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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# Rename temp table
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# Recreate indexes, triggers, and views
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cursor.execute(sql)
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logger.warning(f"Could not recreate dependency: {e}")
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# Commit transaction
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progress_callback(total_rows, total_rows, "Complete")
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# ----------------------------------------
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old_name: Current column name
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new_name: New column name
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"""
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except Exception as e:
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return False
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def _rename_column_recreate(
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def _rename_column_recreate(
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) -> bool:
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# but keeping all columns with one renamed
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# ----------------------------------------
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Similar to pandas: df = df[['col3', 'col1', 'col2']]
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+
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SQLite doesn't support column reordering directly, so this always
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requires table recreation.
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Args:
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table_name: Name of the table
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column_order: List of column names in desired order
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progress_callback: Function for progress updates
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Returns:
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True if successful, False otherwise
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"""
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@@ -295,7 +304,7 @@ class _ColumnMixin:
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# Validate all columns exist
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current_columns = self.get_column_info(table_name)
|
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current_names = {col["name"] for col in current_columns}
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|
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+
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|
if set(column_order) != current_names:
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missing = current_names - set(column_order)
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extra = set(column_order) - current_names
|
|
@@ -304,13 +313,13 @@ class _ColumnMixin:
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if extra:
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314
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logger.error(f"Unknown columns in order: {extra}")
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|
return False
|
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|
-
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+
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|
# Create column map
|
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318
|
column_map = {col["name"]: col for col in current_columns}
|
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-
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+
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cursor = self.cursor
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|
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cursor.execute("BEGIN EXCLUSIVE TRANSACTION")
|
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|
-
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|
+
|
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|
# Build new table definition with reordered columns
|
|
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|
column_defs = []
|
|
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|
for col_name in column_order:
|
|
@@ -323,34 +332,34 @@ class _ColumnMixin:
|
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323
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|
if col["pk"]:
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|
col_def += " PRIMARY KEY"
|
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|
column_defs.append(col_def)
|
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|
-
|
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|
+
|
|
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|
# Create temp table with new column order
|
|
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|
temp_table = f"{table_name}_reorder_{int(time.time())}"
|
|
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338
|
cursor.execute(f"""
|
|
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339
|
CREATE TABLE {temp_table} (
|
|
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|
-
{
|
|
340
|
+
{", ".join(column_defs)}
|
|
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341
|
)
|
|
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342
|
""")
|
|
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|
-
|
|
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|
+
|
|
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344
|
# Copy data
|
|
336
345
|
cursor.execute(f"""
|
|
337
|
-
INSERT INTO {temp_table} ({
|
|
338
|
-
SELECT {
|
|
346
|
+
INSERT INTO {temp_table} ({", ".join(column_order)})
|
|
347
|
+
SELECT {", ".join(column_order)} FROM {table_name}
|
|
339
348
|
""")
|
|
340
|
-
|
|
349
|
+
|
|
341
350
|
# Swap tables
|
|
342
351
|
cursor.execute(f"DROP TABLE {table_name}")
|
|
343
352
|
cursor.execute(f"ALTER TABLE {temp_table} RENAME TO {table_name}")
|
|
344
|
-
|
|
353
|
+
|
|
345
354
|
self.conn.commit()
|
|
346
355
|
logger.info(f"Reordered columns in {table_name}")
|
|
347
356
|
return True
|
|
348
|
-
|
|
357
|
+
|
|
349
358
|
except Exception as e:
|
|
350
359
|
self.conn.rollback()
|
|
351
360
|
logger.error(f"Failed to reorder columns: {e}")
|
|
352
361
|
return False
|
|
353
|
-
|
|
362
|
+
|
|
354
363
|
def sort_columns(
|
|
355
364
|
self,
|
|
356
365
|
table_name: str,
|
|
@@ -360,16 +369,16 @@ class _ColumnMixin:
|
|
|
360
369
|
progress_callback: Optional[callable] = None,
|
|
361
370
|
) -> bool:
|
|
362
371
|
"""Sort columns in a table alphabetically or by custom criteria.
|
|
363
|
-
|
|
372
|
+
|
|
364
373
|
Similar to organizing DataFrame columns systematically.
|
|
365
|
-
|
|
374
|
+
|
|
366
375
|
Args:
|
|
367
376
|
table_name: Name of the table
|
|
368
377
|
alphabetical: Sort columns alphabetically
|
|
369
378
|
reverse: Reverse sort order
|
|
370
379
|
key_columns_first: List of columns to place first (like 'id', 'created_at')
|
|
371
380
|
progress_callback: Function for progress updates
|
|
372
|
-
|
|
381
|
+
|
|
373
382
|
Returns:
|
|
374
383
|
True if successful, False otherwise
|
|
375
384
|
"""
|
|
@@ -377,7 +386,7 @@ class _ColumnMixin:
|
|
|
377
386
|
# Get current columns
|
|
378
387
|
columns = self.get_column_info(table_name)
|
|
379
388
|
column_names = [col["name"] for col in columns]
|
|
380
|
-
|
|
389
|
+
|
|
381
390
|
# Determine new order
|
|
382
391
|
if key_columns_first:
|
|
383
392
|
# Put key columns first, then sort the rest
|
|
@@ -393,18 +402,18 @@ class _ColumnMixin:
|
|
|
393
402
|
if alphabetical
|
|
394
403
|
else column_names
|
|
395
404
|
)
|
|
396
|
-
|
|
405
|
+
|
|
397
406
|
# Use reorder_columns to apply the new order
|
|
398
407
|
return self.reorder_columns(table_name, new_order, progress_callback)
|
|
399
|
-
|
|
408
|
+
|
|
400
409
|
except Exception as e:
|
|
401
410
|
logger.error(f"Failed to sort columns: {e}")
|
|
402
411
|
return False
|
|
403
|
-
|
|
412
|
+
|
|
404
413
|
# ----------------------------------------
|
|
405
414
|
# ADD Operations
|
|
406
415
|
# ----------------------------------------
|
|
407
|
-
|
|
416
|
+
|
|
408
417
|
def add_column(
|
|
409
418
|
self,
|
|
410
419
|
table_name: str,
|
|
@@ -414,14 +423,14 @@ class _ColumnMixin:
|
|
|
414
423
|
not_null: bool = False,
|
|
415
424
|
) -> bool:
|
|
416
425
|
"""Add a new column to the table.
|
|
417
|
-
|
|
426
|
+
|
|
418
427
|
Args:
|
|
419
428
|
table_name: Name of the table
|
|
420
429
|
column_name: Name of new column
|
|
421
430
|
column_type: SQLite type (TEXT, INTEGER, REAL, BLOB)
|
|
422
431
|
default: Default value for the column
|
|
423
432
|
not_null: Whether column should be NOT NULL
|
|
424
|
-
|
|
433
|
+
|
|
425
434
|
Returns:
|
|
426
435
|
True if successful, False otherwise
|
|
427
436
|
"""
|
|
@@ -429,38 +438,38 @@ class _ColumnMixin:
|
|
|
429
438
|
if self.column_exists(table_name, column_name):
|
|
430
439
|
logger.warning(f"Column {column_name} already exists in {table_name}")
|
|
431
440
|
return False
|
|
432
|
-
|
|
441
|
+
|
|
433
442
|
cursor = self.cursor
|
|
434
443
|
col_def = f"{column_name} {column_type}"
|
|
435
|
-
|
|
444
|
+
|
|
436
445
|
if not_null and default is None:
|
|
437
446
|
logger.error("Cannot add NOT NULL column without default value")
|
|
438
447
|
return False
|
|
439
|
-
|
|
448
|
+
|
|
440
449
|
if default is not None:
|
|
441
450
|
if isinstance(default, str):
|
|
442
451
|
col_def += f" DEFAULT '{default}'"
|
|
443
452
|
else:
|
|
444
453
|
col_def += f" DEFAULT {default}"
|
|
445
|
-
|
|
454
|
+
|
|
446
455
|
if not_null:
|
|
447
456
|
col_def += " NOT NULL"
|
|
448
|
-
|
|
457
|
+
|
|
449
458
|
cursor.execute(f"ALTER TABLE {table_name} ADD COLUMN {col_def}")
|
|
450
459
|
self.conn.commit()
|
|
451
|
-
|
|
460
|
+
|
|
452
461
|
logger.info(f"Added column {column_name} to {table_name}")
|
|
453
462
|
return True
|
|
454
|
-
|
|
463
|
+
|
|
455
464
|
except Exception as e:
|
|
456
465
|
self.conn.rollback()
|
|
457
466
|
logger.error(f"Failed to add column: {e}")
|
|
458
467
|
return False
|
|
459
|
-
|
|
468
|
+
|
|
460
469
|
# ----------------------------------------
|
|
461
470
|
# Batch Operations
|
|
462
471
|
# ----------------------------------------
|
|
463
|
-
|
|
472
|
+
|
|
464
473
|
def drop_columns(
|
|
465
474
|
self,
|
|
466
475
|
table_name: str,
|
|
@@ -468,15 +477,15 @@ class _ColumnMixin:
|
|
|
468
477
|
progress_callback: Optional[callable] = None,
|
|
469
478
|
) -> bool:
|
|
470
479
|
"""Drop multiple columns efficiently in one operation.
|
|
471
|
-
|
|
480
|
+
|
|
472
481
|
More efficient than dropping columns one by one as it only
|
|
473
482
|
recreates the table once.
|
|
474
|
-
|
|
483
|
+
|
|
475
484
|
Args:
|
|
476
485
|
table_name: Name of the table
|
|
477
486
|
column_names: List of columns to drop
|
|
478
487
|
progress_callback: Function for progress updates
|
|
479
|
-
|
|
488
|
+
|
|
480
489
|
Returns:
|
|
481
490
|
True if successful, False otherwise
|
|
482
491
|
"""
|
|
@@ -486,24 +495,22 @@ class _ColumnMixin:
|
|
|
486
495
|
if not self.column_exists(table_name, col_name):
|
|
487
496
|
logger.error(f"Column {col_name} does not exist in {table_name}")
|
|
488
497
|
return False
|
|
489
|
-
|
|
498
|
+
|
|
490
499
|
# If native DROP is supported and only one column, use it
|
|
491
500
|
if len(column_names) == 1 and self.supports_drop_column():
|
|
492
501
|
return self.drop_column(table_name, column_names[0])
|
|
493
|
-
|
|
502
|
+
|
|
494
503
|
# Otherwise recreate table without the columns
|
|
495
504
|
cursor = self.cursor
|
|
496
505
|
cursor.execute("BEGIN EXCLUSIVE TRANSACTION")
|
|
497
|
-
|
|
506
|
+
|
|
498
507
|
# Get columns to keep
|
|
499
508
|
columns = self.get_column_info(table_name)
|
|
500
|
-
keep_columns = [
|
|
501
|
-
|
|
502
|
-
]
|
|
503
|
-
|
|
509
|
+
keep_columns = [col for col in columns if col["name"] not in column_names]
|
|
510
|
+
|
|
504
511
|
if not keep_columns:
|
|
505
512
|
raise ValueError("Cannot drop all columns from table")
|
|
506
|
-
|
|
513
|
+
|
|
507
514
|
# Create column definitions
|
|
508
515
|
column_names_keep = [col["name"] for col in keep_columns]
|
|
509
516
|
column_defs = []
|
|
@@ -516,33 +523,33 @@ class _ColumnMixin:
|
|
|
516
523
|
if col["pk"]:
|
|
517
524
|
col_def += " PRIMARY KEY"
|
|
518
525
|
column_defs.append(col_def)
|
|
519
|
-
|
|
526
|
+
|
|
520
527
|
# Create temp table
|
|
521
528
|
temp_table = f"{table_name}_drop_{int(time.time())}"
|
|
522
529
|
cursor.execute(f"""
|
|
523
530
|
CREATE TABLE {temp_table} (
|
|
524
|
-
{
|
|
531
|
+
{", ".join(column_defs)}
|
|
525
532
|
)
|
|
526
533
|
""")
|
|
527
|
-
|
|
534
|
+
|
|
528
535
|
# Copy data
|
|
529
536
|
cursor.execute(f"""
|
|
530
|
-
INSERT INTO {temp_table} ({
|
|
531
|
-
SELECT {
|
|
537
|
+
INSERT INTO {temp_table} ({", ".join(column_names_keep)})
|
|
538
|
+
SELECT {", ".join(column_names_keep)} FROM {table_name}
|
|
532
539
|
""")
|
|
533
|
-
|
|
540
|
+
|
|
534
541
|
# Swap tables
|
|
535
542
|
cursor.execute(f"DROP TABLE {table_name}")
|
|
536
543
|
cursor.execute(f"ALTER TABLE {temp_table} RENAME TO {table_name}")
|
|
537
|
-
|
|
544
|
+
|
|
538
545
|
self.conn.commit()
|
|
539
546
|
logger.info(f"Dropped {len(column_names)} columns from {table_name}")
|
|
540
547
|
return True
|
|
541
|
-
|
|
548
|
+
|
|
542
549
|
except Exception as e:
|
|
543
550
|
self.conn.rollback()
|
|
544
551
|
logger.error(f"Failed to drop multiple columns: {e}")
|
|
545
552
|
return False
|
|
546
553
|
|
|
547
554
|
|
|
548
|
-
# EOF
|
|
555
|
+
# EOF
|