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
@@ -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
  # ----------------------------------------
@@ -215,11 +216,11 @@ def correct_sidak(
215
216
  logger.info("\nDetailed results:")
216
217
  for r in corrected_results:
217
218
  comparison = ""
218
- if 'var_x' in r and 'var_y' in r:
219
+ if "var_x" in r and "var_y" in r:
219
220
  comparison = f"{r['var_x']} vs {r['var_y']}: "
220
- elif 'test_method' in r:
221
+ elif "test_method" in r:
221
222
  comparison = f"{r['test_method']}: "
222
- elif 'comparison' in r:
223
+ elif "comparison" in r:
223
224
  comparison = f"{r['comparison']}: "
224
225
 
225
226
  logger.info(
@@ -236,6 +237,7 @@ def correct_sidak(
236
237
  if plot:
237
238
  if ax is None:
238
239
  import matplotlib.pyplot as plt
240
+
239
241
  fig, ax = plt.subplots(figsize=(10, 6))
240
242
  _plot_sidak(corrected_results, alpha, alpha_adj, m, ax)
241
243
 
@@ -257,23 +259,40 @@ def _plot_sidak(corrected_results, alpha, alpha_adj, m, ax):
257
259
 
258
260
  # Plot original and adjusted p-values
259
261
  ax.scatter(x, pvalues, label="Original p-values", alpha=0.7, s=100, color="C0")
260
- ax.scatter(x, pvalues_adj, label="Adjusted p-values", alpha=0.7, s=100, color="C1", marker="s")
262
+ ax.scatter(
263
+ x,
264
+ pvalues_adj,
265
+ label="Adjusted p-values",
266
+ alpha=0.7,
267
+ s=100,
268
+ color="C1",
269
+ marker="s",
270
+ )
261
271
 
262
272
  # Connect original to adjusted with lines
263
273
  for i in range(m):
264
274
  ax.plot([i, i], [pvalues[i], pvalues_adj[i]], "k-", alpha=0.3, linewidth=0.5)
265
275
 
266
276
  # Add significance thresholds
267
- ax.axhline(alpha, color="red", linestyle="--", linewidth=2, alpha=0.5, label=f"α = {alpha}")
268
- ax.axhline(alpha_adj, color="orange", linestyle="--", linewidth=2, alpha=0.5,
269
- label=f"α_adj = {alpha_adj:.4f}")
277
+ ax.axhline(
278
+ alpha, color="red", linestyle="--", linewidth=2, alpha=0.5, label=f"α = {alpha}"
279
+ )
280
+ ax.axhline(
281
+ alpha_adj,
282
+ color="orange",
283
+ linestyle="--",
284
+ linewidth=2,
285
+ alpha=0.5,
286
+ label=f"α_adj = {alpha_adj:.4f}",
287
+ )
270
288
 
271
289
  # Formatting
272
290
  ax.set_xlabel("Test Index")
273
291
  ax.set_ylabel("P-value")
274
292
  rejections = sum(r["rejected"] for r in corrected_results)
275
- ax.set_title(f"Šidák Correction (m={m} tests)\n"
276
- f"{rejections}/{m} hypotheses rejected")
293
+ ax.set_title(
294
+ f"Šidák Correction (m={m} tests)\n{rejections}/{m} hypotheses rejected"
295
+ )
277
296
  ax.set_yscale("log")
278
297
  ax.grid(True, alpha=0.3)
279
298
  ax.legend()
@@ -289,7 +308,7 @@ def _plot_sidak(corrected_results, alpha, alpha_adj, m, ax):
289
308
  elif "comparison" in r:
290
309
  labels.append(r["comparison"])
291
310
  else:
292
- labels.append(f"Test {len(labels)+1}")
311
+ labels.append(f"Test {len(labels) + 1}")
293
312
  ax.set_xticks(x)
294
313
  ax.set_xticklabels(labels, rotation=45, ha="right", fontsize=8)
295
314
  else:
@@ -309,7 +328,9 @@ def main():
309
328
 
310
329
  # Parse empty args for session
311
330
  parser = argparse.ArgumentParser()
312
- parser.add_argument('--verbose', action='store_true', default=True, help='Enable verbose output')
331
+ parser.add_argument(
332
+ "--verbose", action="store_true", default=True, help="Enable verbose output"
333
+ )
313
334
  args = parser.parse_args([])
314
335
 
315
336
  CONFIG, sys.stdout, sys.stderr, plt, CC, rng_manager = stx.session.start(
@@ -326,9 +347,7 @@ def main():
326
347
  logger.info("=" * 70)
327
348
 
328
349
  # Example 1: Basic usage with 5 independent tests
329
- logger.info(
330
- "\n[Example 1] Basic Šidák correction with 5 independent t-tests"
331
- )
350
+ logger.info("\n[Example 1] Basic Šidák correction with 5 independent t-tests")
332
351
  logger.info("-" * 70)
333
352
 
334
353
  np.random.seed(42)
@@ -410,9 +429,7 @@ def main():
410
429
  logger.info(f"Output type: {type(df_corrected)}")
411
430
  logger.info(f"\nCorrected DataFrame (first 3 rows):")
412
431
  logger.info(
413
- df_corrected[
414
- ["var_x", "var_y", "pvalue", "pvalue_adjusted", "rejected"]
415
- ]
432
+ df_corrected[["var_x", "var_y", "pvalue", "pvalue_adjusted", "rejected"]]
416
433
  .head(3)
417
434
  .to_string()
418
435
  )
@@ -437,7 +454,7 @@ def main():
437
454
 
438
455
  for i, (orig, corr) in enumerate(zip(edge_results, edge_corrected)):
439
456
  logger.info(
440
- f"Test {i+1}: p = {orig['pvalue']:.4f} -> "
457
+ f"Test {i + 1}: p = {orig['pvalue']:.4f} -> "
441
458
  f"p_adj = {corr['pvalue_adjusted']:.4f}"
442
459
  )
443
460
 
@@ -478,9 +495,7 @@ def main():
478
495
  bonf_alpha = alpha / m
479
496
  sidak_alpha = 1.0 - (1.0 - alpha) ** (1.0 / m)
480
497
  ratio = sidak_alpha / bonf_alpha
481
- logger.info(
482
- f"{m:<5} {bonf_alpha:.6f} {sidak_alpha:.6f} {ratio:.4f}"
483
- )
498
+ logger.info(f"{m:<5} {bonf_alpha:.6f} {sidak_alpha:.6f} {ratio:.4f}")
484
499
 
485
500
  logger.info("\nNote: Šidák is always ≥ Bonferroni (more powerful)")
486
501
  logger.info("Difference increases with larger m")
@@ -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
  # ----------------------------------------
@@ -50,6 +51,8 @@ from scitex.decorators import batch_fn, torch_fn
50
51
  logger = logging.getLogger(__name__)
51
52
 
52
53
  """Functions & Classes"""
54
+
55
+
53
56
  # @batch_fn
54
57
  @torch_fn
55
58
  def describe_circular(
@@ -110,17 +113,15 @@ def describe_circular(
110
113
  else:
111
114
  _funcs = [func_candidates[ff] for ff in func_names]
112
115
 
113
- calculated = [
114
- ff(angles, values, dim=dim, keepdims=keepdims) for ff in _funcs
115
- ]
116
+ calculated = [ff(angles, values, dim=dim, keepdims=keepdims) for ff in _funcs]
116
117
 
117
118
  return torch.stack(calculated, dim=-1), func_names
118
119
 
119
120
 
120
121
  def _ensure_more_than_2d(data: torch.Tensor) -> None:
121
- assert (
122
- data.ndim >= 2
123
- ), f"Input tensor must be more than 2 dimensional with batch dimension as first axis, got {data.ndim}"
122
+ assert data.ndim >= 2, (
123
+ f"Input tensor must be more than 2 dimensional with batch dimension as first axis, got {data.ndim}"
124
+ )
124
125
 
125
126
 
126
127
  def _check_angle_units(angles: torch.Tensor) -> None:
@@ -174,9 +175,9 @@ def circular_mean(
174
175
 
175
176
  _ensure_more_than_2d(angles)
176
177
  _check_angle_units(angles)
177
- assert (
178
- angles.shape == values.shape
179
- ), f"angles shape {angles.shape} must match values shape {values.shape}"
178
+ assert angles.shape == values.shape, (
179
+ f"angles shape {angles.shape} must match values shape {values.shape}"
180
+ )
180
181
 
181
182
  dim = axis if dim is None else dim
182
183
  cos_angles = torch.cos(angles)
@@ -189,9 +190,7 @@ def circular_mean(
189
190
  sin_component = sin_component / value_sum
190
191
 
191
192
  mean_angle = torch.atan2(sin_component, cos_component)
192
- mean_angle = torch.where(
193
- mean_angle < 0, mean_angle + 2 * np.pi, mean_angle
194
- )
193
+ mean_angle = torch.where(mean_angle < 0, mean_angle + 2 * np.pi, mean_angle)
195
194
 
196
195
  return mean_angle if keepdims else mean_angle.squeeze(dim)
197
196
 
@@ -230,9 +229,9 @@ def circular_concentration(
230
229
  """
231
230
  _ensure_more_than_2d(angles)
232
231
  _check_angle_units(angles)
233
- assert (
234
- angles.shape == values.shape
235
- ), f"angles shape {angles.shape} must match values shape {values.shape}"
232
+ assert angles.shape == values.shape, (
233
+ f"angles shape {angles.shape} must match values shape {values.shape}"
234
+ )
236
235
 
237
236
  dim = axis if dim is None else dim
238
237
  cos_angles = torch.cos(angles)
@@ -280,9 +279,9 @@ def circular_skewness(
280
279
  """
281
280
  _ensure_more_than_2d(angles)
282
281
  _check_angle_units(angles)
283
- assert (
284
- angles.shape == values.shape
285
- ), f"angles shape {angles.shape} must match values shape {values.shape}"
282
+ assert angles.shape == values.shape, (
283
+ f"angles shape {angles.shape} must match values shape {values.shape}"
284
+ )
286
285
 
287
286
  dim = axis if dim is None else dim
288
287
  cos_angles = torch.cos(angles)
@@ -334,9 +333,9 @@ def circular_kurtosis(
334
333
  """
335
334
  _ensure_more_than_2d(angles)
336
335
  _check_angle_units(angles)
337
- assert (
338
- angles.shape == values.shape
339
- ), f"angles shape {angles.shape} must match values shape {values.shape}"
336
+ assert angles.shape == values.shape, (
337
+ f"angles shape {angles.shape} must match values shape {values.shape}"
338
+ )
340
339
 
341
340
  dim = axis if dim is None else dim
342
341
  cos_angles = torch.cos(angles)
@@ -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
  # ----------------------------------------
@@ -40,13 +41,26 @@ import torch
40
41
  from scitex import logging
41
42
 
42
43
  from scitex.decorators import batch_fn, torch_fn
43
- from ._nan import (nancount, nankurtosis, nanmax, nanmean, nanmin, nanq25,
44
- nanq50, nanq75, nanskewness, nanstd, nanvar)
44
+ from ._nan import (
45
+ nancount,
46
+ nankurtosis,
47
+ nanmax,
48
+ nanmean,
49
+ nanmin,
50
+ nanq25,
51
+ nanq50,
52
+ nanq75,
53
+ nanskewness,
54
+ nanstd,
55
+ nanvar,
56
+ )
45
57
  from ._real import kurtosis, mean, q25, q50, q75, skewness, std
46
58
 
47
59
  logger = logging.getLogger(__name__)
48
60
 
49
61
  """Functions & Classes"""
62
+
63
+
50
64
  def verify_non_leakage(
51
65
  x: torch.Tensor,
52
66
  dim: Optional[Union[int, Tuple[int, ...]]] = None,
@@ -56,9 +70,9 @@ def verify_non_leakage(
56
70
  x_first = x[:1]
57
71
  described_first, _ = describe(x_first, dim=dim)
58
72
 
59
- assert (
60
- described_first.shape == described[:1].shape
61
- ), f"Shape mismatch: {described_first.shape} != {described[:1].shape}"
73
+ assert described_first.shape == described[:1].shape, (
74
+ f"Shape mismatch: {described_first.shape} != {described[:1].shape}"
75
+ )
62
76
 
63
77
  torch.testing.assert_close(
64
78
  described_first,
@@ -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
  # ----------------------------------------
@@ -43,6 +44,8 @@ from scitex.decorators import batch_fn, torch_fn
43
44
  logger = logging.getLogger(__name__)
44
45
 
45
46
  """Functions & Classes"""
47
+
48
+
46
49
  @torch_fn
47
50
  @batch_fn
48
51
  def nanmax(x, axis=-1, dim=None, batch_size=None, keepdims=False):
@@ -155,10 +158,7 @@ def nanzscore(x, axis=-1, dim=None, batch_size=None, keepdims=True):
155
158
  @batch_fn
156
159
  def nankurtosis(x, axis=-1, dim=None, batch_size=None, keepdims=False):
157
160
  zscores = nanzscore(x, axis=axis, keepdims=True)
158
- return (
159
- torch.nanmean(torch.pow(zscores, 4.0), dim=dim, keepdims=keepdims)
160
- - 3.0
161
- )
161
+ return torch.nanmean(torch.pow(zscores, 4.0), dim=dim, keepdims=keepdims) - 3.0
162
162
 
163
163
 
164
164
  @torch_fn
@@ -239,9 +239,7 @@ def nanquantile(x, q, axis=-1, dim=None, batch_size=None, keepdims=False):
239
239
  dim_list = [d if d >= 0 else len(original_shape) + d for d in dim_list]
240
240
 
241
241
  # Determine which dimensions to keep
242
- keep_dims = [
243
- i for i in range(len(original_shape)) if i not in dim_list
244
- ]
242
+ keep_dims = [i for i in range(len(original_shape)) if i not in dim_list]
245
243
 
246
244
  # Permute tensor to move dims to reduce to the end
247
245
  perm_dims = keep_dims + dim_list
@@ -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
  # ----------------------------------------
@@ -43,6 +44,8 @@ from scitex.decorators import torch_fn
43
44
  logger = logging.getLogger(__name__)
44
45
 
45
46
  """Functions & Classes"""
47
+
48
+
46
49
  @torch_fn
47
50
  def mean(x, axis=-1, dim=None, keepdims=False):
48
51
  return x.mean(dim, keepdims=keepdims)
@@ -75,9 +78,7 @@ def skewness(x, axis=-1, dim=None, keepdims=False):
75
78
  @torch_fn
76
79
  def kurtosis(x, axis=-1, dim=None, keepdims=False):
77
80
  zscores = zscore(x, axis=axis, keepdims=True)
78
- return (
79
- torch.mean(torch.pow(zscores, 4.0), dim=dim, keepdims=keepdims) - 3.0
80
- )
81
+ return torch.mean(torch.pow(zscores, 4.0), dim=dim, keepdims=keepdims) - 3.0
81
82
 
82
83
 
83
84
  @torch_fn
@@ -26,16 +26,15 @@ from ._epsilon_squared import epsilon_squared, interpret_epsilon_squared
26
26
 
27
27
  __all__ = [
28
28
  # Parametric
29
- 'cohens_d',
30
- 'interpret_cohens_d',
31
- 'eta_squared',
32
- 'interpret_eta_squared',
33
-
29
+ "cohens_d",
30
+ "interpret_cohens_d",
31
+ "eta_squared",
32
+ "interpret_eta_squared",
34
33
  # Non-parametric
35
- 'cliffs_delta',
36
- 'interpret_cliffs_delta',
37
- 'prob_superiority',
38
- 'interpret_prob_superiority',
39
- 'epsilon_squared',
40
- 'interpret_epsilon_squared',
34
+ "cliffs_delta",
35
+ "interpret_cliffs_delta",
36
+ "prob_superiority",
37
+ "interpret_prob_superiority",
38
+ "epsilon_squared",
39
+ "interpret_epsilon_squared",
41
40
  ]
@@ -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
  # ----------------------------------------
@@ -39,8 +40,7 @@ logger = getLogger(__name__)
39
40
 
40
41
 
41
42
  def cliffs_delta(
42
- x: Union[np.ndarray, pd.Series],
43
- y: Union[np.ndarray, pd.Series]
43
+ x: Union[np.ndarray, pd.Series], y: Union[np.ndarray, pd.Series]
44
44
  ) -> float:
45
45
  """
46
46
  Compute Cliff's delta non-parametric effect size.
@@ -168,13 +168,13 @@ def interpret_cliffs_delta(delta: float) -> str:
168
168
  delta_abs = abs(delta)
169
169
 
170
170
  if delta_abs < 0.147:
171
- return 'negligible'
171
+ return "negligible"
172
172
  elif delta_abs < 0.33:
173
- return 'small'
173
+ return "small"
174
174
  elif delta_abs < 0.474:
175
- return 'medium'
175
+ return "medium"
176
176
  else:
177
- return 'large'
177
+ return "large"
178
178
 
179
179
 
180
180
  """Main function"""
@@ -211,11 +211,16 @@ def main(args):
211
211
  delta_outlier = cliffs_delta(x_outlier, y_outlier)
212
212
 
213
213
  from ._cohens_d import cohens_d
214
+
214
215
  d_normal = cohens_d(x_normal, y_normal)
215
216
  d_outlier = cohens_d(x_outlier, y_outlier)
216
217
 
217
- logger.info(f"Without outlier: Cliff's δ = {delta_normal:.3f}, Cohen's d = {d_normal:.3f}")
218
- logger.info(f"With outlier: Cliff's δ = {delta_outlier:.3f}, Cohen's d = {d_outlier:.3f}")
218
+ logger.info(
219
+ f"Without outlier: Cliff's δ = {delta_normal:.3f}, Cohen's d = {d_normal:.3f}"
220
+ )
221
+ logger.info(
222
+ f"With outlier: Cliff's δ = {delta_outlier:.3f}, Cohen's d = {d_outlier:.3f}"
223
+ )
219
224
  logger.info("Cliff's delta is stable, Cohen's d is inflated by outlier")
220
225
 
221
226
  # Example 3: Different effect sizes
@@ -228,9 +233,7 @@ def main(args):
228
233
  delta = cliffs_delta(control, treatment)
229
234
  interpretation = interpret_cliffs_delta(delta)
230
235
 
231
- logger.info(
232
- f"Shift = {shift:.1f}: δ = {delta:.3f} ({interpretation})"
233
- )
236
+ logger.info(f"Shift = {shift:.1f}: δ = {delta:.3f} ({interpretation})")
234
237
 
235
238
  # Visualization
236
239
  logger.info("\n=== Creating visualization ===")
@@ -242,12 +245,12 @@ def main(args):
242
245
  x_demo = np.random.exponential(2, 200)
243
246
  y_demo = np.random.exponential(3, 200)
244
247
 
245
- ax.hist(x_demo, bins=30, alpha=0.5, label='Group X', density=True)
246
- ax.hist(y_demo, bins=30, alpha=0.5, label='Group Y', density=True)
248
+ ax.hist(x_demo, bins=30, alpha=0.5, label="Group X", density=True)
249
+ ax.hist(y_demo, bins=30, alpha=0.5, label="Group Y", density=True)
247
250
 
248
251
  delta_demo = cliffs_delta(x_demo, y_demo)
249
- ax.set_xlabel('Value')
250
- ax.set_ylabel('Density')
252
+ ax.set_xlabel("Value")
253
+ ax.set_ylabel("Density")
251
254
  ax.set_title(f"Distributions (Cliff's δ = {delta_demo:.2f})")
252
255
  ax.legend()
253
256
 
@@ -256,24 +259,28 @@ def main(args):
256
259
  delta_values = np.linspace(-1, 1, 100)
257
260
  interpretations = [interpret_cliffs_delta(d) for d in delta_values]
258
261
 
259
- color_map = {'negligible': 'lightgray', 'small': 'yellow',
260
- 'medium': 'orange', 'large': 'red'}
262
+ color_map = {
263
+ "negligible": "lightgray",
264
+ "small": "yellow",
265
+ "medium": "orange",
266
+ "large": "red",
267
+ }
261
268
  colors = [color_map[i] for i in interpretations]
262
269
 
263
270
  ax.scatter(delta_values, [0] * len(delta_values), c=colors, s=50, alpha=0.7)
264
271
  ax.set_xlabel("Cliff's δ")
265
272
  ax.set_yticks([])
266
- ax.set_title('Effect Size Interpretation')
267
- ax.axvline(0, color='black', linestyle='-', alpha=0.3)
268
- ax.axvline(0.147, color='black', linestyle='--', alpha=0.3)
269
- ax.axvline(0.33, color='black', linestyle='--', alpha=0.3)
270
- ax.axvline(0.474, color='black', linestyle='--', alpha=0.3)
271
- ax.axvline(-0.147, color='black', linestyle='--', alpha=0.3)
272
- ax.axvline(-0.33, color='black', linestyle='--', alpha=0.3)
273
- ax.axvline(-0.474, color='black', linestyle='--', alpha=0.3)
273
+ ax.set_title("Effect Size Interpretation")
274
+ ax.axvline(0, color="black", linestyle="-", alpha=0.3)
275
+ ax.axvline(0.147, color="black", linestyle="--", alpha=0.3)
276
+ ax.axvline(0.33, color="black", linestyle="--", alpha=0.3)
277
+ ax.axvline(0.474, color="black", linestyle="--", alpha=0.3)
278
+ ax.axvline(-0.147, color="black", linestyle="--", alpha=0.3)
279
+ ax.axvline(-0.33, color="black", linestyle="--", alpha=0.3)
280
+ ax.axvline(-0.474, color="black", linestyle="--", alpha=0.3)
274
281
 
275
282
  stx.plt.tight_layout()
276
- stx.io.save(fig, './cliffs_delta_demo.jpg')
283
+ stx.io.save(fig, "./cliffs_delta_demo.jpg")
277
284
  logger.info("Visualization saved")
278
285
 
279
286
  return 0
@@ -284,11 +291,7 @@ def parse_args():
284
291
  parser = argparse.ArgumentParser(
285
292
  description="Demonstrate Cliff's delta effect size calculation"
286
293
  )
287
- parser.add_argument(
288
- '--verbose',
289
- action='store_true',
290
- help='Enable verbose output'
291
- )
294
+ parser.add_argument("--verbose", action="store_true", help="Enable verbose output")
292
295
  return parser.parse_args()
293
296
 
294
297
 
@@ -319,7 +322,7 @@ def run_main():
319
322
  )
320
323
 
321
324
 
322
- if __name__ == '__main__':
325
+ if __name__ == "__main__":
323
326
  run_main()
324
327
 
325
328
  # 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
  # ----------------------------------------
@@ -42,7 +43,7 @@ def cohens_d(
42
43
  x: Union[np.ndarray, pd.Series],
43
44
  y: Optional[Union[np.ndarray, pd.Series]] = None,
44
45
  paired: bool = False,
45
- correction: Literal['hedges', 'glass', None] = None
46
+ correction: Literal["hedges", "glass", None] = None,
46
47
  ) -> float:
47
48
  """
48
49
  Compute Cohen's d effect size.
@@ -136,7 +137,7 @@ def cohens_d(
136
137
  n1, n2 = len(x), len(y)
137
138
  mean_diff = np.mean(x) - np.mean(y)
138
139
 
139
- if correction == 'glass':
140
+ if correction == "glass":
140
141
  # Glass's delta: use only control group (y) SD
141
142
  d = mean_diff / np.std(y, ddof=1)
142
143
  else:
@@ -147,7 +148,7 @@ def cohens_d(
147
148
  d = mean_diff / pooled_std
148
149
 
149
150
  # Apply Hedges' correction for small samples
150
- if correction == 'hedges':
151
+ if correction == "hedges":
151
152
  # Hedges' g correction factor
152
153
  correction_factor = 1 - (3 / (4 * (n1 + n2) - 9))
153
154
  d = d * correction_factor
@@ -181,13 +182,13 @@ def interpret_cohens_d(d: float) -> str:
181
182
  d_abs = abs(d)
182
183
 
183
184
  if d_abs < 0.2:
184
- return 'negligible'
185
+ return "negligible"
185
186
  elif d_abs < 0.5:
186
- return 'small'
187
+ return "small"
187
188
  elif d_abs < 0.8:
188
- return 'medium'
189
+ return "medium"
189
190
  else:
190
- return 'large'
191
+ return "large"
191
192
 
192
193
 
193
194
  """Main function"""
@@ -220,11 +221,13 @@ def main(args):
220
221
  f"Interpretation: {interpretation}"
221
222
  )
222
223
 
223
- results.append({
224
- 'true_d': true_d,
225
- 'computed_d': computed_d,
226
- 'interpretation': interpretation
227
- })
224
+ results.append(
225
+ {
226
+ "true_d": true_d,
227
+ "computed_d": computed_d,
228
+ "interpretation": interpretation,
229
+ }
230
+ )
228
231
 
229
232
  # Example 2: Paired vs independent
230
233
  logger.info("\n=== Example 2: Paired vs Independent ===")
@@ -249,8 +252,8 @@ def main(args):
249
252
  y_small = np.random.normal(0.5, 1, small_n)
250
253
 
251
254
  d_standard = cohens_d(x_small, y_small)
252
- d_hedges = cohens_d(x_small, y_small, correction='hedges')
253
- d_glass = cohens_d(x_small, y_small, correction='glass')
255
+ d_hedges = cohens_d(x_small, y_small, correction="hedges")
256
+ d_glass = cohens_d(x_small, y_small, correction="glass")
254
257
 
255
258
  logger.info(f"Standard Cohen's d = {d_standard:.3f}")
256
259
  logger.info(f"Hedges' g = {d_hedges:.3f} (corrected for small n)")
@@ -266,31 +269,31 @@ def main(args):
266
269
  control_demo = np.random.normal(0, 1, 1000)
267
270
  treatment_demo = np.random.normal(0.8, 1, 1000)
268
271
 
269
- ax.hist(control_demo, bins=30, alpha=0.5, label='Control', density=True)
270
- ax.hist(treatment_demo, bins=30, alpha=0.5, label='Treatment', density=True)
272
+ ax.hist(control_demo, bins=30, alpha=0.5, label="Control", density=True)
273
+ ax.hist(treatment_demo, bins=30, alpha=0.5, label="Treatment", density=True)
271
274
 
272
275
  d_demo = cohens_d(control_demo, treatment_demo)
273
- ax.axvline(np.mean(control_demo), color='blue', linestyle='--', alpha=0.7)
274
- ax.axvline(np.mean(treatment_demo), color='orange', linestyle='--', alpha=0.7)
276
+ ax.axvline(np.mean(control_demo), color="blue", linestyle="--", alpha=0.7)
277
+ ax.axvline(np.mean(treatment_demo), color="orange", linestyle="--", alpha=0.7)
275
278
 
276
- ax.set_xlabel('Value')
277
- ax.set_ylabel('Density')
279
+ ax.set_xlabel("Value")
280
+ ax.set_ylabel("Density")
278
281
  ax.set_title(f"Distributions (Cohen's d = {d_demo:.2f})")
279
282
  ax.legend()
280
283
 
281
284
  # Plot 2: Effect size comparison
282
285
  ax = axes[1]
283
286
  df_results = pd.DataFrame(results)
284
- ax.scatter(df_results['true_d'], df_results['computed_d'], s=100)
285
- ax.plot([-0.5, 1.5], [-0.5, 1.5], 'k--', alpha=0.5, label='Perfect agreement')
286
- ax.set_xlabel('True Effect Size')
287
+ ax.scatter(df_results["true_d"], df_results["computed_d"], s=100)
288
+ ax.plot([-0.5, 1.5], [-0.5, 1.5], "k--", alpha=0.5, label="Perfect agreement")
289
+ ax.set_xlabel("True Effect Size")
287
290
  ax.set_ylabel("Computed Cohen's d")
288
- ax.set_title('True vs Computed Effect Sizes')
291
+ ax.set_title("True vs Computed Effect Sizes")
289
292
  ax.legend()
290
293
  ax.grid(True, alpha=0.3)
291
294
 
292
295
  stx.plt.tight_layout()
293
- stx.io.save(fig, './cohens_d_demo.jpg')
296
+ stx.io.save(fig, "./cohens_d_demo.jpg")
294
297
  logger.info("Visualization saved")
295
298
 
296
299
  return 0
@@ -301,11 +304,7 @@ def parse_args():
301
304
  parser = argparse.ArgumentParser(
302
305
  description="Demonstrate Cohen's d effect size calculation"
303
306
  )
304
- parser.add_argument(
305
- '--verbose',
306
- action='store_true',
307
- help='Enable verbose output'
308
- )
307
+ parser.add_argument("--verbose", action="store_true", help="Enable verbose output")
309
308
  return parser.parse_args()
310
309
 
311
310
 
@@ -336,7 +335,7 @@ def run_main():
336
335
  )
337
336
 
338
337
 
339
- if __name__ == '__main__':
338
+ if __name__ == "__main__":
340
339
  run_main()
341
340
 
342
341
  # EOF