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
@@ -0,0 +1,901 @@
1
+ #!/usr/bin/env python3
2
+ # -*- coding: utf-8 -*-
3
+ # Timestamp: "2025-12-10 (ywatanabe)"
4
+ # File: /home/ywatanabe/proj/scitex-code/src/scitex/stats/auto/_rules.py
5
+
6
+ """
7
+ Test Rules - Applicability rules for statistical tests.
8
+
9
+ This module defines TestRule dataclass and the TEST_RULES registry that
10
+ maps test names to their applicability conditions. Used by check_applicable()
11
+ to determine which tests can be applied to a given StatContext.
12
+
13
+ The priority field is used for test recommendation - higher priority tests
14
+ are recommended first when multiple tests are applicable.
15
+ """
16
+
17
+ from __future__ import annotations
18
+
19
+ from dataclasses import dataclass, field
20
+ from typing import Dict, Literal, Optional, Set
21
+
22
+ # =============================================================================
23
+ # Type Aliases
24
+ # =============================================================================
25
+
26
+ TestFamily = Literal[
27
+ "parametric",
28
+ "nonparametric",
29
+ "categorical",
30
+ "correlation",
31
+ "normality",
32
+ "effect_size",
33
+ "posthoc",
34
+ "other",
35
+ ]
36
+
37
+
38
+ # =============================================================================
39
+ # TestRule
40
+ # =============================================================================
41
+
42
+
43
+ @dataclass
44
+ class TestRule:
45
+ """
46
+ Applicability rule for a specific statistical test.
47
+
48
+ Each TestRule defines the conditions under which a test is applicable.
49
+ The check_applicable() function uses these rules to filter tests
50
+ for a given StatContext.
51
+
52
+ Parameters
53
+ ----------
54
+ name : str
55
+ Internal name of the test (e.g., "ttest_ind", "brunner_munzel").
56
+ family : TestFamily
57
+ High-level family of the test:
58
+ - "parametric": t-test, ANOVA, etc.
59
+ - "nonparametric": Mann-Whitney, Kruskal-Wallis, etc.
60
+ - "categorical": Chi-square, Fisher's exact, etc.
61
+ - "correlation": Pearson, Spearman, etc.
62
+ - "normality": Shapiro-Wilk, etc.
63
+ - "effect_size": Cohen's d, eta-squared, etc.
64
+ - "posthoc": Tukey, Dunnett, etc.
65
+ - "other": Other tests (Levene, etc.)
66
+ min_groups : int
67
+ Minimum required number of groups.
68
+ max_groups : int or None
69
+ Maximum allowed number of groups. None means no upper bound.
70
+ outcome_types : set of str
71
+ Allowed outcome types for this test.
72
+ supports_paired : bool
73
+ Whether the test supports paired/repeated measures.
74
+ supports_unpaired : bool
75
+ Whether the test supports independent groups.
76
+ design_allowed : set of str
77
+ Allowed designs, e.g., {"between", "within"}.
78
+ requires_control_group : bool
79
+ Whether a dedicated control group is required (e.g., Dunnett).
80
+ min_n_total : int or None
81
+ Minimum total sample size. None means no constraint.
82
+ min_n_per_group : int or None
83
+ Minimum sample size per group.
84
+ needs_normality : bool
85
+ Whether test assumes normality (check normality_ok).
86
+ needs_equal_variance : bool
87
+ Whether test assumes equal variances (check variance_homogeneity_ok).
88
+ min_factors : int or None
89
+ Minimum number of factors.
90
+ max_factors : int or None
91
+ Maximum number of factors.
92
+ priority : int
93
+ Priority score for recommendation. Higher = more recommended.
94
+ Brunner-Munzel has priority 110 as the recommended default for 2 groups.
95
+ description : str
96
+ Human-readable description for tooltips.
97
+
98
+ Examples
99
+ --------
100
+ >>> rule = TestRule(
101
+ ... name="ttest_ind",
102
+ ... family="parametric",
103
+ ... min_groups=2,
104
+ ... max_groups=2,
105
+ ... outcome_types={"continuous"},
106
+ ... supports_paired=False,
107
+ ... supports_unpaired=True,
108
+ ... design_allowed={"between"},
109
+ ... requires_control_group=False,
110
+ ... min_n_total=4,
111
+ ... min_n_per_group=2,
112
+ ... needs_normality=True,
113
+ ... needs_equal_variance=False,
114
+ ... min_factors=1,
115
+ ... max_factors=1,
116
+ ... priority=90,
117
+ ... description="Independent samples t-test (Welch)"
118
+ ... )
119
+ """
120
+
121
+ name: str
122
+ family: TestFamily
123
+ min_groups: int
124
+ max_groups: Optional[int]
125
+ outcome_types: Set[str]
126
+ supports_paired: bool
127
+ supports_unpaired: bool
128
+ design_allowed: Set[str]
129
+ requires_control_group: bool
130
+ min_n_total: Optional[int]
131
+ min_n_per_group: Optional[int]
132
+ needs_normality: bool
133
+ needs_equal_variance: bool
134
+ min_factors: Optional[int]
135
+ max_factors: Optional[int]
136
+ priority: int = 0
137
+ description: str = ""
138
+
139
+
140
+ # =============================================================================
141
+ # TEST_RULES Registry
142
+ # =============================================================================
143
+
144
+ TEST_RULES: Dict[str, TestRule] = {
145
+ # =========================================================================
146
+ # Parametric Tests - Mean Comparisons
147
+ # =========================================================================
148
+
149
+ # Independent 2-sample t-test (Welch)
150
+ "ttest_ind": TestRule(
151
+ name="ttest_ind",
152
+ family="parametric",
153
+ min_groups=2,
154
+ max_groups=2,
155
+ outcome_types={"continuous"},
156
+ supports_paired=False,
157
+ supports_unpaired=True,
158
+ design_allowed={"between"},
159
+ requires_control_group=False,
160
+ min_n_total=4,
161
+ min_n_per_group=2,
162
+ needs_normality=True,
163
+ needs_equal_variance=False, # Welch doesn't require equal variance
164
+ min_factors=1,
165
+ max_factors=1,
166
+ priority=90,
167
+ description="Independent samples t-test (Welch)",
168
+ ),
169
+
170
+ # Paired t-test
171
+ "ttest_rel": TestRule(
172
+ name="ttest_rel",
173
+ family="parametric",
174
+ min_groups=2,
175
+ max_groups=2,
176
+ outcome_types={"continuous"},
177
+ supports_paired=True,
178
+ supports_unpaired=False,
179
+ design_allowed={"within"},
180
+ requires_control_group=False,
181
+ min_n_total=4,
182
+ min_n_per_group=2,
183
+ needs_normality=True,
184
+ needs_equal_variance=False,
185
+ min_factors=1,
186
+ max_factors=1,
187
+ priority=95,
188
+ description="Paired samples t-test",
189
+ ),
190
+
191
+ # One-way ANOVA (between)
192
+ "anova_oneway": TestRule(
193
+ name="anova_oneway",
194
+ family="parametric",
195
+ min_groups=3,
196
+ max_groups=None,
197
+ outcome_types={"continuous"},
198
+ supports_paired=False,
199
+ supports_unpaired=True,
200
+ design_allowed={"between"},
201
+ requires_control_group=False,
202
+ min_n_total=6,
203
+ min_n_per_group=2,
204
+ needs_normality=True,
205
+ needs_equal_variance=True,
206
+ min_factors=1,
207
+ max_factors=1,
208
+ priority=80,
209
+ description="One-way ANOVA (between subjects)",
210
+ ),
211
+
212
+ # Repeated-measures one-way ANOVA
213
+ "anova_rm_oneway": TestRule(
214
+ name="anova_rm_oneway",
215
+ family="parametric",
216
+ min_groups=3,
217
+ max_groups=None,
218
+ outcome_types={"continuous"},
219
+ supports_paired=True,
220
+ supports_unpaired=False,
221
+ design_allowed={"within"},
222
+ requires_control_group=False,
223
+ min_n_total=6,
224
+ min_n_per_group=2,
225
+ needs_normality=True,
226
+ needs_equal_variance=True,
227
+ min_factors=1,
228
+ max_factors=1,
229
+ priority=85,
230
+ description="Repeated-measures one-way ANOVA",
231
+ ),
232
+
233
+ # Welch ANOVA (unequal variances)
234
+ "welch_anova": TestRule(
235
+ name="welch_anova",
236
+ family="parametric",
237
+ min_groups=3,
238
+ max_groups=None,
239
+ outcome_types={"continuous"},
240
+ supports_paired=False,
241
+ supports_unpaired=True,
242
+ design_allowed={"between"},
243
+ requires_control_group=False,
244
+ min_n_total=6,
245
+ min_n_per_group=2,
246
+ needs_normality=True,
247
+ needs_equal_variance=False, # Welch doesn't require equal variance
248
+ min_factors=1,
249
+ max_factors=1,
250
+ priority=82,
251
+ description="Welch's ANOVA (heterogeneous variances)",
252
+ ),
253
+
254
+ # Two-way ANOVA (between)
255
+ "anova_twoway": TestRule(
256
+ name="anova_twoway",
257
+ family="parametric",
258
+ min_groups=2,
259
+ max_groups=None,
260
+ outcome_types={"continuous"},
261
+ supports_paired=False,
262
+ supports_unpaired=True,
263
+ design_allowed={"between"},
264
+ requires_control_group=False,
265
+ min_n_total=8,
266
+ min_n_per_group=2,
267
+ needs_normality=True,
268
+ needs_equal_variance=True,
269
+ min_factors=2,
270
+ max_factors=2,
271
+ priority=78,
272
+ description="Two-way ANOVA (between subjects)",
273
+ ),
274
+
275
+ # Two-way ANOVA (mixed)
276
+ "anova_twoway_mixed": TestRule(
277
+ name="anova_twoway_mixed",
278
+ family="parametric",
279
+ min_groups=2,
280
+ max_groups=None,
281
+ outcome_types={"continuous"},
282
+ supports_paired=True,
283
+ supports_unpaired=True,
284
+ design_allowed={"mixed", "within"},
285
+ requires_control_group=False,
286
+ min_n_total=8,
287
+ min_n_per_group=2,
288
+ needs_normality=True,
289
+ needs_equal_variance=True,
290
+ min_factors=2,
291
+ max_factors=2,
292
+ priority=80,
293
+ description="Two-way mixed-design ANOVA",
294
+ ),
295
+
296
+ # =========================================================================
297
+ # Nonparametric Tests - Rank Comparisons
298
+ # =========================================================================
299
+
300
+ # Brunner-Munzel test (RECOMMENDED DEFAULT for 2 groups)
301
+ "brunner_munzel": TestRule(
302
+ name="brunner_munzel",
303
+ family="nonparametric",
304
+ min_groups=2,
305
+ max_groups=2,
306
+ outcome_types={"continuous", "ordinal"},
307
+ supports_paired=False,
308
+ supports_unpaired=True,
309
+ design_allowed={"between"},
310
+ requires_control_group=False,
311
+ min_n_total=6,
312
+ min_n_per_group=3,
313
+ needs_normality=False,
314
+ needs_equal_variance=False, # Most robust - no assumptions
315
+ min_factors=1,
316
+ max_factors=1,
317
+ priority=110, # HIGHEST PRIORITY - recommended default
318
+ description="Brunner-Munzel test (most robust, recommended)",
319
+ ),
320
+
321
+ # Mann-Whitney U test
322
+ "mannwhitneyu": TestRule(
323
+ name="mannwhitneyu",
324
+ family="nonparametric",
325
+ min_groups=2,
326
+ max_groups=2,
327
+ outcome_types={"continuous", "ordinal"},
328
+ supports_paired=False,
329
+ supports_unpaired=True,
330
+ design_allowed={"between"},
331
+ requires_control_group=False,
332
+ min_n_total=4,
333
+ min_n_per_group=2,
334
+ needs_normality=False,
335
+ needs_equal_variance=False,
336
+ min_factors=1,
337
+ max_factors=1,
338
+ priority=85,
339
+ description="Mann-Whitney U test (rank-sum)",
340
+ ),
341
+
342
+ # Wilcoxon signed-rank test (paired)
343
+ "wilcoxon": TestRule(
344
+ name="wilcoxon",
345
+ family="nonparametric",
346
+ min_groups=2,
347
+ max_groups=2,
348
+ outcome_types={"continuous", "ordinal"},
349
+ supports_paired=True,
350
+ supports_unpaired=False,
351
+ design_allowed={"within"},
352
+ requires_control_group=False,
353
+ min_n_total=4,
354
+ min_n_per_group=2,
355
+ needs_normality=False,
356
+ needs_equal_variance=False,
357
+ min_factors=1,
358
+ max_factors=1,
359
+ priority=90,
360
+ description="Wilcoxon signed-rank test (paired)",
361
+ ),
362
+
363
+ # Kruskal-Wallis (3+ groups, between)
364
+ "kruskal": TestRule(
365
+ name="kruskal",
366
+ family="nonparametric",
367
+ min_groups=3,
368
+ max_groups=None,
369
+ outcome_types={"continuous", "ordinal"},
370
+ supports_paired=False,
371
+ supports_unpaired=True,
372
+ design_allowed={"between"},
373
+ requires_control_group=False,
374
+ min_n_total=6,
375
+ min_n_per_group=2,
376
+ needs_normality=False,
377
+ needs_equal_variance=False,
378
+ min_factors=1,
379
+ max_factors=1,
380
+ priority=75,
381
+ description="Kruskal-Wallis H test",
382
+ ),
383
+
384
+ # Friedman test (3+ groups, within)
385
+ "friedman": TestRule(
386
+ name="friedman",
387
+ family="nonparametric",
388
+ min_groups=3,
389
+ max_groups=None,
390
+ outcome_types={"continuous", "ordinal"},
391
+ supports_paired=True,
392
+ supports_unpaired=False,
393
+ design_allowed={"within"},
394
+ requires_control_group=False,
395
+ min_n_total=6,
396
+ min_n_per_group=2,
397
+ needs_normality=False,
398
+ needs_equal_variance=False,
399
+ min_factors=1,
400
+ max_factors=1,
401
+ priority=80,
402
+ description="Friedman test (repeated measures)",
403
+ ),
404
+
405
+ # =========================================================================
406
+ # Categorical Tests
407
+ # =========================================================================
408
+
409
+ # Chi-square test of independence
410
+ "chi2_independence": TestRule(
411
+ name="chi2_independence",
412
+ family="categorical",
413
+ min_groups=2,
414
+ max_groups=None,
415
+ outcome_types={"binary", "categorical"},
416
+ supports_paired=False,
417
+ supports_unpaired=True,
418
+ design_allowed={"between"},
419
+ requires_control_group=False,
420
+ min_n_total=10,
421
+ min_n_per_group=None, # Uses expected counts
422
+ needs_normality=False,
423
+ needs_equal_variance=False,
424
+ min_factors=1,
425
+ max_factors=None,
426
+ priority=80,
427
+ description="Chi-square test of independence",
428
+ ),
429
+
430
+ # Fisher's exact test (2x2)
431
+ "fisher_exact": TestRule(
432
+ name="fisher_exact",
433
+ family="categorical",
434
+ min_groups=2,
435
+ max_groups=2,
436
+ outcome_types={"binary"},
437
+ supports_paired=False,
438
+ supports_unpaired=True,
439
+ design_allowed={"between"},
440
+ requires_control_group=False,
441
+ min_n_total=1,
442
+ min_n_per_group=1,
443
+ needs_normality=False,
444
+ needs_equal_variance=False,
445
+ min_factors=1,
446
+ max_factors=1,
447
+ priority=90,
448
+ description="Fisher's exact test (2x2)",
449
+ ),
450
+
451
+ # McNemar's test (paired binary)
452
+ "mcnemar": TestRule(
453
+ name="mcnemar",
454
+ family="categorical",
455
+ min_groups=2,
456
+ max_groups=2,
457
+ outcome_types={"binary"},
458
+ supports_paired=True,
459
+ supports_unpaired=False,
460
+ design_allowed={"within"},
461
+ requires_control_group=False,
462
+ min_n_total=4,
463
+ min_n_per_group=2,
464
+ needs_normality=False,
465
+ needs_equal_variance=False,
466
+ min_factors=1,
467
+ max_factors=1,
468
+ priority=85,
469
+ description="McNemar's test (paired binary)",
470
+ ),
471
+
472
+ # =========================================================================
473
+ # Correlation Tests
474
+ # =========================================================================
475
+
476
+ # Pearson correlation
477
+ "pearsonr": TestRule(
478
+ name="pearsonr",
479
+ family="correlation",
480
+ min_groups=1,
481
+ max_groups=1,
482
+ outcome_types={"continuous"},
483
+ supports_paired=True,
484
+ supports_unpaired=True,
485
+ design_allowed={"between", "within", "mixed"},
486
+ requires_control_group=False,
487
+ min_n_total=3,
488
+ min_n_per_group=None,
489
+ needs_normality=True,
490
+ needs_equal_variance=False,
491
+ min_factors=None,
492
+ max_factors=None,
493
+ priority=80,
494
+ description="Pearson correlation coefficient",
495
+ ),
496
+
497
+ # Spearman correlation
498
+ "spearmanr": TestRule(
499
+ name="spearmanr",
500
+ family="correlation",
501
+ min_groups=1,
502
+ max_groups=1,
503
+ outcome_types={"continuous", "ordinal"},
504
+ supports_paired=True,
505
+ supports_unpaired=True,
506
+ design_allowed={"between", "within", "mixed"},
507
+ requires_control_group=False,
508
+ min_n_total=3,
509
+ min_n_per_group=None,
510
+ needs_normality=False,
511
+ needs_equal_variance=False,
512
+ min_factors=None,
513
+ max_factors=None,
514
+ priority=85,
515
+ description="Spearman rank correlation",
516
+ ),
517
+
518
+ # =========================================================================
519
+ # Normality Tests
520
+ # =========================================================================
521
+
522
+ # Shapiro-Wilk test
523
+ "shapiro": TestRule(
524
+ name="shapiro",
525
+ family="normality",
526
+ min_groups=1,
527
+ max_groups=None,
528
+ outcome_types={"continuous"},
529
+ supports_paired=True,
530
+ supports_unpaired=True,
531
+ design_allowed={"between", "within", "mixed"},
532
+ requires_control_group=False,
533
+ min_n_total=3,
534
+ min_n_per_group=None,
535
+ needs_normality=False,
536
+ needs_equal_variance=False,
537
+ min_factors=None,
538
+ max_factors=None,
539
+ priority=60,
540
+ description="Shapiro-Wilk normality test",
541
+ ),
542
+
543
+ # Levene's test for homogeneity of variance
544
+ "levene": TestRule(
545
+ name="levene",
546
+ family="other",
547
+ min_groups=2,
548
+ max_groups=None,
549
+ outcome_types={"continuous"},
550
+ supports_paired=False,
551
+ supports_unpaired=True,
552
+ design_allowed={"between"},
553
+ requires_control_group=False,
554
+ min_n_total=4,
555
+ min_n_per_group=2,
556
+ needs_normality=False,
557
+ needs_equal_variance=False,
558
+ min_factors=1,
559
+ max_factors=None,
560
+ priority=70,
561
+ description="Levene's test for homogeneity of variance",
562
+ ),
563
+
564
+ # =========================================================================
565
+ # Post-hoc Tests
566
+ # =========================================================================
567
+
568
+ # Tukey HSD
569
+ "tukey_hsd": TestRule(
570
+ name="tukey_hsd",
571
+ family="posthoc",
572
+ min_groups=3,
573
+ max_groups=None,
574
+ outcome_types={"continuous"},
575
+ supports_paired=False,
576
+ supports_unpaired=True,
577
+ design_allowed={"between"},
578
+ requires_control_group=False,
579
+ min_n_total=6,
580
+ min_n_per_group=2,
581
+ needs_normality=True,
582
+ needs_equal_variance=True,
583
+ min_factors=1,
584
+ max_factors=1,
585
+ priority=88,
586
+ description="Tukey HSD post-hoc test",
587
+ ),
588
+
589
+ # Dunnett (control vs treatments)
590
+ "dunnett": TestRule(
591
+ name="dunnett",
592
+ family="posthoc",
593
+ min_groups=3,
594
+ max_groups=None,
595
+ outcome_types={"continuous"},
596
+ supports_paired=False,
597
+ supports_unpaired=True,
598
+ design_allowed={"between"},
599
+ requires_control_group=True, # REQUIRES control group
600
+ min_n_total=6,
601
+ min_n_per_group=2,
602
+ needs_normality=True,
603
+ needs_equal_variance=True,
604
+ min_factors=1,
605
+ max_factors=1,
606
+ priority=86,
607
+ description="Dunnett's test (control vs treatments)",
608
+ ),
609
+
610
+ # Games-Howell (unequal variances)
611
+ "games_howell": TestRule(
612
+ name="games_howell",
613
+ family="posthoc",
614
+ min_groups=3,
615
+ max_groups=None,
616
+ outcome_types={"continuous"},
617
+ supports_paired=False,
618
+ supports_unpaired=True,
619
+ design_allowed={"between"},
620
+ requires_control_group=False,
621
+ min_n_total=6,
622
+ min_n_per_group=2,
623
+ needs_normality=True,
624
+ needs_equal_variance=False, # Does NOT require equal variance
625
+ min_factors=1,
626
+ max_factors=1,
627
+ priority=89,
628
+ description="Games-Howell post-hoc (unequal variances)",
629
+ ),
630
+
631
+ # =========================================================================
632
+ # Effect Size Measures
633
+ # =========================================================================
634
+
635
+ # Cohen's d (independent)
636
+ "cohens_d_ind": TestRule(
637
+ name="cohens_d_ind",
638
+ family="effect_size",
639
+ min_groups=2,
640
+ max_groups=2,
641
+ outcome_types={"continuous"},
642
+ supports_paired=False,
643
+ supports_unpaired=True,
644
+ design_allowed={"between"},
645
+ requires_control_group=False,
646
+ min_n_total=4,
647
+ min_n_per_group=2,
648
+ needs_normality=False,
649
+ needs_equal_variance=False,
650
+ min_factors=1,
651
+ max_factors=1,
652
+ priority=90,
653
+ description="Cohen's d (independent samples)",
654
+ ),
655
+
656
+ # Cohen's d (paired)
657
+ "cohens_d_paired": TestRule(
658
+ name="cohens_d_paired",
659
+ family="effect_size",
660
+ min_groups=2,
661
+ max_groups=2,
662
+ outcome_types={"continuous"},
663
+ supports_paired=True,
664
+ supports_unpaired=False,
665
+ design_allowed={"within"},
666
+ requires_control_group=False,
667
+ min_n_total=4,
668
+ min_n_per_group=2,
669
+ needs_normality=False,
670
+ needs_equal_variance=False,
671
+ min_factors=1,
672
+ max_factors=1,
673
+ priority=92,
674
+ description="Cohen's d (paired samples)",
675
+ ),
676
+
677
+ # Hedges' g
678
+ "hedges_g": TestRule(
679
+ name="hedges_g",
680
+ family="effect_size",
681
+ min_groups=2,
682
+ max_groups=2,
683
+ outcome_types={"continuous"},
684
+ supports_paired=False,
685
+ supports_unpaired=True,
686
+ design_allowed={"between"},
687
+ requires_control_group=False,
688
+ min_n_total=4,
689
+ min_n_per_group=2,
690
+ needs_normality=False,
691
+ needs_equal_variance=False,
692
+ min_factors=1,
693
+ max_factors=1,
694
+ priority=88,
695
+ description="Hedges' g (bias-corrected effect size)",
696
+ ),
697
+
698
+ # Cliff's delta
699
+ "cliffs_delta": TestRule(
700
+ name="cliffs_delta",
701
+ family="effect_size",
702
+ min_groups=2,
703
+ max_groups=2,
704
+ outcome_types={"continuous", "ordinal"},
705
+ supports_paired=False,
706
+ supports_unpaired=True,
707
+ design_allowed={"between"},
708
+ requires_control_group=False,
709
+ min_n_total=4,
710
+ min_n_per_group=2,
711
+ needs_normality=False,
712
+ needs_equal_variance=False,
713
+ min_factors=1,
714
+ max_factors=1,
715
+ priority=86,
716
+ description="Cliff's delta (nonparametric effect size)",
717
+ ),
718
+
719
+ # Eta-squared
720
+ "eta_squared": TestRule(
721
+ name="eta_squared",
722
+ family="effect_size",
723
+ min_groups=2,
724
+ max_groups=None,
725
+ outcome_types={"continuous"},
726
+ supports_paired=True,
727
+ supports_unpaired=True,
728
+ design_allowed={"between", "within"},
729
+ requires_control_group=False,
730
+ min_n_total=4,
731
+ min_n_per_group=2,
732
+ needs_normality=False,
733
+ needs_equal_variance=False,
734
+ min_factors=1,
735
+ max_factors=1,
736
+ priority=80,
737
+ description="Eta-squared (variance explained)",
738
+ ),
739
+
740
+ # Partial eta-squared
741
+ "partial_eta_squared": TestRule(
742
+ name="partial_eta_squared",
743
+ family="effect_size",
744
+ min_groups=2,
745
+ max_groups=None,
746
+ outcome_types={"continuous"},
747
+ supports_paired=True,
748
+ supports_unpaired=True,
749
+ design_allowed={"between", "within", "mixed"},
750
+ requires_control_group=False,
751
+ min_n_total=4,
752
+ min_n_per_group=2,
753
+ needs_normality=False,
754
+ needs_equal_variance=False,
755
+ min_factors=1,
756
+ max_factors=None,
757
+ priority=85,
758
+ description="Partial eta-squared (multi-factor designs)",
759
+ ),
760
+
761
+ # Effect size r (for correlations)
762
+ "effect_size_r": TestRule(
763
+ name="effect_size_r",
764
+ family="effect_size",
765
+ min_groups=1,
766
+ max_groups=1,
767
+ outcome_types={"continuous", "ordinal"},
768
+ supports_paired=True,
769
+ supports_unpaired=True,
770
+ design_allowed={"between", "within", "mixed"},
771
+ requires_control_group=False,
772
+ min_n_total=3,
773
+ min_n_per_group=None,
774
+ needs_normality=False,
775
+ needs_equal_variance=False,
776
+ min_factors=None,
777
+ max_factors=None,
778
+ priority=80,
779
+ description="Effect size r (correlation)",
780
+ ),
781
+
782
+ # Odds ratio
783
+ "odds_ratio": TestRule(
784
+ name="odds_ratio",
785
+ family="effect_size",
786
+ min_groups=2,
787
+ max_groups=2,
788
+ outcome_types={"binary"},
789
+ supports_paired=False,
790
+ supports_unpaired=True,
791
+ design_allowed={"between"},
792
+ requires_control_group=False,
793
+ min_n_total=1,
794
+ min_n_per_group=1,
795
+ needs_normality=False,
796
+ needs_equal_variance=False,
797
+ min_factors=1,
798
+ max_factors=1,
799
+ priority=88,
800
+ description="Odds ratio (2x2 table)",
801
+ ),
802
+
803
+ # Risk ratio
804
+ "risk_ratio": TestRule(
805
+ name="risk_ratio",
806
+ family="effect_size",
807
+ min_groups=2,
808
+ max_groups=2,
809
+ outcome_types={"binary"},
810
+ supports_paired=False,
811
+ supports_unpaired=True,
812
+ design_allowed={"between"},
813
+ requires_control_group=False,
814
+ min_n_total=1,
815
+ min_n_per_group=1,
816
+ needs_normality=False,
817
+ needs_equal_variance=False,
818
+ min_factors=1,
819
+ max_factors=1,
820
+ priority=86,
821
+ description="Risk ratio (relative risk)",
822
+ ),
823
+
824
+ # Probability of superiority P(X>Y)
825
+ "prob_superiority": TestRule(
826
+ name="prob_superiority",
827
+ family="effect_size",
828
+ min_groups=2,
829
+ max_groups=2,
830
+ outcome_types={"continuous", "ordinal"},
831
+ supports_paired=False,
832
+ supports_unpaired=True,
833
+ design_allowed={"between"},
834
+ requires_control_group=False,
835
+ min_n_total=4,
836
+ min_n_per_group=2,
837
+ needs_normality=False,
838
+ needs_equal_variance=False,
839
+ min_factors=1,
840
+ max_factors=1,
841
+ priority=84,
842
+ description="Probability of superiority P(X>Y)",
843
+ ),
844
+ }
845
+
846
+
847
+ # =============================================================================
848
+ # Utility Functions
849
+ # =============================================================================
850
+
851
+
852
+ def get_test_rule(name: str) -> Optional[TestRule]:
853
+ """
854
+ Get a TestRule by name.
855
+
856
+ Parameters
857
+ ----------
858
+ name : str
859
+ Test name (e.g., "ttest_ind", "brunner_munzel").
860
+
861
+ Returns
862
+ -------
863
+ TestRule or None
864
+ The TestRule if found, else None.
865
+ """
866
+ return TEST_RULES.get(name)
867
+
868
+
869
+ def list_tests_by_family(family: TestFamily) -> Dict[str, TestRule]:
870
+ """
871
+ Get all tests in a specific family.
872
+
873
+ Parameters
874
+ ----------
875
+ family : TestFamily
876
+ Test family to filter by.
877
+
878
+ Returns
879
+ -------
880
+ dict
881
+ Dictionary of test name -> TestRule for the family.
882
+ """
883
+ return {
884
+ name: rule for name, rule in TEST_RULES.items()
885
+ if rule.family == family
886
+ }
887
+
888
+
889
+ # =============================================================================
890
+ # Public API
891
+ # =============================================================================
892
+
893
+ __all__ = [
894
+ "TestRule",
895
+ "TestFamily",
896
+ "TEST_RULES",
897
+ "get_test_rule",
898
+ "list_tests_by_family",
899
+ ]
900
+
901
+ # EOF