scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scitex/__init__.py +19 -8
- scitex/__main__.py +2 -1
- scitex/__version__.py +1 -1
- scitex/_optional_deps.py +13 -20
- scitex/ai/__init__.py +5 -0
- scitex/ai/_gen_ai/_Anthropic.py +3 -1
- scitex/ai/_gen_ai/_BaseGenAI.py +3 -2
- scitex/ai/_gen_ai/_DeepSeek.py +1 -1
- scitex/ai/_gen_ai/_Google.py +3 -2
- scitex/ai/_gen_ai/_Llama.py +4 -2
- scitex/ai/_gen_ai/_OpenAI.py +3 -1
- scitex/ai/_gen_ai/_PARAMS.py +1 -0
- scitex/ai/_gen_ai/_Perplexity.py +3 -1
- scitex/ai/_gen_ai/__init__.py +1 -0
- scitex/ai/_gen_ai/_format_output_func.py +3 -1
- scitex/ai/classification/CrossValidationExperiment.py +8 -14
- scitex/ai/classification/examples/timeseries_cv_demo.py +128 -112
- scitex/ai/classification/reporters/_BaseClassificationReporter.py +2 -0
- scitex/ai/classification/reporters/_ClassificationReporter.py +30 -45
- scitex/ai/classification/reporters/_MultiClassificationReporter.py +8 -11
- scitex/ai/classification/reporters/_SingleClassificationReporter.py +126 -182
- scitex/ai/classification/reporters/__init__.py +1 -1
- scitex/ai/classification/reporters/reporter_utils/_Plotter.py +213 -119
- scitex/ai/classification/reporters/reporter_utils/__init__.py +28 -36
- scitex/ai/classification/reporters/reporter_utils/aggregation.py +125 -143
- scitex/ai/classification/reporters/reporter_utils/data_models.py +128 -120
- scitex/ai/classification/reporters/reporter_utils/reporting.py +507 -340
- scitex/ai/classification/reporters/reporter_utils/storage.py +4 -1
- scitex/ai/classification/reporters/reporter_utils/validation.py +141 -154
- scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +204 -129
- scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +215 -171
- scitex/ai/classification/timeseries/_TimeSeriesMetadata.py +17 -17
- scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +67 -143
- scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +67 -143
- scitex/ai/classification/timeseries/_TimeSeriesStrategy.py +12 -13
- scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +231 -144
- scitex/ai/classification/timeseries/__init__.py +2 -4
- scitex/ai/classification/timeseries/_normalize_timestamp.py +3 -0
- scitex/ai/clustering/_pca.py +0 -1
- scitex/ai/clustering/_umap.py +1 -2
- scitex/ai/feature_extraction/__init__.py +10 -8
- scitex/ai/feature_extraction/vit.py +0 -1
- scitex/ai/feature_selection/feature_selection.py +3 -8
- scitex/ai/metrics/_calc_conf_mat.py +2 -0
- scitex/ai/metrics/_calc_feature_importance.py +3 -7
- scitex/ai/metrics/_calc_pre_rec_auc.py +5 -5
- scitex/ai/metrics/_calc_roc_auc.py +4 -2
- scitex/ai/metrics/_calc_seizure_prediction_metrics.py +35 -20
- scitex/ai/metrics/_calc_silhouette_score.py +1 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger.py +0 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger2020.py +0 -3
- scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger913A.py +0 -3
- scitex/ai/optim/_optimizers.py +1 -1
- scitex/ai/plt/__init__.py +6 -1
- scitex/ai/plt/_plot_feature_importance.py +1 -3
- scitex/ai/plt/_plot_learning_curve.py +9 -24
- scitex/ai/plt/_plot_optuna_study.py +4 -3
- scitex/ai/plt/_plot_pre_rec_curve.py +9 -15
- scitex/ai/plt/_plot_roc_curve.py +6 -8
- scitex/ai/plt/_stx_conf_mat.py +121 -122
- scitex/ai/sampling/undersample.py +3 -2
- scitex/ai/sklearn/__init__.py +2 -2
- scitex/ai/training/_LearningCurveLogger.py +23 -10
- scitex/ai/utils/_check_params.py +0 -1
- scitex/benchmark/__init__.py +15 -25
- scitex/benchmark/benchmark.py +124 -117
- scitex/benchmark/monitor.py +117 -107
- scitex/benchmark/profiler.py +61 -58
- scitex/bridge/__init__.py +110 -0
- scitex/bridge/_helpers.py +149 -0
- scitex/bridge/_plt_vis.py +529 -0
- scitex/bridge/_protocol.py +283 -0
- scitex/bridge/_stats_plt.py +261 -0
- scitex/bridge/_stats_vis.py +265 -0
- scitex/browser/__init__.py +0 -2
- scitex/browser/auth/__init__.py +0 -0
- scitex/browser/auth/google.py +16 -11
- scitex/browser/automation/CookieHandler.py +2 -3
- scitex/browser/collaboration/__init__.py +3 -0
- scitex/browser/collaboration/auth_helpers.py +3 -1
- scitex/browser/collaboration/collaborative_agent.py +2 -0
- scitex/browser/collaboration/interactive_panel.py +2 -2
- scitex/browser/collaboration/shared_session.py +20 -11
- scitex/browser/collaboration/standard_interactions.py +1 -0
- scitex/browser/core/BrowserMixin.py +12 -30
- scitex/browser/core/ChromeProfileManager.py +9 -24
- scitex/browser/debugging/_browser_logger.py +15 -25
- scitex/browser/debugging/_failure_capture.py +9 -2
- scitex/browser/debugging/_highlight_element.py +15 -6
- scitex/browser/debugging/_show_grid.py +5 -6
- scitex/browser/debugging/_sync_session.py +4 -3
- scitex/browser/debugging/_test_monitor.py +14 -5
- scitex/browser/debugging/_visual_cursor.py +46 -35
- scitex/browser/interaction/click_center.py +4 -3
- scitex/browser/interaction/click_with_fallbacks.py +7 -10
- scitex/browser/interaction/close_popups.py +79 -66
- scitex/browser/interaction/fill_with_fallbacks.py +8 -8
- scitex/browser/pdf/__init__.py +3 -1
- scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +11 -10
- scitex/browser/pdf/detect_chrome_pdf_viewer.py +3 -6
- scitex/browser/remote/CaptchaHandler.py +109 -96
- scitex/browser/remote/ZenRowsAPIClient.py +91 -97
- scitex/browser/remote/ZenRowsBrowserManager.py +138 -112
- scitex/browser/stealth/HumanBehavior.py +4 -9
- scitex/browser/stealth/StealthManager.py +11 -26
- scitex/capture/__init__.py +17 -17
- scitex/capture/__main__.py +2 -3
- scitex/capture/capture.py +23 -51
- scitex/capture/cli.py +14 -39
- scitex/capture/gif.py +5 -9
- scitex/capture/mcp_server.py +7 -20
- scitex/capture/session.py +4 -3
- scitex/capture/utils.py +18 -53
- scitex/cli/__init__.py +1 -1
- scitex/cli/cloud.py +158 -116
- scitex/cli/config.py +224 -0
- scitex/cli/main.py +41 -40
- scitex/cli/scholar.py +60 -27
- scitex/cli/security.py +14 -20
- scitex/cli/web.py +87 -90
- scitex/cli/writer.py +51 -45
- scitex/cloud/__init__.py +14 -11
- scitex/cloud/_matplotlib_hook.py +6 -6
- scitex/config/README.md +313 -0
- scitex/config/{PriorityConfig.py → _PriorityConfig.py} +114 -17
- scitex/config/_ScitexConfig.py +319 -0
- scitex/config/__init__.py +41 -9
- scitex/config/_paths.py +325 -0
- scitex/config/default.yaml +81 -0
- scitex/context/_suppress_output.py +2 -3
- scitex/db/_BaseMixins/_BaseBackupMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseBatchMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseBlobMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseImportExportMixin.py +1 -3
- scitex/db/_BaseMixins/_BaseIndexMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseMaintenanceMixin.py +1 -3
- scitex/db/_BaseMixins/_BaseQueryMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseRowMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseTableMixin.py +3 -1
- scitex/db/_BaseMixins/_BaseTransactionMixin.py +1 -3
- scitex/db/_BaseMixins/__init__.py +1 -1
- scitex/db/__init__.py +9 -1
- scitex/db/__main__.py +8 -21
- scitex/db/_check_health.py +15 -31
- scitex/db/_delete_duplicates.py +7 -4
- scitex/db/_inspect.py +22 -38
- scitex/db/_inspect_optimized.py +89 -85
- scitex/db/_postgresql/_PostgreSQL.py +0 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_BlobMixin.py +3 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_ConnectionMixin.py +1 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_ImportExportMixin.py +1 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_MaintenanceMixin.py +1 -4
- scitex/db/_postgresql/_PostgreSQLMixins/_QueryMixin.py +3 -3
- scitex/db/_postgresql/_PostgreSQLMixins/_RowMixin.py +3 -1
- scitex/db/_postgresql/_PostgreSQLMixins/_TransactionMixin.py +1 -3
- scitex/db/_postgresql/__init__.py +1 -1
- scitex/db/_sqlite3/_SQLite3.py +2 -4
- scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin.py +11 -12
- scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin_v01-need-_hash-col.py +19 -14
- scitex/db/_sqlite3/_SQLite3Mixins/_BatchMixin.py +3 -1
- scitex/db/_sqlite3/_SQLite3Mixins/_BlobMixin.py +7 -7
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin.py +118 -111
- scitex/db/_sqlite3/_SQLite3Mixins/_ConnectionMixin.py +8 -10
- scitex/db/_sqlite3/_SQLite3Mixins/_GitMixin.py +17 -45
- scitex/db/_sqlite3/_SQLite3Mixins/_ImportExportMixin.py +1 -3
- scitex/db/_sqlite3/_SQLite3Mixins/_IndexMixin.py +3 -1
- scitex/db/_sqlite3/_SQLite3Mixins/_QueryMixin.py +3 -4
- scitex/db/_sqlite3/_SQLite3Mixins/_RowMixin.py +9 -9
- scitex/db/_sqlite3/_SQLite3Mixins/_TableMixin.py +18 -11
- scitex/db/_sqlite3/_SQLite3Mixins/__init__.py +1 -0
- scitex/db/_sqlite3/__init__.py +1 -1
- scitex/db/_sqlite3/_delete_duplicates.py +13 -11
- scitex/decorators/__init__.py +29 -4
- scitex/decorators/_auto_order.py +43 -43
- scitex/decorators/_batch_fn.py +12 -6
- scitex/decorators/_cache_disk.py +8 -9
- scitex/decorators/_cache_disk_async.py +8 -7
- scitex/decorators/_combined.py +19 -13
- scitex/decorators/_converters.py +16 -3
- scitex/decorators/_deprecated.py +32 -22
- scitex/decorators/_numpy_fn.py +18 -4
- scitex/decorators/_pandas_fn.py +17 -5
- scitex/decorators/_signal_fn.py +17 -3
- scitex/decorators/_torch_fn.py +32 -15
- scitex/decorators/_xarray_fn.py +23 -9
- scitex/dev/_analyze_code_flow.py +0 -2
- scitex/dict/_DotDict.py +15 -19
- scitex/dict/_flatten.py +1 -0
- scitex/dict/_listed_dict.py +1 -0
- scitex/dict/_pop_keys.py +1 -0
- scitex/dict/_replace.py +1 -0
- scitex/dict/_safe_merge.py +1 -0
- scitex/dict/_to_str.py +2 -3
- scitex/dsp/__init__.py +13 -4
- scitex/dsp/_crop.py +3 -1
- scitex/dsp/_detect_ripples.py +3 -1
- scitex/dsp/_modulation_index.py +3 -1
- scitex/dsp/_time.py +3 -1
- scitex/dsp/_wavelet.py +0 -1
- scitex/dsp/example.py +0 -5
- scitex/dsp/filt.py +4 -0
- scitex/dsp/utils/__init__.py +4 -1
- scitex/dsp/utils/pac.py +3 -3
- scitex/dt/_normalize_timestamp.py +4 -1
- scitex/errors.py +3 -6
- scitex/etc/__init__.py +1 -1
- scitex/gen/_DimHandler.py +6 -6
- scitex/gen/__init__.py +5 -1
- scitex/gen/_deprecated_close.py +1 -0
- scitex/gen/_deprecated_start.py +5 -3
- scitex/gen/_detect_environment.py +44 -41
- scitex/gen/_detect_notebook_path.py +51 -47
- scitex/gen/_embed.py +1 -1
- scitex/gen/_get_notebook_path.py +81 -62
- scitex/gen/_inspect_module.py +0 -1
- scitex/gen/_norm.py +16 -7
- scitex/gen/_norm_cache.py +78 -65
- scitex/gen/_print_config.py +0 -3
- scitex/gen/_src.py +2 -3
- scitex/gen/_title_case.py +3 -2
- scitex/gen/_to_even.py +8 -8
- scitex/gen/_transpose.py +3 -3
- scitex/gen/misc.py +0 -3
- scitex/gists/_SigMacro_processFigure_S.py +2 -2
- scitex/gists/_SigMacro_toBlue.py +2 -2
- scitex/gists/__init__.py +4 -1
- scitex/git/_branch.py +19 -11
- scitex/git/_clone.py +23 -15
- scitex/git/_commit.py +10 -12
- scitex/git/_init.py +15 -38
- scitex/git/_remote.py +9 -3
- scitex/git/_result.py +3 -0
- scitex/git/_retry.py +2 -5
- scitex/git/_types.py +4 -0
- scitex/git/_validation.py +8 -8
- scitex/git/_workflow.py +4 -4
- scitex/io/__init__.py +2 -1
- scitex/io/_glob.py +2 -2
- scitex/io/_json2md.py +3 -3
- scitex/io/_load.py +6 -8
- scitex/io/_load_cache.py +71 -71
- scitex/io/_load_configs.py +2 -3
- scitex/io/_load_modules/_H5Explorer.py +6 -12
- scitex/io/_load_modules/_ZarrExplorer.py +3 -3
- scitex/io/_load_modules/_bibtex.py +62 -63
- scitex/io/_load_modules/_canvas.py +4 -9
- scitex/io/_load_modules/_catboost.py +7 -2
- scitex/io/_load_modules/_hdf5.py +2 -0
- scitex/io/_load_modules/_image.py +5 -1
- scitex/io/_load_modules/_matlab.py +3 -1
- scitex/io/_load_modules/_optuna.py +0 -1
- scitex/io/_load_modules/_pdf.py +38 -29
- scitex/io/_load_modules/_sqlite3.py +1 -0
- scitex/io/_load_modules/_txt.py +2 -0
- scitex/io/_load_modules/_xml.py +9 -9
- scitex/io/_load_modules/_zarr.py +12 -10
- scitex/io/_metadata.py +76 -37
- scitex/io/_qr_utils.py +18 -13
- scitex/io/_save.py +220 -63
- scitex/io/_save_modules/__init__.py +7 -2
- scitex/io/_save_modules/_bibtex.py +66 -61
- scitex/io/_save_modules/_canvas.py +5 -6
- scitex/io/_save_modules/_catboost.py +2 -2
- scitex/io/_save_modules/_csv.py +4 -4
- scitex/io/_save_modules/_excel.py +5 -9
- scitex/io/_save_modules/_hdf5.py +9 -21
- scitex/io/_save_modules/_html.py +5 -5
- scitex/io/_save_modules/_image.py +105 -8
- scitex/io/_save_modules/_joblib.py +2 -2
- scitex/io/_save_modules/_json.py +51 -6
- scitex/io/_save_modules/_listed_dfs_as_csv.py +2 -1
- scitex/io/_save_modules/_listed_scalars_as_csv.py +2 -1
- scitex/io/_save_modules/_matlab.py +2 -2
- scitex/io/_save_modules/_numpy.py +6 -8
- scitex/io/_save_modules/_pickle.py +4 -4
- scitex/io/_save_modules/_plotly.py +3 -3
- scitex/io/_save_modules/_tex.py +23 -25
- scitex/io/_save_modules/_text.py +2 -2
- scitex/io/_save_modules/_yaml.py +9 -9
- scitex/io/_save_modules/_zarr.py +15 -15
- scitex/io/utils/__init__.py +2 -1
- scitex/io/utils/h5_to_zarr.py +173 -155
- scitex/linalg/__init__.py +1 -1
- scitex/linalg/_geometric_median.py +4 -3
- scitex/logging/_Tee.py +5 -7
- scitex/logging/__init__.py +18 -19
- scitex/logging/_config.py +4 -1
- scitex/logging/_context.py +6 -5
- scitex/logging/_formatters.py +2 -3
- scitex/logging/_handlers.py +19 -20
- scitex/logging/_levels.py +9 -17
- scitex/logging/_logger.py +74 -15
- scitex/logging/_print_capture.py +17 -17
- scitex/nn/_BNet.py +1 -3
- scitex/nn/_Filters.py +6 -2
- scitex/nn/_ModulationIndex.py +3 -1
- scitex/nn/_PAC.py +3 -2
- scitex/nn/_PSD.py +0 -1
- scitex/nn/__init__.py +16 -3
- scitex/path/_clean.py +10 -8
- scitex/path/_find.py +1 -1
- scitex/path/_get_spath.py +1 -2
- scitex/path/_mk_spath.py +1 -1
- scitex/path/_symlink.py +5 -10
- scitex/pd/__init__.py +4 -1
- scitex/pd/_force_df.py +24 -24
- scitex/pd/_get_unique.py +1 -0
- scitex/pd/_merge_columns.py +1 -1
- scitex/pd/_round.py +11 -7
- scitex/pd/_to_xy.py +0 -1
- scitex/plt/REQUESTS.md +191 -0
- scitex/plt/__init__.py +185 -87
- scitex/plt/_subplots/_AxesWrapper.py +22 -6
- scitex/plt/_subplots/_AxisWrapper.py +100 -39
- scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +74 -52
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +183 -73
- scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +61 -45
- scitex/plt/_subplots/_AxisWrapperMixins/_TrackingMixin.py +26 -14
- scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +80 -73
- scitex/plt/_subplots/_FigWrapper.py +93 -60
- scitex/plt/_subplots/_SubplotsWrapper.py +135 -68
- scitex/plt/_subplots/__init__.py +10 -0
- scitex/plt/_subplots/_export_as_csv.py +89 -47
- scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +1 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +6 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_bar.py +88 -38
- scitex/plt/_subplots/_export_as_csv_formatters/_format_barh.py +25 -31
- scitex/plt/_subplots/_export_as_csv_formatters/_format_boxplot.py +53 -23
- scitex/plt/_subplots/_export_as_csv_formatters/_format_contour.py +38 -25
- scitex/plt/_subplots/_export_as_csv_formatters/_format_contourf.py +17 -9
- scitex/plt/_subplots/_export_as_csv_formatters/_format_errorbar.py +70 -124
- scitex/plt/_subplots/_export_as_csv_formatters/_format_eventplot.py +12 -10
- scitex/plt/_subplots/_export_as_csv_formatters/_format_fill.py +31 -17
- scitex/plt/_subplots/_export_as_csv_formatters/_format_fill_between.py +33 -21
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hexbin.py +14 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hist.py +43 -29
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hist2d.py +14 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow.py +27 -11
- scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow2d.py +7 -5
- scitex/plt/_subplots/_export_as_csv_formatters/_format_matshow.py +9 -7
- scitex/plt/_subplots/_export_as_csv_formatters/_format_pie.py +15 -6
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot.py +85 -46
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_box.py +52 -27
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_imshow.py +1 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_kde.py +16 -17
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter.py +7 -5
- scitex/plt/_subplots/_export_as_csv_formatters/_format_quiver.py +10 -8
- scitex/plt/_subplots/_export_as_csv_formatters/_format_scatter.py +17 -6
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_barplot.py +43 -26
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_boxplot.py +68 -47
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_heatmap.py +52 -64
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_histplot.py +55 -50
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_jointplot.py +9 -11
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_kdeplot.py +63 -29
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_lineplot.py +4 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_pairplot.py +6 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_scatterplot.py +44 -40
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_stripplot.py +46 -39
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_swarmplot.py +46 -39
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_violinplot.py +75 -94
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stem.py +12 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_step.py +12 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_streamplot.py +10 -8
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_conf_mat.py +17 -15
- scitex/plt/_subplots/_export_as_csv_formatters/_format_stx_ecdf.py +10 -9
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- scitex/template/clone_singularity.py +6 -7
- scitex/template/clone_writer_directory.py +6 -7
- scitex/tex/_preview.py +26 -11
- scitex/tex/_to_vec.py +10 -7
- scitex/torch/__init__.py +11 -1
- scitex/types/_ArrayLike.py +2 -0
- scitex/types/_is_listed_X.py +3 -3
- scitex/units.py +110 -77
- scitex/utils/_compress_hdf5.py +3 -3
- scitex/utils/_email.py +8 -4
- scitex/utils/_notify.py +14 -8
- scitex/utils/_search.py +6 -6
- scitex/utils/_verify_scitex_format.py +17 -42
- scitex/utils/_verify_scitex_format_v01.py +12 -34
- scitex/utils/template.py +4 -3
- scitex/vis/__init__.py +0 -0
- scitex/vis/backend/__init__.py +3 -3
- scitex/vis/backend/{export.py → _export.py} +1 -1
- scitex/vis/backend/{parser.py → _parser.py} +1 -3
- scitex/vis/backend/{render.py → _render.py} +1 -1
- scitex/vis/canvas.py +15 -3
- scitex/vis/editor/__init__.py +0 -0
- scitex/vis/editor/_dearpygui_editor.py +450 -304
- scitex/vis/editor/_defaults.py +114 -123
- scitex/vis/editor/_edit.py +38 -26
- scitex/vis/editor/_flask_editor.py +8 -8
- scitex/vis/editor/_mpl_editor.py +63 -48
- scitex/vis/editor/_qt_editor.py +210 -159
- scitex/vis/editor/_tkinter_editor.py +146 -89
- scitex/vis/editor/flask_editor/__init__.py +10 -10
- scitex/vis/editor/flask_editor/_bbox.py +529 -0
- scitex/vis/editor/flask_editor/{core.py → _core.py} +45 -29
- scitex/vis/editor/flask_editor/_plotter.py +567 -0
- scitex/vis/editor/flask_editor/_renderer.py +393 -0
- scitex/vis/editor/flask_editor/{utils.py → _utils.py} +13 -14
- scitex/vis/editor/flask_editor/templates/__init__.py +5 -5
- scitex/vis/editor/flask_editor/templates/{html.py → _html.py} +234 -16
- scitex/vis/editor/flask_editor/templates/_scripts.py +1261 -0
- scitex/vis/editor/flask_editor/templates/{styles.py → _styles.py} +192 -2
- scitex/vis/io/__init__.py +5 -5
- scitex/vis/io/{canvas.py → _canvas.py} +8 -4
- scitex/vis/io/{data.py → _data.py} +13 -9
- scitex/vis/io/{directory.py → _directory.py} +7 -4
- scitex/vis/io/{export.py → _export.py} +15 -12
- scitex/vis/io/{load.py → _load.py} +1 -1
- scitex/vis/io/{panel.py → _panel.py} +21 -13
- scitex/vis/io/{save.py → _save.py} +0 -0
- scitex/vis/model/__init__.py +7 -7
- scitex/vis/model/{annotations.py → _annotations.py} +2 -4
- scitex/vis/model/{axes.py → _axes.py} +1 -1
- scitex/vis/model/{figure.py → _figure.py} +0 -0
- scitex/vis/model/{guides.py → _guides.py} +1 -1
- scitex/vis/model/{plot.py → _plot.py} +2 -4
- scitex/vis/model/{plot_types.py → _plot_types.py} +0 -0
- scitex/vis/model/{styles.py → _styles.py} +0 -0
- scitex/vis/utils/__init__.py +2 -2
- scitex/vis/utils/{defaults.py → _defaults.py} +1 -2
- scitex/vis/utils/{validate.py → _validate.py} +3 -9
- scitex/web/__init__.py +7 -1
- scitex/web/_scraping.py +54 -38
- scitex/web/_search_pubmed.py +30 -14
- scitex/writer/.legacy/Writer_v01-refactored.py +4 -4
- scitex/writer/.legacy/_compile.py +18 -28
- scitex/writer/Writer.py +8 -21
- scitex/writer/__init__.py +11 -11
- 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-2.7.0.dist-info}/METADATA +4 -10
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/RECORD +1071 -975
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +0 -583
- scitex/plt/_subplots/_export_as_csv_formatters.py +0 -112
- scitex/vis/editor/flask_editor/bbox.py +0 -216
- scitex/vis/editor/flask_editor/plotter.py +0 -130
- scitex/vis/editor/flask_editor/renderer.py +0 -184
- scitex/vis/editor/flask_editor/templates/scripts.py +0 -614
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/WHEEL +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/entry_points.txt +0 -0
- {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/licenses/LICENSE +0 -0
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CSS_STYLES = """
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/* =============================================================================
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background: var(--bg-muted);
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background: var(--bg-surface);
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color: var(--text-primary);
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box-shadow: 0 0 0 1px var(--color-cta);
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width: 20px;
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height: 14px;
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border-radius: 2px;
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border: 1px solid var(--border-default);
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background: linear-gradient(45deg, #ccc 25%, transparent 25%),
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linear-gradient(-45deg, #ccc 25%, transparent 25%),
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linear-gradient(45deg, transparent 75%, #ccc 75%),
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linear-gradient(-45deg, transparent 75%, #ccc 75%);
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background-size: 8px 8px;
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background-position: 0 0, 0 4px, 4px -4px, -4px 0px;
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background-color: #fff;
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/* =============================================================================
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* ============================================================================= */
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"""
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# EOF
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scitex/vis/io/__init__.py
CHANGED
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Schema Version: 2.0.0
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"""
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from .
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from ._directory import (
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canvas_directory_exists,
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from .
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from ._canvas import (
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load_canvas_json,
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update_canvas_json,
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get_canvas_schema_version,
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from .
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from ._panel import (
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remove_panel,
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from datetime import datetime
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canvas_json = load_canvas_json(
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)
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Dictionary mapping file paths to validation results
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from .
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str
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New hash value
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from .
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from .
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from ._directory import get_canvas_directory_path
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{
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}
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)
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@@ -190,7 +194,7 @@ def list_data_files(
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Dictionary mapping file paths to hash values
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"""
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from .
|
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canvas_json = load_canvas_json(project_dir, canvas_name, verify_data_hashes=False)
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@@ -36,7 +36,7 @@ def _normalize_canvas_name(canvas_name: str) -> str:
|
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def _strip_canvas_extension(canvas_name: str) -> str:
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"""Remove .canvas extension from canvas_name."""
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if canvas_name.endswith(CANVAS_EXTENSION):
|
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-
return canvas_name[
|
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return canvas_name[: -len(CANVAS_EXTENSION)]
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@@ -75,8 +75,9 @@ def ensure_canvas_directory(
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# Create empty canvas.json if not exists
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|
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|
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from .
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from ._canvas import _get_empty_canvas_template
|
|
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79
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import json
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+
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# Use the name without extension for canvas_name in JSON
|
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|
base_name = _strip_canvas_extension(canvas_name)
|
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83
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|
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@@ -137,9 +138,11 @@ def list_canvas_directories(
|
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# Find .canvas directories that contain canvas.json
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|
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if (
|
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+
if (
|
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+
item.is_dir()
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and item.name.endswith(CANVAS_EXTENSION)
|
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-
and (item / "canvas.json").exists()
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+
and (item / "canvas.json").exists()
|
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+
):
|
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|
if include_extension:
|
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|
canvas_names.append(item.name)
|
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else:
|
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@@ -42,8 +42,8 @@ def export_canvas_to_file(
|
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Path
|
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43
43
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Path to exported file in exports/ directory
|
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44
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"""
|
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45
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-
from .
|
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46
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-
from .
|
|
45
|
+
from ._directory import get_canvas_directory_path
|
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46
|
+
from ._canvas import load_canvas_json
|
|
47
47
|
|
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48
48
|
canvas_dir = get_canvas_directory_path(project_dir, canvas_name)
|
|
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49
|
canvas_json = load_canvas_json(project_dir, canvas_name, verify_data_hashes=False)
|
|
@@ -130,7 +130,7 @@ def list_canvas_exports(
|
|
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List[Path]
|
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List of paths in exports/ directory
|
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132
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"""
|
|
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from .
|
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+
from ._directory import get_canvas_directory_path
|
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134
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135
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canvas_dir = get_canvas_directory_path(project_dir, canvas_name)
|
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exports_dir = canvas_dir / "exports"
|
|
@@ -179,10 +179,7 @@ def _compose_and_export(
|
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fig.patch.set_facecolor(bg_color)
|
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180
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|
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# Sort panels by z_index
|
|
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|
-
panels = sorted(
|
|
183
|
-
canvas_json.get("panels", []),
|
|
184
|
-
key=lambda p: p.get("z_index", 0)
|
|
185
|
-
)
|
|
182
|
+
panels = sorted(canvas_json.get("panels", []), key=lambda p: p.get("z_index", 0))
|
|
186
183
|
|
|
187
184
|
# Place each panel
|
|
188
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for panel in panels:
|
|
@@ -361,11 +358,14 @@ def _add_panel_label(ax, label: Dict[str, Any]) -> None:
|
|
|
361
358
|
x, y, ha, va = pos_map.get(position, pos_map["top-left"])
|
|
362
359
|
|
|
363
360
|
ax.text(
|
|
364
|
-
x,
|
|
361
|
+
x,
|
|
362
|
+
y,
|
|
363
|
+
text,
|
|
365
364
|
transform=ax.transAxes,
|
|
366
365
|
fontsize=fontsize,
|
|
367
366
|
fontweight=fontweight,
|
|
368
|
-
ha=ha,
|
|
367
|
+
ha=ha,
|
|
368
|
+
va=va,
|
|
369
369
|
)
|
|
370
370
|
|
|
371
371
|
|
|
@@ -385,7 +385,8 @@ def _add_annotations(
|
|
|
385
385
|
y = 1 - pos.get("y_mm", 0) / canvas_height_mm
|
|
386
386
|
|
|
387
387
|
fig.text(
|
|
388
|
-
x,
|
|
388
|
+
x,
|
|
389
|
+
y,
|
|
389
390
|
ann.get("content", ""),
|
|
390
391
|
fontsize=ann.get("fontsize", 10),
|
|
391
392
|
color=ann.get("color", "#000000"),
|
|
@@ -406,7 +407,8 @@ def _add_title(
|
|
|
406
407
|
y = 1 - pos.get("y_mm", 5) / canvas_height_mm
|
|
407
408
|
|
|
408
409
|
fig.text(
|
|
409
|
-
x,
|
|
410
|
+
x,
|
|
411
|
+
y,
|
|
410
412
|
title_config.get("text", ""),
|
|
411
413
|
fontsize=title_config.get("fontsize", 14),
|
|
412
414
|
ha="center",
|
|
@@ -448,7 +450,8 @@ def _add_caption(
|
|
|
448
450
|
wrapped_text = textwrap.fill(text, width=wrap_width)
|
|
449
451
|
|
|
450
452
|
fig.text(
|
|
451
|
-
x,
|
|
453
|
+
x,
|
|
454
|
+
y_norm,
|
|
452
455
|
wrapped_text,
|
|
453
456
|
fontsize=fontsize,
|
|
454
457
|
ha="left",
|
|
@@ -13,9 +13,9 @@ from pathlib import Path
|
|
|
13
13
|
from typing import Dict, Any, Union, List, Optional
|
|
14
14
|
import shutil
|
|
15
15
|
|
|
16
|
-
from .
|
|
17
|
-
from .
|
|
18
|
-
from .
|
|
16
|
+
from ._directory import get_canvas_directory_path
|
|
17
|
+
from ._canvas import load_canvas_json, save_canvas_json
|
|
18
|
+
from ._data import compute_file_hash
|
|
19
19
|
|
|
20
20
|
|
|
21
21
|
def _symlink_or_copy(source: Path, dest: Path, bundle: bool = False) -> None:
|
|
@@ -142,7 +142,9 @@ def add_panel_from_scitex(
|
|
|
142
142
|
canvas_json = load_canvas_json(project_dir, canvas_name, verify_data_hashes=False)
|
|
143
143
|
|
|
144
144
|
# Remove existing panel with same name
|
|
145
|
-
canvas_json["panels"] = [
|
|
145
|
+
canvas_json["panels"] = [
|
|
146
|
+
p for p in canvas_json["panels"] if p.get("name") != panel_name
|
|
147
|
+
]
|
|
146
148
|
|
|
147
149
|
# Add new panel
|
|
148
150
|
canvas_json["panels"].append(panel_entry)
|
|
@@ -153,13 +155,14 @@ def add_panel_from_scitex(
|
|
|
153
155
|
csv_hash = compute_file_hash(panel_dir / "panel.csv")
|
|
154
156
|
# Remove existing reference
|
|
155
157
|
canvas_json["data_files"] = [
|
|
156
|
-
d for d in canvas_json.get("data_files", [])
|
|
157
|
-
if d.get("path") != csv_path
|
|
158
|
+
d for d in canvas_json.get("data_files", []) if d.get("path") != csv_path
|
|
158
159
|
]
|
|
159
|
-
canvas_json["data_files"].append(
|
|
160
|
-
|
|
161
|
-
|
|
162
|
-
|
|
160
|
+
canvas_json["data_files"].append(
|
|
161
|
+
{
|
|
162
|
+
"path": csv_path,
|
|
163
|
+
"hash": csv_hash,
|
|
164
|
+
}
|
|
165
|
+
)
|
|
163
166
|
|
|
164
167
|
save_canvas_json(project_dir, canvas_name, canvas_json)
|
|
165
168
|
|
|
@@ -222,7 +225,9 @@ def add_panel_from_image(
|
|
|
222
225
|
canvas_json = load_canvas_json(project_dir, canvas_name, verify_data_hashes=False)
|
|
223
226
|
|
|
224
227
|
# Remove existing panel with same name
|
|
225
|
-
canvas_json["panels"] = [
|
|
228
|
+
canvas_json["panels"] = [
|
|
229
|
+
p for p in canvas_json["panels"] if p.get("name") != panel_name
|
|
230
|
+
]
|
|
226
231
|
|
|
227
232
|
# Add new panel
|
|
228
233
|
canvas_json["panels"].append(panel_entry)
|
|
@@ -261,11 +266,14 @@ def remove_panel(
|
|
|
261
266
|
canvas_json = load_canvas_json(project_dir, canvas_name, verify_data_hashes=False)
|
|
262
267
|
|
|
263
268
|
original_count = len(canvas_json["panels"])
|
|
264
|
-
canvas_json["panels"] = [
|
|
269
|
+
canvas_json["panels"] = [
|
|
270
|
+
p for p in canvas_json["panels"] if p.get("name") != panel_name
|
|
271
|
+
]
|
|
265
272
|
|
|
266
273
|
# Remove data file references for this panel
|
|
267
274
|
canvas_json["data_files"] = [
|
|
268
|
-
d
|
|
275
|
+
d
|
|
276
|
+
for d in canvas_json.get("data_files", [])
|
|
269
277
|
if not d.get("path", "").startswith(f"panels/{panel_name}/")
|
|
270
278
|
]
|
|
271
279
|
|
|
File without changes
|
scitex/vis/model/__init__.py
CHANGED
|
@@ -8,12 +8,12 @@ This module provides dataclass-based models for representing
|
|
|
8
8
|
publication-quality figures as JSON structures.
|
|
9
9
|
"""
|
|
10
10
|
|
|
11
|
-
from .
|
|
12
|
-
from .
|
|
13
|
-
from .
|
|
14
|
-
from .
|
|
15
|
-
from .
|
|
16
|
-
from .
|
|
11
|
+
from ._figure import FigureModel
|
|
12
|
+
from ._axes import AxesModel
|
|
13
|
+
from ._plot import PlotModel
|
|
14
|
+
from ._guides import GuideModel
|
|
15
|
+
from ._annotations import AnnotationModel
|
|
16
|
+
from ._styles import (
|
|
17
17
|
PlotStyle,
|
|
18
18
|
AxesStyle,
|
|
19
19
|
GuideStyle,
|
|
@@ -24,7 +24,7 @@ from .styles import (
|
|
|
24
24
|
copy_text_style,
|
|
25
25
|
apply_style_to_plots,
|
|
26
26
|
)
|
|
27
|
-
from .
|
|
27
|
+
from ._plot_types import (
|
|
28
28
|
# Registry
|
|
29
29
|
PLOT_TYPE_CONFIGS,
|
|
30
30
|
get_plot_config_class,
|
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
from typing import Optional, Dict, Any, Tuple
|
|
7
7
|
from dataclasses import dataclass, field, asdict
|
|
8
8
|
|
|
9
|
-
from .
|
|
9
|
+
from ._styles import TextStyle
|
|
10
10
|
|
|
11
11
|
|
|
12
12
|
@dataclass
|
|
@@ -94,9 +94,7 @@ class AnnotationModel:
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94
94
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# Type-specific validation
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95
95
|
if self.annotation_type in ["text", "annotate"]:
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96
96
|
if not self.text:
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|
97
|
-
raise ValueError(
|
|
98
|
-
f"{self.annotation_type} requires 'text' parameter"
|
|
99
|
-
)
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|
97
|
+
raise ValueError(f"{self.annotation_type} requires 'text' parameter")
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|
100
98
|
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|
101
99
|
if self.annotation_type == "annotate":
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102
100
|
if self.xytext is None:
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File without changes
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|
@@ -6,7 +6,7 @@
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6
6
|
from typing import Optional, List, Dict, Any
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7
7
|
from dataclasses import dataclass, field, asdict
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8
8
|
|
|
9
|
-
from .
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9
|
+
from ._styles import PlotStyle
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10
10
|
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11
11
|
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12
12
|
@dataclass
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@@ -104,9 +104,7 @@ class PlotModel:
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104
104
|
# Type-specific validation
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|
105
105
|
if self.plot_type in ["heatmap", "imshow"]:
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|
106
106
|
if "z" not in self.data and "img" not in self.data:
|
|
107
|
-
raise ValueError(
|
|
108
|
-
f"{self.plot_type} requires 'z' or 'img' in data"
|
|
109
|
-
)
|
|
107
|
+
raise ValueError(f"{self.plot_type} requires 'z' or 'img' in data")
|
|
110
108
|
|
|
111
109
|
elif self.plot_type in ["line", "scatter", "errorbar"]:
|
|
112
110
|
if "x" not in self.data or "y" not in self.data:
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|
File without changes
|
|
File without changes
|
scitex/vis/utils/__init__.py
CHANGED
|
@@ -8,7 +8,7 @@ Includes validation functions and default templates for
|
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|
8
8
|
common publication formats.
|
|
9
9
|
"""
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|
10
10
|
|
|
11
|
-
from .
|
|
11
|
+
from ._validate import (
|
|
12
12
|
validate_json_structure,
|
|
13
13
|
validate_plot_data,
|
|
14
14
|
check_schema_version,
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|
@@ -16,7 +16,7 @@ from .validate import (
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|
|
16
16
|
validate_axes_layout,
|
|
17
17
|
)
|
|
18
18
|
|
|
19
|
-
from .
|
|
19
|
+
from ._defaults import (
|
|
20
20
|
# Constants
|
|
21
21
|
NATURE_SINGLE_COLUMN_MM,
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|
22
22
|
NATURE_DOUBLE_COLUMN_MM,
|
|
@@ -313,8 +313,7 @@ def get_template(name: str, **kwargs) -> Dict[str, Any]:
|
|
|
313
313
|
"""
|
|
314
314
|
if name not in TEMPLATES:
|
|
315
315
|
raise ValueError(
|
|
316
|
-
f"Unknown template: {name}. "
|
|
317
|
-
f"Available: {list(TEMPLATES.keys())}"
|
|
316
|
+
f"Unknown template: {name}. Available: {list(TEMPLATES.keys())}"
|
|
318
317
|
)
|
|
319
318
|
|
|
320
319
|
return TEMPLATES[name](**kwargs)
|