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
@@ -5,9 +5,8 @@
5
5
  # ----------------------------------------
6
6
  from __future__ import annotations
7
7
  import os
8
- __FILE__ = (
9
- "./src/scitex/scholar/storage/_LibraryManager.py"
10
- )
8
+
9
+ __FILE__ = "./src/scitex/scholar/storage/_LibraryManager.py"
11
10
  __DIR__ = os.path.dirname(__FILE__)
12
11
  # ----------------------------------------
13
12
 
@@ -78,7 +77,7 @@ class LibraryManager:
78
77
 
79
78
  metadata_file = self.library_master_dir / paper_id / "metadata.json"
80
79
  try:
81
- with open(metadata_file, 'r') as f:
80
+ with open(metadata_file, "r") as f:
82
81
  data = json.load(f)
83
82
 
84
83
  # Check nested structure: metadata.url.pdfs
@@ -121,7 +120,7 @@ class LibraryManager:
121
120
  return None
122
121
 
123
122
  try:
124
- with open(metadata_file, 'r') as f:
123
+ with open(metadata_file, "r") as f:
125
124
  data = json.load(f)
126
125
 
127
126
  # Use Paper.from_dict() which handles Pydantic validation
@@ -151,7 +150,7 @@ class LibraryManager:
151
150
  existing_data = {}
152
151
  if metadata_file.exists():
153
152
  try:
154
- with open(metadata_file, 'r') as f:
153
+ with open(metadata_file, "r") as f:
155
154
  existing_data = json.load(f)
156
155
  except Exception:
157
156
  pass
@@ -168,7 +167,7 @@ class LibraryManager:
168
167
  merged_data["container"]["updated_at"] = datetime.now().isoformat()
169
168
 
170
169
  # Save to file
171
- with open(metadata_file, 'w') as f:
170
+ with open(metadata_file, "w") as f:
172
171
  json.dump(merged_data, f, indent=2, ensure_ascii=False)
173
172
 
174
173
  logger.debug(f"Saved paper {paper_id} to storage")
@@ -217,9 +216,7 @@ class LibraryManager:
217
216
  if source and source not in engines_list:
218
217
  engines_list.append(source)
219
218
 
220
- def _convert_to_standardized_metadata(
221
- self, flat_metadata: Dict
222
- ) -> OrderedDict:
219
+ def _convert_to_standardized_metadata(self, flat_metadata: Dict) -> OrderedDict:
223
220
  """Convert flat metadata dict to standardized nested structure with _engines tracking."""
224
221
  standardized = copy.deepcopy(BASE_STRUCTURE)
225
222
 
@@ -289,9 +286,7 @@ class LibraryManager:
289
286
  standardized["citation_count"][year] = cc_value[year]
290
287
  if f"{year}_source" in cc_value:
291
288
  self._add_engine_to_list(
292
- standardized["citation_count"][
293
- f"{year}_engines"
294
- ],
289
+ standardized["citation_count"][f"{year}_engines"],
295
290
  cc_value.get(f"{year}_source"),
296
291
  )
297
292
  else:
@@ -331,9 +326,7 @@ class LibraryManager:
331
326
  standardized["publication"]["first_page"] = first.strip()
332
327
  standardized["publication"]["last_page"] = last.strip()
333
328
  if "publisher" in flat_metadata:
334
- standardized["publication"]["publisher"] = flat_metadata[
335
- "publisher"
336
- ]
329
+ standardized["publication"]["publisher"] = flat_metadata["publisher"]
337
330
 
338
331
  # URL section
339
332
  if "url_doi" in flat_metadata:
@@ -344,9 +337,7 @@ class LibraryManager:
344
337
  standardized["url"]["publisher_engines"], "ScholarURLFinder"
345
338
  )
346
339
  if "url_openurl_query" in flat_metadata:
347
- standardized["url"]["openurl_query"] = flat_metadata[
348
- "url_openurl_query"
349
- ]
340
+ standardized["url"]["openurl_query"] = flat_metadata["url_openurl_query"]
350
341
  if "url_openurl_resolved" in flat_metadata:
351
342
  standardized["url"]["openurl_resolved"] = flat_metadata[
352
343
  "url_openurl_resolved"
@@ -421,9 +412,7 @@ class LibraryManager:
421
412
  stored_year = metadata.get("year")
422
413
  stored_doi = metadata.get("doi")
423
414
 
424
- title_match = self._is_title_similar(
425
- title, stored_title
426
- )
415
+ title_match = self._is_title_similar(title, stored_title)
427
416
  year_match = (
428
417
  not year
429
418
  or not stored_year
@@ -506,12 +495,9 @@ class LibraryManager:
506
495
  year = year or paper_data.metadata.basic.year
507
496
  journal = journal or paper_data.metadata.publication.journal
508
497
  abstract = abstract or paper_data.metadata.basic.abstract
509
- publisher = (
510
- publisher or paper_data.metadata.publication.publisher
511
- )
498
+ publisher = publisher or paper_data.metadata.publication.publisher
512
499
  impact_factor = (
513
- impact_factor
514
- or paper_data.metadata.publication.impact_factor
500
+ impact_factor or paper_data.metadata.publication.impact_factor
515
501
  )
516
502
  library_id = library_id or paper_data.container.library_id
517
503
  elif isinstance(paper_data, dict):
@@ -523,9 +509,7 @@ class LibraryManager:
523
509
  journal = journal or paper_data.get("journal")
524
510
  abstract = abstract or paper_data.get("abstract")
525
511
  publisher = publisher or paper_data.get("publisher")
526
- impact_factor = impact_factor or paper_data.get(
527
- "impact_factor"
528
- )
512
+ impact_factor = impact_factor or paper_data.get("impact_factor")
529
513
  library_id = (
530
514
  library_id
531
515
  or paper_data.get("scitex_id")
@@ -566,9 +550,7 @@ class LibraryManager:
566
550
  "authors": authors or [],
567
551
  "year": year,
568
552
  }
569
- existing_paper_dir = self.dedup_manager.check_for_existing_paper(
570
- check_metadata
571
- )
553
+ existing_paper_dir = self.dedup_manager.check_for_existing_paper(check_metadata)
572
554
 
573
555
  if existing_paper_dir:
574
556
  logger.info(f"Found existing paper: {existing_paper_dir.name}")
@@ -614,9 +596,7 @@ class LibraryManager:
614
596
  if abstract:
615
597
  clean_abstract = TextNormalizer.clean_metadata_text(abstract)
616
598
  elif metadata and metadata.get("abstract"):
617
- clean_abstract = TextNormalizer.clean_metadata_text(
618
- metadata["abstract"]
619
- )
599
+ clean_abstract = TextNormalizer.clean_metadata_text(metadata["abstract"])
620
600
  elif existing_metadata.get("abstract"):
621
601
  clean_abstract = TextNormalizer.clean_metadata_text(
622
602
  existing_metadata["abstract"]
@@ -649,45 +629,31 @@ class LibraryManager:
649
629
  or existing_metadata.get("year_source", "input" if year else None),
650
630
  "authors": existing_metadata.get("authors", authors or []),
651
631
  "authors_source": authors_source
652
- or existing_metadata.get(
653
- "authors_source", "input" if authors else None
654
- ),
632
+ or existing_metadata.get("authors_source", "input" if authors else None),
655
633
  "journal": existing_metadata.get("journal", journal),
656
634
  "journal_source": journal_source
657
- or existing_metadata.get(
658
- "journal_source", "input" if journal else None
659
- ),
635
+ or existing_metadata.get("journal_source", "input" if journal else None),
660
636
  # Additional bibliographic fields from explicit parameters
661
637
  "volume": existing_metadata.get("volume", volume),
662
638
  "issue": existing_metadata.get("issue", issue),
663
639
  "pages": existing_metadata.get("pages", pages),
664
640
  "publisher": existing_metadata.get("publisher", publisher),
665
641
  "issn": existing_metadata.get("issn", issn),
666
- "short_journal": existing_metadata.get(
667
- "short_journal", short_journal
668
- ),
642
+ "short_journal": existing_metadata.get("short_journal", short_journal),
669
643
  # Abstract with source tracking
670
644
  "abstract": existing_metadata.get("abstract", clean_abstract),
671
645
  "abstract_source": abstract_source
672
- or existing_metadata.get(
673
- "abstract_source", "input" if abstract else None
674
- ),
646
+ or existing_metadata.get("abstract_source", "input" if abstract else None),
675
647
  # Enrichment fields
676
- "citation_count": existing_metadata.get(
677
- "citation_count", citation_count
678
- ),
679
- "impact_factor": existing_metadata.get(
680
- "impact_factor", impact_factor
681
- ),
648
+ "citation_count": existing_metadata.get("citation_count", citation_count),
649
+ "impact_factor": existing_metadata.get("impact_factor", impact_factor),
682
650
  "scitex_id": existing_metadata.get(
683
651
  "scitex_id", existing_metadata.get("scholar_id", paper_id)
684
652
  ),
685
653
  "created_at": existing_metadata.get(
686
654
  "created_at", datetime.now().isoformat()
687
655
  ),
688
- "created_by": existing_metadata.get(
689
- "created_by", "SciTeX Scholar"
690
- ),
656
+ "created_by": existing_metadata.get("created_by", "SciTeX Scholar"),
691
657
  "updated_at": datetime.now().isoformat(),
692
658
  "projects": existing_metadata.get(
693
659
  "projects", [] if self.project == "master" else [self.project]
@@ -698,9 +664,7 @@ class LibraryManager:
698
664
  }
699
665
 
700
666
  # Store plain dict version for JSON serialization
701
- comprehensive_metadata_plain = self._dotdict_to_dict(
702
- comprehensive_metadata
703
- )
667
+ comprehensive_metadata_plain = self._dotdict_to_dict(comprehensive_metadata)
704
668
 
705
669
  # Convert to standardized format before saving
706
670
  standardized_metadata = self._convert_to_standardized_metadata(
@@ -734,24 +698,18 @@ class LibraryManager:
734
698
  ),
735
699
  (
736
700
  "projects",
737
- comprehensive_metadata_plain.get(
738
- "projects", []
739
- ),
701
+ comprehensive_metadata_plain.get("projects", []),
740
702
  ),
741
703
  ("master_storage_path", str(master_storage_path)),
742
704
  ("readable_name", readable_name),
743
705
  ("metadata_file", str(master_metadata_file)),
744
706
  (
745
707
  "pdf_downloaded_at",
746
- comprehensive_metadata_plain.get(
747
- "pdf_downloaded_at"
748
- ),
708
+ comprehensive_metadata_plain.get("pdf_downloaded_at"),
749
709
  ),
750
710
  (
751
711
  "pdf_size_bytes",
752
- comprehensive_metadata_plain.get(
753
- "pdf_size_bytes"
754
- ),
712
+ comprehensive_metadata_plain.get("pdf_size_bytes"),
755
713
  ),
756
714
  ]
757
715
  ),
@@ -782,9 +740,7 @@ class LibraryManager:
782
740
  readable_name=readable_name,
783
741
  )
784
742
  except Exception as exc_:
785
- logger.error(
786
- f"Failed to create symlink for {paper_id}: {exc_}"
787
- )
743
+ logger.error(f"Failed to create symlink for {paper_id}: {exc_}")
788
744
 
789
745
  return paper_id
790
746
 
@@ -797,9 +753,7 @@ class LibraryManager:
797
753
  bibtex_source: Optional[str] = None,
798
754
  ) -> None:
799
755
  """Save paper that couldn't be resolved to unresolved directory."""
800
- clean_title = (
801
- TextNormalizer.clean_metadata_text(title) if title else ""
802
- )
756
+ clean_title = TextNormalizer.clean_metadata_text(title) if title else ""
803
757
  unresolved_info = {
804
758
  "title": clean_title,
805
759
  "year": year,
@@ -836,9 +790,7 @@ class LibraryManager:
836
790
  ) -> Dict[str, Dict[str, str]]:
837
791
  """Resolve DOIs and create full Scholar library structure with proper paths."""
838
792
  if not self.single_doi_resolver:
839
- raise ValueError(
840
- "SingleDOIResolver is required for resolving DOIs"
841
- )
793
+ raise ValueError("SingleDOIResolver is required for resolving DOIs")
842
794
 
843
795
  results = {}
844
796
  for paper in papers:
@@ -857,9 +809,7 @@ class LibraryManager:
857
809
  sources=sources,
858
810
  )
859
811
 
860
- enhanced_metadata = self._extract_enhanced_metadata(
861
- doi_result, paper
862
- )
812
+ enhanced_metadata = self._extract_enhanced_metadata(doi_result, paper)
863
813
  paper_info = {**paper, **enhanced_metadata}
864
814
 
865
815
  storage_paths = self._call_path_manager_get_storage_paths(
@@ -886,9 +836,7 @@ class LibraryManager:
886
836
  readable_name=storage_paths["readable_name"],
887
837
  )
888
838
 
889
- bibtex_source_filename = getattr(
890
- self, "_source_filename", "papers"
891
- )
839
+ bibtex_source_filename = getattr(self, "_source_filename", "papers")
892
840
  info_dir = self._create_bibtex_info_structure(
893
841
  project=project,
894
842
  paper_info={**paper, **enhanced_metadata},
@@ -902,9 +850,7 @@ class LibraryManager:
902
850
  "doi": complete_metadata.get("doi"),
903
851
  "master_storage_path": str(storage_path),
904
852
  "project_symlink_path": (
905
- str(project_symlink_path)
906
- if project_symlink_path
907
- else None
853
+ str(project_symlink_path) if project_symlink_path else None
908
854
  ),
909
855
  "readable_name": storage_paths["readable_name"],
910
856
  "metadata_file": str(metadata_file),
@@ -963,14 +909,10 @@ class LibraryManager:
963
909
  or doi_result.get("abstract"),
964
910
  "publisher": metadata_source.get("publisher")
965
911
  or doi_result.get("publisher"),
966
- "volume": metadata_source.get("volume")
967
- or doi_result.get("volume"),
968
- "issue": metadata_source.get("issue")
969
- or doi_result.get("issue"),
970
- "pages": metadata_source.get("pages")
971
- or doi_result.get("pages"),
972
- "issn": metadata_source.get("issn")
973
- or doi_result.get("issn"),
912
+ "volume": metadata_source.get("volume") or doi_result.get("volume"),
913
+ "issue": metadata_source.get("issue") or doi_result.get("issue"),
914
+ "pages": metadata_source.get("pages") or doi_result.get("pages"),
915
+ "issn": metadata_source.get("issn") or doi_result.get("issn"),
974
916
  "short_journal": metadata_source.get("short_journal")
975
917
  or doi_result.get("short_journal"),
976
918
  }
@@ -992,9 +934,7 @@ class LibraryManager:
992
934
  ) -> Dict[str, Any]:
993
935
  """Create complete metadata dictionary with source tracking."""
994
936
  raw_title = enhanced_metadata.get("title") or paper.get("title")
995
- clean_title = (
996
- TextNormalizer.clean_metadata_text(raw_title) if raw_title else ""
997
- )
937
+ clean_title = TextNormalizer.clean_metadata_text(raw_title) if raw_title else ""
998
938
  raw_abstract = None
999
939
  if enhanced_metadata.get("abstract"):
1000
940
  raw_abstract = TextNormalizer.clean_metadata_text(
@@ -1022,8 +962,7 @@ class LibraryManager:
1022
962
  if enhanced_metadata.get("title") != paper.get("title")
1023
963
  else "manual"
1024
964
  ),
1025
- "authors": enhanced_metadata.get("authors")
1026
- or paper.get("authors"),
965
+ "authors": enhanced_metadata.get("authors") or paper.get("authors"),
1027
966
  "authors_source": (
1028
967
  doi_source_value
1029
968
  if enhanced_metadata.get("authors") != paper.get("authors")
@@ -1035,8 +974,7 @@ class LibraryManager:
1035
974
  if enhanced_metadata.get("year") != paper.get("year")
1036
975
  else ("manual" if paper.get("year") else None)
1037
976
  ),
1038
- "journal": enhanced_metadata.get("journal")
1039
- or paper.get("journal"),
977
+ "journal": enhanced_metadata.get("journal") or paper.get("journal"),
1040
978
  "journal_source": (
1041
979
  doi_source_value
1042
980
  if enhanced_metadata.get("journal") != paper.get("journal")
@@ -1099,10 +1037,7 @@ class LibraryManager:
1099
1037
 
1100
1038
  missing_fields = []
1101
1039
  for field, default_value in standard_fields.items():
1102
- if (
1103
- field not in complete_metadata
1104
- or complete_metadata[field] is None
1105
- ):
1040
+ if field not in complete_metadata or complete_metadata[field] is None:
1106
1041
  complete_metadata[field] = default_value
1107
1042
  missing_fields.append(field)
1108
1043
 
@@ -1145,18 +1080,16 @@ class LibraryManager:
1145
1080
  first_author = (
1146
1081
  author_parts[-1] if len(author_parts) > 1 else author_parts[0]
1147
1082
  )
1148
- first_author = "".join(
1149
- c for c in first_author if c.isalnum() or c == "-"
1150
- )[:20]
1083
+ first_author = "".join(c for c in first_author if c.isalnum() or c == "-")[
1084
+ :20
1085
+ ]
1151
1086
 
1152
1087
  # Format year (handle DotDict and other non-int types)
1153
1088
  from scitex.dict import DotDict
1154
1089
 
1155
1090
  if isinstance(year, DotDict):
1156
1091
  # Extract value if it's a DotDict
1157
- year = (
1158
- None # Can't extract year from DotDict structure, use Unknown
1159
- )
1092
+ year = None # Can't extract year from DotDict structure, use Unknown
1160
1093
 
1161
1094
  # Convert to int if it's a string representation
1162
1095
  if isinstance(year, str) and year.isdigit():
@@ -1204,9 +1137,7 @@ class LibraryManager:
1204
1137
  if_val = (
1205
1138
  comprehensive_metadata.get("journal_impact_factor")
1206
1139
  or comprehensive_metadata.get("impact_factor")
1207
- or comprehensive_metadata.get("publication", {}).get(
1208
- "impact_factor"
1209
- )
1140
+ or comprehensive_metadata.get("publication", {}).get("impact_factor")
1210
1141
  )
1211
1142
  if isinstance(if_val, dict):
1212
1143
  if_val = if_val.get("value", 0.0) or 0.0
@@ -1216,9 +1147,7 @@ class LibraryManager:
1216
1147
  # Check PDF status with more granular states
1217
1148
  pdf_files = list(master_storage_path.glob("*.pdf"))
1218
1149
  screenshot_dir = master_storage_path / "screenshots"
1219
- has_screenshots = screenshot_dir.exists() and any(
1220
- screenshot_dir.iterdir()
1221
- )
1150
+ has_screenshots = screenshot_dir.exists() and any(screenshot_dir.iterdir())
1222
1151
  downloading_marker = master_storage_path / ".downloading"
1223
1152
  attempted_marker = master_storage_path / ".download_attempted"
1224
1153
 
@@ -1226,11 +1155,7 @@ class LibraryManager:
1226
1155
  doi = None
1227
1156
  if "metadata" in comprehensive_metadata:
1228
1157
  # Nested structure from file
1229
- doi = (
1230
- comprehensive_metadata.get("metadata", {})
1231
- .get("id", {})
1232
- .get("doi")
1233
- )
1158
+ doi = comprehensive_metadata.get("metadata", {}).get("id", {}).get("doi")
1234
1159
  else:
1235
1160
  # Flat structure (during initial save)
1236
1161
  doi = comprehensive_metadata.get("doi")
@@ -1260,9 +1185,7 @@ class LibraryManager:
1260
1185
  "f": 2,
1261
1186
  "s": 3,
1262
1187
  }
1263
- pdf_status_str = (
1264
- f"{pdf_status_id_map[pdf_status_letter]}{pdf_status_letter}"
1265
- )
1188
+ pdf_status_str = f"{pdf_status_id_map[pdf_status_letter]}{pdf_status_letter}"
1266
1189
  # Format: CC_000000-PDF_s-IF_032-2016-Author-Journal
1267
1190
  # PDF status: r=running, s=successful, f=failed, p=pending
1268
1191
  # readable_name = f"CC_{cc:06d}-PDF_{pdf_status_letter}-IF_{int(if_val):03d}-{year_str}-{first_author}-{journal_clean}"
@@ -1300,9 +1223,7 @@ class LibraryManager:
1300
1223
  with open(metadata_file, "r") as f:
1301
1224
  metadata = json.load(f)
1302
1225
  else:
1303
- logger.warning(
1304
- f"No metadata found for {master_storage_path.name}"
1305
- )
1226
+ logger.warning(f"No metadata found for {master_storage_path.name}")
1306
1227
  return None
1307
1228
 
1308
1229
  # Extract metadata from nested structure if needed
@@ -1368,27 +1289,18 @@ class LibraryManager:
1368
1289
  # Check if this symlink points to the same master entry
1369
1290
  try:
1370
1291
  target = existing_link.resolve()
1371
- if (
1372
- target.name == master_id
1373
- and existing_link.name != readable_name
1374
- ):
1292
+ if target.name == master_id and existing_link.name != readable_name:
1375
1293
  # This is an old symlink for the same paper
1376
- logger.debug(
1377
- f"Removing old symlink: {existing_link.name}"
1378
- )
1294
+ logger.debug(f"Removing old symlink: {existing_link.name}")
1379
1295
  existing_link.unlink()
1380
1296
  except Exception as e:
1381
1297
  # Handle broken symlinks
1382
- logger.debug(
1383
- f"Skipping broken symlink {existing_link.name}: {e}"
1384
- )
1298
+ logger.debug(f"Skipping broken symlink {existing_link.name}: {e}")
1385
1299
  continue
1386
1300
 
1387
1301
  # Create new symlink
1388
1302
  if not symlink_path.exists():
1389
- relative_path = os.path.relpath(
1390
- master_storage_path, project_dir
1391
- )
1303
+ relative_path = os.path.relpath(master_storage_path, project_dir)
1392
1304
  symlink_path.symlink_to(relative_path)
1393
1305
  logger.success(
1394
1306
  f"Created project symlink: {symlink_path} -> {relative_path}"
@@ -1430,9 +1342,7 @@ class LibraryManager:
1430
1342
  year = complete_metadata.get("year", "unknown")
1431
1343
  entry_key = f"{first_author}{year}"
1432
1344
 
1433
- bibtex_entry = self._generate_bibtex_entry(
1434
- complete_metadata, entry_key
1435
- )
1345
+ bibtex_entry = self._generate_bibtex_entry(complete_metadata, entry_key)
1436
1346
 
1437
1347
  if bibtex_file.exists():
1438
1348
  with open(bibtex_file, "a", encoding="utf-8") as file_:
@@ -1463,9 +1373,7 @@ class LibraryManager:
1463
1373
  logger.warning(f"Failed to create BibTeX info structure: {exc_}")
1464
1374
  return None
1465
1375
 
1466
- def _generate_bibtex_entry(
1467
- self, metadata: Dict[str, Any], entry_key: str
1468
- ) -> str:
1376
+ def _generate_bibtex_entry(self, metadata: Dict[str, Any], entry_key: str) -> str:
1469
1377
  """Generate BibTeX entry from metadata."""
1470
1378
  entry_type = "article"
1471
1379
  if metadata.get("journal"):
@@ -1496,24 +1404,16 @@ class LibraryManager:
1496
1404
  if value:
1497
1405
  if isinstance(value, list):
1498
1406
  value = " and ".join(str(val_) for val_ in value)
1499
- value_escaped = (
1500
- str(value).replace("{", "\\{").replace("}", "\\}")
1501
- )
1407
+ value_escaped = str(value).replace("{", "\\{").replace("}", "\\}")
1502
1408
  bibtex += f" {bibtex_field} = {{{value_escaped}}},\n"
1503
1409
 
1504
1410
  source_field = f"{meta_field}_source"
1505
1411
  if source_field in metadata:
1506
1412
  bibtex += f" % {bibtex_field}_source = {metadata[source_field]}\n"
1507
1413
 
1508
- bibtex += (
1509
- f" % scholar_id = {metadata.get('scholar_id', 'unknown')},\n"
1510
- )
1511
- bibtex += (
1512
- f" % created_at = {metadata.get('created_at', 'unknown')},\n"
1513
- )
1514
- bibtex += (
1515
- f" % created_by = {metadata.get('created_by', 'unknown')},\n"
1516
- )
1414
+ bibtex += f" % scholar_id = {metadata.get('scholar_id', 'unknown')},\n"
1415
+ bibtex += f" % created_at = {metadata.get('created_at', 'unknown')},\n"
1416
+ bibtex += f" % created_by = {metadata.get('created_by', 'unknown')},\n"
1517
1417
  bibtex += "}\n"
1518
1418
 
1519
1419
  return bibtex
@@ -1566,14 +1466,12 @@ class LibraryManager:
1566
1466
  paper_id: str = None,
1567
1467
  master_storage_path: Path = None,
1568
1468
  ) -> None:
1569
-
1570
1469
  try:
1571
1470
  if not paper_id or not master_storage_path:
1572
1471
  return
1573
1472
 
1574
1473
  project_lib_path = (
1575
- self.config.path_manager.get_scholar_library_path()
1576
- / self.project
1474
+ self.config.path_manager.get_scholar_library_path() / self.project
1577
1475
  )
1578
1476
  project_lib_path.mkdir(parents=True, exist_ok=True)
1579
1477
 
@@ -1666,14 +1564,10 @@ class LibraryManager:
1666
1564
  return True
1667
1565
 
1668
1566
  except Exception as exc_:
1669
- logger.error(
1670
- f"Error updating library metadata for {paper_id}: {exc_}"
1671
- )
1567
+ logger.error(f"Error updating library metadata for {paper_id}: {exc_}")
1672
1568
  return False
1673
1569
 
1674
- def create_writer_directory_structure(
1675
- self, paper_id: str, project: str
1676
- ) -> Path:
1570
+ def create_writer_directory_structure(self, paper_id: str, project: str) -> Path:
1677
1571
  """Create basic paper directory structure."""
1678
1572
  library_path = self.config.path_manager.library_dir
1679
1573
  paper_dir = library_path / project / paper_id
@@ -1728,9 +1622,7 @@ class LibraryManager:
1728
1622
  ) -> Dict[str, str]:
1729
1623
  """Resolve DOIs and update Scholar library metadata.json files."""
1730
1624
  if not self.single_doi_resolver:
1731
- raise ValueError(
1732
- "SingleDOIResolver is required for resolving DOIs"
1733
- )
1625
+ raise ValueError("SingleDOIResolver is required for resolving DOIs")
1734
1626
 
1735
1627
  results = {}
1736
1628
  for paper in papers_with_ids:
@@ -1769,9 +1661,7 @@ class LibraryManager:
1769
1661
  "title": title,
1770
1662
  "title_source": "input",
1771
1663
  "year": paper.get("year"),
1772
- "year_source": (
1773
- "input" if paper.get("year") else None
1774
- ),
1664
+ "year_source": ("input" if paper.get("year") else None),
1775
1665
  "authors": paper.get("authors"),
1776
1666
  "authors_source": (
1777
1667
  "input" if paper.get("authors") else None
@@ -5,9 +5,8 @@
5
5
  # ----------------------------------------
6
6
  from __future__ import annotations
7
7
  import os
8
- __FILE__ = (
9
- "./src/scitex/scholar/url_finder/ScholarURLFinder.py"
10
- )
8
+
9
+ __FILE__ = "./src/scitex/scholar/url_finder/ScholarURLFinder.py"
11
10
  __DIR__ = os.path.dirname(__FILE__)
12
11
  # ----------------------------------------
13
12
 
@@ -125,10 +124,7 @@ class ScholarURLFinder:
125
124
  for i_strategy, strategy in enumerate(STRATEGIES, 1):
126
125
  # Check if strategy should run for this URL
127
126
  publisher_filter = strategy.get("publisher_filter")
128
- if (
129
- publisher_filter
130
- and publisher_filter.lower() not in base_url.lower()
131
- ):
127
+ if publisher_filter and publisher_filter.lower() not in base_url.lower():
132
128
  # logger.debug(
133
129
  # f"{self.name}: Skipping {strategy['name']} (filtered)"
134
130
  # )
@@ -212,13 +208,9 @@ class ScholarURLFinder:
212
208
  if doi:
213
209
  logger.info(f"{self.name}: Detected DOI: {doi}")
214
210
  async with self._managed_page() as page:
215
- resolved_url = await self.openurl_resolver.resolve_doi(
216
- doi, page
217
- )
211
+ resolved_url = await self.openurl_resolver.resolve_doi(doi, page)
218
212
  if resolved_url:
219
- logger.info(
220
- f"{self.name}: Resolved DOI to: {resolved_url}"
221
- )
213
+ logger.info(f"{self.name}: Resolved DOI to: {resolved_url}")
222
214
  url = resolved_url
223
215
  else:
224
216
  # Fallback to direct DOI URL (works for open access papers like arXiv)
@@ -246,9 +238,7 @@ class ScholarURLFinder:
246
238
  return pdfs
247
239
  except Exception as e:
248
240
  # logger.warning(f"{self.name}: Failed to load page: {e}")
249
- await browser_logger.error(
250
- page, f"{self.name}: Navigation Error {e}"
251
- )
241
+ await browser_logger.error(page, f"{self.name}: Navigation Error {e}")
252
242
  return []
253
243
 
254
244
  async def _find_from_page(
@@ -259,16 +249,12 @@ class ScholarURLFinder:
259
249
  pdfs = await self._find_pdf_urls_with_strategies(page, base_url)
260
250
 
261
251
  if not pdfs:
262
- await browser_logger.warning(
263
- page, f"{self.name}: No PDFs on page"
264
- )
252
+ await browser_logger.warning(page, f"{self.name}: No PDFs on page")
265
253
 
266
254
  return pdfs
267
255
  except Exception as e:
268
256
  # logger.error(f"{self.name}: Error finding PDFs: {e}")
269
- await browser_logger.error(
270
- page, f"{self.name}: PDF Search Error {e}"
271
- )
257
+ await browser_logger.error(page, f"{self.name}: PDF Search Error {e}")
272
258
  return []
273
259
 
274
260
  # ==========================================================================
@@ -335,9 +321,7 @@ if __name__ == "__main__":
335
321
  browser_mode=args.browser_mode,
336
322
  chrome_profile_name=args.chrome_profile,
337
323
  )
338
- _, context = (
339
- await browser_manager.get_authenticated_browser_and_context_async()
340
- )
324
+ _, context = await browser_manager.get_authenticated_browser_and_context_async()
341
325
  # time.sleep(1)
342
326
 
343
327
  # Find PDFs
@@ -50,7 +50,7 @@ async def find_pdf_urls_by_direct_links(
50
50
  await browser_logger.debug(
51
51
  page,
52
52
  f"{func_name}: Found {len(all_urls)} URLs "
53
- f"({len(href_urls)} href, {len(dropdown_urls)} dropdown)"
53
+ f"({len(href_urls)} href, {len(dropdown_urls)} dropdown)",
54
54
  )
55
55
 
56
56
  return list(all_urls)