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: "2025-10-09 21:45:30 (ywatanabe)"
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# File: /home/ywatanabe/proj/scitex_repo/src/scitex/utils/_verify_scitex_format.py
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# ----------------------------------------
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from __future__ import annotations
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import os
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__FILE__ = (
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"./src/scitex/utils/_verify_scitex_format.py"
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)
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__DIR__ = os.path.dirname(__FILE__)
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# ----------------------------------------
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"""
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Verify SciTeX template format compliance for Python files.
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Functionalities:
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- Scans Python files in specified directories
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- Checks for required components (main, parse_args, run_main, if __name__)
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- Checks for optional components (docstrings, sections, verbose params)
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- Generates detailed compliance reports
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- Provides recommendations for non-compliant files
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Dependencies:
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- packages:
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- pathlib
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- dataclasses
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- typing
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- re
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IO:
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- input-files:
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- Python source files (.py)
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- output-files:
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- Compliance report (printed to stdout or saved)
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"""
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"""Imports"""
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import argparse
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import re
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from dataclasses import dataclass
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from pathlib import Path
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from typing import Dict
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from scitex import logging
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logger = logging.getLogger(__name__)
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"""Functions & Classes"""
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@dataclass
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class FileInfo:
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"""Store file information."""
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relative_path: str
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content: str
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size: int
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lines: int
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@dataclass
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class TemplateCompliance:
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"""Store compliance check results."""
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has_main: bool = False
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has_parse_args: bool = False
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has_run_main: bool = False
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has_main_guard: bool = False
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is_run_main_unchanged: bool = False
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has_docstring: bool = False
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has_imports_section: bool = False
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has_functions_classes_section: bool = False
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uses_scitex_session: bool = False
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has_verbose_param: bool = False
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@property
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def is_compliant(self) -> bool:
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"""Check if file is fully compliant."""
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return all(
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[
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self.has_main,
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self.has_parse_args,
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self.has_run_main,
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self.has_main_guard,
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self.is_run_main_unchanged,
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]
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)
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@property
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def compliance_score(self) -> float:
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"""Calculate compliance score (0-1)."""
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checks = [
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self.has_main,
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self.has_parse_args,
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self.has_run_main,
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self.has_main_guard,
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self.is_run_main_unchanged,
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self.has_docstring,
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self.has_imports_section,
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self.has_functions_classes_section,
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self.uses_scitex_session,
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self.has_verbose_param,
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]
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return sum(checks) / len(checks)
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def scan_python_files(
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paths: list[Path], base_dir: Path = None
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) -> Dict[str, FileInfo]:
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"""Scan Python files from filesystem paths.
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Args:
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paths: List of file or directory paths to scan
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base_dir: Base directory for relative path calculation
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Returns:
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Dictionary mapping relative paths to FileInfo objects
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"""
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files = {}
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if base_dir is None:
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base_dir = Path.cwd()
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for path in paths:
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path = Path(path).resolve()
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if path.is_file():
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# Single file
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python_files = [path] if path.suffix == ".py" else []
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elif path.is_dir():
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# Directory - recursively find all .py files
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python_files = list(path.rglob("*.py"))
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else:
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logger.warning(f"Path not found: {path}")
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continue
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for py_file in python_files:
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# Skip template.py, __init__.py, and test files
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if any(
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skip in py_file.name for skip in ["template.py", "__init__.py"]
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):
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continue
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try:
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content = py_file.read_text(encoding="utf-8")
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relative_path = str(py_file.relative_to(base_dir))
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files[relative_path] = FileInfo(
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relative_path=relative_path,
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content=content,
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size=py_file.stat().st_size,
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lines=len(content.splitlines()),
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)
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except Exception as e:
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logger.warning(f"Failed to read {py_file}: {e}")
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return files
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def check_compliance(content: str) -> TemplateCompliance:
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"""Check if content follows template format."""
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compliance = TemplateCompliance()
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# Check for main function
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compliance.has_main = bool(
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re.search(r"^def main\(", content, re.MULTILINE)
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)
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# Check for parse_args function
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compliance.has_parse_args = bool(
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re.search(r"^def parse_args\(", content, re.MULTILINE)
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)
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# Check for run_main function
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compliance.has_run_main = bool(
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re.search(r"^def run_main\(", content, re.MULTILINE)
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)
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# Check for main guard
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compliance.has_main_guard = bool(
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re.search(r'if __name__ == "__main__":', content)
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)
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# Check if run_main follows the exact template format
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compliance.is_run_main_unchanged = _check_run_main_unchanged(content)
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# Check for module docstring
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compliance.has_docstring = bool(re.search(r'"""[\s\S]*?"""', content))
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# Check for section markers
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compliance.has_imports_section = bool(re.search(r'"""Imports"""', content))
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compliance.has_functions_classes_section = bool(
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re.search(r'"""Functions & Classes"""', content)
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)
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# Check for scitex session usage
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compliance.uses_scitex_session = bool(
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re.search(r"stx\.session\.start", content)
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)
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# Check for verbose parameter
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compliance.has_verbose_param = bool(
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re.search(r"verbose\s*[:=]\s*(?:bool|True|False)", content)
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)
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return compliance
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def _check_run_main_unchanged(content: str) -> bool:
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"""Check if run_main function follows the exact template format."""
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# Template run_main signature and key components
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required_patterns = [
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r"def run_main\(\) -> None:",
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r'"""Initialize scitex framework, run main function, and cleanup\."""',
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r"global CONFIG, CC, sys, plt, rng",
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r"import sys",
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r"import matplotlib\.pyplot as plt",
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r"import scitex as stx",
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r"args = parse_args\(\)",
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r"CONFIG, sys\.stdout, sys\.stderr, plt, CC, rng = stx\.session\.start\(",
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r"exit_status = main\(args\)",
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r"stx\.session\.close\(",
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]
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# Check all required patterns are present
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for pattern in required_patterns:
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if not re.search(pattern, content):
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return False
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return True
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def generate_report(results: Dict[str, tuple]) -> str:
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"""Generate compliance report."""
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lines = []
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lines.append("=" * 80)
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lines.append("TEMPLATE COMPLIANCE REPORT")
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lines.append("=" * 80)
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lines.append("")
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# Summary statistics
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total_files = len(results)
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compliant_files = sum(1 for _, c in results.values() if c.is_compliant)
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avg_score = (
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sum(c.compliance_score for _, c in results.values()) / total_files
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if total_files > 0
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else 0
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)
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lines.append(f"Total Python files analyzed: {total_files}")
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if total_files > 0:
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lines.append(
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f"Fully compliant files: {compliant_files} ({compliant_files/total_files*100:.1f}%)"
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)
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lines.append(f"Average compliance score: {avg_score:.1%}")
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else:
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lines.append("No files to analyze")
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lines.append("")
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# Detailed results
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lines.append("=" * 80)
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lines.append("DETAILED RESULTS (sorted by compliance score)")
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lines.append("=" * 80)
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lines.append("")
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# Sort by compliance score (lowest first)
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sorted_results = sorted(
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results.items(), key=lambda x: (x[1][1].compliance_score, x[0])
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)
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for filepath, (file_info, compliance) in sorted_results:
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score = compliance.compliance_score
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# Status indicator
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if compliance.is_compliant:
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status = "✓ COMPLIANT"
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elif score >= 0.5:
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status = "⚠ PARTIAL"
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else:
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status = "✗ NON-COMPLIANT"
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lines.append(f"{status} [{score:.0%}] {filepath}")
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lines.append(
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f" Lines: {file_info.lines}, Size: {file_info.size} bytes"
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)
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# Show missing components
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if not compliance.is_compliant:
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missing = []
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if not compliance.has_main:
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missing.append("main()")
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if not compliance.has_parse_args:
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missing.append("parse_args()")
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if not compliance.has_run_main:
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missing.append("run_main()")
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if not compliance.has_main_guard:
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missing.append("if __name__ == '__main__'")
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if not compliance.is_run_main_unchanged:
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missing.append("run_main() template format")
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if missing:
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lines.append(f" ❌ REQUIRED Missing: {', '.join(missing)}")
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# Show optional items
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optional_missing = []
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if not compliance.has_docstring:
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optional_missing.append("module docstring")
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if not compliance.has_imports_section:
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optional_missing.append("'Imports' section")
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if not compliance.has_functions_classes_section:
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optional_missing.append("'Functions & Classes' section")
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if not compliance.uses_scitex_session:
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optional_missing.append("scitex session")
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if not compliance.has_verbose_param:
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optional_missing.append("verbose parameter")
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if optional_missing:
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lines.append(
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f" ⚠️ OPTIONAL Missing: {', '.join(optional_missing)}"
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)
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lines.append("")
|
|
323
|
+
|
|
324
|
+
# Component breakdown
|
|
325
|
+
lines.append("=" * 80)
|
|
326
|
+
lines.append("COMPONENT BREAKDOWN")
|
|
327
|
+
lines.append("=" * 80)
|
|
328
|
+
lines.append("")
|
|
329
|
+
|
|
330
|
+
components = [
|
|
331
|
+
(
|
|
332
|
+
"✓ main() function",
|
|
333
|
+
sum(1 for _, c in results.values() if c.has_main),
|
|
334
|
+
),
|
|
335
|
+
(
|
|
336
|
+
"✓ parse_args() function",
|
|
337
|
+
sum(1 for _, c in results.values() if c.has_parse_args),
|
|
338
|
+
),
|
|
339
|
+
(
|
|
340
|
+
"✓ run_main() function",
|
|
341
|
+
sum(1 for _, c in results.values() if c.has_run_main),
|
|
342
|
+
),
|
|
343
|
+
(
|
|
344
|
+
"✓ if __name__ == '__main__'",
|
|
345
|
+
sum(1 for _, c in results.values() if c.has_main_guard),
|
|
346
|
+
),
|
|
347
|
+
(
|
|
348
|
+
"✓ run_main() template unchanged",
|
|
349
|
+
sum(1 for _, c in results.values() if c.is_run_main_unchanged),
|
|
350
|
+
),
|
|
351
|
+
(
|
|
352
|
+
" Module docstring",
|
|
353
|
+
sum(1 for _, c in results.values() if c.has_docstring),
|
|
354
|
+
),
|
|
355
|
+
(
|
|
356
|
+
" 'Imports' section",
|
|
357
|
+
sum(1 for _, c in results.values() if c.has_imports_section),
|
|
358
|
+
),
|
|
359
|
+
(
|
|
360
|
+
" 'Functions & Classes'",
|
|
361
|
+
sum(
|
|
362
|
+
1
|
|
363
|
+
for _, c in results.values()
|
|
364
|
+
if c.has_functions_classes_section
|
|
365
|
+
),
|
|
366
|
+
),
|
|
367
|
+
(
|
|
368
|
+
" scitex session",
|
|
369
|
+
sum(1 for _, c in results.values() if c.uses_scitex_session),
|
|
370
|
+
),
|
|
371
|
+
(
|
|
372
|
+
" verbose parameter",
|
|
373
|
+
sum(1 for _, c in results.values() if c.has_verbose_param),
|
|
374
|
+
),
|
|
375
|
+
]
|
|
376
|
+
|
|
377
|
+
for component, count in components:
|
|
378
|
+
percentage = count / total_files * 100 if total_files > 0 else 0
|
|
379
|
+
marker = "REQUIRED" if component.startswith("✓") else "OPTIONAL"
|
|
380
|
+
lines.append(
|
|
381
|
+
f"[{marker}] {component:.<45} {count}/{total_files} ({percentage:.1f}%)"
|
|
382
|
+
)
|
|
383
|
+
|
|
384
|
+
# Recommendations
|
|
385
|
+
lines.append("")
|
|
386
|
+
lines.append("=" * 80)
|
|
387
|
+
lines.append("RECOMMENDATIONS")
|
|
388
|
+
lines.append("=" * 80)
|
|
389
|
+
lines.append("")
|
|
390
|
+
|
|
391
|
+
non_compliant = [
|
|
392
|
+
(path, compliance)
|
|
393
|
+
for path, (_, compliance) in results.items()
|
|
394
|
+
if not compliance.is_compliant
|
|
395
|
+
]
|
|
396
|
+
|
|
397
|
+
if non_compliant:
|
|
398
|
+
lines.append(
|
|
399
|
+
f"Found {len(non_compliant)} non-compliant files that need updates:"
|
|
400
|
+
)
|
|
401
|
+
lines.append("")
|
|
402
|
+
for path, compliance in non_compliant:
|
|
403
|
+
lines.append(f"• {path}")
|
|
404
|
+
fixes = []
|
|
405
|
+
if not compliance.has_main:
|
|
406
|
+
fixes.append(" - Add main(args) function")
|
|
407
|
+
if not compliance.has_parse_args:
|
|
408
|
+
fixes.append(" - Add parse_args() function")
|
|
409
|
+
if not compliance.has_run_main:
|
|
410
|
+
fixes.append(" - Add run_main() function")
|
|
411
|
+
if not compliance.has_main_guard:
|
|
412
|
+
fixes.append(" - Add if __name__ == '__main__': run_main()")
|
|
413
|
+
if not compliance.is_run_main_unchanged:
|
|
414
|
+
fixes.append(
|
|
415
|
+
" - Update run_main() to match template format exactly"
|
|
416
|
+
)
|
|
417
|
+
for fix in fixes:
|
|
418
|
+
lines.append(fix)
|
|
419
|
+
lines.append("")
|
|
420
|
+
else:
|
|
421
|
+
lines.append("✓ All files are compliant! Great job!")
|
|
422
|
+
|
|
423
|
+
return "\n".join(lines)
|
|
424
|
+
|
|
425
|
+
|
|
426
|
+
def main(args):
|
|
427
|
+
"""Verify SciTeX template format compliance."""
|
|
428
|
+
# Determine paths to scan
|
|
429
|
+
if args.paths:
|
|
430
|
+
paths = [Path(p).resolve() for p in args.paths]
|
|
431
|
+
# Determine base_dir from the first path
|
|
432
|
+
if args.base_dir:
|
|
433
|
+
base_dir = Path(args.base_dir).resolve()
|
|
434
|
+
else:
|
|
435
|
+
# Find common parent for all paths
|
|
436
|
+
first_path = paths[0]
|
|
437
|
+
if first_path.is_file():
|
|
438
|
+
base_dir = first_path.parent
|
|
439
|
+
else:
|
|
440
|
+
base_dir = first_path
|
|
441
|
+
else:
|
|
442
|
+
# Default to current directory
|
|
443
|
+
paths = [Path.cwd()]
|
|
444
|
+
base_dir = (
|
|
445
|
+
Path(args.base_dir).resolve() if args.base_dir else Path.cwd()
|
|
446
|
+
)
|
|
447
|
+
|
|
448
|
+
logger.info(f"Scanning paths: {[str(p) for p in paths]}")
|
|
449
|
+
logger.info(f"Base directory: {base_dir}")
|
|
450
|
+
|
|
451
|
+
# Scan Python files
|
|
452
|
+
files = scan_python_files(paths, base_dir)
|
|
453
|
+
logger.info(f"Found {len(files)} Python files")
|
|
454
|
+
|
|
455
|
+
if not files:
|
|
456
|
+
logger.warning("No Python files found to analyze")
|
|
457
|
+
return 1
|
|
458
|
+
|
|
459
|
+
# Check compliance for each file
|
|
460
|
+
results = {}
|
|
461
|
+
for path, file_info in files.items():
|
|
462
|
+
compliance = check_compliance(file_info.content)
|
|
463
|
+
results[path] = (file_info, compliance)
|
|
464
|
+
|
|
465
|
+
# Generate report
|
|
466
|
+
report = generate_report(results)
|
|
467
|
+
logger.info("\n" + report)
|
|
468
|
+
|
|
469
|
+
# Save report if output path specified
|
|
470
|
+
if args.output:
|
|
471
|
+
output_path = Path(args.output)
|
|
472
|
+
output_path.parent.mkdir(parents=True, exist_ok=True)
|
|
473
|
+
output_path.write_text(report)
|
|
474
|
+
logger.success(f"Report saved to: {output_path}")
|
|
475
|
+
|
|
476
|
+
# Return exit status based on compliance
|
|
477
|
+
compliant_count = sum(1 for _, c in results.values() if c.is_compliant)
|
|
478
|
+
if compliant_count == len(results):
|
|
479
|
+
logger.success("All files are compliant!")
|
|
480
|
+
return 0
|
|
481
|
+
else:
|
|
482
|
+
logger.warning(
|
|
483
|
+
f"{len(results) - compliant_count} files need attention"
|
|
484
|
+
)
|
|
485
|
+
return 0 # Still return 0 to avoid breaking pipelines
|
|
486
|
+
|
|
487
|
+
|
|
488
|
+
def parse_args() -> argparse.Namespace:
|
|
489
|
+
"""Parse command line arguments."""
|
|
490
|
+
parser = argparse.ArgumentParser(
|
|
491
|
+
description="Verify SciTeX template format compliance for Python files",
|
|
492
|
+
formatter_class=argparse.RawDescriptionHelpFormatter,
|
|
493
|
+
epilog="""
|
|
494
|
+
Examples:
|
|
495
|
+
# Check current directory
|
|
496
|
+
python -m scitex.utils._verify_scitex_format
|
|
497
|
+
|
|
498
|
+
# Check specific directory
|
|
499
|
+
python -m scitex.utils._verify_scitex_format src/scitex/browser
|
|
500
|
+
|
|
501
|
+
# Check multiple paths
|
|
502
|
+
python -m scitex.utils._verify_scitex_format src/scitex/browser src/scitex/io
|
|
503
|
+
|
|
504
|
+
# Check specific file
|
|
505
|
+
python -m scitex.utils._verify_scitex_format src/scitex/browser/automation/CookieHandler.py
|
|
506
|
+
|
|
507
|
+
# Save report to file
|
|
508
|
+
python -m scitex.utils._verify_scitex_format src/scitex/browser -o report.txt
|
|
509
|
+
""",
|
|
510
|
+
)
|
|
511
|
+
parser.add_argument(
|
|
512
|
+
"paths",
|
|
513
|
+
nargs="*",
|
|
514
|
+
help="Files or directories to check (default: current directory)",
|
|
515
|
+
)
|
|
516
|
+
parser.add_argument(
|
|
517
|
+
"--base-dir",
|
|
518
|
+
"-b",
|
|
519
|
+
type=str,
|
|
520
|
+
default=None,
|
|
521
|
+
help="Base directory for relative path calculation (default: current directory)",
|
|
522
|
+
)
|
|
523
|
+
parser.add_argument(
|
|
524
|
+
"--output",
|
|
525
|
+
"-o",
|
|
526
|
+
type=str,
|
|
527
|
+
default=None,
|
|
528
|
+
help="Output file path for report (default: print to stdout)",
|
|
529
|
+
)
|
|
530
|
+
args = parser.parse_args()
|
|
531
|
+
|
|
532
|
+
# Resolve paths BEFORE scitex session changes working directory
|
|
533
|
+
original_cwd = Path.cwd()
|
|
534
|
+
if args.paths:
|
|
535
|
+
args.paths = [str((original_cwd / p).resolve()) for p in args.paths]
|
|
536
|
+
else:
|
|
537
|
+
args.paths = [str(original_cwd)]
|
|
538
|
+
|
|
539
|
+
if args.base_dir:
|
|
540
|
+
args.base_dir = str((original_cwd / args.base_dir).resolve())
|
|
541
|
+
else:
|
|
542
|
+
# Use the original cwd as base
|
|
543
|
+
args.base_dir = str(original_cwd)
|
|
544
|
+
|
|
545
|
+
if args.output:
|
|
546
|
+
args.output = str((original_cwd / args.output).resolve())
|
|
547
|
+
|
|
548
|
+
return args
|
|
549
|
+
|
|
550
|
+
|
|
551
|
+
def run_main() -> None:
|
|
552
|
+
"""Initialize scitex framework, run main function, and cleanup."""
|
|
553
|
+
global CONFIG, CC, sys, plt, rng
|
|
554
|
+
|
|
555
|
+
import sys
|
|
556
|
+
|
|
557
|
+
import matplotlib.pyplot as plt
|
|
558
|
+
|
|
559
|
+
import scitex as stx
|
|
560
|
+
|
|
561
|
+
args = parse_args()
|
|
562
|
+
|
|
563
|
+
CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
|
|
564
|
+
sys,
|
|
565
|
+
plt,
|
|
566
|
+
args=args,
|
|
567
|
+
file=__FILE__,
|
|
568
|
+
sdir_suffix=None,
|
|
569
|
+
verbose=False,
|
|
570
|
+
agg=True,
|
|
571
|
+
)
|
|
572
|
+
|
|
573
|
+
exit_status = main(args)
|
|
574
|
+
|
|
575
|
+
stx.session.close(
|
|
576
|
+
CONFIG,
|
|
577
|
+
verbose=False,
|
|
578
|
+
notify=False,
|
|
579
|
+
message="",
|
|
580
|
+
exit_status=exit_status,
|
|
581
|
+
)
|
|
582
|
+
|
|
583
|
+
|
|
584
|
+
if __name__ == "__main__":
|
|
585
|
+
run_main()
|
|
586
|
+
|
|
587
|
+
# python -m scitex.utils._verify_scitex_format
|
|
588
|
+
|
|
589
|
+
# EOF
|