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
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  334. scitex/gen/_print_config.py +0 -3
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  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
@@ -5,50 +5,53 @@
5
5
  # ----------------------------------------
6
6
  from __future__ import annotations
7
7
  import os
8
+
8
9
  __FILE__ = __file__
9
10
  __DIR__ = os.path.dirname(__FILE__)
10
11
  # ----------------------------------------
11
12
 
12
- import warnings
13
-
14
13
  import numpy as np
15
14
  import pandas as pd
16
15
  from scitex.pd import to_xyz
17
16
 
17
+ from scitex import logging
18
+
19
+ logger = logging.getLogger(__name__)
20
+
18
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  # Global warning registry to track which warnings have been shown
19
22
  _warning_registry = set()
20
23
 
21
24
  # Mapping of matplotlib/seaborn methods to their scitex equivalents
22
25
  _METHOD_ALTERNATIVES = {
23
26
  # Matplotlib methods
24
- 'imshow': 'plot_imshow',
25
- 'plot': 'plot', # already tracked
26
- 'scatter': 'plot_scatter', # already tracked
27
- 'bar': 'plot_bar', # already tracked
28
- 'barh': 'plot_barh', # already tracked
29
- 'hist': 'hist', # already tracked
30
- 'boxplot': 'stx_box or plot_boxplot',
31
- 'violinplot': 'stx_violin or plot_violinplot',
32
- 'fill_between': 'plot_fill_between',
33
- 'errorbar': 'plot_errorbar',
34
- 'contour': 'plot_contour',
35
- 'heatmap': 'stx_heatmap',
36
-
27
+ "imshow": "plot_imshow",
28
+ "plot": "plot", # already tracked
29
+ "scatter": "plot_scatter", # already tracked
30
+ "bar": "plot_bar", # already tracked
31
+ "barh": "plot_barh", # already tracked
32
+ "hist": "hist", # already tracked
33
+ "boxplot": "stx_box or plot_boxplot",
34
+ "violinplot": "stx_violin or plot_violinplot",
35
+ "fill_between": "plot_fill_between",
36
+ "errorbar": "plot_errorbar",
37
+ "contour": "plot_contour",
38
+ "heatmap": "stx_heatmap",
37
39
  # Seaborn methods (accessed via ax.sns_*)
38
- 'scatterplot': 'sns_scatterplot',
39
- 'lineplot': 'sns_lineplot',
40
- 'barplot': 'sns_barplot',
41
- 'boxplot_sns': 'sns_boxplot',
42
- 'violinplot_sns': 'sns_violinplot',
43
- 'stripplot': 'sns_stripplot',
44
- 'swarmplot': 'sns_swarmplot',
45
- 'histplot': 'sns_histplot',
46
- 'kdeplot': 'sns_kdeplot',
47
- 'heatmap_sns': 'sns_heatmap',
48
- 'jointplot': 'sns_jointplot',
49
- 'pairplot': 'sns_pairplot',
40
+ "scatterplot": "sns_scatterplot",
41
+ "lineplot": "sns_lineplot",
42
+ "barplot": "sns_barplot",
43
+ "boxplot_sns": "sns_boxplot",
44
+ "violinplot_sns": "sns_violinplot",
45
+ "stripplot": "sns_stripplot",
46
+ "swarmplot": "sns_swarmplot",
47
+ "histplot": "sns_histplot",
48
+ "kdeplot": "sns_kdeplot",
49
+ "heatmap_sns": "sns_heatmap",
50
+ "jointplot": "sns_jointplot",
51
+ "pairplot": "sns_pairplot",
50
52
  }
51
53
 
54
+
52
55
  def _warn_once(message, category=UserWarning):
53
56
  """Show a warning only once per runtime.
54
57
 
@@ -58,30 +61,77 @@ def _warn_once(message, category=UserWarning):
58
61
  """
59
62
  if message not in _warning_registry:
60
63
  _warning_registry.add(message)
61
- warnings.warn(message, category, stacklevel=3)
64
+ logger.warning(message)
65
+
62
66
 
63
67
  from ._export_as_csv_formatters import (
64
68
  # Standard matplotlib formatters
65
- _format_annotate, _format_bar, _format_barh, _format_boxplot,
66
- _format_contour, _format_contourf, _format_errorbar, _format_eventplot,
67
- _format_fill, _format_fill_between, _format_hexbin, _format_hist,
68
- _format_hist2d, _format_imshow, _format_imshow2d, _format_matshow,
69
- _format_pie, _format_plot, _format_quiver, _format_scatter, _format_stem,
70
- _format_step, _format_streamplot, _format_text, _format_violin,
69
+ _format_annotate,
70
+ _format_bar,
71
+ _format_barh,
72
+ _format_boxplot,
73
+ _format_contour,
74
+ _format_contourf,
75
+ _format_errorbar,
76
+ _format_eventplot,
77
+ _format_fill,
78
+ _format_fill_between,
79
+ _format_hexbin,
80
+ _format_hist,
81
+ _format_hist2d,
82
+ _format_imshow,
83
+ _format_imshow2d,
84
+ _format_matshow,
85
+ _format_pie,
86
+ _format_plot,
87
+ _format_quiver,
88
+ _format_scatter,
89
+ _format_stem,
90
+ _format_step,
91
+ _format_streamplot,
92
+ _format_text,
93
+ _format_violin,
71
94
  _format_violinplot,
72
95
  # Custom scitex formatters
73
- _format_plot_box, _format_plot_conf_mat, _format_plot_ecdf,
74
- _format_plot_fillv, _format_plot_heatmap, _format_plot_image,
75
- _format_plot_imshow, _format_plot_joyplot, _format_plot_kde,
76
- _format_plot_line, _format_plot_mean_ci, _format_plot_mean_std,
77
- _format_plot_median_iqr, _format_plot_raster, _format_plot_rectangle,
78
- _format_plot_scatter, _format_plot_scatter_hist, _format_plot_shaded_line,
96
+ _format_plot_box,
97
+ _format_plot_conf_mat,
98
+ _format_stx_contour,
99
+ _format_plot_ecdf,
100
+ _format_plot_fillv,
101
+ _format_plot_heatmap,
102
+ _format_plot_image,
103
+ _format_plot_imshow,
104
+ _format_stx_imshow,
105
+ _format_plot_joyplot,
106
+ _format_plot_kde,
107
+ _format_plot_line,
108
+ _format_plot_mean_ci,
109
+ _format_plot_mean_std,
110
+ _format_plot_median_iqr,
111
+ _format_plot_raster,
112
+ _format_plot_rectangle,
113
+ _format_plot_scatter,
114
+ _format_plot_scatter_hist,
115
+ _format_plot_shaded_line,
79
116
  _format_plot_violin,
117
+ # stx_ aliases formatters
118
+ _format_stx_scatter,
119
+ _format_stx_bar,
120
+ _format_stx_barh,
121
+ _format_stx_errorbar,
80
122
  # Seaborn formatters
81
- _format_sns_barplot, _format_sns_boxplot, _format_sns_heatmap,
82
- _format_sns_histplot, _format_sns_jointplot, _format_sns_kdeplot,
83
- _format_sns_lineplot, _format_sns_pairplot, _format_sns_scatterplot,
84
- _format_sns_stripplot, _format_sns_swarmplot, _format_sns_violinplot,
123
+ _format_sns_barplot,
124
+ _format_sns_boxplot,
125
+ _format_sns_heatmap,
126
+ _format_sns_histplot,
127
+ _format_sns_jointplot,
128
+ _format_sns_kdeplot,
129
+ _format_sns_lineplot,
130
+ _format_sns_pairplot,
131
+ _format_sns_scatterplot,
132
+ _format_sns_stripplot,
133
+ _format_sns_swarmplot,
134
+ _format_sns_violinplot,
85
135
  )
86
136
 
87
137
  # Registry mapping method names to their formatter functions
@@ -116,11 +166,13 @@ _FORMATTER_REGISTRY = {
116
166
  # Custom scitex methods
117
167
  "stx_box": _format_plot_box,
118
168
  "stx_conf_mat": _format_plot_conf_mat,
169
+ "stx_contour": _format_stx_contour,
119
170
  "stx_ecdf": _format_plot_ecdf,
120
171
  "stx_fillv": _format_plot_fillv,
121
172
  "stx_heatmap": _format_plot_heatmap,
122
173
  "stx_image": _format_plot_image,
123
174
  "plot_imshow": _format_plot_imshow,
175
+ "stx_imshow": _format_stx_imshow,
124
176
  "stx_joyplot": _format_plot_joyplot,
125
177
  "stx_kde": _format_plot_kde,
126
178
  "stx_line": _format_plot_line,
@@ -133,6 +185,11 @@ _FORMATTER_REGISTRY = {
133
185
  "stx_scatter_hist": _format_plot_scatter_hist,
134
186
  "stx_shaded_line": _format_plot_shaded_line,
135
187
  "stx_violin": _format_plot_violin,
188
+ # stx_ aliases
189
+ "stx_scatter": _format_stx_scatter,
190
+ "stx_bar": _format_stx_bar,
191
+ "stx_barh": _format_stx_barh,
192
+ "stx_errorbar": _format_stx_errorbar,
136
193
  # Seaborn methods (sns_ prefix)
137
194
  "sns_barplot": _format_sns_barplot,
138
195
  "sns_boxplot": _format_sns_boxplot,
@@ -165,9 +222,7 @@ def _to_numpy(data):
165
222
  Data as numpy array
166
223
  """
167
224
  if hasattr(data, "numpy"): # torch tensor
168
- return (
169
- data.detach().numpy() if hasattr(data, "detach") else data.numpy()
170
- )
225
+ return data.detach().numpy() if hasattr(data, "detach") else data.numpy()
171
226
  elif hasattr(data, "values"): # pandas series/dataframe
172
227
  return data.values
173
228
  else:
@@ -187,15 +242,15 @@ def export_as_csv(history_records):
187
242
  ValueError: If no plotting records are found or they cannot be combined.
188
243
  """
189
244
  if len(history_records) <= 0:
190
- warnings.warn("Plotting records not found. Cannot export empty data.")
245
+ logger.warning("Plotting records not found. Cannot export empty data.")
191
246
  return pd.DataFrame() # Return empty DataFrame instead of None
192
247
 
193
248
  dfs = []
194
249
  failed_methods = set() # Track failed methods for helpful warnings
195
250
 
196
- for record in list(history_records.values()):
251
+ for record_index, record in enumerate(list(history_records.values())):
197
252
  try:
198
- formatted_df = format_record(record)
253
+ formatted_df = format_record(record, record_index=record_index)
199
254
  if formatted_df is not None and not formatted_df.empty:
200
255
  dfs.append(formatted_df)
201
256
  else:
@@ -229,7 +284,7 @@ def export_as_csv(history_records):
229
284
  df = pd.concat(dfs_reset, axis=1)
230
285
  return df
231
286
  except Exception as e:
232
- warnings.warn(f"Failed to combine plotting records: {e}")
287
+ logger.warning(f"Failed to combine plotting records: {e}")
233
288
  # Return a DataFrame with metadata about what records were attempted
234
289
  meta_df = pd.DataFrame(
235
290
  {
@@ -244,11 +299,13 @@ def export_as_csv(history_records):
244
299
  return meta_df
245
300
 
246
301
 
247
- def format_record(record):
302
+ def format_record(record, record_index=0):
248
303
  """Route record to the appropriate formatting function based on plot method.
249
304
 
250
305
  Args:
251
306
  record (tuple): Plotting record tuple (id, method, tracked_dict, kwargs).
307
+ record_index (int): Index of this record in the history (used as fallback
308
+ for trace_id when user doesn't provide an explicit id= kwarg).
252
309
 
253
310
  Returns:
254
311
  pd.DataFrame: Formatted data for the plot record.
@@ -314,6 +371,8 @@ def format_record(record):
314
371
  return _format_plot_box(id, tracked_dict, kwargs)
315
372
  elif method == "stx_conf_mat":
316
373
  return _format_plot_conf_mat(id, tracked_dict, kwargs)
374
+ elif method == "stx_contour":
375
+ return _format_stx_contour(id, tracked_dict, kwargs)
317
376
  elif method == "stx_ecdf":
318
377
  return _format_plot_ecdf(id, tracked_dict, kwargs)
319
378
  elif method == "stx_fillv":
@@ -324,6 +383,8 @@ def format_record(record):
324
383
  return _format_plot_image(id, tracked_dict, kwargs)
325
384
  elif method == "plot_imshow":
326
385
  return _format_plot_imshow(id, tracked_dict, kwargs)
386
+ elif method == "stx_imshow":
387
+ return _format_stx_imshow(id, tracked_dict, kwargs)
327
388
  elif method == "stx_joyplot":
328
389
  return _format_plot_joyplot(id, tracked_dict, kwargs)
329
390
  elif method == "stx_kde":
@@ -349,6 +410,16 @@ def format_record(record):
349
410
  elif method == "stx_violin":
350
411
  return _format_plot_violin(id, tracked_dict, kwargs)
351
412
 
413
+ # stx_ aliases
414
+ elif method == "stx_scatter":
415
+ return _format_stx_scatter(id, tracked_dict, kwargs)
416
+ elif method == "stx_bar":
417
+ return _format_stx_bar(id, tracked_dict, kwargs)
418
+ elif method == "stx_barh":
419
+ return _format_stx_barh(id, tracked_dict, kwargs)
420
+ elif method == "stx_errorbar":
421
+ return _format_stx_errorbar(id, tracked_dict, kwargs)
422
+
352
423
  # Seaborn functions (sns_ prefix)
353
424
  elif method == "sns_barplot":
354
425
  return _format_sns_barplot(id, tracked_dict, kwargs)
@@ -381,4 +452,5 @@ def format_record(record):
381
452
  f"Check the feature-request-export-as-csv-functions.md for implementation status."
382
453
  )
383
454
 
455
+
384
456
  # EOF
@@ -4,6 +4,7 @@
4
4
  # File: /data/gpfs/projects/punim2354/ywatanabe/scitex_repo/src/scitex/plt/_subplots/_export_as_csv_formatters/__init__.py
5
5
  # ----------------------------------------
6
6
  import os
7
+
7
8
  __FILE__ = __file__
8
9
  __DIR__ = os.path.dirname(__FILE__)
9
10
  # ----------------------------------------
@@ -40,10 +41,12 @@ from ._format_violinplot import _format_violinplot
40
41
  from ._format_plot_imshow import _format_plot_imshow
41
42
  from ._format_plot_box import _format_plot_box
42
43
  from ._format_stx_conf_mat import _format_plot_conf_mat
44
+ from ._format_stx_contour import _format_stx_contour
43
45
  from ._format_stx_ecdf import _format_plot_ecdf
44
46
  from ._format_stx_fillv import _format_plot_fillv
45
47
  from ._format_stx_heatmap import _format_plot_heatmap
46
48
  from ._format_stx_image import _format_plot_image
49
+ from ._format_stx_imshow import _format_stx_imshow
47
50
  from ._format_stx_joyplot import _format_plot_joyplot
48
51
  from ._format_plot_kde import _format_plot_kde
49
52
  from ._format_stx_line import _format_plot_line
@@ -57,6 +60,12 @@ from ._format_stx_scatter_hist import _format_plot_scatter_hist
57
60
  from ._format_stx_shaded_line import _format_plot_shaded_line
58
61
  from ._format_stx_violin import _format_plot_violin
59
62
 
63
+ # stx_ aliases formatters
64
+ from ._format_stx_scatter import _format_stx_scatter
65
+ from ._format_stx_bar import _format_stx_bar
66
+ from ._format_stx_barh import _format_stx_barh
67
+ from ._format_stx_errorbar import _format_stx_errorbar
68
+
60
69
  # Seaborn formatters (sns_ prefix)
61
70
  from ._format_sns_barplot import _format_sns_barplot
62
71
  from ._format_sns_boxplot import _format_sns_boxplot
@@ -5,28 +5,15 @@
5
5
  # ----------------------------------------
6
6
  from __future__ import annotations
7
7
  import os
8
+
8
9
  __FILE__ = __file__
9
10
  __DIR__ = os.path.dirname(__FILE__)
10
11
  # ----------------------------------------
11
12
 
12
13
  import pandas as pd
13
14
 
14
-
15
- def _make_column_name(id, suffix, method="annotate"):
16
- """Create column name with method descriptor, avoiding duplication.
17
-
18
- For example:
19
- - id="annotate_0", suffix="x" -> "annotate_0_x"
20
- - id="plot_5", suffix="x" -> "plot_5_annotate_x"
21
- """
22
- # Check if method name is already in the ID
23
- id_parts = id.rsplit('_', 1)
24
- if len(id_parts) == 2 and id_parts[0].endswith(method):
25
- # Method already in ID, don't duplicate
26
- return f"{id}_{suffix}"
27
- else:
28
- # Method not in ID, add it for clarity
29
- return f"{id}_{method}_{suffix}"
15
+ from scitex.plt.utils._csv_column_naming import get_csv_column_name
16
+ from ._format_plot import _parse_tracking_id
30
17
 
31
18
 
32
19
  def _format_annotate(id, tracked_dict, kwargs):
@@ -41,6 +28,9 @@ def _format_annotate(id, tracked_dict, kwargs):
41
28
  if not tracked_dict or not isinstance(tracked_dict, dict):
42
29
  return pd.DataFrame()
43
30
 
31
+ # Parse the tracking ID to get axes position and trace ID
32
+ ax_row, ax_col, trace_id = _parse_tracking_id(id)
33
+
44
34
  # Get the args from tracked_dict
45
35
  args = tracked_dict.get("args", [])
46
36
 
@@ -50,15 +40,15 @@ def _format_annotate(id, tracked_dict, kwargs):
50
40
  xy = args[1]
51
41
 
52
42
  # xy should be a tuple (x, y)
53
- if hasattr(xy, '__len__') and len(xy) >= 2:
43
+ if hasattr(xy, "__len__") and len(xy) >= 2:
54
44
  x, y = xy[0], xy[1]
55
45
  else:
56
46
  return pd.DataFrame()
57
47
 
58
48
  data = {
59
- _make_column_name(id, "x"): [x],
60
- _make_column_name(id, "y"): [y],
61
- _make_column_name(id, "content"): [text_content]
49
+ get_csv_column_name("x", ax_row, ax_col, trace_id=trace_id): [x],
50
+ get_csv_column_name("y", ax_row, ax_col, trace_id=trace_id): [y],
51
+ get_csv_column_name("content", ax_row, ax_col, trace_id=trace_id): [text_content],
62
52
  }
63
53
 
64
54
  # Check if xytext was provided (either as third arg or in kwargs)
@@ -68,9 +58,9 @@ def _format_annotate(id, tracked_dict, kwargs):
68
58
  elif "xytext" in kwargs:
69
59
  xytext = kwargs["xytext"]
70
60
 
71
- if xytext is not None and hasattr(xytext, '__len__') and len(xytext) >= 2:
72
- data[_make_column_name(id, "text_x")] = [xytext[0]]
73
- data[_make_column_name(id, "text_y")] = [xytext[1]]
61
+ if xytext is not None and hasattr(xytext, "__len__") and len(xytext) >= 2:
62
+ data[get_csv_column_name("text_x", ax_row, ax_col, trace_id=trace_id)] = [xytext[0]]
63
+ data[get_csv_column_name("text_y", ax_row, ax_col, trace_id=trace_id)] = [xytext[1]]
74
64
 
75
65
  # Create DataFrame with proper column names (use dict with list values)
76
66
  df = pd.DataFrame(data)
@@ -78,4 +68,5 @@ def _format_annotate(id, tracked_dict, kwargs):
78
68
 
79
69
  return pd.DataFrame()
80
70
 
71
+
81
72
  # EOF
@@ -4,6 +4,7 @@
4
4
  # File: /data/gpfs/projects/punim2354/ywatanabe/scitex_repo/src/scitex/plt/_subplots/_export_as_csv_formatters/_format_bar.py
5
5
  # ----------------------------------------
6
6
  import os
7
+
7
8
  __FILE__ = __file__
8
9
  __DIR__ = os.path.dirname(__FILE__)
9
10
  # ----------------------------------------
@@ -11,78 +12,127 @@ __DIR__ = os.path.dirname(__FILE__)
11
12
  import pandas as pd
12
13
  import numpy as np
13
14
 
15
+ from scitex.plt.utils._csv_column_naming import get_csv_column_name
16
+ from ._format_plot import _parse_tracking_id
17
+
18
+
14
19
  def _format_bar(id, tracked_dict, kwargs):
15
20
  """Format data from a bar call for CSV export.
16
-
17
- Simplified to focus only on essential x and y values.
18
-
21
+
22
+ Includes x, y values and optional yerr for error bars.
23
+
19
24
  Args:
20
25
  id: The identifier for the plot
21
26
  tracked_dict: Dictionary of tracked data
22
- kwargs: Original keyword arguments
23
-
27
+ kwargs: Original keyword arguments (may contain yerr)
28
+
24
29
  Returns:
25
- pd.DataFrame: Formatted data ready for CSV export with just x and y values
30
+ pd.DataFrame: Formatted data ready for CSV export with x, y, and optional yerr
26
31
  """
27
32
  # Check if tracked_dict is empty or not a dictionary
28
33
  if not tracked_dict or not isinstance(tracked_dict, dict):
29
34
  return pd.DataFrame()
30
-
35
+
36
+ # Parse tracking ID to get axes position and trace ID
37
+ ax_row, ax_col, trace_id = _parse_tracking_id(id)
38
+
39
+ # Get structured column names
40
+ col_x = get_csv_column_name("x", ax_row, ax_col, trace_id=trace_id)
41
+ col_y = get_csv_column_name("y", ax_row, ax_col, trace_id=trace_id)
42
+ col_yerr = get_csv_column_name("yerr", ax_row, ax_col, trace_id=trace_id)
43
+
44
+ # Extract yerr from kwargs if present
45
+ yerr = kwargs.get("yerr") if kwargs else None
46
+
31
47
  # Check if we have the newer format with bar_data
32
- if 'bar_data' in tracked_dict and isinstance(tracked_dict['bar_data'], pd.DataFrame):
48
+ if "bar_data" in tracked_dict and isinstance(
49
+ tracked_dict["bar_data"], pd.DataFrame
50
+ ):
33
51
  # Use the pre-formatted DataFrame but keep only x and height (y)
34
- df = tracked_dict['bar_data'].copy()
35
-
52
+ df = tracked_dict["bar_data"].copy()
53
+
36
54
  # Keep only essential columns
37
- essential_cols = [col for col in df.columns if col in ['x', 'height']]
55
+ essential_cols = [col for col in df.columns if col in ["x", "height"]]
38
56
  if essential_cols:
39
57
  df = df[essential_cols]
40
-
41
- # Rename height to y for consistency
42
- if 'height' in df.columns:
43
- df = df.rename(columns={'height': 'y'})
44
-
45
- # Add identifier to column names
46
- df.columns = [f"{id}_{col}" for col in df.columns]
58
+
59
+ # Rename using structured naming
60
+ rename_map = {}
61
+ if "x" in df.columns:
62
+ rename_map["x"] = col_x
63
+ if "height" in df.columns:
64
+ rename_map["height"] = col_y
65
+
66
+ df = df.rename(columns=rename_map)
67
+
68
+ # Add yerr if present
69
+ if yerr is not None:
70
+ try:
71
+ yerr_array = np.asarray(yerr)
72
+ if len(yerr_array) == len(df):
73
+ df[col_yerr] = yerr_array
74
+ except (TypeError, ValueError):
75
+ pass
76
+
47
77
  return df
48
-
78
+
49
79
  # Legacy format - get the args from tracked_dict
50
- args = tracked_dict.get('args', [])
51
-
80
+ args = tracked_dict.get("args", [])
81
+
52
82
  # Extract x and y data if available
53
83
  if len(args) >= 2:
54
84
  x, y = args[0], args[1]
55
-
85
+
56
86
  # Convert to arrays if possible for consistent handling
57
87
  try:
58
88
  x_array = np.asarray(x)
59
89
  y_array = np.asarray(y)
60
-
61
- # Create DataFrame with just x and y data
90
+
91
+ # Create DataFrame with structured column names
62
92
  data = {
63
- f"{id}_x": x_array,
64
- f"{id}_y": y_array,
93
+ col_x: x_array,
94
+ col_y: y_array,
65
95
  }
66
-
96
+
97
+ # Add yerr if present
98
+ if yerr is not None:
99
+ try:
100
+ yerr_array = np.asarray(yerr)
101
+ if len(yerr_array) == len(x_array):
102
+ data[col_yerr] = yerr_array
103
+ except (TypeError, ValueError):
104
+ pass
105
+
67
106
  return pd.DataFrame(data)
68
-
107
+
69
108
  except (TypeError, ValueError):
70
109
  # Fall back to direct values if conversion fails
71
- return pd.DataFrame({f"{id}_x": x, f"{id}_y": y})
72
-
110
+ result = {col_x: x, col_y: y}
111
+ if yerr is not None:
112
+ result[col_yerr] = yerr
113
+ return pd.DataFrame(result)
114
+
73
115
  # If we have tracked data in another format (like our MatplotlibPlotMixin bar method)
74
116
  result = {}
75
-
117
+
76
118
  # Check for x position (might be in different keys)
77
- for x_key in ['x', 'xs', 'positions']:
119
+ for x_key in ["x", "xs", "positions"]:
78
120
  if x_key in tracked_dict:
79
- result[f"{id}_x"] = tracked_dict[x_key]
121
+ result[col_x] = tracked_dict[x_key]
80
122
  break
81
-
123
+
82
124
  # Check for y values (might be in different keys)
83
- for y_key in ['y', 'ys', 'height', 'heights', 'values']:
125
+ for y_key in ["y", "ys", "height", "heights", "values"]:
84
126
  if y_key in tracked_dict:
85
- result[f"{id}_y"] = tracked_dict[y_key]
127
+ result[col_y] = tracked_dict[y_key]
86
128
  break
87
-
88
- return pd.DataFrame(result) if result else pd.DataFrame()
129
+
130
+ # Add yerr if present in kwargs
131
+ if yerr is not None and result:
132
+ try:
133
+ yerr_array = np.asarray(yerr)
134
+ result[col_yerr] = yerr_array
135
+ except (TypeError, ValueError):
136
+ pass
137
+
138
+ return pd.DataFrame(result) if result else pd.DataFrame()
@@ -4,61 +4,55 @@
4
4
  # File: /data/gpfs/projects/punim2354/ywatanabe/scitex_repo/src/scitex/plt/_subplots/_export_as_csv_formatters/_format_barh.py
5
5
  # ----------------------------------------
6
6
  import os
7
+
7
8
  __FILE__ = __file__
8
9
  __DIR__ = os.path.dirname(__FILE__)
9
10
  # ----------------------------------------
10
11
 
11
12
  import pandas as pd
12
13
 
13
- def _make_column_name(id, suffix, method="barh"):
14
- """Create column name with method descriptor, avoiding duplication.
14
+ from scitex.plt.utils._csv_column_naming import get_csv_column_name
15
+ from ._format_plot import _parse_tracking_id
15
16
 
16
- For example:
17
- - id="barh_0", suffix="x" -> "barh_0_barh_x"
18
- - id="plot_5", suffix="x" -> "plot_5_barh_x"
19
- """
20
- # Check if method name is already in the ID
21
- id_parts = id.rsplit('_', 1)
22
- if len(id_parts) == 2 and id_parts[0].endswith(method):
23
- # Method already in ID, don't duplicate
24
- return f"{id}_{suffix}"
25
- else:
26
- # Method not in ID, add it for clarity
27
- return f"{id}_{method}_{suffix}"
28
17
 
29
18
  def _format_barh(id, tracked_dict, kwargs):
30
19
  """Format data from a barh call."""
31
20
  # Check if tracked_dict is empty or not a dictionary
32
21
  if not tracked_dict or not isinstance(tracked_dict, dict):
33
22
  return pd.DataFrame()
34
-
23
+
24
+ # Parse tracking ID to get axes position and trace ID
25
+ ax_row, ax_col, trace_id = _parse_tracking_id(id)
26
+
35
27
  # Get the args from tracked_dict
36
- args = tracked_dict.get('args', [])
37
-
28
+ args = tracked_dict.get("args", [])
29
+
38
30
  # Extract x and y data if available
39
31
  if len(args) >= 2:
40
- # Note: in barh, x is height, y is width (visually transposed from bar)
41
- x, y = args[0], args[1]
42
-
32
+ # Note: in barh, first arg is y positions, second is widths (x values)
33
+ y_pos, x_width = args[0], args[1]
34
+
43
35
  # Get xerr from kwargs
44
36
  xerr = kwargs.get("xerr")
45
-
37
+
46
38
  # Convert single values to Series
47
- if isinstance(x, (int, float)):
48
- x = pd.Series(x, name="x")
49
- if isinstance(y, (int, float)):
50
- y = pd.Series(y, name="y")
39
+ if isinstance(y_pos, (int, float)):
40
+ y_pos = pd.Series(y_pos, name="y")
41
+ if isinstance(x_width, (int, float)):
42
+ x_width = pd.Series(x_width, name="x")
51
43
  else:
52
44
  # Not enough arguments
53
45
  return pd.DataFrame()
54
46
 
55
- # Use helper to create descriptive column names without duplication
56
- df = pd.DataFrame(
57
- {_make_column_name(id, "y"): x, _make_column_name(id, "x"): y}
58
- ) # Swap x/y for barh
47
+ # Use structured column naming: ax-row-{row}-col-{col}_trace-id-{id}_variable-{var}
48
+ col_x = get_csv_column_name("x", ax_row, ax_col, trace_id=trace_id)
49
+ col_y = get_csv_column_name("y", ax_row, ax_col, trace_id=trace_id)
50
+
51
+ df = pd.DataFrame({col_y: y_pos, col_x: x_width})
59
52
 
60
53
  if xerr is not None:
61
54
  if isinstance(xerr, (int, float)):
62
55
  xerr = pd.Series(xerr, name="xerr")
63
- df[_make_column_name(id, "xerr")] = xerr
64
- return df
56
+ col_xerr = get_csv_column_name("xerr", ax_row, ax_col, trace_id=trace_id)
57
+ df[col_xerr] = xerr
58
+ return df