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
  345. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_kde.py +16 -17
  346. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter.py +7 -5
  347. scitex/plt/_subplots/_export_as_csv_formatters/_format_quiver.py +10 -8
  348. scitex/plt/_subplots/_export_as_csv_formatters/_format_scatter.py +17 -6
  349. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_barplot.py +43 -26
  350. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_boxplot.py +68 -47
  351. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_heatmap.py +52 -64
  352. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_histplot.py +55 -50
  353. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_jointplot.py +9 -11
  354. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_kdeplot.py +63 -29
  355. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_lineplot.py +4 -4
  356. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_pairplot.py +6 -4
  357. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_scatterplot.py +44 -40
  358. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_stripplot.py +46 -39
  359. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_swarmplot.py +46 -39
  360. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_violinplot.py +75 -94
  361. scitex/plt/_subplots/_export_as_csv_formatters/_format_stem.py +12 -3
  362. scitex/plt/_subplots/_export_as_csv_formatters/_format_step.py +12 -3
  363. scitex/plt/_subplots/_export_as_csv_formatters/_format_streamplot.py +10 -8
  364. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_conf_mat.py +17 -15
  365. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_ecdf.py +10 -9
  366. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_fillv.py +35 -31
  367. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_heatmap.py +18 -18
  368. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_image.py +24 -18
  369. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_joyplot.py +9 -7
  370. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_line.py +34 -23
  371. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_mean_ci.py +15 -13
  372. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_mean_std.py +12 -10
  373. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_median_iqr.py +15 -13
  374. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_raster.py +11 -9
  375. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_rectangle.py +84 -56
  376. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_scatter_hist.py +35 -32
  377. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_shaded_line.py +46 -30
  378. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_violin.py +51 -51
  379. scitex/plt/_subplots/_export_as_csv_formatters/_format_text.py +32 -31
  380. scitex/plt/_subplots/_export_as_csv_formatters/_format_violin.py +34 -31
  381. scitex/plt/_subplots/_export_as_csv_formatters/_format_violinplot.py +44 -37
  382. scitex/plt/_subplots/_export_as_csv_formatters/verify_formatters.py +91 -74
  383. scitex/plt/_tpl.py +6 -5
  384. scitex/plt/ax/_plot/__init__.py +24 -0
  385. scitex/plt/ax/_plot/_add_fitted_line.py +12 -11
  386. scitex/plt/ax/_plot/_plot_circular_hist.py +3 -1
  387. scitex/plt/ax/_plot/_plot_statistical_shaded_line.py +25 -19
  388. scitex/plt/ax/_plot/_stx_conf_mat.py +6 -3
  389. scitex/plt/ax/_plot/_stx_ecdf.py +5 -3
  390. scitex/plt/ax/_plot/_stx_fillv.py +4 -2
  391. scitex/plt/ax/_plot/_stx_heatmap.py +7 -4
  392. scitex/plt/ax/_plot/_stx_image.py +7 -5
  393. scitex/plt/ax/_plot/_stx_joyplot.py +32 -10
  394. scitex/plt/ax/_plot/_stx_raster.py +26 -11
  395. scitex/plt/ax/_plot/_stx_rectangle.py +2 -2
  396. scitex/plt/ax/_plot/_stx_shaded_line.py +15 -11
  397. scitex/plt/ax/_plot/_stx_violin.py +3 -1
  398. scitex/plt/ax/_style/_add_marginal_ax.py +6 -4
  399. scitex/plt/ax/_style/_auto_scale_axis.py +14 -10
  400. scitex/plt/ax/_style/_extend.py +3 -1
  401. scitex/plt/ax/_style/_force_aspect.py +5 -3
  402. scitex/plt/ax/_style/_format_units.py +2 -2
  403. scitex/plt/ax/_style/_hide_spines.py +5 -1
  404. scitex/plt/ax/_style/_map_ticks.py +5 -3
  405. scitex/plt/ax/_style/_rotate_labels.py +5 -4
  406. scitex/plt/ax/_style/_rotate_labels_v01.py +73 -63
  407. scitex/plt/ax/_style/_set_log_scale.py +120 -85
  408. scitex/plt/ax/_style/_set_meta.py +99 -76
  409. scitex/plt/ax/_style/_set_supxyt.py +33 -16
  410. scitex/plt/ax/_style/_set_xyt.py +27 -18
  411. scitex/plt/ax/_style/_share_axes.py +15 -5
  412. scitex/plt/ax/_style/_show_spines.py +58 -57
  413. scitex/plt/ax/_style/_style_barplot.py +1 -1
  414. scitex/plt/ax/_style/_style_boxplot.py +25 -14
  415. scitex/plt/ax/_style/_style_errorbar.py +0 -0
  416. scitex/plt/ax/_style/_style_scatter.py +1 -1
  417. scitex/plt/ax/_style/_style_suptitles.py +3 -3
  418. scitex/plt/ax/_style/_style_violinplot.py +8 -2
  419. scitex/plt/color/__init__.py +34 -2
  420. scitex/plt/color/_add_hue_col.py +1 -0
  421. scitex/plt/color/_colors.py +0 -1
  422. scitex/plt/color/_get_colors_from_conf_matap.py +3 -1
  423. scitex/plt/color/_vizualize_colors.py +0 -1
  424. scitex/plt/docs/FIGURE_ARCHITECTURE.md +155 -97
  425. scitex/plt/gallery/README.md +75 -0
  426. scitex/plt/gallery/__init__.py +29 -0
  427. scitex/plt/gallery/_generate.py +153 -0
  428. scitex/plt/gallery/_plots.py +594 -0
  429. scitex/plt/gallery/_registry.py +153 -0
  430. scitex/plt/styles/__init__.py +9 -9
  431. scitex/plt/styles/_plot_defaults.py +62 -61
  432. scitex/plt/styles/_plot_postprocess.py +126 -77
  433. scitex/plt/styles/_style_loader.py +0 -0
  434. scitex/plt/styles/presets.py +43 -18
  435. scitex/plt/templates/research-master/scitex/vis/gallery/area/fill_between.json +110 -0
  436. scitex/plt/templates/research-master/scitex/vis/gallery/area/fill_betweenx.json +88 -0
  437. scitex/plt/templates/research-master/scitex/vis/gallery/area/stx_fill_between.json +103 -0
  438. scitex/plt/templates/research-master/scitex/vis/gallery/area/stx_fillv.json +106 -0
  439. scitex/plt/templates/research-master/scitex/vis/gallery/categorical/bar.json +92 -0
  440. scitex/plt/templates/research-master/scitex/vis/gallery/categorical/barh.json +92 -0
  441. scitex/plt/templates/research-master/scitex/vis/gallery/categorical/boxplot.json +92 -0
  442. scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_bar.json +84 -0
  443. scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_barh.json +84 -0
  444. scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_box.json +83 -0
  445. scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_boxplot.json +93 -0
  446. scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_violin.json +91 -0
  447. scitex/plt/templates/research-master/scitex/vis/gallery/categorical/stx_violinplot.json +91 -0
  448. scitex/plt/templates/research-master/scitex/vis/gallery/categorical/violinplot.json +91 -0
  449. scitex/plt/templates/research-master/scitex/vis/gallery/contour/contour.json +97 -0
  450. scitex/plt/templates/research-master/scitex/vis/gallery/contour/contourf.json +98 -0
  451. scitex/plt/templates/research-master/scitex/vis/gallery/contour/stx_contour.json +84 -0
  452. scitex/plt/templates/research-master/scitex/vis/gallery/distribution/hist.json +101 -0
  453. scitex/plt/templates/research-master/scitex/vis/gallery/distribution/hist2d.json +96 -0
  454. scitex/plt/templates/research-master/scitex/vis/gallery/distribution/stx_ecdf.json +95 -0
  455. scitex/plt/templates/research-master/scitex/vis/gallery/distribution/stx_joyplot.json +95 -0
  456. scitex/plt/templates/research-master/scitex/vis/gallery/distribution/stx_kde.json +93 -0
  457. scitex/plt/templates/research-master/scitex/vis/gallery/grid/imshow.json +95 -0
  458. scitex/plt/templates/research-master/scitex/vis/gallery/grid/matshow.json +95 -0
  459. scitex/plt/templates/research-master/scitex/vis/gallery/grid/stx_conf_mat.json +83 -0
  460. scitex/plt/templates/research-master/scitex/vis/gallery/grid/stx_heatmap.json +92 -0
  461. scitex/plt/templates/research-master/scitex/vis/gallery/grid/stx_image.json +121 -0
  462. scitex/plt/templates/research-master/scitex/vis/gallery/grid/stx_imshow.json +84 -0
  463. scitex/plt/templates/research-master/scitex/vis/gallery/line/plot.json +110 -0
  464. scitex/plt/templates/research-master/scitex/vis/gallery/line/step.json +92 -0
  465. scitex/plt/templates/research-master/scitex/vis/gallery/line/stx_line.json +95 -0
  466. scitex/plt/templates/research-master/scitex/vis/gallery/line/stx_shaded_line.json +96 -0
  467. scitex/plt/templates/research-master/scitex/vis/gallery/scatter/hexbin.json +95 -0
  468. scitex/plt/templates/research-master/scitex/vis/gallery/scatter/scatter.json +95 -0
  469. scitex/plt/templates/research-master/scitex/vis/gallery/scatter/stem.json +92 -0
  470. scitex/plt/templates/research-master/scitex/vis/gallery/scatter/stx_scatter.json +84 -0
  471. scitex/plt/templates/research-master/scitex/vis/gallery/special/pie.json +94 -0
  472. scitex/plt/templates/research-master/scitex/vis/gallery/special/stx_raster.json +109 -0
  473. scitex/plt/templates/research-master/scitex/vis/gallery/special/stx_rectangle.json +108 -0
  474. scitex/plt/templates/research-master/scitex/vis/gallery/statistical/errorbar.json +93 -0
  475. scitex/plt/templates/research-master/scitex/vis/gallery/statistical/stx_errorbar.json +84 -0
  476. scitex/plt/templates/research-master/scitex/vis/gallery/statistical/stx_mean_ci.json +96 -0
  477. scitex/plt/templates/research-master/scitex/vis/gallery/statistical/stx_mean_std.json +96 -0
  478. scitex/plt/templates/research-master/scitex/vis/gallery/statistical/stx_median_iqr.json +96 -0
  479. scitex/plt/templates/research-master/scitex/vis/gallery/vector/quiver.json +99 -0
  480. scitex/plt/templates/research-master/scitex/vis/gallery/vector/streamplot.json +100 -0
  481. scitex/plt/utils/__init__.py +29 -2
  482. scitex/plt/utils/_close.py +8 -3
  483. scitex/plt/utils/_collect_figure_metadata.py +3031 -265
  484. scitex/plt/utils/_colorbar.py +15 -17
  485. scitex/plt/utils/_configure_mpl.py +22 -14
  486. scitex/plt/utils/_crop.py +60 -27
  487. scitex/plt/utils/_csv_column_naming.py +123 -72
  488. scitex/plt/utils/_dimension_viewer.py +7 -19
  489. scitex/plt/utils/_figure_from_axes_mm.py +70 -16
  490. scitex/plt/utils/_figure_mm.py +3 -2
  491. scitex/plt/utils/_get_actual_font.py +5 -4
  492. scitex/plt/utils/_histogram_utils.py +52 -48
  493. scitex/plt/utils/_is_valid_axis.py +19 -13
  494. scitex/plt/utils/_mk_colorbar.py +3 -3
  495. scitex/plt/utils/_scientific_captions.py +202 -139
  496. scitex/plt/utils/_scitex_config.py +98 -98
  497. scitex/plt/utils/_units.py +0 -0
  498. scitex/plt/utils/metadata/__init__.py +36 -0
  499. scitex/plt/utils/metadata/_artist_extraction.py +119 -0
  500. scitex/plt/utils/metadata/_axes_metadata.py +93 -0
  501. scitex/plt/utils/metadata/_collection_artists.py +292 -0
  502. scitex/plt/utils/metadata/_core.py +208 -0
  503. scitex/plt/utils/metadata/_csv_column_extraction.py +186 -0
  504. scitex/plt/utils/metadata/_csv_hash.py +115 -0
  505. scitex/plt/utils/metadata/_csv_verification.py +95 -0
  506. scitex/plt/utils/metadata/_data_linkage.py +263 -0
  507. scitex/plt/utils/metadata/_dimensions.py +239 -0
  508. scitex/plt/utils/metadata/_figure_metadata.py +58 -0
  509. scitex/plt/utils/metadata/_image_text_artists.py +168 -0
  510. scitex/plt/utils/metadata/_label_parsing.py +82 -0
  511. scitex/plt/utils/metadata/_legend_extraction.py +120 -0
  512. scitex/plt/utils/metadata/_line_artists.py +367 -0
  513. scitex/plt/utils/metadata/_line_semantic_handling.py +173 -0
  514. scitex/plt/utils/metadata/_patch_artists.py +211 -0
  515. scitex/plt/utils/metadata/_plot_content.py +26 -0
  516. scitex/plt/utils/metadata/_plot_type_detection.py +184 -0
  517. scitex/plt/utils/metadata/_precision.py +134 -0
  518. scitex/plt/utils/metadata/_precision_config.py +68 -0
  519. scitex/plt/utils/metadata/_precision_sections.py +211 -0
  520. scitex/plt/utils/metadata/_recipe_extraction.py +267 -0
  521. scitex/plt/utils/metadata/_style_parsing.py +174 -0
  522. scitex/repro/_RandomStateManager.py +33 -38
  523. scitex/repro/__init__.py +16 -7
  524. scitex/repro/_gen_ID.py +7 -9
  525. scitex/repro/_gen_timestamp.py +7 -6
  526. scitex/repro/_hash_array.py +8 -12
  527. scitex/reproduce/__init__.py +1 -1
  528. scitex/resource/_get_processor_usages.py +3 -1
  529. scitex/resource/_log_processor_usages.py +3 -1
  530. scitex/rng/__init__.py +1 -1
  531. scitex/schema/README.md +178 -0
  532. scitex/schema/__init__.py +144 -0
  533. scitex/schema/_canvas.py +444 -0
  534. scitex/schema/_stats.py +762 -0
  535. scitex/schema/_validation.py +590 -0
  536. scitex/scholar/.legacy/Scholar.py +5 -12
  537. scitex/scholar/.legacy/_Scholar.py +66 -99
  538. scitex/scholar/.legacy/_ScholarAPI.py +75 -66
  539. scitex/scholar/.legacy/_tmp/search_engine/_BaseSearchEngine.py +3 -3
  540. scitex/scholar/.legacy/_tmp/search_engine/_UnifiedSearcher.py +4 -9
  541. scitex/scholar/.legacy/_tmp/search_engine/__init__.py +14 -21
  542. scitex/scholar/.legacy/_tmp/search_engine/local/_LocalSearchEngine.py +40 -37
  543. scitex/scholar/.legacy/_tmp/search_engine/local/_VectorSearchEngine.py +31 -28
  544. scitex/scholar/.legacy/_tmp/search_engine/web/_ArxivSearchEngine.py +74 -65
  545. scitex/scholar/.legacy/_tmp/search_engine/web/_CrossRefSearchEngine.py +122 -116
  546. scitex/scholar/.legacy/_tmp/search_engine/web/_GoogleScholarSearchEngine.py +65 -59
  547. scitex/scholar/.legacy/_tmp/search_engine/web/_PubMedSearchEngine.py +121 -107
  548. scitex/scholar/.legacy/_tmp/search_engine/web/_SemanticScholarSearchEngine.py +5 -12
  549. scitex/scholar/.legacy/database/_DatabaseEntry.py +49 -45
  550. scitex/scholar/.legacy/database/_DatabaseIndex.py +131 -94
  551. scitex/scholar/.legacy/database/_LibraryManager.py +65 -63
  552. scitex/scholar/.legacy/database/_PaperDatabase.py +138 -124
  553. scitex/scholar/.legacy/database/_ScholarDatabaseIntegration.py +14 -36
  554. scitex/scholar/.legacy/database/_StorageIntegratedDB.py +192 -156
  555. scitex/scholar/.legacy/database/_ZoteroCompatibleDB.py +300 -237
  556. scitex/scholar/.legacy/database/__init__.py +2 -1
  557. scitex/scholar/.legacy/database/manage.py +92 -84
  558. scitex/scholar/.legacy/lookup/_LookupIndex.py +157 -101
  559. scitex/scholar/.legacy/lookup/__init__.py +2 -1
  560. scitex/scholar/.legacy/metadata/doi/batch/_MetadataHandlerForBatchDOIResolution.py +4 -9
  561. scitex/scholar/.legacy/metadata/doi/batch/_ProgressManagerForBatchDOIResolution.py +10 -23
  562. scitex/scholar/.legacy/metadata/doi/batch/_SourceStatsManagerForBatchDOIResolution.py +4 -9
  563. scitex/scholar/.legacy/metadata/doi/batch/__init__.py +3 -1
  564. scitex/scholar/.legacy/metadata/doi/resolvers/_BatchDOIResolver.py +10 -25
  565. scitex/scholar/.legacy/metadata/doi/resolvers/_BibTeXDOIResolver.py +19 -49
  566. scitex/scholar/.legacy/metadata/doi/resolvers/_DOIResolver.py +1 -0
  567. scitex/scholar/.legacy/metadata/doi/resolvers/_SingleDOIResolver.py +8 -20
  568. scitex/scholar/.legacy/metadata/doi/sources/.combined-SemanticScholarSource/_SemanticScholarSource.py +37 -35
  569. scitex/scholar/.legacy/metadata/doi/sources/.combined-SemanticScholarSource/_SemanticScholarSourceEnhanced.py +49 -37
  570. scitex/scholar/.legacy/metadata/doi/sources/_ArXivSource.py +11 -30
  571. scitex/scholar/.legacy/metadata/doi/sources/_BaseDOISource.py +19 -47
  572. scitex/scholar/.legacy/metadata/doi/sources/_CrossRefLocalSource.py +1 -0
  573. scitex/scholar/.legacy/metadata/doi/sources/_CrossRefSource.py +12 -33
  574. scitex/scholar/.legacy/metadata/doi/sources/_OpenAlexSource.py +8 -20
  575. scitex/scholar/.legacy/metadata/doi/sources/_PubMedSource.py +10 -27
  576. scitex/scholar/.legacy/metadata/doi/sources/_SemanticScholarSource.py +11 -29
  577. scitex/scholar/.legacy/metadata/doi/sources/_SourceManager.py +8 -21
  578. scitex/scholar/.legacy/metadata/doi/sources/_SourceResolutionStrategy.py +24 -55
  579. scitex/scholar/.legacy/metadata/doi/sources/_SourceRotationManager.py +8 -21
  580. scitex/scholar/.legacy/metadata/doi/sources/_URLDOISource.py +9 -16
  581. scitex/scholar/.legacy/metadata/doi/sources/_UnifiedSource.py +8 -22
  582. scitex/scholar/.legacy/metadata/doi/sources/__init__.py +1 -0
  583. scitex/scholar/.legacy/metadata/doi/utils/_PubMedConverter.py +4 -8
  584. scitex/scholar/.legacy/metadata/doi/utils/_RateLimitHandler.py +17 -43
  585. scitex/scholar/.legacy/metadata/doi/utils/_TextNormalizer.py +8 -18
  586. scitex/scholar/.legacy/metadata/doi/utils/_URLDOIExtractor.py +4 -8
  587. scitex/scholar/.legacy/metadata/doi/utils/__init__.py +1 -0
  588. scitex/scholar/.legacy/metadata/doi/utils/_to_complete_metadata_structure.py +1 -0
  589. scitex/scholar/.legacy/metadata/enrichment/_LibraryEnricher.py +2 -3
  590. scitex/scholar/.legacy/metadata/enrichment/enrichers/_ImpactFactorEnricher.py +6 -12
  591. scitex/scholar/.legacy/metadata/enrichment/enrichers/_SmartEnricher.py +5 -10
  592. scitex/scholar/.legacy/metadata/enrichment/sources/_UnifiedMetadataSource.py +4 -5
  593. scitex/scholar/.legacy/metadata/query_to_full_meta_json.py +8 -12
  594. scitex/scholar/.legacy/metadata/urls/_URLMetadataHandler.py +3 -3
  595. scitex/scholar/.legacy/metadata/urls/_ZoteroTranslatorRunner.py +15 -21
  596. scitex/scholar/.legacy/metadata/urls/__init__.py +3 -3
  597. scitex/scholar/.legacy/metadata/urls/_finder.py +4 -6
  598. scitex/scholar/.legacy/metadata/urls/_handler.py +7 -15
  599. scitex/scholar/.legacy/metadata/urls/_resolver.py +6 -12
  600. scitex/scholar/.legacy/search/_Embedder.py +74 -69
  601. scitex/scholar/.legacy/search/_SemanticSearch.py +91 -90
  602. scitex/scholar/.legacy/search/_SemanticSearchEngine.py +104 -109
  603. scitex/scholar/.legacy/search/_UnifiedSearcher.py +530 -471
  604. scitex/scholar/.legacy/search/_VectorDatabase.py +111 -92
  605. scitex/scholar/.legacy/search/__init__.py +1 -0
  606. scitex/scholar/.legacy/storage/_EnhancedStorageManager.py +182 -154
  607. scitex/scholar/.legacy/storage/__init__.py +2 -1
  608. scitex/scholar/__init__.py +0 -2
  609. scitex/scholar/__main__.py +1 -3
  610. scitex/scholar/auth/ScholarAuthManager.py +13 -36
  611. scitex/scholar/auth/core/AuthenticationGateway.py +15 -29
  612. scitex/scholar/auth/core/BrowserAuthenticator.py +22 -57
  613. scitex/scholar/auth/core/StrategyResolver.py +10 -27
  614. scitex/scholar/auth/core/__init__.py +5 -1
  615. scitex/scholar/auth/gateway/_OpenURLLinkFinder.py +11 -21
  616. scitex/scholar/auth/gateway/_OpenURLResolver.py +10 -18
  617. scitex/scholar/auth/gateway/_resolve_functions.py +3 -3
  618. scitex/scholar/auth/providers/BaseAuthenticator.py +1 -0
  619. scitex/scholar/auth/providers/EZProxyAuthenticator.py +7 -14
  620. scitex/scholar/auth/providers/OpenAthensAuthenticator.py +29 -57
  621. scitex/scholar/auth/providers/ShibbolethAuthenticator.py +87 -73
  622. scitex/scholar/auth/session/AuthCacheManager.py +12 -22
  623. scitex/scholar/auth/session/SessionManager.py +4 -6
  624. scitex/scholar/auth/sso/BaseSSOAutomator.py +13 -19
  625. scitex/scholar/auth/sso/OpenAthensSSOAutomator.py +16 -45
  626. scitex/scholar/auth/sso/SSOAutomator.py +8 -15
  627. scitex/scholar/auth/sso/UniversityOfMelbourneSSOAutomator.py +13 -23
  628. scitex/scholar/browser/ScholarBrowserManager.py +31 -56
  629. scitex/scholar/browser/__init__.py +1 -0
  630. scitex/scholar/browser/utils/click_and_wait.py +3 -4
  631. scitex/scholar/browser/utils/close_unwanted_pages.py +4 -7
  632. scitex/scholar/browser/utils/wait_redirects.py +15 -40
  633. scitex/scholar/citation_graph/__init__.py +0 -0
  634. scitex/scholar/citation_graph/builder.py +3 -7
  635. scitex/scholar/citation_graph/database.py +4 -11
  636. scitex/scholar/citation_graph/example.py +5 -10
  637. scitex/scholar/citation_graph/models.py +0 -0
  638. scitex/scholar/cli/_url_utils.py +1 -1
  639. scitex/scholar/cli/chrome.py +5 -3
  640. scitex/scholar/cli/download_pdf.py +13 -14
  641. scitex/scholar/cli/handlers/bibtex_handler.py +4 -12
  642. scitex/scholar/cli/handlers/doi_handler.py +1 -3
  643. scitex/scholar/cli/handlers/project_handler.py +6 -20
  644. scitex/scholar/cli/open_browser.py +41 -39
  645. scitex/scholar/cli/open_browser_auto.py +31 -39
  646. scitex/scholar/cli/open_browser_monitored.py +27 -24
  647. scitex/scholar/config/ScholarConfig.py +5 -8
  648. scitex/scholar/config/__init__.py +1 -0
  649. scitex/scholar/config/core/_CascadeConfig.py +3 -3
  650. scitex/scholar/config/core/_PathManager.py +16 -28
  651. scitex/scholar/core/Paper.py +79 -78
  652. scitex/scholar/core/Papers.py +16 -27
  653. scitex/scholar/core/Scholar.py +98 -229
  654. scitex/scholar/core/journal_normalizer.py +52 -49
  655. scitex/scholar/core/oa_cache.py +27 -23
  656. scitex/scholar/core/open_access.py +17 -8
  657. scitex/scholar/docs/template.py +4 -3
  658. scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/clf_svm.py +0 -0
  659. scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/download.py +0 -0
  660. scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_conf_mat.py +0 -0
  661. scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_digits.py +0 -0
  662. scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_umap_space.py +0 -0
  663. scitex/scholar/examples/00_config.py +10 -9
  664. scitex/scholar/examples/01_auth.py +3 -0
  665. scitex/scholar/examples/02_browser.py +14 -10
  666. scitex/scholar/examples/03_01-engine.py +3 -0
  667. scitex/scholar/examples/03_02-engine-for-bibtex.py +4 -3
  668. scitex/scholar/examples/04_01-url.py +9 -9
  669. scitex/scholar/examples/04_02-url-for-bibtex.py +7 -3
  670. scitex/scholar/examples/04_02-url-for-dois.py +87 -97
  671. scitex/scholar/examples/05_download_pdf.py +10 -4
  672. scitex/scholar/examples/06_find_and_download.py +6 -6
  673. scitex/scholar/examples/06_parse_bibtex.py +17 -17
  674. scitex/scholar/examples/07_storage_integration.py +6 -9
  675. scitex/scholar/examples/99_fullpipeline-for-bibtex.py +14 -15
  676. scitex/scholar/examples/99_fullpipeline-for-one-entry.py +31 -23
  677. scitex/scholar/examples/99_maintenance.py +3 -0
  678. scitex/scholar/examples/dev.py +2 -3
  679. scitex/scholar/examples/zotero_integration.py +11 -18
  680. scitex/scholar/impact_factor/ImpactFactorEngine.py +7 -9
  681. scitex/scholar/impact_factor/estimation/__init__.py +4 -4
  682. scitex/scholar/impact_factor/estimation/core/__init__.py +3 -7
  683. scitex/scholar/impact_factor/estimation/core/cache_manager.py +223 -211
  684. scitex/scholar/impact_factor/estimation/core/calculator.py +165 -131
  685. scitex/scholar/impact_factor/estimation/core/journal_matcher.py +217 -172
  686. scitex/scholar/impact_factor/jcr/ImpactFactorJCREngine.py +6 -14
  687. scitex/scholar/impact_factor/jcr/build_database.py +4 -3
  688. scitex/scholar/integration/base.py +9 -17
  689. scitex/scholar/integration/mendeley/exporter.py +2 -4
  690. scitex/scholar/integration/mendeley/importer.py +3 -3
  691. scitex/scholar/integration/mendeley/linker.py +3 -3
  692. scitex/scholar/integration/mendeley/mapper.py +9 -6
  693. scitex/scholar/integration/zotero/__main__.py +26 -43
  694. scitex/scholar/integration/zotero/exporter.py +15 -11
  695. scitex/scholar/integration/zotero/importer.py +12 -10
  696. scitex/scholar/integration/zotero/linker.py +8 -12
  697. scitex/scholar/integration/zotero/mapper.py +17 -12
  698. scitex/scholar/metadata_engines/.combined-SemanticScholarSource/_SemanticScholarSource.py +37 -35
  699. scitex/scholar/metadata_engines/.combined-SemanticScholarSource/_SemanticScholarSourceEnhanced.py +47 -35
  700. scitex/scholar/metadata_engines/ScholarEngine.py +21 -43
  701. scitex/scholar/metadata_engines/__init__.py +1 -0
  702. scitex/scholar/metadata_engines/individual/ArXivEngine.py +15 -37
  703. scitex/scholar/metadata_engines/individual/CrossRefEngine.py +15 -42
  704. scitex/scholar/metadata_engines/individual/CrossRefLocalEngine.py +24 -45
  705. scitex/scholar/metadata_engines/individual/OpenAlexEngine.py +11 -21
  706. scitex/scholar/metadata_engines/individual/PubMedEngine.py +10 -27
  707. scitex/scholar/metadata_engines/individual/SemanticScholarEngine.py +28 -35
  708. scitex/scholar/metadata_engines/individual/URLDOIEngine.py +11 -22
  709. scitex/scholar/metadata_engines/individual/_BaseDOIEngine.py +20 -49
  710. scitex/scholar/metadata_engines/utils/_PubMedConverter.py +4 -8
  711. scitex/scholar/metadata_engines/utils/_URLDOIExtractor.py +5 -10
  712. scitex/scholar/metadata_engines/utils/__init__.py +2 -0
  713. scitex/scholar/metadata_engines/utils/_metadata2bibtex.py +3 -0
  714. scitex/scholar/metadata_engines/utils/_standardize_metadata.py +2 -3
  715. scitex/scholar/pdf_download/ScholarPDFDownloader.py +25 -37
  716. scitex/scholar/pdf_download/strategies/chrome_pdf_viewer.py +11 -19
  717. scitex/scholar/pdf_download/strategies/direct_download.py +5 -9
  718. scitex/scholar/pdf_download/strategies/manual_download_fallback.py +3 -3
  719. scitex/scholar/pdf_download/strategies/manual_download_utils.py +6 -13
  720. scitex/scholar/pdf_download/strategies/open_access_download.py +49 -31
  721. scitex/scholar/pdf_download/strategies/response_body.py +8 -19
  722. scitex/scholar/pipelines/ScholarPipelineBibTeX.py +9 -18
  723. scitex/scholar/pipelines/ScholarPipelineMetadataParallel.py +25 -26
  724. scitex/scholar/pipelines/ScholarPipelineMetadataSingle.py +62 -23
  725. scitex/scholar/pipelines/ScholarPipelineParallel.py +13 -30
  726. scitex/scholar/pipelines/ScholarPipelineSearchParallel.py +299 -220
  727. scitex/scholar/pipelines/ScholarPipelineSearchSingle.py +202 -165
  728. scitex/scholar/pipelines/ScholarPipelineSingle.py +25 -51
  729. scitex/scholar/pipelines/SearchQueryParser.py +55 -55
  730. scitex/scholar/search_engines/ScholarSearchEngine.py +31 -27
  731. scitex/scholar/search_engines/_BaseSearchEngine.py +20 -23
  732. scitex/scholar/search_engines/individual/ArXivSearchEngine.py +53 -35
  733. scitex/scholar/search_engines/individual/CrossRefSearchEngine.py +47 -40
  734. scitex/scholar/search_engines/individual/OpenAlexSearchEngine.py +55 -50
  735. scitex/scholar/search_engines/individual/PubMedSearchEngine.py +8 -10
  736. scitex/scholar/search_engines/individual/SemanticScholarSearchEngine.py +55 -49
  737. scitex/scholar/storage/BibTeXHandler.py +150 -95
  738. scitex/scholar/storage/PaperIO.py +3 -6
  739. scitex/scholar/storage/ScholarLibrary.py +70 -49
  740. scitex/scholar/storage/_DeduplicationManager.py +52 -25
  741. scitex/scholar/storage/_LibraryCacheManager.py +19 -46
  742. scitex/scholar/storage/_LibraryManager.py +65 -175
  743. scitex/scholar/url_finder/ScholarURLFinder.py +9 -25
  744. scitex/scholar/url_finder/strategies/find_pdf_urls_by_direct_links.py +1 -1
  745. scitex/scholar/url_finder/strategies/find_pdf_urls_by_href.py +6 -10
  746. scitex/scholar/url_finder/strategies/find_pdf_urls_by_navigation.py +4 -6
  747. scitex/scholar/url_finder/strategies/find_pdf_urls_by_publisher_patterns.py +8 -15
  748. scitex/scholar/url_finder/strategies/find_pdf_urls_by_zotero_translators.py +3 -3
  749. scitex/scholar/url_finder/strategies/find_supplementary_urls_by_href.py +3 -3
  750. scitex/scholar/url_finder/translators/core/patterns.py +6 -4
  751. scitex/scholar/url_finder/translators/core/registry.py +6 -9
  752. scitex/scholar/url_finder/translators/individual/BOFiP_Impots.py +60 -52
  753. scitex/scholar/url_finder/translators/individual/Baidu_Scholar.py +54 -62
  754. scitex/scholar/url_finder/translators/individual/Bangkok_Post.py +38 -44
  755. scitex/scholar/url_finder/translators/individual/Baruch_Foundation.py +43 -47
  756. scitex/scholar/url_finder/translators/individual/Beobachter.py +46 -50
  757. scitex/scholar/url_finder/translators/individual/Bezneng_Gajit.py +37 -41
  758. scitex/scholar/url_finder/translators/individual/BibLaTeX.py +59 -52
  759. scitex/scholar/url_finder/translators/individual/BibTeX.py +83 -79
  760. scitex/scholar/url_finder/translators/individual/Biblio_com.py +48 -51
  761. scitex/scholar/url_finder/translators/individual/Bibliontology_RDF.py +58 -56
  762. scitex/scholar/url_finder/translators/individual/Camara_Brasileira_do_Livro_ISBN.py +102 -99
  763. scitex/scholar/url_finder/translators/individual/CanLII.py +49 -43
  764. scitex/scholar/url_finder/translators/individual/Canada_com.py +36 -40
  765. scitex/scholar/url_finder/translators/individual/Canadian_Letters_and_Images.py +43 -43
  766. scitex/scholar/url_finder/translators/individual/Canadiana_ca.py +77 -66
  767. scitex/scholar/url_finder/translators/individual/Cascadilla_Proceedings_Project.py +68 -62
  768. scitex/scholar/url_finder/translators/individual/Central_and_Eastern_European_Online_Library_Journals.py +60 -60
  769. scitex/scholar/url_finder/translators/individual/Champlain_Society_Collection.py +63 -61
  770. scitex/scholar/url_finder/translators/individual/Chicago_Journal_of_Theoretical_Computer_Science.py +74 -58
  771. scitex/scholar/url_finder/translators/individual/Christian_Science_Monitor.py +32 -38
  772. scitex/scholar/url_finder/translators/individual/Columbia_University_Press.py +51 -47
  773. scitex/scholar/url_finder/translators/individual/Common_Place.py +66 -57
  774. scitex/scholar/url_finder/translators/individual/Cornell_LII.py +66 -62
  775. scitex/scholar/url_finder/translators/individual/Cornell_University_Press.py +38 -45
  776. scitex/scholar/url_finder/translators/individual/CourtListener.py +52 -56
  777. scitex/scholar/url_finder/translators/individual/DAI_Zenon.py +53 -54
  778. scitex/scholar/url_finder/translators/individual/access_medicine.py +27 -33
  779. scitex/scholar/url_finder/translators/individual/acm.py +1 -1
  780. scitex/scholar/url_finder/translators/individual/acm_digital_library.py +93 -63
  781. scitex/scholar/url_finder/translators/individual/airiti.py +3 -1
  782. scitex/scholar/url_finder/translators/individual/aosic.py +3 -1
  783. scitex/scholar/url_finder/translators/individual/archive_ouverte_aosic.py +3 -1
  784. scitex/scholar/url_finder/translators/individual/archive_ouverte_en_sciences_de_l_information_et_de_la_communication___aosic_.py +6 -2
  785. scitex/scholar/url_finder/translators/individual/artforum.py +35 -27
  786. scitex/scholar/url_finder/translators/individual/arxiv.py +1 -1
  787. scitex/scholar/url_finder/translators/individual/arxiv_org.py +8 -4
  788. scitex/scholar/url_finder/translators/individual/atlanta_journal_constitution.py +22 -18
  789. scitex/scholar/url_finder/translators/individual/atypon_journals.py +19 -11
  790. scitex/scholar/url_finder/translators/individual/austlii_and_nzlii.py +48 -44
  791. scitex/scholar/url_finder/translators/individual/australian_dictionary_of_biography.py +21 -17
  792. scitex/scholar/url_finder/translators/individual/bailii.py +22 -19
  793. scitex/scholar/url_finder/translators/individual/bbc.py +46 -42
  794. scitex/scholar/url_finder/translators/individual/bbc_genome.py +37 -25
  795. scitex/scholar/url_finder/translators/individual/biblioteca_nacional_de_maestros.py +24 -20
  796. scitex/scholar/url_finder/translators/individual/bibliotheque_archives_nationale_quebec_pistard.py +42 -43
  797. scitex/scholar/url_finder/translators/individual/bibliotheque_archives_nationales_quebec.py +87 -81
  798. scitex/scholar/url_finder/translators/individual/bibliotheque_nationale_france.py +39 -37
  799. scitex/scholar/url_finder/translators/individual/bibsys.py +32 -28
  800. scitex/scholar/url_finder/translators/individual/bioconductor.py +58 -52
  801. scitex/scholar/url_finder/translators/individual/biomed_central.py +23 -15
  802. scitex/scholar/url_finder/translators/individual/biorxiv.py +26 -13
  803. scitex/scholar/url_finder/translators/individual/blogger.py +39 -43
  804. scitex/scholar/url_finder/translators/individual/bloomberg.py +48 -52
  805. scitex/scholar/url_finder/translators/individual/bloomsbury_food_library.py +37 -37
  806. scitex/scholar/url_finder/translators/individual/bluesky.py +30 -28
  807. scitex/scholar/url_finder/translators/individual/bnf_isbn.py +1 -1
  808. scitex/scholar/url_finder/translators/individual/bocc.py +66 -60
  809. scitex/scholar/url_finder/translators/individual/boe.py +52 -52
  810. scitex/scholar/url_finder/translators/individual/brill.py +3 -1
  811. scitex/scholar/url_finder/translators/individual/business_standard.py +36 -38
  812. scitex/scholar/url_finder/translators/individual/cabi_cab_abstracts.py +39 -41
  813. scitex/scholar/url_finder/translators/individual/cambridge.py +3 -1
  814. scitex/scholar/url_finder/translators/individual/cambridge_core.py +30 -24
  815. scitex/scholar/url_finder/translators/individual/caod.py +50 -46
  816. scitex/scholar/url_finder/translators/individual/cbc.py +91 -67
  817. scitex/scholar/url_finder/translators/individual/ccfr_bnf.py +49 -53
  818. scitex/scholar/url_finder/translators/individual/cia_world_factbook.py +43 -33
  819. scitex/scholar/url_finder/translators/individual/crossref_rest.py +208 -174
  820. scitex/scholar/url_finder/translators/individual/current_affairs.py +29 -35
  821. scitex/scholar/url_finder/translators/individual/dabi.py +70 -66
  822. scitex/scholar/url_finder/translators/individual/dagens_nyheter.py +3 -1
  823. scitex/scholar/url_finder/translators/individual/dagstuhl.py +10 -15
  824. scitex/scholar/url_finder/translators/individual/dar_almandumah.py +13 -9
  825. scitex/scholar/url_finder/translators/individual/dart_europe.py +19 -22
  826. scitex/scholar/url_finder/translators/individual/data_gov.py +2 -2
  827. scitex/scholar/url_finder/translators/individual/databrary.py +27 -28
  828. scitex/scholar/url_finder/translators/individual/datacite_json.py +152 -137
  829. scitex/scholar/url_finder/translators/individual/dataverse.py +68 -64
  830. scitex/scholar/url_finder/translators/individual/daum_news.py +38 -38
  831. scitex/scholar/url_finder/translators/individual/dblp.py +4 -8
  832. scitex/scholar/url_finder/translators/individual/dblp_computer_science_bibliography.py +8 -3
  833. scitex/scholar/url_finder/translators/individual/dbpia.py +5 -3
  834. scitex/scholar/url_finder/translators/individual/defense_technical_information_center.py +30 -28
  835. scitex/scholar/url_finder/translators/individual/delpher.py +102 -79
  836. scitex/scholar/url_finder/translators/individual/demographic_research.py +35 -31
  837. scitex/scholar/url_finder/translators/individual/denik_cz.py +58 -54
  838. scitex/scholar/url_finder/translators/individual/depatisnet.py +7 -10
  839. scitex/scholar/url_finder/translators/individual/der_freitag.py +81 -66
  840. scitex/scholar/url_finder/translators/individual/der_spiegel.py +56 -54
  841. scitex/scholar/url_finder/translators/individual/digibib_net.py +3 -1
  842. scitex/scholar/url_finder/translators/individual/digizeitschriften.py +3 -1
  843. scitex/scholar/url_finder/translators/individual/dpla.py +13 -14
  844. scitex/scholar/url_finder/translators/individual/dspace.py +2 -2
  845. scitex/scholar/url_finder/translators/individual/ebrary.py +3 -1
  846. scitex/scholar/url_finder/translators/individual/ebscohost.py +3 -1
  847. scitex/scholar/url_finder/translators/individual/electronic_colloquium_on_computational_complexity.py +3 -1
  848. scitex/scholar/url_finder/translators/individual/elife.py +3 -1
  849. scitex/scholar/url_finder/translators/individual/elsevier_health_journals.py +3 -1
  850. scitex/scholar/url_finder/translators/individual/emerald.py +3 -1
  851. scitex/scholar/url_finder/translators/individual/emerald_insight.py +3 -1
  852. scitex/scholar/url_finder/translators/individual/epicurious.py +3 -1
  853. scitex/scholar/url_finder/translators/individual/eurogamerusgamer.py +3 -1
  854. scitex/scholar/url_finder/translators/individual/fachportal_padagogik.py +3 -1
  855. scitex/scholar/url_finder/translators/individual/frontiers.py +1 -1
  856. scitex/scholar/url_finder/translators/individual/gale_databases.py +3 -1
  857. scitex/scholar/url_finder/translators/individual/gms_german_medical_science.py +6 -2
  858. scitex/scholar/url_finder/translators/individual/ieee_computer_society.py +6 -2
  859. scitex/scholar/url_finder/translators/individual/ieee_xplore.py +41 -35
  860. scitex/scholar/url_finder/translators/individual/inter_research_science_center.py +6 -2
  861. scitex/scholar/url_finder/translators/individual/jisc_historical_texts.py +3 -1
  862. scitex/scholar/url_finder/translators/individual/jstor.py +14 -12
  863. scitex/scholar/url_finder/translators/individual/korean_national_library.py +3 -1
  864. scitex/scholar/url_finder/translators/individual/la_times.py +3 -1
  865. scitex/scholar/url_finder/translators/individual/landesbibliographie_baden_wurttemberg.py +3 -1
  866. scitex/scholar/url_finder/translators/individual/legislative_insight.py +3 -1
  867. scitex/scholar/url_finder/translators/individual/libraries_tasmania.py +3 -1
  868. scitex/scholar/url_finder/translators/individual/library_catalog__koha_.py +3 -1
  869. scitex/scholar/url_finder/translators/individual/lingbuzz.py +2 -2
  870. scitex/scholar/url_finder/translators/individual/max_planck_institute_for_the_history_of_science_virtual_laboratory_library.py +3 -1
  871. scitex/scholar/url_finder/translators/individual/mdpi.py +12 -6
  872. scitex/scholar/url_finder/translators/individual/microbiology_society_journals.py +3 -1
  873. scitex/scholar/url_finder/translators/individual/midas_journals.py +3 -1
  874. scitex/scholar/url_finder/translators/individual/nagoya_university_opac.py +3 -1
  875. scitex/scholar/url_finder/translators/individual/nature_publishing_group.py +32 -19
  876. scitex/scholar/url_finder/translators/individual/ntsb_accident_reports.py +3 -1
  877. scitex/scholar/url_finder/translators/individual/openedition_journals.py +8 -4
  878. scitex/scholar/url_finder/translators/individual/orcid.py +16 -15
  879. scitex/scholar/url_finder/translators/individual/oxford.py +25 -19
  880. scitex/scholar/url_finder/translators/individual/oxford_dictionaries_premium.py +3 -1
  881. scitex/scholar/url_finder/translators/individual/ozon_ru.py +3 -1
  882. scitex/scholar/url_finder/translators/individual/plos.py +9 -12
  883. scitex/scholar/url_finder/translators/individual/polygon.py +3 -1
  884. scitex/scholar/url_finder/translators/individual/primo.py +3 -1
  885. scitex/scholar/url_finder/translators/individual/project_muse.py +3 -1
  886. scitex/scholar/url_finder/translators/individual/pubfactory_journals.py +3 -1
  887. scitex/scholar/url_finder/translators/individual/pubmed.py +71 -65
  888. scitex/scholar/url_finder/translators/individual/pubmed_central.py +8 -6
  889. scitex/scholar/url_finder/translators/individual/rechtspraak_nl.py +3 -1
  890. scitex/scholar/url_finder/translators/individual/sage_journals.py +25 -17
  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
@@ -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
  # ----------------------------------------
@@ -229,7 +230,9 @@ class _BlobMixin:
229
230
 
230
231
  if key:
231
232
  # Load specific key
232
- query = f"SELECT data, compressed, data_type FROM {table_name} WHERE key = ?"
233
+ query = (
234
+ f"SELECT data, compressed, data_type FROM {table_name} WHERE key = ?"
235
+ )
233
236
  params = (key,)
234
237
 
235
238
  if where:
@@ -256,16 +259,12 @@ class _BlobMixin:
256
259
 
257
260
  else:
258
261
  # Load all or filtered
259
- query = (
260
- f"SELECT key, data, compressed, data_type FROM {table_name}"
261
- )
262
+ query = f"SELECT key, data, compressed, data_type FROM {table_name}"
262
263
  if where:
263
264
  query += f" WHERE {where}"
264
265
 
265
266
  results = {}
266
- for key, data_bytes, is_compressed, data_type in self.execute(
267
- query
268
- ):
267
+ for key, data_bytes, is_compressed, data_type in self.execute(query):
269
268
  if is_compressed:
270
269
  data_bytes = zlib.decompress(data_bytes)
271
270
 
@@ -278,4 +277,5 @@ class _BlobMixin:
278
277
 
279
278
  return results
280
279
 
280
+
281
281
  # 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
  # ----------------------------------------
@@ -18,11 +19,11 @@ logger = logging.getLogger(__name__)
18
19
 
19
20
  class _ColumnMixin:
20
21
  """Efficient column operations for SQLite3 databases.
21
-
22
+
22
23
  Handles drop, rename, reorder, add, and modify operations
23
24
  with automatic version detection and optimization.
24
25
  """
25
-
26
+
26
27
  def get_sqlite_version(self) -> Tuple[int, int, int]:
27
28
  """Get SQLite version as tuple (major, minor, patch)."""
28
29
  cursor = self.cursor
@@ -30,42 +31,44 @@ class _ColumnMixin:
30
31
  version_str = cursor.fetchone()[0]
31
32
  parts = version_str.split(".")
32
33
  return tuple(int(p) for p in parts[:3])
33
-
34
+
34
35
  def supports_drop_column(self) -> bool:
35
36
  """Check if SQLite supports DROP COLUMN (3.35.0+)."""
36
37
  version = self.get_sqlite_version()
37
38
  return version >= (3, 35, 0)
38
-
39
+
39
40
  def supports_rename_column(self) -> bool:
40
41
  """Check if SQLite supports RENAME COLUMN (3.25.0+)."""
41
42
  version = self.get_sqlite_version()
42
43
  return version >= (3, 25, 0)
43
-
44
+
44
45
  def get_column_info(self, table_name: str) -> List[Dict[str, Any]]:
45
46
  """Get detailed information about table columns."""
46
47
  cursor = self.cursor
47
48
  cursor.execute(f"PRAGMA table_info({table_name})")
48
49
  columns = []
49
50
  for row in cursor.fetchall():
50
- columns.append({
51
- "cid": row[0],
52
- "name": row[1],
53
- "type": row[2],
54
- "notnull": row[3],
55
- "default": row[4],
56
- "pk": row[5],
57
- })
51
+ columns.append(
52
+ {
53
+ "cid": row[0],
54
+ "name": row[1],
55
+ "type": row[2],
56
+ "notnull": row[3],
57
+ "default": row[4],
58
+ "pk": row[5],
59
+ }
60
+ )
58
61
  return columns
59
-
62
+
60
63
  def column_exists(self, table_name: str, column_name: str) -> bool:
61
64
  """Check if a column exists in the table."""
62
65
  columns = self.get_column_info(table_name)
63
66
  return any(col["name"] == column_name for col in columns)
64
-
67
+
65
68
  # ----------------------------------------
66
69
  # DROP Operations
67
70
  # ----------------------------------------
68
-
71
+
69
72
  def drop_column(
70
73
  self,
71
74
  table_name: str,
@@ -74,13 +77,13 @@ class _ColumnMixin:
74
77
  progress_callback: Optional[callable] = None,
75
78
  ) -> bool:
76
79
  """Drop a column from table, using native or recreation method.
77
-
80
+
78
81
  Args:
79
82
  table_name: Name of the table
80
83
  column_name: Name of column to drop
81
84
  force_recreate: Force table recreation even if native DROP is available
82
85
  progress_callback: Function to call with progress updates
83
-
86
+
84
87
  Returns:
85
88
  True if successful, False otherwise
86
89
  """
@@ -89,17 +92,19 @@ class _ColumnMixin:
89
92
  if not self.column_exists(table_name, column_name):
90
93
  logger.warning(f"Column {column_name} does not exist in {table_name}")
91
94
  return False
92
-
95
+
93
96
  # Use native DROP if available and not forced to recreate
94
97
  if self.supports_drop_column() and not force_recreate:
95
98
  return self._drop_column_native(table_name, column_name)
96
99
  else:
97
- return self._drop_column_recreate(table_name, column_name, progress_callback)
98
-
100
+ return self._drop_column_recreate(
101
+ table_name, column_name, progress_callback
102
+ )
103
+
99
104
  except Exception as e:
100
105
  logger.error(f"Failed to drop column {column_name} from {table_name}: {e}")
101
106
  return False
102
-
107
+
103
108
  def _drop_column_native(self, table_name: str, column_name: str) -> bool:
104
109
  """Drop column using native SQLite ALTER TABLE DROP COLUMN."""
105
110
  try:
@@ -112,7 +117,7 @@ class _ColumnMixin:
112
117
  self.conn.rollback()
113
118
  logger.error(f"Native drop failed: {e}")
114
119
  return False
115
-
120
+
116
121
  def _drop_column_recreate(
117
122
  self,
118
123
  table_name: str,
@@ -124,14 +129,14 @@ class _ColumnMixin:
124
129
  cursor = self.cursor
125
130
  # Start transaction
126
131
  cursor.execute("BEGIN EXCLUSIVE TRANSACTION")
127
-
132
+
128
133
  # Get columns to keep
129
134
  columns = self.get_column_info(table_name)
130
135
  keep_columns = [col for col in columns if col["name"] != column_name]
131
-
136
+
132
137
  if not keep_columns:
133
138
  raise ValueError("Cannot drop all columns from table")
134
-
139
+
135
140
  # Create column list for new table
136
141
  column_names = [col["name"] for col in keep_columns]
137
142
  column_defs = []
@@ -144,38 +149,40 @@ class _ColumnMixin:
144
149
  if col["pk"]:
145
150
  col_def += " PRIMARY KEY"
146
151
  column_defs.append(col_def)
147
-
152
+
148
153
  # Get row count for progress
149
154
  cursor.execute(f"SELECT COUNT(*) FROM {table_name}")
150
155
  total_rows = cursor.fetchone()[0]
151
-
156
+
152
157
  if progress_callback:
153
158
  progress_callback(0, total_rows, "Creating temporary table")
154
-
159
+
155
160
  # Create temporary table
156
161
  temp_table = f"{table_name}_temp_{int(time.time())}"
157
162
  cursor.execute(f"""
158
163
  CREATE TABLE {temp_table} (
159
- {', '.join(column_defs)}
164
+ {", ".join(column_defs)}
160
165
  )
161
166
  """)
162
-
167
+
163
168
  # Copy data in batches for progress reporting
164
169
  batch_size = 10000
165
170
  offset = 0
166
-
171
+
167
172
  while offset < total_rows:
168
173
  cursor.execute(f"""
169
- INSERT INTO {temp_table} ({', '.join(column_names)})
170
- SELECT {', '.join(column_names)}
174
+ INSERT INTO {temp_table} ({", ".join(column_names)})
175
+ SELECT {", ".join(column_names)}
171
176
  FROM {table_name}
172
177
  LIMIT {batch_size} OFFSET {offset}
173
178
  """)
174
-
179
+
175
180
  offset += batch_size
176
181
  if progress_callback:
177
- progress_callback(min(offset, total_rows), total_rows, "Copying data")
178
-
182
+ progress_callback(
183
+ min(offset, total_rows), total_rows, "Copying data"
184
+ )
185
+
179
186
  # Get indexes, triggers, and views
180
187
  cursor.execute(f"""
181
188
  SELECT sql FROM sqlite_master
@@ -184,13 +191,13 @@ class _ColumnMixin:
184
191
  AND sql IS NOT NULL
185
192
  """)
186
193
  dependencies = cursor.fetchall()
187
-
194
+
188
195
  # Drop old table
189
196
  cursor.execute(f"DROP TABLE {table_name}")
190
-
197
+
191
198
  # Rename temp table
192
199
  cursor.execute(f"ALTER TABLE {temp_table} RENAME TO {table_name}")
193
-
200
+
194
201
  # Recreate indexes, triggers, and views
195
202
  for dep in dependencies:
196
203
  sql = dep[0]
@@ -200,33 +207,33 @@ class _ColumnMixin:
200
207
  cursor.execute(sql)
201
208
  except Exception as e:
202
209
  logger.warning(f"Could not recreate dependency: {e}")
203
-
210
+
204
211
  # Commit transaction
205
212
  self.conn.commit()
206
-
213
+
207
214
  if progress_callback:
208
215
  progress_callback(total_rows, total_rows, "Complete")
209
-
216
+
210
217
  logger.info(f"Dropped column {column_name} from {table_name} (recreate)")
211
218
  return True
212
-
219
+
213
220
  except Exception as e:
214
221
  self.conn.rollback()
215
222
  logger.error(f"Table recreation failed: {e}")
216
223
  return False
217
-
224
+
218
225
  # ----------------------------------------
219
226
  # RENAME Operations
220
227
  # ----------------------------------------
221
-
228
+
222
229
  def rename_column(self, table_name: str, old_name: str, new_name: str) -> bool:
223
230
  """Rename a column in the table.
224
-
231
+
225
232
  Args:
226
233
  table_name: Name of the table
227
234
  old_name: Current column name
228
235
  new_name: New column name
229
-
236
+
230
237
  Returns:
231
238
  True if successful, False otherwise
232
239
  """
@@ -234,11 +241,11 @@ class _ColumnMixin:
234
241
  if not self.column_exists(table_name, old_name):
235
242
  logger.error(f"Column {old_name} does not exist in {table_name}")
236
243
  return False
237
-
244
+
238
245
  if self.column_exists(table_name, new_name):
239
246
  logger.error(f"Column {new_name} already exists in {table_name}")
240
247
  return False
241
-
248
+
242
249
  if self.supports_rename_column():
243
250
  # Use native RENAME COLUMN
244
251
  cursor = self.cursor
@@ -252,24 +259,26 @@ class _ColumnMixin:
252
259
  else:
253
260
  # Use table recreation for older versions
254
261
  return self._rename_column_recreate(table_name, old_name, new_name)
255
-
262
+
256
263
  except Exception as e:
257
264
  self.conn.rollback()
258
265
  logger.error(f"Failed to rename column: {e}")
259
266
  return False
260
-
261
- def _rename_column_recreate(self, table_name: str, old_name: str, new_name: str) -> bool:
267
+
268
+ def _rename_column_recreate(
269
+ self, table_name: str, old_name: str, new_name: str
270
+ ) -> bool:
262
271
  """Rename column by recreating the table."""
263
272
  # Similar to drop_column_recreate but with renamed column
264
273
  # Implementation would be similar to _drop_column_recreate
265
274
  # but keeping all columns with one renamed
266
275
  logger.warning("Column rename via recreation not yet implemented")
267
276
  return False
268
-
277
+
269
278
  # ----------------------------------------
270
279
  # REORDER/SORT Operations
271
280
  # ----------------------------------------
272
-
281
+
273
282
  def reorder_columns(
274
283
  self,
275
284
  table_name: str,
@@ -277,17 +286,17 @@ class _ColumnMixin:
277
286
  progress_callback: Optional[callable] = None,
278
287
  ) -> bool:
279
288
  """Reorder columns in a table to match the specified order.
280
-
289
+
281
290
  Similar to pandas: df = df[['col3', 'col1', 'col2']]
282
-
291
+
283
292
  SQLite doesn't support column reordering directly, so this always
284
293
  requires table recreation.
285
-
294
+
286
295
  Args:
287
296
  table_name: Name of the table
288
297
  column_order: List of column names in desired order
289
298
  progress_callback: Function for progress updates
290
-
299
+
291
300
  Returns:
292
301
  True if successful, False otherwise
293
302
  """
@@ -295,7 +304,7 @@ class _ColumnMixin:
295
304
  # Validate all columns exist
296
305
  current_columns = self.get_column_info(table_name)
297
306
  current_names = {col["name"] for col in current_columns}
298
-
307
+
299
308
  if set(column_order) != current_names:
300
309
  missing = current_names - set(column_order)
301
310
  extra = set(column_order) - current_names
@@ -304,13 +313,13 @@ class _ColumnMixin:
304
313
  if extra:
305
314
  logger.error(f"Unknown columns in order: {extra}")
306
315
  return False
307
-
316
+
308
317
  # Create column map
309
318
  column_map = {col["name"]: col for col in current_columns}
310
-
319
+
311
320
  cursor = self.cursor
312
321
  cursor.execute("BEGIN EXCLUSIVE TRANSACTION")
313
-
322
+
314
323
  # Build new table definition with reordered columns
315
324
  column_defs = []
316
325
  for col_name in column_order:
@@ -323,34 +332,34 @@ class _ColumnMixin:
323
332
  if col["pk"]:
324
333
  col_def += " PRIMARY KEY"
325
334
  column_defs.append(col_def)
326
-
335
+
327
336
  # Create temp table with new column order
328
337
  temp_table = f"{table_name}_reorder_{int(time.time())}"
329
338
  cursor.execute(f"""
330
339
  CREATE TABLE {temp_table} (
331
- {', '.join(column_defs)}
340
+ {", ".join(column_defs)}
332
341
  )
333
342
  """)
334
-
343
+
335
344
  # Copy data
336
345
  cursor.execute(f"""
337
- INSERT INTO {temp_table} ({', '.join(column_order)})
338
- SELECT {', '.join(column_order)} FROM {table_name}
346
+ INSERT INTO {temp_table} ({", ".join(column_order)})
347
+ SELECT {", ".join(column_order)} FROM {table_name}
339
348
  """)
340
-
349
+
341
350
  # Swap tables
342
351
  cursor.execute(f"DROP TABLE {table_name}")
343
352
  cursor.execute(f"ALTER TABLE {temp_table} RENAME TO {table_name}")
344
-
353
+
345
354
  self.conn.commit()
346
355
  logger.info(f"Reordered columns in {table_name}")
347
356
  return True
348
-
357
+
349
358
  except Exception as e:
350
359
  self.conn.rollback()
351
360
  logger.error(f"Failed to reorder columns: {e}")
352
361
  return False
353
-
362
+
354
363
  def sort_columns(
355
364
  self,
356
365
  table_name: str,
@@ -360,16 +369,16 @@ class _ColumnMixin:
360
369
  progress_callback: Optional[callable] = None,
361
370
  ) -> bool:
362
371
  """Sort columns in a table alphabetically or by custom criteria.
363
-
372
+
364
373
  Similar to organizing DataFrame columns systematically.
365
-
374
+
366
375
  Args:
367
376
  table_name: Name of the table
368
377
  alphabetical: Sort columns alphabetically
369
378
  reverse: Reverse sort order
370
379
  key_columns_first: List of columns to place first (like 'id', 'created_at')
371
380
  progress_callback: Function for progress updates
372
-
381
+
373
382
  Returns:
374
383
  True if successful, False otherwise
375
384
  """
@@ -377,7 +386,7 @@ class _ColumnMixin:
377
386
  # Get current columns
378
387
  columns = self.get_column_info(table_name)
379
388
  column_names = [col["name"] for col in columns]
380
-
389
+
381
390
  # Determine new order
382
391
  if key_columns_first:
383
392
  # Put key columns first, then sort the rest
@@ -393,18 +402,18 @@ class _ColumnMixin:
393
402
  if alphabetical
394
403
  else column_names
395
404
  )
396
-
405
+
397
406
  # Use reorder_columns to apply the new order
398
407
  return self.reorder_columns(table_name, new_order, progress_callback)
399
-
408
+
400
409
  except Exception as e:
401
410
  logger.error(f"Failed to sort columns: {e}")
402
411
  return False
403
-
412
+
404
413
  # ----------------------------------------
405
414
  # ADD Operations
406
415
  # ----------------------------------------
407
-
416
+
408
417
  def add_column(
409
418
  self,
410
419
  table_name: str,
@@ -414,14 +423,14 @@ class _ColumnMixin:
414
423
  not_null: bool = False,
415
424
  ) -> bool:
416
425
  """Add a new column to the table.
417
-
426
+
418
427
  Args:
419
428
  table_name: Name of the table
420
429
  column_name: Name of new column
421
430
  column_type: SQLite type (TEXT, INTEGER, REAL, BLOB)
422
431
  default: Default value for the column
423
432
  not_null: Whether column should be NOT NULL
424
-
433
+
425
434
  Returns:
426
435
  True if successful, False otherwise
427
436
  """
@@ -429,38 +438,38 @@ class _ColumnMixin:
429
438
  if self.column_exists(table_name, column_name):
430
439
  logger.warning(f"Column {column_name} already exists in {table_name}")
431
440
  return False
432
-
441
+
433
442
  cursor = self.cursor
434
443
  col_def = f"{column_name} {column_type}"
435
-
444
+
436
445
  if not_null and default is None:
437
446
  logger.error("Cannot add NOT NULL column without default value")
438
447
  return False
439
-
448
+
440
449
  if default is not None:
441
450
  if isinstance(default, str):
442
451
  col_def += f" DEFAULT '{default}'"
443
452
  else:
444
453
  col_def += f" DEFAULT {default}"
445
-
454
+
446
455
  if not_null:
447
456
  col_def += " NOT NULL"
448
-
457
+
449
458
  cursor.execute(f"ALTER TABLE {table_name} ADD COLUMN {col_def}")
450
459
  self.conn.commit()
451
-
460
+
452
461
  logger.info(f"Added column {column_name} to {table_name}")
453
462
  return True
454
-
463
+
455
464
  except Exception as e:
456
465
  self.conn.rollback()
457
466
  logger.error(f"Failed to add column: {e}")
458
467
  return False
459
-
468
+
460
469
  # ----------------------------------------
461
470
  # Batch Operations
462
471
  # ----------------------------------------
463
-
472
+
464
473
  def drop_columns(
465
474
  self,
466
475
  table_name: str,
@@ -468,15 +477,15 @@ class _ColumnMixin:
468
477
  progress_callback: Optional[callable] = None,
469
478
  ) -> bool:
470
479
  """Drop multiple columns efficiently in one operation.
471
-
480
+
472
481
  More efficient than dropping columns one by one as it only
473
482
  recreates the table once.
474
-
483
+
475
484
  Args:
476
485
  table_name: Name of the table
477
486
  column_names: List of columns to drop
478
487
  progress_callback: Function for progress updates
479
-
488
+
480
489
  Returns:
481
490
  True if successful, False otherwise
482
491
  """
@@ -486,24 +495,22 @@ class _ColumnMixin:
486
495
  if not self.column_exists(table_name, col_name):
487
496
  logger.error(f"Column {col_name} does not exist in {table_name}")
488
497
  return False
489
-
498
+
490
499
  # If native DROP is supported and only one column, use it
491
500
  if len(column_names) == 1 and self.supports_drop_column():
492
501
  return self.drop_column(table_name, column_names[0])
493
-
502
+
494
503
  # Otherwise recreate table without the columns
495
504
  cursor = self.cursor
496
505
  cursor.execute("BEGIN EXCLUSIVE TRANSACTION")
497
-
506
+
498
507
  # Get columns to keep
499
508
  columns = self.get_column_info(table_name)
500
- keep_columns = [
501
- col for col in columns if col["name"] not in column_names
502
- ]
503
-
509
+ keep_columns = [col for col in columns if col["name"] not in column_names]
510
+
504
511
  if not keep_columns:
505
512
  raise ValueError("Cannot drop all columns from table")
506
-
513
+
507
514
  # Create column definitions
508
515
  column_names_keep = [col["name"] for col in keep_columns]
509
516
  column_defs = []
@@ -516,33 +523,33 @@ class _ColumnMixin:
516
523
  if col["pk"]:
517
524
  col_def += " PRIMARY KEY"
518
525
  column_defs.append(col_def)
519
-
526
+
520
527
  # Create temp table
521
528
  temp_table = f"{table_name}_drop_{int(time.time())}"
522
529
  cursor.execute(f"""
523
530
  CREATE TABLE {temp_table} (
524
- {', '.join(column_defs)}
531
+ {", ".join(column_defs)}
525
532
  )
526
533
  """)
527
-
534
+
528
535
  # Copy data
529
536
  cursor.execute(f"""
530
- INSERT INTO {temp_table} ({', '.join(column_names_keep)})
531
- SELECT {', '.join(column_names_keep)} FROM {table_name}
537
+ INSERT INTO {temp_table} ({", ".join(column_names_keep)})
538
+ SELECT {", ".join(column_names_keep)} FROM {table_name}
532
539
  """)
533
-
540
+
534
541
  # Swap tables
535
542
  cursor.execute(f"DROP TABLE {table_name}")
536
543
  cursor.execute(f"ALTER TABLE {temp_table} RENAME TO {table_name}")
537
-
544
+
538
545
  self.conn.commit()
539
546
  logger.info(f"Dropped {len(column_names)} columns from {table_name}")
540
547
  return True
541
-
548
+
542
549
  except Exception as e:
543
550
  self.conn.rollback()
544
551
  logger.error(f"Failed to drop multiple columns: {e}")
545
552
  return False
546
553
 
547
554
 
548
- # EOF
555
+ # EOF