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
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- 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
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if hasattr(violin_widths, "__iter__"):
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violin_widths = violin_widths[0] if len(violin_widths) > 0 else 0.5
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# Call matplotlib's boxplot directly to avoid recursive post-processing
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# which would override our gray styling with the default blue
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if hasattr(ax,
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mpl_ax = ax._axes_mpl
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else:
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# Style the boxplot: scitex gray fill with black edges for visibility
|
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# Set high z-order so boxplot appears on top of violin bodies
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from scitex.plt.color._PARAMS import HEX
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+
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boxplot_zorder = 10
|
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|
-
for box in bp.get(
|
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-
box.set_facecolor(HEX[
|
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-
box.set_edgecolor(
|
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+
for box in bp.get("boxes", []):
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box.set_facecolor(HEX["gray"]) # Scitex gray fill
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box.set_edgecolor("black")
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box.set_alpha(1.0)
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box.set_linewidth(line_width)
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box.set_zorder(boxplot_zorder)
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for median in bp.get(
|
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median.set_color(
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for median in bp.get("medians", []):
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median.set_color("black") # Black median line
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median.set_linewidth(line_width) # 0.2mm thickness
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median.set_zorder(boxplot_zorder + 1)
|
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-
for whisker in bp.get(
|
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-
whisker.set_color(
|
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+
for whisker in bp.get("whiskers", []):
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whisker.set_color("black")
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whisker.set_linewidth(line_width)
|
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whisker.set_zorder(boxplot_zorder)
|
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-
for cap in bp.get(
|
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cap.set_color(
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for cap in bp.get("caps", []):
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cap.set_color("black")
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cap.set_linewidth(line_width)
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cap.set_zorder(boxplot_zorder)
|
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-
for flier in bp.get(
|
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flier.set_markerfacecolor(
|
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flier.set_markeredgecolor(
|
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for flier in bp.get("fliers", []):
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flier.set_markerfacecolor("none") # No fill (open circles)
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flier.set_markeredgecolor("black")
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flier.set_markersize(marker_size) # 0.8mm
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flier.set_markeredgewidth(line_width) # 0.2mm
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|
flier.set_zorder(boxplot_zorder + 2)
|
|
@@ -274,13 +304,14 @@ def _postprocess_boxplot(result, ax):
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"""Apply styling for boxplots (standalone, not violin overlay)."""
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# Use the centralized style_boxplot function for consistent styling
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from scitex.plt.ax import style_boxplot
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+
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style_boxplot(result)
|
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# Cap width: 33% of box width
|
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-
if
|
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|
+
if "caps" in result and "boxes" in result and len(result["boxes"]) > 0:
|
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|
try:
|
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|
-
cap_width_pts = _calculate_cap_width_from_box(result[
|
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|
-
for cap in result[
|
|
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+
cap_width_pts = _calculate_cap_width_from_box(result["boxes"][0], ax)
|
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+
for cap in result["caps"]:
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|
cap.set_markersize(cap_width_pts)
|
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|
except Exception:
|
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|
pass
|
|
@@ -289,9 +320,9 @@ def _postprocess_boxplot(result, ax):
|
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320
|
def _postprocess_scatter(result, kwargs):
|
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"""Apply styling for scatter plots."""
|
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|
# Apply default 0.8mm marker size if 's' not specified
|
|
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|
-
if
|
|
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|
+
if "s" not in kwargs:
|
|
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324
|
size_pt = mm_to_pt(DEFAULT_MARKER_SIZE_MM)
|
|
294
|
-
marker_area = size_pt
|
|
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|
+
marker_area = size_pt**2
|
|
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326
|
result.set_sizes([marker_area])
|
|
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327
|
|
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328
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|
@@ -306,18 +337,18 @@ def _postprocess_hist(result, ax):
|
|
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|
if len(result) >= 3:
|
|
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|
patches = result[2]
|
|
308
339
|
# Handle both single histogram and stacked histograms
|
|
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|
-
if hasattr(patches,
|
|
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|
+
if hasattr(patches, "__iter__"):
|
|
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341
|
for patch_group in patches:
|
|
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|
-
if hasattr(patch_group,
|
|
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|
+
if hasattr(patch_group, "__iter__"):
|
|
312
343
|
for patch in patch_group:
|
|
313
|
-
patch.set_edgecolor(
|
|
344
|
+
patch.set_edgecolor("black")
|
|
314
345
|
patch.set_linewidth(line_width)
|
|
315
346
|
# Ensure alpha is at least 0.7 for visibility
|
|
316
347
|
if patch.get_alpha() is None or patch.get_alpha() < 0.7:
|
|
317
348
|
patch.set_alpha(1.0)
|
|
318
349
|
else:
|
|
319
350
|
# Single patch
|
|
320
|
-
patch_group.set_edgecolor(
|
|
351
|
+
patch_group.set_edgecolor("black")
|
|
321
352
|
patch_group.set_linewidth(line_width)
|
|
322
353
|
if patch_group.get_alpha() is None or patch_group.get_alpha() < 0.7:
|
|
323
354
|
patch_group.set_alpha(1.0)
|
|
@@ -334,29 +365,38 @@ def _postprocess_fill_between(result, kwargs):
|
|
|
334
365
|
line_width = mm_to_pt(DEFAULT_LINE_WIDTH_MM)
|
|
335
366
|
|
|
336
367
|
# Only set edge if not already specified
|
|
337
|
-
if
|
|
338
|
-
result.set_edgecolor(
|
|
368
|
+
if "edgecolor" not in kwargs and "ec" not in kwargs:
|
|
369
|
+
result.set_edgecolor("none")
|
|
339
370
|
|
|
340
371
|
# Ensure alpha is reasonable (default 0.3 is common for fill_between)
|
|
341
|
-
if
|
|
372
|
+
if "alpha" not in kwargs:
|
|
342
373
|
result.set_alpha(0.3)
|
|
343
374
|
|
|
344
375
|
|
|
345
376
|
def _postprocess_bar(result, ax, kwargs):
|
|
346
377
|
"""Apply styling for bar plots with colors and error bars."""
|
|
347
378
|
# Get scitex palette for coloring (only if color not explicitly set)
|
|
348
|
-
if
|
|
379
|
+
if "color" not in kwargs and "c" not in kwargs:
|
|
349
380
|
from scitex.plt.color._PARAMS import HEX
|
|
350
|
-
|
|
351
|
-
|
|
381
|
+
|
|
382
|
+
palette = [
|
|
383
|
+
HEX["blue"],
|
|
384
|
+
HEX["red"],
|
|
385
|
+
HEX["green"],
|
|
386
|
+
HEX["yellow"],
|
|
387
|
+
HEX["purple"],
|
|
388
|
+
HEX["orange"],
|
|
389
|
+
HEX["lightblue"],
|
|
390
|
+
HEX["pink"],
|
|
391
|
+
]
|
|
352
392
|
|
|
353
393
|
line_width = mm_to_pt(DEFAULT_LINE_WIDTH_MM)
|
|
354
394
|
for i, patch in enumerate(result.patches):
|
|
355
395
|
patch.set_facecolor(palette[i % len(palette)])
|
|
356
|
-
patch.set_edgecolor(
|
|
396
|
+
patch.set_edgecolor("black")
|
|
357
397
|
patch.set_linewidth(line_width)
|
|
358
398
|
|
|
359
|
-
if
|
|
399
|
+
if "yerr" not in kwargs or kwargs["yerr"] is None:
|
|
360
400
|
return
|
|
361
401
|
|
|
362
402
|
try:
|
|
@@ -376,14 +416,14 @@ def _postprocess_bar(result, ax, kwargs):
|
|
|
376
416
|
# Adjust cap width to 33% of bar width
|
|
377
417
|
if len(result.patches) > 0:
|
|
378
418
|
cap_width_pts = _calculate_cap_width_from_bar(
|
|
379
|
-
result.patches[0], ax,
|
|
419
|
+
result.patches[0], ax, "width"
|
|
380
420
|
)
|
|
381
421
|
for cap in caplines[1:]:
|
|
382
422
|
cap.set_markersize(cap_width_pts)
|
|
383
423
|
|
|
384
424
|
# Make error bar lines one-sided
|
|
385
425
|
barlinecols = lines[2]
|
|
386
|
-
_make_errorbar_one_sided(barlinecols,
|
|
426
|
+
_make_errorbar_one_sided(barlinecols, "vertical")
|
|
387
427
|
except Exception:
|
|
388
428
|
pass
|
|
389
429
|
|
|
@@ -391,18 +431,27 @@ def _postprocess_bar(result, ax, kwargs):
|
|
|
391
431
|
def _postprocess_barh(result, ax, kwargs):
|
|
392
432
|
"""Apply styling for horizontal bar plots with colors and error bars."""
|
|
393
433
|
# Get scitex palette for coloring (only if color not explicitly set)
|
|
394
|
-
if
|
|
434
|
+
if "color" not in kwargs and "c" not in kwargs:
|
|
395
435
|
from scitex.plt.color._PARAMS import HEX
|
|
396
|
-
|
|
397
|
-
|
|
436
|
+
|
|
437
|
+
palette = [
|
|
438
|
+
HEX["blue"],
|
|
439
|
+
HEX["red"],
|
|
440
|
+
HEX["green"],
|
|
441
|
+
HEX["yellow"],
|
|
442
|
+
HEX["purple"],
|
|
443
|
+
HEX["orange"],
|
|
444
|
+
HEX["lightblue"],
|
|
445
|
+
HEX["pink"],
|
|
446
|
+
]
|
|
398
447
|
|
|
399
448
|
line_width = mm_to_pt(DEFAULT_LINE_WIDTH_MM)
|
|
400
449
|
for i, patch in enumerate(result.patches):
|
|
401
450
|
patch.set_facecolor(palette[i % len(palette)])
|
|
402
|
-
patch.set_edgecolor(
|
|
451
|
+
patch.set_edgecolor("black")
|
|
403
452
|
patch.set_linewidth(line_width)
|
|
404
453
|
|
|
405
|
-
if
|
|
454
|
+
if "xerr" not in kwargs or kwargs["xerr"] is None:
|
|
406
455
|
return
|
|
407
456
|
|
|
408
457
|
try:
|
|
@@ -422,14 +471,14 @@ def _postprocess_barh(result, ax, kwargs):
|
|
|
422
471
|
# Adjust cap width to 33% of bar height
|
|
423
472
|
if len(result.patches) > 0:
|
|
424
473
|
cap_width_pts = _calculate_cap_width_from_bar(
|
|
425
|
-
result.patches[0], ax,
|
|
474
|
+
result.patches[0], ax, "height"
|
|
426
475
|
)
|
|
427
476
|
for cap in caplines[1:]:
|
|
428
477
|
cap.set_markersize(cap_width_pts)
|
|
429
478
|
|
|
430
479
|
# Make error bar lines one-sided
|
|
431
480
|
barlinecols = lines[2]
|
|
432
|
-
_make_errorbar_one_sided(barlinecols,
|
|
481
|
+
_make_errorbar_one_sided(barlinecols, "horizontal")
|
|
433
482
|
except Exception:
|
|
434
483
|
pass
|
|
435
484
|
|
|
@@ -440,36 +489,36 @@ def _postprocess_barh(result, ax, kwargs):
|
|
|
440
489
|
def _calculate_cap_width_from_box(box, ax):
|
|
441
490
|
"""Calculate cap width as 33% of box width in points."""
|
|
442
491
|
# Get box width from path
|
|
443
|
-
if hasattr(box,
|
|
492
|
+
if hasattr(box, "get_path"):
|
|
444
493
|
path = box.get_path()
|
|
445
494
|
vertices = path.vertices
|
|
446
495
|
x_coords = vertices[:, 0]
|
|
447
496
|
box_width_data = x_coords.max() - x_coords.min()
|
|
448
|
-
elif hasattr(box,
|
|
497
|
+
elif hasattr(box, "get_xdata"):
|
|
449
498
|
x_data = box.get_xdata()
|
|
450
499
|
box_width_data = max(x_data) - min(x_data)
|
|
451
500
|
else:
|
|
452
501
|
box_width_data = 0.5 # Default
|
|
453
502
|
|
|
454
|
-
return _data_width_to_points(box_width_data, ax,
|
|
503
|
+
return _data_width_to_points(box_width_data, ax, "x") * CAP_WIDTH_RATIO
|
|
455
504
|
|
|
456
505
|
|
|
457
506
|
def _calculate_cap_width_from_bar(patch, ax, dimension):
|
|
458
507
|
"""Calculate cap width as 33% of bar width/height in points."""
|
|
459
|
-
if dimension ==
|
|
508
|
+
if dimension == "width":
|
|
460
509
|
bar_size = patch.get_width()
|
|
461
|
-
return _data_width_to_points(bar_size, ax,
|
|
510
|
+
return _data_width_to_points(bar_size, ax, "x") * CAP_WIDTH_RATIO
|
|
462
511
|
else: # height
|
|
463
512
|
bar_size = patch.get_height()
|
|
464
|
-
return _data_width_to_points(bar_size, ax,
|
|
513
|
+
return _data_width_to_points(bar_size, ax, "y") * CAP_WIDTH_RATIO
|
|
465
514
|
|
|
466
515
|
|
|
467
|
-
def _data_width_to_points(data_size, ax, axis=
|
|
516
|
+
def _data_width_to_points(data_size, ax, axis="x"):
|
|
468
517
|
"""Convert a data-space size to points."""
|
|
469
518
|
fig = ax.get_figure()
|
|
470
519
|
bbox = ax.get_position()
|
|
471
520
|
|
|
472
|
-
if axis ==
|
|
521
|
+
if axis == "x":
|
|
473
522
|
ax_size_inches = bbox.width * fig.get_figwidth()
|
|
474
523
|
lim = ax.get_xlim()
|
|
475
524
|
else:
|
|
@@ -487,7 +536,7 @@ def _make_errorbar_one_sided(barlinecols, direction):
|
|
|
487
536
|
return
|
|
488
537
|
|
|
489
538
|
for lc in barlinecols:
|
|
490
|
-
if not hasattr(lc,
|
|
539
|
+
if not hasattr(lc, "get_segments"):
|
|
491
540
|
continue
|
|
492
541
|
|
|
493
542
|
segs = lc.get_segments()
|
|
@@ -496,7 +545,7 @@ def _make_errorbar_one_sided(barlinecols, direction):
|
|
|
496
545
|
if len(seg) < 2:
|
|
497
546
|
continue
|
|
498
547
|
|
|
499
|
-
if direction ==
|
|
548
|
+
if direction == "vertical":
|
|
500
549
|
# Keep upper half
|
|
501
550
|
bottom_y = min(seg[0][1], seg[1][1])
|
|
502
551
|
top_y = max(seg[0][1], seg[1][1])
|
|
File without changes
|
scitex/plt/styles/presets.py
CHANGED
|
@@ -33,9 +33,20 @@ Usage:
|
|
|
33
33
|
"""
|
|
34
34
|
|
|
35
35
|
__all__ = [
|
|
36
|
-
"SCITEX_STYLE",
|
|
37
|
-
"
|
|
36
|
+
"SCITEX_STYLE",
|
|
37
|
+
"STYLE",
|
|
38
|
+
"load_style",
|
|
39
|
+
"save_style",
|
|
40
|
+
"set_style",
|
|
41
|
+
"get_style",
|
|
38
42
|
"resolve_style_value",
|
|
43
|
+
# DPI utilities
|
|
44
|
+
"get_default_dpi",
|
|
45
|
+
"get_display_dpi",
|
|
46
|
+
"get_preview_dpi",
|
|
47
|
+
"DPI_SAVE",
|
|
48
|
+
"DPI_DISPLAY",
|
|
49
|
+
"DPI_PREVIEW",
|
|
39
50
|
]
|
|
40
51
|
|
|
41
52
|
from pathlib import Path
|
|
@@ -54,12 +65,19 @@ def _get_config(yaml_path: Optional[Path] = None) -> PriorityConfig:
|
|
|
54
65
|
global _config
|
|
55
66
|
if _config is None or yaml_path:
|
|
56
67
|
yaml = scitex.io.load(yaml_path or _STYLE_FILE)
|
|
57
|
-
flat = {
|
|
68
|
+
flat = {
|
|
69
|
+
f"{k}.{k2}": v2
|
|
70
|
+
for k, v in yaml.items()
|
|
71
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+
if isinstance(v, dict) and k != "presets"
|
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72
|
+
for k2, v2 in v.items()
|
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73
|
+
}
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58
74
|
_config = PriorityConfig(flat, env_prefix="SCITEX_PLT_", auto_uppercase=True)
|
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59
75
|
return _config
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60
76
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61
77
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62
|
-
def resolve_style_value(
|
|
78
|
+
def resolve_style_value(
|
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79
|
+
key: str, direct_val: Any = None, default: Any = None, type: type = float
|
|
80
|
+
) -> Any:
|
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63
81
|
"""Resolve value with priority: direct → env → yaml → default.
|
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64
82
|
|
|
65
83
|
Key format: 'axes.width_mm' - dots for YAML hierarchy, underscores for env vars.
|
|
@@ -68,30 +86,115 @@ def resolve_style_value(key: str, direct_val: Any = None, default: Any = None, t
|
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68
86
|
return _get_config().resolve(key, direct_val, default, type)
|
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69
87
|
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70
88
|
|
|
89
|
+
# =============================================================================
|
|
90
|
+
# DPI Resolution - Central Source of Truth
|
|
91
|
+
# =============================================================================
|
|
92
|
+
#
|
|
93
|
+
# DPI Priority Chain:
|
|
94
|
+
# 1. Bundle's geometry_px.json (highest - existing figure's actual DPI)
|
|
95
|
+
# 2. User override / session setting
|
|
96
|
+
# 3. SCITEX_STYLE.yaml output.dpi (project default)
|
|
97
|
+
# 4. Hardcoded fallback (only if config missing)
|
|
98
|
+
#
|
|
99
|
+
# Usage:
|
|
100
|
+
# from scitex.plt.styles import get_default_dpi, DPI_SAVE
|
|
101
|
+
#
|
|
102
|
+
# # For saving figures (publication quality)
|
|
103
|
+
# fig.savefig("out.png", dpi=get_default_dpi())
|
|
104
|
+
#
|
|
105
|
+
# # For display/preview (lower resolution)
|
|
106
|
+
# fig.savefig("preview.png", dpi=get_display_dpi())
|
|
107
|
+
#
|
|
108
|
+
# # When loading from bundle, use bundle's DPI:
|
|
109
|
+
# dpi = bundle.get("geometry", {}).get("dpi") or get_default_dpi()
|
|
110
|
+
#
|
|
111
|
+
|
|
112
|
+
# Fallback values (only used if config unavailable)
|
|
113
|
+
_FALLBACK_DPI_SAVE = 300
|
|
114
|
+
_FALLBACK_DPI_DISPLAY = 100
|
|
115
|
+
_FALLBACK_DPI_PREVIEW = 150
|
|
116
|
+
|
|
117
|
+
|
|
118
|
+
def get_default_dpi() -> int:
|
|
119
|
+
"""Get default DPI for saving/publication from config.
|
|
120
|
+
|
|
121
|
+
Priority: SCITEX_STYLE.yaml → env var → fallback 300
|
|
122
|
+
|
|
123
|
+
Returns:
|
|
124
|
+
int: DPI value for publication-quality output
|
|
125
|
+
"""
|
|
126
|
+
return int(resolve_style_value("output.dpi", None, _FALLBACK_DPI_SAVE, int))
|
|
127
|
+
|
|
128
|
+
|
|
129
|
+
def get_display_dpi() -> int:
|
|
130
|
+
"""Get DPI for screen display (lower resolution for speed).
|
|
131
|
+
|
|
132
|
+
Returns approximately 1/3 of save DPI, minimum 100.
|
|
133
|
+
|
|
134
|
+
Returns:
|
|
135
|
+
int: DPI value for screen display
|
|
136
|
+
"""
|
|
137
|
+
save_dpi = get_default_dpi()
|
|
138
|
+
return max(_FALLBACK_DPI_DISPLAY, save_dpi // 3)
|
|
139
|
+
|
|
140
|
+
|
|
141
|
+
def get_preview_dpi() -> int:
|
|
142
|
+
"""Get DPI for editor previews and thumbnails.
|
|
143
|
+
|
|
144
|
+
Returns 1/2 of save DPI, clamped between 100-200.
|
|
145
|
+
|
|
146
|
+
Returns:
|
|
147
|
+
int: DPI value for previews
|
|
148
|
+
"""
|
|
149
|
+
save_dpi = get_default_dpi()
|
|
150
|
+
return max(_FALLBACK_DPI_DISPLAY, min(200, save_dpi // 2))
|
|
151
|
+
|
|
152
|
+
|
|
153
|
+
# Module-level constants (evaluated at import time)
|
|
154
|
+
# Use functions for dynamic resolution, constants for static defaults
|
|
155
|
+
DPI_SAVE = _FALLBACK_DPI_SAVE # Use get_default_dpi() for dynamic
|
|
156
|
+
DPI_DISPLAY = _FALLBACK_DPI_DISPLAY
|
|
157
|
+
DPI_PREVIEW = _FALLBACK_DPI_PREVIEW
|
|
158
|
+
|
|
159
|
+
|
|
71
160
|
def load_style(path: Optional[Union[str, Path]] = None) -> Dict[str, Any]:
|
|
72
161
|
"""Load style from YAML as subplots kwargs."""
|
|
73
162
|
cfg = _get_config(Path(path) if path else None)
|
|
74
163
|
g = lambda k, d, t=float: cfg.resolve(k, None, d, t)
|
|
75
164
|
return {
|
|
76
|
-
"axes_width_mm": g("axes.width_mm", 40),
|
|
165
|
+
"axes_width_mm": g("axes.width_mm", 40),
|
|
166
|
+
"axes_height_mm": g("axes.height_mm", 28),
|
|
77
167
|
"axes_thickness_mm": g("axes.thickness_mm", 0.2),
|
|
78
|
-
"margin_left_mm": g("margins.left_mm", 20),
|
|
79
|
-
"
|
|
80
|
-
"
|
|
81
|
-
"
|
|
168
|
+
"margin_left_mm": g("margins.left_mm", 20),
|
|
169
|
+
"margin_right_mm": g("margins.right_mm", 20),
|
|
170
|
+
"margin_bottom_mm": g("margins.bottom_mm", 20),
|
|
171
|
+
"margin_top_mm": g("margins.top_mm", 20),
|
|
172
|
+
"space_w_mm": g("spacing.horizontal_mm", 8),
|
|
173
|
+
"space_h_mm": g("spacing.vertical_mm", 10),
|
|
174
|
+
"tick_length_mm": g("ticks.length_mm", 0.8),
|
|
175
|
+
"tick_thickness_mm": g("ticks.thickness_mm", 0.2),
|
|
82
176
|
"n_ticks": g("ticks.n_ticks", 4, int),
|
|
83
|
-
"trace_thickness_mm": g("lines.trace_mm", 0.2),
|
|
84
|
-
"
|
|
177
|
+
"trace_thickness_mm": g("lines.trace_mm", 0.2),
|
|
178
|
+
"errorbar_thickness_mm": g("lines.errorbar_mm", 0.2),
|
|
179
|
+
"errorbar_cap_width_mm": g("lines.errorbar_cap_mm", 0.8),
|
|
180
|
+
"bar_edge_thickness_mm": g("lines.bar_edge_mm", 0.2),
|
|
85
181
|
"kde_line_thickness_mm": g("lines.kde_mm", 0.2),
|
|
86
|
-
"scatter_size_mm": g("markers.scatter_mm", 0.8),
|
|
182
|
+
"scatter_size_mm": g("markers.scatter_mm", 0.8),
|
|
183
|
+
"marker_size_mm": g("markers.size_mm", 0.8),
|
|
87
184
|
"font_family": g("fonts.family", "Arial", str),
|
|
88
|
-
"axis_font_size_pt": g("fonts.axis_label_pt", 7),
|
|
89
|
-
"
|
|
90
|
-
"
|
|
91
|
-
"
|
|
185
|
+
"axis_font_size_pt": g("fonts.axis_label_pt", 7),
|
|
186
|
+
"tick_font_size_pt": g("fonts.tick_label_pt", 7),
|
|
187
|
+
"title_font_size_pt": g("fonts.title_pt", 8),
|
|
188
|
+
"suptitle_font_size_pt": g("fonts.suptitle_pt", 8),
|
|
189
|
+
"legend_font_size_pt": g("fonts.legend_pt", 6),
|
|
190
|
+
"annotation_font_size_pt": g("fonts.annotation_pt", 6),
|
|
191
|
+
"label_pad_pt": g("padding.label_pt", 0.5),
|
|
192
|
+
"tick_pad_pt": g("padding.tick_pt", 2.0),
|
|
92
193
|
"title_pad_pt": g("padding.title_pt", 1.0),
|
|
93
|
-
"dpi": g("output.dpi", 300, int),
|
|
94
|
-
"
|
|
194
|
+
"dpi": g("output.dpi", 300, int),
|
|
195
|
+
"transparent": g("output.transparent", True, bool),
|
|
196
|
+
"auto_scale_axes": g("behavior.auto_scale_axes", True, bool),
|
|
197
|
+
"mode": "publication",
|
|
95
198
|
}
|
|
96
199
|
|
|
97
200
|
|