scitex 2.5.0__py3-none-any.whl → 2.7.3__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 (1179) hide show
  1. scitex/__init__.py +25 -10
  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/audio/README.md +52 -0
  66. scitex/audio/__init__.py +384 -0
  67. scitex/audio/__main__.py +129 -0
  68. scitex/audio/_tts.py +334 -0
  69. scitex/audio/engines/__init__.py +44 -0
  70. scitex/audio/engines/base.py +275 -0
  71. scitex/audio/engines/elevenlabs_engine.py +143 -0
  72. scitex/audio/engines/gtts_engine.py +162 -0
  73. scitex/audio/engines/pyttsx3_engine.py +131 -0
  74. scitex/audio/mcp_server.py +757 -0
  75. scitex/benchmark/__init__.py +15 -25
  76. scitex/benchmark/benchmark.py +124 -117
  77. scitex/benchmark/monitor.py +117 -107
  78. scitex/benchmark/profiler.py +61 -58
  79. scitex/bridge/__init__.py +110 -0
  80. scitex/bridge/_helpers.py +149 -0
  81. scitex/bridge/_plt_vis.py +529 -0
  82. scitex/bridge/_protocol.py +283 -0
  83. scitex/bridge/_stats_plt.py +261 -0
  84. scitex/bridge/_stats_vis.py +265 -0
  85. scitex/browser/__init__.py +0 -2
  86. scitex/browser/auth/__init__.py +0 -0
  87. scitex/browser/auth/google.py +16 -11
  88. scitex/browser/automation/CookieHandler.py +2 -3
  89. scitex/browser/collaboration/__init__.py +3 -0
  90. scitex/browser/collaboration/auth_helpers.py +3 -1
  91. scitex/browser/collaboration/collaborative_agent.py +2 -0
  92. scitex/browser/collaboration/interactive_panel.py +2 -2
  93. scitex/browser/collaboration/shared_session.py +20 -11
  94. scitex/browser/collaboration/standard_interactions.py +1 -0
  95. scitex/browser/core/BrowserMixin.py +12 -30
  96. scitex/browser/core/ChromeProfileManager.py +9 -24
  97. scitex/browser/debugging/_browser_logger.py +15 -25
  98. scitex/browser/debugging/_failure_capture.py +9 -2
  99. scitex/browser/debugging/_highlight_element.py +15 -6
  100. scitex/browser/debugging/_show_grid.py +5 -6
  101. scitex/browser/debugging/_sync_session.py +4 -3
  102. scitex/browser/debugging/_test_monitor.py +14 -5
  103. scitex/browser/debugging/_visual_cursor.py +46 -35
  104. scitex/browser/interaction/click_center.py +4 -3
  105. scitex/browser/interaction/click_with_fallbacks.py +7 -10
  106. scitex/browser/interaction/close_popups.py +79 -66
  107. scitex/browser/interaction/fill_with_fallbacks.py +8 -8
  108. scitex/browser/pdf/__init__.py +3 -1
  109. scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +11 -10
  110. scitex/browser/pdf/detect_chrome_pdf_viewer.py +3 -6
  111. scitex/browser/remote/CaptchaHandler.py +109 -96
  112. scitex/browser/remote/ZenRowsAPIClient.py +91 -97
  113. scitex/browser/remote/ZenRowsBrowserManager.py +138 -112
  114. scitex/browser/stealth/HumanBehavior.py +4 -9
  115. scitex/browser/stealth/StealthManager.py +11 -26
  116. scitex/capture/__init__.py +17 -17
  117. scitex/capture/__main__.py +2 -3
  118. scitex/capture/capture.py +23 -51
  119. scitex/capture/cli.py +14 -39
  120. scitex/capture/gif.py +5 -9
  121. scitex/capture/mcp_server.py +7 -20
  122. scitex/capture/session.py +4 -3
  123. scitex/capture/utils.py +18 -53
  124. scitex/cli/__init__.py +1 -1
  125. scitex/cli/cloud.py +158 -116
  126. scitex/cli/config.py +224 -0
  127. scitex/cli/main.py +41 -40
  128. scitex/cli/scholar.py +60 -27
  129. scitex/cli/security.py +14 -20
  130. scitex/cli/web.py +87 -90
  131. scitex/cli/writer.py +51 -45
  132. scitex/cloud/__init__.py +14 -11
  133. scitex/cloud/_matplotlib_hook.py +6 -6
  134. scitex/config/README.md +313 -0
  135. scitex/config/{PriorityConfig.py → _PriorityConfig.py} +114 -17
  136. scitex/config/_ScitexConfig.py +319 -0
  137. scitex/config/__init__.py +41 -9
  138. scitex/config/_paths.py +325 -0
  139. scitex/config/default.yaml +81 -0
  140. scitex/context/_suppress_output.py +2 -3
  141. scitex/db/_BaseMixins/_BaseBackupMixin.py +3 -1
  142. scitex/db/_BaseMixins/_BaseBatchMixin.py +3 -1
  143. scitex/db/_BaseMixins/_BaseBlobMixin.py +3 -1
  144. scitex/db/_BaseMixins/_BaseImportExportMixin.py +1 -3
  145. scitex/db/_BaseMixins/_BaseIndexMixin.py +3 -1
  146. scitex/db/_BaseMixins/_BaseMaintenanceMixin.py +1 -3
  147. scitex/db/_BaseMixins/_BaseQueryMixin.py +3 -1
  148. scitex/db/_BaseMixins/_BaseRowMixin.py +3 -1
  149. scitex/db/_BaseMixins/_BaseTableMixin.py +3 -1
  150. scitex/db/_BaseMixins/_BaseTransactionMixin.py +1 -3
  151. scitex/db/_BaseMixins/__init__.py +1 -1
  152. scitex/db/__init__.py +9 -1
  153. scitex/db/__main__.py +8 -21
  154. scitex/db/_check_health.py +15 -31
  155. scitex/db/_delete_duplicates.py +7 -4
  156. scitex/db/_inspect.py +22 -38
  157. scitex/db/_inspect_optimized.py +89 -85
  158. scitex/db/_postgresql/_PostgreSQL.py +0 -1
  159. scitex/db/_postgresql/_PostgreSQLMixins/_BlobMixin.py +3 -1
  160. scitex/db/_postgresql/_PostgreSQLMixins/_ConnectionMixin.py +1 -3
  161. scitex/db/_postgresql/_PostgreSQLMixins/_ImportExportMixin.py +1 -3
  162. scitex/db/_postgresql/_PostgreSQLMixins/_MaintenanceMixin.py +1 -4
  163. scitex/db/_postgresql/_PostgreSQLMixins/_QueryMixin.py +3 -3
  164. scitex/db/_postgresql/_PostgreSQLMixins/_RowMixin.py +3 -1
  165. scitex/db/_postgresql/_PostgreSQLMixins/_TransactionMixin.py +1 -3
  166. scitex/db/_postgresql/__init__.py +1 -1
  167. scitex/db/_sqlite3/_SQLite3.py +2 -4
  168. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin.py +11 -12
  169. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin_v01-need-_hash-col.py +19 -14
  170. scitex/db/_sqlite3/_SQLite3Mixins/_BatchMixin.py +3 -1
  171. scitex/db/_sqlite3/_SQLite3Mixins/_BlobMixin.py +7 -7
  172. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin.py +118 -111
  173. scitex/db/_sqlite3/_SQLite3Mixins/_ConnectionMixin.py +8 -10
  174. scitex/db/_sqlite3/_SQLite3Mixins/_GitMixin.py +17 -45
  175. scitex/db/_sqlite3/_SQLite3Mixins/_ImportExportMixin.py +1 -3
  176. scitex/db/_sqlite3/_SQLite3Mixins/_IndexMixin.py +3 -1
  177. scitex/db/_sqlite3/_SQLite3Mixins/_QueryMixin.py +3 -4
  178. scitex/db/_sqlite3/_SQLite3Mixins/_RowMixin.py +9 -9
  179. scitex/db/_sqlite3/_SQLite3Mixins/_TableMixin.py +18 -11
  180. scitex/db/_sqlite3/_SQLite3Mixins/__init__.py +1 -0
  181. scitex/db/_sqlite3/__init__.py +1 -1
  182. scitex/db/_sqlite3/_delete_duplicates.py +13 -11
  183. scitex/decorators/__init__.py +29 -4
  184. scitex/decorators/_auto_order.py +43 -43
  185. scitex/decorators/_batch_fn.py +12 -6
  186. scitex/decorators/_cache_disk.py +8 -9
  187. scitex/decorators/_cache_disk_async.py +8 -7
  188. scitex/decorators/_combined.py +19 -13
  189. scitex/decorators/_converters.py +16 -3
  190. scitex/decorators/_deprecated.py +32 -22
  191. scitex/decorators/_numpy_fn.py +18 -4
  192. scitex/decorators/_pandas_fn.py +17 -5
  193. scitex/decorators/_signal_fn.py +17 -3
  194. scitex/decorators/_torch_fn.py +32 -15
  195. scitex/decorators/_xarray_fn.py +23 -9
  196. scitex/dev/_analyze_code_flow.py +0 -2
  197. scitex/dev/plt/__init__.py +272 -0
  198. scitex/dev/plt/plot_mpl_axhline.py +28 -0
  199. scitex/dev/plt/plot_mpl_axhspan.py +28 -0
  200. scitex/dev/plt/plot_mpl_axvline.py +28 -0
  201. scitex/dev/plt/plot_mpl_axvspan.py +28 -0
  202. scitex/dev/plt/plot_mpl_bar.py +29 -0
  203. scitex/dev/plt/plot_mpl_barh.py +29 -0
  204. scitex/dev/plt/plot_mpl_boxplot.py +28 -0
  205. scitex/dev/plt/plot_mpl_contour.py +31 -0
  206. scitex/dev/plt/plot_mpl_contourf.py +31 -0
  207. scitex/dev/plt/plot_mpl_errorbar.py +30 -0
  208. scitex/dev/plt/plot_mpl_eventplot.py +28 -0
  209. scitex/dev/plt/plot_mpl_fill.py +30 -0
  210. scitex/dev/plt/plot_mpl_fill_between.py +31 -0
  211. scitex/dev/plt/plot_mpl_hexbin.py +28 -0
  212. scitex/dev/plt/plot_mpl_hist.py +28 -0
  213. scitex/dev/plt/plot_mpl_hist2d.py +28 -0
  214. scitex/dev/plt/plot_mpl_imshow.py +29 -0
  215. scitex/dev/plt/plot_mpl_pcolormesh.py +31 -0
  216. scitex/dev/plt/plot_mpl_pie.py +29 -0
  217. scitex/dev/plt/plot_mpl_plot.py +29 -0
  218. scitex/dev/plt/plot_mpl_quiver.py +31 -0
  219. scitex/dev/plt/plot_mpl_scatter.py +28 -0
  220. scitex/dev/plt/plot_mpl_stackplot.py +31 -0
  221. scitex/dev/plt/plot_mpl_stem.py +29 -0
  222. scitex/dev/plt/plot_mpl_step.py +29 -0
  223. scitex/dev/plt/plot_mpl_violinplot.py +28 -0
  224. scitex/dev/plt/plot_sns_barplot.py +29 -0
  225. scitex/dev/plt/plot_sns_boxplot.py +29 -0
  226. scitex/dev/plt/plot_sns_heatmap.py +28 -0
  227. scitex/dev/plt/plot_sns_histplot.py +29 -0
  228. scitex/dev/plt/plot_sns_kdeplot.py +29 -0
  229. scitex/dev/plt/plot_sns_lineplot.py +31 -0
  230. scitex/dev/plt/plot_sns_scatterplot.py +29 -0
  231. scitex/dev/plt/plot_sns_stripplot.py +29 -0
  232. scitex/dev/plt/plot_sns_swarmplot.py +29 -0
  233. scitex/dev/plt/plot_sns_violinplot.py +29 -0
  234. scitex/dev/plt/plot_stx_bar.py +29 -0
  235. scitex/dev/plt/plot_stx_barh.py +29 -0
  236. scitex/dev/plt/plot_stx_box.py +28 -0
  237. scitex/dev/plt/plot_stx_boxplot.py +28 -0
  238. scitex/dev/plt/plot_stx_conf_mat.py +28 -0
  239. scitex/dev/plt/plot_stx_contour.py +31 -0
  240. scitex/dev/plt/plot_stx_ecdf.py +28 -0
  241. scitex/dev/plt/plot_stx_errorbar.py +30 -0
  242. scitex/dev/plt/plot_stx_fill_between.py +31 -0
  243. scitex/dev/plt/plot_stx_fillv.py +28 -0
  244. scitex/dev/plt/plot_stx_heatmap.py +28 -0
  245. scitex/dev/plt/plot_stx_image.py +28 -0
  246. scitex/dev/plt/plot_stx_imshow.py +28 -0
  247. scitex/dev/plt/plot_stx_joyplot.py +28 -0
  248. scitex/dev/plt/plot_stx_kde.py +28 -0
  249. scitex/dev/plt/plot_stx_line.py +28 -0
  250. scitex/dev/plt/plot_stx_mean_ci.py +28 -0
  251. scitex/dev/plt/plot_stx_mean_std.py +28 -0
  252. scitex/dev/plt/plot_stx_median_iqr.py +28 -0
  253. scitex/dev/plt/plot_stx_raster.py +28 -0
  254. scitex/dev/plt/plot_stx_rectangle.py +28 -0
  255. scitex/dev/plt/plot_stx_scatter.py +29 -0
  256. scitex/dev/plt/plot_stx_shaded_line.py +29 -0
  257. scitex/dev/plt/plot_stx_violin.py +28 -0
  258. scitex/dev/plt/plot_stx_violinplot.py +28 -0
  259. scitex/dict/_DotDict.py +15 -19
  260. scitex/dict/_flatten.py +1 -0
  261. scitex/dict/_listed_dict.py +1 -0
  262. scitex/dict/_pop_keys.py +1 -0
  263. scitex/dict/_replace.py +1 -0
  264. scitex/dict/_safe_merge.py +1 -0
  265. scitex/dict/_to_str.py +2 -3
  266. scitex/dsp/__init__.py +13 -4
  267. scitex/dsp/_crop.py +3 -1
  268. scitex/dsp/_detect_ripples.py +3 -1
  269. scitex/dsp/_modulation_index.py +3 -1
  270. scitex/dsp/_time.py +3 -1
  271. scitex/dsp/_wavelet.py +0 -1
  272. scitex/dsp/example.py +0 -5
  273. scitex/dsp/filt.py +4 -0
  274. scitex/dsp/utils/__init__.py +4 -1
  275. scitex/dsp/utils/pac.py +3 -3
  276. scitex/dt/_normalize_timestamp.py +4 -1
  277. scitex/errors.py +3 -6
  278. scitex/etc/__init__.py +1 -1
  279. scitex/fig/__init__.py +352 -0
  280. scitex/{vis → fig}/backend/__init__.py +3 -3
  281. scitex/{vis/backend/export.py → fig/backend/_export.py} +1 -1
  282. scitex/{vis/backend/parser.py → fig/backend/_parser.py} +2 -4
  283. scitex/{vis/backend/render.py → fig/backend/_render.py} +1 -1
  284. scitex/{vis → fig}/canvas.py +16 -4
  285. scitex/{vis → fig}/editor/__init__.py +0 -0
  286. scitex/{vis → fig}/editor/_dearpygui_editor.py +450 -304
  287. scitex/fig/editor/_defaults.py +300 -0
  288. scitex/fig/editor/_edit.py +751 -0
  289. scitex/{vis → fig}/editor/_flask_editor.py +8 -8
  290. scitex/{vis → fig}/editor/_mpl_editor.py +63 -48
  291. scitex/{vis → fig}/editor/_qt_editor.py +391 -160
  292. scitex/{vis → fig}/editor/_tkinter_editor.py +146 -89
  293. scitex/fig/editor/flask_editor/__init__.py +21 -0
  294. scitex/fig/editor/flask_editor/_bbox.py +1276 -0
  295. scitex/fig/editor/flask_editor/_core.py +624 -0
  296. scitex/fig/editor/flask_editor/_plotter.py +601 -0
  297. scitex/fig/editor/flask_editor/_renderer.py +739 -0
  298. scitex/{vis/editor/flask_editor/utils.py → fig/editor/flask_editor/_utils.py} +13 -14
  299. scitex/{vis → fig}/editor/flask_editor/templates/__init__.py +6 -6
  300. scitex/fig/editor/flask_editor/templates/_html.py +834 -0
  301. scitex/fig/editor/flask_editor/templates/_scripts.py +3136 -0
  302. scitex/fig/editor/flask_editor/templates/_styles.py +1346 -0
  303. scitex/{vis → fig}/io/__init__.py +18 -6
  304. scitex/fig/io/_bundle.py +973 -0
  305. scitex/{vis/io/canvas.py → fig/io/_canvas.py} +9 -5
  306. scitex/{vis/io/data.py → fig/io/_data.py} +14 -10
  307. scitex/{vis/io/directory.py → fig/io/_directory.py} +7 -4
  308. scitex/{vis/io/export.py → fig/io/_export.py} +16 -13
  309. scitex/{vis/io/load.py → fig/io/_load.py} +2 -2
  310. scitex/{vis/io/panel.py → fig/io/_panel.py} +22 -14
  311. scitex/{vis/io/save.py → fig/io/_save.py} +1 -1
  312. scitex/{vis → fig}/model/__init__.py +8 -8
  313. scitex/{vis/model/annotations.py → fig/model/_annotations.py} +3 -5
  314. scitex/{vis/model/axes.py → fig/model/_axes.py} +2 -2
  315. scitex/{vis/model/figure.py → fig/model/_figure.py} +1 -1
  316. scitex/{vis/model/guides.py → fig/model/_guides.py} +2 -2
  317. scitex/{vis/model/plot.py → fig/model/_plot.py} +3 -5
  318. scitex/{vis/model/plot_types.py → fig/model/_plot_types.py} +0 -0
  319. scitex/{vis/model/styles.py → fig/model/_styles.py} +1 -1
  320. scitex/{vis → fig}/utils/__init__.py +3 -3
  321. scitex/{vis/utils/defaults.py → fig/utils/_defaults.py} +1 -2
  322. scitex/{vis/utils/validate.py → fig/utils/_validate.py} +3 -9
  323. scitex/gen/_DimHandler.py +6 -6
  324. scitex/gen/__init__.py +5 -1
  325. scitex/gen/_deprecated_close.py +1 -0
  326. scitex/gen/_deprecated_start.py +5 -3
  327. scitex/gen/_detect_environment.py +44 -41
  328. scitex/gen/_detect_notebook_path.py +51 -47
  329. scitex/gen/_embed.py +1 -1
  330. scitex/gen/_get_notebook_path.py +81 -62
  331. scitex/gen/_inspect_module.py +0 -1
  332. scitex/gen/_norm.py +16 -7
  333. scitex/gen/_norm_cache.py +78 -65
  334. scitex/gen/_print_config.py +0 -3
  335. scitex/gen/_src.py +2 -3
  336. scitex/gen/_title_case.py +3 -2
  337. scitex/gen/_to_even.py +8 -8
  338. scitex/gen/_transpose.py +3 -3
  339. scitex/gen/misc.py +0 -3
  340. scitex/gists/_SigMacro_processFigure_S.py +2 -2
  341. scitex/gists/_SigMacro_toBlue.py +2 -2
  342. scitex/gists/__init__.py +4 -1
  343. scitex/git/_branch.py +19 -11
  344. scitex/git/_clone.py +23 -15
  345. scitex/git/_commit.py +10 -12
  346. scitex/git/_init.py +15 -38
  347. scitex/git/_remote.py +9 -3
  348. scitex/git/_result.py +3 -0
  349. scitex/git/_retry.py +2 -5
  350. scitex/git/_types.py +4 -0
  351. scitex/git/_validation.py +8 -8
  352. scitex/git/_workflow.py +4 -4
  353. scitex/io/__init__.py +12 -27
  354. scitex/io/_bundle.py +434 -0
  355. scitex/io/_flush.py +5 -2
  356. scitex/io/_glob.py +2 -2
  357. scitex/io/_json2md.py +3 -3
  358. scitex/io/_load.py +104 -8
  359. scitex/io/_load_cache.py +71 -71
  360. scitex/io/_load_configs.py +2 -3
  361. scitex/io/_load_modules/_H5Explorer.py +11 -14
  362. scitex/io/_load_modules/_ZarrExplorer.py +3 -3
  363. scitex/io/_load_modules/_bibtex.py +62 -63
  364. scitex/io/_load_modules/_canvas.py +6 -11
  365. scitex/io/_load_modules/_catboost.py +7 -2
  366. scitex/io/_load_modules/_hdf5.py +2 -0
  367. scitex/io/_load_modules/_image.py +7 -4
  368. scitex/io/_load_modules/_matlab.py +3 -1
  369. scitex/io/_load_modules/_optuna.py +0 -1
  370. scitex/io/_load_modules/_pdf.py +38 -29
  371. scitex/io/_load_modules/_sqlite3.py +1 -0
  372. scitex/io/_load_modules/_txt.py +6 -2
  373. scitex/io/_load_modules/_xml.py +9 -9
  374. scitex/io/_load_modules/_zarr.py +12 -10
  375. scitex/io/_metadata.py +34 -285
  376. scitex/io/_metadata_modules/__init__.py +46 -0
  377. scitex/io/_metadata_modules/_embed.py +70 -0
  378. scitex/io/_metadata_modules/_read.py +64 -0
  379. scitex/io/_metadata_modules/_utils.py +79 -0
  380. scitex/io/_metadata_modules/embed_metadata_jpeg.py +74 -0
  381. scitex/io/_metadata_modules/embed_metadata_pdf.py +53 -0
  382. scitex/io/_metadata_modules/embed_metadata_png.py +26 -0
  383. scitex/io/_metadata_modules/embed_metadata_svg.py +62 -0
  384. scitex/io/_metadata_modules/read_metadata_jpeg.py +57 -0
  385. scitex/io/_metadata_modules/read_metadata_pdf.py +51 -0
  386. scitex/io/_metadata_modules/read_metadata_png.py +39 -0
  387. scitex/io/_metadata_modules/read_metadata_svg.py +44 -0
  388. scitex/io/_qr_utils.py +21 -14
  389. scitex/io/_save.py +755 -80
  390. scitex/io/_save_modules/__init__.py +7 -2
  391. scitex/io/_save_modules/_bibtex.py +66 -61
  392. scitex/io/_save_modules/_canvas.py +8 -9
  393. scitex/io/_save_modules/_catboost.py +2 -2
  394. scitex/io/_save_modules/_csv.py +4 -4
  395. scitex/io/_save_modules/_excel.py +5 -9
  396. scitex/io/_save_modules/_hdf5.py +9 -21
  397. scitex/io/_save_modules/_html.py +5 -5
  398. scitex/io/_save_modules/_image.py +107 -14
  399. scitex/io/_save_modules/_joblib.py +2 -2
  400. scitex/io/_save_modules/_json.py +51 -6
  401. scitex/io/_save_modules/_listed_dfs_as_csv.py +2 -1
  402. scitex/io/_save_modules/_listed_scalars_as_csv.py +2 -1
  403. scitex/io/_save_modules/_matlab.py +2 -2
  404. scitex/io/_save_modules/_numpy.py +6 -8
  405. scitex/io/_save_modules/_pickle.py +4 -4
  406. scitex/io/_save_modules/_plotly.py +3 -3
  407. scitex/io/_save_modules/_tex.py +30 -29
  408. scitex/io/_save_modules/_text.py +2 -2
  409. scitex/io/_save_modules/_yaml.py +9 -9
  410. scitex/io/_save_modules/_zarr.py +15 -15
  411. scitex/io/utils/__init__.py +2 -1
  412. scitex/io/utils/h5_to_zarr.py +183 -163
  413. scitex/linalg/__init__.py +1 -1
  414. scitex/linalg/_geometric_median.py +4 -3
  415. scitex/logging/_Tee.py +5 -7
  416. scitex/logging/__init__.py +18 -19
  417. scitex/logging/_config.py +4 -1
  418. scitex/logging/_context.py +6 -5
  419. scitex/logging/_formatters.py +2 -3
  420. scitex/logging/_handlers.py +19 -20
  421. scitex/logging/_levels.py +9 -17
  422. scitex/logging/_logger.py +74 -15
  423. scitex/logging/_print_capture.py +17 -17
  424. scitex/msword/__init__.py +255 -0
  425. scitex/msword/profiles.py +357 -0
  426. scitex/msword/reader.py +753 -0
  427. scitex/msword/utils.py +289 -0
  428. scitex/msword/writer.py +362 -0
  429. scitex/nn/_BNet.py +1 -3
  430. scitex/nn/_Filters.py +6 -2
  431. scitex/nn/_ModulationIndex.py +3 -1
  432. scitex/nn/_PAC.py +3 -2
  433. scitex/nn/_PSD.py +0 -1
  434. scitex/nn/__init__.py +16 -3
  435. scitex/path/_clean.py +10 -8
  436. scitex/path/_find.py +1 -1
  437. scitex/path/_get_spath.py +1 -2
  438. scitex/path/_mk_spath.py +1 -1
  439. scitex/path/_symlink.py +5 -10
  440. scitex/pd/__init__.py +4 -1
  441. scitex/pd/_force_df.py +24 -24
  442. scitex/pd/_get_unique.py +1 -0
  443. scitex/pd/_merge_columns.py +1 -1
  444. scitex/pd/_round.py +11 -7
  445. scitex/pd/_to_xy.py +0 -1
  446. scitex/plt/__init__.py +190 -89
  447. scitex/plt/_subplots/_AxesWrapper.py +28 -12
  448. scitex/plt/_subplots/_AxisWrapper.py +114 -47
  449. scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin/__init__.py +36 -0
  450. scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin/_labels.py +264 -0
  451. scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin/_metadata.py +213 -0
  452. scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin/_visual.py +128 -0
  453. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/__init__.py +59 -0
  454. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/_base.py +34 -0
  455. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/_scientific.py +593 -0
  456. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/_statistical.py +654 -0
  457. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/_stx_aliases.py +527 -0
  458. scitex/plt/_subplots/_AxisWrapperMixins/_RawMatplotlibMixin.py +321 -0
  459. scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin/__init__.py +33 -0
  460. scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin/_base.py +152 -0
  461. scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin/_wrappers.py +600 -0
  462. scitex/plt/_subplots/_AxisWrapperMixins/_TrackingMixin.py +26 -14
  463. scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +80 -73
  464. scitex/plt/_subplots/_AxisWrapperMixins/__init__.py +79 -5
  465. scitex/plt/_subplots/_FigWrapper.py +97 -64
  466. scitex/plt/_subplots/_SubplotsWrapper.py +161 -84
  467. scitex/plt/_subplots/__init__.py +10 -0
  468. scitex/plt/_subplots/_export_as_csv.py +124 -52
  469. scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +9 -0
  470. scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +14 -23
  471. scitex/plt/_subplots/_export_as_csv_formatters/_format_bar.py +88 -38
  472. scitex/plt/_subplots/_export_as_csv_formatters/_format_barh.py +25 -31
  473. scitex/plt/_subplots/_export_as_csv_formatters/_format_boxplot.py +53 -23
  474. scitex/plt/_subplots/_export_as_csv_formatters/_format_contour.py +38 -25
  475. scitex/plt/_subplots/_export_as_csv_formatters/_format_contourf.py +17 -9
  476. scitex/plt/_subplots/_export_as_csv_formatters/_format_errorbar.py +70 -124
  477. scitex/plt/_subplots/_export_as_csv_formatters/_format_eventplot.py +30 -17
  478. scitex/plt/_subplots/_export_as_csv_formatters/_format_fill.py +31 -17
  479. scitex/plt/_subplots/_export_as_csv_formatters/_format_fill_between.py +33 -21
  480. scitex/plt/_subplots/_export_as_csv_formatters/_format_hexbin.py +14 -4
  481. scitex/plt/_subplots/_export_as_csv_formatters/_format_hist.py +43 -29
  482. scitex/plt/_subplots/_export_as_csv_formatters/_format_hist2d.py +14 -4
  483. scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow.py +27 -11
  484. scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow2d.py +34 -16
  485. scitex/plt/_subplots/_export_as_csv_formatters/_format_matshow.py +16 -8
  486. scitex/plt/_subplots/_export_as_csv_formatters/_format_pie.py +15 -6
  487. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot.py +85 -46
  488. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_box.py +52 -27
  489. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_imshow.py +14 -1
  490. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_kde.py +27 -18
  491. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter.py +14 -5
  492. scitex/plt/_subplots/_export_as_csv_formatters/_format_quiver.py +16 -8
  493. scitex/plt/_subplots/_export_as_csv_formatters/_format_scatter.py +17 -6
  494. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_barplot.py +43 -26
  495. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_boxplot.py +68 -47
  496. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_heatmap.py +52 -64
  497. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_histplot.py +55 -50
  498. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_jointplot.py +23 -10
  499. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_kdeplot.py +63 -29
  500. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_lineplot.py +48 -40
  501. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_pairplot.py +20 -6
  502. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_scatterplot.py +44 -40
  503. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_stripplot.py +46 -39
  504. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_swarmplot.py +46 -39
  505. scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_violinplot.py +75 -94
  506. scitex/plt/_subplots/_export_as_csv_formatters/_format_stem.py +12 -3
  507. scitex/plt/_subplots/_export_as_csv_formatters/_format_step.py +12 -3
  508. scitex/plt/_subplots/_export_as_csv_formatters/_format_streamplot.py +17 -9
  509. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_bar.py +84 -0
  510. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_barh.py +85 -0
  511. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_conf_mat.py +31 -18
  512. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_contour.py +54 -0
  513. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_ecdf.py +24 -11
  514. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_errorbar.py +120 -0
  515. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_fillv.py +35 -31
  516. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_heatmap.py +33 -23
  517. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_image.py +44 -28
  518. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_imshow.py +63 -0
  519. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_joyplot.py +31 -12
  520. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_line.py +34 -23
  521. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_mean_ci.py +32 -26
  522. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_mean_std.py +29 -23
  523. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_median_iqr.py +32 -26
  524. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_raster.py +21 -11
  525. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_rectangle.py +84 -56
  526. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_scatter.py +51 -0
  527. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_scatter_hist.py +46 -34
  528. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_shaded_line.py +46 -30
  529. scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_violin.py +51 -51
  530. scitex/plt/_subplots/_export_as_csv_formatters/_format_text.py +32 -31
  531. scitex/plt/_subplots/_export_as_csv_formatters/_format_violin.py +34 -31
  532. scitex/plt/_subplots/_export_as_csv_formatters/_format_violinplot.py +44 -37
  533. scitex/plt/_subplots/_export_as_csv_formatters/verify_formatters.py +91 -74
  534. scitex/plt/_tpl.py +6 -5
  535. scitex/plt/ax/_plot/__init__.py +24 -0
  536. scitex/plt/ax/_plot/_add_fitted_line.py +12 -11
  537. scitex/plt/ax/_plot/_plot_circular_hist.py +3 -1
  538. scitex/plt/ax/_plot/_plot_statistical_shaded_line.py +25 -19
  539. scitex/plt/ax/_plot/_stx_conf_mat.py +6 -3
  540. scitex/plt/ax/_plot/_stx_ecdf.py +9 -5
  541. scitex/plt/ax/_plot/_stx_fillv.py +4 -2
  542. scitex/plt/ax/_plot/_stx_heatmap.py +7 -4
  543. scitex/plt/ax/_plot/_stx_image.py +7 -5
  544. scitex/plt/ax/_plot/_stx_joyplot.py +32 -10
  545. scitex/plt/ax/_plot/_stx_raster.py +26 -11
  546. scitex/plt/ax/_plot/_stx_rectangle.py +2 -2
  547. scitex/plt/ax/_plot/_stx_shaded_line.py +15 -11
  548. scitex/plt/ax/_plot/_stx_violin.py +3 -1
  549. scitex/plt/ax/_style/_add_marginal_ax.py +6 -4
  550. scitex/plt/ax/_style/_auto_scale_axis.py +14 -10
  551. scitex/plt/ax/_style/_extend.py +3 -1
  552. scitex/plt/ax/_style/_force_aspect.py +5 -3
  553. scitex/plt/ax/_style/_format_units.py +2 -2
  554. scitex/plt/ax/_style/_hide_spines.py +5 -1
  555. scitex/plt/ax/_style/_map_ticks.py +5 -3
  556. scitex/plt/ax/_style/_rotate_labels.py +5 -4
  557. scitex/plt/ax/_style/_rotate_labels_v01.py +73 -63
  558. scitex/plt/ax/_style/_set_log_scale.py +120 -85
  559. scitex/plt/ax/_style/_set_meta.py +99 -76
  560. scitex/plt/ax/_style/_set_supxyt.py +33 -16
  561. scitex/plt/ax/_style/_set_xyt.py +27 -18
  562. scitex/plt/ax/_style/_share_axes.py +15 -5
  563. scitex/plt/ax/_style/_show_spines.py +58 -57
  564. scitex/plt/ax/_style/_style_barplot.py +1 -1
  565. scitex/plt/ax/_style/_style_boxplot.py +25 -14
  566. scitex/plt/ax/_style/_style_errorbar.py +0 -0
  567. scitex/plt/ax/_style/_style_scatter.py +1 -1
  568. scitex/plt/ax/_style/_style_suptitles.py +3 -3
  569. scitex/plt/ax/_style/_style_violinplot.py +8 -2
  570. scitex/plt/color/__init__.py +34 -2
  571. scitex/plt/color/_add_hue_col.py +1 -0
  572. scitex/plt/color/_colors.py +0 -1
  573. scitex/plt/color/_get_colors_from_conf_matap.py +3 -1
  574. scitex/plt/color/_vizualize_colors.py +0 -1
  575. scitex/plt/docs/FIGURE_ARCHITECTURE.md +155 -97
  576. scitex/plt/gallery/README.md +75 -0
  577. scitex/plt/gallery/__init__.py +29 -0
  578. scitex/plt/gallery/_generate.py +560 -0
  579. scitex/plt/gallery/_plots.py +594 -0
  580. scitex/plt/gallery/_registry.py +153 -0
  581. scitex/plt/io/__init__.py +53 -0
  582. scitex/plt/io/_bundle.py +490 -0
  583. scitex/plt/io/_layered_bundle.py +1343 -0
  584. scitex/plt/styles/SCITEX_STYLE.yaml +26 -0
  585. scitex/plt/styles/__init__.py +23 -9
  586. scitex/plt/styles/_plot_defaults.py +62 -61
  587. scitex/plt/styles/_plot_postprocess.py +126 -77
  588. scitex/plt/styles/_style_loader.py +0 -0
  589. scitex/plt/styles/presets.py +121 -18
  590. scitex/plt/utils/__init__.py +42 -3
  591. scitex/plt/utils/_close.py +8 -3
  592. scitex/plt/utils/_collect_figure_metadata.py +3033 -271
  593. scitex/plt/utils/_colorbar.py +15 -17
  594. scitex/plt/utils/_configure_mpl.py +26 -30
  595. scitex/plt/utils/_crop.py +87 -36
  596. scitex/plt/utils/_csv_column_naming.py +177 -72
  597. scitex/plt/utils/_dimension_viewer.py +7 -19
  598. scitex/plt/utils/_figure_from_axes_mm.py +70 -16
  599. scitex/plt/utils/_figure_mm.py +119 -3
  600. scitex/plt/utils/_get_actual_font.py +5 -4
  601. scitex/plt/utils/_histogram_utils.py +52 -48
  602. scitex/plt/utils/_hitmap.py +1643 -0
  603. scitex/plt/utils/_is_valid_axis.py +19 -13
  604. scitex/plt/utils/_mk_colorbar.py +3 -3
  605. scitex/plt/utils/_scientific_captions.py +202 -139
  606. scitex/plt/utils/_scitex_config.py +98 -98
  607. scitex/plt/utils/_units.py +0 -0
  608. scitex/plt/utils/metadata/__init__.py +61 -0
  609. scitex/plt/utils/metadata/_artist_extraction.py +119 -0
  610. scitex/plt/utils/metadata/_axes_metadata.py +93 -0
  611. scitex/plt/utils/metadata/_collection_artists.py +292 -0
  612. scitex/plt/utils/metadata/_core.py +207 -0
  613. scitex/plt/utils/metadata/_csv_column_extraction.py +186 -0
  614. scitex/plt/utils/metadata/_csv_hash.py +115 -0
  615. scitex/plt/utils/metadata/_csv_verification.py +95 -0
  616. scitex/plt/utils/metadata/_data_linkage.py +263 -0
  617. scitex/plt/utils/metadata/_dimensions.py +242 -0
  618. scitex/plt/utils/metadata/_editable_export.py +405 -0
  619. scitex/plt/utils/metadata/_figure_metadata.py +58 -0
  620. scitex/plt/utils/metadata/_geometry_extraction.py +570 -0
  621. scitex/plt/utils/metadata/_image_text_artists.py +168 -0
  622. scitex/plt/utils/metadata/_label_parsing.py +82 -0
  623. scitex/plt/utils/metadata/_legend_extraction.py +120 -0
  624. scitex/plt/utils/metadata/_line_artists.py +367 -0
  625. scitex/plt/utils/metadata/_line_semantic_handling.py +173 -0
  626. scitex/plt/utils/metadata/_patch_artists.py +211 -0
  627. scitex/plt/utils/metadata/_plot_content.py +26 -0
  628. scitex/plt/utils/metadata/_plot_type_detection.py +184 -0
  629. scitex/plt/utils/metadata/_precision.py +134 -0
  630. scitex/plt/utils/metadata/_precision_config.py +68 -0
  631. scitex/plt/utils/metadata/_precision_sections.py +211 -0
  632. scitex/plt/utils/metadata/_recipe_extraction.py +267 -0
  633. scitex/plt/utils/metadata/_style_parsing.py +174 -0
  634. scitex/repro/_RandomStateManager.py +33 -38
  635. scitex/repro/__init__.py +16 -7
  636. scitex/repro/_gen_ID.py +7 -9
  637. scitex/repro/_gen_timestamp.py +7 -6
  638. scitex/repro/_hash_array.py +8 -12
  639. scitex/reproduce/__init__.py +1 -1
  640. scitex/resource/_get_processor_usages.py +3 -1
  641. scitex/resource/_log_processor_usages.py +3 -1
  642. scitex/rng/__init__.py +1 -1
  643. scitex/schema/README.md +178 -0
  644. scitex/schema/__init__.py +237 -0
  645. scitex/schema/_canvas.py +444 -0
  646. scitex/schema/_plot.py +1015 -0
  647. scitex/schema/_stats.py +762 -0
  648. scitex/schema/_validation.py +590 -0
  649. scitex/scholar/.legacy/Scholar.py +5 -12
  650. scitex/scholar/.legacy/_Scholar.py +66 -99
  651. scitex/scholar/.legacy/_ScholarAPI.py +75 -66
  652. scitex/scholar/.legacy/_tmp/search_engine/_BaseSearchEngine.py +3 -3
  653. scitex/scholar/.legacy/_tmp/search_engine/_UnifiedSearcher.py +4 -9
  654. scitex/scholar/.legacy/_tmp/search_engine/__init__.py +14 -21
  655. scitex/scholar/.legacy/_tmp/search_engine/local/_LocalSearchEngine.py +40 -37
  656. scitex/scholar/.legacy/_tmp/search_engine/local/_VectorSearchEngine.py +31 -28
  657. scitex/scholar/.legacy/_tmp/search_engine/web/_ArxivSearchEngine.py +74 -65
  658. scitex/scholar/.legacy/_tmp/search_engine/web/_CrossRefSearchEngine.py +122 -116
  659. scitex/scholar/.legacy/_tmp/search_engine/web/_GoogleScholarSearchEngine.py +65 -59
  660. scitex/scholar/.legacy/_tmp/search_engine/web/_PubMedSearchEngine.py +121 -107
  661. scitex/scholar/.legacy/_tmp/search_engine/web/_SemanticScholarSearchEngine.py +5 -12
  662. scitex/scholar/.legacy/database/_DatabaseEntry.py +49 -45
  663. scitex/scholar/.legacy/database/_DatabaseIndex.py +131 -94
  664. scitex/scholar/.legacy/database/_LibraryManager.py +65 -63
  665. scitex/scholar/.legacy/database/_PaperDatabase.py +138 -124
  666. scitex/scholar/.legacy/database/_ScholarDatabaseIntegration.py +14 -36
  667. scitex/scholar/.legacy/database/_StorageIntegratedDB.py +192 -156
  668. scitex/scholar/.legacy/database/_ZoteroCompatibleDB.py +300 -237
  669. scitex/scholar/.legacy/database/__init__.py +2 -1
  670. scitex/scholar/.legacy/database/manage.py +92 -84
  671. scitex/scholar/.legacy/lookup/_LookupIndex.py +157 -101
  672. scitex/scholar/.legacy/lookup/__init__.py +2 -1
  673. scitex/scholar/.legacy/metadata/doi/batch/_MetadataHandlerForBatchDOIResolution.py +4 -9
  674. scitex/scholar/.legacy/metadata/doi/batch/_ProgressManagerForBatchDOIResolution.py +10 -23
  675. scitex/scholar/.legacy/metadata/doi/batch/_SourceStatsManagerForBatchDOIResolution.py +4 -9
  676. scitex/scholar/.legacy/metadata/doi/batch/__init__.py +3 -1
  677. scitex/scholar/.legacy/metadata/doi/resolvers/_BatchDOIResolver.py +10 -25
  678. scitex/scholar/.legacy/metadata/doi/resolvers/_BibTeXDOIResolver.py +19 -49
  679. scitex/scholar/.legacy/metadata/doi/resolvers/_DOIResolver.py +1 -0
  680. scitex/scholar/.legacy/metadata/doi/resolvers/_SingleDOIResolver.py +8 -20
  681. scitex/scholar/.legacy/metadata/doi/sources/.combined-SemanticScholarSource/_SemanticScholarSource.py +37 -35
  682. scitex/scholar/.legacy/metadata/doi/sources/.combined-SemanticScholarSource/_SemanticScholarSourceEnhanced.py +49 -37
  683. scitex/scholar/.legacy/metadata/doi/sources/_ArXivSource.py +11 -30
  684. scitex/scholar/.legacy/metadata/doi/sources/_BaseDOISource.py +19 -47
  685. scitex/scholar/.legacy/metadata/doi/sources/_CrossRefLocalSource.py +1 -0
  686. scitex/scholar/.legacy/metadata/doi/sources/_CrossRefSource.py +12 -33
  687. scitex/scholar/.legacy/metadata/doi/sources/_OpenAlexSource.py +8 -20
  688. scitex/scholar/.legacy/metadata/doi/sources/_PubMedSource.py +10 -27
  689. scitex/scholar/.legacy/metadata/doi/sources/_SemanticScholarSource.py +11 -29
  690. scitex/scholar/.legacy/metadata/doi/sources/_SourceManager.py +8 -21
  691. scitex/scholar/.legacy/metadata/doi/sources/_SourceResolutionStrategy.py +24 -55
  692. scitex/scholar/.legacy/metadata/doi/sources/_SourceRotationManager.py +8 -21
  693. scitex/scholar/.legacy/metadata/doi/sources/_URLDOISource.py +9 -16
  694. scitex/scholar/.legacy/metadata/doi/sources/_UnifiedSource.py +8 -22
  695. scitex/scholar/.legacy/metadata/doi/sources/__init__.py +1 -0
  696. scitex/scholar/.legacy/metadata/doi/utils/_PubMedConverter.py +4 -8
  697. scitex/scholar/.legacy/metadata/doi/utils/_RateLimitHandler.py +17 -43
  698. scitex/scholar/.legacy/metadata/doi/utils/_TextNormalizer.py +8 -18
  699. scitex/scholar/.legacy/metadata/doi/utils/_URLDOIExtractor.py +4 -8
  700. scitex/scholar/.legacy/metadata/doi/utils/__init__.py +1 -0
  701. scitex/scholar/.legacy/metadata/doi/utils/_to_complete_metadata_structure.py +1 -0
  702. scitex/scholar/.legacy/metadata/enrichment/_LibraryEnricher.py +2 -3
  703. scitex/scholar/.legacy/metadata/enrichment/enrichers/_ImpactFactorEnricher.py +6 -12
  704. scitex/scholar/.legacy/metadata/enrichment/enrichers/_SmartEnricher.py +5 -10
  705. scitex/scholar/.legacy/metadata/enrichment/sources/_UnifiedMetadataSource.py +4 -5
  706. scitex/scholar/.legacy/metadata/query_to_full_meta_json.py +8 -12
  707. scitex/scholar/.legacy/metadata/urls/_URLMetadataHandler.py +3 -3
  708. scitex/scholar/.legacy/metadata/urls/_ZoteroTranslatorRunner.py +15 -21
  709. scitex/scholar/.legacy/metadata/urls/__init__.py +3 -3
  710. scitex/scholar/.legacy/metadata/urls/_finder.py +4 -6
  711. scitex/scholar/.legacy/metadata/urls/_handler.py +7 -15
  712. scitex/scholar/.legacy/metadata/urls/_resolver.py +6 -12
  713. scitex/scholar/.legacy/search/_Embedder.py +74 -69
  714. scitex/scholar/.legacy/search/_SemanticSearch.py +91 -90
  715. scitex/scholar/.legacy/search/_SemanticSearchEngine.py +104 -109
  716. scitex/scholar/.legacy/search/_UnifiedSearcher.py +530 -471
  717. scitex/scholar/.legacy/search/_VectorDatabase.py +111 -92
  718. scitex/scholar/.legacy/search/__init__.py +1 -0
  719. scitex/scholar/.legacy/storage/_EnhancedStorageManager.py +182 -154
  720. scitex/scholar/.legacy/storage/__init__.py +2 -1
  721. scitex/scholar/__init__.py +0 -2
  722. scitex/scholar/__main__.py +1 -3
  723. scitex/scholar/auth/ScholarAuthManager.py +13 -36
  724. scitex/scholar/auth/core/AuthenticationGateway.py +15 -29
  725. scitex/scholar/auth/core/BrowserAuthenticator.py +22 -57
  726. scitex/scholar/auth/core/StrategyResolver.py +10 -27
  727. scitex/scholar/auth/core/__init__.py +5 -1
  728. scitex/scholar/auth/gateway/_OpenURLLinkFinder.py +11 -21
  729. scitex/scholar/auth/gateway/_OpenURLResolver.py +10 -18
  730. scitex/scholar/auth/gateway/_resolve_functions.py +3 -3
  731. scitex/scholar/auth/providers/BaseAuthenticator.py +1 -0
  732. scitex/scholar/auth/providers/EZProxyAuthenticator.py +7 -14
  733. scitex/scholar/auth/providers/OpenAthensAuthenticator.py +29 -57
  734. scitex/scholar/auth/providers/ShibbolethAuthenticator.py +87 -73
  735. scitex/scholar/auth/session/AuthCacheManager.py +12 -22
  736. scitex/scholar/auth/session/SessionManager.py +4 -6
  737. scitex/scholar/auth/sso/BaseSSOAutomator.py +13 -19
  738. scitex/scholar/auth/sso/OpenAthensSSOAutomator.py +16 -45
  739. scitex/scholar/auth/sso/SSOAutomator.py +8 -15
  740. scitex/scholar/auth/sso/UniversityOfMelbourneSSOAutomator.py +13 -23
  741. scitex/scholar/browser/ScholarBrowserManager.py +31 -56
  742. scitex/scholar/browser/__init__.py +1 -0
  743. scitex/scholar/browser/utils/click_and_wait.py +3 -4
  744. scitex/scholar/browser/utils/close_unwanted_pages.py +4 -7
  745. scitex/scholar/browser/utils/wait_redirects.py +15 -40
  746. scitex/scholar/citation_graph/__init__.py +0 -0
  747. scitex/scholar/citation_graph/builder.py +3 -7
  748. scitex/scholar/citation_graph/database.py +4 -11
  749. scitex/scholar/citation_graph/example.py +5 -10
  750. scitex/scholar/citation_graph/models.py +0 -0
  751. scitex/scholar/cli/_url_utils.py +1 -1
  752. scitex/scholar/cli/chrome.py +5 -3
  753. scitex/scholar/cli/download_pdf.py +13 -14
  754. scitex/scholar/cli/handlers/bibtex_handler.py +4 -12
  755. scitex/scholar/cli/handlers/doi_handler.py +1 -3
  756. scitex/scholar/cli/handlers/project_handler.py +6 -20
  757. scitex/scholar/cli/open_browser.py +41 -39
  758. scitex/scholar/cli/open_browser_auto.py +31 -39
  759. scitex/scholar/cli/open_browser_monitored.py +27 -24
  760. scitex/scholar/config/ScholarConfig.py +5 -8
  761. scitex/scholar/config/__init__.py +1 -0
  762. scitex/scholar/config/core/_CascadeConfig.py +3 -3
  763. scitex/scholar/config/core/_PathManager.py +16 -28
  764. scitex/scholar/core/Paper.py +79 -78
  765. scitex/scholar/core/Papers.py +16 -27
  766. scitex/scholar/core/Scholar.py +98 -229
  767. scitex/scholar/core/journal_normalizer.py +52 -49
  768. scitex/scholar/core/oa_cache.py +27 -23
  769. scitex/scholar/core/open_access.py +17 -8
  770. scitex/scholar/docs/template.py +4 -3
  771. scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/clf_svm.py +0 -0
  772. scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/download.py +0 -0
  773. scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_conf_mat.py +0 -0
  774. scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_digits.py +0 -0
  775. scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_umap_space.py +0 -0
  776. scitex/scholar/examples/00_config.py +10 -9
  777. scitex/scholar/examples/01_auth.py +3 -0
  778. scitex/scholar/examples/02_browser.py +14 -10
  779. scitex/scholar/examples/03_01-engine.py +3 -0
  780. scitex/scholar/examples/03_02-engine-for-bibtex.py +4 -3
  781. scitex/scholar/examples/04_01-url.py +9 -9
  782. scitex/scholar/examples/04_02-url-for-bibtex.py +7 -3
  783. scitex/scholar/examples/04_02-url-for-dois.py +87 -97
  784. scitex/scholar/examples/05_download_pdf.py +10 -4
  785. scitex/scholar/examples/06_find_and_download.py +6 -6
  786. scitex/scholar/examples/06_parse_bibtex.py +17 -17
  787. scitex/scholar/examples/07_storage_integration.py +6 -9
  788. scitex/scholar/examples/99_fullpipeline-for-bibtex.py +14 -15
  789. scitex/scholar/examples/99_fullpipeline-for-one-entry.py +31 -23
  790. scitex/scholar/examples/99_maintenance.py +3 -0
  791. scitex/scholar/examples/dev.py +2 -3
  792. scitex/scholar/examples/zotero_integration.py +11 -18
  793. scitex/scholar/impact_factor/ImpactFactorEngine.py +7 -9
  794. scitex/scholar/impact_factor/estimation/__init__.py +4 -4
  795. scitex/scholar/impact_factor/estimation/core/__init__.py +3 -7
  796. scitex/scholar/impact_factor/estimation/core/cache_manager.py +223 -211
  797. scitex/scholar/impact_factor/estimation/core/calculator.py +165 -131
  798. scitex/scholar/impact_factor/estimation/core/journal_matcher.py +217 -172
  799. scitex/scholar/impact_factor/jcr/ImpactFactorJCREngine.py +6 -14
  800. scitex/scholar/impact_factor/jcr/build_database.py +4 -3
  801. scitex/scholar/integration/base.py +9 -17
  802. scitex/scholar/integration/mendeley/exporter.py +2 -4
  803. scitex/scholar/integration/mendeley/importer.py +3 -3
  804. scitex/scholar/integration/mendeley/linker.py +3 -3
  805. scitex/scholar/integration/mendeley/mapper.py +9 -6
  806. scitex/scholar/integration/zotero/__main__.py +26 -43
  807. scitex/scholar/integration/zotero/exporter.py +15 -11
  808. scitex/scholar/integration/zotero/importer.py +12 -10
  809. scitex/scholar/integration/zotero/linker.py +8 -12
  810. scitex/scholar/integration/zotero/mapper.py +17 -12
  811. scitex/scholar/metadata_engines/.combined-SemanticScholarSource/_SemanticScholarSource.py +37 -35
  812. scitex/scholar/metadata_engines/.combined-SemanticScholarSource/_SemanticScholarSourceEnhanced.py +47 -35
  813. scitex/scholar/metadata_engines/ScholarEngine.py +21 -43
  814. scitex/scholar/metadata_engines/__init__.py +1 -0
  815. scitex/scholar/metadata_engines/individual/ArXivEngine.py +15 -37
  816. scitex/scholar/metadata_engines/individual/CrossRefEngine.py +15 -42
  817. scitex/scholar/metadata_engines/individual/CrossRefLocalEngine.py +24 -45
  818. scitex/scholar/metadata_engines/individual/OpenAlexEngine.py +11 -21
  819. scitex/scholar/metadata_engines/individual/PubMedEngine.py +10 -27
  820. scitex/scholar/metadata_engines/individual/SemanticScholarEngine.py +28 -35
  821. scitex/scholar/metadata_engines/individual/URLDOIEngine.py +11 -22
  822. scitex/scholar/metadata_engines/individual/_BaseDOIEngine.py +20 -49
  823. scitex/scholar/metadata_engines/utils/_PubMedConverter.py +4 -8
  824. scitex/scholar/metadata_engines/utils/_URLDOIExtractor.py +5 -10
  825. scitex/scholar/metadata_engines/utils/__init__.py +2 -0
  826. scitex/scholar/metadata_engines/utils/_metadata2bibtex.py +3 -0
  827. scitex/scholar/metadata_engines/utils/_standardize_metadata.py +2 -3
  828. scitex/scholar/pdf_download/ScholarPDFDownloader.py +25 -37
  829. scitex/scholar/pdf_download/strategies/chrome_pdf_viewer.py +11 -19
  830. scitex/scholar/pdf_download/strategies/direct_download.py +5 -9
  831. scitex/scholar/pdf_download/strategies/manual_download_fallback.py +3 -3
  832. scitex/scholar/pdf_download/strategies/manual_download_utils.py +6 -13
  833. scitex/scholar/pdf_download/strategies/open_access_download.py +49 -31
  834. scitex/scholar/pdf_download/strategies/response_body.py +8 -19
  835. scitex/scholar/pipelines/ScholarPipelineBibTeX.py +9 -18
  836. scitex/scholar/pipelines/ScholarPipelineMetadataParallel.py +25 -26
  837. scitex/scholar/pipelines/ScholarPipelineMetadataSingle.py +62 -23
  838. scitex/scholar/pipelines/ScholarPipelineParallel.py +13 -30
  839. scitex/scholar/pipelines/ScholarPipelineSearchParallel.py +299 -220
  840. scitex/scholar/pipelines/ScholarPipelineSearchSingle.py +202 -165
  841. scitex/scholar/pipelines/ScholarPipelineSingle.py +25 -51
  842. scitex/scholar/pipelines/SearchQueryParser.py +55 -55
  843. scitex/scholar/search_engines/ScholarSearchEngine.py +31 -27
  844. scitex/scholar/search_engines/_BaseSearchEngine.py +20 -23
  845. scitex/scholar/search_engines/individual/ArXivSearchEngine.py +53 -35
  846. scitex/scholar/search_engines/individual/CrossRefSearchEngine.py +47 -40
  847. scitex/scholar/search_engines/individual/OpenAlexSearchEngine.py +55 -50
  848. scitex/scholar/search_engines/individual/PubMedSearchEngine.py +8 -10
  849. scitex/scholar/search_engines/individual/SemanticScholarSearchEngine.py +55 -49
  850. scitex/scholar/storage/BibTeXHandler.py +150 -95
  851. scitex/scholar/storage/PaperIO.py +3 -6
  852. scitex/scholar/storage/ScholarLibrary.py +70 -49
  853. scitex/scholar/storage/_DeduplicationManager.py +52 -25
  854. scitex/scholar/storage/_LibraryCacheManager.py +19 -46
  855. scitex/scholar/storage/_LibraryManager.py +65 -175
  856. scitex/scholar/url_finder/ScholarURLFinder.py +9 -25
  857. scitex/scholar/url_finder/strategies/find_pdf_urls_by_direct_links.py +1 -1
  858. scitex/scholar/url_finder/strategies/find_pdf_urls_by_href.py +6 -10
  859. scitex/scholar/url_finder/strategies/find_pdf_urls_by_navigation.py +4 -6
  860. scitex/scholar/url_finder/strategies/find_pdf_urls_by_publisher_patterns.py +8 -15
  861. scitex/scholar/url_finder/strategies/find_pdf_urls_by_zotero_translators.py +3 -3
  862. scitex/scholar/url_finder/strategies/find_supplementary_urls_by_href.py +3 -3
  863. scitex/scholar/url_finder/translators/core/patterns.py +6 -4
  864. scitex/scholar/url_finder/translators/core/registry.py +6 -9
  865. scitex/scholar/url_finder/translators/individual/BOFiP_Impots.py +60 -52
  866. scitex/scholar/url_finder/translators/individual/Baidu_Scholar.py +54 -62
  867. scitex/scholar/url_finder/translators/individual/Bangkok_Post.py +38 -44
  868. scitex/scholar/url_finder/translators/individual/Baruch_Foundation.py +43 -47
  869. scitex/scholar/url_finder/translators/individual/Beobachter.py +46 -50
  870. scitex/scholar/url_finder/translators/individual/Bezneng_Gajit.py +37 -41
  871. scitex/scholar/url_finder/translators/individual/BibLaTeX.py +59 -52
  872. scitex/scholar/url_finder/translators/individual/BibTeX.py +83 -79
  873. scitex/scholar/url_finder/translators/individual/Biblio_com.py +48 -51
  874. scitex/scholar/url_finder/translators/individual/Bibliontology_RDF.py +58 -56
  875. scitex/scholar/url_finder/translators/individual/Camara_Brasileira_do_Livro_ISBN.py +102 -99
  876. scitex/scholar/url_finder/translators/individual/CanLII.py +49 -43
  877. scitex/scholar/url_finder/translators/individual/Canada_com.py +36 -40
  878. scitex/scholar/url_finder/translators/individual/Canadian_Letters_and_Images.py +43 -43
  879. scitex/scholar/url_finder/translators/individual/Canadiana_ca.py +77 -66
  880. scitex/scholar/url_finder/translators/individual/Cascadilla_Proceedings_Project.py +68 -62
  881. scitex/scholar/url_finder/translators/individual/Central_and_Eastern_European_Online_Library_Journals.py +60 -60
  882. scitex/scholar/url_finder/translators/individual/Champlain_Society_Collection.py +63 -61
  883. scitex/scholar/url_finder/translators/individual/Chicago_Journal_of_Theoretical_Computer_Science.py +74 -58
  884. scitex/scholar/url_finder/translators/individual/Christian_Science_Monitor.py +32 -38
  885. scitex/scholar/url_finder/translators/individual/Columbia_University_Press.py +51 -47
  886. scitex/scholar/url_finder/translators/individual/Common_Place.py +66 -57
  887. scitex/scholar/url_finder/translators/individual/Cornell_LII.py +66 -62
  888. scitex/scholar/url_finder/translators/individual/Cornell_University_Press.py +38 -45
  889. scitex/scholar/url_finder/translators/individual/CourtListener.py +52 -56
  890. scitex/scholar/url_finder/translators/individual/DAI_Zenon.py +53 -54
  891. scitex/scholar/url_finder/translators/individual/access_medicine.py +27 -33
  892. scitex/scholar/url_finder/translators/individual/acm.py +1 -1
  893. scitex/scholar/url_finder/translators/individual/acm_digital_library.py +93 -63
  894. scitex/scholar/url_finder/translators/individual/airiti.py +3 -1
  895. scitex/scholar/url_finder/translators/individual/aosic.py +3 -1
  896. scitex/scholar/url_finder/translators/individual/archive_ouverte_aosic.py +3 -1
  897. scitex/scholar/url_finder/translators/individual/archive_ouverte_en_sciences_de_l_information_et_de_la_communication___aosic_.py +6 -2
  898. scitex/scholar/url_finder/translators/individual/artforum.py +35 -27
  899. scitex/scholar/url_finder/translators/individual/arxiv.py +1 -1
  900. scitex/scholar/url_finder/translators/individual/arxiv_org.py +8 -4
  901. scitex/scholar/url_finder/translators/individual/atlanta_journal_constitution.py +22 -18
  902. scitex/scholar/url_finder/translators/individual/atypon_journals.py +19 -11
  903. scitex/scholar/url_finder/translators/individual/austlii_and_nzlii.py +48 -44
  904. scitex/scholar/url_finder/translators/individual/australian_dictionary_of_biography.py +21 -17
  905. scitex/scholar/url_finder/translators/individual/bailii.py +22 -19
  906. scitex/scholar/url_finder/translators/individual/bbc.py +46 -42
  907. scitex/scholar/url_finder/translators/individual/bbc_genome.py +37 -25
  908. scitex/scholar/url_finder/translators/individual/biblioteca_nacional_de_maestros.py +24 -20
  909. scitex/scholar/url_finder/translators/individual/bibliotheque_archives_nationale_quebec_pistard.py +42 -43
  910. scitex/scholar/url_finder/translators/individual/bibliotheque_archives_nationales_quebec.py +87 -81
  911. scitex/scholar/url_finder/translators/individual/bibliotheque_nationale_france.py +39 -37
  912. scitex/scholar/url_finder/translators/individual/bibsys.py +32 -28
  913. scitex/scholar/url_finder/translators/individual/bioconductor.py +58 -52
  914. scitex/scholar/url_finder/translators/individual/biomed_central.py +23 -15
  915. scitex/scholar/url_finder/translators/individual/biorxiv.py +26 -13
  916. scitex/scholar/url_finder/translators/individual/blogger.py +39 -43
  917. scitex/scholar/url_finder/translators/individual/bloomberg.py +48 -52
  918. scitex/scholar/url_finder/translators/individual/bloomsbury_food_library.py +37 -37
  919. scitex/scholar/url_finder/translators/individual/bluesky.py +30 -28
  920. scitex/scholar/url_finder/translators/individual/bnf_isbn.py +1 -1
  921. scitex/scholar/url_finder/translators/individual/bocc.py +66 -60
  922. scitex/scholar/url_finder/translators/individual/boe.py +52 -52
  923. scitex/scholar/url_finder/translators/individual/brill.py +3 -1
  924. scitex/scholar/url_finder/translators/individual/business_standard.py +36 -38
  925. scitex/scholar/url_finder/translators/individual/cabi_cab_abstracts.py +39 -41
  926. scitex/scholar/url_finder/translators/individual/cambridge.py +3 -1
  927. scitex/scholar/url_finder/translators/individual/cambridge_core.py +30 -24
  928. scitex/scholar/url_finder/translators/individual/caod.py +50 -46
  929. scitex/scholar/url_finder/translators/individual/cbc.py +91 -67
  930. scitex/scholar/url_finder/translators/individual/ccfr_bnf.py +49 -53
  931. scitex/scholar/url_finder/translators/individual/cia_world_factbook.py +43 -33
  932. scitex/scholar/url_finder/translators/individual/crossref_rest.py +208 -174
  933. scitex/scholar/url_finder/translators/individual/current_affairs.py +29 -35
  934. scitex/scholar/url_finder/translators/individual/dabi.py +70 -66
  935. scitex/scholar/url_finder/translators/individual/dagens_nyheter.py +3 -1
  936. scitex/scholar/url_finder/translators/individual/dagstuhl.py +10 -15
  937. scitex/scholar/url_finder/translators/individual/dar_almandumah.py +13 -9
  938. scitex/scholar/url_finder/translators/individual/dart_europe.py +19 -22
  939. scitex/scholar/url_finder/translators/individual/data_gov.py +2 -2
  940. scitex/scholar/url_finder/translators/individual/databrary.py +27 -28
  941. scitex/scholar/url_finder/translators/individual/datacite_json.py +152 -137
  942. scitex/scholar/url_finder/translators/individual/dataverse.py +68 -64
  943. scitex/scholar/url_finder/translators/individual/daum_news.py +38 -38
  944. scitex/scholar/url_finder/translators/individual/dblp.py +4 -8
  945. scitex/scholar/url_finder/translators/individual/dblp_computer_science_bibliography.py +8 -3
  946. scitex/scholar/url_finder/translators/individual/dbpia.py +5 -3
  947. scitex/scholar/url_finder/translators/individual/defense_technical_information_center.py +30 -28
  948. scitex/scholar/url_finder/translators/individual/delpher.py +102 -79
  949. scitex/scholar/url_finder/translators/individual/demographic_research.py +35 -31
  950. scitex/scholar/url_finder/translators/individual/denik_cz.py +58 -54
  951. scitex/scholar/url_finder/translators/individual/depatisnet.py +7 -10
  952. scitex/scholar/url_finder/translators/individual/der_freitag.py +81 -66
  953. scitex/scholar/url_finder/translators/individual/der_spiegel.py +56 -54
  954. scitex/scholar/url_finder/translators/individual/digibib_net.py +3 -1
  955. scitex/scholar/url_finder/translators/individual/digizeitschriften.py +3 -1
  956. scitex/scholar/url_finder/translators/individual/dpla.py +13 -14
  957. scitex/scholar/url_finder/translators/individual/dspace.py +2 -2
  958. scitex/scholar/url_finder/translators/individual/ebrary.py +3 -1
  959. scitex/scholar/url_finder/translators/individual/ebscohost.py +3 -1
  960. scitex/scholar/url_finder/translators/individual/electronic_colloquium_on_computational_complexity.py +3 -1
  961. scitex/scholar/url_finder/translators/individual/elife.py +3 -1
  962. scitex/scholar/url_finder/translators/individual/elsevier_health_journals.py +3 -1
  963. scitex/scholar/url_finder/translators/individual/emerald.py +3 -1
  964. scitex/scholar/url_finder/translators/individual/emerald_insight.py +3 -1
  965. scitex/scholar/url_finder/translators/individual/epicurious.py +3 -1
  966. scitex/scholar/url_finder/translators/individual/eurogamerusgamer.py +3 -1
  967. scitex/scholar/url_finder/translators/individual/fachportal_padagogik.py +3 -1
  968. scitex/scholar/url_finder/translators/individual/frontiers.py +1 -1
  969. scitex/scholar/url_finder/translators/individual/gale_databases.py +3 -1
  970. scitex/scholar/url_finder/translators/individual/gms_german_medical_science.py +6 -2
  971. scitex/scholar/url_finder/translators/individual/ieee_computer_society.py +6 -2
  972. scitex/scholar/url_finder/translators/individual/ieee_xplore.py +41 -35
  973. scitex/scholar/url_finder/translators/individual/inter_research_science_center.py +6 -2
  974. scitex/scholar/url_finder/translators/individual/jisc_historical_texts.py +3 -1
  975. scitex/scholar/url_finder/translators/individual/jstor.py +14 -12
  976. scitex/scholar/url_finder/translators/individual/korean_national_library.py +3 -1
  977. scitex/scholar/url_finder/translators/individual/la_times.py +3 -1
  978. scitex/scholar/url_finder/translators/individual/landesbibliographie_baden_wurttemberg.py +3 -1
  979. scitex/scholar/url_finder/translators/individual/legislative_insight.py +3 -1
  980. scitex/scholar/url_finder/translators/individual/libraries_tasmania.py +3 -1
  981. scitex/scholar/url_finder/translators/individual/library_catalog__koha_.py +3 -1
  982. scitex/scholar/url_finder/translators/individual/lingbuzz.py +2 -2
  983. scitex/scholar/url_finder/translators/individual/max_planck_institute_for_the_history_of_science_virtual_laboratory_library.py +3 -1
  984. scitex/scholar/url_finder/translators/individual/mdpi.py +12 -6
  985. scitex/scholar/url_finder/translators/individual/microbiology_society_journals.py +3 -1
  986. scitex/scholar/url_finder/translators/individual/midas_journals.py +3 -1
  987. scitex/scholar/url_finder/translators/individual/nagoya_university_opac.py +3 -1
  988. scitex/scholar/url_finder/translators/individual/nature_publishing_group.py +32 -19
  989. scitex/scholar/url_finder/translators/individual/ntsb_accident_reports.py +3 -1
  990. scitex/scholar/url_finder/translators/individual/openedition_journals.py +8 -4
  991. scitex/scholar/url_finder/translators/individual/orcid.py +16 -15
  992. scitex/scholar/url_finder/translators/individual/oxford.py +25 -19
  993. scitex/scholar/url_finder/translators/individual/oxford_dictionaries_premium.py +3 -1
  994. scitex/scholar/url_finder/translators/individual/ozon_ru.py +3 -1
  995. scitex/scholar/url_finder/translators/individual/plos.py +9 -12
  996. scitex/scholar/url_finder/translators/individual/polygon.py +3 -1
  997. scitex/scholar/url_finder/translators/individual/primo.py +3 -1
  998. scitex/scholar/url_finder/translators/individual/project_muse.py +3 -1
  999. scitex/scholar/url_finder/translators/individual/pubfactory_journals.py +3 -1
  1000. scitex/scholar/url_finder/translators/individual/pubmed.py +71 -65
  1001. scitex/scholar/url_finder/translators/individual/pubmed_central.py +8 -6
  1002. scitex/scholar/url_finder/translators/individual/rechtspraak_nl.py +3 -1
  1003. scitex/scholar/url_finder/translators/individual/sage_journals.py +25 -17
  1004. scitex/scholar/url_finder/translators/individual/sciencedirect.py +36 -17
  1005. scitex/scholar/url_finder/translators/individual/semantics_visual_library.py +3 -1
  1006. scitex/scholar/url_finder/translators/individual/silverchair.py +70 -52
  1007. scitex/scholar/url_finder/translators/individual/sora.py +3 -1
  1008. scitex/scholar/url_finder/translators/individual/springer.py +15 -11
  1009. scitex/scholar/url_finder/translators/individual/ssrn.py +3 -3
  1010. scitex/scholar/url_finder/translators/individual/stanford_encyclopedia_of_philosophy.py +3 -1
  1011. scitex/scholar/url_finder/translators/individual/superlib.py +3 -1
  1012. scitex/scholar/url_finder/translators/individual/treesearch.py +3 -1
  1013. scitex/scholar/url_finder/translators/individual/university_of_chicago_press_books.py +3 -1
  1014. scitex/scholar/url_finder/translators/individual/vlex.py +3 -1
  1015. scitex/scholar/url_finder/translators/individual/web_of_science.py +3 -1
  1016. scitex/scholar/url_finder/translators/individual/web_of_science_nextgen.py +3 -1
  1017. scitex/scholar/url_finder/translators/individual/wiley.py +31 -25
  1018. scitex/scholar/url_finder/translators/individual/wilson_center_digital_archive.py +3 -1
  1019. scitex/scholar/utils/bibtex/_parse_bibtex.py +3 -3
  1020. scitex/scholar/utils/cleanup/_cleanup_scholar_processes.py +5 -9
  1021. scitex/scholar/utils/text/_TextNormalizer.py +249 -176
  1022. scitex/scholar/utils/validation/DOIValidator.py +31 -28
  1023. scitex/scholar/utils/validation/__init__.py +0 -0
  1024. scitex/scholar/utils/validation/validate_library_dois.py +61 -57
  1025. scitex/scholar/zotero/__init__.py +1 -1
  1026. scitex/security/cli.py +7 -20
  1027. scitex/security/github.py +45 -32
  1028. scitex/session/__init__.py +8 -9
  1029. scitex/session/_decorator.py +49 -42
  1030. scitex/session/_lifecycle.py +39 -39
  1031. scitex/session/_manager.py +24 -20
  1032. scitex/sh/__init__.py +4 -3
  1033. scitex/sh/_execute.py +10 -7
  1034. scitex/sh/_security.py +3 -3
  1035. scitex/sh/_types.py +2 -3
  1036. scitex/stats/__init__.py +174 -6
  1037. scitex/stats/_schema.py +42 -569
  1038. scitex/stats/auto/__init__.py +188 -0
  1039. scitex/stats/auto/_context.py +331 -0
  1040. scitex/stats/auto/_formatting.py +679 -0
  1041. scitex/stats/auto/_rules.py +901 -0
  1042. scitex/stats/auto/_selector.py +554 -0
  1043. scitex/stats/auto/_styles.py +721 -0
  1044. scitex/stats/correct/__init__.py +4 -4
  1045. scitex/stats/correct/_correct_bonferroni.py +43 -34
  1046. scitex/stats/correct/_correct_fdr.py +14 -40
  1047. scitex/stats/correct/_correct_fdr_.py +39 -46
  1048. scitex/stats/correct/_correct_holm.py +14 -32
  1049. scitex/stats/correct/_correct_sidak.py +36 -21
  1050. scitex/stats/descriptive/_circular.py +20 -21
  1051. scitex/stats/descriptive/_describe.py +19 -5
  1052. scitex/stats/descriptive/_nan.py +5 -7
  1053. scitex/stats/descriptive/_real.py +4 -3
  1054. scitex/stats/effect_sizes/__init__.py +10 -11
  1055. scitex/stats/effect_sizes/_cliffs_delta.py +35 -32
  1056. scitex/stats/effect_sizes/_cohens_d.py +30 -31
  1057. scitex/stats/effect_sizes/_epsilon_squared.py +19 -22
  1058. scitex/stats/effect_sizes/_eta_squared.py +23 -27
  1059. scitex/stats/effect_sizes/_prob_superiority.py +18 -21
  1060. scitex/stats/io/__init__.py +29 -0
  1061. scitex/stats/io/_bundle.py +156 -0
  1062. scitex/stats/posthoc/__init__.py +3 -3
  1063. scitex/stats/posthoc/_dunnett.py +75 -55
  1064. scitex/stats/posthoc/_games_howell.py +61 -43
  1065. scitex/stats/posthoc/_tukey_hsd.py +42 -34
  1066. scitex/stats/power/__init__.py +2 -2
  1067. scitex/stats/power/_power.py +56 -56
  1068. scitex/stats/tests/__init__.py +1 -1
  1069. scitex/stats/tests/correlation/__init__.py +1 -1
  1070. scitex/stats/tests/correlation/_test_pearson.py +28 -38
  1071. scitex/stats/utils/__init__.py +14 -17
  1072. scitex/stats/utils/_effect_size.py +85 -78
  1073. scitex/stats/utils/_formatters.py +49 -43
  1074. scitex/stats/utils/_normalizers.py +7 -14
  1075. scitex/stats/utils/_power.py +56 -56
  1076. scitex/str/__init__.py +1 -0
  1077. scitex/str/_clean_path.py +3 -3
  1078. scitex/str/_factor_out_digits.py +86 -58
  1079. scitex/str/_format_plot_text.py +180 -111
  1080. scitex/str/_latex.py +19 -19
  1081. scitex/str/_latex_fallback.py +9 -10
  1082. scitex/str/_parse.py +3 -6
  1083. scitex/str/_print_debug.py +13 -13
  1084. scitex/str/_printc.py +2 -0
  1085. scitex/str/_search.py +3 -3
  1086. scitex/template/.legacy/_clone_project.py +9 -13
  1087. scitex/template/__init__.py +10 -2
  1088. scitex/template/_clone_project.py +7 -2
  1089. scitex/template/_copy.py +1 -0
  1090. scitex/template/_customize.py +3 -6
  1091. scitex/template/_git_strategy.py +2 -3
  1092. scitex/template/_rename.py +1 -0
  1093. scitex/template/clone_pip_project.py +6 -7
  1094. scitex/template/clone_research.py +7 -10
  1095. scitex/template/clone_singularity.py +6 -7
  1096. scitex/template/clone_writer_directory.py +6 -7
  1097. scitex/tex/__init__.py +4 -0
  1098. scitex/tex/_export.py +890 -0
  1099. scitex/tex/_preview.py +26 -11
  1100. scitex/tex/_to_vec.py +10 -7
  1101. scitex/torch/__init__.py +11 -1
  1102. scitex/types/_ArrayLike.py +2 -0
  1103. scitex/types/_is_listed_X.py +3 -3
  1104. scitex/units.py +110 -77
  1105. scitex/utils/_compress_hdf5.py +3 -3
  1106. scitex/utils/_email.py +8 -4
  1107. scitex/utils/_notify.py +14 -8
  1108. scitex/utils/_search.py +6 -6
  1109. scitex/utils/_verify_scitex_format.py +17 -42
  1110. scitex/utils/_verify_scitex_format_v01.py +12 -34
  1111. scitex/utils/template.py +4 -3
  1112. scitex/web/__init__.py +7 -1
  1113. scitex/web/_scraping.py +54 -38
  1114. scitex/web/_search_pubmed.py +30 -14
  1115. scitex/writer/.legacy/Writer_v01-refactored.py +4 -4
  1116. scitex/writer/.legacy/_compile.py +18 -28
  1117. scitex/writer/Writer.py +8 -21
  1118. scitex/writer/__init__.py +11 -11
  1119. scitex/writer/_clone_writer_project.py +2 -6
  1120. scitex/writer/_compile/__init__.py +1 -0
  1121. scitex/writer/_compile/_parser.py +1 -0
  1122. scitex/writer/_compile/_runner.py +35 -38
  1123. scitex/writer/_compile/_validator.py +1 -0
  1124. scitex/writer/_compile/manuscript.py +1 -0
  1125. scitex/writer/_compile/revision.py +1 -0
  1126. scitex/writer/_compile/supplementary.py +1 -0
  1127. scitex/writer/_compile_async.py +5 -12
  1128. scitex/writer/_project/__init__.py +1 -0
  1129. scitex/writer/_project/_create.py +10 -25
  1130. scitex/writer/_project/_trees.py +4 -9
  1131. scitex/writer/_project/_validate.py +2 -3
  1132. scitex/writer/_validate_tree_structures.py +7 -18
  1133. scitex/writer/dataclasses/__init__.py +8 -10
  1134. scitex/writer/dataclasses/config/_CONSTANTS.py +2 -3
  1135. scitex/writer/dataclasses/config/_WriterConfig.py +4 -9
  1136. scitex/writer/dataclasses/contents/_ManuscriptContents.py +14 -25
  1137. scitex/writer/dataclasses/contents/_RevisionContents.py +21 -16
  1138. scitex/writer/dataclasses/contents/_SupplementaryContents.py +21 -24
  1139. scitex/writer/dataclasses/core/_Document.py +2 -3
  1140. scitex/writer/dataclasses/core/_DocumentSection.py +8 -23
  1141. scitex/writer/dataclasses/results/_CompilationResult.py +2 -3
  1142. scitex/writer/dataclasses/results/_LaTeXIssue.py +3 -6
  1143. scitex/writer/dataclasses/results/_SaveSectionsResponse.py +20 -9
  1144. scitex/writer/dataclasses/results/_SectionReadResponse.py +24 -10
  1145. scitex/writer/dataclasses/tree/_ConfigTree.py +7 -4
  1146. scitex/writer/dataclasses/tree/_ManuscriptTree.py +10 -13
  1147. scitex/writer/dataclasses/tree/_RevisionTree.py +16 -17
  1148. scitex/writer/dataclasses/tree/_ScriptsTree.py +10 -5
  1149. scitex/writer/dataclasses/tree/_SharedTree.py +10 -13
  1150. scitex/writer/dataclasses/tree/_SupplementaryTree.py +15 -14
  1151. scitex/writer/utils/.legacy_git_retry.py +3 -8
  1152. scitex/writer/utils/_parse_latex_logs.py +2 -3
  1153. scitex/writer/utils/_parse_script_args.py +20 -23
  1154. scitex/writer/utils/_watch.py +5 -5
  1155. {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/METADATA +14 -10
  1156. {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/RECORD +1149 -985
  1157. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +0 -583
  1158. scitex/io/memo.md +0 -2827
  1159. scitex/plt/_subplots/TODO.md +0 -53
  1160. scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +0 -537
  1161. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +0 -1499
  1162. scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +0 -431
  1163. scitex/plt/_subplots/_export_as_csv_formatters.py +0 -112
  1164. scitex/vis/__init__.py +0 -177
  1165. scitex/vis/editor/_defaults.py +0 -244
  1166. scitex/vis/editor/_edit.py +0 -378
  1167. scitex/vis/editor/flask_editor/__init__.py +0 -21
  1168. scitex/vis/editor/flask_editor/bbox.py +0 -216
  1169. scitex/vis/editor/flask_editor/core.py +0 -152
  1170. scitex/vis/editor/flask_editor/plotter.py +0 -130
  1171. scitex/vis/editor/flask_editor/renderer.py +0 -184
  1172. scitex/vis/editor/flask_editor/templates/html.py +0 -295
  1173. scitex/vis/editor/flask_editor/templates/scripts.py +0 -614
  1174. scitex/vis/editor/flask_editor/templates/styles.py +0 -549
  1175. /scitex/{vis → fig}/README.md +0 -0
  1176. /scitex/{vis → fig}/docs/CANVAS_ARCHITECTURE.md +0 -0
  1177. {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/WHEEL +0 -0
  1178. {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/entry_points.txt +0 -0
  1179. {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/licenses/LICENSE +0 -0
@@ -0,0 +1,594 @@
1
+ #!/usr/bin/env python3
2
+ # -*- coding: utf-8 -*-
3
+ # Timestamp: "2025-12-08 23:30:00 (ywatanabe)"
4
+ # File: /home/ywatanabe/proj/scitex-code/src/scitex/plt/gallery/_plots.py
5
+
6
+ """Plot definitions for gallery generation."""
7
+
8
+ import numpy as np
9
+
10
+
11
+ # =============================================================================
12
+ # Line Plots
13
+ # =============================================================================
14
+ def plot_plot(fig, ax, stx):
15
+ """ax.plot() - Basic line plot."""
16
+ time_sec = np.linspace(0, 2 * np.pi, 100)
17
+ ax.plot(time_sec, np.sin(time_sec), "b-", label="sin", id="sine_wave")
18
+ ax.plot(time_sec, np.cos(time_sec), "r--", label="cos", id="cosine_wave")
19
+ ax.set_xyt(x="Time [s]", y="Amplitude [a.u.]", t="ax.plot()")
20
+ ax.legend(frameon=False, fontsize=6)
21
+ return fig, ax
22
+
23
+
24
+ def plot_step(fig, ax, stx):
25
+ """ax.step() - Step plot."""
26
+ time_ms = np.arange(20)
27
+ voltage_mv = np.random.randint(0, 5, 20)
28
+ ax.step(time_ms, voltage_mv, where="mid", id="digital_signal")
29
+ ax.set_xyt(x="Time [ms]", y="Voltage [mV]", t="ax.step()")
30
+ return fig, ax
31
+
32
+
33
+ def plot_stx_line(fig, ax, stx):
34
+ """ax.stx_line() - Simple line from 1D array."""
35
+ np.random.seed(42)
36
+ signal_amplitude = np.sin(np.linspace(0, 4 * np.pi, 100)) + np.random.normal(
37
+ 0, 0.1, 100
38
+ )
39
+ ax.stx_line(signal_amplitude, id="eeg_signal", label="Signal")
40
+ ax.set_xyt(x="Sample", y="Amplitude [μV]", t="ax.stx_line()")
41
+ ax.legend(frameon=False, fontsize=6)
42
+ return fig, ax
43
+
44
+
45
+ def plot_stx_shaded_line(fig, ax, stx):
46
+ """ax.stx_shaded_line() - Line with shaded region."""
47
+ np.random.seed(42)
48
+ time_sec = np.linspace(0, 10, 100)
49
+ mean_value = np.sin(time_sec)
50
+ lower_bound = mean_value - 0.3
51
+ upper_bound = mean_value + 0.3
52
+ ax.stx_shaded_line(
53
+ time_sec, mean_value, lower_bound, upper_bound, id="confidence_band"
54
+ )
55
+ ax.set_xyt(x="Time [s]", y="Response [a.u.]", t="ax.stx_shaded_line()")
56
+ return fig, ax
57
+
58
+
59
+ # =============================================================================
60
+ # Statistical Summaries
61
+ # =============================================================================
62
+ def plot_stx_mean_std(fig, ax, stx):
63
+ """ax.stx_mean_std() - Mean ± standard deviation."""
64
+ np.random.seed(42)
65
+ n_trials, n_timepoints = 50, 100
66
+ trials_data = np.sin(np.linspace(0, 2 * np.pi, n_timepoints)) + np.random.normal(
67
+ 0, 0.3, (n_trials, n_timepoints)
68
+ )
69
+ ax.stx_mean_std(trials_data, id="trial_average")
70
+ ax.set_xyt(x="Time [ms]", y="Amplitude [μV]", t="ax.stx_mean_std()")
71
+ return fig, ax
72
+
73
+
74
+ def plot_stx_mean_ci(fig, ax, stx):
75
+ """ax.stx_mean_ci() - Mean with confidence interval."""
76
+ np.random.seed(42)
77
+ n_subjects, n_timepoints = 30, 100
78
+ subjects_data = np.sin(np.linspace(0, 2 * np.pi, n_timepoints)) + np.random.normal(
79
+ 0, 0.4, (n_subjects, n_timepoints)
80
+ )
81
+ ax.stx_mean_ci(subjects_data, id="group_average")
82
+ ax.set_xyt(x="Time [ms]", y="BOLD [%]", t="ax.stx_mean_ci()")
83
+ return fig, ax
84
+
85
+
86
+ def plot_stx_median_iqr(fig, ax, stx):
87
+ """ax.stx_median_iqr() - Median with interquartile range."""
88
+ np.random.seed(42)
89
+ n_samples, n_timepoints = 40, 100
90
+ samples_data = np.exp(np.linspace(0, 2, n_timepoints)) + np.random.exponential(
91
+ 0.5, (n_samples, n_timepoints)
92
+ )
93
+ ax.stx_median_iqr(samples_data, id="reaction_times")
94
+ ax.set_xyt(x="Trial", y="RT [ms]", t="ax.stx_median_iqr()")
95
+ return fig, ax
96
+
97
+
98
+ def plot_errorbar(fig, ax, stx):
99
+ """ax.errorbar() - Error bars."""
100
+ conditions = np.arange(5)
101
+ accuracy_mean = [0.75, 0.82, 0.88, 0.91, 0.85]
102
+ accuracy_std = [0.08, 0.06, 0.05, 0.04, 0.07]
103
+ ax.errorbar(
104
+ conditions, accuracy_mean, yerr=accuracy_std, fmt="o-", capsize=3, id="accuracy"
105
+ )
106
+ ax.set_xyt(x="Condition", y="Accuracy", t="ax.errorbar()")
107
+ return fig, ax
108
+
109
+
110
+ def plot_stx_errorbar(fig, ax, stx):
111
+ """ax.stx_errorbar() - Error bars with x, y, yerr."""
112
+ np.random.seed(42)
113
+ x = np.arange(5)
114
+ y = np.array([0.7, 0.8, 0.85, 0.9, 0.82])
115
+ yerr = np.array([0.05, 0.04, 0.03, 0.04, 0.06])
116
+ ax.stx_errorbar(x, y, yerr=yerr, id="group_accuracy", fmt="o-", capsize=3)
117
+ ax.set_xyt(x="Condition", y="Accuracy", t="ax.stx_errorbar()")
118
+ return fig, ax
119
+
120
+
121
+ # =============================================================================
122
+ # Distributions
123
+ # =============================================================================
124
+ def plot_hist(fig, ax, stx):
125
+ """ax.hist() - Histogram."""
126
+ np.random.seed(42)
127
+ reaction_times = np.random.normal(450, 80, 1000)
128
+ ax.hist(reaction_times, bins=30, alpha=0.7, edgecolor="black", id="rt_distribution")
129
+ ax.set_xyt(x="Reaction Time [ms]", y="Count", t="ax.hist()")
130
+ return fig, ax
131
+
132
+
133
+ def plot_hist2d(fig, ax, stx):
134
+ """ax.hist2d() - 2D histogram."""
135
+ np.random.seed(42)
136
+ x_position = np.random.normal(0, 1, 5000)
137
+ y_position = np.random.normal(0, 1, 5000)
138
+ ax.hist2d(x_position, y_position, bins=30, cmap="viridis", id="position_density")
139
+ ax.set_xyt(x="X Position [cm]", y="Y Position [cm]", t="ax.hist2d()")
140
+ return fig, ax
141
+
142
+
143
+ def plot_stx_kde(fig, ax, stx):
144
+ """ax.stx_kde() - Kernel density estimation."""
145
+ np.random.seed(42)
146
+ scores = np.concatenate(
147
+ [np.random.normal(70, 10, 500), np.random.normal(85, 8, 300)]
148
+ )
149
+ ax.stx_kde(scores, id="score_distribution")
150
+ ax.set_xyt(x="Score", y="Density", t="ax.stx_kde()")
151
+ return fig, ax
152
+
153
+
154
+ def plot_stx_ecdf(fig, ax, stx):
155
+ """ax.stx_ecdf() - Empirical CDF."""
156
+ np.random.seed(42)
157
+ latencies = np.random.exponential(50, 500)
158
+ ax.stx_ecdf(latencies, id="latency_cdf")
159
+ ax.set_xyt(x="Latency [ms]", y="Cumulative Probability", t="ax.stx_ecdf()")
160
+ return fig, ax
161
+
162
+
163
+ def plot_stx_joyplot(fig, ax, stx):
164
+ """ax.stx_joyplot() - Ridge/joy plot."""
165
+ np.random.seed(42)
166
+ n_groups = 5
167
+ data_groups = [np.random.normal(i * 0.5, 0.8, 200) for i in range(n_groups)]
168
+ ax.stx_joyplot(data_groups, id="distributions_by_group")
169
+ ax.set_xyt(x="Value", y="Group", t="ax.stx_joyplot()")
170
+ return fig, ax
171
+
172
+
173
+ # =============================================================================
174
+ # Categorical
175
+ # =============================================================================
176
+ def plot_bar(fig, ax, stx):
177
+ """ax.bar() - Bar chart."""
178
+ categories = ["A", "B", "C", "D"]
179
+ values = [23, 45, 56, 78]
180
+ ax.bar(categories, values, id="category_counts")
181
+ ax.set_xyt(x="Category", y="Count", t="ax.bar()")
182
+ return fig, ax
183
+
184
+
185
+ def plot_barh(fig, ax, stx):
186
+ """ax.barh() - Horizontal bar chart."""
187
+ methods = ["Method A", "Method B", "Method C", "Method D"]
188
+ accuracy = [0.85, 0.92, 0.78, 0.88]
189
+ ax.barh(methods, accuracy, id="method_comparison")
190
+ ax.set_xyt(x="Accuracy", y="Method", t="ax.barh()")
191
+ return fig, ax
192
+
193
+
194
+ def plot_stx_bar(fig, ax, stx):
195
+ """ax.stx_bar() - Bar chart with x and height."""
196
+ x = ["A", "B", "C", "D"]
197
+ height = [0.7, 0.8, 0.85, 0.9]
198
+ ax.stx_bar(x, height, id="condition_means")
199
+ ax.set_xyt(x="Condition", y="Performance", t="ax.stx_bar()")
200
+ return fig, ax
201
+
202
+
203
+ def plot_stx_barh(fig, ax, stx):
204
+ """ax.stx_barh() - Horizontal bar with y and width."""
205
+ y = ["Method A", "Method B", "Method C", "Method D"]
206
+ width = [0.75, 0.82, 0.88, 0.91]
207
+ ax.stx_barh(y, width, id="method_performance")
208
+ ax.set_xyt(x="Accuracy", y="Method", t="ax.stx_barh()")
209
+ return fig, ax
210
+
211
+
212
+ def plot_boxplot(fig, ax, stx):
213
+ """ax.boxplot() - Box plot."""
214
+ np.random.seed(42)
215
+ group_a = np.random.normal(100, 15, 50)
216
+ group_b = np.random.normal(110, 20, 50)
217
+ group_c = np.random.normal(95, 10, 50)
218
+ ax.boxplot(
219
+ [group_a, group_b, group_c],
220
+ labels=["Control", "Treatment A", "Treatment B"],
221
+ id="treatment_comparison",
222
+ )
223
+ ax.set_xyt(x="Group", y="Response", t="ax.boxplot()")
224
+ return fig, ax
225
+
226
+
227
+ def plot_violinplot(fig, ax, stx):
228
+ """ax.violinplot() - Violin plot."""
229
+ np.random.seed(42)
230
+ data = [np.random.normal(0, std, 100) for std in [1, 2, 1.5, 2.5]]
231
+ ax.violinplot(data, showmeans=True, showmedians=True, id="distribution_comparison")
232
+ ax.set_xyt(x="Condition", y="Value", t="ax.violinplot()")
233
+ return fig, ax
234
+
235
+
236
+ def plot_stx_box(fig, ax, stx):
237
+ """ax.stx_box() - Box plot from 2D array."""
238
+ np.random.seed(42)
239
+ n_subjects, n_conditions = 30, 4
240
+ data = np.random.normal([50, 55, 48, 60], 10, (n_subjects, n_conditions))
241
+ ax.stx_box(data, id="condition_distributions")
242
+ ax.set_xyt(x="Condition", y="Score", t="ax.stx_box()")
243
+ return fig, ax
244
+
245
+
246
+ def plot_stx_violin(fig, ax, stx):
247
+ """ax.stx_violin() - Violin plot from list of arrays."""
248
+ np.random.seed(42)
249
+ data = [
250
+ np.random.normal(0, 1, 100),
251
+ np.random.normal(0.5, 1.2, 100),
252
+ np.random.normal(1, 0.8, 100),
253
+ ]
254
+ ax.stx_violin(data, id="effect_distributions")
255
+ ax.set_xyt(x="Condition", y="Effect Size", t="ax.stx_violin()")
256
+ return fig, ax
257
+
258
+
259
+ def plot_stx_boxplot(fig, ax, stx):
260
+ """ax.stx_boxplot() - Enhanced box plot."""
261
+ np.random.seed(42)
262
+ data = [np.random.exponential(scale, 100) for scale in [1, 1.5, 2, 1.2]]
263
+ ax.stx_boxplot(data, id="skewed_distributions")
264
+ ax.set_xyt(x="Group", y="Value", t="ax.stx_boxplot()")
265
+ return fig, ax
266
+
267
+
268
+ def plot_stx_violinplot(fig, ax, stx):
269
+ """ax.stx_violinplot() - Enhanced violin plot."""
270
+ np.random.seed(42)
271
+ data = [
272
+ np.concatenate([np.random.normal(-1, 0.5, 50), np.random.normal(1, 0.5, 50)])
273
+ for _ in range(3)
274
+ ]
275
+ ax.stx_violinplot(data, id="bimodal_distributions")
276
+ ax.set_xyt(x="Condition", y="Value", t="ax.stx_violinplot()")
277
+ return fig, ax
278
+
279
+
280
+ # =============================================================================
281
+ # Scatter & Points
282
+ # =============================================================================
283
+ def plot_scatter(fig, ax, stx):
284
+ """ax.scatter() - Scatter plot."""
285
+ np.random.seed(42)
286
+ age = np.random.uniform(20, 80, 100)
287
+ response_time = 200 + age * 2 + np.random.normal(0, 30, 100)
288
+ ax.scatter(age, response_time, alpha=0.6, id="age_rt_correlation")
289
+ ax.set_xyt(x="Age [years]", y="Response Time [ms]", t="ax.scatter()")
290
+ return fig, ax
291
+
292
+
293
+ def plot_stx_scatter(fig, ax, stx):
294
+ """ax.stx_scatter() - Enhanced scatter plot."""
295
+ np.random.seed(42)
296
+ x_feature = np.random.normal(0, 1, 150)
297
+ y_feature = 0.7 * x_feature + np.random.normal(0, 0.5, 150)
298
+ ax.stx_scatter(x_feature, y_feature, id="feature_correlation")
299
+ ax.set_xyt(x="Feature X", y="Feature Y", t="ax.stx_scatter()")
300
+ return fig, ax
301
+
302
+
303
+ def plot_stem(fig, ax, stx):
304
+ """ax.stem() - Stem plot."""
305
+ frequencies = np.arange(0, 50, 5)
306
+ power_spectrum = np.abs(np.random.normal(0, 1, 10)) ** 2
307
+ ax.stem(frequencies, power_spectrum, id="frequency_spectrum")
308
+ ax.set_xyt(x="Frequency [Hz]", y="Power [dB]", t="ax.stem()")
309
+ return fig, ax
310
+
311
+
312
+ def plot_hexbin(fig, ax, stx):
313
+ """ax.hexbin() - Hexagonal binning."""
314
+ np.random.seed(42)
315
+ x_coord = np.random.normal(0, 2, 10000)
316
+ y_coord = np.random.normal(0, 2, 10000)
317
+ ax.hexbin(x_coord, y_coord, gridsize=20, cmap="YlOrRd", id="density_map")
318
+ ax.set_xyt(x="X", y="Y", t="ax.hexbin()")
319
+ return fig, ax
320
+
321
+
322
+ # =============================================================================
323
+ # Area & Fill
324
+ # =============================================================================
325
+ def plot_fill_between(fig, ax, stx):
326
+ """ax.fill_between() - Filled area between curves."""
327
+ time = np.linspace(0, 10, 100)
328
+ upper = np.sin(time) + 0.5
329
+ lower = np.sin(time) - 0.5
330
+ ax.fill_between(time, lower, upper, alpha=0.3, id="confidence_region")
331
+ ax.plot(time, np.sin(time), "b-", id="mean_line")
332
+ ax.set_xyt(x="Time [s]", y="Value", t="ax.fill_between()")
333
+ return fig, ax
334
+
335
+
336
+ def plot_fill_betweenx(fig, ax, stx):
337
+ """ax.fill_betweenx() - Horizontal filled area."""
338
+ y = np.linspace(0, 10, 100)
339
+ x1 = np.sin(y)
340
+ x2 = np.sin(y) + 1
341
+ ax.fill_betweenx(y, x1, x2, alpha=0.3, id="horizontal_band")
342
+ ax.set_xyt(x="Value", y="Depth [m]", t="ax.fill_betweenx()")
343
+ return fig, ax
344
+
345
+
346
+ def plot_stx_fill_between(fig, ax, stx):
347
+ """ax.stx_fill_between() - Enhanced fill between."""
348
+ np.random.seed(42)
349
+ time = np.linspace(0, 5, 50)
350
+ mean = np.sin(time * 2)
351
+ std = 0.3 + 0.1 * np.abs(np.sin(time))
352
+ ax.stx_fill_between(time, mean - std, mean + std, id="uncertainty_band")
353
+ ax.plot(time, mean, "k-", linewidth=1, id="central_estimate")
354
+ ax.set_xyt(x="Time [s]", y="Estimate", t="ax.stx_fill_between()")
355
+ return fig, ax
356
+
357
+
358
+ def plot_stx_fillv(fig, ax, stx):
359
+ """ax.stx_fillv() - Vertical fill regions."""
360
+ time = np.linspace(0, 10, 100)
361
+ signal = np.sin(time * 2)
362
+ ax.plot(time, signal, "b-", id="signal")
363
+ ax.stx_fillv([2, 6], [4, 8], alpha=0.3, color="red", id="stimulus_periods")
364
+ ax.set_xyt(x="Time [s]", y="Amplitude", t="ax.stx_fillv()")
365
+ return fig, ax
366
+
367
+
368
+ # =============================================================================
369
+ # Grid & Matrix
370
+ # =============================================================================
371
+ def plot_imshow(fig, ax, stx):
372
+ """ax.imshow() - Image display."""
373
+ np.random.seed(42)
374
+ image_data = np.random.rand(20, 20)
375
+ im = ax.imshow(image_data, cmap="viridis", id="random_image")
376
+ fig.colorbar(im, ax=ax, shrink=0.8)
377
+ ax.set_xyt(x="X", y="Y", t="ax.imshow()")
378
+ return fig, ax
379
+
380
+
381
+ def plot_matshow(fig, ax, stx):
382
+ """ax.matshow() - Matrix display."""
383
+ np.random.seed(42)
384
+ correlation_matrix = np.corrcoef(np.random.rand(5, 100))
385
+ im = ax.matshow(correlation_matrix, cmap="RdBu_r", id="correlation_matrix")
386
+ fig.colorbar(im, ax=ax, shrink=0.8)
387
+ ax.set_xyt(x="Variable", y="Variable", t="ax.matshow()")
388
+ return fig, ax
389
+
390
+
391
+ def plot_stx_imshow(fig, ax, stx):
392
+ """ax.stx_imshow() - Enhanced image display."""
393
+ np.random.seed(42)
394
+ brain_slice = np.random.rand(64, 64) * 100
395
+ ax.stx_imshow(brain_slice, cmap="hot", id="brain_activity")
396
+ ax.set_xyt(x="X [voxels]", y="Y [voxels]", t="ax.stx_imshow()")
397
+ return fig, ax
398
+
399
+
400
+ def plot_stx_image(fig, ax, stx):
401
+ """ax.stx_image() - Image from 2D array."""
402
+ np.random.seed(42)
403
+ grayscale_image = np.random.rand(32, 32)
404
+ ax.stx_image(grayscale_image, id="grayscale_image")
405
+ ax.set_xyt(x="X", y="Y", t="ax.stx_image()")
406
+ return fig, ax
407
+
408
+
409
+ def plot_stx_heatmap(fig, ax, stx):
410
+ """ax.stx_heatmap() - Annotated heatmap."""
411
+ np.random.seed(42)
412
+ data = np.random.rand(5, 5)
413
+ ax.stx_heatmap(data, id="annotated_heatmap")
414
+ ax.set_xyt(x="Feature", y="Sample", t="ax.stx_heatmap()")
415
+ return fig, ax
416
+
417
+
418
+ def plot_stx_conf_mat(fig, ax, stx):
419
+ """ax.stx_conf_mat() - Confusion matrix."""
420
+ np.random.seed(42)
421
+ conf_matrix = np.array([[45, 5, 2], [3, 42, 8], [1, 6, 48]])
422
+ ax.stx_conf_mat(conf_matrix, id="classification_results")
423
+ ax.set_xyt(x="Predicted", y="Actual", t="ax.stx_conf_mat()")
424
+ return fig, ax
425
+
426
+
427
+ # =============================================================================
428
+ # Contours
429
+ # =============================================================================
430
+ def plot_contour(fig, ax, stx):
431
+ """ax.contour() - Contour lines."""
432
+ x = np.linspace(-3, 3, 100)
433
+ y = np.linspace(-3, 3, 100)
434
+ X, Y = np.meshgrid(x, y)
435
+ Z = np.sin(X) * np.cos(Y)
436
+ cs = ax.contour(X, Y, Z, levels=10, id="contour_lines")
437
+ ax.clabel(cs, inline=True, fontsize=6)
438
+ ax.set_xyt(x="X", y="Y", t="ax.contour()")
439
+ return fig, ax
440
+
441
+
442
+ def plot_contourf(fig, ax, stx):
443
+ """ax.contourf() - Filled contours."""
444
+ x = np.linspace(-3, 3, 100)
445
+ y = np.linspace(-3, 3, 100)
446
+ X, Y = np.meshgrid(x, y)
447
+ Z = np.exp(-(X**2 + Y**2) / 2)
448
+ cf = ax.contourf(X, Y, Z, levels=20, cmap="viridis", id="gaussian_2d")
449
+ fig.colorbar(cf, ax=ax, shrink=0.8)
450
+ ax.set_xyt(x="X", y="Y", t="ax.contourf()")
451
+ return fig, ax
452
+
453
+
454
+ def plot_stx_contour(fig, ax, stx):
455
+ """ax.stx_contour() - Enhanced contour plot."""
456
+ np.random.seed(42)
457
+ x = np.linspace(-2, 2, 50)
458
+ y = np.linspace(-2, 2, 50)
459
+ X, Y = np.meshgrid(x, y)
460
+ Z = X * np.exp(-(X**2) - Y**2)
461
+ ax.stx_contour(X, Y, Z, id="potential_field")
462
+ ax.set_xyt(x="X", y="Y", t="ax.stx_contour()")
463
+ return fig, ax
464
+
465
+
466
+ # =============================================================================
467
+ # Vector Fields
468
+ # =============================================================================
469
+ def plot_quiver(fig, ax, stx):
470
+ """ax.quiver() - Vector field."""
471
+ x = np.linspace(-2, 2, 10)
472
+ y = np.linspace(-2, 2, 10)
473
+ X, Y = np.meshgrid(x, y)
474
+ U = -Y
475
+ V = X
476
+ ax.quiver(X, Y, U, V, id="rotation_field")
477
+ ax.set_xyt(x="X", y="Y", t="ax.quiver()")
478
+ return fig, ax
479
+
480
+
481
+ def plot_streamplot(fig, ax, stx):
482
+ """ax.streamplot() - Streamlines."""
483
+ x = np.linspace(-2, 2, 30)
484
+ y = np.linspace(-2, 2, 30)
485
+ X, Y = np.meshgrid(x, y)
486
+ U = -1 - X**2 + Y
487
+ V = 1 + X - Y**2
488
+ ax.streamplot(X, Y, U, V, density=1, id="flow_field")
489
+ ax.set_xyt(x="X", y="Y", t="ax.streamplot()")
490
+ return fig, ax
491
+
492
+
493
+ # =============================================================================
494
+ # Special
495
+ # =============================================================================
496
+ def plot_pie(fig, ax, stx):
497
+ """ax.pie() - Pie chart."""
498
+ sizes = [30, 25, 20, 15, 10]
499
+ labels = ["Category A", "Category B", "Category C", "Category D", "Category E"]
500
+ ax.pie(sizes, labels=labels, autopct="%1.1f%%", id="category_breakdown")
501
+ ax.set_title("ax.pie()")
502
+ return fig, ax
503
+
504
+
505
+ def plot_stx_raster(fig, ax, stx):
506
+ """ax.stx_raster() - Spike raster plot."""
507
+ np.random.seed(42)
508
+ n_neurons, n_timepoints = 20, 1000
509
+ spike_times = [
510
+ np.sort(
511
+ np.random.choice(n_timepoints, np.random.randint(10, 50), replace=False)
512
+ )
513
+ for _ in range(n_neurons)
514
+ ]
515
+ ax.stx_raster(spike_times, id="neural_spikes")
516
+ ax.set_xyt(x="Time [ms]", y="Neuron", t="ax.stx_raster()")
517
+ return fig, ax
518
+
519
+
520
+ def plot_stx_rectangle(fig, ax, stx):
521
+ """ax.stx_rectangle() - Rectangle annotation."""
522
+ np.random.seed(42)
523
+ time = np.linspace(0, 10, 200)
524
+ signal = np.sin(time * 2) + np.random.normal(0, 0.1, 200)
525
+ ax.plot(time, signal, "b-", alpha=0.7, id="signal")
526
+ ax.stx_rectangle(2, -0.5, 2, 1.5, alpha=0.3, color="red", id="region_of_interest")
527
+ ax.set_xyt(x="Time [s]", y="Amplitude", t="ax.stx_rectangle()")
528
+ return fig, ax
529
+
530
+
531
+ # =============================================================================
532
+ # Plot Registry
533
+ # =============================================================================
534
+ PLOT_FUNCTIONS = {
535
+ # Line
536
+ "plot": plot_plot,
537
+ "step": plot_step,
538
+ "stx_line": plot_stx_line,
539
+ "stx_shaded_line": plot_stx_shaded_line,
540
+ # Statistical
541
+ "stx_mean_std": plot_stx_mean_std,
542
+ "stx_mean_ci": plot_stx_mean_ci,
543
+ "stx_median_iqr": plot_stx_median_iqr,
544
+ "errorbar": plot_errorbar,
545
+ "stx_errorbar": plot_stx_errorbar,
546
+ # Distribution
547
+ "hist": plot_hist,
548
+ "hist2d": plot_hist2d,
549
+ "stx_kde": plot_stx_kde,
550
+ "stx_ecdf": plot_stx_ecdf,
551
+ "stx_joyplot": plot_stx_joyplot,
552
+ # Categorical
553
+ "bar": plot_bar,
554
+ "barh": plot_barh,
555
+ "stx_bar": plot_stx_bar,
556
+ "stx_barh": plot_stx_barh,
557
+ "boxplot": plot_boxplot,
558
+ "violinplot": plot_violinplot,
559
+ "stx_box": plot_stx_box,
560
+ "stx_violin": plot_stx_violin,
561
+ "stx_boxplot": plot_stx_boxplot,
562
+ "stx_violinplot": plot_stx_violinplot,
563
+ # Scatter
564
+ "scatter": plot_scatter,
565
+ "stx_scatter": plot_stx_scatter,
566
+ "stem": plot_stem,
567
+ "hexbin": plot_hexbin,
568
+ # Area
569
+ "fill_between": plot_fill_between,
570
+ "fill_betweenx": plot_fill_betweenx,
571
+ "stx_fill_between": plot_stx_fill_between,
572
+ "stx_fillv": plot_stx_fillv,
573
+ # Grid
574
+ "imshow": plot_imshow,
575
+ "matshow": plot_matshow,
576
+ "stx_imshow": plot_stx_imshow,
577
+ "stx_image": plot_stx_image,
578
+ "stx_heatmap": plot_stx_heatmap,
579
+ "stx_conf_mat": plot_stx_conf_mat,
580
+ # Contour
581
+ "contour": plot_contour,
582
+ "contourf": plot_contourf,
583
+ "stx_contour": plot_stx_contour,
584
+ # Vector
585
+ "quiver": plot_quiver,
586
+ "streamplot": plot_streamplot,
587
+ # Special
588
+ "pie": plot_pie,
589
+ "stx_raster": plot_stx_raster,
590
+ "stx_rectangle": plot_stx_rectangle,
591
+ }
592
+
593
+
594
+ # EOF