scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scitex/__init__.py +19 -8
- scitex/__main__.py +2 -1
- scitex/__version__.py +1 -1
- scitex/_optional_deps.py +13 -20
- scitex/ai/__init__.py +5 -0
- scitex/ai/_gen_ai/_Anthropic.py +3 -1
- scitex/ai/_gen_ai/_BaseGenAI.py +3 -2
- scitex/ai/_gen_ai/_DeepSeek.py +1 -1
- scitex/ai/_gen_ai/_Google.py +3 -2
- scitex/ai/_gen_ai/_Llama.py +4 -2
- scitex/ai/_gen_ai/_OpenAI.py +3 -1
- scitex/ai/_gen_ai/_PARAMS.py +1 -0
- scitex/ai/_gen_ai/_Perplexity.py +3 -1
- scitex/ai/_gen_ai/__init__.py +1 -0
- scitex/ai/_gen_ai/_format_output_func.py +3 -1
- scitex/ai/classification/CrossValidationExperiment.py +8 -14
- scitex/ai/classification/examples/timeseries_cv_demo.py +128 -112
- scitex/ai/classification/reporters/_BaseClassificationReporter.py +2 -0
- scitex/ai/classification/reporters/_ClassificationReporter.py +30 -45
- scitex/ai/classification/reporters/_MultiClassificationReporter.py +8 -11
- scitex/ai/classification/reporters/_SingleClassificationReporter.py +126 -182
- scitex/ai/classification/reporters/__init__.py +1 -1
- scitex/ai/classification/reporters/reporter_utils/_Plotter.py +213 -119
- scitex/ai/classification/reporters/reporter_utils/__init__.py +28 -36
- scitex/ai/classification/reporters/reporter_utils/aggregation.py +125 -143
- scitex/ai/classification/reporters/reporter_utils/data_models.py +128 -120
- scitex/ai/classification/reporters/reporter_utils/reporting.py +507 -340
- scitex/ai/classification/reporters/reporter_utils/storage.py +4 -1
- scitex/ai/classification/reporters/reporter_utils/validation.py +141 -154
- scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +204 -129
- scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +215 -171
- scitex/ai/classification/timeseries/_TimeSeriesMetadata.py +17 -17
- scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +67 -143
- scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +67 -143
- scitex/ai/classification/timeseries/_TimeSeriesStrategy.py +12 -13
- scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +231 -144
- scitex/ai/classification/timeseries/__init__.py +2 -4
- scitex/ai/classification/timeseries/_normalize_timestamp.py +3 -0
- scitex/ai/clustering/_pca.py +0 -1
- scitex/ai/clustering/_umap.py +1 -2
- scitex/ai/feature_extraction/__init__.py +10 -8
- scitex/ai/feature_extraction/vit.py +0 -1
- scitex/ai/feature_selection/feature_selection.py +3 -8
- scitex/ai/metrics/_calc_conf_mat.py +2 -0
- scitex/ai/metrics/_calc_feature_importance.py +3 -7
- scitex/ai/metrics/_calc_pre_rec_auc.py +5 -5
- scitex/ai/metrics/_calc_roc_auc.py +4 -2
- scitex/ai/metrics/_calc_seizure_prediction_metrics.py +35 -20
- scitex/ai/metrics/_calc_silhouette_score.py +1 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger.py +0 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger2020.py +0 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger913A.py +0 -3
- scitex/ai/optim/_optimizers.py +1 -1
- scitex/ai/plt/__init__.py +6 -1
- scitex/ai/plt/_plot_feature_importance.py +1 -3
- scitex/ai/plt/_plot_learning_curve.py +9 -24
- scitex/ai/plt/_plot_optuna_study.py +4 -3
- scitex/ai/plt/_plot_pre_rec_curve.py +9 -15
- scitex/ai/plt/_plot_roc_curve.py +6 -8
- scitex/ai/plt/_stx_conf_mat.py +121 -122
- scitex/ai/sampling/undersample.py +3 -2
- scitex/ai/sklearn/__init__.py +2 -2
- scitex/ai/training/_LearningCurveLogger.py +23 -10
- scitex/ai/utils/_check_params.py +0 -1
- scitex/benchmark/__init__.py +15 -25
- scitex/benchmark/benchmark.py +124 -117
- scitex/benchmark/monitor.py +117 -107
- scitex/benchmark/profiler.py +61 -58
- scitex/bridge/__init__.py +110 -0
- scitex/bridge/_helpers.py +149 -0
- scitex/bridge/_plt_vis.py +529 -0
- scitex/bridge/_protocol.py +283 -0
- scitex/bridge/_stats_plt.py +261 -0
- scitex/bridge/_stats_vis.py +265 -0
- scitex/browser/__init__.py +0 -2
- scitex/browser/auth/__init__.py +0 -0
- scitex/browser/auth/google.py +16 -11
- scitex/browser/automation/CookieHandler.py +2 -3
- scitex/browser/collaboration/__init__.py +3 -0
- scitex/browser/collaboration/auth_helpers.py +3 -1
- scitex/browser/collaboration/collaborative_agent.py +2 -0
- scitex/browser/collaboration/interactive_panel.py +2 -2
- scitex/browser/collaboration/shared_session.py +20 -11
- scitex/browser/collaboration/standard_interactions.py +1 -0
- scitex/browser/core/BrowserMixin.py +12 -30
- scitex/browser/core/ChromeProfileManager.py +9 -24
- scitex/browser/debugging/_browser_logger.py +15 -25
- scitex/browser/debugging/_failure_capture.py +9 -2
- scitex/browser/debugging/_highlight_element.py +15 -6
- scitex/browser/debugging/_show_grid.py +5 -6
- scitex/browser/debugging/_sync_session.py +4 -3
- scitex/browser/debugging/_test_monitor.py +14 -5
- scitex/browser/debugging/_visual_cursor.py +46 -35
- scitex/browser/interaction/click_center.py +4 -3
- scitex/browser/interaction/click_with_fallbacks.py +7 -10
- scitex/browser/interaction/close_popups.py +79 -66
- scitex/browser/interaction/fill_with_fallbacks.py +8 -8
- scitex/browser/pdf/__init__.py +3 -1
- scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +11 -10
- scitex/browser/pdf/detect_chrome_pdf_viewer.py +3 -6
- scitex/browser/remote/CaptchaHandler.py +109 -96
- scitex/browser/remote/ZenRowsAPIClient.py +91 -97
- scitex/browser/remote/ZenRowsBrowserManager.py +138 -112
- scitex/browser/stealth/HumanBehavior.py +4 -9
- scitex/browser/stealth/StealthManager.py +11 -26
- scitex/capture/__init__.py +17 -17
- scitex/capture/__main__.py +2 -3
- scitex/capture/capture.py +23 -51
- scitex/capture/cli.py +14 -39
- scitex/capture/gif.py +5 -9
- scitex/capture/mcp_server.py +7 -20
- scitex/capture/session.py +4 -3
- scitex/capture/utils.py +18 -53
- scitex/cli/__init__.py +1 -1
- scitex/cli/cloud.py +158 -116
- scitex/cli/config.py +224 -0
- scitex/cli/main.py +41 -40
- scitex/cli/scholar.py +60 -27
- scitex/cli/security.py +14 -20
- scitex/cli/web.py +87 -90
- scitex/cli/writer.py +51 -45
- scitex/cloud/__init__.py +14 -11
- scitex/cloud/_matplotlib_hook.py +6 -6
- scitex/config/README.md +313 -0
- scitex/config/{PriorityConfig.py → _PriorityConfig.py} +114 -17
- scitex/config/_ScitexConfig.py +319 -0
- scitex/config/__init__.py +41 -9
- scitex/config/_paths.py +325 -0
- scitex/config/default.yaml +81 -0
- scitex/context/_suppress_output.py +2 -3
- scitex/db/_BaseMixins/_BaseBackupMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseBatchMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseBlobMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseImportExportMixin.py +1 -3
- scitex/db/_BaseMixins/_BaseIndexMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseMaintenanceMixin.py +1 -3
- scitex/db/_BaseMixins/_BaseQueryMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseRowMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseTableMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseTransactionMixin.py +1 -3
- scitex/db/_BaseMixins/__init__.py +1 -1
- scitex/db/__init__.py +9 -1
- scitex/db/__main__.py +8 -21
- scitex/db/_check_health.py +15 -31
- scitex/db/_delete_duplicates.py +7 -4
- scitex/db/_inspect.py +22 -38
- scitex/db/_inspect_optimized.py +89 -85
- scitex/db/_postgresql/_PostgreSQL.py +0 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_BlobMixin.py +3 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_ConnectionMixin.py +1 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_ImportExportMixin.py +1 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_MaintenanceMixin.py +1 -4
- scitex/db/_postgresql/_PostgreSQLMixins/_QueryMixin.py +3 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_RowMixin.py +3 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_TransactionMixin.py +1 -3
- scitex/db/_postgresql/__init__.py +1 -1
- scitex/db/_sqlite3/_SQLite3.py +2 -4
- scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin.py +11 -12
- scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin_v01-need-_hash-col.py +19 -14
- scitex/db/_sqlite3/_SQLite3Mixins/_BatchMixin.py +3 -1
- scitex/db/_sqlite3/_SQLite3Mixins/_BlobMixin.py +7 -7
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin.py +118 -111
- scitex/db/_sqlite3/_SQLite3Mixins/_ConnectionMixin.py +8 -10
- scitex/db/_sqlite3/_SQLite3Mixins/_GitMixin.py +17 -45
- scitex/db/_sqlite3/_SQLite3Mixins/_ImportExportMixin.py +1 -3
- scitex/db/_sqlite3/_SQLite3Mixins/_IndexMixin.py +3 -1
- scitex/db/_sqlite3/_SQLite3Mixins/_QueryMixin.py +3 -4
- scitex/db/_sqlite3/_SQLite3Mixins/_RowMixin.py +9 -9
- scitex/db/_sqlite3/_SQLite3Mixins/_TableMixin.py +18 -11
- scitex/db/_sqlite3/_SQLite3Mixins/__init__.py +1 -0
- scitex/db/_sqlite3/__init__.py +1 -1
- scitex/db/_sqlite3/_delete_duplicates.py +13 -11
- scitex/decorators/__init__.py +29 -4
- scitex/decorators/_auto_order.py +43 -43
- scitex/decorators/_batch_fn.py +12 -6
- scitex/decorators/_cache_disk.py +8 -9
- scitex/decorators/_cache_disk_async.py +8 -7
- scitex/decorators/_combined.py +19 -13
- scitex/decorators/_converters.py +16 -3
- scitex/decorators/_deprecated.py +32 -22
- scitex/decorators/_numpy_fn.py +18 -4
- scitex/decorators/_pandas_fn.py +17 -5
- scitex/decorators/_signal_fn.py +17 -3
- scitex/decorators/_torch_fn.py +32 -15
- scitex/decorators/_xarray_fn.py +23 -9
- scitex/dev/_analyze_code_flow.py +0 -2
- scitex/dict/_DotDict.py +15 -19
- scitex/dict/_flatten.py +1 -0
- scitex/dict/_listed_dict.py +1 -0
- scitex/dict/_pop_keys.py +1 -0
- scitex/dict/_replace.py +1 -0
- scitex/dict/_safe_merge.py +1 -0
- scitex/dict/_to_str.py +2 -3
- scitex/dsp/__init__.py +13 -4
- scitex/dsp/_crop.py +3 -1
- scitex/dsp/_detect_ripples.py +3 -1
- scitex/dsp/_modulation_index.py +3 -1
- scitex/dsp/_time.py +3 -1
- scitex/dsp/_wavelet.py +0 -1
- scitex/dsp/example.py +0 -5
- scitex/dsp/filt.py +4 -0
- scitex/dsp/utils/__init__.py +4 -1
- scitex/dsp/utils/pac.py +3 -3
- scitex/dt/_normalize_timestamp.py +4 -1
- scitex/errors.py +3 -6
- scitex/etc/__init__.py +1 -1
- scitex/gen/_DimHandler.py +6 -6
- scitex/gen/__init__.py +5 -1
- scitex/gen/_deprecated_close.py +1 -0
- scitex/gen/_deprecated_start.py +5 -3
- scitex/gen/_detect_environment.py +44 -41
- scitex/gen/_detect_notebook_path.py +51 -47
- scitex/gen/_embed.py +1 -1
- scitex/gen/_get_notebook_path.py +81 -62
- scitex/gen/_inspect_module.py +0 -1
- scitex/gen/_norm.py +16 -7
- scitex/gen/_norm_cache.py +78 -65
- scitex/gen/_print_config.py +0 -3
- scitex/gen/_src.py +2 -3
- scitex/gen/_title_case.py +3 -2
- scitex/gen/_to_even.py +8 -8
- scitex/gen/_transpose.py +3 -3
- scitex/gen/misc.py +0 -3
- scitex/gists/_SigMacro_processFigure_S.py +2 -2
- scitex/gists/_SigMacro_toBlue.py +2 -2
- scitex/gists/__init__.py +4 -1
- scitex/git/_branch.py +19 -11
- scitex/git/_clone.py +23 -15
- scitex/git/_commit.py +10 -12
- scitex/git/_init.py +15 -38
- scitex/git/_remote.py +9 -3
- scitex/git/_result.py +3 -0
- scitex/git/_retry.py +2 -5
- scitex/git/_types.py +4 -0
- scitex/git/_validation.py +8 -8
- scitex/git/_workflow.py +4 -4
- scitex/io/__init__.py +2 -1
- scitex/io/_glob.py +2 -2
- scitex/io/_json2md.py +3 -3
- scitex/io/_load.py +6 -8
- scitex/io/_load_cache.py +71 -71
- scitex/io/_load_configs.py +2 -3
- scitex/io/_load_modules/_H5Explorer.py +6 -12
- scitex/io/_load_modules/_ZarrExplorer.py +3 -3
- scitex/io/_load_modules/_bibtex.py +62 -63
- scitex/io/_load_modules/_canvas.py +4 -9
- scitex/io/_load_modules/_catboost.py +7 -2
- scitex/io/_load_modules/_hdf5.py +2 -0
- scitex/io/_load_modules/_image.py +5 -1
- scitex/io/_load_modules/_matlab.py +3 -1
- scitex/io/_load_modules/_optuna.py +0 -1
- scitex/io/_load_modules/_pdf.py +38 -29
- scitex/io/_load_modules/_sqlite3.py +1 -0
- scitex/io/_load_modules/_txt.py +2 -0
- scitex/io/_load_modules/_xml.py +9 -9
- scitex/io/_load_modules/_zarr.py +12 -10
- scitex/io/_metadata.py +76 -37
- scitex/io/_qr_utils.py +18 -13
- scitex/io/_save.py +220 -63
- scitex/io/_save_modules/__init__.py +7 -2
- scitex/io/_save_modules/_bibtex.py +66 -61
- scitex/io/_save_modules/_canvas.py +5 -6
- scitex/io/_save_modules/_catboost.py +2 -2
- scitex/io/_save_modules/_csv.py +4 -4
- scitex/io/_save_modules/_excel.py +5 -9
- scitex/io/_save_modules/_hdf5.py +9 -21
- scitex/io/_save_modules/_html.py +5 -5
- scitex/io/_save_modules/_image.py +105 -8
- scitex/io/_save_modules/_joblib.py +2 -2
- scitex/io/_save_modules/_json.py +51 -6
- scitex/io/_save_modules/_listed_dfs_as_csv.py +2 -1
- scitex/io/_save_modules/_listed_scalars_as_csv.py +2 -1
- scitex/io/_save_modules/_matlab.py +2 -2
- scitex/io/_save_modules/_numpy.py +6 -8
- scitex/io/_save_modules/_pickle.py +4 -4
- scitex/io/_save_modules/_plotly.py +3 -3
- scitex/io/_save_modules/_tex.py +23 -25
- scitex/io/_save_modules/_text.py +2 -2
- scitex/io/_save_modules/_yaml.py +9 -9
- scitex/io/_save_modules/_zarr.py +15 -15
- scitex/io/utils/__init__.py +2 -1
- scitex/io/utils/h5_to_zarr.py +173 -155
- scitex/linalg/__init__.py +1 -1
- scitex/linalg/_geometric_median.py +4 -3
- scitex/logging/_Tee.py +5 -7
- scitex/logging/__init__.py +18 -19
- scitex/logging/_config.py +4 -1
- scitex/logging/_context.py +6 -5
- scitex/logging/_formatters.py +2 -3
- scitex/logging/_handlers.py +19 -20
- scitex/logging/_levels.py +9 -17
- scitex/logging/_logger.py +74 -15
- scitex/logging/_print_capture.py +17 -17
- scitex/nn/_BNet.py +1 -3
- scitex/nn/_Filters.py +6 -2
- scitex/nn/_ModulationIndex.py +3 -1
- scitex/nn/_PAC.py +3 -2
- scitex/nn/_PSD.py +0 -1
- scitex/nn/__init__.py +16 -3
- scitex/path/_clean.py +10 -8
- scitex/path/_find.py +1 -1
- scitex/path/_get_spath.py +1 -2
- scitex/path/_mk_spath.py +1 -1
- scitex/path/_symlink.py +5 -10
- scitex/pd/__init__.py +4 -1
- scitex/pd/_force_df.py +24 -24
- scitex/pd/_get_unique.py +1 -0
- scitex/pd/_merge_columns.py +1 -1
- scitex/pd/_round.py +11 -7
- scitex/pd/_to_xy.py +0 -1
- scitex/plt/REQUESTS.md +191 -0
- scitex/plt/__init__.py +185 -87
- scitex/plt/_subplots/_AxesWrapper.py +22 -6
- scitex/plt/_subplots/_AxisWrapper.py +100 -39
- scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +74 -52
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +183 -73
- scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +61 -45
- scitex/plt/_subplots/_AxisWrapperMixins/_TrackingMixin.py +26 -14
- scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +80 -73
- scitex/plt/_subplots/_FigWrapper.py +93 -60
- scitex/plt/_subplots/_SubplotsWrapper.py +135 -68
- scitex/plt/_subplots/__init__.py +10 -0
- scitex/plt/_subplots/_export_as_csv.py +89 -47
- scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +1 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +6 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_bar.py +88 -38
- scitex/plt/_subplots/_export_as_csv_formatters/_format_barh.py +25 -31
- scitex/plt/_subplots/_export_as_csv_formatters/_format_boxplot.py +53 -23
- scitex/plt/_subplots/_export_as_csv_formatters/_format_contour.py +38 -25
- scitex/plt/_subplots/_export_as_csv_formatters/_format_contourf.py +17 -9
- scitex/plt/_subplots/_export_as_csv_formatters/_format_errorbar.py +70 -124
- scitex/plt/_subplots/_export_as_csv_formatters/_format_eventplot.py +12 -10
- scitex/plt/_subplots/_export_as_csv_formatters/_format_fill.py +31 -17
- scitex/plt/_subplots/_export_as_csv_formatters/_format_fill_between.py +33 -21
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hexbin.py +14 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hist.py +43 -29
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hist2d.py +14 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow.py +27 -11
- scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow2d.py +7 -5
- scitex/plt/_subplots/_export_as_csv_formatters/_format_matshow.py +9 -7
- scitex/plt/_subplots/_export_as_csv_formatters/_format_pie.py +15 -6
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot.py +85 -46
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_box.py +52 -27
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_imshow.py +1 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_kde.py +16 -17
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter.py +7 -5
- scitex/plt/_subplots/_export_as_csv_formatters/_format_quiver.py +10 -8
- scitex/plt/_subplots/_export_as_csv_formatters/_format_scatter.py +17 -6
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_barplot.py +43 -26
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_boxplot.py +68 -47
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_heatmap.py +52 -64
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_histplot.py +55 -50
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_jointplot.py +9 -11
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_kdeplot.py +63 -29
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_lineplot.py +4 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_pairplot.py +6 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_scatterplot.py +44 -40
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_stripplot.py +46 -39
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_swarmplot.py +46 -39
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_violinplot.py +75 -94
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stem.py +12 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_step.py +12 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_streamplot.py +10 -8
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_conf_mat.py +17 -15
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_ecdf.py +10 -9
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- scitex/tex/_preview.py +26 -11
- scitex/tex/_to_vec.py +10 -7
- scitex/torch/__init__.py +11 -1
- scitex/types/_ArrayLike.py +2 -0
- scitex/types/_is_listed_X.py +3 -3
- scitex/units.py +110 -77
- scitex/utils/_compress_hdf5.py +3 -3
- scitex/utils/_email.py +8 -4
- scitex/utils/_notify.py +14 -8
- scitex/utils/_search.py +6 -6
- scitex/utils/_verify_scitex_format.py +17 -42
- scitex/utils/_verify_scitex_format_v01.py +12 -34
- scitex/utils/template.py +4 -3
- scitex/vis/__init__.py +0 -0
- scitex/vis/backend/__init__.py +3 -3
- scitex/vis/backend/{export.py → _export.py} +1 -1
- scitex/vis/backend/{parser.py → _parser.py} +1 -3
- scitex/vis/backend/{render.py → _render.py} +1 -1
- scitex/vis/canvas.py +15 -3
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- scitex/vis/editor/_dearpygui_editor.py +450 -304
- scitex/vis/editor/_defaults.py +114 -123
- scitex/vis/editor/_edit.py +38 -26
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- scitex/vis/editor/flask_editor/_bbox.py +529 -0
- scitex/vis/editor/flask_editor/{core.py → _core.py} +45 -29
- scitex/vis/editor/flask_editor/_plotter.py +567 -0
- scitex/vis/editor/flask_editor/_renderer.py +393 -0
- scitex/vis/editor/flask_editor/{utils.py → _utils.py} +13 -14
- scitex/vis/editor/flask_editor/templates/__init__.py +5 -5
- scitex/vis/editor/flask_editor/templates/{html.py → _html.py} +234 -16
- scitex/vis/editor/flask_editor/templates/_scripts.py +1261 -0
- scitex/vis/editor/flask_editor/templates/{styles.py → _styles.py} +192 -2
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- scitex/vis/io/{canvas.py → _canvas.py} +8 -4
- scitex/vis/io/{data.py → _data.py} +13 -9
- scitex/vis/io/{directory.py → _directory.py} +7 -4
- scitex/vis/io/{export.py → _export.py} +15 -12
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- scitex/vis/io/{panel.py → _panel.py} +21 -13
- scitex/vis/io/{save.py → _save.py} +0 -0
- scitex/vis/model/__init__.py +7 -7
- scitex/vis/model/{annotations.py → _annotations.py} +2 -4
- scitex/vis/model/{axes.py → _axes.py} +1 -1
- scitex/vis/model/{figure.py → _figure.py} +0 -0
- scitex/vis/model/{guides.py → _guides.py} +1 -1
- scitex/vis/model/{plot.py → _plot.py} +2 -4
- scitex/vis/model/{plot_types.py → _plot_types.py} +0 -0
- scitex/vis/model/{styles.py → _styles.py} +0 -0
- scitex/vis/utils/__init__.py +2 -2
- scitex/vis/utils/{defaults.py → _defaults.py} +1 -2
- scitex/vis/utils/{validate.py → _validate.py} +3 -9
- scitex/web/__init__.py +7 -1
- scitex/web/_scraping.py +54 -38
- scitex/web/_search_pubmed.py +30 -14
- scitex/writer/.legacy/Writer_v01-refactored.py +4 -4
- scitex/writer/.legacy/_compile.py +18 -28
- scitex/writer/Writer.py +8 -21
- scitex/writer/__init__.py +11 -11
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- scitex/writer/dataclasses/__init__.py +8 -10
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- scitex/writer/dataclasses/results/_SaveSectionsResponse.py +20 -9
- scitex/writer/dataclasses/results/_SectionReadResponse.py +24 -10
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- scitex/writer/dataclasses/tree/_ManuscriptTree.py +10 -13
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- scitex/writer/dataclasses/tree/_SupplementaryTree.py +15 -14
- scitex/writer/utils/.legacy_git_retry.py +3 -8
- scitex/writer/utils/_parse_latex_logs.py +2 -3
- scitex/writer/utils/_parse_script_args.py +20 -23
- scitex/writer/utils/_watch.py +5 -5
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/METADATA +4 -10
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/RECORD +1071 -975
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +0 -583
- scitex/plt/_subplots/_export_as_csv_formatters.py +0 -112
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- scitex/vis/editor/flask_editor/plotter.py +0 -130
- scitex/vis/editor/flask_editor/renderer.py +0 -184
- scitex/vis/editor/flask_editor/templates/scripts.py +0 -614
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/WHEEL +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/entry_points.txt +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/licenses/LICENSE +0 -0
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class TextNormalizer:
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"""Normalize text for better matching in academic paper searches."""
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# LaTeX to Unicode mappings
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LATEX_UNICODE_MAP = {
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# Common accented characters
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r"\{\\\"u\}": "ü",
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r"\{\\\"U\}": "Ü",
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r"\{\\\"o\}": "ö",
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r"\{\\\"O\}": "Ö",
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r"\{\\\"a\}": "ä",
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r"\{\\\"A\}": "Ä",
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r"\{\\\"e\}": "ë",
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r"\{\\\"E\}": "Ë",
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r"\{\\\"i\}": "ï",
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r"\{\\\"I\}": "Ï",
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# Circumflex
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r"\{\\^e\}": "ê",
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r"\{\\^E\}": "Ê",
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r"\{\\^a\}": "â",
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r"\{\\^A\}": "Â",
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r"\{\\^o\}": "ô",
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r"\{\\^O\}": "Ô",
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r"\{\\^u\}": "û",
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r"\{\\^U\}": "Û",
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r"\{\\^i\}": "î",
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r"\{\\^I\}": "Î",
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# Grave accent
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r"\{\\`e\}": "è",
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r"\{\\`E\}": "È",
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r"\{\\`a\}": "à",
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r"\{\\`A\}": "À",
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r"\{\\`o\}": "ò",
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r"\{\\`O\}": "Ò",
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r"\{\\`u\}": "ù",
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r"\{\\`U\}": "Ù",
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r"\{\\`i\}": "ì",
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r"\{\\`I\}": "Ì",
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# Acute accent
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r"\{\\\'e\}": "é",
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r"\{\\\'E\}": "É",
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r"\{\\\'a\}": "á",
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r"\{\\\'A\}": "Á",
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r"\{\\\'o\}": "ó",
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r"\{\\\'O\}": "Ó",
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r"\{\\\'u\}": "ú",
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r"\{\\\'U\}": "Ú",
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r"\{\\\'i\}": "í",
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r"\{\\\'I\}": "Í",
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# Tilde
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r"\{\\~n\}": "ñ",
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r"\{\\~N\}": "Ñ",
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r"\{\\~a\}": "ã",
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r"\{\\~A\}": "Ã",
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r"\{\\~o\}": "õ",
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r"\{\\~O\}": "Õ",
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# Cedilla
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r"\{\\c c\}": "ç",
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r"\{\\c C\}": "Ç",
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# Ring
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r"\{\\aa\}": "å",
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r"\{\\AA\}": "Å",
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# Slash
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r"\{\\o\}": "ø",
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r"\{\\O\}": "Ø",
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# Special characters
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r"\{ss\}": "ß",
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r"\{ae\}": "æ",
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r"\{AE\}": "Æ",
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r"\{oe\}": "œ",
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r"\{OE\}": "Œ",
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# Czech/Slovak
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r"\{\\v c\}": "č",
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r"\{\\v C\}": "Č",
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r"\{\\v r\}": "ř",
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r"\{\\v R\}": "Ř",
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r"\{\\v s\}": "š",
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r"\{\\v S\}": "Š",
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r"\{\\v z\}": "ž",
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r"\{\\v Z\}": "Ž",
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r"\{\\v n\}": "ň",
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r"\{\\v N\}": "Ň",
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r"\{\\v t\}": "ť",
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r"\{\\v T\}": "Ť",
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r"\{\\v d\}": "ď",
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r"\{\\v D\}": "Ď",
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r"\{\\v l\}": "ľ",
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# Polish
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r"\{\\\\l\}": "ł",
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# Hungarian
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r"\{\\\\H\{o\}\}": "ő",
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r"\{\\\\H\{O\}\}": "Ő",
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r"\{\\\\H\{u\}\}": "ű",
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r"\{\\\\H\{U\}\}": "Ű",
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}
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@classmethod
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def normalize_for_search(cls, text: str, preserve_case: bool = False) -> str:
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"""Normalize text for academic paper search matching.
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Args:
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preserve_case: Whether to preserve original case
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Returns:
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Normalized text suitable for fuzzy matching
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"""
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return ""
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# Convert LaTeX sequences to Unicode
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normalized = cls._convert_latex_to_unicode(text)
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# Unicode normalization (decompose accented characters)
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normalized = unicodedata.normalize(
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normalized = unicodedata.normalize("NFKD", normalized)
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# Convert to lowercase unless preserving case
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normalized = normalized.lower()
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# Remove extra whitespace
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normalized = re.sub(r
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normalized = re.sub(r"\s+", " ", normalized).strip()
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@classmethod
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def normalize_for_fuzzy_matching(cls, text: str) -> str:
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"""Aggressive normalization for fuzzy title matching.
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Heavily normalized text for fuzzy matching
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"""
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# Start with search normalization
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normalized = cls.normalize_for_search(text, preserve_case=False)
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# Remove punctuation and special characters
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normalized = re.sub(r"[^\w\s]", " ", normalized)
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# Remove common stopwords that don't affect meaning
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stopwords = {
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}
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words = [w for w in normalized.split() if w not in stopwords and len(w) > 1]
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return
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+
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return " ".join(words)
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+
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@classmethod
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def normalize_author_name(cls, name: str) -> str:
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"""Normalize author names for better matching.
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-
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+
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Args:
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name: Author name to normalize
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-
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+
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Returns:
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Normalized author name
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"""
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if not name:
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return ""
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-
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+
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# Convert LaTeX to Unicode
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normalized = cls._convert_latex_to_unicode(name)
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-
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+
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# Unicode normalization
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-
normalized = unicodedata.normalize(
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-
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+
normalized = unicodedata.normalize("NFKD", normalized)
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+
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# Handle common name formats
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# "Last, First Middle" -> "First Middle Last"
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-
if
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parts = normalized.split(
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+
if "," in normalized:
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+
parts = normalized.split(",", 1)
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if len(parts) == 2:
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last_name = parts[0].strip()
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first_names = parts[1].strip()
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normalized = f"{first_names} {last_name}"
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+
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# Remove extra whitespace
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normalized = re.sub(r
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-
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+
normalized = re.sub(r"\s+", " ", normalized).strip()
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return normalized
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-
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-
@classmethod
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+
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+
@classmethod
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def _convert_latex_to_unicode(cls, text: str) -> str:
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"""Convert LaTeX sequences to Unicode characters.
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+
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Args:
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text: Text containing LaTeX sequences
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-
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+
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Returns:
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Text with LaTeX converted to Unicode
|
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"""
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result = text
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-
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+
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# Handle common patterns from academic papers first
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common_patterns = [
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# Handle H{"u}lsemann style (without escaping)
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-
(r
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-
(r
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-
(r
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+
(r"H\{\"u\}", "Hü"),
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+
(r"H\{\"o\}", "Hö"),
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+
(r"H\{\"a\}", "Hä"),
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251
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# Handle with braces
|
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|
-
(r
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202
|
-
(r
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203
|
-
(r
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|
204
|
-
(r
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205
|
-
(r
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252
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+
(r"\{\"u\}", "ü"),
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+
(r"\{\"U\}", "Ü"),
|
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+
(r"\{\"o\}", "ö"),
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+
(r"\{\"O\}", "Ö"),
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+
(r"\{\"a\}", "ä"),
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+
(r"\{\"A\}", "Ä"),
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+
(r"\{\"e\}", "ë"),
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+
(r"\{\"E\}", "Ë"),
|
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+
(r"\{\"i\}", "ï"),
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+
(r"\{\"I\}", "Ï"),
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206
262
|
# Circumflex
|
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207
|
-
(r
|
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208
|
-
(r
|
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209
|
-
(r
|
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210
|
-
(r
|
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211
|
-
(r
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263
|
+
(r"\{\^e\}", "ê"),
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+
(r"\{\^E\}", "Ê"),
|
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+
(r"\{\^a\}", "â"),
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+
(r"\{\^A\}", "Â"),
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+
(r"\{\^o\}", "ô"),
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+
(r"\{\^O\}", "Ô"),
|
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|
+
(r"\{\^u\}", "û"),
|
|
270
|
+
(r"\{\^U\}", "Û"),
|
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271
|
+
(r"\{\^i\}", "î"),
|
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272
|
+
(r"\{\^I\}", "Î"),
|
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212
273
|
# Grave accent
|
|
213
|
-
(r
|
|
214
|
-
(r
|
|
215
|
-
(r
|
|
216
|
-
(r
|
|
217
|
-
(r
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|
274
|
+
(r"\{\`e\}", "è"),
|
|
275
|
+
(r"\{\`E\}", "È"),
|
|
276
|
+
(r"\{\`a\}", "à"),
|
|
277
|
+
(r"\{\`A\}", "À"),
|
|
278
|
+
(r"\{\`o\}", "ò"),
|
|
279
|
+
(r"\{\`O\}", "Ò"),
|
|
280
|
+
(r"\{\`u\}", "ù"),
|
|
281
|
+
(r"\{\`U\}", "Ù"),
|
|
282
|
+
(r"\{\`i\}", "ì"),
|
|
283
|
+
(r"\{\`I\}", "Ì"),
|
|
218
284
|
# Acute accent
|
|
219
|
-
(r
|
|
220
|
-
(r
|
|
221
|
-
(r
|
|
222
|
-
(r
|
|
223
|
-
(r
|
|
285
|
+
(r"\{\'e\}", "é"),
|
|
286
|
+
(r"\{\'E\}", "É"),
|
|
287
|
+
(r"\{\'a\}", "á"),
|
|
288
|
+
(r"\{\'A\}", "Á"),
|
|
289
|
+
(r"\{\'o\}", "ó"),
|
|
290
|
+
(r"\{\'O\}", "Ó"),
|
|
291
|
+
(r"\{\'u\}", "ú"),
|
|
292
|
+
(r"\{\'U\}", "Ú"),
|
|
293
|
+
(r"\{\'i\}", "í"),
|
|
294
|
+
(r"\{\'I\}", "Í"),
|
|
224
295
|
]
|
|
225
|
-
|
|
296
|
+
|
|
226
297
|
# Apply common patterns first
|
|
227
298
|
for pattern, replacement in common_patterns:
|
|
228
299
|
result = re.sub(pattern, replacement, result)
|
|
229
|
-
|
|
300
|
+
|
|
230
301
|
# Then apply the full mapping with proper escaping
|
|
231
302
|
for latex_seq, unicode_char in cls.LATEX_UNICODE_MAP.items():
|
|
232
303
|
result = re.sub(latex_seq, unicode_char, result)
|
|
233
|
-
|
|
304
|
+
|
|
234
305
|
return result
|
|
235
|
-
|
|
306
|
+
|
|
236
307
|
@classmethod
|
|
237
308
|
def calculate_title_similarity(cls, title1: str, title2: str) -> float:
|
|
238
309
|
"""Calculate similarity between two academic paper titles.
|
|
239
|
-
|
|
310
|
+
|
|
240
311
|
Args:
|
|
241
312
|
title1: First title
|
|
242
313
|
title2: Second title
|
|
243
|
-
|
|
314
|
+
|
|
244
315
|
Returns:
|
|
245
316
|
Similarity score between 0 and 1
|
|
246
317
|
"""
|
|
247
318
|
if not title1 or not title2:
|
|
248
319
|
return 0.0
|
|
249
|
-
|
|
320
|
+
|
|
250
321
|
# Normalize both titles for comparison
|
|
251
322
|
norm1 = cls.normalize_for_fuzzy_matching(title1)
|
|
252
323
|
norm2 = cls.normalize_for_fuzzy_matching(title2)
|
|
253
|
-
|
|
324
|
+
|
|
254
325
|
if norm1 == norm2:
|
|
255
326
|
return 1.0
|
|
256
|
-
|
|
327
|
+
|
|
257
328
|
# Calculate word-based Jaccard similarity
|
|
258
329
|
words1 = set(norm1.split())
|
|
259
330
|
words2 = set(norm2.split())
|
|
260
|
-
|
|
331
|
+
|
|
261
332
|
if not words1 or not words2:
|
|
262
333
|
return 0.0
|
|
263
|
-
|
|
334
|
+
|
|
264
335
|
intersection = len(words1 & words2)
|
|
265
336
|
union = len(words1 | words2)
|
|
266
|
-
|
|
337
|
+
|
|
267
338
|
return intersection / union if union > 0 else 0.0
|
|
268
|
-
|
|
339
|
+
|
|
269
340
|
@classmethod
|
|
270
|
-
def is_likely_same_title(
|
|
341
|
+
def is_likely_same_title(
|
|
342
|
+
cls, title1: str, title2: str, threshold: float = 0.8
|
|
343
|
+
) -> bool:
|
|
271
344
|
"""Check if two titles likely refer to the same paper.
|
|
272
|
-
|
|
345
|
+
|
|
273
346
|
Args:
|
|
274
347
|
title1: First title
|
|
275
348
|
title2: Second title
|
|
276
349
|
threshold: Similarity threshold (0-1)
|
|
277
|
-
|
|
350
|
+
|
|
278
351
|
Returns:
|
|
279
352
|
True if titles are likely the same paper
|
|
280
353
|
"""
|
|
@@ -284,20 +357,20 @@ class TextNormalizer:
|
|
|
284
357
|
@classmethod
|
|
285
358
|
def normalize_title(cls, title: str, remove_trailing_period: bool = True) -> str:
|
|
286
359
|
"""Normalize paper title for storage and comparison.
|
|
287
|
-
|
|
360
|
+
|
|
288
361
|
This method provides consistent title normalization across the Scholar system:
|
|
289
362
|
- Removes BibTeX braces: {Title} -> Title
|
|
290
363
|
- Converts LaTeX sequences to Unicode
|
|
291
364
|
- Normalizes whitespace
|
|
292
365
|
- Optionally removes trailing periods
|
|
293
|
-
|
|
366
|
+
|
|
294
367
|
Args:
|
|
295
368
|
title: Paper title to normalize
|
|
296
369
|
remove_trailing_period: Whether to remove trailing period (default: True)
|
|
297
|
-
|
|
370
|
+
|
|
298
371
|
Returns:
|
|
299
372
|
Normalized title string
|
|
300
|
-
|
|
373
|
+
|
|
301
374
|
Examples:
|
|
302
375
|
>>> TextNormalizer.normalize_title("{Deep Learning in Neural Networks.}")
|
|
303
376
|
"Deep Learning in Neural Networks"
|
|
@@ -306,38 +379,38 @@ class TextNormalizer:
|
|
|
306
379
|
"""
|
|
307
380
|
if not title:
|
|
308
381
|
return ""
|
|
309
|
-
|
|
382
|
+
|
|
310
383
|
# Remove BibTeX braces
|
|
311
|
-
normalized = title.strip(
|
|
312
|
-
|
|
384
|
+
normalized = title.strip("{}")
|
|
385
|
+
|
|
313
386
|
# Convert LaTeX sequences to Unicode
|
|
314
387
|
normalized = cls._convert_latex_to_unicode(normalized)
|
|
315
|
-
|
|
388
|
+
|
|
316
389
|
# Unicode normalization
|
|
317
|
-
normalized = unicodedata.normalize(
|
|
318
|
-
|
|
390
|
+
normalized = unicodedata.normalize("NFKD", normalized)
|
|
391
|
+
|
|
319
392
|
# Normalize whitespace
|
|
320
|
-
normalized = re.sub(r
|
|
321
|
-
|
|
393
|
+
normalized = re.sub(r"\s+", " ", normalized).strip()
|
|
394
|
+
|
|
322
395
|
# Remove trailing period if requested
|
|
323
|
-
if remove_trailing_period and normalized.endswith(
|
|
324
|
-
normalized = normalized.rstrip(
|
|
325
|
-
|
|
396
|
+
if remove_trailing_period and normalized.endswith("."):
|
|
397
|
+
normalized = normalized.rstrip(".")
|
|
398
|
+
|
|
326
399
|
return normalized
|
|
327
400
|
|
|
328
401
|
@classmethod
|
|
329
402
|
def strip_html_tags(cls, text: str) -> str:
|
|
330
403
|
"""Strip HTML/XML tags from text.
|
|
331
|
-
|
|
404
|
+
|
|
332
405
|
This method removes HTML and XML tags commonly found in academic metadata
|
|
333
406
|
such as abstracts and titles retrieved from APIs.
|
|
334
|
-
|
|
407
|
+
|
|
335
408
|
Args:
|
|
336
409
|
text: Text containing HTML/XML tags
|
|
337
|
-
|
|
410
|
+
|
|
338
411
|
Returns:
|
|
339
412
|
Text with HTML/XML tags removed
|
|
340
|
-
|
|
413
|
+
|
|
341
414
|
Examples:
|
|
342
415
|
>>> TextNormalizer.strip_html_tags("<p>Abstract <i>text</i> here.</p>")
|
|
343
416
|
"Abstract text here."
|
|
@@ -346,62 +419,62 @@ class TextNormalizer:
|
|
|
346
419
|
"""
|
|
347
420
|
if not text:
|
|
348
421
|
return ""
|
|
349
|
-
|
|
422
|
+
|
|
350
423
|
# Remove HTML/XML tags using regex
|
|
351
424
|
# This pattern matches opening and closing tags
|
|
352
|
-
clean_text = re.sub(r
|
|
353
|
-
|
|
425
|
+
clean_text = re.sub(r"<[^>]+>", "", text)
|
|
426
|
+
|
|
354
427
|
# Clean up any HTML entities that might remain
|
|
355
428
|
html_entities = {
|
|
356
|
-
|
|
357
|
-
|
|
358
|
-
|
|
359
|
-
|
|
360
|
-
|
|
361
|
-
|
|
362
|
-
|
|
363
|
-
|
|
429
|
+
"&": "&",
|
|
430
|
+
"<": "<",
|
|
431
|
+
">": ">",
|
|
432
|
+
""": '"',
|
|
433
|
+
"'": "'",
|
|
434
|
+
" ": " ",
|
|
435
|
+
"'": "'",
|
|
436
|
+
""": '"',
|
|
364
437
|
}
|
|
365
|
-
|
|
438
|
+
|
|
366
439
|
for entity, replacement in html_entities.items():
|
|
367
440
|
clean_text = clean_text.replace(entity, replacement)
|
|
368
|
-
|
|
441
|
+
|
|
369
442
|
# Normalize whitespace after tag removal
|
|
370
|
-
clean_text = re.sub(r
|
|
371
|
-
|
|
443
|
+
clean_text = re.sub(r"\s+", " ", clean_text).strip()
|
|
444
|
+
|
|
372
445
|
return clean_text
|
|
373
446
|
|
|
374
447
|
@classmethod
|
|
375
448
|
def clean_metadata_text(cls, text: str) -> str:
|
|
376
449
|
"""Comprehensive cleaning for metadata text fields.
|
|
377
|
-
|
|
450
|
+
|
|
378
451
|
This combines HTML tag stripping, LaTeX conversion, and normalization
|
|
379
452
|
specifically for metadata fields like titles and abstracts.
|
|
380
|
-
|
|
453
|
+
|
|
381
454
|
Args:
|
|
382
455
|
text: Raw metadata text
|
|
383
|
-
|
|
456
|
+
|
|
384
457
|
Returns:
|
|
385
458
|
Cleaned and normalized text
|
|
386
459
|
"""
|
|
387
460
|
if not text:
|
|
388
461
|
return ""
|
|
389
|
-
|
|
462
|
+
|
|
390
463
|
# First strip HTML/XML tags
|
|
391
464
|
cleaned = cls.strip_html_tags(text)
|
|
392
|
-
|
|
465
|
+
|
|
393
466
|
# Convert LaTeX sequences to Unicode (needed before normalization)
|
|
394
467
|
cleaned = cls._convert_latex_to_unicode(cleaned)
|
|
395
|
-
|
|
468
|
+
|
|
396
469
|
# Then apply Unicode normalization and whitespace cleanup
|
|
397
470
|
# Use NFC to keep composed characters like ü together
|
|
398
|
-
cleaned = unicodedata.normalize(
|
|
399
|
-
cleaned = re.sub(r
|
|
400
|
-
|
|
471
|
+
cleaned = unicodedata.normalize("NFC", cleaned)
|
|
472
|
+
cleaned = re.sub(r"\s+", " ", cleaned).strip()
|
|
473
|
+
|
|
401
474
|
return cleaned
|
|
402
475
|
|
|
403
476
|
|
|
404
477
|
# Export
|
|
405
478
|
__all__ = ["TextNormalizer"]
|
|
406
479
|
|
|
407
|
-
# EOF
|
|
480
|
+
# EOF
|