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
scitex/tex/_export.py
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#!/usr/bin/env python3
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Export SciTeX writer documents to LaTeX format.
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This module converts the intermediate document format (from scitex.msword
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Export a SciTeX writer document to LaTeX format.
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SciTeX writer document structure containing:
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LaTeX document class (article, report, book, etc.).
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export_images : bool
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Path
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Examples
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--------
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effective_class = preset["document_class"]
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# Combine packages
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all_packages = extra_packages + (packages or [])
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162
|
+
# Build LaTeX content
|
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163
|
+
latex_content = _build_latex_document(
|
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164
|
+
blocks=blocks,
|
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165
|
+
metadata=metadata,
|
|
166
|
+
references=references,
|
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167
|
+
document_class=effective_class,
|
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168
|
+
class_options=effective_options,
|
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169
|
+
packages=all_packages if all_packages else None,
|
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170
|
+
preamble=preamble,
|
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171
|
+
image_map=image_map,
|
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172
|
+
use_bibtex=use_bibtex,
|
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173
|
+
output_stem=output_path.stem,
|
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174
|
+
)
|
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175
|
+
|
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176
|
+
# Write to file
|
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177
|
+
output_path.write_text(latex_content, encoding="utf-8")
|
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178
|
+
|
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179
|
+
# Generate .bib file if using bibtex
|
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180
|
+
if use_bibtex and references:
|
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181
|
+
bib_path = output_path.with_suffix(".bib")
|
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182
|
+
bib_content = _generate_bibtex(references)
|
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183
|
+
bib_path.write_text(bib_content, encoding="utf-8")
|
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184
|
+
|
|
185
|
+
return output_path
|
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186
|
+
|
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187
|
+
|
|
188
|
+
def _generate_bibtex(references: List[Dict[str, Any]]) -> str:
|
|
189
|
+
"""Generate BibTeX content from references."""
|
|
190
|
+
entries = []
|
|
191
|
+
for ref in references:
|
|
192
|
+
num = ref.get("number", len(entries) + 1)
|
|
193
|
+
text = ref.get("text", ref.get("raw", ""))
|
|
194
|
+
|
|
195
|
+
# Basic entry - in practice, would parse author/title/year
|
|
196
|
+
entry = f"""@misc{{ref{num},
|
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197
|
+
note = {{{text}}}
|
|
198
|
+
}}"""
|
|
199
|
+
entries.append(entry)
|
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200
|
+
|
|
201
|
+
return "\n\n".join(entries)
|
|
202
|
+
|
|
203
|
+
|
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204
|
+
def _write_images_to_dir(
|
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205
|
+
images: List[Dict[str, Any]],
|
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206
|
+
image_dir: Path,
|
|
207
|
+
tex_parent: Path,
|
|
208
|
+
) -> Dict[str, str]:
|
|
209
|
+
"""
|
|
210
|
+
Write images to directory and return hash->relative_path mapping.
|
|
211
|
+
|
|
212
|
+
Parameters
|
|
213
|
+
----------
|
|
214
|
+
images : list
|
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215
|
+
List of image dicts with 'hash', 'extension', 'data' keys.
|
|
216
|
+
image_dir : Path
|
|
217
|
+
Directory to write images to.
|
|
218
|
+
tex_parent : Path
|
|
219
|
+
Parent directory of the .tex file (for relative paths).
|
|
220
|
+
|
|
221
|
+
Returns
|
|
222
|
+
-------
|
|
223
|
+
dict
|
|
224
|
+
Mapping from image hash to relative path for LaTeX.
|
|
225
|
+
"""
|
|
226
|
+
image_map = {}
|
|
227
|
+
fig_counter = 0
|
|
228
|
+
|
|
229
|
+
for img in images:
|
|
230
|
+
img_hash = img.get("hash")
|
|
231
|
+
ext = img.get("extension", ".png")
|
|
232
|
+
data = img.get("data")
|
|
233
|
+
|
|
234
|
+
if data is None or img_hash is None:
|
|
235
|
+
continue
|
|
236
|
+
|
|
237
|
+
# Skip duplicates (same hash = same image content)
|
|
238
|
+
if img_hash in image_map:
|
|
239
|
+
continue
|
|
240
|
+
|
|
241
|
+
fig_counter += 1
|
|
242
|
+
filename = f"fig_{fig_counter}{ext}"
|
|
243
|
+
filepath = image_dir / filename
|
|
244
|
+
|
|
245
|
+
# Write image data
|
|
246
|
+
filepath.write_bytes(data)
|
|
247
|
+
|
|
248
|
+
# Store relative path from tex file location
|
|
249
|
+
try:
|
|
250
|
+
rel_path = filepath.relative_to(tex_parent)
|
|
251
|
+
except ValueError:
|
|
252
|
+
rel_path = filepath
|
|
253
|
+
|
|
254
|
+
image_map[img_hash] = str(rel_path)
|
|
255
|
+
|
|
256
|
+
return image_map
|
|
257
|
+
|
|
258
|
+
|
|
259
|
+
def _build_latex_document(
|
|
260
|
+
blocks: List[Dict[str, Any]],
|
|
261
|
+
metadata: Dict[str, Any],
|
|
262
|
+
references: List[Dict[str, Any]],
|
|
263
|
+
document_class: str,
|
|
264
|
+
class_options: Optional[List[str]] = None,
|
|
265
|
+
packages: Optional[List[str]] = None,
|
|
266
|
+
preamble: Optional[str] = None,
|
|
267
|
+
image_map: Optional[Dict[str, str]] = None,
|
|
268
|
+
use_bibtex: bool = False,
|
|
269
|
+
output_stem: str = "document",
|
|
270
|
+
) -> str:
|
|
271
|
+
"""Build complete LaTeX document content."""
|
|
272
|
+
if image_map is None:
|
|
273
|
+
image_map = {}
|
|
274
|
+
lines = []
|
|
275
|
+
|
|
276
|
+
# Document class with options
|
|
277
|
+
if class_options:
|
|
278
|
+
opts = ",".join(class_options)
|
|
279
|
+
lines.append(f"\\documentclass[{opts}]{{{document_class}}}")
|
|
280
|
+
else:
|
|
281
|
+
lines.append(f"\\documentclass{{{document_class}}}")
|
|
282
|
+
lines.append("")
|
|
283
|
+
|
|
284
|
+
# Default packages
|
|
285
|
+
default_packages = [
|
|
286
|
+
"inputenc",
|
|
287
|
+
"fontenc",
|
|
288
|
+
"amsmath",
|
|
289
|
+
"amssymb",
|
|
290
|
+
"graphicx",
|
|
291
|
+
"hyperref",
|
|
292
|
+
]
|
|
293
|
+
|
|
294
|
+
# Package options
|
|
295
|
+
package_options = {
|
|
296
|
+
"inputenc": "utf8",
|
|
297
|
+
"fontenc": "T1",
|
|
298
|
+
}
|
|
299
|
+
|
|
300
|
+
for pkg in default_packages:
|
|
301
|
+
opt = package_options.get(pkg)
|
|
302
|
+
if opt:
|
|
303
|
+
lines.append(f"\\usepackage[{opt}]{{{pkg}}}")
|
|
304
|
+
else:
|
|
305
|
+
lines.append(f"\\usepackage{{{pkg}}}")
|
|
306
|
+
|
|
307
|
+
# Additional packages
|
|
308
|
+
if packages:
|
|
309
|
+
for pkg in packages:
|
|
310
|
+
if pkg not in default_packages:
|
|
311
|
+
lines.append(f"\\usepackage{{{pkg}}}")
|
|
312
|
+
|
|
313
|
+
lines.append("")
|
|
314
|
+
|
|
315
|
+
# Metadata
|
|
316
|
+
if metadata.get("title"):
|
|
317
|
+
title = _escape_latex(metadata["title"])
|
|
318
|
+
lines.append(f"\\title{{{title}}}")
|
|
319
|
+
if metadata.get("author"):
|
|
320
|
+
author = _escape_latex(metadata["author"])
|
|
321
|
+
lines.append(f"\\author{{{author}}}")
|
|
322
|
+
|
|
323
|
+
lines.append("")
|
|
324
|
+
|
|
325
|
+
# Additional preamble
|
|
326
|
+
if preamble:
|
|
327
|
+
lines.append(preamble)
|
|
328
|
+
lines.append("")
|
|
329
|
+
|
|
330
|
+
# Begin document
|
|
331
|
+
lines.append("\\begin{document}")
|
|
332
|
+
lines.append("")
|
|
333
|
+
|
|
334
|
+
# Title
|
|
335
|
+
if metadata.get("title"):
|
|
336
|
+
lines.append("\\maketitle")
|
|
337
|
+
lines.append("")
|
|
338
|
+
|
|
339
|
+
# Track list state for proper itemize/enumerate environments
|
|
340
|
+
in_list = False
|
|
341
|
+
list_type = None
|
|
342
|
+
|
|
343
|
+
# Process blocks
|
|
344
|
+
for i, block in enumerate(blocks):
|
|
345
|
+
btype = block.get("type")
|
|
346
|
+
|
|
347
|
+
# Handle list transitions
|
|
348
|
+
if btype == "list-item":
|
|
349
|
+
item_list_type = block.get("list_type", "unordered")
|
|
350
|
+
if not in_list:
|
|
351
|
+
env = "enumerate" if item_list_type == "ordered" else "itemize"
|
|
352
|
+
lines.append(f"\\begin{{{env}}}")
|
|
353
|
+
in_list = True
|
|
354
|
+
list_type = item_list_type
|
|
355
|
+
elif in_list:
|
|
356
|
+
# Close list environment
|
|
357
|
+
env = "enumerate" if list_type == "ordered" else "itemize"
|
|
358
|
+
lines.append(f"\\end{{{env}}}")
|
|
359
|
+
lines.append("")
|
|
360
|
+
in_list = False
|
|
361
|
+
list_type = None
|
|
362
|
+
|
|
363
|
+
block_latex = _convert_block_to_latex(block, image_map)
|
|
364
|
+
if block_latex:
|
|
365
|
+
lines.append(block_latex)
|
|
366
|
+
|
|
367
|
+
# Close any open list
|
|
368
|
+
if in_list:
|
|
369
|
+
env = "enumerate" if list_type == "ordered" else "itemize"
|
|
370
|
+
lines.append(f"\\end{{{env}}}")
|
|
371
|
+
lines.append("")
|
|
372
|
+
|
|
373
|
+
# References section
|
|
374
|
+
if references:
|
|
375
|
+
lines.append("")
|
|
376
|
+
if use_bibtex:
|
|
377
|
+
lines.append(f"\\bibliographystyle{{plain}}")
|
|
378
|
+
lines.append(f"\\bibliography{{{output_stem}}}")
|
|
379
|
+
else:
|
|
380
|
+
lines.append("\\begin{thebibliography}{99}")
|
|
381
|
+
for ref in references:
|
|
382
|
+
ref_latex = _convert_reference_to_latex(ref)
|
|
383
|
+
if ref_latex:
|
|
384
|
+
lines.append(ref_latex)
|
|
385
|
+
lines.append("\\end{thebibliography}")
|
|
386
|
+
|
|
387
|
+
# End document
|
|
388
|
+
lines.append("")
|
|
389
|
+
lines.append("\\end{document}")
|
|
390
|
+
|
|
391
|
+
return "\n".join(lines)
|
|
392
|
+
|
|
393
|
+
|
|
394
|
+
def _convert_block_to_latex(
|
|
395
|
+
block: Dict[str, Any],
|
|
396
|
+
image_map: Optional[Dict[str, str]] = None,
|
|
397
|
+
) -> Optional[str]:
|
|
398
|
+
"""Convert a single block to LaTeX."""
|
|
399
|
+
if image_map is None:
|
|
400
|
+
image_map = {}
|
|
401
|
+
|
|
402
|
+
btype = block.get("type", "paragraph")
|
|
403
|
+
text = block.get("text", "")
|
|
404
|
+
|
|
405
|
+
if not text and btype not in ("table", "image", "caption", "equation"):
|
|
406
|
+
return None
|
|
407
|
+
|
|
408
|
+
if btype == "heading":
|
|
409
|
+
return _convert_heading(block)
|
|
410
|
+
elif btype == "paragraph":
|
|
411
|
+
return _convert_paragraph(block)
|
|
412
|
+
elif btype == "caption":
|
|
413
|
+
return _convert_caption(block, image_map)
|
|
414
|
+
elif btype == "table":
|
|
415
|
+
return _convert_table(block)
|
|
416
|
+
elif btype == "image":
|
|
417
|
+
return _convert_image(block, image_map)
|
|
418
|
+
elif btype == "list-item":
|
|
419
|
+
return _convert_list_item(block)
|
|
420
|
+
elif btype == "equation":
|
|
421
|
+
return _convert_equation(block)
|
|
422
|
+
elif btype == "reference-paragraph":
|
|
423
|
+
# Skip - handled separately in references section
|
|
424
|
+
return None
|
|
425
|
+
else:
|
|
426
|
+
# Default: treat as paragraph
|
|
427
|
+
return _escape_latex(text) + "\n"
|
|
428
|
+
|
|
429
|
+
|
|
430
|
+
def _convert_equation(block: Dict[str, Any]) -> str:
|
|
431
|
+
"""Convert an equation block to LaTeX."""
|
|
432
|
+
latex = block.get("latex", "")
|
|
433
|
+
text = block.get("text", "")
|
|
434
|
+
|
|
435
|
+
if latex:
|
|
436
|
+
# Use the converted LaTeX from OMML
|
|
437
|
+
return f"\\begin{{equation}}\n{latex}\n\\end{{equation}}\n"
|
|
438
|
+
elif text:
|
|
439
|
+
# Fallback: wrap text in equation environment
|
|
440
|
+
return f"\\begin{{equation}}\n{_escape_latex(text)}\n\\end{{equation}}\n"
|
|
441
|
+
return ""
|
|
442
|
+
|
|
443
|
+
|
|
444
|
+
def _convert_heading(block: Dict[str, Any]) -> str:
|
|
445
|
+
"""Convert a heading block to LaTeX."""
|
|
446
|
+
level = block.get("level", 1)
|
|
447
|
+
text = _escape_latex(block.get("text", ""))
|
|
448
|
+
|
|
449
|
+
# Map heading levels to LaTeX commands
|
|
450
|
+
level_commands = {
|
|
451
|
+
1: "section",
|
|
452
|
+
2: "subsection",
|
|
453
|
+
3: "subsubsection",
|
|
454
|
+
4: "paragraph",
|
|
455
|
+
5: "subparagraph",
|
|
456
|
+
}
|
|
457
|
+
|
|
458
|
+
command = level_commands.get(level, "paragraph")
|
|
459
|
+
return f"\\{command}{{{text}}}\n"
|
|
460
|
+
|
|
461
|
+
|
|
462
|
+
def _convert_paragraph(block: Dict[str, Any]) -> str:
|
|
463
|
+
"""Convert a paragraph block to LaTeX."""
|
|
464
|
+
runs = block.get("runs", [])
|
|
465
|
+
|
|
466
|
+
if runs:
|
|
467
|
+
# Build paragraph from formatted runs
|
|
468
|
+
parts = []
|
|
469
|
+
for run in runs:
|
|
470
|
+
run_text = _escape_latex(run.get("text", ""))
|
|
471
|
+
if run.get("bold"):
|
|
472
|
+
run_text = f"\\textbf{{{run_text}}}"
|
|
473
|
+
if run.get("italic"):
|
|
474
|
+
run_text = f"\\textit{{{run_text}}}"
|
|
475
|
+
if run.get("underline"):
|
|
476
|
+
run_text = f"\\underline{{{run_text}}}"
|
|
477
|
+
parts.append(run_text)
|
|
478
|
+
return "".join(parts) + "\n"
|
|
479
|
+
else:
|
|
480
|
+
return _escape_latex(block.get("text", "")) + "\n"
|
|
481
|
+
|
|
482
|
+
|
|
483
|
+
def _convert_caption(
|
|
484
|
+
block: Dict[str, Any],
|
|
485
|
+
image_map: Optional[Dict[str, str]] = None,
|
|
486
|
+
) -> str:
|
|
487
|
+
"""Convert a caption block to LaTeX figure/table environment."""
|
|
488
|
+
if image_map is None:
|
|
489
|
+
image_map = {}
|
|
490
|
+
|
|
491
|
+
caption_type = block.get("caption_type", "")
|
|
492
|
+
number = block.get("number", "")
|
|
493
|
+
caption_text = _escape_latex(block.get("caption_text", block.get("text", "")))
|
|
494
|
+
image_hash = block.get("image_hash")
|
|
495
|
+
|
|
496
|
+
if caption_type == "figure":
|
|
497
|
+
# Check if we have an associated image
|
|
498
|
+
image_path = None
|
|
499
|
+
if image_hash and image_hash in image_map:
|
|
500
|
+
image_path = image_map[image_hash]
|
|
501
|
+
|
|
502
|
+
lines = [
|
|
503
|
+
"\\begin{figure}[htbp]",
|
|
504
|
+
"\\centering",
|
|
505
|
+
]
|
|
506
|
+
|
|
507
|
+
if image_path:
|
|
508
|
+
# Remove extension for includegraphics
|
|
509
|
+
image_path_no_ext = image_path.rsplit(".", 1)[0] if "." in image_path else image_path
|
|
510
|
+
lines.append(f"\\includegraphics[width=0.8\\textwidth]{{{image_path_no_ext}}}")
|
|
511
|
+
else:
|
|
512
|
+
lines.append(f"% Image placeholder for Figure {number}")
|
|
513
|
+
|
|
514
|
+
lines.extend([
|
|
515
|
+
f"\\caption{{{caption_text}}}",
|
|
516
|
+
f"\\label{{fig:{number}}}",
|
|
517
|
+
"\\end{figure}",
|
|
518
|
+
"",
|
|
519
|
+
])
|
|
520
|
+
return "\n".join(lines)
|
|
521
|
+
|
|
522
|
+
elif caption_type == "table":
|
|
523
|
+
# Table captions - typically above the table
|
|
524
|
+
return f"% Table {number}: {caption_text}\n"
|
|
525
|
+
|
|
526
|
+
else:
|
|
527
|
+
return f"% Caption: {caption_text}\n"
|
|
528
|
+
|
|
529
|
+
|
|
530
|
+
def _convert_image(
|
|
531
|
+
block: Dict[str, Any],
|
|
532
|
+
image_map: Optional[Dict[str, str]] = None,
|
|
533
|
+
) -> str:
|
|
534
|
+
"""Convert an image block to LaTeX includegraphics."""
|
|
535
|
+
if image_map is None:
|
|
536
|
+
image_map = {}
|
|
537
|
+
|
|
538
|
+
image_hash = block.get("image_hash") or block.get("hash")
|
|
539
|
+
width = block.get("width", "0.8\\textwidth")
|
|
540
|
+
|
|
541
|
+
if image_hash and image_hash in image_map:
|
|
542
|
+
image_path = image_map[image_hash]
|
|
543
|
+
# Remove extension for includegraphics
|
|
544
|
+
image_path_no_ext = image_path.rsplit(".", 1)[0] if "." in image_path else image_path
|
|
545
|
+
|
|
546
|
+
lines = [
|
|
547
|
+
"\\begin{figure}[htbp]",
|
|
548
|
+
"\\centering",
|
|
549
|
+
f"\\includegraphics[width={width}]{{{image_path_no_ext}}}",
|
|
550
|
+
"\\end{figure}",
|
|
551
|
+
"",
|
|
552
|
+
]
|
|
553
|
+
return "\n".join(lines)
|
|
554
|
+
|
|
555
|
+
return "% Image placeholder\n"
|
|
556
|
+
|
|
557
|
+
|
|
558
|
+
def _convert_table(block: Dict[str, Any]) -> str:
|
|
559
|
+
"""Convert a table block to LaTeX."""
|
|
560
|
+
rows = block.get("rows", [])
|
|
561
|
+
if not rows:
|
|
562
|
+
return ""
|
|
563
|
+
|
|
564
|
+
num_cols = len(rows[0]) if rows else 0
|
|
565
|
+
col_spec = "|" + "c|" * num_cols
|
|
566
|
+
|
|
567
|
+
lines = [
|
|
568
|
+
"\\begin{table}[htbp]",
|
|
569
|
+
"\\centering",
|
|
570
|
+
f"\\begin{{tabular}}{{{col_spec}}}",
|
|
571
|
+
"\\hline",
|
|
572
|
+
]
|
|
573
|
+
|
|
574
|
+
for i, row in enumerate(rows):
|
|
575
|
+
escaped_cells = [_escape_latex(str(cell)) for cell in row]
|
|
576
|
+
lines.append(" & ".join(escaped_cells) + " \\\\")
|
|
577
|
+
lines.append("\\hline")
|
|
578
|
+
|
|
579
|
+
lines.extend([
|
|
580
|
+
"\\end{tabular}",
|
|
581
|
+
"\\end{table}",
|
|
582
|
+
"",
|
|
583
|
+
])
|
|
584
|
+
|
|
585
|
+
return "\n".join(lines)
|
|
586
|
+
|
|
587
|
+
|
|
588
|
+
def _convert_list_item(block: Dict[str, Any]) -> str:
|
|
589
|
+
"""Convert a list item to LaTeX."""
|
|
590
|
+
text = _escape_latex(block.get("text", ""))
|
|
591
|
+
return f"\\item {text}\n"
|
|
592
|
+
|
|
593
|
+
|
|
594
|
+
def _convert_reference_to_latex(ref: Dict[str, Any]) -> str:
|
|
595
|
+
"""Convert a reference entry to LaTeX bibitem."""
|
|
596
|
+
number = ref.get("number")
|
|
597
|
+
text = _escape_latex(ref.get("text", ref.get("raw", "")))
|
|
598
|
+
|
|
599
|
+
if number:
|
|
600
|
+
return f"\\bibitem{{ref{number}}} {text}"
|
|
601
|
+
else:
|
|
602
|
+
return f"\\bibitem{{}} {text}"
|
|
603
|
+
|
|
604
|
+
|
|
605
|
+
def _escape_latex(text: str) -> str:
|
|
606
|
+
"""Escape special LaTeX characters."""
|
|
607
|
+
if not text:
|
|
608
|
+
return ""
|
|
609
|
+
|
|
610
|
+
# Characters that need escaping in LaTeX
|
|
611
|
+
replacements = [
|
|
612
|
+
("\\", "\\textbackslash{}"),
|
|
613
|
+
("&", "\\&"),
|
|
614
|
+
("%", "\\%"),
|
|
615
|
+
("$", "\\$"),
|
|
616
|
+
("#", "\\#"),
|
|
617
|
+
("_", "\\_"),
|
|
618
|
+
("{", "\\{"),
|
|
619
|
+
("}", "\\}"),
|
|
620
|
+
("~", "\\textasciitilde{}"),
|
|
621
|
+
("^", "\\textasciicircum{}"),
|
|
622
|
+
]
|
|
623
|
+
|
|
624
|
+
# Apply replacements (order matters - backslash first)
|
|
625
|
+
result = text
|
|
626
|
+
for old, new in replacements:
|
|
627
|
+
# Skip if already escaped
|
|
628
|
+
if old == "\\":
|
|
629
|
+
# Don't escape existing LaTeX commands
|
|
630
|
+
result = re.sub(r'(?<!\\)\\(?![a-zA-Z{])', new, result)
|
|
631
|
+
else:
|
|
632
|
+
result = result.replace(old, new)
|
|
633
|
+
|
|
634
|
+
return result
|
|
635
|
+
|
|
636
|
+
|
|
637
|
+
@dataclass
|
|
638
|
+
class CompileResult:
|
|
639
|
+
"""Result of LaTeX compilation.
|
|
640
|
+
|
|
641
|
+
Attributes
|
|
642
|
+
----------
|
|
643
|
+
success : bool
|
|
644
|
+
Whether compilation succeeded.
|
|
645
|
+
pdf_path : Path | None
|
|
646
|
+
Path to generated PDF, or None if failed.
|
|
647
|
+
exit_code : int
|
|
648
|
+
Process exit code.
|
|
649
|
+
stdout : str
|
|
650
|
+
Standard output from compiler.
|
|
651
|
+
stderr : str
|
|
652
|
+
Standard error from compiler.
|
|
653
|
+
log_content : str
|
|
654
|
+
Content of .log file if available.
|
|
655
|
+
errors : list[str]
|
|
656
|
+
Extracted error messages.
|
|
657
|
+
warnings : list[str]
|
|
658
|
+
Extracted warning messages.
|
|
659
|
+
"""
|
|
660
|
+
success: bool
|
|
661
|
+
pdf_path: Optional[Path]
|
|
662
|
+
exit_code: int
|
|
663
|
+
stdout: str
|
|
664
|
+
stderr: str
|
|
665
|
+
log_content: str = ""
|
|
666
|
+
errors: List[str] = None
|
|
667
|
+
warnings: List[str] = None
|
|
668
|
+
|
|
669
|
+
def __post_init__(self):
|
|
670
|
+
if self.errors is None:
|
|
671
|
+
self.errors = []
|
|
672
|
+
if self.warnings is None:
|
|
673
|
+
self.warnings = []
|
|
674
|
+
|
|
675
|
+
|
|
676
|
+
def compile_tex(
|
|
677
|
+
tex_path: str | Path,
|
|
678
|
+
output_dir: Optional[str | Path] = None,
|
|
679
|
+
compiler: str = "pdflatex",
|
|
680
|
+
runs: int = 2,
|
|
681
|
+
clean: bool = True,
|
|
682
|
+
timeout: int = 120,
|
|
683
|
+
) -> CompileResult:
|
|
684
|
+
"""
|
|
685
|
+
Compile a LaTeX file to PDF.
|
|
686
|
+
|
|
687
|
+
Parameters
|
|
688
|
+
----------
|
|
689
|
+
tex_path : str | Path
|
|
690
|
+
Path to the .tex file.
|
|
691
|
+
output_dir : str | Path | None
|
|
692
|
+
Output directory for PDF. If None, uses same directory as tex file.
|
|
693
|
+
compiler : str
|
|
694
|
+
LaTeX compiler to use: "pdflatex", "xelatex", "lualatex", or "latexmk".
|
|
695
|
+
Default is "pdflatex".
|
|
696
|
+
runs : int
|
|
697
|
+
Number of compilation passes (for references/ToC). Default is 2.
|
|
698
|
+
Ignored if compiler is "latexmk".
|
|
699
|
+
clean : bool
|
|
700
|
+
Remove auxiliary files (.aux, .log, .out, etc.) after compilation.
|
|
701
|
+
Default is True.
|
|
702
|
+
timeout : int
|
|
703
|
+
Timeout in seconds for each compilation pass. Default is 120.
|
|
704
|
+
|
|
705
|
+
Returns
|
|
706
|
+
-------
|
|
707
|
+
CompileResult
|
|
708
|
+
Compilation result with success status, PDF path, and logs.
|
|
709
|
+
|
|
710
|
+
Examples
|
|
711
|
+
--------
|
|
712
|
+
>>> from scitex.tex import compile_tex
|
|
713
|
+
>>> result = compile_tex("manuscript.tex")
|
|
714
|
+
>>> if result.success:
|
|
715
|
+
... print(f"PDF created: {result.pdf_path}")
|
|
716
|
+
... else:
|
|
717
|
+
... print(f"Errors: {result.errors}")
|
|
718
|
+
|
|
719
|
+
>>> # Use latexmk for automatic multi-pass compilation
|
|
720
|
+
>>> result = compile_tex("manuscript.tex", compiler="latexmk")
|
|
721
|
+
|
|
722
|
+
Notes
|
|
723
|
+
-----
|
|
724
|
+
Requires LaTeX to be installed on the system (texlive, miktex, etc.).
|
|
725
|
+
"""
|
|
726
|
+
tex_path = Path(tex_path).absolute()
|
|
727
|
+
|
|
728
|
+
if not tex_path.exists():
|
|
729
|
+
return CompileResult(
|
|
730
|
+
success=False,
|
|
731
|
+
pdf_path=None,
|
|
732
|
+
exit_code=1,
|
|
733
|
+
stdout="",
|
|
734
|
+
stderr=f"File not found: {tex_path}",
|
|
735
|
+
errors=[f"File not found: {tex_path}"],
|
|
736
|
+
)
|
|
737
|
+
|
|
738
|
+
# Determine output directory
|
|
739
|
+
if output_dir is None:
|
|
740
|
+
output_dir = tex_path.parent
|
|
741
|
+
else:
|
|
742
|
+
output_dir = Path(output_dir).absolute()
|
|
743
|
+
output_dir.mkdir(parents=True, exist_ok=True)
|
|
744
|
+
|
|
745
|
+
# Check if compiler is available
|
|
746
|
+
compiler_cmd = shutil.which(compiler)
|
|
747
|
+
if compiler_cmd is None:
|
|
748
|
+
return CompileResult(
|
|
749
|
+
success=False,
|
|
750
|
+
pdf_path=None,
|
|
751
|
+
exit_code=127,
|
|
752
|
+
stdout="",
|
|
753
|
+
stderr=f"Compiler not found: {compiler}",
|
|
754
|
+
errors=[f"Compiler not found: {compiler}. Install texlive or miktex."],
|
|
755
|
+
)
|
|
756
|
+
|
|
757
|
+
# Build command
|
|
758
|
+
if compiler == "latexmk":
|
|
759
|
+
cmd = [
|
|
760
|
+
compiler,
|
|
761
|
+
"-pdf",
|
|
762
|
+
"-interaction=nonstopmode",
|
|
763
|
+
f"-output-directory={output_dir}",
|
|
764
|
+
str(tex_path),
|
|
765
|
+
]
|
|
766
|
+
runs = 1 # latexmk handles multi-pass
|
|
767
|
+
else:
|
|
768
|
+
cmd = [
|
|
769
|
+
compiler,
|
|
770
|
+
"-interaction=nonstopmode",
|
|
771
|
+
"-halt-on-error",
|
|
772
|
+
f"-output-directory={output_dir}",
|
|
773
|
+
str(tex_path),
|
|
774
|
+
]
|
|
775
|
+
|
|
776
|
+
# Run compilation
|
|
777
|
+
stdout_all = []
|
|
778
|
+
stderr_all = []
|
|
779
|
+
exit_code = 0
|
|
780
|
+
|
|
781
|
+
for run_num in range(runs):
|
|
782
|
+
try:
|
|
783
|
+
result = subprocess.run(
|
|
784
|
+
cmd,
|
|
785
|
+
cwd=tex_path.parent,
|
|
786
|
+
capture_output=True,
|
|
787
|
+
text=True,
|
|
788
|
+
timeout=timeout,
|
|
789
|
+
)
|
|
790
|
+
stdout_all.append(f"=== Pass {run_num + 1} ===\n{result.stdout}")
|
|
791
|
+
stderr_all.append(result.stderr)
|
|
792
|
+
exit_code = result.returncode
|
|
793
|
+
|
|
794
|
+
# If compilation failed, don't continue
|
|
795
|
+
if exit_code != 0:
|
|
796
|
+
break
|
|
797
|
+
|
|
798
|
+
except subprocess.TimeoutExpired:
|
|
799
|
+
return CompileResult(
|
|
800
|
+
success=False,
|
|
801
|
+
pdf_path=None,
|
|
802
|
+
exit_code=124,
|
|
803
|
+
stdout="\n".join(stdout_all),
|
|
804
|
+
stderr=f"Compilation timed out after {timeout} seconds",
|
|
805
|
+
errors=[f"Compilation timed out after {timeout} seconds"],
|
|
806
|
+
)
|
|
807
|
+
except Exception as e:
|
|
808
|
+
return CompileResult(
|
|
809
|
+
success=False,
|
|
810
|
+
pdf_path=None,
|
|
811
|
+
exit_code=1,
|
|
812
|
+
stdout="\n".join(stdout_all),
|
|
813
|
+
stderr=str(e),
|
|
814
|
+
errors=[str(e)],
|
|
815
|
+
)
|
|
816
|
+
|
|
817
|
+
# Check for output PDF
|
|
818
|
+
pdf_name = tex_path.stem + ".pdf"
|
|
819
|
+
pdf_path = output_dir / pdf_name
|
|
820
|
+
|
|
821
|
+
# Read log file for detailed errors/warnings
|
|
822
|
+
log_path = output_dir / (tex_path.stem + ".log")
|
|
823
|
+
log_content = ""
|
|
824
|
+
errors = []
|
|
825
|
+
warnings = []
|
|
826
|
+
|
|
827
|
+
if log_path.exists():
|
|
828
|
+
try:
|
|
829
|
+
log_content = log_path.read_text(encoding="utf-8", errors="replace")
|
|
830
|
+
errors, warnings = _parse_latex_log(log_content)
|
|
831
|
+
except Exception:
|
|
832
|
+
pass
|
|
833
|
+
|
|
834
|
+
# Clean auxiliary files
|
|
835
|
+
if clean:
|
|
836
|
+
aux_extensions = [".aux", ".log", ".out", ".toc", ".lof", ".lot",
|
|
837
|
+
".bbl", ".blg", ".fls", ".fdb_latexmk", ".synctex.gz"]
|
|
838
|
+
for ext in aux_extensions:
|
|
839
|
+
aux_file = output_dir / (tex_path.stem + ext)
|
|
840
|
+
if aux_file.exists():
|
|
841
|
+
try:
|
|
842
|
+
aux_file.unlink()
|
|
843
|
+
except Exception:
|
|
844
|
+
pass
|
|
845
|
+
|
|
846
|
+
success = exit_code == 0 and pdf_path.exists()
|
|
847
|
+
|
|
848
|
+
return CompileResult(
|
|
849
|
+
success=success,
|
|
850
|
+
pdf_path=pdf_path if pdf_path.exists() else None,
|
|
851
|
+
exit_code=exit_code,
|
|
852
|
+
stdout="\n".join(stdout_all),
|
|
853
|
+
stderr="\n".join(stderr_all),
|
|
854
|
+
log_content=log_content,
|
|
855
|
+
errors=errors,
|
|
856
|
+
warnings=warnings,
|
|
857
|
+
)
|
|
858
|
+
|
|
859
|
+
|
|
860
|
+
def _parse_latex_log(log_content: str) -> Tuple[List[str], List[str]]:
|
|
861
|
+
"""Parse LaTeX log file for errors and warnings."""
|
|
862
|
+
errors = []
|
|
863
|
+
warnings = []
|
|
864
|
+
|
|
865
|
+
lines = log_content.split("\n")
|
|
866
|
+
|
|
867
|
+
for i, line in enumerate(lines):
|
|
868
|
+
# Error patterns
|
|
869
|
+
if line.startswith("!"):
|
|
870
|
+
# Collect multi-line error message
|
|
871
|
+
error_lines = [line]
|
|
872
|
+
for j in range(i + 1, min(i + 5, len(lines))):
|
|
873
|
+
if lines[j].startswith("l.") or lines[j].strip() == "":
|
|
874
|
+
break
|
|
875
|
+
error_lines.append(lines[j])
|
|
876
|
+
errors.append(" ".join(error_lines))
|
|
877
|
+
|
|
878
|
+
elif "Error:" in line or "Fatal error" in line:
|
|
879
|
+
errors.append(line.strip())
|
|
880
|
+
|
|
881
|
+
# Warning patterns
|
|
882
|
+
elif "Warning:" in line:
|
|
883
|
+
warnings.append(line.strip())
|
|
884
|
+
elif "Underfull" in line or "Overfull" in line:
|
|
885
|
+
warnings.append(line.strip())
|
|
886
|
+
|
|
887
|
+
return errors, warnings
|
|
888
|
+
|
|
889
|
+
|
|
890
|
+
__all__ = ["export_tex", "compile_tex", "CompileResult"]
|