scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1091) hide show
  1. scitex/__init__.py +19 -8
  2. scitex/__main__.py +2 -1
  3. scitex/__version__.py +1 -1
  4. scitex/_optional_deps.py +13 -20
  5. scitex/ai/__init__.py +5 -0
  6. scitex/ai/_gen_ai/_Anthropic.py +3 -1
  7. scitex/ai/_gen_ai/_BaseGenAI.py +3 -2
  8. scitex/ai/_gen_ai/_DeepSeek.py +1 -1
  9. scitex/ai/_gen_ai/_Google.py +3 -2
  10. scitex/ai/_gen_ai/_Llama.py +4 -2
  11. scitex/ai/_gen_ai/_OpenAI.py +3 -1
  12. scitex/ai/_gen_ai/_PARAMS.py +1 -0
  13. scitex/ai/_gen_ai/_Perplexity.py +3 -1
  14. scitex/ai/_gen_ai/__init__.py +1 -0
  15. scitex/ai/_gen_ai/_format_output_func.py +3 -1
  16. scitex/ai/classification/CrossValidationExperiment.py +8 -14
  17. scitex/ai/classification/examples/timeseries_cv_demo.py +128 -112
  18. scitex/ai/classification/reporters/_BaseClassificationReporter.py +2 -0
  19. scitex/ai/classification/reporters/_ClassificationReporter.py +30 -45
  20. scitex/ai/classification/reporters/_MultiClassificationReporter.py +8 -11
  21. scitex/ai/classification/reporters/_SingleClassificationReporter.py +126 -182
  22. scitex/ai/classification/reporters/__init__.py +1 -1
  23. scitex/ai/classification/reporters/reporter_utils/_Plotter.py +213 -119
  24. scitex/ai/classification/reporters/reporter_utils/__init__.py +28 -36
  25. scitex/ai/classification/reporters/reporter_utils/aggregation.py +125 -143
  26. scitex/ai/classification/reporters/reporter_utils/data_models.py +128 -120
  27. scitex/ai/classification/reporters/reporter_utils/reporting.py +507 -340
  28. scitex/ai/classification/reporters/reporter_utils/storage.py +4 -1
  29. scitex/ai/classification/reporters/reporter_utils/validation.py +141 -154
  30. scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +204 -129
  31. scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +215 -171
  32. scitex/ai/classification/timeseries/_TimeSeriesMetadata.py +17 -17
  33. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +67 -143
  34. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +67 -143
  35. scitex/ai/classification/timeseries/_TimeSeriesStrategy.py +12 -13
  36. scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +231 -144
  37. scitex/ai/classification/timeseries/__init__.py +2 -4
  38. scitex/ai/classification/timeseries/_normalize_timestamp.py +3 -0
  39. scitex/ai/clustering/_pca.py +0 -1
  40. scitex/ai/clustering/_umap.py +1 -2
  41. scitex/ai/feature_extraction/__init__.py +10 -8
  42. scitex/ai/feature_extraction/vit.py +0 -1
  43. scitex/ai/feature_selection/feature_selection.py +3 -8
  44. scitex/ai/metrics/_calc_conf_mat.py +2 -0
  45. scitex/ai/metrics/_calc_feature_importance.py +3 -7
  46. scitex/ai/metrics/_calc_pre_rec_auc.py +5 -5
  47. scitex/ai/metrics/_calc_roc_auc.py +4 -2
  48. scitex/ai/metrics/_calc_seizure_prediction_metrics.py +35 -20
  49. scitex/ai/metrics/_calc_silhouette_score.py +1 -3
  50. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger.py +0 -3
  51. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger2020.py +0 -3
  52. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger913A.py +0 -3
  53. scitex/ai/optim/_optimizers.py +1 -1
  54. scitex/ai/plt/__init__.py +6 -1
  55. scitex/ai/plt/_plot_feature_importance.py +1 -3
  56. scitex/ai/plt/_plot_learning_curve.py +9 -24
  57. scitex/ai/plt/_plot_optuna_study.py +4 -3
  58. scitex/ai/plt/_plot_pre_rec_curve.py +9 -15
  59. scitex/ai/plt/_plot_roc_curve.py +6 -8
  60. scitex/ai/plt/_stx_conf_mat.py +121 -122
  61. scitex/ai/sampling/undersample.py +3 -2
  62. scitex/ai/sklearn/__init__.py +2 -2
  63. scitex/ai/training/_LearningCurveLogger.py +23 -10
  64. scitex/ai/utils/_check_params.py +0 -1
  65. scitex/benchmark/__init__.py +15 -25
  66. scitex/benchmark/benchmark.py +124 -117
  67. scitex/benchmark/monitor.py +117 -107
  68. scitex/benchmark/profiler.py +61 -58
  69. scitex/bridge/__init__.py +110 -0
  70. scitex/bridge/_helpers.py +149 -0
  71. scitex/bridge/_plt_vis.py +529 -0
  72. scitex/bridge/_protocol.py +283 -0
  73. scitex/bridge/_stats_plt.py +261 -0
  74. scitex/bridge/_stats_vis.py +265 -0
  75. scitex/browser/__init__.py +0 -2
  76. scitex/browser/auth/__init__.py +0 -0
  77. scitex/browser/auth/google.py +16 -11
  78. scitex/browser/automation/CookieHandler.py +2 -3
  79. scitex/browser/collaboration/__init__.py +3 -0
  80. scitex/browser/collaboration/auth_helpers.py +3 -1
  81. scitex/browser/collaboration/collaborative_agent.py +2 -0
  82. scitex/browser/collaboration/interactive_panel.py +2 -2
  83. scitex/browser/collaboration/shared_session.py +20 -11
  84. scitex/browser/collaboration/standard_interactions.py +1 -0
  85. scitex/browser/core/BrowserMixin.py +12 -30
  86. scitex/browser/core/ChromeProfileManager.py +9 -24
  87. scitex/browser/debugging/_browser_logger.py +15 -25
  88. scitex/browser/debugging/_failure_capture.py +9 -2
  89. scitex/browser/debugging/_highlight_element.py +15 -6
  90. scitex/browser/debugging/_show_grid.py +5 -6
  91. scitex/browser/debugging/_sync_session.py +4 -3
  92. scitex/browser/debugging/_test_monitor.py +14 -5
  93. scitex/browser/debugging/_visual_cursor.py +46 -35
  94. scitex/browser/interaction/click_center.py +4 -3
  95. scitex/browser/interaction/click_with_fallbacks.py +7 -10
  96. scitex/browser/interaction/close_popups.py +79 -66
  97. scitex/browser/interaction/fill_with_fallbacks.py +8 -8
  98. scitex/browser/pdf/__init__.py +3 -1
  99. scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +11 -10
  100. scitex/browser/pdf/detect_chrome_pdf_viewer.py +3 -6
  101. scitex/browser/remote/CaptchaHandler.py +109 -96
  102. scitex/browser/remote/ZenRowsAPIClient.py +91 -97
  103. scitex/browser/remote/ZenRowsBrowserManager.py +138 -112
  104. scitex/browser/stealth/HumanBehavior.py +4 -9
  105. scitex/browser/stealth/StealthManager.py +11 -26
  106. scitex/capture/__init__.py +17 -17
  107. scitex/capture/__main__.py +2 -3
  108. scitex/capture/capture.py +23 -51
  109. scitex/capture/cli.py +14 -39
  110. scitex/capture/gif.py +5 -9
  111. scitex/capture/mcp_server.py +7 -20
  112. scitex/capture/session.py +4 -3
  113. scitex/capture/utils.py +18 -53
  114. scitex/cli/__init__.py +1 -1
  115. scitex/cli/cloud.py +158 -116
  116. scitex/cli/config.py +224 -0
  117. scitex/cli/main.py +41 -40
  118. scitex/cli/scholar.py +60 -27
  119. scitex/cli/security.py +14 -20
  120. scitex/cli/web.py +87 -90
  121. scitex/cli/writer.py +51 -45
  122. scitex/cloud/__init__.py +14 -11
  123. scitex/cloud/_matplotlib_hook.py +6 -6
  124. scitex/config/README.md +313 -0
  125. scitex/config/{PriorityConfig.py → _PriorityConfig.py} +114 -17
  126. scitex/config/_ScitexConfig.py +319 -0
  127. scitex/config/__init__.py +41 -9
  128. scitex/config/_paths.py +325 -0
  129. scitex/config/default.yaml +81 -0
  130. scitex/context/_suppress_output.py +2 -3
  131. scitex/db/_BaseMixins/_BaseBackupMixin.py +3 -1
  132. scitex/db/_BaseMixins/_BaseBatchMixin.py +3 -1
  133. scitex/db/_BaseMixins/_BaseBlobMixin.py +3 -1
  134. scitex/db/_BaseMixins/_BaseImportExportMixin.py +1 -3
  135. scitex/db/_BaseMixins/_BaseIndexMixin.py +3 -1
  136. scitex/db/_BaseMixins/_BaseMaintenanceMixin.py +1 -3
  137. scitex/db/_BaseMixins/_BaseQueryMixin.py +3 -1
  138. scitex/db/_BaseMixins/_BaseRowMixin.py +3 -1
  139. scitex/db/_BaseMixins/_BaseTableMixin.py +3 -1
  140. scitex/db/_BaseMixins/_BaseTransactionMixin.py +1 -3
  141. scitex/db/_BaseMixins/__init__.py +1 -1
  142. scitex/db/__init__.py +9 -1
  143. scitex/db/__main__.py +8 -21
  144. scitex/db/_check_health.py +15 -31
  145. scitex/db/_delete_duplicates.py +7 -4
  146. scitex/db/_inspect.py +22 -38
  147. scitex/db/_inspect_optimized.py +89 -85
  148. scitex/db/_postgresql/_PostgreSQL.py +0 -1
  149. scitex/db/_postgresql/_PostgreSQLMixins/_BlobMixin.py +3 -1
  150. scitex/db/_postgresql/_PostgreSQLMixins/_ConnectionMixin.py +1 -3
  151. scitex/db/_postgresql/_PostgreSQLMixins/_ImportExportMixin.py +1 -3
  152. scitex/db/_postgresql/_PostgreSQLMixins/_MaintenanceMixin.py +1 -4
  153. scitex/db/_postgresql/_PostgreSQLMixins/_QueryMixin.py +3 -3
  154. scitex/db/_postgresql/_PostgreSQLMixins/_RowMixin.py +3 -1
  155. scitex/db/_postgresql/_PostgreSQLMixins/_TransactionMixin.py +1 -3
  156. scitex/db/_postgresql/__init__.py +1 -1
  157. scitex/db/_sqlite3/_SQLite3.py +2 -4
  158. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin.py +11 -12
  159. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin_v01-need-_hash-col.py +19 -14
  160. scitex/db/_sqlite3/_SQLite3Mixins/_BatchMixin.py +3 -1
  161. scitex/db/_sqlite3/_SQLite3Mixins/_BlobMixin.py +7 -7
  162. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin.py +118 -111
  163. scitex/db/_sqlite3/_SQLite3Mixins/_ConnectionMixin.py +8 -10
  164. scitex/db/_sqlite3/_SQLite3Mixins/_GitMixin.py +17 -45
  165. scitex/db/_sqlite3/_SQLite3Mixins/_ImportExportMixin.py +1 -3
  166. scitex/db/_sqlite3/_SQLite3Mixins/_IndexMixin.py +3 -1
  167. scitex/db/_sqlite3/_SQLite3Mixins/_QueryMixin.py +3 -4
  168. scitex/db/_sqlite3/_SQLite3Mixins/_RowMixin.py +9 -9
  169. scitex/db/_sqlite3/_SQLite3Mixins/_TableMixin.py +18 -11
  170. scitex/db/_sqlite3/_SQLite3Mixins/__init__.py +1 -0
  171. scitex/db/_sqlite3/__init__.py +1 -1
  172. scitex/db/_sqlite3/_delete_duplicates.py +13 -11
  173. scitex/decorators/__init__.py +29 -4
  174. scitex/decorators/_auto_order.py +43 -43
  175. scitex/decorators/_batch_fn.py +12 -6
  176. scitex/decorators/_cache_disk.py +8 -9
  177. scitex/decorators/_cache_disk_async.py +8 -7
  178. scitex/decorators/_combined.py +19 -13
  179. scitex/decorators/_converters.py +16 -3
  180. scitex/decorators/_deprecated.py +32 -22
  181. scitex/decorators/_numpy_fn.py +18 -4
  182. scitex/decorators/_pandas_fn.py +17 -5
  183. scitex/decorators/_signal_fn.py +17 -3
  184. scitex/decorators/_torch_fn.py +32 -15
  185. scitex/decorators/_xarray_fn.py +23 -9
  186. scitex/dev/_analyze_code_flow.py +0 -2
  187. scitex/dict/_DotDict.py +15 -19
  188. scitex/dict/_flatten.py +1 -0
  189. scitex/dict/_listed_dict.py +1 -0
  190. scitex/dict/_pop_keys.py +1 -0
  191. scitex/dict/_replace.py +1 -0
  192. scitex/dict/_safe_merge.py +1 -0
  193. scitex/dict/_to_str.py +2 -3
  194. scitex/dsp/__init__.py +13 -4
  195. scitex/dsp/_crop.py +3 -1
  196. scitex/dsp/_detect_ripples.py +3 -1
  197. scitex/dsp/_modulation_index.py +3 -1
  198. scitex/dsp/_time.py +3 -1
  199. scitex/dsp/_wavelet.py +0 -1
  200. scitex/dsp/example.py +0 -5
  201. scitex/dsp/filt.py +4 -0
  202. scitex/dsp/utils/__init__.py +4 -1
  203. scitex/dsp/utils/pac.py +3 -3
  204. scitex/dt/_normalize_timestamp.py +4 -1
  205. scitex/errors.py +3 -6
  206. scitex/etc/__init__.py +1 -1
  207. scitex/gen/_DimHandler.py +6 -6
  208. scitex/gen/__init__.py +5 -1
  209. scitex/gen/_deprecated_close.py +1 -0
  210. scitex/gen/_deprecated_start.py +5 -3
  211. scitex/gen/_detect_environment.py +44 -41
  212. scitex/gen/_detect_notebook_path.py +51 -47
  213. scitex/gen/_embed.py +1 -1
  214. scitex/gen/_get_notebook_path.py +81 -62
  215. scitex/gen/_inspect_module.py +0 -1
  216. scitex/gen/_norm.py +16 -7
  217. scitex/gen/_norm_cache.py +78 -65
  218. scitex/gen/_print_config.py +0 -3
  219. scitex/gen/_src.py +2 -3
  220. scitex/gen/_title_case.py +3 -2
  221. scitex/gen/_to_even.py +8 -8
  222. scitex/gen/_transpose.py +3 -3
  223. scitex/gen/misc.py +0 -3
  224. scitex/gists/_SigMacro_processFigure_S.py +2 -2
  225. scitex/gists/_SigMacro_toBlue.py +2 -2
  226. scitex/gists/__init__.py +4 -1
  227. scitex/git/_branch.py +19 -11
  228. scitex/git/_clone.py +23 -15
  229. scitex/git/_commit.py +10 -12
  230. scitex/git/_init.py +15 -38
  231. scitex/git/_remote.py +9 -3
  232. scitex/git/_result.py +3 -0
  233. scitex/git/_retry.py +2 -5
  234. scitex/git/_types.py +4 -0
  235. scitex/git/_validation.py +8 -8
  236. scitex/git/_workflow.py +4 -4
  237. scitex/io/__init__.py +2 -1
  238. scitex/io/_glob.py +2 -2
  239. scitex/io/_json2md.py +3 -3
  240. scitex/io/_load.py +6 -8
  241. scitex/io/_load_cache.py +71 -71
  242. scitex/io/_load_configs.py +2 -3
  243. scitex/io/_load_modules/_H5Explorer.py +6 -12
  244. scitex/io/_load_modules/_ZarrExplorer.py +3 -3
  245. scitex/io/_load_modules/_bibtex.py +62 -63
  246. scitex/io/_load_modules/_canvas.py +4 -9
  247. scitex/io/_load_modules/_catboost.py +7 -2
  248. scitex/io/_load_modules/_hdf5.py +2 -0
  249. scitex/io/_load_modules/_image.py +5 -1
  250. scitex/io/_load_modules/_matlab.py +3 -1
  251. scitex/io/_load_modules/_optuna.py +0 -1
  252. scitex/io/_load_modules/_pdf.py +38 -29
  253. scitex/io/_load_modules/_sqlite3.py +1 -0
  254. scitex/io/_load_modules/_txt.py +2 -0
  255. scitex/io/_load_modules/_xml.py +9 -9
  256. scitex/io/_load_modules/_zarr.py +12 -10
  257. scitex/io/_metadata.py +76 -37
  258. scitex/io/_qr_utils.py +18 -13
  259. scitex/io/_save.py +220 -63
  260. scitex/io/_save_modules/__init__.py +7 -2
  261. scitex/io/_save_modules/_bibtex.py +66 -61
  262. scitex/io/_save_modules/_canvas.py +5 -6
  263. scitex/io/_save_modules/_catboost.py +2 -2
  264. scitex/io/_save_modules/_csv.py +4 -4
  265. scitex/io/_save_modules/_excel.py +5 -9
  266. scitex/io/_save_modules/_hdf5.py +9 -21
  267. scitex/io/_save_modules/_html.py +5 -5
  268. scitex/io/_save_modules/_image.py +105 -8
  269. scitex/io/_save_modules/_joblib.py +2 -2
  270. scitex/io/_save_modules/_json.py +51 -6
  271. scitex/io/_save_modules/_listed_dfs_as_csv.py +2 -1
  272. scitex/io/_save_modules/_listed_scalars_as_csv.py +2 -1
  273. scitex/io/_save_modules/_matlab.py +2 -2
  274. scitex/io/_save_modules/_numpy.py +6 -8
  275. scitex/io/_save_modules/_pickle.py +4 -4
  276. scitex/io/_save_modules/_plotly.py +3 -3
  277. scitex/io/_save_modules/_tex.py +23 -25
  278. scitex/io/_save_modules/_text.py +2 -2
  279. scitex/io/_save_modules/_yaml.py +9 -9
  280. scitex/io/_save_modules/_zarr.py +15 -15
  281. scitex/io/utils/__init__.py +2 -1
  282. scitex/io/utils/h5_to_zarr.py +173 -155
  283. scitex/linalg/__init__.py +1 -1
  284. scitex/linalg/_geometric_median.py +4 -3
  285. scitex/logging/_Tee.py +5 -7
  286. scitex/logging/__init__.py +18 -19
  287. scitex/logging/_config.py +4 -1
  288. scitex/logging/_context.py +6 -5
  289. scitex/logging/_formatters.py +2 -3
  290. scitex/logging/_handlers.py +19 -20
  291. scitex/logging/_levels.py +9 -17
  292. scitex/logging/_logger.py +74 -15
  293. scitex/logging/_print_capture.py +17 -17
  294. scitex/nn/_BNet.py +1 -3
  295. scitex/nn/_Filters.py +6 -2
  296. scitex/nn/_ModulationIndex.py +3 -1
  297. scitex/nn/_PAC.py +3 -2
  298. scitex/nn/_PSD.py +0 -1
  299. scitex/nn/__init__.py +16 -3
  300. scitex/path/_clean.py +10 -8
  301. scitex/path/_find.py +1 -1
  302. scitex/path/_get_spath.py +1 -2
  303. scitex/path/_mk_spath.py +1 -1
  304. scitex/path/_symlink.py +5 -10
  305. scitex/pd/__init__.py +4 -1
  306. scitex/pd/_force_df.py +24 -24
  307. scitex/pd/_get_unique.py +1 -0
  308. scitex/pd/_merge_columns.py +1 -1
  309. scitex/pd/_round.py +11 -7
  310. scitex/pd/_to_xy.py +0 -1
  311. scitex/plt/REQUESTS.md +191 -0
  312. scitex/plt/__init__.py +185 -87
  313. scitex/plt/_subplots/_AxesWrapper.py +22 -6
  314. scitex/plt/_subplots/_AxisWrapper.py +100 -39
  315. scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +74 -52
  316. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +183 -73
  317. scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +61 -45
  318. scitex/plt/_subplots/_AxisWrapperMixins/_TrackingMixin.py +26 -14
  319. scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +80 -73
  320. scitex/plt/_subplots/_FigWrapper.py +93 -60
  321. scitex/plt/_subplots/_SubplotsWrapper.py +135 -68
  322. scitex/plt/_subplots/__init__.py +10 -0
  323. scitex/plt/_subplots/_export_as_csv.py +89 -47
  324. scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +1 -0
  325. scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +6 -4
  326. scitex/plt/_subplots/_export_as_csv_formatters/_format_bar.py +88 -38
  327. scitex/plt/_subplots/_export_as_csv_formatters/_format_barh.py +25 -31
  328. scitex/plt/_subplots/_export_as_csv_formatters/_format_boxplot.py +53 -23
  329. scitex/plt/_subplots/_export_as_csv_formatters/_format_contour.py +38 -25
  330. scitex/plt/_subplots/_export_as_csv_formatters/_format_contourf.py +17 -9
  331. scitex/plt/_subplots/_export_as_csv_formatters/_format_errorbar.py +70 -124
  332. scitex/plt/_subplots/_export_as_csv_formatters/_format_eventplot.py +12 -10
  333. scitex/plt/_subplots/_export_as_csv_formatters/_format_fill.py +31 -17
  334. scitex/plt/_subplots/_export_as_csv_formatters/_format_fill_between.py +33 -21
  335. scitex/plt/_subplots/_export_as_csv_formatters/_format_hexbin.py +14 -4
  336. scitex/plt/_subplots/_export_as_csv_formatters/_format_hist.py +43 -29
  337. scitex/plt/_subplots/_export_as_csv_formatters/_format_hist2d.py +14 -4
  338. scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow.py +27 -11
  339. scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow2d.py +7 -5
  340. scitex/plt/_subplots/_export_as_csv_formatters/_format_matshow.py +9 -7
  341. scitex/plt/_subplots/_export_as_csv_formatters/_format_pie.py +15 -6
  342. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot.py +85 -46
  343. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_box.py +52 -27
  344. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_imshow.py +1 -0
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  891. scitex/scholar/url_finder/translators/individual/sciencedirect.py +36 -17
  892. scitex/scholar/url_finder/translators/individual/semantics_visual_library.py +3 -1
  893. scitex/scholar/url_finder/translators/individual/silverchair.py +70 -52
  894. scitex/scholar/url_finder/translators/individual/sora.py +3 -1
  895. scitex/scholar/url_finder/translators/individual/springer.py +15 -11
  896. scitex/scholar/url_finder/translators/individual/ssrn.py +3 -3
  897. scitex/scholar/url_finder/translators/individual/stanford_encyclopedia_of_philosophy.py +3 -1
  898. scitex/scholar/url_finder/translators/individual/superlib.py +3 -1
  899. scitex/scholar/url_finder/translators/individual/treesearch.py +3 -1
  900. scitex/scholar/url_finder/translators/individual/university_of_chicago_press_books.py +3 -1
  901. scitex/scholar/url_finder/translators/individual/vlex.py +3 -1
  902. scitex/scholar/url_finder/translators/individual/web_of_science.py +3 -1
  903. scitex/scholar/url_finder/translators/individual/web_of_science_nextgen.py +3 -1
  904. scitex/scholar/url_finder/translators/individual/wiley.py +31 -25
  905. scitex/scholar/url_finder/translators/individual/wilson_center_digital_archive.py +3 -1
  906. scitex/scholar/utils/bibtex/_parse_bibtex.py +3 -3
  907. scitex/scholar/utils/cleanup/_cleanup_scholar_processes.py +5 -9
  908. scitex/scholar/utils/text/_TextNormalizer.py +249 -176
  909. scitex/scholar/utils/validation/DOIValidator.py +31 -28
  910. scitex/scholar/utils/validation/__init__.py +0 -0
  911. scitex/scholar/utils/validation/validate_library_dois.py +61 -57
  912. scitex/scholar/zotero/__init__.py +1 -1
  913. scitex/security/cli.py +7 -20
  914. scitex/security/github.py +45 -32
  915. scitex/session/__init__.py +8 -9
  916. scitex/session/_decorator.py +49 -42
  917. scitex/session/_lifecycle.py +39 -39
  918. scitex/session/_manager.py +24 -20
  919. scitex/sh/__init__.py +4 -3
  920. scitex/sh/_execute.py +10 -7
  921. scitex/sh/_security.py +3 -3
  922. scitex/sh/_types.py +2 -3
  923. scitex/stats/__init__.py +57 -6
  924. scitex/stats/_schema.py +42 -569
  925. scitex/stats/auto/__init__.py +188 -0
  926. scitex/stats/auto/_context.py +331 -0
  927. scitex/stats/auto/_formatting.py +679 -0
  928. scitex/stats/auto/_rules.py +901 -0
  929. scitex/stats/auto/_selector.py +554 -0
  930. scitex/stats/auto/_styles.py +721 -0
  931. scitex/stats/correct/__init__.py +4 -4
  932. scitex/stats/correct/_correct_bonferroni.py +43 -34
  933. scitex/stats/correct/_correct_fdr.py +14 -40
  934. scitex/stats/correct/_correct_fdr_.py +39 -46
  935. scitex/stats/correct/_correct_holm.py +14 -32
  936. scitex/stats/correct/_correct_sidak.py +36 -21
  937. scitex/stats/descriptive/_circular.py +20 -21
  938. scitex/stats/descriptive/_describe.py +19 -5
  939. scitex/stats/descriptive/_nan.py +5 -7
  940. scitex/stats/descriptive/_real.py +4 -3
  941. scitex/stats/effect_sizes/__init__.py +10 -11
  942. scitex/stats/effect_sizes/_cliffs_delta.py +35 -32
  943. scitex/stats/effect_sizes/_cohens_d.py +30 -31
  944. scitex/stats/effect_sizes/_epsilon_squared.py +19 -22
  945. scitex/stats/effect_sizes/_eta_squared.py +23 -27
  946. scitex/stats/effect_sizes/_prob_superiority.py +18 -21
  947. scitex/stats/posthoc/__init__.py +3 -3
  948. scitex/stats/posthoc/_dunnett.py +75 -55
  949. scitex/stats/posthoc/_games_howell.py +61 -43
  950. scitex/stats/posthoc/_tukey_hsd.py +42 -34
  951. scitex/stats/power/__init__.py +2 -2
  952. scitex/stats/power/_power.py +56 -56
  953. scitex/stats/tests/__init__.py +1 -1
  954. scitex/stats/tests/correlation/__init__.py +1 -1
  955. scitex/stats/tests/correlation/_test_pearson.py +28 -38
  956. scitex/stats/utils/__init__.py +14 -17
  957. scitex/stats/utils/_effect_size.py +85 -78
  958. scitex/stats/utils/_formatters.py +49 -43
  959. scitex/stats/utils/_normalizers.py +7 -14
  960. scitex/stats/utils/_power.py +56 -56
  961. scitex/str/__init__.py +1 -0
  962. scitex/str/_clean_path.py +3 -3
  963. scitex/str/_factor_out_digits.py +86 -58
  964. scitex/str/_format_plot_text.py +180 -111
  965. scitex/str/_latex.py +19 -19
  966. scitex/str/_latex_fallback.py +9 -10
  967. scitex/str/_parse.py +3 -6
  968. scitex/str/_print_debug.py +13 -13
  969. scitex/str/_printc.py +2 -0
  970. scitex/str/_search.py +3 -3
  971. scitex/template/.legacy/_clone_project.py +9 -13
  972. scitex/template/__init__.py +10 -2
  973. scitex/template/_clone_project.py +7 -2
  974. scitex/template/_copy.py +1 -0
  975. scitex/template/_customize.py +3 -6
  976. scitex/template/_git_strategy.py +2 -3
  977. scitex/template/_rename.py +1 -0
  978. scitex/template/clone_pip_project.py +6 -7
  979. scitex/template/clone_research.py +7 -10
  980. scitex/template/clone_singularity.py +6 -7
  981. scitex/template/clone_writer_directory.py +6 -7
  982. scitex/tex/_preview.py +26 -11
  983. scitex/tex/_to_vec.py +10 -7
  984. scitex/torch/__init__.py +11 -1
  985. scitex/types/_ArrayLike.py +2 -0
  986. scitex/types/_is_listed_X.py +3 -3
  987. scitex/units.py +110 -77
  988. scitex/utils/_compress_hdf5.py +3 -3
  989. scitex/utils/_email.py +8 -4
  990. scitex/utils/_notify.py +14 -8
  991. scitex/utils/_search.py +6 -6
  992. scitex/utils/_verify_scitex_format.py +17 -42
  993. scitex/utils/_verify_scitex_format_v01.py +12 -34
  994. scitex/utils/template.py +4 -3
  995. scitex/vis/__init__.py +0 -0
  996. scitex/vis/backend/__init__.py +3 -3
  997. scitex/vis/backend/{export.py → _export.py} +1 -1
  998. scitex/vis/backend/{parser.py → _parser.py} +1 -3
  999. scitex/vis/backend/{render.py → _render.py} +1 -1
  1000. scitex/vis/canvas.py +15 -3
  1001. scitex/vis/editor/__init__.py +0 -0
  1002. scitex/vis/editor/_dearpygui_editor.py +450 -304
  1003. scitex/vis/editor/_defaults.py +114 -123
  1004. scitex/vis/editor/_edit.py +38 -26
  1005. scitex/vis/editor/_flask_editor.py +8 -8
  1006. scitex/vis/editor/_mpl_editor.py +63 -48
  1007. scitex/vis/editor/_qt_editor.py +210 -159
  1008. scitex/vis/editor/_tkinter_editor.py +146 -89
  1009. scitex/vis/editor/flask_editor/__init__.py +10 -10
  1010. scitex/vis/editor/flask_editor/_bbox.py +529 -0
  1011. scitex/vis/editor/flask_editor/{core.py → _core.py} +45 -29
  1012. scitex/vis/editor/flask_editor/_plotter.py +567 -0
  1013. scitex/vis/editor/flask_editor/_renderer.py +393 -0
  1014. scitex/vis/editor/flask_editor/{utils.py → _utils.py} +13 -14
  1015. scitex/vis/editor/flask_editor/templates/__init__.py +5 -5
  1016. scitex/vis/editor/flask_editor/templates/{html.py → _html.py} +234 -16
  1017. scitex/vis/editor/flask_editor/templates/_scripts.py +1261 -0
  1018. scitex/vis/editor/flask_editor/templates/{styles.py → _styles.py} +192 -2
  1019. scitex/vis/io/__init__.py +5 -5
  1020. scitex/vis/io/{canvas.py → _canvas.py} +8 -4
  1021. scitex/vis/io/{data.py → _data.py} +13 -9
  1022. scitex/vis/io/{directory.py → _directory.py} +7 -4
  1023. scitex/vis/io/{export.py → _export.py} +15 -12
  1024. scitex/vis/io/{load.py → _load.py} +1 -1
  1025. scitex/vis/io/{panel.py → _panel.py} +21 -13
  1026. scitex/vis/io/{save.py → _save.py} +0 -0
  1027. scitex/vis/model/__init__.py +7 -7
  1028. scitex/vis/model/{annotations.py → _annotations.py} +2 -4
  1029. scitex/vis/model/{axes.py → _axes.py} +1 -1
  1030. scitex/vis/model/{figure.py → _figure.py} +0 -0
  1031. scitex/vis/model/{guides.py → _guides.py} +1 -1
  1032. scitex/vis/model/{plot.py → _plot.py} +2 -4
  1033. scitex/vis/model/{plot_types.py → _plot_types.py} +0 -0
  1034. scitex/vis/model/{styles.py → _styles.py} +0 -0
  1035. scitex/vis/utils/__init__.py +2 -2
  1036. scitex/vis/utils/{defaults.py → _defaults.py} +1 -2
  1037. scitex/vis/utils/{validate.py → _validate.py} +3 -9
  1038. scitex/web/__init__.py +7 -1
  1039. scitex/web/_scraping.py +54 -38
  1040. scitex/web/_search_pubmed.py +30 -14
  1041. scitex/writer/.legacy/Writer_v01-refactored.py +4 -4
  1042. scitex/writer/.legacy/_compile.py +18 -28
  1043. scitex/writer/Writer.py +8 -21
  1044. scitex/writer/__init__.py +11 -11
  1045. scitex/writer/_clone_writer_project.py +2 -6
  1046. scitex/writer/_compile/__init__.py +1 -0
  1047. scitex/writer/_compile/_parser.py +1 -0
  1048. scitex/writer/_compile/_runner.py +35 -38
  1049. scitex/writer/_compile/_validator.py +1 -0
  1050. scitex/writer/_compile/manuscript.py +1 -0
  1051. scitex/writer/_compile/revision.py +1 -0
  1052. scitex/writer/_compile/supplementary.py +1 -0
  1053. scitex/writer/_compile_async.py +5 -12
  1054. scitex/writer/_project/__init__.py +1 -0
  1055. scitex/writer/_project/_create.py +10 -25
  1056. scitex/writer/_project/_trees.py +4 -9
  1057. scitex/writer/_project/_validate.py +2 -3
  1058. scitex/writer/_validate_tree_structures.py +7 -18
  1059. scitex/writer/dataclasses/__init__.py +8 -10
  1060. scitex/writer/dataclasses/config/_CONSTANTS.py +2 -3
  1061. scitex/writer/dataclasses/config/_WriterConfig.py +4 -9
  1062. scitex/writer/dataclasses/contents/_ManuscriptContents.py +14 -25
  1063. scitex/writer/dataclasses/contents/_RevisionContents.py +21 -16
  1064. scitex/writer/dataclasses/contents/_SupplementaryContents.py +21 -24
  1065. scitex/writer/dataclasses/core/_Document.py +2 -3
  1066. scitex/writer/dataclasses/core/_DocumentSection.py +8 -23
  1067. scitex/writer/dataclasses/results/_CompilationResult.py +2 -3
  1068. scitex/writer/dataclasses/results/_LaTeXIssue.py +3 -6
  1069. scitex/writer/dataclasses/results/_SaveSectionsResponse.py +20 -9
  1070. scitex/writer/dataclasses/results/_SectionReadResponse.py +24 -10
  1071. scitex/writer/dataclasses/tree/_ConfigTree.py +7 -4
  1072. scitex/writer/dataclasses/tree/_ManuscriptTree.py +10 -13
  1073. scitex/writer/dataclasses/tree/_RevisionTree.py +16 -17
  1074. scitex/writer/dataclasses/tree/_ScriptsTree.py +10 -5
  1075. scitex/writer/dataclasses/tree/_SharedTree.py +10 -13
  1076. scitex/writer/dataclasses/tree/_SupplementaryTree.py +15 -14
  1077. scitex/writer/utils/.legacy_git_retry.py +3 -8
  1078. scitex/writer/utils/_parse_latex_logs.py +2 -3
  1079. scitex/writer/utils/_parse_script_args.py +20 -23
  1080. scitex/writer/utils/_watch.py +5 -5
  1081. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/METADATA +4 -10
  1082. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/RECORD +1071 -975
  1083. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +0 -583
  1084. scitex/plt/_subplots/_export_as_csv_formatters.py +0 -112
  1085. scitex/vis/editor/flask_editor/bbox.py +0 -216
  1086. scitex/vis/editor/flask_editor/plotter.py +0 -130
  1087. scitex/vis/editor/flask_editor/renderer.py +0 -184
  1088. scitex/vis/editor/flask_editor/templates/scripts.py +0 -614
  1089. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/WHEEL +0 -0
  1090. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/entry_points.txt +0 -0
  1091. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/licenses/LICENSE +0 -0
@@ -0,0 +1,529 @@
1
+ #!/usr/bin/env python3
2
+ # -*- coding: utf-8 -*-
3
+ # File: ./src/scitex/vis/editor/flask_editor/bbox.py
4
+ """Bounding box extraction for figure elements."""
5
+
6
+ from typing import Dict, Any
7
+
8
+
9
+ def extract_bboxes(
10
+ fig, ax, renderer, img_width: int, img_height: int
11
+ ) -> Dict[str, Any]:
12
+ """Extract bounding boxes for all figure elements (single-axis)."""
13
+ from matplotlib.transforms import Bbox
14
+
15
+ # Get figure tight bbox in inches
16
+ fig_bbox = fig.get_tightbbox(renderer)
17
+ tight_x0 = fig_bbox.x0
18
+ tight_y0 = fig_bbox.y0
19
+ tight_width = fig_bbox.width
20
+ tight_height = fig_bbox.height
21
+
22
+ # bbox_inches='tight' adds pad_inches (default 0.1) around the tight bbox
23
+ pad_inches = 0.1
24
+ saved_width_inches = tight_width + 2 * pad_inches
25
+ saved_height_inches = tight_height + 2 * pad_inches
26
+
27
+ # Scale factors for converting inches to pixels
28
+ scale_x = img_width / saved_width_inches
29
+ scale_y = img_height / saved_height_inches
30
+
31
+ bboxes = {}
32
+
33
+ def get_element_bbox(element, name):
34
+ """Get element bbox in image pixel coordinates."""
35
+ try:
36
+ bbox = element.get_window_extent(renderer)
37
+
38
+ elem_x0_inches = bbox.x0 / fig.dpi
39
+ elem_x1_inches = bbox.x1 / fig.dpi
40
+ elem_y0_inches = bbox.y0 / fig.dpi
41
+ elem_y1_inches = bbox.y1 / fig.dpi
42
+
43
+ x0_rel = elem_x0_inches - tight_x0 + pad_inches
44
+ x1_rel = elem_x1_inches - tight_x0 + pad_inches
45
+ y0_rel = saved_height_inches - (elem_y1_inches - tight_y0 + pad_inches)
46
+ y1_rel = saved_height_inches - (elem_y0_inches - tight_y0 + pad_inches)
47
+
48
+ bboxes[name] = {
49
+ "x0": max(0, int(x0_rel * scale_x)),
50
+ "y0": max(0, int(y0_rel * scale_y)),
51
+ "x1": min(img_width, int(x1_rel * scale_x)),
52
+ "y1": min(img_height, int(y1_rel * scale_y)),
53
+ "label": name.replace("_", " ").title(),
54
+ }
55
+ except Exception as e:
56
+ print(f"Error getting bbox for {name}: {e}")
57
+
58
+ def bbox_to_img_coords(bbox):
59
+ """Convert matplotlib bbox to image pixel coordinates."""
60
+ x0_inches = bbox.x0 / fig.dpi
61
+ y0_inches = bbox.y0 / fig.dpi
62
+ x1_inches = bbox.x1 / fig.dpi
63
+ y1_inches = bbox.y1 / fig.dpi
64
+ x0_rel = x0_inches - tight_x0 + pad_inches
65
+ y0_rel = y0_inches - tight_y0 + pad_inches
66
+ x1_rel = x1_inches - tight_x0 + pad_inches
67
+ y1_rel = y1_inches - tight_y0 + pad_inches
68
+ return {
69
+ "x0": int(x0_rel * scale_x),
70
+ "y0": int((saved_height_inches - y1_rel) * scale_y),
71
+ "x1": int(x1_rel * scale_x),
72
+ "y1": int((saved_height_inches - y0_rel) * scale_y),
73
+ }
74
+
75
+ # Get bboxes for title, labels
76
+ if ax.title.get_text():
77
+ get_element_bbox(ax.title, "title")
78
+ if ax.xaxis.label.get_text():
79
+ get_element_bbox(ax.xaxis.label, "xlabel")
80
+ if ax.yaxis.label.get_text():
81
+ get_element_bbox(ax.yaxis.label, "ylabel")
82
+
83
+ # Get axis bboxes
84
+ _extract_axis_bboxes(ax, renderer, bboxes, bbox_to_img_coords, Bbox)
85
+
86
+ # Get legend bbox
87
+ legend = ax.get_legend()
88
+ if legend:
89
+ get_element_bbox(legend, "legend")
90
+
91
+ # Get trace (line) bboxes
92
+ _extract_trace_bboxes(
93
+ ax,
94
+ fig,
95
+ renderer,
96
+ bboxes,
97
+ get_element_bbox,
98
+ tight_x0,
99
+ tight_y0,
100
+ saved_height_inches,
101
+ scale_x,
102
+ scale_y,
103
+ pad_inches,
104
+ )
105
+
106
+ return bboxes
107
+
108
+
109
+ def extract_bboxes_multi(
110
+ fig, axes_map: Dict[str, Any], renderer, img_width: int, img_height: int
111
+ ) -> Dict[str, Any]:
112
+ """Extract bounding boxes for all elements in a multi-axis figure.
113
+
114
+ Args:
115
+ fig: Matplotlib figure
116
+ axes_map: Dict mapping axis IDs (e.g., 'ax_00') to matplotlib Axes objects
117
+ renderer: Matplotlib renderer
118
+ img_width: Image width in pixels
119
+ img_height: Image height in pixels
120
+
121
+ Returns:
122
+ Dict with bboxes keyed by "{ax_id}_{element_type}" (e.g., "ax_00_xlabel")
123
+ """
124
+ from matplotlib.transforms import Bbox
125
+
126
+ # Get figure tight bbox in inches
127
+ fig_bbox = fig.get_tightbbox(renderer)
128
+ tight_x0 = fig_bbox.x0
129
+ tight_y0 = fig_bbox.y0
130
+ tight_width = fig_bbox.width
131
+ tight_height = fig_bbox.height
132
+
133
+ # bbox_inches='tight' adds pad_inches (default 0.1) around the tight bbox
134
+ pad_inches = 0.1
135
+ saved_width_inches = tight_width + 2 * pad_inches
136
+ saved_height_inches = tight_height + 2 * pad_inches
137
+
138
+ # Scale factors for converting inches to pixels
139
+ scale_x = img_width / saved_width_inches
140
+ scale_y = img_height / saved_height_inches
141
+
142
+ bboxes = {}
143
+
144
+ def get_element_bbox(element, name, ax_id, current_ax=None):
145
+ """Get element bbox in image pixel coordinates."""
146
+ import numpy as np
147
+ full_name = f"{ax_id}_{name}"
148
+ try:
149
+ bbox = element.get_window_extent(renderer)
150
+
151
+ # Check for invalid bbox (infinity or NaN)
152
+ if not (np.isfinite(bbox.x0) and np.isfinite(bbox.x1) and
153
+ np.isfinite(bbox.y0) and np.isfinite(bbox.y1)):
154
+ # Try to get bbox from data for scatter/collection elements
155
+ if hasattr(element, 'get_offsets') and current_ax is not None:
156
+ offsets = element.get_offsets()
157
+ if len(offsets) > 0 and np.isfinite(offsets).all():
158
+ # Use axis transform to get display coordinates
159
+ display_coords = current_ax.transData.transform(offsets)
160
+ x0 = display_coords[:, 0].min()
161
+ x1 = display_coords[:, 0].max()
162
+ y0 = display_coords[:, 1].min()
163
+ y1 = display_coords[:, 1].max()
164
+ if np.isfinite([x0, x1, y0, y1]).all():
165
+ from matplotlib.transforms import Bbox
166
+ bbox = Bbox.from_extents(x0, y0, x1, y1)
167
+ else:
168
+ return # Skip this element
169
+ else:
170
+ return # Skip this element
171
+ else:
172
+ return # Skip this element
173
+
174
+ elem_x0_inches = bbox.x0 / fig.dpi
175
+ elem_x1_inches = bbox.x1 / fig.dpi
176
+ elem_y0_inches = bbox.y0 / fig.dpi
177
+ elem_y1_inches = bbox.y1 / fig.dpi
178
+
179
+ x0_rel = elem_x0_inches - tight_x0 + pad_inches
180
+ x1_rel = elem_x1_inches - tight_x0 + pad_inches
181
+ y0_rel = saved_height_inches - (elem_y1_inches - tight_y0 + pad_inches)
182
+ y1_rel = saved_height_inches - (elem_y0_inches - tight_y0 + pad_inches)
183
+
184
+ # Clamp values to avoid overflow
185
+ x0_px = max(0, min(img_width, int(x0_rel * scale_x)))
186
+ y0_px = max(0, min(img_height, int(y0_rel * scale_y)))
187
+ x1_px = max(0, min(img_width, int(x1_rel * scale_x)))
188
+ y1_px = max(0, min(img_height, int(y1_rel * scale_y)))
189
+
190
+ bboxes[full_name] = {
191
+ "x0": x0_px,
192
+ "y0": y0_px,
193
+ "x1": x1_px,
194
+ "y1": y1_px,
195
+ "label": f"{ax_id}: {name.replace('_', ' ').title()}",
196
+ "ax_id": ax_id,
197
+ }
198
+ except Exception as e:
199
+ print(f"Error getting bbox for {full_name}: {e}")
200
+
201
+ def bbox_to_img_coords(bbox):
202
+ """Convert matplotlib bbox to image pixel coordinates."""
203
+ x0_inches = bbox.x0 / fig.dpi
204
+ y0_inches = bbox.y0 / fig.dpi
205
+ x1_inches = bbox.x1 / fig.dpi
206
+ y1_inches = bbox.y1 / fig.dpi
207
+ x0_rel = x0_inches - tight_x0 + pad_inches
208
+ y0_rel = y0_inches - tight_y0 + pad_inches
209
+ x1_rel = x1_inches - tight_x0 + pad_inches
210
+ y1_rel = y1_inches - tight_y0 + pad_inches
211
+ return {
212
+ "x0": int(x0_rel * scale_x),
213
+ "y0": int((saved_height_inches - y1_rel) * scale_y),
214
+ "x1": int(x1_rel * scale_x),
215
+ "y1": int((saved_height_inches - y0_rel) * scale_y),
216
+ }
217
+
218
+ # Extract bboxes for each axis
219
+ for ax_id, ax in axes_map.items():
220
+ # Get axes bounding box (the entire panel area)
221
+ try:
222
+ ax_bbox = ax.get_window_extent(renderer)
223
+ coords = bbox_to_img_coords(ax_bbox)
224
+ bboxes[f"{ax_id}_panel"] = {
225
+ **coords,
226
+ "label": f"Panel {ax_id}",
227
+ "ax_id": ax_id,
228
+ "is_panel": True,
229
+ }
230
+ except Exception as e:
231
+ print(f"Error getting panel bbox for {ax_id}: {e}")
232
+
233
+ # Get bboxes for title, labels
234
+ if ax.title.get_text():
235
+ get_element_bbox(ax.title, "title", ax_id, ax)
236
+ if ax.xaxis.label.get_text():
237
+ get_element_bbox(ax.xaxis.label, "xlabel", ax_id, ax)
238
+ if ax.yaxis.label.get_text():
239
+ get_element_bbox(ax.yaxis.label, "ylabel", ax_id, ax)
240
+
241
+ # Get legend bbox
242
+ legend = ax.get_legend()
243
+ if legend:
244
+ get_element_bbox(legend, "legend", ax_id, ax)
245
+
246
+ # Get trace (line) bboxes
247
+ _extract_trace_bboxes_for_axis(
248
+ ax,
249
+ ax_id,
250
+ fig,
251
+ renderer,
252
+ bboxes,
253
+ get_element_bbox,
254
+ tight_x0,
255
+ tight_y0,
256
+ saved_height_inches,
257
+ scale_x,
258
+ scale_y,
259
+ pad_inches,
260
+ )
261
+
262
+ return bboxes
263
+
264
+
265
+ def _extract_trace_bboxes_for_axis(
266
+ ax,
267
+ ax_id,
268
+ fig,
269
+ renderer,
270
+ bboxes,
271
+ get_element_bbox,
272
+ tight_x0,
273
+ tight_y0,
274
+ saved_height_inches,
275
+ scale_x,
276
+ scale_y,
277
+ pad_inches,
278
+ ):
279
+ """Extract bboxes for all data elements in a specific axis.
280
+
281
+ Handles:
282
+ - Lines (plot, errorbar lines)
283
+ - Scatter points (PathCollection)
284
+ - Fill areas (PolyCollection from fill_between)
285
+ - Bars (Rectangle patches)
286
+ """
287
+ import numpy as np
288
+
289
+ def coords_to_img_points(data_coords):
290
+ """Convert data coordinates to image pixel coordinates."""
291
+ if len(data_coords) == 0:
292
+ return []
293
+ transform = ax.transData
294
+ points_display = transform.transform(data_coords)
295
+ points_img = []
296
+ for px, py in points_display:
297
+ # Skip invalid points (NaN, infinity)
298
+ if not np.isfinite(px) or not np.isfinite(py):
299
+ continue
300
+ px_inches = px / fig.dpi
301
+ py_inches = py / fig.dpi
302
+ x_rel = px_inches - tight_x0 + pad_inches
303
+ y_rel = saved_height_inches - (py_inches - tight_y0 + pad_inches)
304
+ # Clamp to reasonable bounds to avoid overflow
305
+ x_img = max(-10000, min(10000, int(x_rel * scale_x)))
306
+ y_img = max(-10000, min(10000, int(y_rel * scale_y)))
307
+ points_img.append([x_img, y_img])
308
+ # Downsample if too many
309
+ if len(points_img) > 100:
310
+ step = len(points_img) // 100
311
+ points_img = points_img[::step]
312
+ return points_img
313
+
314
+ # 1. Extract lines (plot, errorbar lines, etc.)
315
+ line_idx = 0
316
+ for line in ax.get_lines():
317
+ try:
318
+ label = line.get_label()
319
+ if label.startswith("_"):
320
+ continue
321
+
322
+ trace_name = f"trace_{line_idx}"
323
+ full_name = f"{ax_id}_{trace_name}"
324
+ get_element_bbox(line, trace_name, ax_id, ax)
325
+
326
+ if full_name in bboxes:
327
+ bboxes[full_name]["label"] = f"{ax_id}: {label or f'Line {line_idx}'}"
328
+ bboxes[full_name]["trace_idx"] = line_idx
329
+ bboxes[full_name]["element_type"] = "line"
330
+
331
+ xdata, ydata = line.get_xdata(), line.get_ydata()
332
+ if len(xdata) > 0:
333
+ bboxes[full_name]["points"] = coords_to_img_points(
334
+ list(zip(xdata, ydata))
335
+ )
336
+ line_idx += 1
337
+ except Exception as e:
338
+ print(f"Error getting line bbox for {ax_id}: {e}")
339
+
340
+ # 2. Extract collections (scatter, fill_between, etc.)
341
+ coll_idx = 0
342
+ for coll in ax.collections:
343
+ try:
344
+ label = coll.get_label()
345
+ if label.startswith("_"):
346
+ # Still extract unlabeled collections but with generic name
347
+ label = None
348
+
349
+ coll_type = type(coll).__name__
350
+ if coll_type == "PathCollection":
351
+ # Scatter points
352
+ element_name = f"scatter_{coll_idx}"
353
+ full_name = f"{ax_id}_{element_name}"
354
+ get_element_bbox(coll, element_name, ax_id, ax)
355
+
356
+ if full_name in bboxes:
357
+ bboxes[full_name]["label"] = f"{ax_id}: {label or f'Scatter {coll_idx}'}"
358
+ bboxes[full_name]["element_type"] = "scatter"
359
+
360
+ # Get scatter point positions
361
+ offsets = coll.get_offsets()
362
+ if len(offsets) > 0:
363
+ bboxes[full_name]["points"] = coords_to_img_points(offsets)
364
+
365
+ elif coll_type == "PolyCollection":
366
+ # Fill areas (fill_between, etc.)
367
+ element_name = f"fill_{coll_idx}"
368
+ full_name = f"{ax_id}_{element_name}"
369
+ get_element_bbox(coll, element_name, ax_id, ax)
370
+
371
+ if full_name in bboxes:
372
+ bboxes[full_name]["label"] = f"{ax_id}: {label or f'Fill {coll_idx}'}"
373
+ bboxes[full_name]["element_type"] = "fill"
374
+
375
+ coll_idx += 1
376
+ except Exception as e:
377
+ print(f"Error getting collection bbox for {ax_id}: {e}")
378
+
379
+ # 3. Extract patches (bars, rectangles, etc.)
380
+ patch_idx = 0
381
+ for patch in ax.patches:
382
+ try:
383
+ label = patch.get_label()
384
+ patch_type = type(patch).__name__
385
+
386
+ if patch_type == "Rectangle":
387
+ # Bar chart bars
388
+ element_name = f"bar_{patch_idx}"
389
+ full_name = f"{ax_id}_{element_name}"
390
+ get_element_bbox(patch, element_name, ax_id, ax)
391
+
392
+ if full_name in bboxes:
393
+ bboxes[full_name]["label"] = f"{ax_id}: {label or f'Bar {patch_idx}'}"
394
+ bboxes[full_name]["element_type"] = "bar"
395
+
396
+ patch_idx += 1
397
+ except Exception as e:
398
+ print(f"Error getting patch bbox for {ax_id}: {e}")
399
+
400
+
401
+ def _extract_axis_bboxes(ax, renderer, bboxes, bbox_to_img_coords, Bbox):
402
+ """Extract bboxes for X and Y axis elements."""
403
+ try:
404
+ # X-axis: combine spine and tick labels into one bbox
405
+ x_axis_bboxes = []
406
+ for ticklabel in ax.xaxis.get_ticklabels():
407
+ if ticklabel.get_visible():
408
+ try:
409
+ tb = ticklabel.get_window_extent(renderer)
410
+ if tb.width > 0:
411
+ x_axis_bboxes.append(tb)
412
+ except Exception:
413
+ pass
414
+ for tick in ax.xaxis.get_major_ticks():
415
+ if tick.tick1line.get_visible():
416
+ try:
417
+ tb = tick.tick1line.get_window_extent(renderer)
418
+ if tb.width > 0 or tb.height > 0:
419
+ x_axis_bboxes.append(tb)
420
+ except Exception:
421
+ pass
422
+ spine_bbox = ax.spines["bottom"].get_window_extent(renderer)
423
+ if spine_bbox.width > 0:
424
+ if x_axis_bboxes:
425
+ tick_union = Bbox.union(x_axis_bboxes)
426
+ constrained_spine = Bbox.from_extents(
427
+ tick_union.x0, spine_bbox.y0, tick_union.x1, spine_bbox.y1
428
+ )
429
+ x_axis_bboxes.append(constrained_spine)
430
+ else:
431
+ x_axis_bboxes.append(spine_bbox)
432
+ if x_axis_bboxes:
433
+ combined = Bbox.union(x_axis_bboxes)
434
+ bboxes["xaxis_ticks"] = bbox_to_img_coords(combined)
435
+ bboxes["xaxis_ticks"]["label"] = "X Spine & Ticks"
436
+
437
+ # Y-axis: combine spine and tick labels into one bbox
438
+ y_axis_bboxes = []
439
+ for ticklabel in ax.yaxis.get_ticklabels():
440
+ if ticklabel.get_visible():
441
+ try:
442
+ tb = ticklabel.get_window_extent(renderer)
443
+ if tb.width > 0:
444
+ y_axis_bboxes.append(tb)
445
+ except Exception:
446
+ pass
447
+ for tick in ax.yaxis.get_major_ticks():
448
+ if tick.tick1line.get_visible():
449
+ try:
450
+ tb = tick.tick1line.get_window_extent(renderer)
451
+ if tb.width > 0 or tb.height > 0:
452
+ y_axis_bboxes.append(tb)
453
+ except Exception:
454
+ pass
455
+ spine_bbox = ax.spines["left"].get_window_extent(renderer)
456
+ if spine_bbox.height > 0:
457
+ if y_axis_bboxes:
458
+ tick_union = Bbox.union(y_axis_bboxes)
459
+ constrained_spine = Bbox.from_extents(
460
+ spine_bbox.x0, tick_union.y0, spine_bbox.x1, tick_union.y1
461
+ )
462
+ y_axis_bboxes.append(constrained_spine)
463
+ else:
464
+ y_axis_bboxes.append(spine_bbox)
465
+ if y_axis_bboxes:
466
+ combined = Bbox.union(y_axis_bboxes)
467
+ padded = Bbox.from_extents(
468
+ combined.x0 - 10, combined.y0 - 5, combined.x1 + 5, combined.y1 + 5
469
+ )
470
+ bboxes["yaxis_ticks"] = bbox_to_img_coords(padded)
471
+ bboxes["yaxis_ticks"]["label"] = "Y Spine & Ticks"
472
+
473
+ except Exception as e:
474
+ print(f"Error getting axis bboxes: {e}")
475
+
476
+
477
+ def _extract_trace_bboxes(
478
+ ax,
479
+ fig,
480
+ renderer,
481
+ bboxes,
482
+ get_element_bbox,
483
+ tight_x0,
484
+ tight_y0,
485
+ saved_height_inches,
486
+ scale_x,
487
+ scale_y,
488
+ pad_inches,
489
+ ):
490
+ """Extract bboxes for trace (line) elements with proximity detection points."""
491
+ for idx, line in enumerate(ax.get_lines()):
492
+ try:
493
+ label = line.get_label()
494
+ if label.startswith("_"):
495
+ continue
496
+ get_element_bbox(line, f"trace_{idx}")
497
+ if f"trace_{idx}" in bboxes:
498
+ bboxes[f"trace_{idx}"]["label"] = label or f"Trace {idx}"
499
+ bboxes[f"trace_{idx}"]["trace_idx"] = idx
500
+
501
+ # Get line data points in pixel coordinates for proximity detection
502
+ xdata, ydata = line.get_xdata(), line.get_ydata()
503
+ if len(xdata) > 0:
504
+ transform = ax.transData
505
+ points_display = transform.transform(list(zip(xdata, ydata)))
506
+
507
+ points_img = []
508
+ for px, py in points_display:
509
+ px_inches = px / fig.dpi
510
+ py_inches = py / fig.dpi
511
+ x_rel = px_inches - tight_x0 + pad_inches
512
+ y_rel = saved_height_inches - (
513
+ py_inches - tight_y0 + pad_inches
514
+ )
515
+ x_img = int(x_rel * scale_x)
516
+ y_img = int(y_rel * scale_y)
517
+ points_img.append([x_img, y_img])
518
+
519
+ # Downsample points if too many
520
+ if len(points_img) > 100:
521
+ step = len(points_img) // 100
522
+ points_img = points_img[::step]
523
+
524
+ bboxes[f"trace_{idx}"]["points"] = points_img
525
+ except Exception as e:
526
+ print(f"Error getting trace bbox: {e}")
527
+
528
+
529
+ # EOF
@@ -10,8 +10,8 @@ import json
10
10
  import threading
11
11
  import webbrowser
12
12
 
13
- from .utils import find_available_port, kill_process_on_port, check_port_available
14
- from .renderer import render_preview_with_bboxes
13
+ from ._utils import find_available_port, kill_process_on_port, check_port_available
14
+ from ._renderer import render_preview_with_bboxes
15
15
  from .templates import build_html_template
16
16
 
17
17
 
@@ -47,6 +47,7 @@ class WebEditor:
47
47
 
48
48
  # Get SciTeX defaults and merge with metadata
49
49
  from .._defaults import get_scitex_defaults, extract_defaults_from_metadata
50
+
50
51
  self.scitex_defaults = get_scitex_defaults()
51
52
  self.metadata_defaults = extract_defaults_from_metadata(metadata)
52
53
 
@@ -64,13 +65,16 @@ class WebEditor:
64
65
  try:
65
66
  from flask import Flask, render_template_string, request, jsonify
66
67
  except ImportError:
67
- raise ImportError("Flask is required for web editor. Install: pip install flask")
68
+ raise ImportError(
69
+ "Flask is required for web editor. Install: pip install flask"
70
+ )
68
71
 
69
72
  # Handle port conflicts
70
73
  if not check_port_available(self._requested_port):
71
74
  print(f"Port {self._requested_port} is in use. Attempting to free it...")
72
75
  if kill_process_on_port(self._requested_port):
73
76
  import time
77
+
74
78
  time.sleep(0.5)
75
79
  self.port = self._requested_port
76
80
  print(f"Successfully freed port {self.port}")
@@ -82,71 +86,83 @@ class WebEditor:
82
86
 
83
87
  app = Flask(__name__)
84
88
  editor = self
85
- html_template = build_html_template()
86
89
 
87
- @app.route('/')
90
+ @app.route("/")
88
91
  def index():
92
+ # Rebuild template each time for hot reload support
93
+ html_template = build_html_template()
89
94
  return render_template_string(
90
95
  html_template,
91
96
  filename=str(editor.json_path.resolve()),
92
- overrides=json.dumps(editor.current_overrides)
97
+ overrides=json.dumps(editor.current_overrides),
93
98
  )
94
99
 
95
- @app.route('/preview')
100
+ @app.route("/preview")
96
101
  def preview():
97
102
  """Generate figure preview as base64 PNG with element bboxes."""
98
103
  img_data, bboxes, img_size = render_preview_with_bboxes(
99
- editor.csv_data, editor.current_overrides
104
+ editor.csv_data, editor.current_overrides,
105
+ metadata=editor.metadata
100
106
  )
101
- return jsonify({'image': img_data, 'bboxes': bboxes, 'img_size': img_size})
107
+ return jsonify({"image": img_data, "bboxes": bboxes, "img_size": img_size})
102
108
 
103
- @app.route('/update', methods=['POST'])
109
+ @app.route("/update", methods=["POST"])
104
110
  def update():
105
111
  """Update overrides and return new preview."""
106
112
  data = request.json
107
- editor.current_overrides.update(data.get('overrides', {}))
113
+ editor.current_overrides.update(data.get("overrides", {}))
108
114
  editor._user_modified = True
109
115
  img_data, bboxes, img_size = render_preview_with_bboxes(
110
- editor.csv_data, editor.current_overrides
116
+ editor.csv_data, editor.current_overrides,
117
+ metadata=editor.metadata
118
+ )
119
+ return jsonify(
120
+ {
121
+ "image": img_data,
122
+ "bboxes": bboxes,
123
+ "img_size": img_size,
124
+ "status": "updated",
125
+ }
111
126
  )
112
- return jsonify({
113
- 'image': img_data,
114
- 'bboxes': bboxes,
115
- 'img_size': img_size,
116
- 'status': 'updated'
117
- })
118
-
119
- @app.route('/save', methods=['POST'])
127
+
128
+ @app.route("/save", methods=["POST"])
120
129
  def save():
121
130
  """Save to .manual.json."""
122
131
  from .._edit import save_manual_overrides
132
+
123
133
  try:
124
- manual_path = save_manual_overrides(editor.json_path, editor.current_overrides)
125
- return jsonify({'status': 'saved', 'path': str(manual_path)})
134
+ manual_path = save_manual_overrides(
135
+ editor.json_path, editor.current_overrides
136
+ )
137
+ return jsonify({"status": "saved", "path": str(manual_path)})
126
138
  except Exception as e:
127
- return jsonify({'status': 'error', 'message': str(e)}), 500
139
+ return jsonify({"status": "error", "message": str(e)}), 500
128
140
 
129
- @app.route('/shutdown', methods=['POST'])
141
+ @app.route("/shutdown", methods=["POST"])
130
142
  def shutdown():
131
143
  """Shutdown the server."""
132
- func = request.environ.get('werkzeug.server.shutdown')
144
+ func = request.environ.get("werkzeug.server.shutdown")
133
145
  if func is None:
134
- raise RuntimeError('Not running with Werkzeug Server')
146
+ raise RuntimeError("Not running with Werkzeug Server")
135
147
  func()
136
- return jsonify({'status': 'shutdown'})
148
+ return jsonify({"status": "shutdown"})
137
149
 
138
150
  # Open browser after short delay
139
151
  def open_browser():
140
152
  import time
153
+
141
154
  time.sleep(0.5)
142
- webbrowser.open(f'http://127.0.0.1:{self.port}')
155
+ webbrowser.open(f"http://127.0.0.1:{self.port}")
143
156
 
144
157
  threading.Thread(target=open_browser, daemon=True).start()
145
158
 
146
159
  print(f"Starting SciTeX Editor at http://127.0.0.1:{self.port}")
147
160
  print("Press Ctrl+C to stop")
148
161
 
149
- app.run(host='127.0.0.1', port=self.port, debug=False, use_reloader=False)
162
+ # Note: use_reloader=False because the reloader re-runs the entire script
163
+ # which causes infinite loops when the demo generates figures
164
+ # Templates are rebuilt on each page refresh anyway
165
+ app.run(host="127.0.0.1", port=self.port, debug=False, use_reloader=False)
150
166
 
151
167
 
152
168
  # EOF