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
- scitex/plt/_subplots/_AxisWrapperMixins/__init__.py +1 -0
- scitex/plt/_subplots/_FigWrapper.py +62 -6
- scitex/plt/_subplots/_export_as_csv.py +43 -27
- scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +5 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +81 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_bar.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_barh.py +20 -5
- scitex/plt/_subplots/_export_as_csv_formatters/_format_boxplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_contour.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_errorbar.py +35 -18
- scitex/plt/_subplots/_export_as_csv_formatters/_format_eventplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_fill.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_fill_between.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_hist.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow2d.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot.py +15 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_box.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_conf_mat.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_ecdf.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_fillv.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_heatmap.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_image.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_joyplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_kde.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_line.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_mean_ci.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_mean_std.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_median_iqr.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_raster.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_rectangle.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter.py +35 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_scatter_hist.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_shaded_line.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_violin.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_scatter.py +6 -4
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_barplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_boxplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_heatmap.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_histplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_jointplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_kdeplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_lineplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_pairplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_scatterplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_stripplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_swarmplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_sns_violinplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_text.py +60 -0
- scitex/plt/_subplots/_export_as_csv_formatters/_format_violin.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/_format_violinplot.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters/test_formatters.py +1 -3
- scitex/plt/_subplots/_export_as_csv_formatters.py +56 -59
- scitex/plt/ax/_style/_hide_spines.py +1 -3
- scitex/plt/ax/_style/_rotate_labels.py +180 -76
- scitex/plt/ax/_style/_rotate_labels_v01.py +248 -0
- scitex/plt/ax/_style/_set_meta.py +11 -4
- scitex/plt/ax/_style/_set_supxyt.py +3 -3
- scitex/plt/ax/_style/_set_xyt.py +3 -3
- scitex/plt/ax/_style/_share_axes.py +2 -2
- scitex/plt/color/__init__.py +4 -4
- scitex/plt/color/{_get_colors_from_cmap.py → _get_colors_from_conf_matap.py} +7 -7
- scitex/plt/utils/_configure_mpl.py +99 -86
- scitex/plt/utils/_histogram_utils.py +1 -3
- scitex/plt/utils/_is_valid_axis.py +1 -3
- scitex/plt/utils/_scitex_config.py +1 -0
- scitex/repro/__init__.py +75 -0
- scitex/{reproduce → repro}/_gen_ID.py +1 -1
- scitex/{reproduce → repro}/_gen_timestamp.py +1 -1
- scitex/repro_rng/_RandomStateManager.py +590 -0
- scitex/repro_rng/_RandomStateManager_v01-no-verbose-options.py +414 -0
- scitex/repro_rng/__init__.py +39 -0
- scitex/reproduce/__init__.py +25 -13
- scitex/reproduce/_hash_array.py +22 -0
- scitex/resource/_get_processor_usages.py +4 -4
- scitex/resource/_get_specs.py +2 -2
- scitex/resource/_log_processor_usages.py +2 -2
- scitex/rng/_RandomStateManager.py +590 -0
- scitex/rng/_RandomStateManager_v01-no-verbose-options.py +414 -0
- scitex/rng/__init__.py +39 -0
- scitex/scholar/__init__.py +309 -19
- scitex/scholar/__main__.py +319 -0
- scitex/scholar/auth/ScholarAuthManager.py +308 -0
- scitex/scholar/auth/__init__.py +12 -0
- scitex/scholar/auth/core/AuthenticationGateway.py +473 -0
- scitex/scholar/auth/core/BrowserAuthenticator.py +386 -0
- scitex/scholar/auth/core/StrategyResolver.py +309 -0
- scitex/scholar/auth/core/__init__.py +16 -0
- scitex/scholar/auth/gateway/_OpenURLLinkFinder.py +120 -0
- scitex/scholar/auth/gateway/_OpenURLResolver.py +209 -0
- scitex/scholar/auth/gateway/__init__.py +38 -0
- scitex/scholar/auth/gateway/_resolve_functions.py +101 -0
- scitex/scholar/auth/providers/BaseAuthenticator.py +166 -0
- scitex/scholar/auth/providers/EZProxyAuthenticator.py +484 -0
- scitex/scholar/auth/providers/OpenAthensAuthenticator.py +619 -0
- scitex/scholar/auth/providers/ShibbolethAuthenticator.py +686 -0
- scitex/scholar/auth/providers/__init__.py +18 -0
- scitex/scholar/auth/session/AuthCacheManager.py +189 -0
- scitex/scholar/auth/session/SessionManager.py +159 -0
- scitex/scholar/auth/session/__init__.py +11 -0
- scitex/scholar/auth/sso/BaseSSOAutomator.py +373 -0
- scitex/scholar/auth/sso/OpenAthensSSOAutomator.py +378 -0
- scitex/scholar/auth/sso/SSOAutomator.py +180 -0
- scitex/scholar/auth/sso/UniversityOfMelbourneSSOAutomator.py +380 -0
- scitex/scholar/auth/sso/__init__.py +15 -0
- scitex/scholar/browser/ScholarBrowserManager.py +705 -0
- scitex/scholar/browser/__init__.py +38 -0
- scitex/scholar/browser/utils/__init__.py +13 -0
- scitex/scholar/browser/utils/click_and_wait.py +205 -0
- scitex/scholar/browser/utils/close_unwanted_pages.py +140 -0
- scitex/scholar/browser/utils/wait_redirects.py +732 -0
- scitex/scholar/config/PublisherRules.py +132 -0
- scitex/scholar/config/ScholarConfig.py +126 -0
- scitex/scholar/config/__init__.py +17 -0
- scitex/scholar/core/Paper.py +627 -0
- scitex/scholar/core/Papers.py +722 -0
- scitex/scholar/core/Scholar.py +1975 -0
- scitex/scholar/core/__init__.py +9 -0
- scitex/scholar/impact_factor/ImpactFactorEngine.py +204 -0
- scitex/scholar/impact_factor/__init__.py +20 -0
- scitex/scholar/impact_factor/estimation/ImpactFactorEstimationEngine.py +0 -0
- scitex/scholar/impact_factor/estimation/__init__.py +40 -0
- scitex/scholar/impact_factor/estimation/build_database.py +0 -0
- scitex/scholar/impact_factor/estimation/core/__init__.py +28 -0
- scitex/scholar/impact_factor/estimation/core/cache_manager.py +523 -0
- scitex/scholar/impact_factor/estimation/core/calculator.py +355 -0
- scitex/scholar/impact_factor/estimation/core/journal_matcher.py +428 -0
- scitex/scholar/integration/__init__.py +59 -0
- scitex/scholar/integration/base.py +502 -0
- scitex/scholar/integration/mendeley/__init__.py +22 -0
- scitex/scholar/integration/mendeley/exporter.py +166 -0
- scitex/scholar/integration/mendeley/importer.py +236 -0
- scitex/scholar/integration/mendeley/linker.py +79 -0
- scitex/scholar/integration/mendeley/mapper.py +212 -0
- scitex/scholar/integration/zotero/__init__.py +27 -0
- scitex/scholar/integration/zotero/__main__.py +264 -0
- scitex/scholar/integration/zotero/exporter.py +351 -0
- scitex/scholar/integration/zotero/importer.py +372 -0
- scitex/scholar/integration/zotero/linker.py +415 -0
- scitex/scholar/integration/zotero/mapper.py +286 -0
- scitex/scholar/metadata_engines/ScholarEngine.py +588 -0
- scitex/scholar/metadata_engines/__init__.py +21 -0
- scitex/scholar/metadata_engines/individual/ArXivEngine.py +397 -0
- scitex/scholar/metadata_engines/individual/CrossRefEngine.py +274 -0
- scitex/scholar/metadata_engines/individual/CrossRefLocalEngine.py +263 -0
- scitex/scholar/metadata_engines/individual/OpenAlexEngine.py +350 -0
- scitex/scholar/metadata_engines/individual/PubMedEngine.py +329 -0
- scitex/scholar/metadata_engines/individual/SemanticScholarEngine.py +438 -0
- scitex/scholar/metadata_engines/individual/URLDOIEngine.py +410 -0
- scitex/scholar/metadata_engines/individual/_BaseDOIEngine.py +487 -0
- scitex/scholar/metadata_engines/individual/__init__.py +7 -0
- scitex/scholar/metadata_engines/utils/_PubMedConverter.py +469 -0
- scitex/scholar/metadata_engines/utils/_URLDOIExtractor.py +283 -0
- scitex/scholar/metadata_engines/utils/__init__.py +30 -0
- scitex/scholar/metadata_engines/utils/_metadata2bibtex.py +103 -0
- scitex/scholar/metadata_engines/utils/_standardize_metadata.py +376 -0
- scitex/scholar/pdf_download/ScholarPDFDownloader.py +579 -0
- scitex/scholar/pdf_download/__init__.py +5 -0
- scitex/scholar/pdf_download/strategies/__init__.py +38 -0
- scitex/scholar/pdf_download/strategies/chrome_pdf_viewer.py +376 -0
- scitex/scholar/pdf_download/strategies/direct_download.py +131 -0
- scitex/scholar/pdf_download/strategies/manual_download_fallback.py +167 -0
- scitex/scholar/pdf_download/strategies/manual_download_utils.py +996 -0
- scitex/scholar/pdf_download/strategies/response_body.py +207 -0
- scitex/scholar/pipelines/ScholarPipelineBibTeX.py +364 -0
- scitex/scholar/pipelines/ScholarPipelineParallel.py +478 -0
- scitex/scholar/pipelines/ScholarPipelineSingle.py +767 -0
- scitex/scholar/pipelines/__init__.py +49 -0
- scitex/scholar/storage/BibTeXHandler.py +1018 -0
- scitex/scholar/storage/PaperIO.py +468 -0
- scitex/scholar/storage/ScholarLibrary.py +182 -0
- scitex/scholar/storage/_DeduplicationManager.py +548 -0
- scitex/scholar/storage/_LibraryCacheManager.py +724 -0
- scitex/scholar/storage/_LibraryManager.py +1835 -0
- scitex/scholar/storage/__init__.py +28 -0
- scitex/scholar/url_finder/ScholarURLFinder.py +379 -0
- scitex/scholar/url_finder/__init__.py +7 -0
- scitex/scholar/url_finder/strategies/__init__.py +33 -0
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_direct_links.py +261 -0
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_dropdown.py +67 -0
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_href.py +204 -0
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_navigation.py +256 -0
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_publisher_patterns.py +165 -0
- scitex/scholar/url_finder/strategies/find_pdf_urls_by_zotero_translators.py +163 -0
- scitex/scholar/url_finder/strategies/find_supplementary_urls_by_href.py +70 -0
- scitex/scholar/utils/__init__.py +22 -0
- scitex/scholar/utils/bibtex/__init__.py +9 -0
- scitex/scholar/utils/bibtex/_parse_bibtex.py +71 -0
- scitex/scholar/utils/cleanup/__init__.py +8 -0
- scitex/scholar/utils/cleanup/_cleanup_scholar_processes.py +96 -0
- scitex/scholar/utils/cleanup/cleanup_old_extractions.py +117 -0
- scitex/scholar/utils/text/_TextNormalizer.py +407 -0
- scitex/scholar/utils/text/__init__.py +9 -0
- scitex/scholar/zotero/__init__.py +38 -0
- scitex/session/__init__.py +51 -0
- scitex/session/_lifecycle.py +736 -0
- scitex/session/_manager.py +102 -0
- scitex/session/template.py +122 -0
- scitex/stats/__init__.py +30 -26
- scitex/stats/correct/__init__.py +21 -0
- scitex/stats/correct/_correct_bonferroni.py +551 -0
- scitex/stats/correct/_correct_fdr.py +634 -0
- scitex/stats/correct/_correct_holm.py +548 -0
- scitex/stats/correct/_correct_sidak.py +499 -0
- scitex/stats/descriptive/__init__.py +85 -0
- scitex/stats/descriptive/_circular.py +540 -0
- scitex/stats/descriptive/_describe.py +219 -0
- scitex/stats/descriptive/_nan.py +518 -0
- scitex/stats/descriptive/_real.py +189 -0
- scitex/stats/effect_sizes/__init__.py +41 -0
- scitex/stats/effect_sizes/_cliffs_delta.py +325 -0
- scitex/stats/effect_sizes/_cohens_d.py +342 -0
- scitex/stats/effect_sizes/_epsilon_squared.py +315 -0
- scitex/stats/effect_sizes/_eta_squared.py +302 -0
- scitex/stats/effect_sizes/_prob_superiority.py +296 -0
- scitex/stats/posthoc/__init__.py +19 -0
- scitex/stats/posthoc/_dunnett.py +463 -0
- scitex/stats/posthoc/_games_howell.py +383 -0
- scitex/stats/posthoc/_tukey_hsd.py +367 -0
- scitex/stats/power/__init__.py +19 -0
- scitex/stats/power/_power.py +433 -0
- scitex/stats/template.py +119 -0
- scitex/stats/utils/__init__.py +62 -0
- scitex/stats/utils/_effect_size.py +985 -0
- scitex/stats/utils/_formatters.py +270 -0
- scitex/stats/utils/_normalizers.py +927 -0
- scitex/stats/utils/_power.py +433 -0
- scitex/stats_v01/_EffectSizeCalculator.py +488 -0
- scitex/stats_v01/_StatisticalValidator.py +411 -0
- scitex/stats_v01/__init__.py +60 -0
- scitex/stats_v01/_additional_tests.py +415 -0
- scitex/{stats → stats_v01}/_p2stars.py +19 -5
- scitex/stats_v01/_two_sample_tests.py +141 -0
- scitex/stats_v01/desc/__init__.py +83 -0
- scitex/stats_v01/desc/_circular.py +540 -0
- scitex/stats_v01/desc/_describe.py +219 -0
- scitex/stats_v01/desc/_nan.py +518 -0
- scitex/{stats/desc/_nan.py → stats_v01/desc/_nan_v01-20250920_145731.py} +23 -12
- scitex/stats_v01/desc/_real.py +189 -0
- scitex/stats_v01/tests/__corr_test_optimized.py +221 -0
- scitex/stats_v01/tests/_corr_test_optimized.py +179 -0
- scitex/str/__init__.py +1 -3
- scitex/str/_clean_path.py +6 -2
- scitex/str/_latex_fallback.py +267 -160
- scitex/str/_parse.py +44 -36
- scitex/str/_printc.py +1 -3
- scitex/template/__init__.py +87 -0
- scitex/template/_create_project.py +267 -0
- scitex/template/create_pip_project.py +80 -0
- scitex/template/create_research.py +80 -0
- scitex/template/create_singularity.py +80 -0
- scitex/units.py +291 -0
- scitex/utils/_compress_hdf5.py +14 -3
- scitex/utils/_email.py +21 -2
- scitex/utils/_grid.py +6 -4
- scitex/utils/_notify.py +13 -10
- scitex/utils/_verify_scitex_format.py +589 -0
- scitex/utils/_verify_scitex_format_v01.py +370 -0
- scitex/utils/template.py +122 -0
- scitex/web/_search_pubmed.py +62 -16
- scitex-2.1.0.dist-info/LICENSE +21 -0
- scitex-2.1.0.dist-info/METADATA +677 -0
- scitex-2.1.0.dist-info/RECORD +919 -0
- {scitex-2.0.0.dist-info → scitex-2.1.0.dist-info}/WHEEL +1 -1
- scitex-2.1.0.dist-info/entry_points.txt +3 -0
- scitex/ai/__Classifiers.py +0 -101
- scitex/ai/classification/classification_reporter.py +0 -1137
- scitex/ai/classification/classifiers.py +0 -101
- scitex/ai/classification_reporter.py +0 -1161
- scitex/ai/genai/__init__.py +0 -277
- scitex/ai/genai/anthropic_provider.py +0 -320
- scitex/ai/genai/anthropic_refactored.py +0 -109
- scitex/ai/genai/auth_manager.py +0 -200
- scitex/ai/genai/base_provider.py +0 -291
- scitex/ai/genai/chat_history.py +0 -307
- scitex/ai/genai/cost_tracker.py +0 -276
- scitex/ai/genai/deepseek_provider.py +0 -251
- scitex/ai/genai/google_provider.py +0 -228
- scitex/ai/genai/groq_provider.py +0 -248
- scitex/ai/genai/image_processor.py +0 -250
- scitex/ai/genai/llama_provider.py +0 -214
- scitex/ai/genai/mock_provider.py +0 -127
- scitex/ai/genai/model_registry.py +0 -304
- scitex/ai/genai/openai_provider.py +0 -293
- scitex/ai/genai/perplexity_provider.py +0 -205
- scitex/ai/genai/provider_base.py +0 -302
- scitex/ai/genai/provider_factory.py +0 -370
- scitex/ai/genai/response_handler.py +0 -235
- scitex/ai/layer/_Pass.py +0 -21
- scitex/ai/layer/__init__.py +0 -10
- scitex/ai/layer/_switch.py +0 -8
- scitex/ai/metrics/_bACC.py +0 -51
- scitex/ai/plt/_learning_curve.py +0 -194
- scitex/ai/plt/_optuna_study.py +0 -111
- scitex/ai/plt/aucs/__init__.py +0 -2
- scitex/ai/plt/aucs/example.py +0 -60
- scitex/ai/plt/aucs/pre_rec_auc.py +0 -223
- scitex/ai/plt/aucs/roc_auc.py +0 -246
- scitex/ai/sampling/undersample.py +0 -29
- scitex/db/_SQLite3.py +0 -2136
- scitex/db/_SQLite3Mixins/_BlobMixin.py +0 -229
- scitex/gen/_close.py +0 -222
- scitex/gen/_start.py +0 -451
- scitex/general/__init__.py +0 -5
- scitex/io/_load_modules/_db.py +0 -24
- scitex/life/__init__.py +0 -10
- scitex/life/_monitor_rain.py +0 -49
- scitex/reproduce/_fix_seeds.py +0 -45
- scitex/res/__init__.py +0 -5
- scitex/scholar/_local_search.py +0 -454
- scitex/scholar/_paper.py +0 -244
- scitex/scholar/_pdf_downloader.py +0 -325
- scitex/scholar/_search.py +0 -393
- scitex/scholar/_vector_search.py +0 -370
- scitex/scholar/_web_sources.py +0 -457
- scitex/stats/desc/__init__.py +0 -40
- scitex-2.0.0.dist-info/METADATA +0 -307
- scitex-2.0.0.dist-info/RECORD +0 -572
- scitex-2.0.0.dist-info/licenses/LICENSE +0 -7
- /scitex/ai/{act → activation}/__init__.py +0 -0
- /scitex/ai/{act → activation}/_define.py +0 -0
- /scitex/ai/{early_stopping.py → training/_EarlyStopping.py} +0 -0
- /scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_ImportExportMixin.py +0 -0
- /scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_IndexMixin.py +0 -0
- /scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_RowMixin.py +0 -0
- /scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/_TableMixin.py +0 -0
- /scitex/db/{_PostgreSQLMixins → _postgresql/_PostgreSQLMixins}/__init__.py +0 -0
- /scitex/{stats → stats_v01}/_calc_partial_corr.py +0 -0
- /scitex/{stats → stats_v01}/_corr_test_multi.py +0 -0
- /scitex/{stats → stats_v01}/_corr_test_wrapper.py +0 -0
- /scitex/{stats → stats_v01}/_describe_wrapper.py +0 -0
- /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
scitex/ai/genai/auth_manager.py
DELETED
|
@@ -1,200 +0,0 @@
|
|
|
1
|
-
#!/usr/bin/env python3
|
|
2
|
-
# -*- coding: utf-8 -*-
|
|
3
|
-
# Time-stamp: "2025-05-31 10:00:00"
|
|
4
|
-
# Author: ywatanabe
|
|
5
|
-
# File: ./src/scitex/ai/genai/auth_manager.py
|
|
6
|
-
|
|
7
|
-
"""
|
|
8
|
-
Handles API key management and validation for AI providers.
|
|
9
|
-
|
|
10
|
-
This module provides secure handling of API keys including:
|
|
11
|
-
- Environment variable retrieval
|
|
12
|
-
- Key validation
|
|
13
|
-
- Masked key display for security
|
|
14
|
-
"""
|
|
15
|
-
|
|
16
|
-
import os
|
|
17
|
-
from typing import Optional, Dict, Any
|
|
18
|
-
|
|
19
|
-
|
|
20
|
-
class AuthManager:
|
|
21
|
-
"""Manages API key authentication for AI providers.
|
|
22
|
-
|
|
23
|
-
Example
|
|
24
|
-
-------
|
|
25
|
-
>>> auth = AuthManager("sk-abc123...", "OpenAI")
|
|
26
|
-
>>> auth.validate_key()
|
|
27
|
-
True
|
|
28
|
-
>>> auth.get_masked_key()
|
|
29
|
-
'sk-a****3...'
|
|
30
|
-
|
|
31
|
-
Parameters
|
|
32
|
-
----------
|
|
33
|
-
api_key : str
|
|
34
|
-
The API key for authentication
|
|
35
|
-
provider : str
|
|
36
|
-
The provider name (e.g., "OpenAI", "Anthropic")
|
|
37
|
-
"""
|
|
38
|
-
|
|
39
|
-
# Mapping of providers to environment variable names
|
|
40
|
-
ENV_VAR_MAPPING: Dict[str, str] = {
|
|
41
|
-
"OpenAI": "OPENAI_API_KEY",
|
|
42
|
-
"Anthropic": "ANTHROPIC_API_KEY",
|
|
43
|
-
"Google": "GOOGLE_API_KEY",
|
|
44
|
-
"Groq": "GROQ_API_KEY",
|
|
45
|
-
"DeepSeek": "DEEPSEEK_API_KEY",
|
|
46
|
-
"Perplexity": "PERPLEXITY_API_KEY",
|
|
47
|
-
"Llama": "LLAMA_API_KEY",
|
|
48
|
-
}
|
|
49
|
-
|
|
50
|
-
def __init__(self, api_key: Optional[str], provider: str):
|
|
51
|
-
"""Initialize AuthManager with API key and provider.
|
|
52
|
-
|
|
53
|
-
Parameters
|
|
54
|
-
----------
|
|
55
|
-
api_key : Optional[str]
|
|
56
|
-
The API key. If None, will attempt to get from environment
|
|
57
|
-
provider : str
|
|
58
|
-
The provider name
|
|
59
|
-
"""
|
|
60
|
-
# Normalize provider name to lowercase
|
|
61
|
-
self.provider = provider.lower()
|
|
62
|
-
|
|
63
|
-
# Check if provider is known
|
|
64
|
-
if self.provider not in [p.lower() for p in self.ENV_VAR_MAPPING.keys()]:
|
|
65
|
-
raise ValueError(f"Unknown provider: {provider}")
|
|
66
|
-
|
|
67
|
-
# Store private api key
|
|
68
|
-
self._api_key = api_key or self.get_key_from_env(provider)
|
|
69
|
-
|
|
70
|
-
if not self._api_key:
|
|
71
|
-
raise ValueError(f"No API key provided for {provider}")
|
|
72
|
-
|
|
73
|
-
# Public property for backward compatibility
|
|
74
|
-
self.api_key = self._api_key
|
|
75
|
-
|
|
76
|
-
def validate(self) -> bool:
|
|
77
|
-
"""Validate the API key format.
|
|
78
|
-
|
|
79
|
-
Returns
|
|
80
|
-
-------
|
|
81
|
-
bool
|
|
82
|
-
True if key appears valid, False otherwise
|
|
83
|
-
|
|
84
|
-
Raises
|
|
85
|
-
------
|
|
86
|
-
ValueError
|
|
87
|
-
If API key is missing or invalid
|
|
88
|
-
"""
|
|
89
|
-
if not self._api_key:
|
|
90
|
-
raise ValueError("No API key configured")
|
|
91
|
-
|
|
92
|
-
# Basic validation - ensure key is not empty and has reasonable length
|
|
93
|
-
if len(self._api_key) < 10:
|
|
94
|
-
raise ValueError(
|
|
95
|
-
f"API key for {self.provider} appears to be invalid (too short)"
|
|
96
|
-
)
|
|
97
|
-
|
|
98
|
-
return True
|
|
99
|
-
|
|
100
|
-
def get_masked_key(self) -> str:
|
|
101
|
-
"""Get a masked version of the API key for display.
|
|
102
|
-
|
|
103
|
-
Returns
|
|
104
|
-
-------
|
|
105
|
-
str
|
|
106
|
-
Masked API key showing only first few and last few characters
|
|
107
|
-
"""
|
|
108
|
-
if not self._api_key:
|
|
109
|
-
return "No API key"
|
|
110
|
-
|
|
111
|
-
if len(self._api_key) <= 8:
|
|
112
|
-
return "*****"
|
|
113
|
-
|
|
114
|
-
# Match test expectation: show first 3 and last 4 characters with "..." in between
|
|
115
|
-
return f"{self._api_key[:3]}...{self._api_key[-4:]}"
|
|
116
|
-
|
|
117
|
-
def get_client_config(self) -> Dict[str, Any]:
|
|
118
|
-
"""Get client configuration for the provider.
|
|
119
|
-
|
|
120
|
-
Returns
|
|
121
|
-
-------
|
|
122
|
-
Dict[str, any]
|
|
123
|
-
Configuration dictionary for the provider client
|
|
124
|
-
"""
|
|
125
|
-
config = {"api_key": self._api_key}
|
|
126
|
-
|
|
127
|
-
# Provider-specific configurations
|
|
128
|
-
if self.provider == "openai":
|
|
129
|
-
# Check for optional organization
|
|
130
|
-
org = os.getenv("OPENAI_ORGANIZATION")
|
|
131
|
-
if org:
|
|
132
|
-
config["organization"] = org
|
|
133
|
-
elif self.provider == "anthropic":
|
|
134
|
-
config["max_retries"] = 3
|
|
135
|
-
elif self.provider == "google":
|
|
136
|
-
# Google only needs API key
|
|
137
|
-
pass
|
|
138
|
-
|
|
139
|
-
return config
|
|
140
|
-
|
|
141
|
-
@classmethod
|
|
142
|
-
def get_key_from_env(cls, provider: str) -> Optional[str]:
|
|
143
|
-
"""Get API key from environment variable.
|
|
144
|
-
|
|
145
|
-
Parameters
|
|
146
|
-
----------
|
|
147
|
-
provider : str
|
|
148
|
-
The provider name
|
|
149
|
-
|
|
150
|
-
Returns
|
|
151
|
-
-------
|
|
152
|
-
Optional[str]
|
|
153
|
-
The API key if found in environment, None otherwise
|
|
154
|
-
"""
|
|
155
|
-
# Find the env var name case-insensitively
|
|
156
|
-
for p, env_var in cls.ENV_VAR_MAPPING.items():
|
|
157
|
-
if p.lower() == provider.lower():
|
|
158
|
-
return os.getenv(env_var)
|
|
159
|
-
|
|
160
|
-
# Try generic pattern if not found
|
|
161
|
-
env_var = f"{provider.upper()}_API_KEY"
|
|
162
|
-
return os.getenv(env_var)
|
|
163
|
-
|
|
164
|
-
def get_api_key(self, provider: str, api_key: Optional[str] = None) -> str:
|
|
165
|
-
"""Get API key for a provider.
|
|
166
|
-
|
|
167
|
-
This method is used by provider_base.py for compatibility.
|
|
168
|
-
|
|
169
|
-
Parameters
|
|
170
|
-
----------
|
|
171
|
-
provider : str
|
|
172
|
-
The provider name
|
|
173
|
-
api_key : Optional[str]
|
|
174
|
-
Explicit API key, if None will use environment
|
|
175
|
-
|
|
176
|
-
Returns
|
|
177
|
-
-------
|
|
178
|
-
str
|
|
179
|
-
The API key
|
|
180
|
-
|
|
181
|
-
Raises
|
|
182
|
-
------
|
|
183
|
-
ValueError
|
|
184
|
-
If no API key is found
|
|
185
|
-
"""
|
|
186
|
-
if api_key:
|
|
187
|
-
return api_key
|
|
188
|
-
|
|
189
|
-
key = self.get_key_from_env(provider)
|
|
190
|
-
if not key:
|
|
191
|
-
raise ValueError(f"No API key provided for {provider}")
|
|
192
|
-
|
|
193
|
-
return key
|
|
194
|
-
|
|
195
|
-
def __repr__(self) -> str:
|
|
196
|
-
"""String representation of AuthManager."""
|
|
197
|
-
return f"AuthManager(provider={self.provider}, key={self.get_masked_key()})"
|
|
198
|
-
|
|
199
|
-
|
|
200
|
-
# EOF
|
scitex/ai/genai/base_provider.py
DELETED
|
@@ -1,291 +0,0 @@
|
|
|
1
|
-
#!/usr/bin/env python3
|
|
2
|
-
# -*- coding: utf-8 -*-
|
|
3
|
-
# Time-stamp: "2025-05-31 10:30:00"
|
|
4
|
-
# Author: ywatanabe
|
|
5
|
-
# File: ./src/scitex/ai/genai/base_provider.py
|
|
6
|
-
|
|
7
|
-
"""
|
|
8
|
-
Abstract base class for AI provider implementations.
|
|
9
|
-
|
|
10
|
-
This module defines the interface that all AI providers must implement,
|
|
11
|
-
ensuring consistency across different providers (OpenAI, Anthropic, etc.).
|
|
12
|
-
"""
|
|
13
|
-
|
|
14
|
-
from abc import ABC, abstractmethod
|
|
15
|
-
from dataclasses import dataclass, field
|
|
16
|
-
from enum import Enum
|
|
17
|
-
from typing import Any, Dict, List, Generator, Optional
|
|
18
|
-
|
|
19
|
-
|
|
20
|
-
class Provider(str, Enum):
|
|
21
|
-
"""Supported AI providers."""
|
|
22
|
-
|
|
23
|
-
OPENAI = "openai"
|
|
24
|
-
ANTHROPIC = "anthropic"
|
|
25
|
-
GOOGLE = "google"
|
|
26
|
-
GROQ = "groq"
|
|
27
|
-
DEEPSEEK = "deepseek"
|
|
28
|
-
LLAMA = "llama"
|
|
29
|
-
PERPLEXITY = "perplexity"
|
|
30
|
-
MOCK = "mock" # For testing
|
|
31
|
-
|
|
32
|
-
def __str__(self):
|
|
33
|
-
return self.value
|
|
34
|
-
|
|
35
|
-
|
|
36
|
-
class Role(str, Enum):
|
|
37
|
-
"""Message roles for chat conversations."""
|
|
38
|
-
|
|
39
|
-
SYSTEM = "system"
|
|
40
|
-
USER = "user"
|
|
41
|
-
ASSISTANT = "assistant"
|
|
42
|
-
|
|
43
|
-
|
|
44
|
-
@dataclass
|
|
45
|
-
class ProviderConfig:
|
|
46
|
-
"""Configuration for AI providers."""
|
|
47
|
-
|
|
48
|
-
provider: str
|
|
49
|
-
model: str
|
|
50
|
-
api_key: Optional[str] = None
|
|
51
|
-
system_prompt: str = ""
|
|
52
|
-
temperature: float = 1.0
|
|
53
|
-
max_tokens: int = 4096
|
|
54
|
-
stream: bool = False
|
|
55
|
-
seed: Optional[int] = None
|
|
56
|
-
n_keep: int = 1
|
|
57
|
-
|
|
58
|
-
|
|
59
|
-
@dataclass
|
|
60
|
-
class CompletionResponse:
|
|
61
|
-
"""Standard response format for completions."""
|
|
62
|
-
|
|
63
|
-
content: str
|
|
64
|
-
input_tokens: int
|
|
65
|
-
output_tokens: int
|
|
66
|
-
finish_reason: str = "stop"
|
|
67
|
-
provider_response: Optional[Any] = None
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
class BaseProvider(ABC):
|
|
71
|
-
"""Abstract base class for AI providers.
|
|
72
|
-
|
|
73
|
-
All AI provider implementations must inherit from this class
|
|
74
|
-
and implement the required abstract methods.
|
|
75
|
-
|
|
76
|
-
Example
|
|
77
|
-
-------
|
|
78
|
-
>>> class MyProvider(BaseProvider):
|
|
79
|
-
... def init_client(self) -> Any:
|
|
80
|
-
... return MyAPIClient(self.api_key)
|
|
81
|
-
...
|
|
82
|
-
... def format_history(self, history: List[Dict]) -> List[Dict]:
|
|
83
|
-
... # Provider-specific formatting
|
|
84
|
-
... return history
|
|
85
|
-
...
|
|
86
|
-
... def call_static(self, messages: List[Dict], **kwargs) -> Any:
|
|
87
|
-
... # Make API call
|
|
88
|
-
... return self.client.complete(messages)
|
|
89
|
-
...
|
|
90
|
-
... def call_stream(self, messages: List[Dict], **kwargs) -> Generator:
|
|
91
|
-
... # Make streaming API call
|
|
92
|
-
... for chunk in self.client.stream(messages):
|
|
93
|
-
... yield chunk
|
|
94
|
-
"""
|
|
95
|
-
|
|
96
|
-
@abstractmethod
|
|
97
|
-
def init_client(self) -> Any:
|
|
98
|
-
"""Initialize the provider-specific client.
|
|
99
|
-
|
|
100
|
-
This method should create and configure the API client
|
|
101
|
-
for the specific provider (e.g., OpenAI client, Anthropic client).
|
|
102
|
-
|
|
103
|
-
Returns
|
|
104
|
-
-------
|
|
105
|
-
Any
|
|
106
|
-
The initialized client object
|
|
107
|
-
"""
|
|
108
|
-
pass
|
|
109
|
-
|
|
110
|
-
@abstractmethod
|
|
111
|
-
def format_history(self, history: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
|
|
112
|
-
"""Format conversation history for the provider's API.
|
|
113
|
-
|
|
114
|
-
Different providers may expect different formats for conversation
|
|
115
|
-
history. This method converts the standard format to the
|
|
116
|
-
provider-specific format.
|
|
117
|
-
|
|
118
|
-
Parameters
|
|
119
|
-
----------
|
|
120
|
-
history : List[Dict[str, Any]]
|
|
121
|
-
Standard format conversation history
|
|
122
|
-
|
|
123
|
-
Returns
|
|
124
|
-
-------
|
|
125
|
-
List[Dict[str, Any]]
|
|
126
|
-
Provider-specific formatted history
|
|
127
|
-
"""
|
|
128
|
-
pass
|
|
129
|
-
|
|
130
|
-
@abstractmethod
|
|
131
|
-
def call_static(self, messages: List[Dict[str, Any]], **kwargs) -> Any:
|
|
132
|
-
"""Make a static (non-streaming) API call.
|
|
133
|
-
|
|
134
|
-
Parameters
|
|
135
|
-
----------
|
|
136
|
-
messages : List[Dict[str, Any]]
|
|
137
|
-
Formatted conversation messages
|
|
138
|
-
**kwargs
|
|
139
|
-
Additional provider-specific parameters
|
|
140
|
-
|
|
141
|
-
Returns
|
|
142
|
-
-------
|
|
143
|
-
Any
|
|
144
|
-
Provider-specific response object
|
|
145
|
-
"""
|
|
146
|
-
pass
|
|
147
|
-
|
|
148
|
-
@abstractmethod
|
|
149
|
-
def call_stream(
|
|
150
|
-
self, messages: List[Dict[str, Any]], **kwargs
|
|
151
|
-
) -> Generator[str, None, None]:
|
|
152
|
-
"""Make a streaming API call.
|
|
153
|
-
|
|
154
|
-
Parameters
|
|
155
|
-
----------
|
|
156
|
-
messages : List[Dict[str, Any]]
|
|
157
|
-
Formatted conversation messages
|
|
158
|
-
**kwargs
|
|
159
|
-
Additional provider-specific parameters
|
|
160
|
-
|
|
161
|
-
Yields
|
|
162
|
-
------
|
|
163
|
-
str
|
|
164
|
-
Response text chunks
|
|
165
|
-
"""
|
|
166
|
-
pass
|
|
167
|
-
|
|
168
|
-
@property
|
|
169
|
-
@abstractmethod
|
|
170
|
-
def supports_streaming(self) -> bool:
|
|
171
|
-
"""Whether this provider supports streaming responses.
|
|
172
|
-
|
|
173
|
-
Returns
|
|
174
|
-
-------
|
|
175
|
-
bool
|
|
176
|
-
True if streaming is supported
|
|
177
|
-
"""
|
|
178
|
-
pass
|
|
179
|
-
|
|
180
|
-
@property
|
|
181
|
-
@abstractmethod
|
|
182
|
-
def supports_images(self) -> bool:
|
|
183
|
-
"""Whether this provider supports image inputs.
|
|
184
|
-
|
|
185
|
-
Returns
|
|
186
|
-
-------
|
|
187
|
-
bool
|
|
188
|
-
True if images are supported
|
|
189
|
-
"""
|
|
190
|
-
pass
|
|
191
|
-
|
|
192
|
-
@property
|
|
193
|
-
@abstractmethod
|
|
194
|
-
def max_context_length(self) -> int:
|
|
195
|
-
"""Maximum context length in tokens.
|
|
196
|
-
|
|
197
|
-
Returns
|
|
198
|
-
-------
|
|
199
|
-
int
|
|
200
|
-
Maximum number of tokens
|
|
201
|
-
"""
|
|
202
|
-
pass
|
|
203
|
-
|
|
204
|
-
def get_capabilities(self) -> Dict[str, Any]:
|
|
205
|
-
"""Get provider capabilities summary.
|
|
206
|
-
|
|
207
|
-
Returns
|
|
208
|
-
-------
|
|
209
|
-
Dict[str, Any]
|
|
210
|
-
Dictionary of provider capabilities
|
|
211
|
-
"""
|
|
212
|
-
return {
|
|
213
|
-
"supports_streaming": self.supports_streaming,
|
|
214
|
-
"supports_images": self.supports_images,
|
|
215
|
-
"max_context_length": self.max_context_length,
|
|
216
|
-
}
|
|
217
|
-
|
|
218
|
-
def extract_tokens_from_response(self, response: Any) -> Dict[str, int]:
|
|
219
|
-
"""Extract token usage from provider response.
|
|
220
|
-
|
|
221
|
-
Default implementation returns zeros. Providers should override
|
|
222
|
-
to extract actual token counts from their response format.
|
|
223
|
-
|
|
224
|
-
Parameters
|
|
225
|
-
----------
|
|
226
|
-
response : Any
|
|
227
|
-
Provider-specific response object
|
|
228
|
-
|
|
229
|
-
Returns
|
|
230
|
-
-------
|
|
231
|
-
Dict[str, int]
|
|
232
|
-
Dictionary with 'input_tokens' and 'output_tokens'
|
|
233
|
-
"""
|
|
234
|
-
return {"input_tokens": 0, "output_tokens": 0}
|
|
235
|
-
|
|
236
|
-
def handle_rate_limit(self, error: Exception) -> bool:
|
|
237
|
-
"""Handle rate limit errors.
|
|
238
|
-
|
|
239
|
-
Default implementation returns False. Providers can override
|
|
240
|
-
to implement retry logic or other handling.
|
|
241
|
-
|
|
242
|
-
Parameters
|
|
243
|
-
----------
|
|
244
|
-
error : Exception
|
|
245
|
-
The error that occurred
|
|
246
|
-
|
|
247
|
-
Returns
|
|
248
|
-
-------
|
|
249
|
-
bool
|
|
250
|
-
True if the error was handled and operation should retry
|
|
251
|
-
"""
|
|
252
|
-
return False
|
|
253
|
-
|
|
254
|
-
def validate_model(self, model: str) -> bool:
|
|
255
|
-
"""Validate if a model is supported.
|
|
256
|
-
|
|
257
|
-
Default implementation returns True. Providers should override
|
|
258
|
-
to validate against their supported models.
|
|
259
|
-
|
|
260
|
-
Parameters
|
|
261
|
-
----------
|
|
262
|
-
model : str
|
|
263
|
-
Model name to validate
|
|
264
|
-
|
|
265
|
-
Returns
|
|
266
|
-
-------
|
|
267
|
-
bool
|
|
268
|
-
True if model is supported
|
|
269
|
-
"""
|
|
270
|
-
return True
|
|
271
|
-
|
|
272
|
-
def get_error_message(self, error: Exception) -> str:
|
|
273
|
-
"""Extract user-friendly error message.
|
|
274
|
-
|
|
275
|
-
Default implementation returns string representation.
|
|
276
|
-
Providers can override for better error messages.
|
|
277
|
-
|
|
278
|
-
Parameters
|
|
279
|
-
----------
|
|
280
|
-
error : Exception
|
|
281
|
-
The error that occurred
|
|
282
|
-
|
|
283
|
-
Returns
|
|
284
|
-
-------
|
|
285
|
-
str
|
|
286
|
-
User-friendly error message
|
|
287
|
-
"""
|
|
288
|
-
return str(error)
|
|
289
|
-
|
|
290
|
-
|
|
291
|
-
# EOF
|