scitex 2.0.0__py2.py3-none-any.whl → 2.1.0__py2.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 +53 -15
- scitex/__main__.py +72 -26
- scitex/__version__.py +1 -1
- scitex/_sh.py +145 -23
- scitex/ai/__init__.py +30 -16
- scitex/ai/_gen_ai/_Anthropic.py +5 -7
- scitex/ai/_gen_ai/_BaseGenAI.py +2 -2
- scitex/ai/_gen_ai/_DeepSeek.py +10 -2
- scitex/ai/_gen_ai/_Google.py +2 -2
- scitex/ai/_gen_ai/_Llama.py +2 -2
- scitex/ai/_gen_ai/_OpenAI.py +2 -2
- scitex/ai/_gen_ai/_PARAMS.py +51 -65
- scitex/ai/_gen_ai/_Perplexity.py +2 -2
- scitex/ai/_gen_ai/__init__.py +25 -14
- scitex/ai/_gen_ai/_format_output_func.py +4 -4
- scitex/ai/classification/{classifier_server.py → Classifier.py} +5 -5
- scitex/ai/classification/CrossValidationExperiment.py +374 -0
- scitex/ai/classification/__init__.py +43 -4
- scitex/ai/classification/reporters/_BaseClassificationReporter.py +281 -0
- scitex/ai/classification/reporters/_ClassificationReporter.py +773 -0
- scitex/ai/classification/reporters/_MultiClassificationReporter.py +406 -0
- scitex/ai/classification/reporters/_SingleClassificationReporter.py +1834 -0
- scitex/ai/classification/reporters/__init__.py +11 -0
- scitex/ai/classification/reporters/reporter_utils/_Plotter.py +1028 -0
- scitex/ai/classification/reporters/reporter_utils/__init__.py +80 -0
- scitex/ai/classification/reporters/reporter_utils/aggregation.py +457 -0
- scitex/ai/classification/reporters/reporter_utils/data_models.py +313 -0
- scitex/ai/classification/reporters/reporter_utils/reporting.py +1056 -0
- scitex/ai/classification/reporters/reporter_utils/storage.py +221 -0
- scitex/ai/classification/reporters/reporter_utils/validation.py +395 -0
- scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +568 -0
- scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +688 -0
- scitex/ai/classification/timeseries/_TimeSeriesMetadata.py +139 -0
- scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +1716 -0
- scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +1685 -0
- scitex/ai/classification/timeseries/_TimeSeriesStrategy.py +84 -0
- scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +610 -0
- scitex/ai/classification/timeseries/__init__.py +39 -0
- scitex/ai/classification/timeseries/_normalize_timestamp.py +436 -0
- scitex/ai/clustering/_umap.py +2 -2
- scitex/ai/feature_extraction/vit.py +1 -0
- scitex/ai/feature_selection/__init__.py +30 -0
- scitex/ai/feature_selection/feature_selection.py +364 -0
- scitex/ai/loss/multi_task_loss.py +1 -1
- scitex/ai/metrics/__init__.py +51 -4
- scitex/ai/metrics/_calc_bacc.py +61 -0
- scitex/ai/metrics/_calc_bacc_from_conf_mat.py +38 -0
- scitex/ai/metrics/_calc_clf_report.py +78 -0
- scitex/ai/metrics/_calc_conf_mat.py +93 -0
- scitex/ai/metrics/_calc_feature_importance.py +183 -0
- scitex/ai/metrics/_calc_mcc.py +61 -0
- scitex/ai/metrics/_calc_pre_rec_auc.py +116 -0
- scitex/ai/metrics/_calc_roc_auc.py +110 -0
- scitex/ai/metrics/_calc_seizure_prediction_metrics.py +490 -0
- scitex/ai/metrics/{silhoute_score_block.py → _calc_silhouette_score.py} +15 -8
- scitex/ai/metrics/_normalize_labels.py +83 -0
- scitex/ai/plt/__init__.py +47 -8
- scitex/ai/plt/{_conf_mat.py → _plot_conf_mat.py} +158 -87
- scitex/ai/plt/_plot_feature_importance.py +323 -0
- scitex/ai/plt/_plot_learning_curve.py +345 -0
- scitex/ai/plt/_plot_optuna_study.py +225 -0
- scitex/ai/plt/_plot_pre_rec_curve.py +290 -0
- scitex/ai/plt/_plot_roc_curve.py +255 -0
- scitex/ai/training/{learning_curve_logger.py → _LearningCurveLogger.py} +197 -213
- scitex/ai/training/__init__.py +2 -2
- scitex/ai/utils/grid_search.py +3 -3
- scitex/benchmark/__init__.py +52 -0
- scitex/benchmark/benchmark.py +400 -0
- scitex/benchmark/monitor.py +370 -0
- scitex/benchmark/profiler.py +297 -0
- scitex/browser/__init__.py +48 -0
- scitex/browser/automation/CookieHandler.py +216 -0
- scitex/browser/automation/__init__.py +7 -0
- scitex/browser/collaboration/__init__.py +55 -0
- scitex/browser/collaboration/auth_helpers.py +94 -0
- scitex/browser/collaboration/collaborative_agent.py +136 -0
- scitex/browser/collaboration/credential_manager.py +188 -0
- scitex/browser/collaboration/interactive_panel.py +400 -0
- scitex/browser/collaboration/persistent_browser.py +170 -0
- scitex/browser/collaboration/shared_session.py +383 -0
- scitex/browser/collaboration/standard_interactions.py +246 -0
- scitex/browser/collaboration/visual_feedback.py +181 -0
- scitex/browser/core/BrowserMixin.py +326 -0
- scitex/browser/core/ChromeProfileManager.py +446 -0
- scitex/browser/core/__init__.py +9 -0
- scitex/browser/debugging/__init__.py +18 -0
- scitex/browser/debugging/_browser_logger.py +657 -0
- scitex/browser/debugging/_highlight_element.py +143 -0
- scitex/browser/debugging/_show_grid.py +154 -0
- scitex/browser/interaction/__init__.py +24 -0
- scitex/browser/interaction/click_center.py +149 -0
- scitex/browser/interaction/click_with_fallbacks.py +206 -0
- scitex/browser/interaction/close_popups.py +498 -0
- scitex/browser/interaction/fill_with_fallbacks.py +209 -0
- scitex/browser/pdf/__init__.py +14 -0
- scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +200 -0
- scitex/browser/pdf/detect_chrome_pdf_viewer.py +198 -0
- scitex/browser/remote/CaptchaHandler.py +434 -0
- scitex/browser/remote/ZenRowsAPIClient.py +347 -0
- scitex/browser/remote/ZenRowsBrowserManager.py +570 -0
- scitex/browser/remote/__init__.py +11 -0
- scitex/browser/stealth/HumanBehavior.py +344 -0
- scitex/browser/stealth/StealthManager.py +1008 -0
- scitex/browser/stealth/__init__.py +9 -0
- scitex/browser/template.py +122 -0
- scitex/capture/__init__.py +110 -0
- scitex/capture/__main__.py +25 -0
- scitex/capture/capture.py +848 -0
- scitex/capture/cli.py +233 -0
- scitex/capture/gif.py +344 -0
- scitex/capture/mcp_server.py +961 -0
- scitex/capture/session.py +70 -0
- scitex/capture/utils.py +705 -0
- scitex/cli/__init__.py +17 -0
- scitex/cli/cloud.py +447 -0
- scitex/cli/main.py +42 -0
- scitex/cli/scholar.py +280 -0
- scitex/context/_suppress_output.py +5 -3
- scitex/db/__init__.py +30 -3
- scitex/db/__main__.py +75 -0
- scitex/db/_check_health.py +381 -0
- scitex/db/_delete_duplicates.py +25 -386
- scitex/db/_inspect.py +335 -114
- scitex/db/_inspect_optimized.py +301 -0
- scitex/db/{_PostgreSQL.py → _postgresql/_PostgreSQL.py} +3 -3
- scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_BackupMixin.py +1 -1
- scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_BatchMixin.py +1 -1
- scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_BlobMixin.py +1 -1
- scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_ConnectionMixin.py +1 -1
- scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_MaintenanceMixin.py +1 -1
- scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_QueryMixin.py +1 -1
- scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_SchemaMixin.py +1 -1
- scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_TransactionMixin.py +1 -1
- scitex/db/_postgresql/__init__.py +6 -0
- scitex/db/_sqlite3/_SQLite3.py +210 -0
- scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin.py +581 -0
- scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin_v01-need-_hash-col.py +517 -0
- scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_BatchMixin.py +1 -1
- scitex/db/_sqlite3/_SQLite3Mixins/_BlobMixin.py +281 -0
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin.py +548 -0
- scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +583 -0
- scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_ConnectionMixin.py +29 -13
- scitex/db/_sqlite3/_SQLite3Mixins/_GitMixin.py +583 -0
- scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_ImportExportMixin.py +1 -1
- scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_IndexMixin.py +1 -1
- scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_MaintenanceMixin.py +2 -1
- scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_QueryMixin.py +37 -10
- scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_RowMixin.py +46 -6
- scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_TableMixin.py +56 -10
- scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/_TransactionMixin.py +1 -1
- scitex/db/{_SQLite3Mixins → _sqlite3/_SQLite3Mixins}/__init__.py +14 -2
- scitex/db/_sqlite3/__init__.py +7 -0
- scitex/db/_sqlite3/_delete_duplicates.py +274 -0
- scitex/decorators/__init__.py +2 -0
- scitex/decorators/_cache_disk.py +13 -5
- scitex/decorators/_cache_disk_async.py +49 -0
- scitex/decorators/_deprecated.py +175 -10
- scitex/decorators/_timeout.py +1 -1
- scitex/dev/_analyze_code_flow.py +2 -2
- scitex/dict/_DotDict.py +73 -15
- scitex/dict/_DotDict_v01-not-handling-recursive-instantiations.py +442 -0
- scitex/dict/_DotDict_v02-not-serializing-Path-object.py +446 -0
- scitex/dict/__init__.py +2 -0
- scitex/dict/_flatten.py +27 -0
- scitex/dsp/_crop.py +2 -2
- scitex/dsp/_demo_sig.py +2 -2
- scitex/dsp/_detect_ripples.py +2 -2
- scitex/dsp/_hilbert.py +2 -2
- scitex/dsp/_listen.py +6 -6
- scitex/dsp/_modulation_index.py +2 -2
- scitex/dsp/_pac.py +1 -1
- scitex/dsp/_psd.py +2 -2
- scitex/dsp/_resample.py +2 -1
- scitex/dsp/_time.py +3 -2
- scitex/dsp/_wavelet.py +3 -2
- scitex/dsp/add_noise.py +2 -2
- scitex/dsp/example.py +1 -0
- scitex/dsp/filt.py +10 -9
- scitex/dsp/template.py +3 -2
- scitex/dsp/utils/_differential_bandpass_filters.py +1 -1
- scitex/dsp/utils/pac.py +2 -2
- scitex/dt/_normalize_timestamp.py +432 -0
- scitex/errors.py +572 -0
- scitex/gen/_DimHandler.py +2 -2
- scitex/gen/__init__.py +37 -7
- scitex/gen/_deprecated_close.py +80 -0
- scitex/gen/_deprecated_start.py +26 -0
- scitex/gen/_detect_environment.py +152 -0
- scitex/gen/_detect_notebook_path.py +169 -0
- scitex/gen/_embed.py +6 -2
- scitex/gen/_get_notebook_path.py +257 -0
- scitex/gen/_less.py +1 -1
- scitex/gen/_list_packages.py +2 -2
- scitex/gen/_norm.py +44 -9
- scitex/gen/_norm_cache.py +269 -0
- scitex/gen/_src.py +3 -5
- scitex/gen/_title_case.py +3 -3
- scitex/io/__init__.py +28 -6
- scitex/io/_glob.py +13 -7
- scitex/io/_load.py +108 -21
- scitex/io/_load_cache.py +303 -0
- scitex/io/_load_configs.py +40 -15
- scitex/io/{_H5Explorer.py → _load_modules/_H5Explorer.py} +80 -17
- scitex/io/_load_modules/_ZarrExplorer.py +114 -0
- scitex/io/_load_modules/_bibtex.py +207 -0
- scitex/io/_load_modules/_hdf5.py +53 -178
- scitex/io/_load_modules/_json.py +5 -3
- scitex/io/_load_modules/_pdf.py +871 -16
- scitex/io/_load_modules/_sqlite3.py +15 -0
- scitex/io/_load_modules/_txt.py +41 -12
- scitex/io/_load_modules/_yaml.py +4 -3
- scitex/io/_load_modules/_zarr.py +126 -0
- scitex/io/_save.py +429 -171
- scitex/io/_save_modules/__init__.py +6 -0
- scitex/io/_save_modules/_bibtex.py +194 -0
- scitex/io/_save_modules/_csv.py +8 -4
- scitex/io/_save_modules/_excel.py +174 -15
- scitex/io/_save_modules/_hdf5.py +251 -226
- scitex/io/_save_modules/_image.py +1 -3
- scitex/io/_save_modules/_json.py +49 -4
- scitex/io/_save_modules/_listed_dfs_as_csv.py +1 -3
- scitex/io/_save_modules/_listed_scalars_as_csv.py +1 -3
- scitex/io/_save_modules/_tex.py +277 -0
- scitex/io/_save_modules/_yaml.py +42 -3
- scitex/io/_save_modules/_zarr.py +160 -0
- scitex/io/utils/__init__.py +20 -0
- scitex/io/utils/h5_to_zarr.py +616 -0
- scitex/linalg/_geometric_median.py +6 -2
- scitex/{gen/_tee.py → logging/_Tee.py} +43 -84
- scitex/logging/__init__.py +122 -0
- scitex/logging/_config.py +158 -0
- scitex/logging/_context.py +103 -0
- scitex/logging/_formatters.py +128 -0
- scitex/logging/_handlers.py +64 -0
- scitex/logging/_levels.py +35 -0
- scitex/logging/_logger.py +163 -0
- scitex/logging/_print_capture.py +95 -0
- scitex/ml/__init__.py +69 -0
- scitex/{ai/genai/anthropic.py → ml/_gen_ai/_Anthropic.py} +13 -19
- scitex/{ai/genai/base_genai.py → ml/_gen_ai/_BaseGenAI.py} +5 -5
- scitex/{ai/genai/deepseek.py → ml/_gen_ai/_DeepSeek.py} +11 -16
- scitex/{ai/genai/google.py → ml/_gen_ai/_Google.py} +7 -15
- scitex/{ai/genai/groq.py → ml/_gen_ai/_Groq.py} +1 -8
- scitex/{ai/genai/llama.py → ml/_gen_ai/_Llama.py} +3 -16
- scitex/{ai/genai/openai.py → ml/_gen_ai/_OpenAI.py} +3 -3
- scitex/{ai/genai/params.py → ml/_gen_ai/_PARAMS.py} +51 -65
- scitex/{ai/genai/perplexity.py → ml/_gen_ai/_Perplexity.py} +3 -14
- scitex/ml/_gen_ai/__init__.py +43 -0
- scitex/{ai/genai/calc_cost.py → ml/_gen_ai/_calc_cost.py} +1 -1
- scitex/{ai/genai/format_output_func.py → ml/_gen_ai/_format_output_func.py} +4 -4
- scitex/{ai/genai/genai_factory.py → ml/_gen_ai/_genai_factory.py} +8 -8
- scitex/ml/activation/__init__.py +8 -0
- scitex/ml/activation/_define.py +11 -0
- scitex/{ai/classifier_server.py → ml/classification/Classifier.py} +5 -5
- scitex/ml/classification/CrossValidationExperiment.py +374 -0
- scitex/ml/classification/__init__.py +46 -0
- scitex/ml/classification/reporters/_BaseClassificationReporter.py +281 -0
- scitex/ml/classification/reporters/_ClassificationReporter.py +773 -0
- scitex/ml/classification/reporters/_MultiClassificationReporter.py +406 -0
- scitex/ml/classification/reporters/_SingleClassificationReporter.py +1834 -0
- scitex/ml/classification/reporters/__init__.py +11 -0
- scitex/ml/classification/reporters/reporter_utils/_Plotter.py +1028 -0
- scitex/ml/classification/reporters/reporter_utils/__init__.py +80 -0
- scitex/ml/classification/reporters/reporter_utils/aggregation.py +457 -0
- scitex/ml/classification/reporters/reporter_utils/data_models.py +313 -0
- scitex/ml/classification/reporters/reporter_utils/reporting.py +1056 -0
- scitex/ml/classification/reporters/reporter_utils/storage.py +221 -0
- scitex/ml/classification/reporters/reporter_utils/validation.py +395 -0
- scitex/ml/classification/timeseries/_TimeSeriesBlockingSplit.py +568 -0
- scitex/ml/classification/timeseries/_TimeSeriesCalendarSplit.py +688 -0
- scitex/ml/classification/timeseries/_TimeSeriesMetadata.py +139 -0
- scitex/ml/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +1716 -0
- scitex/ml/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +1685 -0
- scitex/ml/classification/timeseries/_TimeSeriesStrategy.py +84 -0
- scitex/ml/classification/timeseries/_TimeSeriesStratifiedSplit.py +610 -0
- scitex/ml/classification/timeseries/__init__.py +39 -0
- scitex/ml/classification/timeseries/_normalize_timestamp.py +436 -0
- scitex/ml/clustering/__init__.py +11 -0
- scitex/ml/clustering/_pca.py +115 -0
- scitex/ml/clustering/_umap.py +376 -0
- scitex/ml/feature_extraction/__init__.py +56 -0
- scitex/ml/feature_extraction/vit.py +149 -0
- scitex/ml/feature_selection/__init__.py +30 -0
- scitex/ml/feature_selection/feature_selection.py +364 -0
- scitex/ml/loss/_L1L2Losses.py +34 -0
- scitex/ml/loss/__init__.py +12 -0
- scitex/ml/loss/multi_task_loss.py +47 -0
- scitex/ml/metrics/__init__.py +56 -0
- scitex/ml/metrics/_calc_bacc.py +61 -0
- scitex/ml/metrics/_calc_bacc_from_conf_mat.py +38 -0
- scitex/ml/metrics/_calc_clf_report.py +78 -0
- scitex/ml/metrics/_calc_conf_mat.py +93 -0
- scitex/ml/metrics/_calc_feature_importance.py +183 -0
- scitex/ml/metrics/_calc_mcc.py +61 -0
- scitex/ml/metrics/_calc_pre_rec_auc.py +116 -0
- scitex/ml/metrics/_calc_roc_auc.py +110 -0
- scitex/ml/metrics/_calc_seizure_prediction_metrics.py +490 -0
- scitex/ml/metrics/_calc_silhouette_score.py +503 -0
- scitex/ml/metrics/_normalize_labels.py +83 -0
- scitex/ml/optim/Ranger_Deep_Learning_Optimizer/__init__.py +0 -0
- scitex/ml/optim/Ranger_Deep_Learning_Optimizer/ranger/__init__.py +3 -0
- scitex/ml/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger.py +207 -0
- scitex/ml/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger2020.py +238 -0
- scitex/ml/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger913A.py +215 -0
- scitex/ml/optim/Ranger_Deep_Learning_Optimizer/ranger/rangerqh.py +184 -0
- scitex/ml/optim/Ranger_Deep_Learning_Optimizer/setup.py +24 -0
- scitex/ml/optim/__init__.py +13 -0
- scitex/ml/optim/_get_set.py +31 -0
- scitex/ml/optim/_optimizers.py +71 -0
- scitex/ml/plt/__init__.py +60 -0
- scitex/ml/plt/_plot_conf_mat.py +663 -0
- scitex/ml/plt/_plot_feature_importance.py +323 -0
- scitex/ml/plt/_plot_learning_curve.py +345 -0
- scitex/ml/plt/_plot_optuna_study.py +225 -0
- scitex/ml/plt/_plot_pre_rec_curve.py +290 -0
- scitex/ml/plt/_plot_roc_curve.py +255 -0
- scitex/ml/sk/__init__.py +11 -0
- scitex/ml/sk/_clf.py +58 -0
- scitex/ml/sk/_to_sktime.py +100 -0
- scitex/ml/sklearn/__init__.py +26 -0
- scitex/ml/sklearn/clf.py +58 -0
- scitex/ml/sklearn/to_sktime.py +100 -0
- scitex/{ai/training/early_stopping.py → ml/training/_EarlyStopping.py} +1 -2
- scitex/{ai → ml/training}/_LearningCurveLogger.py +198 -242
- scitex/ml/training/__init__.py +7 -0
- scitex/ml/utils/__init__.py +22 -0
- scitex/ml/utils/_check_params.py +50 -0
- scitex/ml/utils/_default_dataset.py +46 -0
- scitex/ml/utils/_format_samples_for_sktime.py +26 -0
- scitex/ml/utils/_label_encoder.py +134 -0
- scitex/ml/utils/_merge_labels.py +22 -0
- scitex/ml/utils/_sliding_window_data_augmentation.py +11 -0
- scitex/ml/utils/_under_sample.py +51 -0
- scitex/ml/utils/_verify_n_gpus.py +16 -0
- scitex/ml/utils/grid_search.py +148 -0
- scitex/nn/_BNet.py +15 -9
- scitex/nn/_Filters.py +2 -2
- scitex/nn/_ModulationIndex.py +2 -2
- scitex/nn/_PAC.py +1 -1
- scitex/nn/_Spectrogram.py +12 -3
- scitex/nn/__init__.py +9 -10
- scitex/path/__init__.py +18 -0
- scitex/path/_clean.py +4 -0
- scitex/path/_find.py +9 -4
- scitex/path/_symlink.py +348 -0
- scitex/path/_version.py +4 -3
- scitex/pd/__init__.py +2 -0
- scitex/pd/_get_unique.py +99 -0
- scitex/plt/__init__.py +114 -5
- scitex/plt/_subplots/_AxesWrapper.py +1 -3
- scitex/plt/_subplots/_AxisWrapper.py +7 -3
- scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +47 -13
- scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +160 -2
- scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +26 -4
- scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +322 -0
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- /scitex/{stats → stats_v01}/_multiple_corrections.py +0 -0
- /scitex/{stats → stats_v01}/_nan_stats.py +0 -0
- /scitex/{stats → stats_v01}/_p2stars_wrapper.py +0 -0
- /scitex/{stats → stats_v01}/_statistical_tests.py +0 -0
- /scitex/{stats/desc/_describe.py → stats_v01/desc/_describe_v01-20250920_145731.py} +0 -0
- /scitex/{stats/desc/_real.py → stats_v01/desc/_real_v01-20250920_145731.py} +0 -0
- /scitex/{stats → stats_v01}/multiple/__init__.py +0 -0
- /scitex/{stats → stats_v01}/multiple/_bonferroni_correction.py +0 -0
- /scitex/{stats → stats_v01}/multiple/_fdr_correction.py +0 -0
- /scitex/{stats → stats_v01}/multiple/_multicompair.py +0 -0
- /scitex/{stats → stats_v01}/tests/__corr_test.py +0 -0
- /scitex/{stats → stats_v01}/tests/__corr_test_multi.py +0 -0
- /scitex/{stats → stats_v01}/tests/__corr_test_single.py +0 -0
- /scitex/{stats → stats_v01}/tests/__init__.py +0 -0
- /scitex/{stats → stats_v01}/tests/_brunner_munzel_test.py +0 -0
- /scitex/{stats → stats_v01}/tests/_nocorrelation_test.py +0 -0
- /scitex/{stats → stats_v01}/tests/_smirnov_grubbs.py +0 -0
- {scitex-2.0.0.dist-info → scitex-2.1.0.dist-info}/top_level.txt +0 -0
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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# Timestamp: "2025-10-01 20:28:19 (ywatanabe)"
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# File: /ssh:sp:/home/ywatanabe/proj/scitex_repo/src/scitex/stats/utils/_normalizers.py
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# ----------------------------------------
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from __future__ import annotations
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import os
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__FILE__ = __file__
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__DIR__ = os.path.dirname(__FILE__)
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# ----------------------------------------
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"""
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Output format normalization utilities for scitex.stats.
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Provides functions to convert between dict and DataFrame formats,
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ensuring consistent output structure across all statistical tests.
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"""
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from typing import Any, Dict, List, Literal, Optional, Union
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import numpy as np
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import pandas as pd
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# Standard columns for statistical test outputs
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STANDARD_COLUMNS = [
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"test_method",
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"statistic_name",
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"statistic",
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"alternative",
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"n_samples",
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"n_x",
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"n_y",
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"n_pairs",
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"var_x",
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"var_y",
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"pvalue",
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"pvalue_adjusted",
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"pstars",
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"alpha",
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"alpha_adjusted",
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"rejected",
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"effect_size",
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"effect_size_metric",
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"effect_size_interpretation",
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"effect_size_secondary",
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"effect_size_secondary_metric",
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"effect_size_secondary_interpretation",
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"power",
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"H0",
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]
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# Default values for standard columns
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STANDARD_DEFAULTS = {
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"alternative": "two-sided",
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"pstars": "ns",
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"rejected": False,
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"alpha": 0.05,
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"alpha_adjusted": np.nan,
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"pvalue_adjusted": np.nan,
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"power": np.nan,
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"n_samples": np.nan,
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"n_x": np.nan,
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"n_y": np.nan,
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"n_pairs": np.nan,
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"var_x": "",
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"var_y": "",
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}
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# Column types
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COLUMN_TYPES = {
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"test_method": str,
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"statistic_name": str,
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"statistic": float,
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"alternative": str,
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"n_samples": "Int64", # Nullable integer
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"n_x": "Int64",
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"n_y": "Int64",
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"n_pairs": "Int64",
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"var_x": str,
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"var_y": str,
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"pvalue": float,
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"pvalue_adjusted": float,
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"pstars": str,
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"alpha": float,
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"alpha_adjusted": float,
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"rejected": bool,
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"effect_size": float,
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"effect_size_metric": str,
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"effect_size_interpretation": str,
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"effect_size_secondary": float,
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"effect_size_secondary_metric": str,
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"effect_size_secondary_interpretation": str,
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"power": float,
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"H0": str,
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}
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def normalize_result(
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result: Dict[str, Any], fill_missing: bool = True
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) -> Dict[str, Any]:
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"""
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Normalize a test result dictionary to standard format.
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Parameters
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----------
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result : dict
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Result dictionary from a statistical test
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fill_missing : bool, default True
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Whether to fill missing standard columns with defaults
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Returns
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-------
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dict
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Normalized result dictionary
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Examples
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--------
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>>> result = {'pvalue': 0.023, 'statistic': 2.45}
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>>> normalized = normalize_result(result)
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>>> 'pstars' in normalized
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True
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"""
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normalized = result.copy()
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if fill_missing:
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for col, default in STANDARD_DEFAULTS.items():
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if col not in normalized:
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normalized[col] = default
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# Use adjusted pvalue if available, otherwise use raw pvalue
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pvalue_for_decision = normalized.get(
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"pvalue_adjusted", normalized.get("pvalue")
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)
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alpha_for_decision = normalized.get(
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"alpha_adjusted", normalized.get("alpha", 0.05)
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)
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# Compute pstars based on adjusted pvalue if available
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if "pstars" not in normalized and pvalue_for_decision is not None:
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from ._formatters import p2stars
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normalized["pstars"] = p2stars(pvalue_for_decision)
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# Compute rejected based on adjusted criteria if available
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if "rejected" not in normalized and pvalue_for_decision is not None:
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normalized["rejected"] = pvalue_for_decision < alpha_for_decision
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return normalized
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def to_dataframe(
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results: Union[Dict[str, Any], List[Dict[str, Any]]],
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normalize: bool = True,
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) -> pd.DataFrame:
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"""
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Convert test result(s) to DataFrame.
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Parameters
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----------
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results : dict or list of dict
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Single result dict or list of result dicts
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normalize : bool, default True
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Whether to normalize results before conversion
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Returns
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-------
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pd.DataFrame
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DataFrame with one row per result
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Examples
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--------
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>>> result = {'var_x': 'A', 'var_y': 'B', 'pvalue': 0.01}
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>>> df = to_dataframe(result)
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>>> df.shape
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(1, ...)
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>>> results = [result1, result2, result3]
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>>> df = to_dataframe(results)
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>>> len(df)
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3
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"""
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# Handle single dict
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if isinstance(results, dict):
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results = [results]
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# Normalize if requested
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if normalize:
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results = [normalize_result(r) for r in results]
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# Convert to DataFrame
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df = pd.DataFrame(results)
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return df
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def force_dataframe(
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results: Union[Dict[str, Any], List[Dict[str, Any]], pd.DataFrame],
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columns: Optional[List[str]] = None,
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fill_na: bool = True,
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defaults: Optional[Dict[str, Any]] = None,
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enforce_types: bool = True,
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) -> pd.DataFrame:
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"""
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Ensure DataFrame output with consistent columns and types.
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This is the main function for normalizing statistical test outputs
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to a standard DataFrame format.
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Parameters
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----------
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results : dict, list of dict, or DataFrame
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Test result(s) to normalize
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columns : list of str, optional
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Columns to include. If None, uses all columns in results.
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If specified, ensures these columns exist (adds with NaN if missing).
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fill_na : bool, default True
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Whether to fill NaN values with defaults
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defaults : dict, optional
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Custom default values. Merged with STANDARD_DEFAULTS.
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enforce_types : bool, default True
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Whether to enforce correct dtypes for standard columns
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Returns
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-------
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pd.DataFrame
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Normalized DataFrame with consistent format
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Examples
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--------
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>>> # Basic usage
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>>> results = [
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... {'var_x': 'A', 'pvalue': 0.01},
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... {'var_x': 'B', 'pvalue': 0.05, 'effect_size': 0.5},
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... ]
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>>> df = force_dataframe(results)
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>>> 'effect_size' in df.columns
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True
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>>> df['effect_size'].isna().sum()
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1
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>>> # Specify required columns
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>>> df = force_dataframe(
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... results,
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... columns=['var_x', 'pvalue', 'pstars', 'rejected']
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... )
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>>> set(df.columns) >= {'var_x', 'pvalue', 'pstars', 'rejected'}
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True
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>>> # Custom defaults
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>>> df = force_dataframe(
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... results,
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... defaults={'effect_size': 0.0, 'pstars': 'ns'}
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... )
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"""
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# Convert to DataFrame if needed
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if not isinstance(results, pd.DataFrame):
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df = to_dataframe(results, normalize=True)
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else:
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df = results.copy()
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# Merge custom defaults with standard defaults
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all_defaults = STANDARD_DEFAULTS.copy()
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if defaults:
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all_defaults.update(defaults)
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# Ensure specified columns exist
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if columns:
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for col in columns:
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if col not in df.columns:
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default_val = all_defaults.get(col, np.nan)
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df[col] = default_val
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# Fill NaN values with defaults
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if fill_na:
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for col, default_val in all_defaults.items():
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if col in df.columns:
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df[col] = df[col].fillna(default_val)
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# Enforce types for standard columns
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if enforce_types:
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for col, dtype in COLUMN_TYPES.items():
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if col in df.columns:
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try:
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df[col] = df[col].astype(dtype)
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except (ValueError, TypeError):
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# Skip if conversion fails
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pass
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return df
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def to_dict(df: pd.DataFrame, row: int = 0) -> Dict[str, Any]:
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"""
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Convert DataFrame row to dictionary.
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Parameters
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----------
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df : pd.DataFrame
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DataFrame containing test results
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row : int, default 0
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Row index to convert
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Returns
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-------
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dict
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Dictionary representation of the row
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Examples
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--------
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>>> df = pd.DataFrame({'pvalue': [0.01, 0.05], 'var_x': ['A', 'B']})
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>>> result = to_dict(df, row=1)
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>>> result['var_x']
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'B'
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"""
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return df.iloc[row].to_dict()
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def combine_results(
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results_list: List[Union[Dict, pd.DataFrame]], **kwargs
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) -> pd.DataFrame:
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"""
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Combine multiple test results into a single DataFrame.
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Parameters
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----------
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results_list : list
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List of result dicts or DataFrames
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**kwargs : dict
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Additional arguments passed to force_dataframe
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Returns
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-------
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pd.DataFrame
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Combined DataFrame with all results
|
|
335
|
+
|
|
336
|
+
Examples
|
|
337
|
+
--------
|
|
338
|
+
>>> r1 = test_ttest_ind(x1, y1, var_x='Control', var_y='Treatment')
|
|
339
|
+
>>> r2 = test_ttest_ind(x2, y2, var_x='Placebo', var_y='Drug')
|
|
340
|
+
>>> df = combine_results([r1, r2])
|
|
341
|
+
>>> len(df)
|
|
342
|
+
2
|
|
343
|
+
"""
|
|
344
|
+
# Convert all to DataFrames
|
|
345
|
+
dfs = []
|
|
346
|
+
for result in results_list:
|
|
347
|
+
if isinstance(result, dict):
|
|
348
|
+
df = to_dataframe(result)
|
|
349
|
+
elif isinstance(result, pd.DataFrame):
|
|
350
|
+
df = result
|
|
351
|
+
else:
|
|
352
|
+
raise TypeError(f"Expected dict or DataFrame, got {type(result)}")
|
|
353
|
+
dfs.append(df)
|
|
354
|
+
|
|
355
|
+
# Concatenate
|
|
356
|
+
combined = pd.concat(dfs, ignore_index=True)
|
|
357
|
+
|
|
358
|
+
# Normalize
|
|
359
|
+
return force_dataframe(combined, **kwargs)
|
|
360
|
+
|
|
361
|
+
|
|
362
|
+
def export_results(
|
|
363
|
+
results: Union[Dict[str, Any], List[Dict[str, Any]], pd.DataFrame],
|
|
364
|
+
path: str,
|
|
365
|
+
format: Optional[str] = None,
|
|
366
|
+
**kwargs,
|
|
367
|
+
) -> str:
|
|
368
|
+
"""
|
|
369
|
+
Export test results to various formats.
|
|
370
|
+
|
|
371
|
+
Parameters
|
|
372
|
+
----------
|
|
373
|
+
results : dict, list of dict, or DataFrame
|
|
374
|
+
Test results to export
|
|
375
|
+
path : str
|
|
376
|
+
Output file path
|
|
377
|
+
format : str, optional
|
|
378
|
+
Output format: 'csv', 'txt', 'json', 'xlsx', 'latex'
|
|
379
|
+
If None, inferred from path extension
|
|
380
|
+
**kwargs : dict
|
|
381
|
+
Additional arguments passed to export function
|
|
382
|
+
|
|
383
|
+
Returns
|
|
384
|
+
-------
|
|
385
|
+
str
|
|
386
|
+
Path to exported file
|
|
387
|
+
|
|
388
|
+
Examples
|
|
389
|
+
--------
|
|
390
|
+
>>> result = test_ttest_ind(x, y)
|
|
391
|
+
>>> export_results(result, 'results.csv')
|
|
392
|
+
'results.csv'
|
|
393
|
+
|
|
394
|
+
>>> # Multiple results
|
|
395
|
+
>>> results = [result1, result2, result3]
|
|
396
|
+
>>> export_results(results, 'results.xlsx')
|
|
397
|
+
'results.xlsx'
|
|
398
|
+
|
|
399
|
+
>>> # LaTeX table
|
|
400
|
+
>>> export_results(results, 'results.tex', format='latex')
|
|
401
|
+
'results.tex'
|
|
402
|
+
"""
|
|
403
|
+
import os
|
|
404
|
+
|
|
405
|
+
# Infer format from extension if not provided
|
|
406
|
+
if format is None:
|
|
407
|
+
_, ext = os.path.splitext(path)
|
|
408
|
+
format = ext.lstrip(".").lower()
|
|
409
|
+
|
|
410
|
+
# Convert to DataFrame
|
|
411
|
+
if not isinstance(results, pd.DataFrame):
|
|
412
|
+
df = force_dataframe(results)
|
|
413
|
+
else:
|
|
414
|
+
df = results
|
|
415
|
+
|
|
416
|
+
# Export based on format
|
|
417
|
+
if format == "csv":
|
|
418
|
+
df.to_csv(path, index=False, **kwargs)
|
|
419
|
+
# Add signature as comment
|
|
420
|
+
with open(path, "a") as f:
|
|
421
|
+
f.write(f"\n# {_get_scitex_signature('excel')}\n")
|
|
422
|
+
elif format in ["txt", "tsv"]:
|
|
423
|
+
df.to_csv(path, index=False, sep="\t", **kwargs)
|
|
424
|
+
# Add signature
|
|
425
|
+
with open(path, "a") as f:
|
|
426
|
+
f.write(f"\n{_get_scitex_signature('text')}")
|
|
427
|
+
elif format == "json":
|
|
428
|
+
# Export JSON with metadata
|
|
429
|
+
import json
|
|
430
|
+
|
|
431
|
+
data = {
|
|
432
|
+
"data": df.to_dict("records"),
|
|
433
|
+
"metadata": {
|
|
434
|
+
"generated_by": "SciTeX Stats",
|
|
435
|
+
"timestamp": _get_scitex_signature("excel").split(" | ")[1],
|
|
436
|
+
"description": "Professional Statistical Analysis Framework for Scientific Computing",
|
|
437
|
+
},
|
|
438
|
+
}
|
|
439
|
+
with open(path, "w") as f:
|
|
440
|
+
json.dump(data, f, indent=2, **kwargs)
|
|
441
|
+
elif format == "xlsx":
|
|
442
|
+
df.to_excel(path, index=False, **kwargs)
|
|
443
|
+
elif format in ["latex", "tex"]:
|
|
444
|
+
latex_str = df.to_latex(index=False, **kwargs)
|
|
445
|
+
# Add signature as LaTeX comment
|
|
446
|
+
latex_str += f"\n% {_get_scitex_signature('excel')}\n"
|
|
447
|
+
with open(path, "w") as f:
|
|
448
|
+
f.write(latex_str)
|
|
449
|
+
else:
|
|
450
|
+
raise ValueError(
|
|
451
|
+
f"Unsupported format: {format}. "
|
|
452
|
+
f"Use 'csv', 'txt', 'json', 'xlsx', or 'latex'"
|
|
453
|
+
)
|
|
454
|
+
|
|
455
|
+
return path
|
|
456
|
+
|
|
457
|
+
|
|
458
|
+
def export_excel_styled(
|
|
459
|
+
results: Union[Dict[str, Any], List[Dict[str, Any]], pd.DataFrame],
|
|
460
|
+
path: str,
|
|
461
|
+
**kwargs,
|
|
462
|
+
) -> str:
|
|
463
|
+
""" """
|
|
464
|
+
pass
|
|
465
|
+
|
|
466
|
+
|
|
467
|
+
def export_report(
|
|
468
|
+
results: Union[Dict[str, Any], List[Dict[str, Any]], pd.DataFrame],
|
|
469
|
+
path: str,
|
|
470
|
+
title: str = "Statistical Analysis Report",
|
|
471
|
+
include_summary: bool = True,
|
|
472
|
+
**kwargs,
|
|
473
|
+
) -> str:
|
|
474
|
+
"""
|
|
475
|
+
Export formatted report with colored highlights.
|
|
476
|
+
|
|
477
|
+
Parameters
|
|
478
|
+
----------
|
|
479
|
+
results : dict, list of dict, or DataFrame
|
|
480
|
+
Test results to export
|
|
481
|
+
path : str
|
|
482
|
+
Output file path (supports .html, .md, .txt)
|
|
483
|
+
title : str, default "Statistical Analysis Report"
|
|
484
|
+
Report title
|
|
485
|
+
include_summary : bool, default True
|
|
486
|
+
Whether to include summary statistics
|
|
487
|
+
**kwargs : dict
|
|
488
|
+
Additional arguments
|
|
489
|
+
|
|
490
|
+
Returns
|
|
491
|
+
-------
|
|
492
|
+
str
|
|
493
|
+
Path to exported file
|
|
494
|
+
|
|
495
|
+
Notes
|
|
496
|
+
-----
|
|
497
|
+
Report includes:
|
|
498
|
+
- Summary statistics (counts of significant results)
|
|
499
|
+
- Full results table with color-coded significance
|
|
500
|
+
- Automatic detection of output format from extension
|
|
501
|
+
|
|
502
|
+
Examples
|
|
503
|
+
--------
|
|
504
|
+
>>> results = [result1, result2, result3]
|
|
505
|
+
>>> export_report(results, 'report.html', title='My Analysis')
|
|
506
|
+
'report.html'
|
|
507
|
+
|
|
508
|
+
>>> export_report(results, 'report.md') # Markdown format
|
|
509
|
+
'report.md'
|
|
510
|
+
"""
|
|
511
|
+
import os
|
|
512
|
+
|
|
513
|
+
# Convert to DataFrame
|
|
514
|
+
if not isinstance(results, pd.DataFrame):
|
|
515
|
+
df = force_dataframe(results)
|
|
516
|
+
else:
|
|
517
|
+
df = results
|
|
518
|
+
|
|
519
|
+
# Detect format
|
|
520
|
+
_, ext = os.path.splitext(path)
|
|
521
|
+
format_type = ext.lstrip(".").lower()
|
|
522
|
+
|
|
523
|
+
# Generate report based on format
|
|
524
|
+
if format_type == "html":
|
|
525
|
+
return _export_report_html(df, path, title, include_summary)
|
|
526
|
+
elif format_type == "md":
|
|
527
|
+
return _export_report_markdown(df, path, title, include_summary)
|
|
528
|
+
else: # txt or other
|
|
529
|
+
return _export_report_text(df, path, title, include_summary)
|
|
530
|
+
|
|
531
|
+
|
|
532
|
+
def _get_scitex_signature(format_type="html"):
|
|
533
|
+
"""Generate SciTeX Stats signature for branding."""
|
|
534
|
+
import datetime
|
|
535
|
+
|
|
536
|
+
timestamp = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
|
|
537
|
+
|
|
538
|
+
if format_type == "html":
|
|
539
|
+
return f"""
|
|
540
|
+
<div style="margin-top: 30px; padding-top: 20px; border-top: 2px solid #ddd; text-align: center; color: #666; font-size: 12px;">
|
|
541
|
+
<p>Generated by <strong style="color: #4CAF50;">SciTeX Stats</strong> | {timestamp}</p>
|
|
542
|
+
<p style="font-size: 10px;">Professional Statistical Analysis Framework for Scientific Computing</p>
|
|
543
|
+
</div>
|
|
544
|
+
"""
|
|
545
|
+
elif format_type == "markdown":
|
|
546
|
+
return f"\n\n---\n\n*Generated by **SciTeX Stats** | {timestamp}*\n\n*Professional Statistical Analysis Framework for Scientific Computing*\n"
|
|
547
|
+
elif format_type == "text":
|
|
548
|
+
return f"\n\n{'='*80}\nGenerated by SciTeX Stats | {timestamp}\nProfessional Statistical Analysis Framework for Scientific Computing\n{'='*80}\n"
|
|
549
|
+
else:
|
|
550
|
+
return f"Generated by SciTeX Stats | {timestamp}"
|
|
551
|
+
|
|
552
|
+
|
|
553
|
+
def _export_report_html(df, path, title, include_summary):
|
|
554
|
+
"""Generate HTML report with styling."""
|
|
555
|
+
# Generate summary
|
|
556
|
+
summary_html = ""
|
|
557
|
+
if include_summary and "pvalue" in df.columns:
|
|
558
|
+
n_total = len(df)
|
|
559
|
+
n_sig_001 = (df["pvalue"] < 0.001).sum()
|
|
560
|
+
n_sig_01 = ((df["pvalue"] >= 0.001) & (df["pvalue"] < 0.01)).sum()
|
|
561
|
+
n_sig_05 = ((df["pvalue"] >= 0.01) & (df["pvalue"] < 0.05)).sum()
|
|
562
|
+
n_ns = (df["pvalue"] >= 0.05).sum()
|
|
563
|
+
|
|
564
|
+
summary_html = f"""
|
|
565
|
+
<div class="summary">
|
|
566
|
+
<h2>Summary</h2>
|
|
567
|
+
<ul>
|
|
568
|
+
<li>Total tests: {n_total}</li>
|
|
569
|
+
<li style="color: #FF6B6B; font-weight: bold;">p < 0.001 (***): {n_sig_001}</li>
|
|
570
|
+
<li style="color: #FFA500; font-weight: bold;">p < 0.01 (**): {n_sig_01}</li>
|
|
571
|
+
<li style="color: #FFE66D; font-weight: bold;">p < 0.05 (*): {n_sig_05}</li>
|
|
572
|
+
<li style="color: #999;">p >= 0.05 (ns): {n_ns}</li>
|
|
573
|
+
</ul>
|
|
574
|
+
</div>
|
|
575
|
+
"""
|
|
576
|
+
|
|
577
|
+
# Style function for DataFrame
|
|
578
|
+
def style_pvalue(val):
|
|
579
|
+
if pd.isna(val):
|
|
580
|
+
return ""
|
|
581
|
+
if val < 0.001:
|
|
582
|
+
return (
|
|
583
|
+
"background-color: #FF6B6B; font-weight: bold; color: white;"
|
|
584
|
+
)
|
|
585
|
+
elif val < 0.01:
|
|
586
|
+
return (
|
|
587
|
+
"background-color: #FFA500; font-weight: bold; color: white;"
|
|
588
|
+
)
|
|
589
|
+
elif val < 0.05:
|
|
590
|
+
return "background-color: #FFE66D; font-weight: bold;"
|
|
591
|
+
else:
|
|
592
|
+
return "background-color: #E8E8E8;"
|
|
593
|
+
|
|
594
|
+
# Apply styling
|
|
595
|
+
if "pvalue" in df.columns:
|
|
596
|
+
styled = df.style.applymap(style_pvalue, subset=["pvalue"])
|
|
597
|
+
else:
|
|
598
|
+
styled = df.style
|
|
599
|
+
|
|
600
|
+
# Generate HTML
|
|
601
|
+
table_html = styled.to_html()
|
|
602
|
+
|
|
603
|
+
html_content = f"""
|
|
604
|
+
<!DOCTYPE html>
|
|
605
|
+
<html>
|
|
606
|
+
<head>
|
|
607
|
+
<title>{title}</title>
|
|
608
|
+
<style>
|
|
609
|
+
body {{
|
|
610
|
+
font-family: Arial, sans-serif;
|
|
611
|
+
margin: 20px;
|
|
612
|
+
background-color: #f5f5f5;
|
|
613
|
+
}}
|
|
614
|
+
h1 {{
|
|
615
|
+
color: #333;
|
|
616
|
+
border-bottom: 3px solid #4CAF50;
|
|
617
|
+
padding-bottom: 10px;
|
|
618
|
+
}}
|
|
619
|
+
.summary {{
|
|
620
|
+
background-color: white;
|
|
621
|
+
padding: 15px;
|
|
622
|
+
border-radius: 5px;
|
|
623
|
+
margin-bottom: 20px;
|
|
624
|
+
box-shadow: 0 2px 4px rgba(0,0,0,0.1);
|
|
625
|
+
}}
|
|
626
|
+
table {{
|
|
627
|
+
border-collapse: collapse;
|
|
628
|
+
width: 100%;
|
|
629
|
+
background-color: white;
|
|
630
|
+
box-shadow: 0 2px 4px rgba(0,0,0,0.1);
|
|
631
|
+
}}
|
|
632
|
+
th {{
|
|
633
|
+
background-color: #4CAF50;
|
|
634
|
+
color: white;
|
|
635
|
+
padding: 12px;
|
|
636
|
+
text-align: left;
|
|
637
|
+
}}
|
|
638
|
+
td {{
|
|
639
|
+
padding: 10px;
|
|
640
|
+
border-bottom: 1px solid #ddd;
|
|
641
|
+
}}
|
|
642
|
+
tr:hover {{
|
|
643
|
+
background-color: #f5f5f5;
|
|
644
|
+
}}
|
|
645
|
+
</style>
|
|
646
|
+
</head>
|
|
647
|
+
<body>
|
|
648
|
+
<h1>{title}</h1>
|
|
649
|
+
{summary_html}
|
|
650
|
+
<h2>Results</h2>
|
|
651
|
+
{table_html}
|
|
652
|
+
{_get_scitex_signature('html')}
|
|
653
|
+
</body>
|
|
654
|
+
</html>
|
|
655
|
+
"""
|
|
656
|
+
|
|
657
|
+
with open(path, "w") as f:
|
|
658
|
+
f.write(html_content)
|
|
659
|
+
|
|
660
|
+
return path
|
|
661
|
+
|
|
662
|
+
|
|
663
|
+
def _export_report_markdown(df, path, title, include_summary):
|
|
664
|
+
"""Generate Markdown report."""
|
|
665
|
+
lines = [f"# {title}\n"]
|
|
666
|
+
|
|
667
|
+
# Summary
|
|
668
|
+
if include_summary and "pvalue" in df.columns:
|
|
669
|
+
n_total = len(df)
|
|
670
|
+
n_sig = (df["pvalue"] < 0.05).sum()
|
|
671
|
+
n_ns = (df["pvalue"] >= 0.05).sum()
|
|
672
|
+
|
|
673
|
+
lines.append("## Summary\n")
|
|
674
|
+
lines.append(f"- Total tests: {n_total}")
|
|
675
|
+
lines.append(f"- Significant (p < 0.05): {n_sig}")
|
|
676
|
+
lines.append(f"- Non-significant (p >= 0.05): {n_ns}\n")
|
|
677
|
+
|
|
678
|
+
# Table
|
|
679
|
+
lines.append("## Results\n")
|
|
680
|
+
lines.append(df.to_markdown(index=False))
|
|
681
|
+
|
|
682
|
+
# Add signature
|
|
683
|
+
lines.append(_get_scitex_signature("markdown"))
|
|
684
|
+
|
|
685
|
+
with open(path, "w") as f:
|
|
686
|
+
f.write("\n".join(lines))
|
|
687
|
+
|
|
688
|
+
return path
|
|
689
|
+
|
|
690
|
+
|
|
691
|
+
def _export_report_text(df, path, title, include_summary):
|
|
692
|
+
"""Generate plain text report."""
|
|
693
|
+
lines = [title, "=" * len(title), ""]
|
|
694
|
+
|
|
695
|
+
# Summary
|
|
696
|
+
if include_summary and "pvalue" in df.columns:
|
|
697
|
+
n_total = len(df)
|
|
698
|
+
n_sig = (df["pvalue"] < 0.05).sum()
|
|
699
|
+
|
|
700
|
+
lines.append("SUMMARY")
|
|
701
|
+
lines.append(f"Total tests: {n_total}")
|
|
702
|
+
lines.append(f"Significant: {n_sig}")
|
|
703
|
+
lines.append("")
|
|
704
|
+
|
|
705
|
+
# Table
|
|
706
|
+
lines.append("RESULTS")
|
|
707
|
+
lines.append(df.to_string(index=False))
|
|
708
|
+
|
|
709
|
+
# Add signature
|
|
710
|
+
lines.append(_get_scitex_signature("text"))
|
|
711
|
+
|
|
712
|
+
with open(path, "w") as f:
|
|
713
|
+
f.write("\n".join(lines))
|
|
714
|
+
|
|
715
|
+
return path
|
|
716
|
+
|
|
717
|
+
|
|
718
|
+
def export_summary(
|
|
719
|
+
results: Union[Dict[str, Any], List[Dict[str, Any]], pd.DataFrame],
|
|
720
|
+
path: str,
|
|
721
|
+
columns: Optional[List[str]] = None,
|
|
722
|
+
format: Optional[str] = None,
|
|
723
|
+
**kwargs,
|
|
724
|
+
) -> str:
|
|
725
|
+
"""
|
|
726
|
+
Export summary of test results (selected columns only).
|
|
727
|
+
|
|
728
|
+
Parameters
|
|
729
|
+
----------
|
|
730
|
+
results : dict, list of dict, or DataFrame
|
|
731
|
+
Test results to export
|
|
732
|
+
path : str
|
|
733
|
+
Output file path
|
|
734
|
+
columns : list of str, optional
|
|
735
|
+
Columns to include. Default: key columns for reporting
|
|
736
|
+
format : str, optional
|
|
737
|
+
Output format (inferred from extension if None)
|
|
738
|
+
**kwargs : dict
|
|
739
|
+
Additional arguments passed to export function
|
|
740
|
+
|
|
741
|
+
Returns
|
|
742
|
+
-------
|
|
743
|
+
str
|
|
744
|
+
Path to exported file
|
|
745
|
+
|
|
746
|
+
Examples
|
|
747
|
+
--------
|
|
748
|
+
>>> # Export only key columns
|
|
749
|
+
>>> export_summary(results, 'summary.csv')
|
|
750
|
+
'summary.csv'
|
|
751
|
+
|
|
752
|
+
>>> # Custom columns
|
|
753
|
+
>>> export_summary(
|
|
754
|
+
... results,
|
|
755
|
+
... 'summary.xlsx',
|
|
756
|
+
... columns=['var_x', 'var_y', 'pvalue', 'effect_size']
|
|
757
|
+
... )
|
|
758
|
+
'summary.xlsx'
|
|
759
|
+
"""
|
|
760
|
+
# Default summary columns
|
|
761
|
+
if columns is None:
|
|
762
|
+
columns = [
|
|
763
|
+
"test_method",
|
|
764
|
+
"var_x",
|
|
765
|
+
"var_y",
|
|
766
|
+
"n_x",
|
|
767
|
+
"n_y",
|
|
768
|
+
"statistic",
|
|
769
|
+
"pvalue",
|
|
770
|
+
"pstars",
|
|
771
|
+
"rejected",
|
|
772
|
+
"effect_size",
|
|
773
|
+
"effect_size_metric",
|
|
774
|
+
"effect_size_interpretation",
|
|
775
|
+
]
|
|
776
|
+
|
|
777
|
+
# Convert to DataFrame
|
|
778
|
+
if not isinstance(results, pd.DataFrame):
|
|
779
|
+
df = force_dataframe(results)
|
|
780
|
+
else:
|
|
781
|
+
df = results
|
|
782
|
+
|
|
783
|
+
# Select columns (only those that exist)
|
|
784
|
+
available_cols = [col for col in columns if col in df.columns]
|
|
785
|
+
df_summary = df[available_cols]
|
|
786
|
+
|
|
787
|
+
# Export
|
|
788
|
+
return export_results(df_summary, path, format=format, **kwargs)
|
|
789
|
+
|
|
790
|
+
|
|
791
|
+
def convert_results(
|
|
792
|
+
results: Union[Dict[str, Any], List[Dict[str, Any]], pd.DataFrame],
|
|
793
|
+
return_as: Literal[
|
|
794
|
+
"dict",
|
|
795
|
+
"dataframe",
|
|
796
|
+
"markdown",
|
|
797
|
+
"json",
|
|
798
|
+
"latex",
|
|
799
|
+
"html",
|
|
800
|
+
"text",
|
|
801
|
+
] = "dict",
|
|
802
|
+
**kwargs,
|
|
803
|
+
) -> Union[dict, List[dict], pd.DataFrame, str]:
|
|
804
|
+
"""
|
|
805
|
+
Convert statistical test results to specified format.
|
|
806
|
+
|
|
807
|
+
This is a pure format converter - does NOT save files.
|
|
808
|
+
For saving, use scitex.io.save() after conversion.
|
|
809
|
+
|
|
810
|
+
Parameters
|
|
811
|
+
----------
|
|
812
|
+
results : dict, list of dict, or DataFrame
|
|
813
|
+
Test results to convert
|
|
814
|
+
return_as : str, default 'dict'
|
|
815
|
+
Output format:
|
|
816
|
+
- 'dict': Python dictionary (single result) or list of dicts (multiple)
|
|
817
|
+
- 'dataframe': pandas DataFrame
|
|
818
|
+
- 'markdown': Markdown table string
|
|
819
|
+
- 'json': JSON string
|
|
820
|
+
- 'latex': LaTeX table string
|
|
821
|
+
- 'html': HTML table string
|
|
822
|
+
- 'text': Plain text table string
|
|
823
|
+
**kwargs : dict
|
|
824
|
+
Additional arguments passed to format functions
|
|
825
|
+
|
|
826
|
+
Returns
|
|
827
|
+
-------
|
|
828
|
+
output : dict, list, DataFrame, or str
|
|
829
|
+
Converted results in requested format
|
|
830
|
+
|
|
831
|
+
Notes
|
|
832
|
+
-----
|
|
833
|
+
This function only handles format conversion. To save results to files,
|
|
834
|
+
convert to DataFrame first, then use scitex.io.save():
|
|
835
|
+
|
|
836
|
+
>>> df = convert_results(results, return_as='dataframe')
|
|
837
|
+
>>> stx.io.save(df, 'results.xlsx')
|
|
838
|
+
|
|
839
|
+
Examples
|
|
840
|
+
--------
|
|
841
|
+
>>> result = {'pvalue': 0.01, 'var_x': 'A', 'var_y': 'B'}
|
|
842
|
+
|
|
843
|
+
# Convert to different formats
|
|
844
|
+
>>> convert_results(result, return_as='dict')
|
|
845
|
+
{'pvalue': 0.01, 'var_x': 'A', 'var_y': 'B'}
|
|
846
|
+
|
|
847
|
+
>>> df = convert_results(result, return_as='dataframe')
|
|
848
|
+
# Returns DataFrame
|
|
849
|
+
|
|
850
|
+
>>> convert_results(result, return_as='markdown')
|
|
851
|
+
'| var_x | var_y | pvalue |\\n|-------|-------|--------|...'
|
|
852
|
+
|
|
853
|
+
>>> latex_str = convert_results(result, return_as='latex')
|
|
854
|
+
|
|
855
|
+
# To save to file, use stx.io.save
|
|
856
|
+
>>> import scitex as stx
|
|
857
|
+
>>> df = convert_results(result, return_as='dataframe')
|
|
858
|
+
>>> stx.io.save(df, 'results.xlsx') # Uses stx.io.save for file operations
|
|
859
|
+
"""
|
|
860
|
+
# Handle each format - pure conversion, no file I/O
|
|
861
|
+
if return_as == "dict":
|
|
862
|
+
if isinstance(results, dict):
|
|
863
|
+
return results
|
|
864
|
+
elif isinstance(results, list):
|
|
865
|
+
return results
|
|
866
|
+
elif isinstance(results, pd.DataFrame):
|
|
867
|
+
return (
|
|
868
|
+
results.to_dict("records")
|
|
869
|
+
if len(results) > 1
|
|
870
|
+
else to_dict(results, row=0)
|
|
871
|
+
)
|
|
872
|
+
|
|
873
|
+
elif return_as == "dataframe":
|
|
874
|
+
return force_dataframe(results)
|
|
875
|
+
|
|
876
|
+
elif return_as == "markdown":
|
|
877
|
+
df_out = force_dataframe(results)
|
|
878
|
+
return df_out.to_markdown(index=False, **kwargs)
|
|
879
|
+
|
|
880
|
+
elif return_as == "json":
|
|
881
|
+
df_out = force_dataframe(results)
|
|
882
|
+
return df_out.to_json(orient="records", indent=2, **kwargs)
|
|
883
|
+
|
|
884
|
+
elif return_as == "latex":
|
|
885
|
+
df_out = force_dataframe(results)
|
|
886
|
+
return df_out.to_latex(index=False, **kwargs)
|
|
887
|
+
|
|
888
|
+
elif return_as == "html":
|
|
889
|
+
df_out = force_dataframe(results)
|
|
890
|
+
return df_out.to_html(index=False, **kwargs)
|
|
891
|
+
|
|
892
|
+
elif return_as == "text":
|
|
893
|
+
df_out = force_dataframe(results)
|
|
894
|
+
return df_out.to_string(index=False, **kwargs)
|
|
895
|
+
|
|
896
|
+
elif return_as == "csv":
|
|
897
|
+
df_out = force_dataframe(results)
|
|
898
|
+
return df_out.to_csv(index=False, **kwargs)
|
|
899
|
+
|
|
900
|
+
else:
|
|
901
|
+
raise ValueError(
|
|
902
|
+
f"Unknown return_as format: {return_as}. "
|
|
903
|
+
f"Use 'dict', 'dataframe', 'markdown', 'json', 'latex', 'html', or 'text'"
|
|
904
|
+
)
|
|
905
|
+
|
|
906
|
+
|
|
907
|
+
# Convenience alias
|
|
908
|
+
as_dataframe = force_dataframe
|
|
909
|
+
|
|
910
|
+
__all__ = [
|
|
911
|
+
"normalize_result",
|
|
912
|
+
"to_dataframe",
|
|
913
|
+
"force_dataframe",
|
|
914
|
+
"to_dict",
|
|
915
|
+
"combine_results",
|
|
916
|
+
"convert_results",
|
|
917
|
+
"export_results",
|
|
918
|
+
"export_summary",
|
|
919
|
+
"export_excel_styled",
|
|
920
|
+
"export_report",
|
|
921
|
+
"as_dataframe",
|
|
922
|
+
"STANDARD_COLUMNS",
|
|
923
|
+
"STANDARD_DEFAULTS",
|
|
924
|
+
"COLUMN_TYPES",
|
|
925
|
+
]
|
|
926
|
+
|
|
927
|
+
# EOF
|