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
@@ -32,7 +32,8 @@ try:
32
32
  except Exception:
33
33
  # Search for Arial font files and register them
34
34
  arial_paths = [
35
- f for f in fm.findSystemFonts()
35
+ f
36
+ for f in fm.findSystemFonts()
36
37
  if os.path.basename(f).lower().startswith("arial")
37
38
  ]
38
39
 
@@ -53,11 +54,17 @@ except Exception:
53
54
  # Configure matplotlib to use Arial if available
54
55
  if _arial_enabled:
55
56
  mpl.rcParams["font.family"] = "Arial"
56
- mpl.rcParams["font.sans-serif"] = ["Arial", "Helvetica", "DejaVu Sans", "Liberation Sans"]
57
+ mpl.rcParams["font.sans-serif"] = [
58
+ "Arial",
59
+ "Helvetica",
60
+ "DejaVu Sans",
61
+ "Liberation Sans",
62
+ ]
57
63
  else:
58
64
  # Warn about missing Arial
59
65
  try:
60
66
  from scitex.logging import getLogger
67
+
61
68
  _logger = getLogger(__name__)
62
69
  _logger.warning(
63
70
  "Arial font not found. Using fallback fonts (Helvetica/DejaVu Sans). "
@@ -66,11 +73,12 @@ else:
66
73
  except:
67
74
  # If scitex.logging not available, use standard warnings
68
75
  import warnings
76
+
69
77
  warnings.warn(
70
78
  "Arial font not found. Using fallback fonts (Helvetica/DejaVu Sans). "
71
79
  "For publication figures with Arial: sudo apt-get install ttf-mscorefonts-installer && fc-cache -fv",
72
80
  UserWarning,
73
- stacklevel=2
81
+ stacklevel=2,
74
82
  )
75
83
 
76
84
 
@@ -116,7 +124,7 @@ class SubplotsWrapper:
116
124
  dpi=None,
117
125
  styles=None, # List of style dicts for per-axes control
118
126
  transparent=None, # Transparent background (default: from SCITEX_STYLE.yaml)
119
- **kwargs
127
+ **kwargs,
120
128
  ):
121
129
  """
122
130
  Create figure and axes with optional millimeter-based control.
@@ -216,34 +224,69 @@ class SubplotsWrapper:
216
224
  """
217
225
 
218
226
  # Use resolve_style_value for priority: direct → yaml → env → default
219
- from scitex.plt.styles import resolve_style_value as _resolve, SCITEX_STYLE as _S
227
+ from scitex.plt.styles import (
228
+ resolve_style_value as _resolve,
229
+ SCITEX_STYLE as _S,
230
+ )
220
231
 
221
232
  # Resolve all style values with proper priority chain
222
- axes_width_mm = _resolve('axes.width_mm', axes_width_mm, _S.get('axes_width_mm'))
223
- axes_height_mm = _resolve('axes.height_mm', axes_height_mm, _S.get('axes_height_mm'))
224
- margin_left_mm = _resolve('margins.left_mm', margin_left_mm, _S.get('margin_left_mm'))
225
- margin_right_mm = _resolve('margins.right_mm', margin_right_mm, _S.get('margin_right_mm'))
226
- margin_bottom_mm = _resolve('margins.bottom_mm', margin_bottom_mm, _S.get('margin_bottom_mm'))
227
- margin_top_mm = _resolve('margins.top_mm', margin_top_mm, _S.get('margin_top_mm'))
228
- space_w_mm = _resolve('spacing.horizontal_mm', space_w_mm, _S.get('space_w_mm'))
229
- space_h_mm = _resolve('spacing.vertical_mm', space_h_mm, _S.get('space_h_mm'))
230
- axes_thickness_mm = _resolve('axes.thickness_mm', axes_thickness_mm, _S.get('axes_thickness_mm'))
231
- tick_length_mm = _resolve('ticks.length_mm', tick_length_mm, _S.get('tick_length_mm'))
232
- tick_thickness_mm = _resolve('ticks.thickness_mm', tick_thickness_mm, _S.get('tick_thickness_mm'))
233
- trace_thickness_mm = _resolve('lines.trace_mm', trace_thickness_mm, _S.get('trace_thickness_mm'))
234
- marker_size_mm = _resolve('markers.size_mm', marker_size_mm, _S.get('marker_size_mm'))
235
- axis_font_size_pt = _resolve('fonts.axis_label_pt', axis_font_size_pt, _S.get('axis_font_size_pt'))
236
- tick_font_size_pt = _resolve('fonts.tick_label_pt', tick_font_size_pt, _S.get('tick_font_size_pt'))
237
- title_font_size_pt = _resolve('fonts.title_pt', title_font_size_pt, _S.get('title_font_size_pt'))
238
- legend_font_size_pt = _resolve('fonts.legend_pt', legend_font_size_pt, _S.get('legend_font_size_pt'))
239
- suptitle_font_size_pt = _resolve('fonts.suptitle_pt', suptitle_font_size_pt, _S.get('suptitle_font_size_pt'))
240
- n_ticks = _resolve('ticks.n_ticks', n_ticks, _S.get('n_ticks'), int)
241
- dpi = _resolve('output.dpi', dpi, _S.get('dpi'), int)
233
+ axes_width_mm = _resolve(
234
+ "axes.width_mm", axes_width_mm, _S.get("axes_width_mm")
235
+ )
236
+ axes_height_mm = _resolve(
237
+ "axes.height_mm", axes_height_mm, _S.get("axes_height_mm")
238
+ )
239
+ margin_left_mm = _resolve(
240
+ "margins.left_mm", margin_left_mm, _S.get("margin_left_mm")
241
+ )
242
+ margin_right_mm = _resolve(
243
+ "margins.right_mm", margin_right_mm, _S.get("margin_right_mm")
244
+ )
245
+ margin_bottom_mm = _resolve(
246
+ "margins.bottom_mm", margin_bottom_mm, _S.get("margin_bottom_mm")
247
+ )
248
+ margin_top_mm = _resolve(
249
+ "margins.top_mm", margin_top_mm, _S.get("margin_top_mm")
250
+ )
251
+ space_w_mm = _resolve("spacing.horizontal_mm", space_w_mm, _S.get("space_w_mm"))
252
+ space_h_mm = _resolve("spacing.vertical_mm", space_h_mm, _S.get("space_h_mm"))
253
+ axes_thickness_mm = _resolve(
254
+ "axes.thickness_mm", axes_thickness_mm, _S.get("axes_thickness_mm")
255
+ )
256
+ tick_length_mm = _resolve(
257
+ "ticks.length_mm", tick_length_mm, _S.get("tick_length_mm")
258
+ )
259
+ tick_thickness_mm = _resolve(
260
+ "ticks.thickness_mm", tick_thickness_mm, _S.get("tick_thickness_mm")
261
+ )
262
+ trace_thickness_mm = _resolve(
263
+ "lines.trace_mm", trace_thickness_mm, _S.get("trace_thickness_mm")
264
+ )
265
+ marker_size_mm = _resolve(
266
+ "markers.size_mm", marker_size_mm, _S.get("marker_size_mm")
267
+ )
268
+ axis_font_size_pt = _resolve(
269
+ "fonts.axis_label_pt", axis_font_size_pt, _S.get("axis_font_size_pt")
270
+ )
271
+ tick_font_size_pt = _resolve(
272
+ "fonts.tick_label_pt", tick_font_size_pt, _S.get("tick_font_size_pt")
273
+ )
274
+ title_font_size_pt = _resolve(
275
+ "fonts.title_pt", title_font_size_pt, _S.get("title_font_size_pt")
276
+ )
277
+ legend_font_size_pt = _resolve(
278
+ "fonts.legend_pt", legend_font_size_pt, _S.get("legend_font_size_pt")
279
+ )
280
+ suptitle_font_size_pt = _resolve(
281
+ "fonts.suptitle_pt", suptitle_font_size_pt, _S.get("suptitle_font_size_pt")
282
+ )
283
+ n_ticks = _resolve("ticks.n_ticks", n_ticks, _S.get("n_ticks"), int)
284
+ dpi = _resolve("output.dpi", dpi, _S.get("dpi"), int)
242
285
  # Resolve transparent from YAML (default: True in SCITEX_STYLE.yaml)
243
286
  if transparent is None:
244
- transparent = _S.get('transparent', True)
287
+ transparent = _S.get("transparent", True)
245
288
  if mode is None:
246
- mode = _S.get('mode', 'publication')
289
+ mode = _S.get("mode", "publication")
247
290
 
248
291
  # Always use mm-control pathway with SCITEX_STYLE defaults
249
292
  if True:
@@ -276,7 +319,7 @@ class SubplotsWrapper:
276
319
  dpi=dpi,
277
320
  styles=styles,
278
321
  transparent=transparent,
279
- **kwargs
322
+ **kwargs,
280
323
  )
281
324
 
282
325
  def _create_with_mm_control(
@@ -312,7 +355,7 @@ class SubplotsWrapper:
312
355
  dpi=None,
313
356
  styles=None,
314
357
  transparent=None, # Resolved from caller
315
- **kwargs
358
+ **kwargs,
316
359
  ):
317
360
  """Create figure with mm-based control over axes dimensions."""
318
361
  from scitex.plt.utils import mm_to_inch, apply_style_mm
@@ -327,7 +370,7 @@ class SubplotsWrapper:
327
370
  n_axes = nrows * ncols
328
371
 
329
372
  # Apply mode-specific defaults
330
- if mode == 'display':
373
+ if mode == "display":
331
374
  scale_factor = 3.0
332
375
  dpi = dpi or 100
333
376
  else: # publication or None
@@ -337,18 +380,26 @@ class SubplotsWrapper:
337
380
  # Set defaults - if value is provided, apply scaling; if not, use scaled default
338
381
  if axes_width_mm is None:
339
382
  axes_width_mm = 30.0 * scale_factor
340
- elif mode == 'display':
383
+ elif mode == "display":
341
384
  axes_width_mm = axes_width_mm * scale_factor
342
385
 
343
386
  if axes_height_mm is None:
344
387
  axes_height_mm = 21.0 * scale_factor
345
- elif mode == 'display':
388
+ elif mode == "display":
346
389
  axes_height_mm = axes_height_mm * scale_factor
347
390
 
348
- margin_left_mm = margin_left_mm if margin_left_mm is not None else (5.0 * scale_factor)
349
- margin_right_mm = margin_right_mm if margin_right_mm is not None else (2.0 * scale_factor)
350
- margin_bottom_mm = margin_bottom_mm if margin_bottom_mm is not None else (5.0 * scale_factor)
351
- margin_top_mm = margin_top_mm if margin_top_mm is not None else (2.0 * scale_factor)
391
+ margin_left_mm = (
392
+ margin_left_mm if margin_left_mm is not None else (5.0 * scale_factor)
393
+ )
394
+ margin_right_mm = (
395
+ margin_right_mm if margin_right_mm is not None else (2.0 * scale_factor)
396
+ )
397
+ margin_bottom_mm = (
398
+ margin_bottom_mm if margin_bottom_mm is not None else (5.0 * scale_factor)
399
+ )
400
+ margin_top_mm = (
401
+ margin_top_mm if margin_top_mm is not None else (2.0 * scale_factor)
402
+ )
352
403
  space_w_mm = space_w_mm if space_w_mm is not None else (3.0 * scale_factor)
353
404
  space_h_mm = space_h_mm if space_h_mm is not None else (3.0 * scale_factor)
354
405
 
@@ -356,14 +407,18 @@ class SubplotsWrapper:
356
407
  if isinstance(axes_width_mm, (list, tuple)):
357
408
  ax_widths_mm = list(axes_width_mm)
358
409
  if len(ax_widths_mm) != n_axes:
359
- raise ValueError(f"axes_width_mm list length ({len(ax_widths_mm)}) must match nrows*ncols ({n_axes})")
410
+ raise ValueError(
411
+ f"axes_width_mm list length ({len(ax_widths_mm)}) must match nrows*ncols ({n_axes})"
412
+ )
360
413
  else:
361
414
  ax_widths_mm = [axes_width_mm] * n_axes
362
415
 
363
416
  if isinstance(axes_height_mm, (list, tuple)):
364
417
  ax_heights_mm = list(axes_height_mm)
365
418
  if len(ax_heights_mm) != n_axes:
366
- raise ValueError(f"axes_height_mm list length ({len(ax_heights_mm)}) must match nrows*ncols ({n_axes})")
419
+ raise ValueError(
420
+ f"axes_height_mm list length ({len(ax_heights_mm)}) must match nrows*ncols ({n_axes})"
421
+ )
367
422
  else:
368
423
  ax_heights_mm = [axes_height_mm] * n_axes
369
424
 
@@ -392,7 +447,7 @@ class SubplotsWrapper:
392
447
  figsize_inch = (mm_to_inch(total_width_mm), mm_to_inch(total_height_mm))
393
448
  if transparent:
394
449
  # Transparent background for publication figures
395
- self._fig_mpl = plt.figure(figsize=figsize_inch, dpi=dpi, facecolor='none')
450
+ self._fig_mpl = plt.figure(figsize=figsize_inch, dpi=dpi, facecolor="none")
396
451
  else:
397
452
  self._fig_mpl = plt.figure(figsize=figsize_inch, dpi=dpi)
398
453
 
@@ -404,12 +459,18 @@ class SubplotsWrapper:
404
459
  for col in range(ncols):
405
460
  # Calculate position for this axes
406
461
  # Left position: left margin + sum of previous column widths + spacing
407
- left_mm = margin_left_mm + max_widths_per_col[:col].sum() + col * space_w_mm
462
+ left_mm = (
463
+ margin_left_mm + max_widths_per_col[:col].sum() + col * space_w_mm
464
+ )
408
465
 
409
466
  # Bottom position: bottom margin + sum of heights above this row + spacing
410
467
  # (rows are counted from top in matplotlib)
411
468
  rows_below = nrows - row - 1
412
- bottom_mm = margin_bottom_mm + max_heights_per_row[row+1:].sum() + rows_below * space_h_mm
469
+ bottom_mm = (
470
+ margin_bottom_mm
471
+ + max_heights_per_row[row + 1 :].sum()
472
+ + rows_below * space_h_mm
473
+ )
413
474
 
414
475
  # Convert to figure coordinates [0-1]
415
476
  left = left_mm / total_width_mm
@@ -425,10 +486,10 @@ class SubplotsWrapper:
425
486
 
426
487
  # Tag with metadata
427
488
  ax_mpl._scitex_metadata = {
428
- 'created_with': 'scitex.plt.subplots (mm-control)',
429
- 'mode': mode or 'publication',
430
- 'axes_size_mm': (ax_widths_mm[ax_idx], ax_heights_mm[ax_idx]),
431
- 'position_in_grid': (row, col),
489
+ "created_with": "scitex.plt.subplots",
490
+ "mode": mode or "publication",
491
+ "axes_size_mm": (ax_widths_mm[ax_idx], ax_heights_mm[ax_idx]),
492
+ "position_in_grid": (row, col),
432
493
  }
433
494
 
434
495
  ax_idx += 1
@@ -440,7 +501,9 @@ class SubplotsWrapper:
440
501
  if styles is not None:
441
502
  if isinstance(styles, list):
442
503
  if len(styles) != n_axes:
443
- raise ValueError(f"styles list length ({len(styles)}) must match nrows*ncols ({n_axes})")
504
+ raise ValueError(
505
+ f"styles list length ({len(styles)}) must match nrows*ncols ({n_axes})"
506
+ )
444
507
  style_dict = styles[i]
445
508
  else:
446
509
  style_dict = styles
@@ -448,39 +511,39 @@ class SubplotsWrapper:
448
511
  # Build style dict from individual parameters
449
512
  style_dict = {}
450
513
  if axes_thickness_mm is not None:
451
- style_dict['axis_thickness_mm'] = axes_thickness_mm
514
+ style_dict["axis_thickness_mm"] = axes_thickness_mm
452
515
  if tick_length_mm is not None:
453
- style_dict['tick_length_mm'] = tick_length_mm
516
+ style_dict["tick_length_mm"] = tick_length_mm
454
517
  if tick_thickness_mm is not None:
455
- style_dict['tick_thickness_mm'] = tick_thickness_mm
518
+ style_dict["tick_thickness_mm"] = tick_thickness_mm
456
519
  if trace_thickness_mm is not None:
457
- style_dict['trace_thickness_mm'] = trace_thickness_mm
520
+ style_dict["trace_thickness_mm"] = trace_thickness_mm
458
521
  if marker_size_mm is not None:
459
- style_dict['marker_size_mm'] = marker_size_mm
522
+ style_dict["marker_size_mm"] = marker_size_mm
460
523
  if axis_font_size_pt is not None:
461
- style_dict['axis_font_size_pt'] = axis_font_size_pt
524
+ style_dict["axis_font_size_pt"] = axis_font_size_pt
462
525
  if tick_font_size_pt is not None:
463
- style_dict['tick_font_size_pt'] = tick_font_size_pt
526
+ style_dict["tick_font_size_pt"] = tick_font_size_pt
464
527
  if title_font_size_pt is not None:
465
- style_dict['title_font_size_pt'] = title_font_size_pt
528
+ style_dict["title_font_size_pt"] = title_font_size_pt
466
529
  if legend_font_size_pt is not None:
467
- style_dict['legend_font_size_pt'] = legend_font_size_pt
530
+ style_dict["legend_font_size_pt"] = legend_font_size_pt
468
531
  if suptitle_font_size_pt is not None:
469
- style_dict['suptitle_font_size_pt'] = suptitle_font_size_pt
532
+ style_dict["suptitle_font_size_pt"] = suptitle_font_size_pt
470
533
  if label_pad_pt is not None:
471
- style_dict['label_pad_pt'] = label_pad_pt
534
+ style_dict["label_pad_pt"] = label_pad_pt
472
535
  if tick_pad_pt is not None:
473
- style_dict['tick_pad_pt'] = tick_pad_pt
536
+ style_dict["tick_pad_pt"] = tick_pad_pt
474
537
  if title_pad_pt is not None:
475
- style_dict['title_pad_pt'] = title_pad_pt
538
+ style_dict["title_pad_pt"] = title_pad_pt
476
539
  if font_family is not None:
477
- style_dict['font_family'] = font_family
540
+ style_dict["font_family"] = font_family
478
541
  if n_ticks is not None:
479
- style_dict['n_ticks'] = n_ticks
542
+ style_dict["n_ticks"] = n_ticks
480
543
 
481
544
  # Extract suptitle font size if available
482
- if 'suptitle_font_size_pt' in style_dict:
483
- suptitle_font_size_pt_value = style_dict['suptitle_font_size_pt']
545
+ if "suptitle_font_size_pt" in style_dict:
546
+ suptitle_font_size_pt_value = style_dict["suptitle_font_size_pt"]
484
547
  else:
485
548
  suptitle_font_size_pt_value = None
486
549
 
@@ -488,7 +551,7 @@ class SubplotsWrapper:
488
551
  if style_dict:
489
552
  apply_style_mm(ax_mpl, style_dict)
490
553
  # Add style to metadata
491
- ax_mpl._scitex_metadata['style_mm'] = style_dict
554
+ ax_mpl._scitex_metadata["style_mm"] = style_dict
492
555
 
493
556
  # Store suptitle font size in figure metadata for later use
494
557
  if suptitle_font_size_pt_value is not None:
@@ -505,13 +568,17 @@ class SubplotsWrapper:
505
568
  ax_mpl_scalar = axes_array_mpl.item()
506
569
  self._axis_scitex = AxisWrapper(self._fig_scitex, ax_mpl_scalar, track)
507
570
  self._fig_scitex.axes = self._axis_scitex
571
+ # Store reference to scitex wrapper on matplotlib axes for metadata collection
572
+ ax_mpl_scalar._scitex_wrapper = self._axis_scitex
508
573
  return self._fig_scitex, self._axis_scitex
509
574
 
510
575
  # Handle multiple axes case
511
- axes_flat_scitex_list = [
512
- AxisWrapper(self._fig_scitex, ax_mpl, track)
513
- for ax_mpl in axes_mpl_list
514
- ]
576
+ axes_flat_scitex_list = []
577
+ for ax_mpl in axes_mpl_list:
578
+ ax_scitex = AxisWrapper(self._fig_scitex, ax_mpl, track)
579
+ # Store reference to scitex wrapper on matplotlib axes for metadata collection
580
+ ax_mpl._scitex_wrapper = ax_scitex
581
+ axes_flat_scitex_list.append(ax_scitex)
515
582
 
516
583
  axes_array_scitex = np.array(axes_flat_scitex_list).reshape(nrows, ncols)
517
584
  self._axes_scitex = AxesWrapper(self._fig_scitex, axes_array_scitex)
@@ -9,6 +9,16 @@ __FILE__ = "./src/scitex/plt/_subplots/__init__.py"
9
9
  __DIR__ = os.path.dirname(__FILE__)
10
10
  # ----------------------------------------
11
11
 
12
+ # Import wrapper classes
13
+ from ._FigWrapper import FigWrapper
14
+ from ._AxisWrapper import AxisWrapper
15
+ from ._AxesWrapper import AxesWrapper
16
+
17
+ # Backward-compatible aliases
18
+ _FigWrapper = FigWrapper
19
+ _AxisWrapper = AxisWrapper
20
+ _AxesWrapper = AxesWrapper
21
+
12
22
  # Import export_as_csv module functions
13
23
  from ._export_as_csv import export_as_csv, format_record
14
24
 
@@ -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
  # ----------------------------------------
@@ -21,34 +22,34 @@ _warning_registry = set()
21
22
  # Mapping of matplotlib/seaborn methods to their scitex equivalents
22
23
  _METHOD_ALTERNATIVES = {
23
24
  # Matplotlib methods
24
- 'imshow': 'plot_imshow',
25
- 'plot': 'plot', # already tracked
26
- 'scatter': 'plot_scatter', # already tracked
27
- 'bar': 'plot_bar', # already tracked
28
- 'barh': 'plot_barh', # already tracked
29
- 'hist': 'hist', # already tracked
30
- 'boxplot': 'stx_box or plot_boxplot',
31
- 'violinplot': 'stx_violin or plot_violinplot',
32
- 'fill_between': 'plot_fill_between',
33
- 'errorbar': 'plot_errorbar',
34
- 'contour': 'plot_contour',
35
- 'heatmap': 'stx_heatmap',
36
-
25
+ "imshow": "plot_imshow",
26
+ "plot": "plot", # already tracked
27
+ "scatter": "plot_scatter", # already tracked
28
+ "bar": "plot_bar", # already tracked
29
+ "barh": "plot_barh", # already tracked
30
+ "hist": "hist", # already tracked
31
+ "boxplot": "stx_box or plot_boxplot",
32
+ "violinplot": "stx_violin or plot_violinplot",
33
+ "fill_between": "plot_fill_between",
34
+ "errorbar": "plot_errorbar",
35
+ "contour": "plot_contour",
36
+ "heatmap": "stx_heatmap",
37
37
  # Seaborn methods (accessed via ax.sns_*)
38
- 'scatterplot': 'sns_scatterplot',
39
- 'lineplot': 'sns_lineplot',
40
- 'barplot': 'sns_barplot',
41
- 'boxplot_sns': 'sns_boxplot',
42
- 'violinplot_sns': 'sns_violinplot',
43
- 'stripplot': 'sns_stripplot',
44
- 'swarmplot': 'sns_swarmplot',
45
- 'histplot': 'sns_histplot',
46
- 'kdeplot': 'sns_kdeplot',
47
- 'heatmap_sns': 'sns_heatmap',
48
- 'jointplot': 'sns_jointplot',
49
- 'pairplot': 'sns_pairplot',
38
+ "scatterplot": "sns_scatterplot",
39
+ "lineplot": "sns_lineplot",
40
+ "barplot": "sns_barplot",
41
+ "boxplot_sns": "sns_boxplot",
42
+ "violinplot_sns": "sns_violinplot",
43
+ "stripplot": "sns_stripplot",
44
+ "swarmplot": "sns_swarmplot",
45
+ "histplot": "sns_histplot",
46
+ "kdeplot": "sns_kdeplot",
47
+ "heatmap_sns": "sns_heatmap",
48
+ "jointplot": "sns_jointplot",
49
+ "pairplot": "sns_pairplot",
50
50
  }
51
51
 
52
+
52
53
  def _warn_once(message, category=UserWarning):
53
54
  """Show a warning only once per runtime.
54
55
 
@@ -60,28 +61,68 @@ def _warn_once(message, category=UserWarning):
60
61
  _warning_registry.add(message)
61
62
  warnings.warn(message, category, stacklevel=3)
62
63
 
64
+
63
65
  from ._export_as_csv_formatters import (
64
66
  # Standard matplotlib formatters
65
- _format_annotate, _format_bar, _format_barh, _format_boxplot,
66
- _format_contour, _format_contourf, _format_errorbar, _format_eventplot,
67
- _format_fill, _format_fill_between, _format_hexbin, _format_hist,
68
- _format_hist2d, _format_imshow, _format_imshow2d, _format_matshow,
69
- _format_pie, _format_plot, _format_quiver, _format_scatter, _format_stem,
70
- _format_step, _format_streamplot, _format_text, _format_violin,
67
+ _format_annotate,
68
+ _format_bar,
69
+ _format_barh,
70
+ _format_boxplot,
71
+ _format_contour,
72
+ _format_contourf,
73
+ _format_errorbar,
74
+ _format_eventplot,
75
+ _format_fill,
76
+ _format_fill_between,
77
+ _format_hexbin,
78
+ _format_hist,
79
+ _format_hist2d,
80
+ _format_imshow,
81
+ _format_imshow2d,
82
+ _format_matshow,
83
+ _format_pie,
84
+ _format_plot,
85
+ _format_quiver,
86
+ _format_scatter,
87
+ _format_stem,
88
+ _format_step,
89
+ _format_streamplot,
90
+ _format_text,
91
+ _format_violin,
71
92
  _format_violinplot,
72
93
  # Custom scitex formatters
73
- _format_plot_box, _format_plot_conf_mat, _format_plot_ecdf,
74
- _format_plot_fillv, _format_plot_heatmap, _format_plot_image,
75
- _format_plot_imshow, _format_plot_joyplot, _format_plot_kde,
76
- _format_plot_line, _format_plot_mean_ci, _format_plot_mean_std,
77
- _format_plot_median_iqr, _format_plot_raster, _format_plot_rectangle,
78
- _format_plot_scatter, _format_plot_scatter_hist, _format_plot_shaded_line,
94
+ _format_plot_box,
95
+ _format_plot_conf_mat,
96
+ _format_plot_ecdf,
97
+ _format_plot_fillv,
98
+ _format_plot_heatmap,
99
+ _format_plot_image,
100
+ _format_plot_imshow,
101
+ _format_plot_joyplot,
102
+ _format_plot_kde,
103
+ _format_plot_line,
104
+ _format_plot_mean_ci,
105
+ _format_plot_mean_std,
106
+ _format_plot_median_iqr,
107
+ _format_plot_raster,
108
+ _format_plot_rectangle,
109
+ _format_plot_scatter,
110
+ _format_plot_scatter_hist,
111
+ _format_plot_shaded_line,
79
112
  _format_plot_violin,
80
113
  # Seaborn formatters
81
- _format_sns_barplot, _format_sns_boxplot, _format_sns_heatmap,
82
- _format_sns_histplot, _format_sns_jointplot, _format_sns_kdeplot,
83
- _format_sns_lineplot, _format_sns_pairplot, _format_sns_scatterplot,
84
- _format_sns_stripplot, _format_sns_swarmplot, _format_sns_violinplot,
114
+ _format_sns_barplot,
115
+ _format_sns_boxplot,
116
+ _format_sns_heatmap,
117
+ _format_sns_histplot,
118
+ _format_sns_jointplot,
119
+ _format_sns_kdeplot,
120
+ _format_sns_lineplot,
121
+ _format_sns_pairplot,
122
+ _format_sns_scatterplot,
123
+ _format_sns_stripplot,
124
+ _format_sns_swarmplot,
125
+ _format_sns_violinplot,
85
126
  )
86
127
 
87
128
  # Registry mapping method names to their formatter functions
@@ -165,9 +206,7 @@ def _to_numpy(data):
165
206
  Data as numpy array
166
207
  """
167
208
  if hasattr(data, "numpy"): # torch tensor
168
- return (
169
- data.detach().numpy() if hasattr(data, "detach") else data.numpy()
170
- )
209
+ return data.detach().numpy() if hasattr(data, "detach") else data.numpy()
171
210
  elif hasattr(data, "values"): # pandas series/dataframe
172
211
  return data.values
173
212
  else:
@@ -193,9 +232,9 @@ def export_as_csv(history_records):
193
232
  dfs = []
194
233
  failed_methods = set() # Track failed methods for helpful warnings
195
234
 
196
- for record in list(history_records.values()):
235
+ for record_index, record in enumerate(list(history_records.values())):
197
236
  try:
198
- formatted_df = format_record(record)
237
+ formatted_df = format_record(record, record_index=record_index)
199
238
  if formatted_df is not None and not formatted_df.empty:
200
239
  dfs.append(formatted_df)
201
240
  else:
@@ -244,11 +283,13 @@ def export_as_csv(history_records):
244
283
  return meta_df
245
284
 
246
285
 
247
- def format_record(record):
286
+ def format_record(record, record_index=0):
248
287
  """Route record to the appropriate formatting function based on plot method.
249
288
 
250
289
  Args:
251
290
  record (tuple): Plotting record tuple (id, method, tracked_dict, kwargs).
291
+ record_index (int): Index of this record in the history (used as fallback
292
+ for trace_id when user doesn't provide an explicit id= kwarg).
252
293
 
253
294
  Returns:
254
295
  pd.DataFrame: Formatted data for the plot record.
@@ -381,4 +422,5 @@ def format_record(record):
381
422
  f"Check the feature-request-export-as-csv-functions.md for implementation status."
382
423
  )
383
424
 
425
+
384
426
  # EOF
@@ -4,6 +4,7 @@
4
4
  # File: /data/gpfs/projects/punim2354/ywatanabe/scitex_repo/src/scitex/plt/_subplots/_export_as_csv_formatters/__init__.py
5
5
  # ----------------------------------------
6
6
  import os
7
+
7
8
  __FILE__ = __file__
8
9
  __DIR__ = os.path.dirname(__FILE__)
9
10
  # ----------------------------------------
@@ -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
  # ----------------------------------------
@@ -20,7 +21,7 @@ def _make_column_name(id, suffix, method="annotate"):
20
21
  - id="plot_5", suffix="x" -> "plot_5_annotate_x"
21
22
  """
22
23
  # Check if method name is already in the ID
23
- id_parts = id.rsplit('_', 1)
24
+ id_parts = id.rsplit("_", 1)
24
25
  if len(id_parts) == 2 and id_parts[0].endswith(method):
25
26
  # Method already in ID, don't duplicate
26
27
  return f"{id}_{suffix}"
@@ -50,7 +51,7 @@ def _format_annotate(id, tracked_dict, kwargs):
50
51
  xy = args[1]
51
52
 
52
53
  # xy should be a tuple (x, y)
53
- if hasattr(xy, '__len__') and len(xy) >= 2:
54
+ if hasattr(xy, "__len__") and len(xy) >= 2:
54
55
  x, y = xy[0], xy[1]
55
56
  else:
56
57
  return pd.DataFrame()
@@ -58,7 +59,7 @@ def _format_annotate(id, tracked_dict, kwargs):
58
59
  data = {
59
60
  _make_column_name(id, "x"): [x],
60
61
  _make_column_name(id, "y"): [y],
61
- _make_column_name(id, "content"): [text_content]
62
+ _make_column_name(id, "content"): [text_content],
62
63
  }
63
64
 
64
65
  # Check if xytext was provided (either as third arg or in kwargs)
@@ -68,7 +69,7 @@ def _format_annotate(id, tracked_dict, kwargs):
68
69
  elif "xytext" in kwargs:
69
70
  xytext = kwargs["xytext"]
70
71
 
71
- if xytext is not None and hasattr(xytext, '__len__') and len(xytext) >= 2:
72
+ if xytext is not None and hasattr(xytext, "__len__") and len(xytext) >= 2:
72
73
  data[_make_column_name(id, "text_x")] = [xytext[0]]
73
74
  data[_make_column_name(id, "text_y")] = [xytext[1]]
74
75
 
@@ -78,4 +79,5 @@ def _format_annotate(id, tracked_dict, kwargs):
78
79
 
79
80
  return pd.DataFrame()
80
81
 
82
+
81
83
  # EOF