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.
- scitex/__init__.py +25 -10
- 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/audio/README.md +52 -0
- scitex/audio/__init__.py +384 -0
- scitex/audio/__main__.py +129 -0
- scitex/audio/_tts.py +334 -0
- scitex/audio/engines/__init__.py +44 -0
- scitex/audio/engines/base.py +275 -0
- scitex/audio/engines/elevenlabs_engine.py +143 -0
- scitex/audio/engines/gtts_engine.py +162 -0
- scitex/audio/engines/pyttsx3_engine.py +131 -0
- scitex/audio/mcp_server.py +757 -0
- 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/dev/plt/__init__.py +272 -0
- scitex/dev/plt/plot_mpl_axhline.py +28 -0
- scitex/dev/plt/plot_mpl_axhspan.py +28 -0
- scitex/dev/plt/plot_mpl_axvline.py +28 -0
- scitex/dev/plt/plot_mpl_axvspan.py +28 -0
- scitex/dev/plt/plot_mpl_bar.py +29 -0
- scitex/dev/plt/plot_mpl_barh.py +29 -0
- scitex/dev/plt/plot_mpl_boxplot.py +28 -0
- scitex/dev/plt/plot_mpl_contour.py +31 -0
- scitex/dev/plt/plot_mpl_contourf.py +31 -0
- scitex/dev/plt/plot_mpl_errorbar.py +30 -0
- scitex/dev/plt/plot_mpl_eventplot.py +28 -0
- scitex/dev/plt/plot_mpl_fill.py +30 -0
- scitex/dev/plt/plot_mpl_fill_between.py +31 -0
- scitex/dev/plt/plot_mpl_hexbin.py +28 -0
- scitex/dev/plt/plot_mpl_hist.py +28 -0
- scitex/dev/plt/plot_mpl_hist2d.py +28 -0
- scitex/dev/plt/plot_mpl_imshow.py +29 -0
- scitex/dev/plt/plot_mpl_pcolormesh.py +31 -0
- scitex/dev/plt/plot_mpl_pie.py +29 -0
- scitex/dev/plt/plot_mpl_plot.py +29 -0
- scitex/dev/plt/plot_mpl_quiver.py +31 -0
- scitex/dev/plt/plot_mpl_scatter.py +28 -0
- scitex/dev/plt/plot_mpl_stackplot.py +31 -0
- scitex/dev/plt/plot_mpl_stem.py +29 -0
- scitex/dev/plt/plot_mpl_step.py +29 -0
- scitex/dev/plt/plot_mpl_violinplot.py +28 -0
- scitex/dev/plt/plot_sns_barplot.py +29 -0
- scitex/dev/plt/plot_sns_boxplot.py +29 -0
- scitex/dev/plt/plot_sns_heatmap.py +28 -0
- scitex/dev/plt/plot_sns_histplot.py +29 -0
- scitex/dev/plt/plot_sns_kdeplot.py +29 -0
- scitex/dev/plt/plot_sns_lineplot.py +31 -0
- scitex/dev/plt/plot_sns_scatterplot.py +29 -0
- scitex/dev/plt/plot_sns_stripplot.py +29 -0
- scitex/dev/plt/plot_sns_swarmplot.py +29 -0
- scitex/dev/plt/plot_sns_violinplot.py +29 -0
- scitex/dev/plt/plot_stx_bar.py +29 -0
- scitex/dev/plt/plot_stx_barh.py +29 -0
- scitex/dev/plt/plot_stx_box.py +28 -0
- scitex/dev/plt/plot_stx_boxplot.py +28 -0
- scitex/dev/plt/plot_stx_conf_mat.py +28 -0
- scitex/dev/plt/plot_stx_contour.py +31 -0
- scitex/dev/plt/plot_stx_ecdf.py +28 -0
- scitex/dev/plt/plot_stx_errorbar.py +30 -0
- scitex/dev/plt/plot_stx_fill_between.py +31 -0
- scitex/dev/plt/plot_stx_fillv.py +28 -0
- scitex/dev/plt/plot_stx_heatmap.py +28 -0
- scitex/dev/plt/plot_stx_image.py +28 -0
- scitex/dev/plt/plot_stx_imshow.py +28 -0
- scitex/dev/plt/plot_stx_joyplot.py +28 -0
- scitex/dev/plt/plot_stx_kde.py +28 -0
- scitex/dev/plt/plot_stx_line.py +28 -0
- scitex/dev/plt/plot_stx_mean_ci.py +28 -0
- scitex/dev/plt/plot_stx_mean_std.py +28 -0
- scitex/dev/plt/plot_stx_median_iqr.py +28 -0
- scitex/dev/plt/plot_stx_raster.py +28 -0
- scitex/dev/plt/plot_stx_rectangle.py +28 -0
- scitex/dev/plt/plot_stx_scatter.py +29 -0
- scitex/dev/plt/plot_stx_shaded_line.py +29 -0
- scitex/dev/plt/plot_stx_violin.py +28 -0
- scitex/dev/plt/plot_stx_violinplot.py +28 -0
- 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/fig/__init__.py +352 -0
- scitex/{vis → fig}/backend/__init__.py +3 -3
- scitex/{vis/backend/export.py → fig/backend/_export.py} +1 -1
- scitex/{vis/backend/parser.py → fig/backend/_parser.py} +2 -4
- scitex/{vis/backend/render.py → fig/backend/_render.py} +1 -1
- scitex/{vis → fig}/canvas.py +16 -4
- scitex/{vis → fig}/editor/__init__.py +0 -0
- scitex/{vis → fig}/editor/_dearpygui_editor.py +450 -304
- scitex/fig/editor/_defaults.py +300 -0
- scitex/fig/editor/_edit.py +751 -0
- scitex/{vis → fig}/editor/_flask_editor.py +8 -8
- scitex/{vis → fig}/editor/_mpl_editor.py +63 -48
- scitex/{vis → fig}/editor/_qt_editor.py +391 -160
- scitex/{vis → fig}/editor/_tkinter_editor.py +146 -89
- scitex/fig/editor/flask_editor/__init__.py +21 -0
- scitex/fig/editor/flask_editor/_bbox.py +1276 -0
- scitex/fig/editor/flask_editor/_core.py +624 -0
- scitex/fig/editor/flask_editor/_plotter.py +601 -0
- scitex/fig/editor/flask_editor/_renderer.py +739 -0
- scitex/{vis/editor/flask_editor/utils.py → fig/editor/flask_editor/_utils.py} +13 -14
- scitex/{vis → fig}/editor/flask_editor/templates/__init__.py +6 -6
- scitex/fig/editor/flask_editor/templates/_html.py +834 -0
- scitex/fig/editor/flask_editor/templates/_scripts.py +3136 -0
- scitex/fig/editor/flask_editor/templates/_styles.py +1346 -0
- scitex/{vis → fig}/io/__init__.py +18 -6
- scitex/fig/io/_bundle.py +973 -0
- scitex/{vis/io/canvas.py → fig/io/_canvas.py} +9 -5
- scitex/{vis/io/data.py → fig/io/_data.py} +14 -10
- scitex/{vis/io/directory.py → fig/io/_directory.py} +7 -4
- scitex/{vis/io/export.py → fig/io/_export.py} +16 -13
- scitex/{vis/io/load.py → fig/io/_load.py} +2 -2
- scitex/{vis/io/panel.py → fig/io/_panel.py} +22 -14
- scitex/{vis/io/save.py → fig/io/_save.py} +1 -1
- scitex/{vis → fig}/model/__init__.py +8 -8
- scitex/{vis/model/annotations.py → fig/model/_annotations.py} +3 -5
- scitex/{vis/model/axes.py → fig/model/_axes.py} +2 -2
- scitex/{vis/model/figure.py → fig/model/_figure.py} +1 -1
- scitex/{vis/model/guides.py → fig/model/_guides.py} +2 -2
- scitex/{vis/model/plot.py → fig/model/_plot.py} +3 -5
- scitex/{vis/model/plot_types.py → fig/model/_plot_types.py} +0 -0
- scitex/{vis/model/styles.py → fig/model/_styles.py} +1 -1
- scitex/{vis → fig}/utils/__init__.py +3 -3
- scitex/{vis/utils/defaults.py → fig/utils/_defaults.py} +1 -2
- scitex/{vis/utils/validate.py → fig/utils/_validate.py} +3 -9
- 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 +12 -27
- scitex/io/_bundle.py +434 -0
- scitex/io/_flush.py +5 -2
- scitex/io/_glob.py +2 -2
- scitex/io/_json2md.py +3 -3
- scitex/io/_load.py +104 -8
- scitex/io/_load_cache.py +71 -71
- scitex/io/_load_configs.py +2 -3
- scitex/io/_load_modules/_H5Explorer.py +11 -14
- scitex/io/_load_modules/_ZarrExplorer.py +3 -3
- scitex/io/_load_modules/_bibtex.py +62 -63
- scitex/io/_load_modules/_canvas.py +6 -11
- scitex/io/_load_modules/_catboost.py +7 -2
- scitex/io/_load_modules/_hdf5.py +2 -0
- scitex/io/_load_modules/_image.py +7 -4
- 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 +6 -2
- scitex/io/_load_modules/_xml.py +9 -9
- scitex/io/_load_modules/_zarr.py +12 -10
- scitex/io/_metadata.py +34 -285
- scitex/io/_metadata_modules/__init__.py +46 -0
- scitex/io/_metadata_modules/_embed.py +70 -0
- scitex/io/_metadata_modules/_read.py +64 -0
- scitex/io/_metadata_modules/_utils.py +79 -0
- scitex/io/_metadata_modules/embed_metadata_jpeg.py +74 -0
- scitex/io/_metadata_modules/embed_metadata_pdf.py +53 -0
- scitex/io/_metadata_modules/embed_metadata_png.py +26 -0
- scitex/io/_metadata_modules/embed_metadata_svg.py +62 -0
- scitex/io/_metadata_modules/read_metadata_jpeg.py +57 -0
- scitex/io/_metadata_modules/read_metadata_pdf.py +51 -0
- scitex/io/_metadata_modules/read_metadata_png.py +39 -0
- scitex/io/_metadata_modules/read_metadata_svg.py +44 -0
- scitex/io/_qr_utils.py +21 -14
- scitex/io/_save.py +755 -80
- scitex/io/_save_modules/__init__.py +7 -2
- scitex/io/_save_modules/_bibtex.py +66 -61
- scitex/io/_save_modules/_canvas.py +8 -9
- 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 +107 -14
- 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 +30 -29
- 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 +183 -163
- 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/msword/__init__.py +255 -0
- scitex/msword/profiles.py +357 -0
- scitex/msword/reader.py +753 -0
- scitex/msword/utils.py +289 -0
- scitex/msword/writer.py +362 -0
- 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/__init__.py +190 -89
- scitex/plt/_subplots/_AxesWrapper.py +28 -12
- scitex/plt/_subplots/_AxisWrapper.py +114 -47
- scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin/__init__.py +36 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin/_labels.py +264 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin/_metadata.py +213 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin/_visual.py +128 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/__init__.py +59 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/_base.py +34 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/_scientific.py +593 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/_statistical.py +654 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin/_stx_aliases.py +527 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_RawMatplotlibMixin.py +321 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin/__init__.py +33 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin/_base.py +152 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin/_wrappers.py +600 -0
- scitex/plt/_subplots/_AxisWrapperMixins/_TrackingMixin.py +26 -14
- scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +80 -73
- scitex/plt/_subplots/_AxisWrapperMixins/__init__.py +79 -5
- scitex/plt/_subplots/_FigWrapper.py +97 -64
- scitex/plt/_subplots/_SubplotsWrapper.py +161 -84
- scitex/plt/_subplots/__init__.py +10 -0
- scitex/plt/_subplots/_export_as_csv.py +124 -52
- scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +9 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +14 -23
- 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 +30 -17
- 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 +34 -16
- scitex/plt/_subplots/_export_as_csv_formatters/_format_matshow.py +16 -8
- 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 +14 -1
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_kde.py +27 -18
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter.py +14 -5
- scitex/plt/_subplots/_export_as_csv_formatters/_format_quiver.py +16 -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 +23 -10
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_kdeplot.py +63 -29
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_lineplot.py +48 -40
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_pairplot.py +20 -6
- 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 +17 -9
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_bar.py +84 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_barh.py +85 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_conf_mat.py +31 -18
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_contour.py +54 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_ecdf.py +24 -11
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_errorbar.py +120 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_fillv.py +35 -31
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_heatmap.py +33 -23
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_image.py +44 -28
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_imshow.py +63 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_joyplot.py +31 -12
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_line.py +34 -23
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_mean_ci.py +32 -26
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_mean_std.py +29 -23
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_median_iqr.py +32 -26
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_raster.py +21 -11
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_rectangle.py +84 -56
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_scatter.py +51 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_scatter_hist.py +46 -34
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_shaded_line.py +46 -30
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_violin.py +51 -51
- scitex/plt/_subplots/_export_as_csv_formatters/_format_text.py +32 -31
- scitex/plt/_subplots/_export_as_csv_formatters/_format_violin.py +34 -31
- scitex/plt/_subplots/_export_as_csv_formatters/_format_violinplot.py +44 -37
- scitex/plt/_subplots/_export_as_csv_formatters/verify_formatters.py +91 -74
- scitex/plt/_tpl.py +6 -5
- scitex/plt/ax/_plot/__init__.py +24 -0
- scitex/plt/ax/_plot/_add_fitted_line.py +12 -11
- scitex/plt/ax/_plot/_plot_circular_hist.py +3 -1
- scitex/plt/ax/_plot/_plot_statistical_shaded_line.py +25 -19
- scitex/plt/ax/_plot/_stx_conf_mat.py +6 -3
- scitex/plt/ax/_plot/_stx_ecdf.py +9 -5
- scitex/plt/ax/_plot/_stx_fillv.py +4 -2
- scitex/plt/ax/_plot/_stx_heatmap.py +7 -4
- scitex/plt/ax/_plot/_stx_image.py +7 -5
- scitex/plt/ax/_plot/_stx_joyplot.py +32 -10
- scitex/plt/ax/_plot/_stx_raster.py +26 -11
- scitex/plt/ax/_plot/_stx_rectangle.py +2 -2
- scitex/plt/ax/_plot/_stx_shaded_line.py +15 -11
- scitex/plt/ax/_plot/_stx_violin.py +3 -1
- scitex/plt/ax/_style/_add_marginal_ax.py +6 -4
- scitex/plt/ax/_style/_auto_scale_axis.py +14 -10
- scitex/plt/ax/_style/_extend.py +3 -1
- scitex/plt/ax/_style/_force_aspect.py +5 -3
- scitex/plt/ax/_style/_format_units.py +2 -2
- scitex/plt/ax/_style/_hide_spines.py +5 -1
- scitex/plt/ax/_style/_map_ticks.py +5 -3
- scitex/plt/ax/_style/_rotate_labels.py +5 -4
- scitex/plt/ax/_style/_rotate_labels_v01.py +73 -63
- scitex/plt/ax/_style/_set_log_scale.py +120 -85
- scitex/plt/ax/_style/_set_meta.py +99 -76
- scitex/plt/ax/_style/_set_supxyt.py +33 -16
- scitex/plt/ax/_style/_set_xyt.py +27 -18
- scitex/plt/ax/_style/_share_axes.py +15 -5
- scitex/plt/ax/_style/_show_spines.py +58 -57
- scitex/plt/ax/_style/_style_barplot.py +1 -1
- scitex/plt/ax/_style/_style_boxplot.py +25 -14
- scitex/plt/ax/_style/_style_errorbar.py +0 -0
- scitex/plt/ax/_style/_style_scatter.py +1 -1
- scitex/plt/ax/_style/_style_suptitles.py +3 -3
- scitex/plt/ax/_style/_style_violinplot.py +8 -2
- scitex/plt/color/__init__.py +34 -2
- scitex/plt/color/_add_hue_col.py +1 -0
- scitex/plt/color/_colors.py +0 -1
- scitex/plt/color/_get_colors_from_conf_matap.py +3 -1
- scitex/plt/color/_vizualize_colors.py +0 -1
- scitex/plt/docs/FIGURE_ARCHITECTURE.md +155 -97
- scitex/plt/gallery/README.md +75 -0
- scitex/plt/gallery/__init__.py +29 -0
- scitex/plt/gallery/_generate.py +560 -0
- scitex/plt/gallery/_plots.py +594 -0
- scitex/plt/gallery/_registry.py +153 -0
- scitex/plt/io/__init__.py +53 -0
- scitex/plt/io/_bundle.py +490 -0
- scitex/plt/io/_layered_bundle.py +1343 -0
- scitex/plt/styles/SCITEX_STYLE.yaml +26 -0
- scitex/plt/styles/__init__.py +23 -9
- scitex/plt/styles/_plot_defaults.py +62 -61
- scitex/plt/styles/_plot_postprocess.py +126 -77
- scitex/plt/styles/_style_loader.py +0 -0
- scitex/plt/styles/presets.py +121 -18
- scitex/plt/utils/__init__.py +42 -3
- scitex/plt/utils/_close.py +8 -3
- scitex/plt/utils/_collect_figure_metadata.py +3033 -271
- scitex/plt/utils/_colorbar.py +15 -17
- scitex/plt/utils/_configure_mpl.py +26 -30
- scitex/plt/utils/_crop.py +87 -36
- scitex/plt/utils/_csv_column_naming.py +177 -72
- scitex/plt/utils/_dimension_viewer.py +7 -19
- scitex/plt/utils/_figure_from_axes_mm.py +70 -16
- scitex/plt/utils/_figure_mm.py +119 -3
- scitex/plt/utils/_get_actual_font.py +5 -4
- scitex/plt/utils/_histogram_utils.py +52 -48
- scitex/plt/utils/_hitmap.py +1643 -0
- scitex/plt/utils/_is_valid_axis.py +19 -13
- scitex/plt/utils/_mk_colorbar.py +3 -3
- scitex/plt/utils/_scientific_captions.py +202 -139
- scitex/plt/utils/_scitex_config.py +98 -98
- scitex/plt/utils/_units.py +0 -0
- scitex/plt/utils/metadata/__init__.py +61 -0
- scitex/plt/utils/metadata/_artist_extraction.py +119 -0
- scitex/plt/utils/metadata/_axes_metadata.py +93 -0
- scitex/plt/utils/metadata/_collection_artists.py +292 -0
- scitex/plt/utils/metadata/_core.py +207 -0
- scitex/plt/utils/metadata/_csv_column_extraction.py +186 -0
- scitex/plt/utils/metadata/_csv_hash.py +115 -0
- scitex/plt/utils/metadata/_csv_verification.py +95 -0
- scitex/plt/utils/metadata/_data_linkage.py +263 -0
- scitex/plt/utils/metadata/_dimensions.py +242 -0
- scitex/plt/utils/metadata/_editable_export.py +405 -0
- scitex/plt/utils/metadata/_figure_metadata.py +58 -0
- scitex/plt/utils/metadata/_geometry_extraction.py +570 -0
- scitex/plt/utils/metadata/_image_text_artists.py +168 -0
- scitex/plt/utils/metadata/_label_parsing.py +82 -0
- scitex/plt/utils/metadata/_legend_extraction.py +120 -0
- scitex/plt/utils/metadata/_line_artists.py +367 -0
- scitex/plt/utils/metadata/_line_semantic_handling.py +173 -0
- scitex/plt/utils/metadata/_patch_artists.py +211 -0
- scitex/plt/utils/metadata/_plot_content.py +26 -0
- scitex/plt/utils/metadata/_plot_type_detection.py +184 -0
- scitex/plt/utils/metadata/_precision.py +134 -0
- scitex/plt/utils/metadata/_precision_config.py +68 -0
- scitex/plt/utils/metadata/_precision_sections.py +211 -0
- scitex/plt/utils/metadata/_recipe_extraction.py +267 -0
- scitex/plt/utils/metadata/_style_parsing.py +174 -0
- scitex/repro/_RandomStateManager.py +33 -38
- scitex/repro/__init__.py +16 -7
- scitex/repro/_gen_ID.py +7 -9
- scitex/repro/_gen_timestamp.py +7 -6
- scitex/repro/_hash_array.py +8 -12
- scitex/reproduce/__init__.py +1 -1
- scitex/resource/_get_processor_usages.py +3 -1
- scitex/resource/_log_processor_usages.py +3 -1
- scitex/rng/__init__.py +1 -1
- scitex/schema/README.md +178 -0
- scitex/schema/__init__.py +237 -0
- scitex/schema/_canvas.py +444 -0
- scitex/schema/_plot.py +1015 -0
- scitex/schema/_stats.py +762 -0
- scitex/schema/_validation.py +590 -0
- scitex/scholar/.legacy/Scholar.py +5 -12
- scitex/scholar/.legacy/_Scholar.py +66 -99
- scitex/scholar/.legacy/_ScholarAPI.py +75 -66
- scitex/scholar/.legacy/_tmp/search_engine/_BaseSearchEngine.py +3 -3
- scitex/scholar/.legacy/_tmp/search_engine/_UnifiedSearcher.py +4 -9
- scitex/scholar/.legacy/_tmp/search_engine/__init__.py +14 -21
- scitex/scholar/.legacy/_tmp/search_engine/local/_LocalSearchEngine.py +40 -37
- scitex/scholar/.legacy/_tmp/search_engine/local/_VectorSearchEngine.py +31 -28
- scitex/scholar/.legacy/_tmp/search_engine/web/_ArxivSearchEngine.py +74 -65
- scitex/scholar/.legacy/_tmp/search_engine/web/_CrossRefSearchEngine.py +122 -116
- scitex/scholar/.legacy/_tmp/search_engine/web/_GoogleScholarSearchEngine.py +65 -59
- scitex/scholar/.legacy/_tmp/search_engine/web/_PubMedSearchEngine.py +121 -107
- scitex/scholar/.legacy/_tmp/search_engine/web/_SemanticScholarSearchEngine.py +5 -12
- scitex/scholar/.legacy/database/_DatabaseEntry.py +49 -45
- scitex/scholar/.legacy/database/_DatabaseIndex.py +131 -94
- scitex/scholar/.legacy/database/_LibraryManager.py +65 -63
- scitex/scholar/.legacy/database/_PaperDatabase.py +138 -124
- scitex/scholar/.legacy/database/_ScholarDatabaseIntegration.py +14 -36
- scitex/scholar/.legacy/database/_StorageIntegratedDB.py +192 -156
- scitex/scholar/.legacy/database/_ZoteroCompatibleDB.py +300 -237
- scitex/scholar/.legacy/database/__init__.py +2 -1
- scitex/scholar/.legacy/database/manage.py +92 -84
- scitex/scholar/.legacy/lookup/_LookupIndex.py +157 -101
- scitex/scholar/.legacy/lookup/__init__.py +2 -1
- scitex/scholar/.legacy/metadata/doi/batch/_MetadataHandlerForBatchDOIResolution.py +4 -9
- scitex/scholar/.legacy/metadata/doi/batch/_ProgressManagerForBatchDOIResolution.py +10 -23
- scitex/scholar/.legacy/metadata/doi/batch/_SourceStatsManagerForBatchDOIResolution.py +4 -9
- scitex/scholar/.legacy/metadata/doi/batch/__init__.py +3 -1
- scitex/scholar/.legacy/metadata/doi/resolvers/_BatchDOIResolver.py +10 -25
- scitex/scholar/.legacy/metadata/doi/resolvers/_BibTeXDOIResolver.py +19 -49
- scitex/scholar/.legacy/metadata/doi/resolvers/_DOIResolver.py +1 -0
- scitex/scholar/.legacy/metadata/doi/resolvers/_SingleDOIResolver.py +8 -20
- scitex/scholar/.legacy/metadata/doi/sources/.combined-SemanticScholarSource/_SemanticScholarSource.py +37 -35
- scitex/scholar/.legacy/metadata/doi/sources/.combined-SemanticScholarSource/_SemanticScholarSourceEnhanced.py +49 -37
- scitex/scholar/.legacy/metadata/doi/sources/_ArXivSource.py +11 -30
- scitex/scholar/.legacy/metadata/doi/sources/_BaseDOISource.py +19 -47
- scitex/scholar/.legacy/metadata/doi/sources/_CrossRefLocalSource.py +1 -0
- scitex/scholar/.legacy/metadata/doi/sources/_CrossRefSource.py +12 -33
- scitex/scholar/.legacy/metadata/doi/sources/_OpenAlexSource.py +8 -20
- scitex/scholar/.legacy/metadata/doi/sources/_PubMedSource.py +10 -27
- scitex/scholar/.legacy/metadata/doi/sources/_SemanticScholarSource.py +11 -29
- scitex/scholar/.legacy/metadata/doi/sources/_SourceManager.py +8 -21
- scitex/scholar/.legacy/metadata/doi/sources/_SourceResolutionStrategy.py +24 -55
- scitex/scholar/.legacy/metadata/doi/sources/_SourceRotationManager.py +8 -21
- scitex/scholar/.legacy/metadata/doi/sources/_URLDOISource.py +9 -16
- scitex/scholar/.legacy/metadata/doi/sources/_UnifiedSource.py +8 -22
- scitex/scholar/.legacy/metadata/doi/sources/__init__.py +1 -0
- scitex/scholar/.legacy/metadata/doi/utils/_PubMedConverter.py +4 -8
- scitex/scholar/.legacy/metadata/doi/utils/_RateLimitHandler.py +17 -43
- scitex/scholar/.legacy/metadata/doi/utils/_TextNormalizer.py +8 -18
- scitex/scholar/.legacy/metadata/doi/utils/_URLDOIExtractor.py +4 -8
- scitex/scholar/.legacy/metadata/doi/utils/__init__.py +1 -0
- scitex/scholar/.legacy/metadata/doi/utils/_to_complete_metadata_structure.py +1 -0
- scitex/scholar/.legacy/metadata/enrichment/_LibraryEnricher.py +2 -3
- scitex/scholar/.legacy/metadata/enrichment/enrichers/_ImpactFactorEnricher.py +6 -12
- scitex/scholar/.legacy/metadata/enrichment/enrichers/_SmartEnricher.py +5 -10
- scitex/scholar/.legacy/metadata/enrichment/sources/_UnifiedMetadataSource.py +4 -5
- scitex/scholar/.legacy/metadata/query_to_full_meta_json.py +8 -12
- scitex/scholar/.legacy/metadata/urls/_URLMetadataHandler.py +3 -3
- scitex/scholar/.legacy/metadata/urls/_ZoteroTranslatorRunner.py +15 -21
- scitex/scholar/.legacy/metadata/urls/__init__.py +3 -3
- scitex/scholar/.legacy/metadata/urls/_finder.py +4 -6
- scitex/scholar/.legacy/metadata/urls/_handler.py +7 -15
- scitex/scholar/.legacy/metadata/urls/_resolver.py +6 -12
- scitex/scholar/.legacy/search/_Embedder.py +74 -69
- scitex/scholar/.legacy/search/_SemanticSearch.py +91 -90
- scitex/scholar/.legacy/search/_SemanticSearchEngine.py +104 -109
- scitex/scholar/.legacy/search/_UnifiedSearcher.py +530 -471
- scitex/scholar/.legacy/search/_VectorDatabase.py +111 -92
- scitex/scholar/.legacy/search/__init__.py +1 -0
- scitex/scholar/.legacy/storage/_EnhancedStorageManager.py +182 -154
- scitex/scholar/.legacy/storage/__init__.py +2 -1
- scitex/scholar/__init__.py +0 -2
- scitex/scholar/__main__.py +1 -3
- scitex/scholar/auth/ScholarAuthManager.py +13 -36
- scitex/scholar/auth/core/AuthenticationGateway.py +15 -29
- scitex/scholar/auth/core/BrowserAuthenticator.py +22 -57
- scitex/scholar/auth/core/StrategyResolver.py +10 -27
- scitex/scholar/auth/core/__init__.py +5 -1
- scitex/scholar/auth/gateway/_OpenURLLinkFinder.py +11 -21
- scitex/scholar/auth/gateway/_OpenURLResolver.py +10 -18
- scitex/scholar/auth/gateway/_resolve_functions.py +3 -3
- scitex/scholar/auth/providers/BaseAuthenticator.py +1 -0
- scitex/scholar/auth/providers/EZProxyAuthenticator.py +7 -14
- scitex/scholar/auth/providers/OpenAthensAuthenticator.py +29 -57
- scitex/scholar/auth/providers/ShibbolethAuthenticator.py +87 -73
- scitex/scholar/auth/session/AuthCacheManager.py +12 -22
- scitex/scholar/auth/session/SessionManager.py +4 -6
- scitex/scholar/auth/sso/BaseSSOAutomator.py +13 -19
- scitex/scholar/auth/sso/OpenAthensSSOAutomator.py +16 -45
- scitex/scholar/auth/sso/SSOAutomator.py +8 -15
- scitex/scholar/auth/sso/UniversityOfMelbourneSSOAutomator.py +13 -23
- scitex/scholar/browser/ScholarBrowserManager.py +31 -56
- scitex/scholar/browser/__init__.py +1 -0
- scitex/scholar/browser/utils/click_and_wait.py +3 -4
- scitex/scholar/browser/utils/close_unwanted_pages.py +4 -7
- scitex/scholar/browser/utils/wait_redirects.py +15 -40
- scitex/scholar/citation_graph/__init__.py +0 -0
- scitex/scholar/citation_graph/builder.py +3 -7
- scitex/scholar/citation_graph/database.py +4 -11
- scitex/scholar/citation_graph/example.py +5 -10
- scitex/scholar/citation_graph/models.py +0 -0
- scitex/scholar/cli/_url_utils.py +1 -1
- scitex/scholar/cli/chrome.py +5 -3
- scitex/scholar/cli/download_pdf.py +13 -14
- scitex/scholar/cli/handlers/bibtex_handler.py +4 -12
- scitex/scholar/cli/handlers/doi_handler.py +1 -3
- scitex/scholar/cli/handlers/project_handler.py +6 -20
- scitex/scholar/cli/open_browser.py +41 -39
- scitex/scholar/cli/open_browser_auto.py +31 -39
- scitex/scholar/cli/open_browser_monitored.py +27 -24
- scitex/scholar/config/ScholarConfig.py +5 -8
- scitex/scholar/config/__init__.py +1 -0
- scitex/scholar/config/core/_CascadeConfig.py +3 -3
- scitex/scholar/config/core/_PathManager.py +16 -28
- scitex/scholar/core/Paper.py +79 -78
- scitex/scholar/core/Papers.py +16 -27
- scitex/scholar/core/Scholar.py +98 -229
- scitex/scholar/core/journal_normalizer.py +52 -49
- scitex/scholar/core/oa_cache.py +27 -23
- scitex/scholar/core/open_access.py +17 -8
- scitex/scholar/docs/template.py +4 -3
- scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/clf_svm.py +0 -0
- scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/download.py +0 -0
- scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_conf_mat.py +0 -0
- scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_digits.py +0 -0
- scitex/scholar/docs/to_claude/examples/example-python-project-scitex/scripts/mnist/plot_umap_space.py +0 -0
- scitex/scholar/examples/00_config.py +10 -9
- scitex/scholar/examples/01_auth.py +3 -0
- scitex/scholar/examples/02_browser.py +14 -10
- scitex/scholar/examples/03_01-engine.py +3 -0
- scitex/scholar/examples/03_02-engine-for-bibtex.py +4 -3
- scitex/scholar/examples/04_01-url.py +9 -9
- scitex/scholar/examples/04_02-url-for-bibtex.py +7 -3
- scitex/scholar/examples/04_02-url-for-dois.py +87 -97
- scitex/scholar/examples/05_download_pdf.py +10 -4
- scitex/scholar/examples/06_find_and_download.py +6 -6
- scitex/scholar/examples/06_parse_bibtex.py +17 -17
- scitex/scholar/examples/07_storage_integration.py +6 -9
- scitex/scholar/examples/99_fullpipeline-for-bibtex.py +14 -15
- scitex/scholar/examples/99_fullpipeline-for-one-entry.py +31 -23
- scitex/scholar/examples/99_maintenance.py +3 -0
- scitex/scholar/examples/dev.py +2 -3
- scitex/scholar/examples/zotero_integration.py +11 -18
- scitex/scholar/impact_factor/ImpactFactorEngine.py +7 -9
- scitex/scholar/impact_factor/estimation/__init__.py +4 -4
- scitex/scholar/impact_factor/estimation/core/__init__.py +3 -7
- scitex/scholar/impact_factor/estimation/core/cache_manager.py +223 -211
- scitex/scholar/impact_factor/estimation/core/calculator.py +165 -131
- scitex/scholar/impact_factor/estimation/core/journal_matcher.py +217 -172
- scitex/scholar/impact_factor/jcr/ImpactFactorJCREngine.py +6 -14
- scitex/scholar/impact_factor/jcr/build_database.py +4 -3
- scitex/scholar/integration/base.py +9 -17
- scitex/scholar/integration/mendeley/exporter.py +2 -4
- scitex/scholar/integration/mendeley/importer.py +3 -3
- scitex/scholar/integration/mendeley/linker.py +3 -3
- scitex/scholar/integration/mendeley/mapper.py +9 -6
- scitex/scholar/integration/zotero/__main__.py +26 -43
- scitex/scholar/integration/zotero/exporter.py +15 -11
- scitex/scholar/integration/zotero/importer.py +12 -10
- scitex/scholar/integration/zotero/linker.py +8 -12
- scitex/scholar/integration/zotero/mapper.py +17 -12
- scitex/scholar/metadata_engines/.combined-SemanticScholarSource/_SemanticScholarSource.py +37 -35
- scitex/scholar/metadata_engines/.combined-SemanticScholarSource/_SemanticScholarSourceEnhanced.py +47 -35
- scitex/scholar/metadata_engines/ScholarEngine.py +21 -43
- scitex/scholar/metadata_engines/__init__.py +1 -0
- scitex/scholar/metadata_engines/individual/ArXivEngine.py +15 -37
- scitex/scholar/metadata_engines/individual/CrossRefEngine.py +15 -42
- scitex/scholar/metadata_engines/individual/CrossRefLocalEngine.py +24 -45
- scitex/scholar/metadata_engines/individual/OpenAlexEngine.py +11 -21
- scitex/scholar/metadata_engines/individual/PubMedEngine.py +10 -27
- scitex/scholar/metadata_engines/individual/SemanticScholarEngine.py +28 -35
- scitex/scholar/metadata_engines/individual/URLDOIEngine.py +11 -22
- scitex/scholar/metadata_engines/individual/_BaseDOIEngine.py +20 -49
- scitex/scholar/metadata_engines/utils/_PubMedConverter.py +4 -8
- scitex/scholar/metadata_engines/utils/_URLDOIExtractor.py +5 -10
- scitex/scholar/metadata_engines/utils/__init__.py +2 -0
- scitex/scholar/metadata_engines/utils/_metadata2bibtex.py +3 -0
- scitex/scholar/metadata_engines/utils/_standardize_metadata.py +2 -3
- scitex/scholar/pdf_download/ScholarPDFDownloader.py +25 -37
- scitex/scholar/pdf_download/strategies/chrome_pdf_viewer.py +11 -19
- scitex/scholar/pdf_download/strategies/direct_download.py +5 -9
- scitex/scholar/pdf_download/strategies/manual_download_fallback.py +3 -3
- scitex/scholar/pdf_download/strategies/manual_download_utils.py +6 -13
- scitex/scholar/pdf_download/strategies/open_access_download.py +49 -31
- scitex/scholar/pdf_download/strategies/response_body.py +8 -19
- scitex/scholar/pipelines/ScholarPipelineBibTeX.py +9 -18
- scitex/scholar/pipelines/ScholarPipelineMetadataParallel.py +25 -26
- scitex/scholar/pipelines/ScholarPipelineMetadataSingle.py +62 -23
- scitex/scholar/pipelines/ScholarPipelineParallel.py +13 -30
- scitex/scholar/pipelines/ScholarPipelineSearchParallel.py +299 -220
- scitex/scholar/pipelines/ScholarPipelineSearchSingle.py +202 -165
- scitex/scholar/pipelines/ScholarPipelineSingle.py +25 -51
- scitex/scholar/pipelines/SearchQueryParser.py +55 -55
- scitex/scholar/search_engines/ScholarSearchEngine.py +31 -27
- scitex/scholar/search_engines/_BaseSearchEngine.py +20 -23
- scitex/scholar/search_engines/individual/ArXivSearchEngine.py +53 -35
- scitex/scholar/search_engines/individual/CrossRefSearchEngine.py +47 -40
- scitex/scholar/search_engines/individual/OpenAlexSearchEngine.py +55 -50
- scitex/scholar/search_engines/individual/PubMedSearchEngine.py +8 -10
- scitex/scholar/search_engines/individual/SemanticScholarSearchEngine.py +55 -49
- scitex/scholar/storage/BibTeXHandler.py +150 -95
- scitex/scholar/storage/PaperIO.py +3 -6
- scitex/scholar/storage/ScholarLibrary.py +70 -49
- scitex/scholar/storage/_DeduplicationManager.py +52 -25
- scitex/scholar/storage/_LibraryCacheManager.py +19 -46
- scitex/scholar/storage/_LibraryManager.py +65 -175
- scitex/scholar/url_finder/ScholarURLFinder.py +9 -25
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_direct_links.py +1 -1
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_href.py +6 -10
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_navigation.py +4 -6
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_publisher_patterns.py +8 -15
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_zotero_translators.py +3 -3
- scitex/scholar/url_finder/strategies/find_supplementary_urls_by_href.py +3 -3
- scitex/scholar/url_finder/translators/core/patterns.py +6 -4
- scitex/scholar/url_finder/translators/core/registry.py +6 -9
- scitex/scholar/url_finder/translators/individual/BOFiP_Impots.py +60 -52
- scitex/scholar/url_finder/translators/individual/Baidu_Scholar.py +54 -62
- scitex/scholar/url_finder/translators/individual/Bangkok_Post.py +38 -44
- scitex/scholar/url_finder/translators/individual/Baruch_Foundation.py +43 -47
- scitex/scholar/url_finder/translators/individual/Beobachter.py +46 -50
- scitex/scholar/url_finder/translators/individual/Bezneng_Gajit.py +37 -41
- scitex/scholar/url_finder/translators/individual/BibLaTeX.py +59 -52
- scitex/scholar/url_finder/translators/individual/BibTeX.py +83 -79
- scitex/scholar/url_finder/translators/individual/Biblio_com.py +48 -51
- scitex/scholar/url_finder/translators/individual/Bibliontology_RDF.py +58 -56
- scitex/scholar/url_finder/translators/individual/Camara_Brasileira_do_Livro_ISBN.py +102 -99
- scitex/scholar/url_finder/translators/individual/CanLII.py +49 -43
- scitex/scholar/url_finder/translators/individual/Canada_com.py +36 -40
- scitex/scholar/url_finder/translators/individual/Canadian_Letters_and_Images.py +43 -43
- scitex/scholar/url_finder/translators/individual/Canadiana_ca.py +77 -66
- scitex/scholar/url_finder/translators/individual/Cascadilla_Proceedings_Project.py +68 -62
- scitex/scholar/url_finder/translators/individual/Central_and_Eastern_European_Online_Library_Journals.py +60 -60
- scitex/scholar/url_finder/translators/individual/Champlain_Society_Collection.py +63 -61
- scitex/scholar/url_finder/translators/individual/Chicago_Journal_of_Theoretical_Computer_Science.py +74 -58
- scitex/scholar/url_finder/translators/individual/Christian_Science_Monitor.py +32 -38
- scitex/scholar/url_finder/translators/individual/Columbia_University_Press.py +51 -47
- scitex/scholar/url_finder/translators/individual/Common_Place.py +66 -57
- scitex/scholar/url_finder/translators/individual/Cornell_LII.py +66 -62
- scitex/scholar/url_finder/translators/individual/Cornell_University_Press.py +38 -45
- scitex/scholar/url_finder/translators/individual/CourtListener.py +52 -56
- scitex/scholar/url_finder/translators/individual/DAI_Zenon.py +53 -54
- scitex/scholar/url_finder/translators/individual/access_medicine.py +27 -33
- scitex/scholar/url_finder/translators/individual/acm.py +1 -1
- scitex/scholar/url_finder/translators/individual/acm_digital_library.py +93 -63
- scitex/scholar/url_finder/translators/individual/airiti.py +3 -1
- scitex/scholar/url_finder/translators/individual/aosic.py +3 -1
- scitex/scholar/url_finder/translators/individual/archive_ouverte_aosic.py +3 -1
- scitex/scholar/url_finder/translators/individual/archive_ouverte_en_sciences_de_l_information_et_de_la_communication___aosic_.py +6 -2
- scitex/scholar/url_finder/translators/individual/artforum.py +35 -27
- scitex/scholar/url_finder/translators/individual/arxiv.py +1 -1
- scitex/scholar/url_finder/translators/individual/arxiv_org.py +8 -4
- scitex/scholar/url_finder/translators/individual/atlanta_journal_constitution.py +22 -18
- scitex/scholar/url_finder/translators/individual/atypon_journals.py +19 -11
- scitex/scholar/url_finder/translators/individual/austlii_and_nzlii.py +48 -44
- scitex/scholar/url_finder/translators/individual/australian_dictionary_of_biography.py +21 -17
- scitex/scholar/url_finder/translators/individual/bailii.py +22 -19
- scitex/scholar/url_finder/translators/individual/bbc.py +46 -42
- scitex/scholar/url_finder/translators/individual/bbc_genome.py +37 -25
- scitex/scholar/url_finder/translators/individual/biblioteca_nacional_de_maestros.py +24 -20
- scitex/scholar/url_finder/translators/individual/bibliotheque_archives_nationale_quebec_pistard.py +42 -43
- scitex/scholar/url_finder/translators/individual/bibliotheque_archives_nationales_quebec.py +87 -81
- scitex/scholar/url_finder/translators/individual/bibliotheque_nationale_france.py +39 -37
- scitex/scholar/url_finder/translators/individual/bibsys.py +32 -28
- scitex/scholar/url_finder/translators/individual/bioconductor.py +58 -52
- scitex/scholar/url_finder/translators/individual/biomed_central.py +23 -15
- scitex/scholar/url_finder/translators/individual/biorxiv.py +26 -13
- scitex/scholar/url_finder/translators/individual/blogger.py +39 -43
- scitex/scholar/url_finder/translators/individual/bloomberg.py +48 -52
- scitex/scholar/url_finder/translators/individual/bloomsbury_food_library.py +37 -37
- scitex/scholar/url_finder/translators/individual/bluesky.py +30 -28
- scitex/scholar/url_finder/translators/individual/bnf_isbn.py +1 -1
- scitex/scholar/url_finder/translators/individual/bocc.py +66 -60
- scitex/scholar/url_finder/translators/individual/boe.py +52 -52
- scitex/scholar/url_finder/translators/individual/brill.py +3 -1
- scitex/scholar/url_finder/translators/individual/business_standard.py +36 -38
- scitex/scholar/url_finder/translators/individual/cabi_cab_abstracts.py +39 -41
- scitex/scholar/url_finder/translators/individual/cambridge.py +3 -1
- scitex/scholar/url_finder/translators/individual/cambridge_core.py +30 -24
- scitex/scholar/url_finder/translators/individual/caod.py +50 -46
- scitex/scholar/url_finder/translators/individual/cbc.py +91 -67
- scitex/scholar/url_finder/translators/individual/ccfr_bnf.py +49 -53
- scitex/scholar/url_finder/translators/individual/cia_world_factbook.py +43 -33
- scitex/scholar/url_finder/translators/individual/crossref_rest.py +208 -174
- scitex/scholar/url_finder/translators/individual/current_affairs.py +29 -35
- scitex/scholar/url_finder/translators/individual/dabi.py +70 -66
- scitex/scholar/url_finder/translators/individual/dagens_nyheter.py +3 -1
- scitex/scholar/url_finder/translators/individual/dagstuhl.py +10 -15
- scitex/scholar/url_finder/translators/individual/dar_almandumah.py +13 -9
- scitex/scholar/url_finder/translators/individual/dart_europe.py +19 -22
- scitex/scholar/url_finder/translators/individual/data_gov.py +2 -2
- scitex/scholar/url_finder/translators/individual/databrary.py +27 -28
- scitex/scholar/url_finder/translators/individual/datacite_json.py +152 -137
- scitex/scholar/url_finder/translators/individual/dataverse.py +68 -64
- scitex/scholar/url_finder/translators/individual/daum_news.py +38 -38
- scitex/scholar/url_finder/translators/individual/dblp.py +4 -8
- scitex/scholar/url_finder/translators/individual/dblp_computer_science_bibliography.py +8 -3
- scitex/scholar/url_finder/translators/individual/dbpia.py +5 -3
- scitex/scholar/url_finder/translators/individual/defense_technical_information_center.py +30 -28
- scitex/scholar/url_finder/translators/individual/delpher.py +102 -79
- scitex/scholar/url_finder/translators/individual/demographic_research.py +35 -31
- scitex/scholar/url_finder/translators/individual/denik_cz.py +58 -54
- scitex/scholar/url_finder/translators/individual/depatisnet.py +7 -10
- scitex/scholar/url_finder/translators/individual/der_freitag.py +81 -66
- scitex/scholar/url_finder/translators/individual/der_spiegel.py +56 -54
- scitex/scholar/url_finder/translators/individual/digibib_net.py +3 -1
- scitex/scholar/url_finder/translators/individual/digizeitschriften.py +3 -1
- scitex/scholar/url_finder/translators/individual/dpla.py +13 -14
- scitex/scholar/url_finder/translators/individual/dspace.py +2 -2
- scitex/scholar/url_finder/translators/individual/ebrary.py +3 -1
- scitex/scholar/url_finder/translators/individual/ebscohost.py +3 -1
- scitex/scholar/url_finder/translators/individual/electronic_colloquium_on_computational_complexity.py +3 -1
- scitex/scholar/url_finder/translators/individual/elife.py +3 -1
- scitex/scholar/url_finder/translators/individual/elsevier_health_journals.py +3 -1
- scitex/scholar/url_finder/translators/individual/emerald.py +3 -1
- scitex/scholar/url_finder/translators/individual/emerald_insight.py +3 -1
- scitex/scholar/url_finder/translators/individual/epicurious.py +3 -1
- scitex/scholar/url_finder/translators/individual/eurogamerusgamer.py +3 -1
- scitex/scholar/url_finder/translators/individual/fachportal_padagogik.py +3 -1
- scitex/scholar/url_finder/translators/individual/frontiers.py +1 -1
- scitex/scholar/url_finder/translators/individual/gale_databases.py +3 -1
- scitex/scholar/url_finder/translators/individual/gms_german_medical_science.py +6 -2
- scitex/scholar/url_finder/translators/individual/ieee_computer_society.py +6 -2
- scitex/scholar/url_finder/translators/individual/ieee_xplore.py +41 -35
- scitex/scholar/url_finder/translators/individual/inter_research_science_center.py +6 -2
- scitex/scholar/url_finder/translators/individual/jisc_historical_texts.py +3 -1
- scitex/scholar/url_finder/translators/individual/jstor.py +14 -12
- scitex/scholar/url_finder/translators/individual/korean_national_library.py +3 -1
- scitex/scholar/url_finder/translators/individual/la_times.py +3 -1
- scitex/scholar/url_finder/translators/individual/landesbibliographie_baden_wurttemberg.py +3 -1
- scitex/scholar/url_finder/translators/individual/legislative_insight.py +3 -1
- scitex/scholar/url_finder/translators/individual/libraries_tasmania.py +3 -1
- scitex/scholar/url_finder/translators/individual/library_catalog__koha_.py +3 -1
- scitex/scholar/url_finder/translators/individual/lingbuzz.py +2 -2
- scitex/scholar/url_finder/translators/individual/max_planck_institute_for_the_history_of_science_virtual_laboratory_library.py +3 -1
- scitex/scholar/url_finder/translators/individual/mdpi.py +12 -6
- scitex/scholar/url_finder/translators/individual/microbiology_society_journals.py +3 -1
- scitex/scholar/url_finder/translators/individual/midas_journals.py +3 -1
- scitex/scholar/url_finder/translators/individual/nagoya_university_opac.py +3 -1
- scitex/scholar/url_finder/translators/individual/nature_publishing_group.py +32 -19
- scitex/scholar/url_finder/translators/individual/ntsb_accident_reports.py +3 -1
- scitex/scholar/url_finder/translators/individual/openedition_journals.py +8 -4
- scitex/scholar/url_finder/translators/individual/orcid.py +16 -15
- scitex/scholar/url_finder/translators/individual/oxford.py +25 -19
- scitex/scholar/url_finder/translators/individual/oxford_dictionaries_premium.py +3 -1
- scitex/scholar/url_finder/translators/individual/ozon_ru.py +3 -1
- scitex/scholar/url_finder/translators/individual/plos.py +9 -12
- scitex/scholar/url_finder/translators/individual/polygon.py +3 -1
- scitex/scholar/url_finder/translators/individual/primo.py +3 -1
- scitex/scholar/url_finder/translators/individual/project_muse.py +3 -1
- scitex/scholar/url_finder/translators/individual/pubfactory_journals.py +3 -1
- scitex/scholar/url_finder/translators/individual/pubmed.py +71 -65
- scitex/scholar/url_finder/translators/individual/pubmed_central.py +8 -6
- scitex/scholar/url_finder/translators/individual/rechtspraak_nl.py +3 -1
- scitex/scholar/url_finder/translators/individual/sage_journals.py +25 -17
- scitex/scholar/url_finder/translators/individual/sciencedirect.py +36 -17
- scitex/scholar/url_finder/translators/individual/semantics_visual_library.py +3 -1
- scitex/scholar/url_finder/translators/individual/silverchair.py +70 -52
- scitex/scholar/url_finder/translators/individual/sora.py +3 -1
- scitex/scholar/url_finder/translators/individual/springer.py +15 -11
- scitex/scholar/url_finder/translators/individual/ssrn.py +3 -3
- scitex/scholar/url_finder/translators/individual/stanford_encyclopedia_of_philosophy.py +3 -1
- scitex/scholar/url_finder/translators/individual/superlib.py +3 -1
- scitex/scholar/url_finder/translators/individual/treesearch.py +3 -1
- scitex/scholar/url_finder/translators/individual/university_of_chicago_press_books.py +3 -1
- scitex/scholar/url_finder/translators/individual/vlex.py +3 -1
- scitex/scholar/url_finder/translators/individual/web_of_science.py +3 -1
- scitex/scholar/url_finder/translators/individual/web_of_science_nextgen.py +3 -1
- scitex/scholar/url_finder/translators/individual/wiley.py +31 -25
- scitex/scholar/url_finder/translators/individual/wilson_center_digital_archive.py +3 -1
- scitex/scholar/utils/bibtex/_parse_bibtex.py +3 -3
- scitex/scholar/utils/cleanup/_cleanup_scholar_processes.py +5 -9
- scitex/scholar/utils/text/_TextNormalizer.py +249 -176
- scitex/scholar/utils/validation/DOIValidator.py +31 -28
- scitex/scholar/utils/validation/__init__.py +0 -0
- scitex/scholar/utils/validation/validate_library_dois.py +61 -57
- scitex/scholar/zotero/__init__.py +1 -1
- scitex/security/cli.py +7 -20
- scitex/security/github.py +45 -32
- scitex/session/__init__.py +8 -9
- scitex/session/_decorator.py +49 -42
- scitex/session/_lifecycle.py +39 -39
- scitex/session/_manager.py +24 -20
- scitex/sh/__init__.py +4 -3
- scitex/sh/_execute.py +10 -7
- scitex/sh/_security.py +3 -3
- scitex/sh/_types.py +2 -3
- scitex/stats/__init__.py +174 -6
- scitex/stats/_schema.py +42 -569
- scitex/stats/auto/__init__.py +188 -0
- scitex/stats/auto/_context.py +331 -0
- scitex/stats/auto/_formatting.py +679 -0
- scitex/stats/auto/_rules.py +901 -0
- scitex/stats/auto/_selector.py +554 -0
- scitex/stats/auto/_styles.py +721 -0
- scitex/stats/correct/__init__.py +4 -4
- scitex/stats/correct/_correct_bonferroni.py +43 -34
- scitex/stats/correct/_correct_fdr.py +14 -40
- scitex/stats/correct/_correct_fdr_.py +39 -46
- scitex/stats/correct/_correct_holm.py +14 -32
- scitex/stats/correct/_correct_sidak.py +36 -21
- scitex/stats/descriptive/_circular.py +20 -21
- scitex/stats/descriptive/_describe.py +19 -5
- scitex/stats/descriptive/_nan.py +5 -7
- scitex/stats/descriptive/_real.py +4 -3
- scitex/stats/effect_sizes/__init__.py +10 -11
- scitex/stats/effect_sizes/_cliffs_delta.py +35 -32
- scitex/stats/effect_sizes/_cohens_d.py +30 -31
- scitex/stats/effect_sizes/_epsilon_squared.py +19 -22
- scitex/stats/effect_sizes/_eta_squared.py +23 -27
- scitex/stats/effect_sizes/_prob_superiority.py +18 -21
- scitex/stats/io/__init__.py +29 -0
- scitex/stats/io/_bundle.py +156 -0
- scitex/stats/posthoc/__init__.py +3 -3
- scitex/stats/posthoc/_dunnett.py +75 -55
- scitex/stats/posthoc/_games_howell.py +61 -43
- scitex/stats/posthoc/_tukey_hsd.py +42 -34
- scitex/stats/power/__init__.py +2 -2
- scitex/stats/power/_power.py +56 -56
- scitex/stats/tests/__init__.py +1 -1
- scitex/stats/tests/correlation/__init__.py +1 -1
- scitex/stats/tests/correlation/_test_pearson.py +28 -38
- scitex/stats/utils/__init__.py +14 -17
- scitex/stats/utils/_effect_size.py +85 -78
- scitex/stats/utils/_formatters.py +49 -43
- scitex/stats/utils/_normalizers.py +7 -14
- scitex/stats/utils/_power.py +56 -56
- scitex/str/__init__.py +1 -0
- scitex/str/_clean_path.py +3 -3
- scitex/str/_factor_out_digits.py +86 -58
- scitex/str/_format_plot_text.py +180 -111
- scitex/str/_latex.py +19 -19
- scitex/str/_latex_fallback.py +9 -10
- scitex/str/_parse.py +3 -6
- scitex/str/_print_debug.py +13 -13
- scitex/str/_printc.py +2 -0
- scitex/str/_search.py +3 -3
- scitex/template/.legacy/_clone_project.py +9 -13
- scitex/template/__init__.py +10 -2
- scitex/template/_clone_project.py +7 -2
- scitex/template/_copy.py +1 -0
- scitex/template/_customize.py +3 -6
- scitex/template/_git_strategy.py +2 -3
- scitex/template/_rename.py +1 -0
- scitex/template/clone_pip_project.py +6 -7
- scitex/template/clone_research.py +7 -10
- scitex/template/clone_singularity.py +6 -7
- scitex/template/clone_writer_directory.py +6 -7
- scitex/tex/__init__.py +4 -0
- scitex/tex/_export.py +890 -0
- 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/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
- scitex/writer/_clone_writer_project.py +2 -6
- scitex/writer/_compile/__init__.py +1 -0
- scitex/writer/_compile/_parser.py +1 -0
- scitex/writer/_compile/_runner.py +35 -38
- scitex/writer/_compile/_validator.py +1 -0
- scitex/writer/_compile/manuscript.py +1 -0
- scitex/writer/_compile/revision.py +1 -0
- scitex/writer/_compile/supplementary.py +1 -0
- scitex/writer/_compile_async.py +5 -12
- scitex/writer/_project/__init__.py +1 -0
- scitex/writer/_project/_create.py +10 -25
- scitex/writer/_project/_trees.py +4 -9
- scitex/writer/_project/_validate.py +2 -3
- scitex/writer/_validate_tree_structures.py +7 -18
- scitex/writer/dataclasses/__init__.py +8 -10
- scitex/writer/dataclasses/config/_CONSTANTS.py +2 -3
- scitex/writer/dataclasses/config/_WriterConfig.py +4 -9
- scitex/writer/dataclasses/contents/_ManuscriptContents.py +14 -25
- scitex/writer/dataclasses/contents/_RevisionContents.py +21 -16
- scitex/writer/dataclasses/contents/_SupplementaryContents.py +21 -24
- scitex/writer/dataclasses/core/_Document.py +2 -3
- scitex/writer/dataclasses/core/_DocumentSection.py +8 -23
- scitex/writer/dataclasses/results/_CompilationResult.py +2 -3
- scitex/writer/dataclasses/results/_LaTeXIssue.py +3 -6
- scitex/writer/dataclasses/results/_SaveSectionsResponse.py +20 -9
- scitex/writer/dataclasses/results/_SectionReadResponse.py +24 -10
- scitex/writer/dataclasses/tree/_ConfigTree.py +7 -4
- scitex/writer/dataclasses/tree/_ManuscriptTree.py +10 -13
- scitex/writer/dataclasses/tree/_RevisionTree.py +16 -17
- scitex/writer/dataclasses/tree/_ScriptsTree.py +10 -5
- scitex/writer/dataclasses/tree/_SharedTree.py +10 -13
- 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-2.7.3.dist-info}/METADATA +14 -10
- {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/RECORD +1149 -985
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +0 -583
- scitex/io/memo.md +0 -2827
- scitex/plt/_subplots/TODO.md +0 -53
- scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +0 -537
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +0 -1499
- scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +0 -431
- scitex/plt/_subplots/_export_as_csv_formatters.py +0 -112
- scitex/vis/__init__.py +0 -177
- scitex/vis/editor/_defaults.py +0 -244
- scitex/vis/editor/_edit.py +0 -378
- scitex/vis/editor/flask_editor/__init__.py +0 -21
- scitex/vis/editor/flask_editor/bbox.py +0 -216
- scitex/vis/editor/flask_editor/core.py +0 -152
- scitex/vis/editor/flask_editor/plotter.py +0 -130
- scitex/vis/editor/flask_editor/renderer.py +0 -184
- scitex/vis/editor/flask_editor/templates/html.py +0 -295
- scitex/vis/editor/flask_editor/templates/scripts.py +0 -614
- scitex/vis/editor/flask_editor/templates/styles.py +0 -549
- /scitex/{vis → fig}/README.md +0 -0
- /scitex/{vis → fig}/docs/CANVAS_ARCHITECTURE.md +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/WHEEL +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/entry_points.txt +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.3.dist-info}/licenses/LICENSE +0 -0
|
@@ -1,614 +0,0 @@
|
|
|
1
|
-
#!/usr/bin/env python3
|
|
2
|
-
# -*- coding: utf-8 -*-
|
|
3
|
-
# File: ./src/scitex/vis/editor/flask_editor/templates/scripts.py
|
|
4
|
-
"""JavaScript for the Flask editor UI."""
|
|
5
|
-
|
|
6
|
-
JS_SCRIPTS = '''
|
|
7
|
-
let overrides = {{ overrides|safe }};
|
|
8
|
-
let traces = overrides.traces || [];
|
|
9
|
-
let elementBboxes = {};
|
|
10
|
-
let imgSize = {width: 0, height: 0};
|
|
11
|
-
let hoveredElement = null;
|
|
12
|
-
let selectedElement = null;
|
|
13
|
-
|
|
14
|
-
// Hover system - client-side hit testing
|
|
15
|
-
function initHoverSystem() {
|
|
16
|
-
const container = document.getElementById('preview-container');
|
|
17
|
-
const img = document.getElementById('preview-img');
|
|
18
|
-
|
|
19
|
-
img.addEventListener('mousemove', (e) => {
|
|
20
|
-
if (imgSize.width === 0 || imgSize.height === 0) return;
|
|
21
|
-
|
|
22
|
-
const rect = img.getBoundingClientRect();
|
|
23
|
-
const x = e.clientX - rect.left;
|
|
24
|
-
const y = e.clientY - rect.top;
|
|
25
|
-
|
|
26
|
-
const scaleX = imgSize.width / rect.width;
|
|
27
|
-
const scaleY = imgSize.height / rect.height;
|
|
28
|
-
const imgX = x * scaleX;
|
|
29
|
-
const imgY = y * scaleY;
|
|
30
|
-
|
|
31
|
-
const element = findElementAt(imgX, imgY);
|
|
32
|
-
if (element !== hoveredElement) {
|
|
33
|
-
hoveredElement = element;
|
|
34
|
-
updateOverlay();
|
|
35
|
-
}
|
|
36
|
-
});
|
|
37
|
-
|
|
38
|
-
img.addEventListener('mouseleave', () => {
|
|
39
|
-
hoveredElement = null;
|
|
40
|
-
updateOverlay();
|
|
41
|
-
});
|
|
42
|
-
|
|
43
|
-
img.addEventListener('click', (e) => {
|
|
44
|
-
if (hoveredElement) {
|
|
45
|
-
selectedElement = hoveredElement;
|
|
46
|
-
updateOverlay();
|
|
47
|
-
scrollToSection(selectedElement);
|
|
48
|
-
}
|
|
49
|
-
});
|
|
50
|
-
|
|
51
|
-
img.addEventListener('load', () => {
|
|
52
|
-
updateOverlay();
|
|
53
|
-
});
|
|
54
|
-
}
|
|
55
|
-
|
|
56
|
-
function findElementAt(x, y) {
|
|
57
|
-
const matches = [];
|
|
58
|
-
for (const [name, bbox] of Object.entries(elementBboxes)) {
|
|
59
|
-
if (!name.startsWith('trace_')) {
|
|
60
|
-
if (x >= bbox.x0 && x <= bbox.x1 && y >= bbox.y0 && y <= bbox.y1) {
|
|
61
|
-
const area = (bbox.x1 - bbox.x0) * (bbox.y1 - bbox.y0);
|
|
62
|
-
matches.push({name, area});
|
|
63
|
-
}
|
|
64
|
-
}
|
|
65
|
-
}
|
|
66
|
-
if (matches.length > 0) {
|
|
67
|
-
matches.sort((a, b) => a.area - b.area);
|
|
68
|
-
return matches[0].name;
|
|
69
|
-
}
|
|
70
|
-
|
|
71
|
-
const PROXIMITY_THRESHOLD = 15;
|
|
72
|
-
let closestTrace = null;
|
|
73
|
-
let minDistance = Infinity;
|
|
74
|
-
|
|
75
|
-
for (const [name, bbox] of Object.entries(elementBboxes)) {
|
|
76
|
-
if (name.startsWith('trace_') && bbox.points) {
|
|
77
|
-
if (x >= bbox.x0 && x <= bbox.x1 && y >= bbox.y0 && y <= bbox.y1) {
|
|
78
|
-
const dist = distanceToLine(x, y, bbox.points);
|
|
79
|
-
if (dist < minDistance) {
|
|
80
|
-
minDistance = dist;
|
|
81
|
-
closestTrace = name;
|
|
82
|
-
}
|
|
83
|
-
}
|
|
84
|
-
}
|
|
85
|
-
}
|
|
86
|
-
|
|
87
|
-
if (closestTrace && minDistance <= PROXIMITY_THRESHOLD) {
|
|
88
|
-
return closestTrace;
|
|
89
|
-
}
|
|
90
|
-
|
|
91
|
-
return null;
|
|
92
|
-
}
|
|
93
|
-
|
|
94
|
-
function distanceToLine(px, py, points) {
|
|
95
|
-
let minDist = Infinity;
|
|
96
|
-
for (let i = 0; i < points.length - 1; i++) {
|
|
97
|
-
const [x1, y1] = points[i];
|
|
98
|
-
const [x2, y2] = points[i + 1];
|
|
99
|
-
const dist = distanceToSegment(px, py, x1, y1, x2, y2);
|
|
100
|
-
if (dist < minDist) minDist = dist;
|
|
101
|
-
}
|
|
102
|
-
return minDist;
|
|
103
|
-
}
|
|
104
|
-
|
|
105
|
-
function distanceToSegment(px, py, x1, y1, x2, y2) {
|
|
106
|
-
const dx = x2 - x1;
|
|
107
|
-
const dy = y2 - y1;
|
|
108
|
-
const lenSq = dx * dx + dy * dy;
|
|
109
|
-
|
|
110
|
-
if (lenSq === 0) {
|
|
111
|
-
return Math.sqrt((px - x1) ** 2 + (py - y1) ** 2);
|
|
112
|
-
}
|
|
113
|
-
|
|
114
|
-
let t = ((px - x1) * dx + (py - y1) * dy) / lenSq;
|
|
115
|
-
t = Math.max(0, Math.min(1, t));
|
|
116
|
-
|
|
117
|
-
const projX = x1 + t * dx;
|
|
118
|
-
const projY = y1 + t * dy;
|
|
119
|
-
|
|
120
|
-
return Math.sqrt((px - projX) ** 2 + (py - projY) ** 2);
|
|
121
|
-
}
|
|
122
|
-
|
|
123
|
-
function drawTracePath(bbox, scaleX, scaleY, type) {
|
|
124
|
-
if (!bbox.points || bbox.points.length < 2) return '';
|
|
125
|
-
|
|
126
|
-
const points = bbox.points;
|
|
127
|
-
let pathD = `M ${points[0][0] * scaleX} ${points[0][1] * scaleY}`;
|
|
128
|
-
for (let i = 1; i < points.length; i++) {
|
|
129
|
-
pathD += ` L ${points[i][0] * scaleX} ${points[i][1] * scaleY}`;
|
|
130
|
-
}
|
|
131
|
-
|
|
132
|
-
const className = type === 'hover' ? 'hover-path' : 'selected-path';
|
|
133
|
-
const labelX = points[0][0] * scaleX;
|
|
134
|
-
const labelY = points[0][1] * scaleY - 8;
|
|
135
|
-
const labelClass = type === 'hover' ? 'hover-label' : 'selected-label';
|
|
136
|
-
|
|
137
|
-
return `<path class="${className}" d="${pathD}"/>` +
|
|
138
|
-
`<text class="${labelClass}" x="${labelX}" y="${labelY}">${bbox.label}</text>`;
|
|
139
|
-
}
|
|
140
|
-
|
|
141
|
-
function updateOverlay() {
|
|
142
|
-
const overlay = document.getElementById('hover-overlay');
|
|
143
|
-
const img = document.getElementById('preview-img');
|
|
144
|
-
const rect = img.getBoundingClientRect();
|
|
145
|
-
|
|
146
|
-
overlay.setAttribute('width', rect.width);
|
|
147
|
-
overlay.setAttribute('height', rect.height);
|
|
148
|
-
|
|
149
|
-
const scaleX = rect.width / imgSize.width;
|
|
150
|
-
const scaleY = rect.height / imgSize.height;
|
|
151
|
-
|
|
152
|
-
let svg = '';
|
|
153
|
-
|
|
154
|
-
if (hoveredElement && hoveredElement !== selectedElement) {
|
|
155
|
-
const bbox = elementBboxes[hoveredElement];
|
|
156
|
-
if (bbox) {
|
|
157
|
-
if (hoveredElement.startsWith('trace_') && bbox.points) {
|
|
158
|
-
svg += drawTracePath(bbox, scaleX, scaleY, 'hover');
|
|
159
|
-
} else {
|
|
160
|
-
const x = bbox.x0 * scaleX - 2;
|
|
161
|
-
const y = bbox.y0 * scaleY - 2;
|
|
162
|
-
const w = (bbox.x1 - bbox.x0) * scaleX + 4;
|
|
163
|
-
const h = (bbox.y1 - bbox.y0) * scaleY + 4;
|
|
164
|
-
svg += `<rect class="hover-rect" x="${x}" y="${y}" width="${w}" height="${h}" rx="2"/>`;
|
|
165
|
-
svg += `<text class="hover-label" x="${x}" y="${y - 4}">${bbox.label}</text>`;
|
|
166
|
-
}
|
|
167
|
-
}
|
|
168
|
-
}
|
|
169
|
-
|
|
170
|
-
if (selectedElement) {
|
|
171
|
-
const bbox = elementBboxes[selectedElement];
|
|
172
|
-
if (bbox) {
|
|
173
|
-
if (selectedElement.startsWith('trace_') && bbox.points) {
|
|
174
|
-
svg += drawTracePath(bbox, scaleX, scaleY, 'selected');
|
|
175
|
-
} else {
|
|
176
|
-
const x = bbox.x0 * scaleX - 2;
|
|
177
|
-
const y = bbox.y0 * scaleY - 2;
|
|
178
|
-
const w = (bbox.x1 - bbox.x0) * scaleX + 4;
|
|
179
|
-
const h = (bbox.y1 - bbox.y0) * scaleY + 4;
|
|
180
|
-
svg += `<rect class="selected-rect" x="${x}" y="${y}" width="${w}" height="${h}" rx="2"/>`;
|
|
181
|
-
svg += `<text class="selected-label" x="${x}" y="${y - 4}">${bbox.label}</text>`;
|
|
182
|
-
}
|
|
183
|
-
}
|
|
184
|
-
}
|
|
185
|
-
|
|
186
|
-
overlay.innerHTML = svg;
|
|
187
|
-
}
|
|
188
|
-
|
|
189
|
-
function expandSection(sectionId) {
|
|
190
|
-
document.querySelectorAll('.section').forEach(section => {
|
|
191
|
-
const header = section.querySelector('.section-header');
|
|
192
|
-
const content = section.querySelector('.section-content');
|
|
193
|
-
if (section.id === sectionId) {
|
|
194
|
-
header?.classList.remove('collapsed');
|
|
195
|
-
content?.classList.remove('collapsed');
|
|
196
|
-
} else if (header?.classList.contains('section-toggle')) {
|
|
197
|
-
header?.classList.add('collapsed');
|
|
198
|
-
content?.classList.add('collapsed');
|
|
199
|
-
}
|
|
200
|
-
});
|
|
201
|
-
}
|
|
202
|
-
|
|
203
|
-
function scrollToSection(elementName) {
|
|
204
|
-
const elementToSection = {
|
|
205
|
-
'title': 'section-labels',
|
|
206
|
-
'xlabel': 'section-labels',
|
|
207
|
-
'ylabel': 'section-labels',
|
|
208
|
-
'xaxis_ticks': 'section-ticks',
|
|
209
|
-
'yaxis_ticks': 'section-ticks',
|
|
210
|
-
'legend': 'section-legend'
|
|
211
|
-
};
|
|
212
|
-
|
|
213
|
-
const fieldMap = {
|
|
214
|
-
'title': 'title',
|
|
215
|
-
'xlabel': 'xlabel',
|
|
216
|
-
'ylabel': 'ylabel',
|
|
217
|
-
'xaxis_ticks': 'x_n_ticks',
|
|
218
|
-
'yaxis_ticks': 'y_n_ticks',
|
|
219
|
-
'legend': 'legend_visible'
|
|
220
|
-
};
|
|
221
|
-
|
|
222
|
-
if (elementName.startsWith('trace_')) {
|
|
223
|
-
expandSection('section-traces');
|
|
224
|
-
const traceIdx = elementBboxes[elementName]?.trace_idx;
|
|
225
|
-
if (traceIdx !== undefined) {
|
|
226
|
-
const traceColors = document.querySelectorAll('.trace-color');
|
|
227
|
-
if (traceColors[traceIdx]) {
|
|
228
|
-
setTimeout(() => {
|
|
229
|
-
traceColors[traceIdx].scrollIntoView({behavior: 'smooth', block: 'center'});
|
|
230
|
-
traceColors[traceIdx].click();
|
|
231
|
-
}, 100);
|
|
232
|
-
}
|
|
233
|
-
}
|
|
234
|
-
return;
|
|
235
|
-
}
|
|
236
|
-
|
|
237
|
-
const sectionId = elementToSection[elementName];
|
|
238
|
-
if (sectionId) {
|
|
239
|
-
expandSection(sectionId);
|
|
240
|
-
}
|
|
241
|
-
|
|
242
|
-
const fieldId = fieldMap[elementName];
|
|
243
|
-
if (fieldId) {
|
|
244
|
-
const field = document.getElementById(fieldId);
|
|
245
|
-
if (field) {
|
|
246
|
-
setTimeout(() => {
|
|
247
|
-
field.scrollIntoView({behavior: 'smooth', block: 'center'});
|
|
248
|
-
field.focus();
|
|
249
|
-
}, 100);
|
|
250
|
-
}
|
|
251
|
-
}
|
|
252
|
-
}
|
|
253
|
-
|
|
254
|
-
// Theme management
|
|
255
|
-
function toggleTheme() {
|
|
256
|
-
const html = document.documentElement;
|
|
257
|
-
const current = html.getAttribute('data-theme');
|
|
258
|
-
const next = current === 'dark' ? 'light' : 'dark';
|
|
259
|
-
html.setAttribute('data-theme', next);
|
|
260
|
-
document.getElementById('theme-icon').innerHTML = next === 'dark' ? '☾' : '☼';
|
|
261
|
-
localStorage.setItem('scitex-editor-theme', next);
|
|
262
|
-
}
|
|
263
|
-
|
|
264
|
-
// Collapsible sections
|
|
265
|
-
function toggleSection(header) {
|
|
266
|
-
header.classList.toggle('collapsed');
|
|
267
|
-
const content = header.nextElementSibling;
|
|
268
|
-
content.classList.toggle('collapsed');
|
|
269
|
-
}
|
|
270
|
-
|
|
271
|
-
function toggleCustomLegendPosition() {
|
|
272
|
-
const legendLoc = document.getElementById('legend_loc').value;
|
|
273
|
-
const customCoordsDiv = document.getElementById('custom-legend-coords');
|
|
274
|
-
customCoordsDiv.style.display = legendLoc === 'custom' ? 'flex' : 'none';
|
|
275
|
-
}
|
|
276
|
-
|
|
277
|
-
// Initialize fields
|
|
278
|
-
document.addEventListener('DOMContentLoaded', () => {
|
|
279
|
-
// Load saved theme
|
|
280
|
-
const savedTheme = localStorage.getItem('scitex-editor-theme');
|
|
281
|
-
if (savedTheme) {
|
|
282
|
-
document.documentElement.setAttribute('data-theme', savedTheme);
|
|
283
|
-
document.getElementById('theme-icon').innerHTML = savedTheme === 'dark' ? '☾' : '☼';
|
|
284
|
-
}
|
|
285
|
-
|
|
286
|
-
// Labels
|
|
287
|
-
if (overrides.title) document.getElementById('title').value = overrides.title;
|
|
288
|
-
if (overrides.xlabel) document.getElementById('xlabel').value = overrides.xlabel;
|
|
289
|
-
if (overrides.ylabel) document.getElementById('ylabel').value = overrides.ylabel;
|
|
290
|
-
|
|
291
|
-
// Axis limits
|
|
292
|
-
if (overrides.xlim) {
|
|
293
|
-
document.getElementById('xmin').value = overrides.xlim[0];
|
|
294
|
-
document.getElementById('xmax').value = overrides.xlim[1];
|
|
295
|
-
}
|
|
296
|
-
if (overrides.ylim) {
|
|
297
|
-
document.getElementById('ymin').value = overrides.ylim[0];
|
|
298
|
-
document.getElementById('ymax').value = overrides.ylim[1];
|
|
299
|
-
}
|
|
300
|
-
|
|
301
|
-
// Traces
|
|
302
|
-
document.getElementById('linewidth').value = overrides.linewidth || 1.0;
|
|
303
|
-
updateTracesList();
|
|
304
|
-
|
|
305
|
-
// Legend
|
|
306
|
-
document.getElementById('legend_visible').checked = overrides.legend_visible !== false;
|
|
307
|
-
document.getElementById('legend_loc').value = overrides.legend_loc || 'best';
|
|
308
|
-
document.getElementById('legend_frameon').checked = overrides.legend_frameon || false;
|
|
309
|
-
document.getElementById('legend_fontsize').value = overrides.legend_fontsize || 6;
|
|
310
|
-
document.getElementById('legend_x').value = overrides.legend_x !== undefined ? overrides.legend_x : 0.5;
|
|
311
|
-
document.getElementById('legend_y').value = overrides.legend_y !== undefined ? overrides.legend_y : 0.5;
|
|
312
|
-
toggleCustomLegendPosition();
|
|
313
|
-
|
|
314
|
-
// Ticks
|
|
315
|
-
document.getElementById('x_n_ticks').value = overrides.x_n_ticks || overrides.n_ticks || 4;
|
|
316
|
-
document.getElementById('y_n_ticks').value = overrides.y_n_ticks || overrides.n_ticks || 4;
|
|
317
|
-
document.getElementById('hide_x_ticks').checked = overrides.hide_x_ticks || false;
|
|
318
|
-
document.getElementById('hide_y_ticks').checked = overrides.hide_y_ticks || false;
|
|
319
|
-
document.getElementById('tick_fontsize').value = overrides.tick_fontsize || 7;
|
|
320
|
-
document.getElementById('tick_length').value = overrides.tick_length || 0.8;
|
|
321
|
-
document.getElementById('tick_width').value = overrides.tick_width || 0.2;
|
|
322
|
-
document.getElementById('tick_direction').value = overrides.tick_direction || 'out';
|
|
323
|
-
|
|
324
|
-
// Style
|
|
325
|
-
document.getElementById('grid').checked = overrides.grid || false;
|
|
326
|
-
document.getElementById('hide_top_spine').checked = overrides.hide_top_spine !== false;
|
|
327
|
-
document.getElementById('hide_right_spine').checked = overrides.hide_right_spine !== false;
|
|
328
|
-
document.getElementById('axis_width').value = overrides.axis_width || 0.2;
|
|
329
|
-
document.getElementById('axis_fontsize').value = overrides.axis_fontsize || 7;
|
|
330
|
-
document.getElementById('facecolor').value = overrides.facecolor || '#ffffff';
|
|
331
|
-
document.getElementById('facecolor_text').value = overrides.facecolor || '#ffffff';
|
|
332
|
-
document.getElementById('transparent').checked = overrides.transparent !== false;
|
|
333
|
-
|
|
334
|
-
// Dimensions
|
|
335
|
-
if (overrides.fig_size) {
|
|
336
|
-
document.getElementById('fig_width').value = Math.round(overrides.fig_size[0] * 100) / 100;
|
|
337
|
-
document.getElementById('fig_height').value = Math.round(overrides.fig_size[1] * 100) / 100;
|
|
338
|
-
}
|
|
339
|
-
document.getElementById('dpi').value = overrides.dpi || 300;
|
|
340
|
-
|
|
341
|
-
// Sync color inputs
|
|
342
|
-
document.getElementById('facecolor').addEventListener('input', (e) => {
|
|
343
|
-
document.getElementById('facecolor_text').value = e.target.value;
|
|
344
|
-
});
|
|
345
|
-
document.getElementById('facecolor_text').addEventListener('change', (e) => {
|
|
346
|
-
document.getElementById('facecolor').value = e.target.value;
|
|
347
|
-
});
|
|
348
|
-
|
|
349
|
-
updateAnnotationsList();
|
|
350
|
-
updatePreview();
|
|
351
|
-
initHoverSystem();
|
|
352
|
-
setAutoUpdateInterval();
|
|
353
|
-
});
|
|
354
|
-
|
|
355
|
-
// Traces list management
|
|
356
|
-
function updateTracesList() {
|
|
357
|
-
const list = document.getElementById('traces-list');
|
|
358
|
-
if (!traces || traces.length === 0) {
|
|
359
|
-
list.innerHTML = '<div style="padding: 10px; color: var(--text-muted); font-size: 0.85em;">No traces found in metadata</div>';
|
|
360
|
-
return;
|
|
361
|
-
}
|
|
362
|
-
|
|
363
|
-
list.innerHTML = traces.map((t, i) => `
|
|
364
|
-
<div class="trace-item">
|
|
365
|
-
<input type="color" class="trace-color" value="${t.color || '#1f77b4'}"
|
|
366
|
-
onchange="updateTraceColor(${i}, this.value)">
|
|
367
|
-
<span class="trace-label">${t.label || t.id || 'Trace ' + (i+1)}</span>
|
|
368
|
-
<div class="trace-style">
|
|
369
|
-
<select onchange="updateTraceStyle(${i}, this.value)">
|
|
370
|
-
<option value="-" ${t.linestyle === '-' ? 'selected' : ''}>Solid</option>
|
|
371
|
-
<option value="--" ${t.linestyle === '--' ? 'selected' : ''}>Dashed</option>
|
|
372
|
-
<option value=":" ${t.linestyle === ':' ? 'selected' : ''}>Dotted</option>
|
|
373
|
-
<option value="-." ${t.linestyle === '-.' ? 'selected' : ''}>Dash-dot</option>
|
|
374
|
-
</select>
|
|
375
|
-
</div>
|
|
376
|
-
</div>
|
|
377
|
-
`).join('');
|
|
378
|
-
}
|
|
379
|
-
|
|
380
|
-
function updateTraceColor(idx, color) {
|
|
381
|
-
if (traces[idx]) {
|
|
382
|
-
traces[idx].color = color;
|
|
383
|
-
scheduleUpdate();
|
|
384
|
-
}
|
|
385
|
-
}
|
|
386
|
-
|
|
387
|
-
function updateTraceStyle(idx, style) {
|
|
388
|
-
if (traces[idx]) {
|
|
389
|
-
traces[idx].linestyle = style;
|
|
390
|
-
scheduleUpdate();
|
|
391
|
-
}
|
|
392
|
-
}
|
|
393
|
-
|
|
394
|
-
function collectOverrides() {
|
|
395
|
-
const o = {};
|
|
396
|
-
|
|
397
|
-
// Labels
|
|
398
|
-
const title = document.getElementById('title').value;
|
|
399
|
-
const xlabel = document.getElementById('xlabel').value;
|
|
400
|
-
const ylabel = document.getElementById('ylabel').value;
|
|
401
|
-
if (title) o.title = title;
|
|
402
|
-
if (xlabel) o.xlabel = xlabel;
|
|
403
|
-
if (ylabel) o.ylabel = ylabel;
|
|
404
|
-
|
|
405
|
-
// Axis limits
|
|
406
|
-
const xmin = document.getElementById('xmin').value;
|
|
407
|
-
const xmax = document.getElementById('xmax').value;
|
|
408
|
-
if (xmin !== '' && xmax !== '') o.xlim = [parseFloat(xmin), parseFloat(xmax)];
|
|
409
|
-
|
|
410
|
-
const ymin = document.getElementById('ymin').value;
|
|
411
|
-
const ymax = document.getElementById('ymax').value;
|
|
412
|
-
if (ymin !== '' && ymax !== '') o.ylim = [parseFloat(ymin), parseFloat(ymax)];
|
|
413
|
-
|
|
414
|
-
// Traces
|
|
415
|
-
o.linewidth = parseFloat(document.getElementById('linewidth').value) || 1.0;
|
|
416
|
-
o.traces = traces;
|
|
417
|
-
|
|
418
|
-
// Legend
|
|
419
|
-
o.legend_visible = document.getElementById('legend_visible').checked;
|
|
420
|
-
o.legend_loc = document.getElementById('legend_loc').value;
|
|
421
|
-
o.legend_frameon = document.getElementById('legend_frameon').checked;
|
|
422
|
-
o.legend_fontsize = parseInt(document.getElementById('legend_fontsize').value) || 6;
|
|
423
|
-
o.legend_x = parseFloat(document.getElementById('legend_x').value) || 0.5;
|
|
424
|
-
o.legend_y = parseFloat(document.getElementById('legend_y').value) || 0.5;
|
|
425
|
-
|
|
426
|
-
// Ticks
|
|
427
|
-
o.x_n_ticks = parseInt(document.getElementById('x_n_ticks').value) || 4;
|
|
428
|
-
o.y_n_ticks = parseInt(document.getElementById('y_n_ticks').value) || 4;
|
|
429
|
-
o.hide_x_ticks = document.getElementById('hide_x_ticks').checked;
|
|
430
|
-
o.hide_y_ticks = document.getElementById('hide_y_ticks').checked;
|
|
431
|
-
o.tick_fontsize = parseInt(document.getElementById('tick_fontsize').value) || 7;
|
|
432
|
-
o.tick_length = parseFloat(document.getElementById('tick_length').value) || 0.8;
|
|
433
|
-
o.tick_width = parseFloat(document.getElementById('tick_width').value) || 0.2;
|
|
434
|
-
o.tick_direction = document.getElementById('tick_direction').value;
|
|
435
|
-
|
|
436
|
-
// Style
|
|
437
|
-
o.grid = document.getElementById('grid').checked;
|
|
438
|
-
o.hide_top_spine = document.getElementById('hide_top_spine').checked;
|
|
439
|
-
o.hide_right_spine = document.getElementById('hide_right_spine').checked;
|
|
440
|
-
o.axis_width = parseFloat(document.getElementById('axis_width').value) || 0.2;
|
|
441
|
-
o.axis_fontsize = parseInt(document.getElementById('axis_fontsize').value) || 7;
|
|
442
|
-
o.facecolor = document.getElementById('facecolor').value;
|
|
443
|
-
o.transparent = document.getElementById('transparent').checked;
|
|
444
|
-
|
|
445
|
-
// Dimensions
|
|
446
|
-
o.fig_size = [
|
|
447
|
-
parseFloat(document.getElementById('fig_width').value) || 3.15,
|
|
448
|
-
parseFloat(document.getElementById('fig_height').value) || 2.68
|
|
449
|
-
];
|
|
450
|
-
o.dpi = parseInt(document.getElementById('dpi').value) || 300;
|
|
451
|
-
|
|
452
|
-
// Annotations
|
|
453
|
-
o.annotations = overrides.annotations || [];
|
|
454
|
-
|
|
455
|
-
return o;
|
|
456
|
-
}
|
|
457
|
-
|
|
458
|
-
async function updatePreview() {
|
|
459
|
-
setStatus('Updating...', false);
|
|
460
|
-
overrides = collectOverrides();
|
|
461
|
-
try {
|
|
462
|
-
const resp = await fetch('/update', {
|
|
463
|
-
method: 'POST',
|
|
464
|
-
headers: {'Content-Type': 'application/json'},
|
|
465
|
-
body: JSON.stringify({overrides})
|
|
466
|
-
});
|
|
467
|
-
const data = await resp.json();
|
|
468
|
-
document.getElementById('preview-img').src = 'data:image/png;base64,' + data.image;
|
|
469
|
-
|
|
470
|
-
if (data.bboxes) {
|
|
471
|
-
elementBboxes = data.bboxes;
|
|
472
|
-
}
|
|
473
|
-
if (data.img_size) {
|
|
474
|
-
imgSize = data.img_size;
|
|
475
|
-
}
|
|
476
|
-
|
|
477
|
-
selectedElement = null;
|
|
478
|
-
hoveredElement = null;
|
|
479
|
-
updateOverlay();
|
|
480
|
-
|
|
481
|
-
setStatus('Preview updated', false);
|
|
482
|
-
} catch (e) {
|
|
483
|
-
setStatus('Error: ' + e.message, true);
|
|
484
|
-
}
|
|
485
|
-
}
|
|
486
|
-
|
|
487
|
-
async function saveManual() {
|
|
488
|
-
setStatus('Saving...', false);
|
|
489
|
-
try {
|
|
490
|
-
const resp = await fetch('/save', {
|
|
491
|
-
method: 'POST',
|
|
492
|
-
headers: {'Content-Type': 'application/json'}
|
|
493
|
-
});
|
|
494
|
-
const data = await resp.json();
|
|
495
|
-
if (data.status === 'saved') {
|
|
496
|
-
setStatus('Saved: ' + data.path.split('/').pop(), false);
|
|
497
|
-
} else {
|
|
498
|
-
setStatus('Error: ' + data.message, true);
|
|
499
|
-
}
|
|
500
|
-
} catch (e) {
|
|
501
|
-
setStatus('Error: ' + e.message, true);
|
|
502
|
-
}
|
|
503
|
-
}
|
|
504
|
-
|
|
505
|
-
function resetOverrides() {
|
|
506
|
-
if (confirm('Reset all changes to original values?')) {
|
|
507
|
-
location.reload();
|
|
508
|
-
}
|
|
509
|
-
}
|
|
510
|
-
|
|
511
|
-
function addAnnotation() {
|
|
512
|
-
const text = document.getElementById('annot-text').value;
|
|
513
|
-
if (!text) return;
|
|
514
|
-
const x = parseFloat(document.getElementById('annot-x').value) || 0.5;
|
|
515
|
-
const y = parseFloat(document.getElementById('annot-y').value) || 0.5;
|
|
516
|
-
const size = parseInt(document.getElementById('annot-size').value) || 8;
|
|
517
|
-
if (!overrides.annotations) overrides.annotations = [];
|
|
518
|
-
overrides.annotations.push({type: 'text', text, x, y, fontsize: size});
|
|
519
|
-
document.getElementById('annot-text').value = '';
|
|
520
|
-
updateAnnotationsList();
|
|
521
|
-
updatePreview();
|
|
522
|
-
}
|
|
523
|
-
|
|
524
|
-
function removeAnnotation(idx) {
|
|
525
|
-
overrides.annotations.splice(idx, 1);
|
|
526
|
-
updateAnnotationsList();
|
|
527
|
-
updatePreview();
|
|
528
|
-
}
|
|
529
|
-
|
|
530
|
-
function updateAnnotationsList() {
|
|
531
|
-
const list = document.getElementById('annotations-list');
|
|
532
|
-
const annotations = overrides.annotations || [];
|
|
533
|
-
if (annotations.length === 0) {
|
|
534
|
-
list.innerHTML = '';
|
|
535
|
-
return;
|
|
536
|
-
}
|
|
537
|
-
list.innerHTML = annotations.map((a, i) =>
|
|
538
|
-
`<div class="annotation-item">
|
|
539
|
-
<span>${a.text.substring(0, 25)}${a.text.length > 25 ? '...' : ''} (${a.x.toFixed(2)}, ${a.y.toFixed(2)})</span>
|
|
540
|
-
<button onclick="removeAnnotation(${i})">Remove</button>
|
|
541
|
-
</div>`
|
|
542
|
-
).join('');
|
|
543
|
-
}
|
|
544
|
-
|
|
545
|
-
function setStatus(msg, isError = false) {
|
|
546
|
-
const el = document.getElementById('status');
|
|
547
|
-
el.textContent = msg;
|
|
548
|
-
el.classList.toggle('error', isError);
|
|
549
|
-
}
|
|
550
|
-
|
|
551
|
-
// Debounced auto-update
|
|
552
|
-
let updateTimer = null;
|
|
553
|
-
const DEBOUNCE_DELAY = 500;
|
|
554
|
-
|
|
555
|
-
function scheduleUpdate() {
|
|
556
|
-
if (updateTimer) clearTimeout(updateTimer);
|
|
557
|
-
updateTimer = setTimeout(() => {
|
|
558
|
-
updatePreview();
|
|
559
|
-
}, DEBOUNCE_DELAY);
|
|
560
|
-
}
|
|
561
|
-
|
|
562
|
-
// Auto-update on input changes
|
|
563
|
-
document.querySelectorAll('input[type="text"], input[type="number"]').forEach(el => {
|
|
564
|
-
el.addEventListener('input', scheduleUpdate);
|
|
565
|
-
el.addEventListener('keypress', (e) => {
|
|
566
|
-
if (e.key === 'Enter') {
|
|
567
|
-
if (updateTimer) clearTimeout(updateTimer);
|
|
568
|
-
updatePreview();
|
|
569
|
-
}
|
|
570
|
-
});
|
|
571
|
-
});
|
|
572
|
-
|
|
573
|
-
document.querySelectorAll('input[type="checkbox"], select').forEach(el => {
|
|
574
|
-
el.addEventListener('change', () => {
|
|
575
|
-
if (updateTimer) clearTimeout(updateTimer);
|
|
576
|
-
updatePreview();
|
|
577
|
-
});
|
|
578
|
-
});
|
|
579
|
-
|
|
580
|
-
document.querySelectorAll('input[type="color"]').forEach(el => {
|
|
581
|
-
el.addEventListener('change', () => {
|
|
582
|
-
if (updateTimer) clearTimeout(updateTimer);
|
|
583
|
-
updatePreview();
|
|
584
|
-
});
|
|
585
|
-
});
|
|
586
|
-
|
|
587
|
-
// Ctrl+S keyboard shortcut to save
|
|
588
|
-
document.addEventListener('keydown', (e) => {
|
|
589
|
-
if ((e.ctrlKey || e.metaKey) && e.key === 's') {
|
|
590
|
-
e.preventDefault();
|
|
591
|
-
saveManual();
|
|
592
|
-
}
|
|
593
|
-
});
|
|
594
|
-
|
|
595
|
-
// Auto-update interval system
|
|
596
|
-
let autoUpdateIntervalId = null;
|
|
597
|
-
|
|
598
|
-
function setAutoUpdateInterval() {
|
|
599
|
-
if (autoUpdateIntervalId) {
|
|
600
|
-
clearInterval(autoUpdateIntervalId);
|
|
601
|
-
autoUpdateIntervalId = null;
|
|
602
|
-
}
|
|
603
|
-
|
|
604
|
-
const intervalMs = parseInt(document.getElementById('auto_update_interval').value);
|
|
605
|
-
if (intervalMs > 0) {
|
|
606
|
-
autoUpdateIntervalId = setInterval(() => {
|
|
607
|
-
updatePreview();
|
|
608
|
-
}, intervalMs);
|
|
609
|
-
}
|
|
610
|
-
}
|
|
611
|
-
'''
|
|
612
|
-
|
|
613
|
-
|
|
614
|
-
# EOF
|