metadata()
300
+
301
+ logger.info(f"Cleanup completed: removed {removed_count} expired entries")
302
+ return removed_count
303
+
304
+ def cleanup_by_size(self) -> int:
305
+ """Remove oldest entries if cache exceeds size limit"""
306
+ current_size = self.get_cache_size()
307
+ if current_size <= self.max_cache_size_bytes:
308
+ return 0
309
+
310
+ logger.info(f"Cache size ({current_size / 1024 / 1024:.1f}MB) exceeds limit, cleaning up")
311
+
312
+ # Sort entries by creation time (oldest first)
313
+ entries_by_age = sorted(
314
+ self.metadata['entries'].items(),
315
+ key=lambda x: x[1]['created_at']
316
+ )
317
+
318
+ removed_count = 0
319
+ for cache_key, entry in entries_by_age:
320
+ if self._remove_cache_entry(cache_key):
321
+ removed_count += 1
322
+ current_size = self.get_cache_size()
323
+ if current_size <= self.max_cache_size_bytes:
324
+ break
325
+
326
+ logger.info(f"Size cleanup completed: removed {removed_count} entries")
327
+ return removed_count
328
+
329
+ def clear_all(self, cache_type: Optional[str] = None) -> int:
330
+ """Clear all cache entries or entries of specific type"""
331
+ removed_count = 0
332
+
333
+ if cache_type:
334
+ # Clear specific type
335
+ cache_keys = [
336
+ key for key, entry in self.metadata['entries'].items()
337
+ if entry['cache_type'] == cache_type
338
+ ]
339
+ logger.info(f"Clearing all {cache_type} cache entries")
340
+ else:
341
+ # Clear all
342
+ cache_keys = list(self.metadata['entries'].keys())
343
+ logger.info("Clearing all cache entries")
344
+
345
+ for cache_key in cache_keys:
346
+ if self._remove_cache_entry(cache_key):
347
+ removed_count += 1
348
+
349
+ logger.info(f"Cleared {removed_count} cache entries")
350
+ return removed_count
351
+
352
+ def get_cache_size(self) -> int:
353
+ """Get total cache size in bytes"""
354
+ total_size = 0
355
+ for entry in self.metadata['entries'].values():
356
+ cache_path = Path(entry['file_path'])
357
+ if cache_path.exists():
358
+ total_size += cache_path.stat().st_size
359
+
360
+ # Add metadata file size
361
+ if self.metadata_file.exists():
362
+ total_size += self.metadata_file.stat().st_size
363
+
364
+ return total_size
365
+
366
+ def get_statistics(self) -> Dict:
367
+ """Get cache usage statistics"""
368
+ stats = self.metadata['statistics'].copy()
369
+ stats.update({
370
+ 'total_entries': len(self.metadata['entries']),
371
+ 'cache_size_mb': self.get_cache_size() / 1024 / 1024,
372
+ 'cache_size_limit_mb': self.max_cache_size_bytes / 1024 / 1024,
373
+ 'hit_rate': (
374
+ stats['cache_hits'] / stats['total_gets']
375
+ if stats['total_gets'] > 0 else 0.0
376
+ ),
377
+ 'last_cleanup': self.metadata.get('last_cleanup'),
378
+ 'entries_by_type': {}
379
+ })
380
+
381
+ # Count entries by type
382
+ for entry in self.metadata['entries'].values():
383
+ cache_type = entry['cache_type']
384
+ stats['entries_by_type'][cache_type] = stats['entries_by_type'].get(cache_type, 0) + 1
385
+
386
+ return stats
387
+
388
+ def list_entries(self, cache_type: Optional[str] = None) -> List[Dict]:
389
+ """List cache entries with metadata"""
390
+ entries = []
391
+
392
+ for cache_key, entry in self.metadata['entries'].items():
393
+ if cache_type is None or entry['cache_type'] == cache_type:
394
+ entry_info = entry.copy()
395
+ entry_info['cache_key'] = cache_key
396
+ entry_info['expired'] = datetime.now() > datetime.fromisoformat(entry['expires_at'])
397
+ entries.append(entry_info)
398
+
399
+ return entries
400
+
401
+
402
+ def main():
403
+ """Demonstration of CacheManager functionality"""
404
+ logger.info("Starting Cache Manager demonstration")
405
+
406
+ # Initialize cache manager
407
+ cache = CacheManager(cache_dir="/tmp/demo_cache", max_cache_size_mb=10)
408
+
409
+ logger.info("Testing cache operations")
410
+ logger.info("=" * 40)
411
+
412
+ # Test basic set/get operations
413
+ logger.info("1. Testing basic cache operations")
414
+
415
+ test_data = {
416
+ 'journal_name': 'Nature',
417
+ 'impact_factor': 49.962,
418
+ 'year': 2023,
419
+ 'metadata': {
420
+ 'publisher': 'Nature Publishing Group',
421
+ 'issn': ['0028-0836', '1476-4687']
422
+ }
423
+ }
424
+
425
+ # Set cache entry
426
+ success = cache.set('nature_2023_if', test_data, ttl=300, cache_type='impact_factors')
427
+ logger.info(f"Cache set successful: {success}")
428
+
429
+ # Get cache entry
430
+ retrieved_data = cache.get('nature_2023_if', cache_type='impact_factors')
431
+ logger.info(f"Cache get successful: {retrieved_data is not None}")
432
+ if retrieved_data:
433
+ logger.info(f"Retrieved journal: {retrieved_data['journal_name']}")
434
+
435
+ logger.info("")
436
+
437
+ # Test different cache types
438
+ logger.info("2. Testing different cache types")
439
+
440
+ cache_types = ['api_responses', 'impact_factors', 'journal_data', 'search_results']
441
+ for i, cache_type in enumerate(cache_types):
442
+ key = f"test_key_{i}"
443
+ value = f"test_value_{i}_for_{cache_type}"
444
+ cache.set(key, value, cache_type=cache_type)
445
+ logger.info(f"Stored in {cache_type}: {key}")
446
+
447
+ logger.info("")
448
+
449
+ # Test serialization types
450
+ logger.info("3. Testing serialization types")
451
+
452
+ # JSON serialization (default)
453
+ json_data = {'type': 'json', 'numbers': [1, 2, 3], 'nested': {'key': 'value'}}
454
+ cache.set('json_test', json_data, cache_type='journal_data')
455
+
456
+ # Pickle serialization
457
+ pickle_data = {'type': 'pickle', 'complex_object': datetime.now()}
458
+ cache.set('pickle_test', pickle_data, cache_type='journal_data', use_pickle=True)
459
+
460
+ # Verify both work
461
+ json_retrieved = cache.get('json_test', cache_type='journal_data')
462
+ pickle_retrieved = cache.get('pickle_test', cache_type='journal_data')
463
+
464
+ logger.info(f"JSON serialization works: {json_retrieved is not None}")
465
+ logger.info(f"Pickle serialization works: {pickle_retrieved is not None}")
466
+ logger.info("")
467
+
468
+ # Test cache statistics
469
+ logger.info("4. Cache statistics")
470
+ stats = cache.get_statistics()
471
+ logger.info(f"Total entries: {stats['total_entries']}")
472
+ logger.info(f"Cache size: {stats['cache_size_mb']:.3f} MB")
473
+ logger.info(f"Hit rate: {stats['hit_rate']:.1%}")
474
+ logger.info(f"Entries by type: {stats['entries_by_type']}")
475
+ logger.info("")
476
+
477
+ # Test cache listing
478
+ logger.info("5. Cache entry listing")
479
+ entries = cache.list_entries()
480
+ logger.info(f"Found {len(entries)} cache entries:")
481
+ for entry in entries[:3]: # Show first 3
482
+ logger.info(f" {entry['key']} [{entry['cache_type']}] - expires: {entry['expires_at'][:19]}")
483
+ logger.info("")
484
+
485
+ # Test expiration (simulate with short TTL)
486
+ logger.info("6. Testing cache expiration")
487
+ cache.set('expire_test', 'will expire soon', ttl=1) # 1 second TTL
488
+
489
+ # Immediate retrieval should work
490
+ immediate = cache.get('expire_test')
491
+ logger.info(f"Immediate retrieval: {'Success' if immediate else 'Failed'}")
492
+
493
+ # Wait for expiration
494
+ time.sleep(2)
495
+ expired = cache.get('expire_test')
496
+ logger.info(f"After expiration: {'Success' if expired else 'Failed (as expected)'}")
497
+ logger.info("")
498
+
499
+ # Test cleanup operations
500
+ logger.info("7. Testing cleanup operations")
501
+
502
+ # Add some entries with short TTL
503
+ for i in range(5):
504
+ cache.set(f'temp_{i}', f'temporary_data_{i}', ttl=1)
505
+
506
+ time.sleep(2) # Let them expire
507
+
508
+ # Cleanup expired entries
509
+ removed = cache.cleanup_expired()
510
+ logger.info(f"Cleaned up {removed} expired entries")
511
+
512
+ # Final statistics
513
+ final_stats = cache.get_statistics()
514
+ logger.info(f"Final cache entries: {final_stats['total_entries']}")
515
+ logger.info("")
516
+
517
+ logger.success("Cache Manager demonstration completed")
518
+
519
+
520
+ if __name__ == "__main__":
521
+ main()
522
+
523
+ # EOF