scitex 2.5.0__py3-none-any.whl → 2.7.0__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 (1091) hide show
  1. scitex/__init__.py +19 -8
  2. scitex/__main__.py +2 -1
  3. scitex/__version__.py +1 -1
  4. scitex/_optional_deps.py +13 -20
  5. scitex/ai/__init__.py +5 -0
  6. scitex/ai/_gen_ai/_Anthropic.py +3 -1
  7. scitex/ai/_gen_ai/_BaseGenAI.py +3 -2
  8. scitex/ai/_gen_ai/_DeepSeek.py +1 -1
  9. scitex/ai/_gen_ai/_Google.py +3 -2
  10. scitex/ai/_gen_ai/_Llama.py +4 -2
  11. scitex/ai/_gen_ai/_OpenAI.py +3 -1
  12. scitex/ai/_gen_ai/_PARAMS.py +1 -0
  13. scitex/ai/_gen_ai/_Perplexity.py +3 -1
  14. scitex/ai/_gen_ai/__init__.py +1 -0
  15. scitex/ai/_gen_ai/_format_output_func.py +3 -1
  16. scitex/ai/classification/CrossValidationExperiment.py +8 -14
  17. scitex/ai/classification/examples/timeseries_cv_demo.py +128 -112
  18. scitex/ai/classification/reporters/_BaseClassificationReporter.py +2 -0
  19. scitex/ai/classification/reporters/_ClassificationReporter.py +30 -45
  20. scitex/ai/classification/reporters/_MultiClassificationReporter.py +8 -11
  21. scitex/ai/classification/reporters/_SingleClassificationReporter.py +126 -182
  22. scitex/ai/classification/reporters/__init__.py +1 -1
  23. scitex/ai/classification/reporters/reporter_utils/_Plotter.py +213 -119
  24. scitex/ai/classification/reporters/reporter_utils/__init__.py +28 -36
  25. scitex/ai/classification/reporters/reporter_utils/aggregation.py +125 -143
  26. scitex/ai/classification/reporters/reporter_utils/data_models.py +128 -120
  27. scitex/ai/classification/reporters/reporter_utils/reporting.py +507 -340
  28. scitex/ai/classification/reporters/reporter_utils/storage.py +4 -1
  29. scitex/ai/classification/reporters/reporter_utils/validation.py +141 -154
  30. scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +204 -129
  31. scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +215 -171
  32. scitex/ai/classification/timeseries/_TimeSeriesMetadata.py +17 -17
  33. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +67 -143
  34. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +67 -143
  35. scitex/ai/classification/timeseries/_TimeSeriesStrategy.py +12 -13
  36. scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +231 -144
  37. scitex/ai/classification/timeseries/__init__.py +2 -4
  38. scitex/ai/classification/timeseries/_normalize_timestamp.py +3 -0
  39. scitex/ai/clustering/_pca.py +0 -1
  40. scitex/ai/clustering/_umap.py +1 -2
  41. scitex/ai/feature_extraction/__init__.py +10 -8
  42. scitex/ai/feature_extraction/vit.py +0 -1
  43. scitex/ai/feature_selection/feature_selection.py +3 -8
  44. scitex/ai/metrics/_calc_conf_mat.py +2 -0
  45. scitex/ai/metrics/_calc_feature_importance.py +3 -7
  46. scitex/ai/metrics/_calc_pre_rec_auc.py +5 -5
  47. scitex/ai/metrics/_calc_roc_auc.py +4 -2
  48. scitex/ai/metrics/_calc_seizure_prediction_metrics.py +35 -20
  49. scitex/ai/metrics/_calc_silhouette_score.py +1 -3
  50. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger.py +0 -3
  51. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger2020.py +0 -3
  52. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger913A.py +0 -3
  53. scitex/ai/optim/_optimizers.py +1 -1
  54. scitex/ai/plt/__init__.py +6 -1
  55. scitex/ai/plt/_plot_feature_importance.py +1 -3
  56. scitex/ai/plt/_plot_learning_curve.py +9 -24
  57. scitex/ai/plt/_plot_optuna_study.py +4 -3
  58. scitex/ai/plt/_plot_pre_rec_curve.py +9 -15
  59. scitex/ai/plt/_plot_roc_curve.py +6 -8
  60. scitex/ai/plt/_stx_conf_mat.py +121 -122
  61. scitex/ai/sampling/undersample.py +3 -2
  62. scitex/ai/sklearn/__init__.py +2 -2
  63. scitex/ai/training/_LearningCurveLogger.py +23 -10
  64. scitex/ai/utils/_check_params.py +0 -1
  65. scitex/benchmark/__init__.py +15 -25
  66. scitex/benchmark/benchmark.py +124 -117
  67. scitex/benchmark/monitor.py +117 -107
  68. scitex/benchmark/profiler.py +61 -58
  69. scitex/bridge/__init__.py +110 -0
  70. scitex/bridge/_helpers.py +149 -0
  71. scitex/bridge/_plt_vis.py +529 -0
  72. scitex/bridge/_protocol.py +283 -0
  73. scitex/bridge/_stats_plt.py +261 -0
  74. scitex/bridge/_stats_vis.py +265 -0
  75. scitex/browser/__init__.py +0 -2
  76. scitex/browser/auth/__init__.py +0 -0
  77. scitex/browser/auth/google.py +16 -11
  78. scitex/browser/automation/CookieHandler.py +2 -3
  79. scitex/browser/collaboration/__init__.py +3 -0
  80. scitex/browser/collaboration/auth_helpers.py +3 -1
  81. scitex/browser/collaboration/collaborative_agent.py +2 -0
  82. scitex/browser/collaboration/interactive_panel.py +2 -2
  83. scitex/browser/collaboration/shared_session.py +20 -11
  84. scitex/browser/collaboration/standard_interactions.py +1 -0
  85. scitex/browser/core/BrowserMixin.py +12 -30
  86. scitex/browser/core/ChromeProfileManager.py +9 -24
  87. scitex/browser/debugging/_browser_logger.py +15 -25
  88. scitex/browser/debugging/_failure_capture.py +9 -2
  89. scitex/browser/debugging/_highlight_element.py +15 -6
  90. scitex/browser/debugging/_show_grid.py +5 -6
  91. scitex/browser/debugging/_sync_session.py +4 -3
  92. scitex/browser/debugging/_test_monitor.py +14 -5
  93. scitex/browser/debugging/_visual_cursor.py +46 -35
  94. scitex/browser/interaction/click_center.py +4 -3
  95. scitex/browser/interaction/click_with_fallbacks.py +7 -10
  96. scitex/browser/interaction/close_popups.py +79 -66
  97. scitex/browser/interaction/fill_with_fallbacks.py +8 -8
  98. scitex/browser/pdf/__init__.py +3 -1
  99. scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +11 -10
  100. scitex/browser/pdf/detect_chrome_pdf_viewer.py +3 -6
  101. scitex/browser/remote/CaptchaHandler.py +109 -96
  102. scitex/browser/remote/ZenRowsAPIClient.py +91 -97
  103. scitex/browser/remote/ZenRowsBrowserManager.py +138 -112
  104. scitex/browser/stealth/HumanBehavior.py +4 -9
  105. scitex/browser/stealth/StealthManager.py +11 -26
  106. scitex/capture/__init__.py +17 -17
  107. scitex/capture/__main__.py +2 -3
  108. scitex/capture/capture.py +23 -51
  109. scitex/capture/cli.py +14 -39
  110. scitex/capture/gif.py +5 -9
  111. scitex/capture/mcp_server.py +7 -20
  112. scitex/capture/session.py +4 -3
  113. scitex/capture/utils.py +18 -53
  114. scitex/cli/__init__.py +1 -1
  115. scitex/cli/cloud.py +158 -116
  116. scitex/cli/config.py +224 -0
  117. scitex/cli/main.py +41 -40
  118. scitex/cli/scholar.py +60 -27
  119. scitex/cli/security.py +14 -20
  120. scitex/cli/web.py +87 -90
  121. scitex/cli/writer.py +51 -45
  122. scitex/cloud/__init__.py +14 -11
  123. scitex/cloud/_matplotlib_hook.py +6 -6
  124. scitex/config/README.md +313 -0
  125. scitex/config/{PriorityConfig.py → _PriorityConfig.py} +114 -17
  126. scitex/config/_ScitexConfig.py +319 -0
  127. scitex/config/__init__.py +41 -9
  128. scitex/config/_paths.py +325 -0
  129. scitex/config/default.yaml +81 -0
  130. scitex/context/_suppress_output.py +2 -3
  131. scitex/db/_BaseMixins/_BaseBackupMixin.py +3 -1
  132. scitex/db/_BaseMixins/_BaseBatchMixin.py +3 -1
  133. scitex/db/_BaseMixins/_BaseBlobMixin.py +3 -1
  134. scitex/db/_BaseMixins/_BaseImportExportMixin.py +1 -3
  135. scitex/db/_BaseMixins/_BaseIndexMixin.py +3 -1
  136. scitex/db/_BaseMixins/_BaseMaintenanceMixin.py +1 -3
  137. scitex/db/_BaseMixins/_BaseQueryMixin.py +3 -1
  138. scitex/db/_BaseMixins/_BaseRowMixin.py +3 -1
  139. scitex/db/_BaseMixins/_BaseTableMixin.py +3 -1
  140. scitex/db/_BaseMixins/_BaseTransactionMixin.py +1 -3
  141. scitex/db/_BaseMixins/__init__.py +1 -1
  142. scitex/db/__init__.py +9 -1
  143. scitex/db/__main__.py +8 -21
  144. scitex/db/_check_health.py +15 -31
  145. scitex/db/_delete_duplicates.py +7 -4
  146. scitex/db/_inspect.py +22 -38
  147. scitex/db/_inspect_optimized.py +89 -85
  148. scitex/db/_postgresql/_PostgreSQL.py +0 -1
  149. scitex/db/_postgresql/_PostgreSQLMixins/_BlobMixin.py +3 -1
  150. scitex/db/_postgresql/_PostgreSQLMixins/_ConnectionMixin.py +1 -3
  151. scitex/db/_postgresql/_PostgreSQLMixins/_ImportExportMixin.py +1 -3
  152. scitex/db/_postgresql/_PostgreSQLMixins/_MaintenanceMixin.py +1 -4
  153. scitex/db/_postgresql/_PostgreSQLMixins/_QueryMixin.py +3 -3
  154. scitex/db/_postgresql/_PostgreSQLMixins/_RowMixin.py +3 -1
  155. scitex/db/_postgresql/_PostgreSQLMixins/_TransactionMixin.py +1 -3
  156. scitex/db/_postgresql/__init__.py +1 -1
  157. scitex/db/_sqlite3/_SQLite3.py +2 -4
  158. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin.py +11 -12
  159. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin_v01-need-_hash-col.py +19 -14
  160. scitex/db/_sqlite3/_SQLite3Mixins/_BatchMixin.py +3 -1
  161. scitex/db/_sqlite3/_SQLite3Mixins/_BlobMixin.py +7 -7
  162. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin.py +118 -111
  163. scitex/db/_sqlite3/_SQLite3Mixins/_ConnectionMixin.py +8 -10
  164. scitex/db/_sqlite3/_SQLite3Mixins/_GitMixin.py +17 -45
  165. scitex/db/_sqlite3/_SQLite3Mixins/_ImportExportMixin.py +1 -3
  166. scitex/db/_sqlite3/_SQLite3Mixins/_IndexMixin.py +3 -1
  167. scitex/db/_sqlite3/_SQLite3Mixins/_QueryMixin.py +3 -4
  168. scitex/db/_sqlite3/_SQLite3Mixins/_RowMixin.py +9 -9
  169. scitex/db/_sqlite3/_SQLite3Mixins/_TableMixin.py +18 -11
  170. scitex/db/_sqlite3/_SQLite3Mixins/__init__.py +1 -0
  171. scitex/db/_sqlite3/__init__.py +1 -1
  172. scitex/db/_sqlite3/_delete_duplicates.py +13 -11
  173. scitex/decorators/__init__.py +29 -4
  174. scitex/decorators/_auto_order.py +43 -43
  175. scitex/decorators/_batch_fn.py +12 -6
  176. scitex/decorators/_cache_disk.py +8 -9
  177. scitex/decorators/_cache_disk_async.py +8 -7
  178. scitex/decorators/_combined.py +19 -13
  179. scitex/decorators/_converters.py +16 -3
  180. scitex/decorators/_deprecated.py +32 -22
  181. scitex/decorators/_numpy_fn.py +18 -4
  182. scitex/decorators/_pandas_fn.py +17 -5
  183. scitex/decorators/_signal_fn.py +17 -3
  184. scitex/decorators/_torch_fn.py +32 -15
  185. scitex/decorators/_xarray_fn.py +23 -9
  186. scitex/dev/_analyze_code_flow.py +0 -2
  187. scitex/dict/_DotDict.py +15 -19
  188. scitex/dict/_flatten.py +1 -0
  189. scitex/dict/_listed_dict.py +1 -0
  190. scitex/dict/_pop_keys.py +1 -0
  191. scitex/dict/_replace.py +1 -0
  192. scitex/dict/_safe_merge.py +1 -0
  193. scitex/dict/_to_str.py +2 -3
  194. scitex/dsp/__init__.py +13 -4
  195. scitex/dsp/_crop.py +3 -1
  196. scitex/dsp/_detect_ripples.py +3 -1
  197. scitex/dsp/_modulation_index.py +3 -1
  198. scitex/dsp/_time.py +3 -1
  199. scitex/dsp/_wavelet.py +0 -1
  200. scitex/dsp/example.py +0 -5
  201. scitex/dsp/filt.py +4 -0
  202. scitex/dsp/utils/__init__.py +4 -1
  203. scitex/dsp/utils/pac.py +3 -3
  204. scitex/dt/_normalize_timestamp.py +4 -1
  205. scitex/errors.py +3 -6
  206. scitex/etc/__init__.py +1 -1
  207. scitex/gen/_DimHandler.py +6 -6
  208. scitex/gen/__init__.py +5 -1
  209. scitex/gen/_deprecated_close.py +1 -0
  210. scitex/gen/_deprecated_start.py +5 -3
  211. scitex/gen/_detect_environment.py +44 -41
  212. scitex/gen/_detect_notebook_path.py +51 -47
  213. scitex/gen/_embed.py +1 -1
  214. scitex/gen/_get_notebook_path.py +81 -62
  215. scitex/gen/_inspect_module.py +0 -1
  216. scitex/gen/_norm.py +16 -7
  217. scitex/gen/_norm_cache.py +78 -65
  218. scitex/gen/_print_config.py +0 -3
  219. scitex/gen/_src.py +2 -3
  220. scitex/gen/_title_case.py +3 -2
  221. scitex/gen/_to_even.py +8 -8
  222. scitex/gen/_transpose.py +3 -3
  223. scitex/gen/misc.py +0 -3
  224. scitex/gists/_SigMacro_processFigure_S.py +2 -2
  225. scitex/gists/_SigMacro_toBlue.py +2 -2
  226. scitex/gists/__init__.py +4 -1
  227. scitex/git/_branch.py +19 -11
  228. scitex/git/_clone.py +23 -15
  229. scitex/git/_commit.py +10 -12
  230. scitex/git/_init.py +15 -38
  231. scitex/git/_remote.py +9 -3
  232. scitex/git/_result.py +3 -0
  233. scitex/git/_retry.py +2 -5
  234. scitex/git/_types.py +4 -0
  235. scitex/git/_validation.py +8 -8
  236. scitex/git/_workflow.py +4 -4
  237. scitex/io/__init__.py +2 -1
  238. scitex/io/_glob.py +2 -2
  239. scitex/io/_json2md.py +3 -3
  240. scitex/io/_load.py +6 -8
  241. scitex/io/_load_cache.py +71 -71
  242. scitex/io/_load_configs.py +2 -3
  243. scitex/io/_load_modules/_H5Explorer.py +6 -12
  244. scitex/io/_load_modules/_ZarrExplorer.py +3 -3
  245. scitex/io/_load_modules/_bibtex.py +62 -63
  246. scitex/io/_load_modules/_canvas.py +4 -9
  247. scitex/io/_load_modules/_catboost.py +7 -2
  248. scitex/io/_load_modules/_hdf5.py +2 -0
  249. scitex/io/_load_modules/_image.py +5 -1
  250. scitex/io/_load_modules/_matlab.py +3 -1
  251. scitex/io/_load_modules/_optuna.py +0 -1
  252. scitex/io/_load_modules/_pdf.py +38 -29
  253. scitex/io/_load_modules/_sqlite3.py +1 -0
  254. scitex/io/_load_modules/_txt.py +2 -0
  255. scitex/io/_load_modules/_xml.py +9 -9
  256. scitex/io/_load_modules/_zarr.py +12 -10
  257. scitex/io/_metadata.py +76 -37
  258. scitex/io/_qr_utils.py +18 -13
  259. scitex/io/_save.py +220 -63
  260. scitex/io/_save_modules/__init__.py +7 -2
  261. scitex/io/_save_modules/_bibtex.py +66 -61
  262. scitex/io/_save_modules/_canvas.py +5 -6
  263. scitex/io/_save_modules/_catboost.py +2 -2
  264. scitex/io/_save_modules/_csv.py +4 -4
  265. scitex/io/_save_modules/_excel.py +5 -9
  266. scitex/io/_save_modules/_hdf5.py +9 -21
  267. scitex/io/_save_modules/_html.py +5 -5
  268. scitex/io/_save_modules/_image.py +105 -8
  269. scitex/io/_save_modules/_joblib.py +2 -2
  270. scitex/io/_save_modules/_json.py +51 -6
  271. scitex/io/_save_modules/_listed_dfs_as_csv.py +2 -1
  272. scitex/io/_save_modules/_listed_scalars_as_csv.py +2 -1
  273. scitex/io/_save_modules/_matlab.py +2 -2
  274. scitex/io/_save_modules/_numpy.py +6 -8
  275. scitex/io/_save_modules/_pickle.py +4 -4
  276. scitex/io/_save_modules/_plotly.py +3 -3
  277. scitex/io/_save_modules/_tex.py +23 -25
  278. scitex/io/_save_modules/_text.py +2 -2
  279. scitex/io/_save_modules/_yaml.py +9 -9
  280. scitex/io/_save_modules/_zarr.py +15 -15
  281. scitex/io/utils/__init__.py +2 -1
  282. scitex/io/utils/h5_to_zarr.py +173 -155
  283. scitex/linalg/__init__.py +1 -1
  284. scitex/linalg/_geometric_median.py +4 -3
  285. scitex/logging/_Tee.py +5 -7
  286. scitex/logging/__init__.py +18 -19
  287. scitex/logging/_config.py +4 -1
  288. scitex/logging/_context.py +6 -5
  289. scitex/logging/_formatters.py +2 -3
  290. scitex/logging/_handlers.py +19 -20
  291. scitex/logging/_levels.py +9 -17
  292. scitex/logging/_logger.py +74 -15
  293. scitex/logging/_print_capture.py +17 -17
  294. scitex/nn/_BNet.py +1 -3
  295. scitex/nn/_Filters.py +6 -2
  296. scitex/nn/_ModulationIndex.py +3 -1
  297. scitex/nn/_PAC.py +3 -2
  298. scitex/nn/_PSD.py +0 -1
  299. scitex/nn/__init__.py +16 -3
  300. scitex/path/_clean.py +10 -8
  301. scitex/path/_find.py +1 -1
  302. scitex/path/_get_spath.py +1 -2
  303. scitex/path/_mk_spath.py +1 -1
  304. scitex/path/_symlink.py +5 -10
  305. scitex/pd/__init__.py +4 -1
  306. scitex/pd/_force_df.py +24 -24
  307. scitex/pd/_get_unique.py +1 -0
  308. scitex/pd/_merge_columns.py +1 -1
  309. scitex/pd/_round.py +11 -7
  310. scitex/pd/_to_xy.py +0 -1
  311. scitex/plt/REQUESTS.md +191 -0
  312. scitex/plt/__init__.py +185 -87
  313. scitex/plt/_subplots/_AxesWrapper.py +22 -6
  314. scitex/plt/_subplots/_AxisWrapper.py +100 -39
  315. scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +74 -52
  316. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +183 -73
  317. scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +61 -45
  318. scitex/plt/_subplots/_AxisWrapperMixins/_TrackingMixin.py +26 -14
  319. scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +80 -73
  320. scitex/plt/_subplots/_FigWrapper.py +93 -60
  321. scitex/plt/_subplots/_SubplotsWrapper.py +135 -68
  322. scitex/plt/_subplots/__init__.py +10 -0
  323. scitex/plt/_subplots/_export_as_csv.py +89 -47
  324. scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +1 -0
  325. scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +6 -4
  326. scitex/plt/_subplots/_export_as_csv_formatters/_format_bar.py +88 -38
  327. scitex/plt/_subplots/_export_as_csv_formatters/_format_barh.py +25 -31
  328. scitex/plt/_subplots/_export_as_csv_formatters/_format_boxplot.py +53 -23
  329. scitex/plt/_subplots/_export_as_csv_formatters/_format_contour.py +38 -25
  330. scitex/plt/_subplots/_export_as_csv_formatters/_format_contourf.py +17 -9
  331. scitex/plt/_subplots/_export_as_csv_formatters/_format_errorbar.py +70 -124
  332. scitex/plt/_subplots/_export_as_csv_formatters/_format_eventplot.py +12 -10
  333. scitex/plt/_subplots/_export_as_csv_formatters/_format_fill.py +31 -17
  334. scitex/plt/_subplots/_export_as_csv_formatters/_format_fill_between.py +33 -21
  335. scitex/plt/_subplots/_export_as_csv_formatters/_format_hexbin.py +14 -4
  336. scitex/plt/_subplots/_export_as_csv_formatters/_format_hist.py +43 -29
  337. scitex/plt/_subplots/_export_as_csv_formatters/_format_hist2d.py +14 -4
  338. scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow.py +27 -11
  339. scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow2d.py +7 -5
  340. scitex/plt/_subplots/_export_as_csv_formatters/_format_matshow.py +9 -7
  341. scitex/plt/_subplots/_export_as_csv_formatters/_format_pie.py +15 -6
  342. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot.py +85 -46
  343. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_box.py +52 -27
  344. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_imshow.py +1 -0
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  891. scitex/scholar/url_finder/translators/individual/sciencedirect.py +36 -17
  892. scitex/scholar/url_finder/translators/individual/semantics_visual_library.py +3 -1
  893. scitex/scholar/url_finder/translators/individual/silverchair.py +70 -52
  894. scitex/scholar/url_finder/translators/individual/sora.py +3 -1
  895. scitex/scholar/url_finder/translators/individual/springer.py +15 -11
  896. scitex/scholar/url_finder/translators/individual/ssrn.py +3 -3
  897. scitex/scholar/url_finder/translators/individual/stanford_encyclopedia_of_philosophy.py +3 -1
  898. scitex/scholar/url_finder/translators/individual/superlib.py +3 -1
  899. scitex/scholar/url_finder/translators/individual/treesearch.py +3 -1
  900. scitex/scholar/url_finder/translators/individual/university_of_chicago_press_books.py +3 -1
  901. scitex/scholar/url_finder/translators/individual/vlex.py +3 -1
  902. scitex/scholar/url_finder/translators/individual/web_of_science.py +3 -1
  903. scitex/scholar/url_finder/translators/individual/web_of_science_nextgen.py +3 -1
  904. scitex/scholar/url_finder/translators/individual/wiley.py +31 -25
  905. scitex/scholar/url_finder/translators/individual/wilson_center_digital_archive.py +3 -1
  906. scitex/scholar/utils/bibtex/_parse_bibtex.py +3 -3
  907. scitex/scholar/utils/cleanup/_cleanup_scholar_processes.py +5 -9
  908. scitex/scholar/utils/text/_TextNormalizer.py +249 -176
  909. scitex/scholar/utils/validation/DOIValidator.py +31 -28
  910. scitex/scholar/utils/validation/__init__.py +0 -0
  911. scitex/scholar/utils/validation/validate_library_dois.py +61 -57
  912. scitex/scholar/zotero/__init__.py +1 -1
  913. scitex/security/cli.py +7 -20
  914. scitex/security/github.py +45 -32
  915. scitex/session/__init__.py +8 -9
  916. scitex/session/_decorator.py +49 -42
  917. scitex/session/_lifecycle.py +39 -39
  918. scitex/session/_manager.py +24 -20
  919. scitex/sh/__init__.py +4 -3
  920. scitex/sh/_execute.py +10 -7
  921. scitex/sh/_security.py +3 -3
  922. scitex/sh/_types.py +2 -3
  923. scitex/stats/__init__.py +57 -6
  924. scitex/stats/_schema.py +42 -569
  925. scitex/stats/auto/__init__.py +188 -0
  926. scitex/stats/auto/_context.py +331 -0
  927. scitex/stats/auto/_formatting.py +679 -0
  928. scitex/stats/auto/_rules.py +901 -0
  929. scitex/stats/auto/_selector.py +554 -0
  930. scitex/stats/auto/_styles.py +721 -0
  931. scitex/stats/correct/__init__.py +4 -4
  932. scitex/stats/correct/_correct_bonferroni.py +43 -34
  933. scitex/stats/correct/_correct_fdr.py +14 -40
  934. scitex/stats/correct/_correct_fdr_.py +39 -46
  935. scitex/stats/correct/_correct_holm.py +14 -32
  936. scitex/stats/correct/_correct_sidak.py +36 -21
  937. scitex/stats/descriptive/_circular.py +20 -21
  938. scitex/stats/descriptive/_describe.py +19 -5
  939. scitex/stats/descriptive/_nan.py +5 -7
  940. scitex/stats/descriptive/_real.py +4 -3
  941. scitex/stats/effect_sizes/__init__.py +10 -11
  942. scitex/stats/effect_sizes/_cliffs_delta.py +35 -32
  943. scitex/stats/effect_sizes/_cohens_d.py +30 -31
  944. scitex/stats/effect_sizes/_epsilon_squared.py +19 -22
  945. scitex/stats/effect_sizes/_eta_squared.py +23 -27
  946. scitex/stats/effect_sizes/_prob_superiority.py +18 -21
  947. scitex/stats/posthoc/__init__.py +3 -3
  948. scitex/stats/posthoc/_dunnett.py +75 -55
  949. scitex/stats/posthoc/_games_howell.py +61 -43
  950. scitex/stats/posthoc/_tukey_hsd.py +42 -34
  951. scitex/stats/power/__init__.py +2 -2
  952. scitex/stats/power/_power.py +56 -56
  953. scitex/stats/tests/__init__.py +1 -1
  954. scitex/stats/tests/correlation/__init__.py +1 -1
  955. scitex/stats/tests/correlation/_test_pearson.py +28 -38
  956. scitex/stats/utils/__init__.py +14 -17
  957. scitex/stats/utils/_effect_size.py +85 -78
  958. scitex/stats/utils/_formatters.py +49 -43
  959. scitex/stats/utils/_normalizers.py +7 -14
  960. scitex/stats/utils/_power.py +56 -56
  961. scitex/str/__init__.py +1 -0
  962. scitex/str/_clean_path.py +3 -3
  963. scitex/str/_factor_out_digits.py +86 -58
  964. scitex/str/_format_plot_text.py +180 -111
  965. scitex/str/_latex.py +19 -19
  966. scitex/str/_latex_fallback.py +9 -10
  967. scitex/str/_parse.py +3 -6
  968. scitex/str/_print_debug.py +13 -13
  969. scitex/str/_printc.py +2 -0
  970. scitex/str/_search.py +3 -3
  971. scitex/template/.legacy/_clone_project.py +9 -13
  972. scitex/template/__init__.py +10 -2
  973. scitex/template/_clone_project.py +7 -2
  974. scitex/template/_copy.py +1 -0
  975. scitex/template/_customize.py +3 -6
  976. scitex/template/_git_strategy.py +2 -3
  977. scitex/template/_rename.py +1 -0
  978. scitex/template/clone_pip_project.py +6 -7
  979. scitex/template/clone_research.py +7 -10
  980. scitex/template/clone_singularity.py +6 -7
  981. scitex/template/clone_writer_directory.py +6 -7
  982. scitex/tex/_preview.py +26 -11
  983. scitex/tex/_to_vec.py +10 -7
  984. scitex/torch/__init__.py +11 -1
  985. scitex/types/_ArrayLike.py +2 -0
  986. scitex/types/_is_listed_X.py +3 -3
  987. scitex/units.py +110 -77
  988. scitex/utils/_compress_hdf5.py +3 -3
  989. scitex/utils/_email.py +8 -4
  990. scitex/utils/_notify.py +14 -8
  991. scitex/utils/_search.py +6 -6
  992. scitex/utils/_verify_scitex_format.py +17 -42
  993. scitex/utils/_verify_scitex_format_v01.py +12 -34
  994. scitex/utils/template.py +4 -3
  995. scitex/vis/__init__.py +0 -0
  996. scitex/vis/backend/__init__.py +3 -3
  997. scitex/vis/backend/{export.py → _export.py} +1 -1
  998. scitex/vis/backend/{parser.py → _parser.py} +1 -3
  999. scitex/vis/backend/{render.py → _render.py} +1 -1
  1000. scitex/vis/canvas.py +15 -3
  1001. scitex/vis/editor/__init__.py +0 -0
  1002. scitex/vis/editor/_dearpygui_editor.py +450 -304
  1003. scitex/vis/editor/_defaults.py +114 -123
  1004. scitex/vis/editor/_edit.py +38 -26
  1005. scitex/vis/editor/_flask_editor.py +8 -8
  1006. scitex/vis/editor/_mpl_editor.py +63 -48
  1007. scitex/vis/editor/_qt_editor.py +210 -159
  1008. scitex/vis/editor/_tkinter_editor.py +146 -89
  1009. scitex/vis/editor/flask_editor/__init__.py +10 -10
  1010. scitex/vis/editor/flask_editor/_bbox.py +529 -0
  1011. scitex/vis/editor/flask_editor/{core.py → _core.py} +45 -29
  1012. scitex/vis/editor/flask_editor/_plotter.py +567 -0
  1013. scitex/vis/editor/flask_editor/_renderer.py +393 -0
  1014. scitex/vis/editor/flask_editor/{utils.py → _utils.py} +13 -14
  1015. scitex/vis/editor/flask_editor/templates/__init__.py +5 -5
  1016. scitex/vis/editor/flask_editor/templates/{html.py → _html.py} +234 -16
  1017. scitex/vis/editor/flask_editor/templates/_scripts.py +1261 -0
  1018. scitex/vis/editor/flask_editor/templates/{styles.py → _styles.py} +192 -2
  1019. scitex/vis/io/__init__.py +5 -5
  1020. scitex/vis/io/{canvas.py → _canvas.py} +8 -4
  1021. scitex/vis/io/{data.py → _data.py} +13 -9
  1022. scitex/vis/io/{directory.py → _directory.py} +7 -4
  1023. scitex/vis/io/{export.py → _export.py} +15 -12
  1024. scitex/vis/io/{load.py → _load.py} +1 -1
  1025. scitex/vis/io/{panel.py → _panel.py} +21 -13
  1026. scitex/vis/io/{save.py → _save.py} +0 -0
  1027. scitex/vis/model/__init__.py +7 -7
  1028. scitex/vis/model/{annotations.py → _annotations.py} +2 -4
  1029. scitex/vis/model/{axes.py → _axes.py} +1 -1
  1030. scitex/vis/model/{figure.py → _figure.py} +0 -0
  1031. scitex/vis/model/{guides.py → _guides.py} +1 -1
  1032. scitex/vis/model/{plot.py → _plot.py} +2 -4
  1033. scitex/vis/model/{plot_types.py → _plot_types.py} +0 -0
  1034. scitex/vis/model/{styles.py → _styles.py} +0 -0
  1035. scitex/vis/utils/__init__.py +2 -2
  1036. scitex/vis/utils/{defaults.py → _defaults.py} +1 -2
  1037. scitex/vis/utils/{validate.py → _validate.py} +3 -9
  1038. scitex/web/__init__.py +7 -1
  1039. scitex/web/_scraping.py +54 -38
  1040. scitex/web/_search_pubmed.py +30 -14
  1041. scitex/writer/.legacy/Writer_v01-refactored.py +4 -4
  1042. scitex/writer/.legacy/_compile.py +18 -28
  1043. scitex/writer/Writer.py +8 -21
  1044. scitex/writer/__init__.py +11 -11
  1045. scitex/writer/_clone_writer_project.py +2 -6
  1046. scitex/writer/_compile/__init__.py +1 -0
  1047. scitex/writer/_compile/_parser.py +1 -0
  1048. scitex/writer/_compile/_runner.py +35 -38
  1049. scitex/writer/_compile/_validator.py +1 -0
  1050. scitex/writer/_compile/manuscript.py +1 -0
  1051. scitex/writer/_compile/revision.py +1 -0
  1052. scitex/writer/_compile/supplementary.py +1 -0
  1053. scitex/writer/_compile_async.py +5 -12
  1054. scitex/writer/_project/__init__.py +1 -0
  1055. scitex/writer/_project/_create.py +10 -25
  1056. scitex/writer/_project/_trees.py +4 -9
  1057. scitex/writer/_project/_validate.py +2 -3
  1058. scitex/writer/_validate_tree_structures.py +7 -18
  1059. scitex/writer/dataclasses/__init__.py +8 -10
  1060. scitex/writer/dataclasses/config/_CONSTANTS.py +2 -3
  1061. scitex/writer/dataclasses/config/_WriterConfig.py +4 -9
  1062. scitex/writer/dataclasses/contents/_ManuscriptContents.py +14 -25
  1063. scitex/writer/dataclasses/contents/_RevisionContents.py +21 -16
  1064. scitex/writer/dataclasses/contents/_SupplementaryContents.py +21 -24
  1065. scitex/writer/dataclasses/core/_Document.py +2 -3
  1066. scitex/writer/dataclasses/core/_DocumentSection.py +8 -23
  1067. scitex/writer/dataclasses/results/_CompilationResult.py +2 -3
  1068. scitex/writer/dataclasses/results/_LaTeXIssue.py +3 -6
  1069. scitex/writer/dataclasses/results/_SaveSectionsResponse.py +20 -9
  1070. scitex/writer/dataclasses/results/_SectionReadResponse.py +24 -10
  1071. scitex/writer/dataclasses/tree/_ConfigTree.py +7 -4
  1072. scitex/writer/dataclasses/tree/_ManuscriptTree.py +10 -13
  1073. scitex/writer/dataclasses/tree/_RevisionTree.py +16 -17
  1074. scitex/writer/dataclasses/tree/_ScriptsTree.py +10 -5
  1075. scitex/writer/dataclasses/tree/_SharedTree.py +10 -13
  1076. scitex/writer/dataclasses/tree/_SupplementaryTree.py +15 -14
  1077. scitex/writer/utils/.legacy_git_retry.py +3 -8
  1078. scitex/writer/utils/_parse_latex_logs.py +2 -3
  1079. scitex/writer/utils/_parse_script_args.py +20 -23
  1080. scitex/writer/utils/_watch.py +5 -5
  1081. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/METADATA +4 -10
  1082. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/RECORD +1071 -975
  1083. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +0 -583
  1084. scitex/plt/_subplots/_export_as_csv_formatters.py +0 -112
  1085. scitex/vis/editor/flask_editor/bbox.py +0 -216
  1086. scitex/vis/editor/flask_editor/plotter.py +0 -130
  1087. scitex/vis/editor/flask_editor/renderer.py +0 -184
  1088. scitex/vis/editor/flask_editor/templates/scripts.py +0 -614
  1089. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/WHEEL +0 -0
  1090. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/entry_points.txt +0 -0
  1091. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/licenses/LICENSE +0 -0
@@ -36,6 +36,7 @@ logger = logging.getLogger(__name__)
36
36
 
37
37
  class ShibbolethError(ScholarError):
38
38
  """Raised when Shibboleth authentication fails."""
39
+
39
40
  pass
40
41
 
41
42
 
@@ -101,9 +102,11 @@ class ShibbolethAuthenticator(BaseAuthenticator):
101
102
  cache_dir or Path.home() / ".scitex" / "scholar" / "shibboleth_sessions"
102
103
  )
103
104
  self.cache_dir.mkdir(parents=True, exist_ok=True)
104
-
105
+
105
106
  # Session file path
106
- self.session_file = self.cache_dir / f"session_{self._get_session_async_key()}.json"
107
+ self.session_file = (
108
+ self.cache_dir / f"session_{self._get_session_async_key()}.json"
109
+ )
107
110
 
108
111
  # Session management
109
112
  self._cookies: Dict[str, str] = {}
@@ -119,7 +122,7 @@ class ShibbolethAuthenticator(BaseAuthenticator):
119
122
  "https://ds.aai.switch.ch", # Swiss federation
120
123
  "https://discovery.shibboleth.net", # Generic discovery
121
124
  ]
122
-
125
+
123
126
  # Common IdP login patterns
124
127
  self.idp_patterns = {
125
128
  "username_field": [
@@ -144,7 +147,7 @@ class ShibbolethAuthenticator(BaseAuthenticator):
144
147
  "button:has-text('Sign in')",
145
148
  ],
146
149
  }
147
-
150
+
148
151
  # Load existing session
149
152
  self._load_session()
150
153
 
@@ -163,7 +166,7 @@ class ShibbolethAuthenticator(BaseAuthenticator):
163
166
  try:
164
167
  with open(self.session_file, "r") as f:
165
168
  data = json.load(f)
166
-
169
+
167
170
  # Check if session is expired
168
171
  expiry_str = data.get("expiry")
169
172
  if expiry_str:
@@ -238,45 +241,47 @@ class ShibbolethAuthenticator(BaseAuthenticator):
238
241
 
239
242
  # Get resource URL to access (triggers Shibboleth flow)
240
243
  resource_url = kwargs.get("resource_url", "https://www.nature.com/siteindex")
241
-
242
- logger.info(f"Authenticating with Shibboleth for {self.institution or 'institution'}")
244
+
245
+ logger.info(
246
+ f"Authenticating with Shibboleth for {self.institution or 'institution'}"
247
+ )
243
248
 
244
249
  async with async_playwright() as p:
245
250
  browser = await p.chromium.launch(
246
251
  headless=not self.debug_mode,
247
- args=['--disable-blink-features=AutomationControlled']
252
+ args=["--disable-blink-features=AutomationControlled"],
248
253
  )
249
-
254
+
250
255
  try:
251
256
  context = await browser.new_context(
252
- user_agent='Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36'
257
+ user_agent="Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36"
253
258
  )
254
259
  page = await context.new_page()
255
-
260
+
256
261
  # Step 1: Access protected resource
257
262
  await page.goto(resource_url, wait_until="networkidle")
258
-
263
+
259
264
  # Step 2: Look for institutional login option
260
265
  login_found = await self._find_institutional_login_async(page)
261
-
266
+
262
267
  if login_found:
263
268
  # Click institutional login
264
269
  await login_found.click()
265
270
  await page.wait_for_load_state("networkidle")
266
-
271
+
267
272
  # Step 3: Handle WAYF/Discovery Service
268
273
  wayf_handled = await self._handle_wayf_selection_async(page)
269
-
274
+
270
275
  if not wayf_handled and not self.idp_url:
271
276
  raise ShibbolethError("Could not find institution selection page")
272
-
277
+
273
278
  # Step 4: Handle IdP login
274
279
  if self.idp_url and page.url.startswith(self.idp_url):
275
280
  await self._handle_idp_login_async(page)
276
281
  else:
277
282
  # Try to detect and handle IdP automatically
278
283
  await self._handle_idp_login_async(page)
279
-
284
+
280
285
  # Step 5: Wait for redirect back to resource
281
286
  try:
282
287
  await page.wait_for_function(
@@ -285,35 +290,35 @@ class ShibbolethAuthenticator(BaseAuthenticator):
285
290
  !window.location.href.includes('wayf') &&
286
291
  !window.location.href.includes('discovery');
287
292
  }}""",
288
- timeout=30000
293
+ timeout=30000,
289
294
  )
290
295
  except:
291
296
  # Continue anyway - might still be authenticate_async
292
297
  pass
293
-
298
+
294
299
  # Extract cookies and SAML attributes
295
300
  cookies = await context.cookies()
296
-
301
+
297
302
  # Try to extract SAML attributes from page or headers
298
303
  self._saml_attributes = await self._extract_saml_attributes_async(page)
299
-
304
+
300
305
  # Convert cookies
301
306
  self._cookies = {c["name"]: c["value"] for c in cookies}
302
307
  self._full_cookies = cookies
303
-
308
+
304
309
  # Set session expiry (typically 8-12 hours for Shibboleth)
305
310
  self._session_expiry = datetime.now() + timedelta(hours=8)
306
-
311
+
307
312
  # Save session
308
313
  self._save_session_async()
309
-
314
+
310
315
  logger.info(f"{self.name}: Shibboleth authentication successful")
311
316
  return {
312
317
  "cookies": self._cookies,
313
318
  "full_cookies": self._full_cookies,
314
319
  "saml_attributes": self._saml_attributes,
315
320
  }
316
-
321
+
317
322
  except Exception as e:
318
323
  logger.error(f"Shibboleth authentication failed: {e}")
319
324
  raise ShibbolethError(f"Authentication failed: {str(e)}")
@@ -333,13 +338,13 @@ class ShibbolethAuthenticator(BaseAuthenticator):
333
338
  "a[href*='wayf']",
334
339
  "a[href*='idp']",
335
340
  ]
336
-
341
+
337
342
  for selector in selectors:
338
343
  element = await page.query_selector(selector)
339
344
  if element and await element.is_visible():
340
345
  logger.debug(f"Found institutional login: {selector}")
341
346
  return element
342
-
347
+
343
348
  return None
344
349
 
345
350
  async def _handle_wayf_selection_async(self, page: Page) -> bool:
@@ -348,15 +353,16 @@ class ShibbolethAuthenticator(BaseAuthenticator):
348
353
  wayf_indicators = ["wayf", "discovery", "ds.", "where are you from"]
349
354
  current_url = page.url.lower()
350
355
  page_content = await page.content()
351
-
352
- is_wayf = any(ind in current_url for ind in wayf_indicators) or \
353
- any(ind in page_content.lower() for ind in wayf_indicators)
354
-
356
+
357
+ is_wayf = any(ind in current_url for ind in wayf_indicators) or any(
358
+ ind in page_content.lower() for ind in wayf_indicators
359
+ )
360
+
355
361
  if not is_wayf:
356
362
  return False
357
-
363
+
358
364
  logger.info(f"{self.name}: Detected WAYF/Discovery Service page")
359
-
365
+
360
366
  # Try to find institution selector
361
367
  if self.institution:
362
368
  # Search for institution in dropdown/list
@@ -365,43 +371,48 @@ class ShibbolethAuthenticator(BaseAuthenticator):
365
371
  f"a:has-text('{self.institution}')",
366
372
  f"li:has-text('{self.institution}')",
367
373
  ]
368
-
374
+
369
375
  for selector in selectors:
370
376
  element = await page.query_selector(selector)
371
377
  if element:
372
378
  # If it's an option, select it
373
379
  if await element.evaluate("el => el.tagName") == "OPTION":
374
380
  select = await element.evaluate_handle("el => el.parentElement")
375
- await select.select_option(value=await element.get_attribute("value"))
381
+ await select.select_option(
382
+ value=await element.get_attribute("value")
383
+ )
376
384
  # Find and click submit button
377
- submit = await page.query_selector("button[type='submit'], input[type='submit']")
385
+ submit = await page.query_selector(
386
+ "button[type='submit'], input[type='submit']"
387
+ )
378
388
  if submit:
379
389
  await submit.click()
380
390
  else:
381
391
  # Direct click
382
392
  await element.click()
383
-
393
+
384
394
  await page.wait_for_load_state("networkidle")
385
395
  return True
386
-
396
+
387
397
  # If automated selection fails, might need manual intervention
388
398
  if self.debug_mode:
389
399
  logger.info(f"{self.name}: Please select your institution manually")
390
400
  await asyncio.sleep(30) # Give time for manual selection
391
-
401
+
392
402
  return False
393
403
 
394
404
  async def _handle_idp_login_async(self, page: Page) -> None:
395
405
  """Handle login at the Identity Provider."""
396
406
  logger.info(f"{self.name}: Handling IdP login page")
397
-
407
+
398
408
  # Get credentials
399
409
  if not self.username:
400
410
  self.username = input("Shibboleth username: ")
401
411
  if not self.password:
402
412
  import getpass
413
+
403
414
  self.password = getpass.getpass("Shibboleth password: ")
404
-
415
+
405
416
  # Try each username field pattern
406
417
  username_filled = False
407
418
  for selector in self.idp_patterns["username_field"]:
@@ -410,10 +421,10 @@ class ShibbolethAuthenticator(BaseAuthenticator):
410
421
  await field.fill(self.username)
411
422
  username_filled = True
412
423
  break
413
-
424
+
414
425
  if not username_filled:
415
426
  raise ShibbolethError("Could not find username field")
416
-
427
+
417
428
  # Try each password field pattern
418
429
  password_filled = False
419
430
  for selector in self.idp_patterns["password_field"]:
@@ -422,24 +433,24 @@ class ShibbolethAuthenticator(BaseAuthenticator):
422
433
  await field.fill(self.password)
423
434
  password_filled = True
424
435
  break
425
-
436
+
426
437
  if not password_filled:
427
438
  raise ShibbolethError("Could not find password field")
428
-
439
+
429
440
  # Try each submit button pattern
430
441
  for selector in self.idp_patterns["submit_button"]:
431
442
  button = await page.query_selector(selector)
432
443
  if button and await button.is_visible():
433
444
  await button.click()
434
445
  break
435
-
446
+
436
447
  # Wait for authentication to complete
437
448
  await page.wait_for_load_state("networkidle")
438
449
 
439
450
  async def _extract_saml_attributes_async(self, page: Page) -> Dict[str, Any]:
440
451
  """Try to extract SAML attributes from the page."""
441
452
  attributes = {}
442
-
453
+
443
454
  try:
444
455
  # Some SPs expose attributes in meta tags
445
456
  meta_tags = await page.query_selector_all("meta[name^='shib-']")
@@ -449,20 +460,20 @@ class ShibbolethAuthenticator(BaseAuthenticator):
449
460
  if name and content:
450
461
  attr_name = name.replace("shib-", "")
451
462
  attributes[attr_name] = content
452
-
463
+
453
464
  # Check for common attribute patterns in page
454
465
  if not attributes:
455
466
  # Try to find email/eppn
456
- email_pattern = r'[\w._%+-]+@[\w.-]+\.[a-zA-Z]{2,}'
467
+ email_pattern = r"[\w._%+-]+@[\w.-]+\.[a-zA-Z]{2,}"
457
468
  page_text = await page.text_content()
458
469
  if page_text:
459
470
  emails = re.findall(email_pattern, page_text)
460
471
  if emails and self.username in emails[0]:
461
472
  attributes["eppn"] = emails[0]
462
-
473
+
463
474
  except Exception as e:
464
475
  logger.debug(f"Could not extract SAML attributes: {e}")
465
-
476
+
466
477
  return attributes
467
478
 
468
479
  async def is_authenticate_async(self, verify_live: bool = False) -> bool:
@@ -478,48 +489,48 @@ class ShibbolethAuthenticator(BaseAuthenticator):
478
489
  # Check if we have session data
479
490
  if not self._cookies or not self._session_expiry:
480
491
  return False
481
-
492
+
482
493
  # Check if session is expired
483
494
  if datetime.now() > self._session_expiry:
484
495
  logger.info(f"{self.name}: Shibboleth session expired")
485
496
  return False
486
-
497
+
487
498
  # If requested, verify session is still valid
488
499
  if verify_live:
489
500
  try:
490
501
  async with async_playwright() as p:
491
502
  browser = await p.chromium.launch(headless=True)
492
503
  context = await browser.new_context()
493
-
504
+
494
505
  # Add cookies
495
506
  await context.add_cookies(self._full_cookies)
496
-
507
+
497
508
  page = await context.new_page()
498
-
509
+
499
510
  # Try to access a protected resource
500
511
  test_url = "https://www.nature.com/nature"
501
512
  response = await page.goto(test_url, wait_until="networkidle")
502
-
513
+
503
514
  # Check if we're redirected to login
504
515
  is_valid = not any(
505
- ind in page.url.lower()
516
+ ind in page.url.lower()
506
517
  for ind in ["login", "wayf", "idp", "shibboleth"]
507
518
  )
508
-
519
+
509
520
  await browser.close()
510
-
521
+
511
522
  if not is_valid:
512
523
  logger.info(f"{self.name}: Shibboleth session no longer valid")
513
524
  self._cookies = {}
514
525
  self._full_cookies = []
515
526
  self._session_expiry = None
516
-
527
+
517
528
  return is_valid
518
-
529
+
519
530
  except Exception as e:
520
531
  logger.warn(f"Failed to verify session: {e}")
521
532
  return False
522
-
533
+
523
534
  return True
524
535
 
525
536
  async def get_auth_headers_async(self) -> Dict[str, str]:
@@ -561,17 +572,17 @@ class ShibbolethAuthenticator(BaseAuthenticator):
561
572
  self._full_cookies = []
562
573
  self._session_expiry = None
563
574
  self._saml_attributes = {}
564
-
575
+
565
576
  # Remove session file
566
577
  if self.session_file.exists():
567
578
  self.session_file.unlink()
568
-
579
+
569
580
  logger.info(f"{self.name}: Logged out from Shibboleth")
570
581
 
571
582
  async def get_session_info_async(self) -> Dict[str, Any]:
572
583
  """Get information about current session."""
573
584
  is_authenticate_async = await self.is_authenticate_async()
574
-
585
+
575
586
  return {
576
587
  "authenticate_async": is_authenticate_async,
577
588
  "provider": "Shibboleth",
@@ -580,7 +591,9 @@ class ShibbolethAuthenticator(BaseAuthenticator):
580
591
  "idp_url": self.idp_url,
581
592
  "entity_id": self.entity_id,
582
593
  "saml_attributes": self._saml_attributes,
583
- "session_expiry": self._session_expiry.isoformat() if self._session_expiry else None,
594
+ "session_expiry": self._session_expiry.isoformat()
595
+ if self._session_expiry
596
+ else None,
584
597
  "cookies_count": len(self._cookies),
585
598
  }
586
599
 
@@ -671,16 +684,17 @@ class ShibbolethAuthenticator(BaseAuthenticator):
671
684
  p = await async_playwright().start()
672
685
  browser = await p.chromium.launch(
673
686
  headless=not self.debug_mode,
674
- args=['--disable-blink-features=AutomationControlled']
687
+ args=["--disable-blink-features=AutomationControlled"],
675
688
  )
676
-
689
+
677
690
  context = await browser.new_context(
678
- user_agent='Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36'
691
+ user_agent="Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36"
679
692
  )
680
-
693
+
681
694
  # Add authentication cookies
682
695
  await context.add_cookies(self._full_cookies)
683
-
696
+
684
697
  return browser, context
685
698
 
686
- # EOF
699
+
700
+ # EOF
@@ -5,9 +5,8 @@
5
5
  # ----------------------------------------
6
6
  from __future__ import annotations
7
7
  import os
8
- __FILE__ = (
9
- "./src/scitex/scholar/auth/utils/AuthCacheManager.py"
10
- )
8
+
9
+ __FILE__ = "./src/scitex/scholar/auth/utils/AuthCacheManager.py"
11
10
  __DIR__ = os.path.dirname(__FILE__)
12
11
  # ----------------------------------------
13
12
 
@@ -61,13 +60,13 @@ class AuthCacheManager:
61
60
  os.chmod(self.cache_dir, 0o700)
62
61
  except OSError:
63
62
  # Permission denied in WSL or other systems where chmod may not work
64
- logger.debug(f"{self.name}: Could not set directory permissions: {self.cache_dir}")
63
+ logger.debug(
64
+ f"{self.name}: Could not set directory permissions: {self.cache_dir}"
65
+ )
65
66
 
66
67
  self.email = email
67
68
 
68
- async def save_session_async(
69
- self, session_manager: SessionManager
70
- ) -> bool:
69
+ async def save_session_async(self, session_manager: SessionManager) -> bool:
71
70
  """Save session data to cache file."""
72
71
  try:
73
72
  cache_data = self._create_cache_data(session_manager)
@@ -77,23 +76,17 @@ class AuthCacheManager:
77
76
 
78
77
  # Set secure permissions
79
78
  os.chmod(self.cache_json, 0o600)
80
- logger.info(
81
- f"{self.name}: Session saved to: {self.cache_json}"
82
- )
79
+ logger.info(f"{self.name}: Session saved to: {self.cache_json}")
83
80
  return True
84
81
 
85
82
  except Exception as e:
86
83
  logger.error(f"{self.name}: Failed to save session cache: {e}")
87
84
  return False
88
85
 
89
- async def load_session_async(
90
- self, session_manager: SessionManager
91
- ) -> bool:
86
+ async def load_session_async(self, session_manager: SessionManager) -> bool:
92
87
  """Load session data from cache file."""
93
88
  if not Path(self.cache_json).exists():
94
- logger.debug(
95
- f"{self.name}: No session cache found at {self.cache_json}"
96
- )
89
+ logger.debug(f"{self.name}: No session cache found at {self.cache_json}")
97
90
  return False
98
91
 
99
92
  try:
@@ -121,9 +114,7 @@ class AuthCacheManager:
121
114
  try:
122
115
  if self.cache_json.exists():
123
116
  self.cache_json.unlink()
124
- logger.info(
125
- f"{self.name}: Cleared cache file: {self.cache_json}"
126
- )
117
+ logger.info(f"{self.name}: Cleared cache file: {self.cache_json}")
127
118
  return True
128
119
  except Exception as e:
129
120
  logger.error(f"{self.name}: Failed to clear cache: {e}")
@@ -137,9 +128,7 @@ class AuthCacheManager:
137
128
  """Get lock file path."""
138
129
  return self.cache_json_lock
139
130
 
140
- def _create_cache_data(
141
- self, session_manager: SessionManager
142
- ) -> Dict[str, Any]:
131
+ def _create_cache_data(self, session_manager: SessionManager) -> Dict[str, Any]:
143
132
  """Create cache data dictionary from session manager."""
144
133
  expiry = session_manager.get_session_async_expiry()
145
134
  return {
@@ -193,4 +182,5 @@ class AuthCacheManager:
193
182
 
194
183
  session_manager.set_session_data(cookies, full_cookies, expiry)
195
184
 
185
+
196
186
  # EOF
@@ -5,9 +5,8 @@
5
5
  # ----------------------------------------
6
6
  from __future__ import annotations
7
7
  import os
8
- __FILE__ = (
9
- "./src/scitex/scholar/auth/library/_SessionManager.py"
10
- )
8
+
9
+ __FILE__ = "./src/scitex/scholar/auth/library/_SessionManager.py"
11
10
  __DIR__ = os.path.dirname(__FILE__)
12
11
  # ----------------------------------------
13
12
 
@@ -98,9 +97,7 @@ class SessionManager:
98
97
  "has_cookies": bool(self._cookies),
99
98
  "cookie_count": len(self._cookies),
100
99
  "expiry": (
101
- self._session_expiry.isoformat()
102
- if self._session_expiry
103
- else None
100
+ self._session_expiry.isoformat() if self._session_expiry else None
104
101
  ),
105
102
  "expired": self.is_session_expired(),
106
103
  "time_remaining": self._get_time_remaining(),
@@ -156,4 +153,5 @@ class SessionManager:
156
153
  "expiry": self._session_expiry,
157
154
  }
158
155
 
156
+
159
157
  # EOF
@@ -5,6 +5,7 @@
5
5
  # ----------------------------------------
6
6
  from __future__ import annotations
7
7
  import os
8
+
8
9
  __FILE__ = __file__
9
10
  __DIR__ = os.path.dirname(__FILE__)
10
11
  # ----------------------------------------
@@ -92,9 +93,7 @@ class BaseSSOAutomator(ABC):
92
93
  )
93
94
 
94
95
  # Session management
95
- self._session_dir = (
96
- Path.home() / ".scitex" / "scholar" / "sso_sessions"
97
- )
96
+ self._session_dir = Path.home() / ".scitex" / "scholar" / "sso_sessions"
98
97
  self._session_dir.mkdir(parents=True, exist_ok=True)
99
98
 
100
99
  self.logger = logger
@@ -135,9 +134,7 @@ class BaseSSOAutomator(ABC):
135
134
  if not self.is_sso_page(current_url):
136
135
  return True
137
136
 
138
- self.logger.info(
139
- f"Detected {self.get_institution_name()} SSO page"
140
- )
137
+ self.logger.info(f"Detected {self.get_institution_name()} SSO page")
141
138
 
142
139
  # Try to restore session first
143
140
  if self.use_persistent_session:
@@ -250,9 +247,7 @@ class BaseSSOAutomator(ABC):
250
247
  if success:
251
248
  self.logger.info(f"User notification sent: {event_type}")
252
249
  else:
253
- self.logger.warning(
254
- f"Failed to send user notification: {event_type}"
255
- )
250
+ self.logger.warning(f"Failed to send user notification: {event_type}")
256
251
 
257
252
  except Exception as e:
258
253
  self.logger.warning(f"Failed to send user notification: {str(e)}")
@@ -287,16 +282,14 @@ Action Required:
287
282
  System: SciTeX Scholar Module
288
283
  Institution: {institution}
289
284
  Status: Awaiting 2FA approval
290
- Timeout: {kwargs.get('timeout', 'Unknown')} seconds
285
+ Timeout: {kwargs.get("timeout", "Unknown")} seconds
291
286
 
292
287
  This is an automated notification from the SciTeX Scholar authentication system.
293
288
  """.strip()
294
289
  priority = "high"
295
290
 
296
291
  elif event_type == "authentication_success":
297
- subject = (
298
- f"SciTeX Scholar: Authentication Successful - {institution}"
299
- )
292
+ subject = f"SciTeX Scholar: Authentication Successful - {institution}"
300
293
  message = f"""
301
294
  {institution} SSO Authentication Complete
302
295
 
@@ -304,8 +297,8 @@ Your authentication has been completed successfully.
304
297
 
305
298
  Details:
306
299
  - Institution: {institution}
307
- - Session expires: {kwargs.get('expires_at', 'Unknown')}
308
- - Cookies saved: {kwargs.get('cookie_count', 'Unknown')}
300
+ - Session expires: {kwargs.get("expires_at", "Unknown")}
301
+ - Cookies saved: {kwargs.get("cookie_count", "Unknown")}
309
302
 
310
303
  System: SciTeX Scholar Module
311
304
  Status: Authenticated
@@ -323,7 +316,7 @@ Authentication was not completed successfully.
323
316
 
324
317
  Details:
325
318
  - Institution: {institution}
326
- - Error: {kwargs.get('error', 'Unknown error')}
319
+ - Error: {kwargs.get("error", "Unknown error")}
327
320
  - Retry available: Yes
328
321
 
329
322
  System: SciTeX Scholar Module
@@ -342,8 +335,8 @@ Your authentication session has expired and will need to be renewed.
342
335
 
343
336
  Details:
344
337
  - Institution: {institution}
345
- - Expired at: {kwargs.get('expired_at', 'Unknown')}
346
- - Auto-renewal: {kwargs.get('auto_renewal', 'Disabled')}
338
+ - Expired at: {kwargs.get("expired_at", "Unknown")}
339
+ - Auto-renewal: {kwargs.get("auto_renewal", "Disabled")}
347
340
 
348
341
  System: SciTeX Scholar Module
349
342
  Status: Session expired
@@ -358,7 +351,7 @@ Authentication will be required for the next access.
358
351
  message = f"""
359
352
  {institution} SSO Notification
360
353
 
361
- Event: {event_type.replace('_', ' ').title()}
354
+ Event: {event_type.replace("_", " ").title()}
362
355
  Institution: {institution}
363
356
  Context: {kwargs}
364
357
 
@@ -370,4 +363,5 @@ This is an automated notification from the SciTeX Scholar authentication system.
370
363
 
371
364
  return subject, message, priority
372
365
 
366
+
373
367
  # EOF