├── .ci ├── check_channels_ssot.sh ├── check_experiments_shims.sh ├── check_meta_schema.sh ├── check_no_compat.sh ├── check_no_lightning.sh ├── check_no_parallel_impl.sh ├── check_no_sys_path.sh └── check_script_arguments.sh ├── .claude ├── global-CLAUDE.md └── guidelines.md ├── .coveragerc ├── .coveragerc.data ├── .coveragerc.unit ├── .cursorrules ├── .env.example ├── .gitattributes ├── .githooks └── pre-push ├── .github └── workflows │ ├── ci.yml │ ├── claude.yml │ └── no-lightning.yml ├── .gitignore ├── .importlinter ├── .pre-commit-config.yaml ├── .pre-commit-hooks ├── check-duplicate-classes.py ├── check_hardcoded_paths.py └── safe_torch_load.py ├── .rgignore ├── .secrets.baseline ├── AGENTS.md ├── CHANGELOG.md ├── CLAUDE.md ├── Dockerfile ├── IDEAL_REFERENCE_SEIZURE_TRANSFORMER_DATAFLOW.md ├── LICENSE ├── Makefile ├── README.md ├── README_V2.md ├── RELEASE_v2.0.0.md ├── ROADMAP.md ├── SEIZURE_TRANSFORMER_CURRENT_STATUS.md ├── SEIZURE_TRANSFORMER_GAPS_AND_FIX_PLAN.md ├── TECHNICAL_DEBT.md ├── TUEV_METRICS_SSOT.md ├── TUEV_PREPROCESSING_SPECS.md ├── TUEV_REFERENCE.md ├── TUEV_REPRODUCTION_REPORT.md ├── conftest.py ├── data ├── README.md ├── datasets │ ├── tuab │ │ └── .gitkeep │ └── tuev │ │ └── .gitkeep └── models │ └── pretrained │ └── .gitkeep ├── docker-compose.yml ├── docs ├── API.md ├── ARCHITECTURE.md ├── CHANNELS.md ├── CI_CD_SETUP.md ├── CLEANUP_PLAN.md ├── EVALUATION_METRICS.md ├── MIGRATION_GUIDE.md ├── QUICK_START.md ├── README.md ├── TESTING.md ├── TRAINING.md ├── TUH_CORPUS_GUIDE.md ├── UNITS.md ├── archive │ ├── ANSWER.md │ ├── CI_VS_SCRIPTS_CLARIFICATION.md │ ├── CLASS_IMBALANCE_ANALYSIS.md │ ├── CLEANUP_TODO.md │ ├── CODEBASE_AUDIT.md │ ├── README_OLD.md │ ├── REMAINING_DEBT.md │ ├── SCRIPTS_CLEANUP_PLAN.md │ ├── ci_cd_fixes │ │ ├── CI_CD_100_PERCENT_STATUS.md │ │ ├── CI_CD_ANALYSIS.md │ │ ├── CI_CD_FINAL_AUDIT.md │ │ ├── FIX_SUMMARY.md │ │ └── SENIOR_AUDIT_PITCH.md │ ├── completed │ │ ├── ARCHITECTURE_CLARIFICATION.md │ │ ├── ARCHITECTURE_UNIFICATION_COMPLETED.md │ │ ├── CHANGELOG.md │ │ ├── EEGPT_DEPENDENCY_MAP.md │ │ ├── LICENSE │ │ ├── LITERATURE_VS_DOCS_COMPARISON.md │ │ ├── README_CHANGES_SUMMARY.md │ │ ├── SENIOR_AUDITOR_PITCH.md │ │ ├── TECHNICAL_DEBT.md │ │ ├── TECH_DEBT_IMPLEMENTATION_PLAN.md │ │ ├── TUEV_IMPLEMENTATION_SPEC.md │ │ └── tuev_fixes_2025_09_05 │ │ │ ├── P0_TUEV_AUTOREJECT_MONTAGE_FIX.md │ │ │ ├── P0_TUEV_COMPLETE_FIX.md │ │ │ ├── P1_TUEV_RANSAC_NUMPY_WARNINGS.md │ │ │ └── README.md │ ├── implementation │ │ └── 2025-09-sleep-edf-alignment │ │ │ ├── ALIGNMENT_STATUS.md │ │ │ ├── ARCHITECTURE_AUDIT.md │ │ │ ├── CACHE_PATH_ANALYSIS.md │ │ │ ├── CLEANUP_STATUS.md │ │ │ ├── CLEAN_FIX_PROPOSAL.md │ │ │ ├── COVERAGE_STRATEGY.md │ │ │ ├── CRASH_FACTS_ONLY.md │ │ │ ├── CRASH_FIX_PLAN.md │ │ │ ├── CRASH_INVESTIGATION.md │ │ │ ├── CURRENT_ALIGNMENT_STATUS.md │ │ │ ├── DIVERGENCE_FIX_ACTION_PLAN.md │ │ │ ├── FINAL_ALIGNMENT_ACTION_PLAN.md │ │ │ ├── FINAL_POLISH_CHECKLIST.md │ │ │ ├── FULL_ALIGNMENT_COMPLETE.md │ │ │ ├── IMPLEMENTATION_COMPLETE.md │ │ │ ├── MERGE_READY_SUMMARY.md │ │ │ ├── PARALLEL_PATHS_COMPLETE.md │ │ │ ├── PARALLEL_PATHS_VERIFIED.md │ │ │ ├── PATH_AUDIT.md │ │ │ ├── README.md │ │ │ ├── SLEEP_EDF_FIX_PLAN.md │ │ │ ├── TEST_DATA_DIVERGENCE_PLAN.md │ │ │ ├── TEST_SUITE_INVESTIGATION.md │ │ │ ├── TEST_SUITE_REORGANIZATION_PLAN.md │ │ │ └── TUAB_TUEV_ALIGNMENT_PLAN.md │ ├── mne_general_docs │ │ ├── MNE_AUDIT_PACKAGE_README.md │ │ ├── MNE_AUTOREJECT_IMPLEMENTATION_GUIDE.md │ │ ├── MNE_AUTOREJECT_SYNERGY.md │ │ ├── MNE_CRITICAL_GAPS_ANALYSIS.md │ │ ├── MNE_IMPLEMENTATION_PLAN.md │ │ ├── MNE_INTEGRATION_STRATEGY.md │ │ └── MNE_PREPROCESSING_PIPELINE.md │ ├── seizure_transformer │ │ ├── CURRENT_SEIZURE_TRANSFORMER_DATAFLOW.md │ │ ├── INTENDED_SEIZURE_TRANSFORMER_APPLICATION.md │ │ ├── README.md │ │ ├── SEIZURE_TRANSFORMER_CONSOLIDATION_PLAN.md │ │ ├── SEIZURE_TRANSFORMER_POSTMORTEM.md │ │ ├── TUSZ_IMPLEMENTATION.md │ │ ├── TUSZ_OSS_SUMMARY.md │ │ ├── TUSZ_ROADMAP.md │ │ └── TUSZ_SPEC.md │ ├── technical-debt │ │ ├── P0_CRITICAL_FIXES_COMPLETED.md │ │ ├── P1_FIXES_COMPLETED.md │ │ ├── P2_TECHNICAL_DEBT_SPRINTS_1-3_COMPLETED.md │ │ └── TECHNICAL_DEBT_ORIGINAL.md │ └── tuev_old │ │ ├── TUEV_CHANNEL_MISMATCH_ANALYSIS.md │ │ ├── TUEV_DIVERGENCE_ANALYSIS.md │ │ ├── TUEV_IMPLEMENTATION_PLAN.md │ │ ├── TUEV_INVESTIGATION.md │ │ └── TUEV_TROUBLESHOOTING_GUIDE.md ├── external_references │ ├── AUTOREJECT_COMPLETE_GUIDE.md │ ├── AUTOREJECT_TUAB_SPECIFIC.md │ ├── MNE_AUTOREJECT_INTEGRATION.md │ ├── MNE_PREPROCESSING_GUIDE.md │ └── README.md ├── internal │ └── email-templates.md ├── tuev │ ├── PAPER_PARITY_STATUS.md │ ├── archive │ │ ├── TUEV_FPZ_DISCREPANCY.md │ │ ├── TUEV_LOW_BAC_INVESTIGATION.md │ │ └── TUEV_PAPER_PARITY_IMPLEMENTATION_PLAN.md │ └── archived │ │ ├── EEGPT_TUEV_ACTUAL_DATA_FLOW.md │ │ ├── TUEV.md │ │ ├── TUEV_FINAL_VERDICT.md │ │ ├── TUEV_GAP_ANALYSIS.md │ │ ├── TUEV_IMBALANCE_MITIGATION.md │ │ ├── TUEV_METRICS_SSOT.md │ │ ├── TUEV_REFERENCE.md │ │ └── TUEV_REPRODUCTION_REPORT.md └── tusz │ └── archive │ ├── TUSZ_ARCHITECTURE_DECISION.md │ ├── TUSZ_BRAINSTORMING.md │ ├── TUSZ_TEMPORAL_IMPLEMENTATION.md │ └── TUSZ_WRAPPER_INTEGRATION_PLAN.md ├── examples └── end_to_end_pipeline.py ├── experiments ├── README.md ├── eegpt_linear_probe │ ├── README.md │ ├── TUEV_TRAINING_GUIDE.md │ ├── WORKSPACE_STATUS.md │ ├── archive │ │ ├── 2025-09-09_pre_paper_parity │ │ │ ├── ARCHIVE_README.md │ │ │ ├── docs │ │ │ │ ├── MAPPER_INTEGRATION.md │ │ │ │ ├── TRAINING_AUDIT.md │ │ │ │ └── test_channel_enforcement.py │ │ │ ├── output │ │ │ │ ├── smoke_20250901_171359 │ │ │ │ │ └── config.yaml │ │ │ │ ├── smoke_test │ │ │ │ │ └── config.yaml │ │ │ │ ├── smoke_test_20250901_171035 │ │ │ │ │ ├── config.yaml │ │ │ │ │ └── smoke_config.yaml │ │ │ │ ├── tuab_mne_20250829_214405 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuab_mne_20250829_214639 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuab_mne_20250901_172911 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuab_mne_20250903_104056 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuab_mne_20250904_015242 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuab_mne_20250904_015544 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuev_mne_20250905_025104 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuev_mne_20250905_025215 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuev_mne_20250905_025410 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuev_mne_20250905_124159 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuev_mne_20250905_124333 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuev_mne_20250905_124553 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuev_mne_20250908_113817 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuev_mne_fixed_20250905_141349 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuev_mne_fixed_20250905_142926 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuev_mne_fixed_20250905_143030 │ │ │ │ │ └── config.yaml │ │ │ │ ├── tuev_mne_fixed_20250905_143154 │ │ │ │ │ └── config.yaml │ │ │ │ └── tuev_v4_clean_20250905_213850 │ │ │ │ │ └── config.yaml │ │ │ └── scripts │ │ │ │ ├── build_mne_cache.sh │ │ │ │ ├── clean_tuev_restart.sh │ │ │ │ ├── launch_tuev_cache.sh │ │ │ │ └── launch_tuev_mne.sh │ │ ├── fix_history │ │ │ ├── CHANNEL_FIX_SUMMARY.md │ │ │ ├── EXPERIMENTS_ANALYSIS.md │ │ │ ├── FINAL_AUDIT_BEFORE_LAUNCH.md │ │ │ ├── FINAL_FIX_SUMMARY.md │ │ │ ├── FIX_AUDIT_SUMMARY.md │ │ │ ├── IMPORT_FIX_DOCUMENTATION.md │ │ │ ├── READY_FOR_AUDIT.md │ │ │ ├── TECH_DEBT_CRITICAL.md │ │ │ ├── TUEV_FINAL_CHECKLIST.md │ │ │ ├── TUEV_FIXES_SUMMARY.md │ │ │ └── TUEV_POLISH_SUMMARY.md │ │ └── old_tests │ │ │ ├── test_collate_functions.py │ │ │ ├── test_normalization_fix.py │ │ │ ├── test_tuev_bipolar.py │ │ │ └── test_tuev_implementation.py │ ├── balanced_training.out │ ├── balanced_training_fixed.out │ ├── configs │ │ ├── archive │ │ │ ├── README.md │ │ │ ├── tuev.yaml │ │ │ └── tuev_smoke_test.yaml │ │ ├── tuab.yaml │ │ ├── tuab_smoke_test.yaml │ │ └── tuev_paper_parity.yaml │ ├── docs_archive │ │ ├── ARCHIVE_NOTE.md │ │ ├── CHANNEL_SPECIFICATIONS.md │ │ ├── MNE_INTEGRATION_README.md │ │ └── README.md │ ├── mne_integration │ │ ├── __init__.py │ │ └── cache_builder.py │ ├── scripts │ │ ├── launch_tuab_mne.sh │ │ ├── launch_tuev_safe.sh │ │ ├── monitor_mne_training.sh │ │ └── run_smoke_test.sh │ ├── train_tuab_mne.py │ └── train_tuev_events.py └── seizure_transformer │ ├── test_quick.py │ └── train_tusz.py ├── literature ├── README.md ├── _archive │ ├── convert_mne_pdfs.py │ ├── convert_mne_pdfs_pypdf.py │ ├── convert_pdf_to_md.py │ ├── convert_seizure_preprocessing.py │ ├── convert_seizure_pymupdf.py │ ├── convert_seizure_transformer.py │ └── convert_seizure_with_marker.py ├── docx │ ├── TUAB-THESIS.docx │ ├── TUSZ-BOOK.docx │ ├── electrodes_and_channels_v30.docx │ └── picone-2021-objective-evaluation-metrics.docx ├── markdown │ ├── ALFEE │ │ ├── ALFEE.md │ │ └── README.md │ ├── EEGPT │ │ ├── EEGPT.md │ │ ├── _page_13_Figure_2.jpeg │ │ ├── _page_14_Figure_4.jpeg │ │ ├── _page_14_Figure_6.jpeg │ │ ├── _page_15_Figure_2.jpeg │ │ ├── _page_15_Figure_4.jpeg │ │ ├── _page_22_Figure_0.jpeg │ │ ├── _page_22_Figure_2.jpeg │ │ ├── _page_23_Figure_2.jpeg │ │ ├── _page_23_Figure_5.jpeg │ │ ├── _page_24_Figure_0.jpeg │ │ ├── _page_24_Figure_2.jpeg │ │ ├── _page_24_Figure_6.jpeg │ │ ├── _page_25_Figure_0.jpeg │ │ ├── _page_3_Figure_0.jpeg │ │ ├── _page_4_Figure_7.jpeg │ │ ├── _page_5_Figure_0.jpeg │ │ └── _page_8_Figure_6.jpeg │ ├── MNE-Python │ │ ├── MNE-Python.md │ │ └── README.md │ ├── MNE-SOFTWARE │ │ ├── MNE-SOFTWARE.md │ │ └── README.md │ ├── NeuroLM │ │ ├── NeuroLM.md │ │ └── README.md │ ├── README.md │ ├── autoreject │ │ ├── _page_0_Picture_0.jpeg │ │ ├── _page_22_Figure_2.jpeg │ │ ├── _page_23_Figure_2.jpeg │ │ ├── _page_24_Figure_2.jpeg │ │ ├── _page_25_Figure_2.jpeg │ │ ├── _page_26_Figure_2.jpeg │ │ ├── _page_27_Figure_2.jpeg │ │ ├── _page_28_Figure_2.jpeg │ │ ├── _page_29_Figure_2.jpeg │ │ └── autoreject.md │ ├── evaluation-metrics │ │ ├── media │ │ │ └── media │ │ │ │ ├── image1.png │ │ │ │ ├── image10.png │ │ │ │ ├── image3.png │ │ │ │ ├── image5.png │ │ │ │ ├── image6.png │ │ │ │ ├── image7.png │ │ │ │ ├── image8.png │ │ │ │ └── image9.png │ │ └── picone-2021-objective-evaluation-metrics.md │ ├── seizure_preprocessing │ │ ├── seizure_preprocessing.md │ │ ├── seizure_preprocessing.pdf-2-0.png │ │ └── seizure_preprocessing.pdf-2-1.png │ ├── seizure_transformer │ │ ├── SEIZURE_TRANSFORMER.md │ │ ├── SEIZURE_TRANSFORMER.pdf-2-0.png │ │ ├── SEIZURE_TRANSFORMER.pdf-2-1.png │ │ ├── SEIZURE_TRANSFORMER.pdf-3-0.png │ │ ├── SEIZURE_TRANSFORMER.pdf-3-1.png │ │ ├── SEIZURE_TRANSFORMER.pdf-3-2.png │ │ ├── SEIZURE_TRANSFORMER.pdf-3-3.png │ │ ├── SEIZURE_TRANSFORMER.pdf-3-4.png │ │ ├── SEIZURE_TRANSFORMER.pdf-3-5.png │ │ ├── SEIZURE_TRANSFORMER.pdf-4-0.png │ │ ├── SEIZURE_TRANSFORMER.pdf-4-1.png │ │ ├── SEIZURE_TRANSFORMER.pdf-4-3.png │ │ ├── SEIZURE_TRANSFORMER.pdf-4-4.png │ │ ├── SEIZURE_TRANSFORMER.pdf-4-5.png │ │ ├── SeizureTransformer.md │ │ ├── figure_4_0.png │ │ ├── figure_4_1.png │ │ ├── figure_4_2.png │ │ ├── figure_4_3.png │ │ └── figure_4_4.png │ ├── tuab │ │ ├── lopez-2017-tuab-thesis.md │ │ └── media │ │ │ └── media │ │ │ ├── image10.png │ │ │ ├── image11.png │ │ │ ├── image12.png │ │ │ ├── image13.png │ │ │ ├── image14.png │ │ │ ├── image15.png │ │ │ ├── image16.png │ │ │ ├── image17.png │ │ │ ├── image18.png │ │ │ ├── image19.png │ │ │ ├── image2.png │ │ │ ├── image3.png │ │ │ ├── image4.PNG │ │ │ ├── image5.png │ │ │ ├── image6.png │ │ │ ├── image7.png │ │ │ ├── image8.png │ │ │ └── image9.png │ ├── tusz │ │ ├── media │ │ │ └── media │ │ │ │ ├── image1.png │ │ │ │ ├── image2.png │ │ │ │ ├── image3.png │ │ │ │ ├── image4.png │ │ │ │ └── image5.png │ │ └── shah-2018-tusz-book-chapter.md │ ├── yasa-figures │ │ ├── _page_0_Picture_0.jpeg │ │ ├── _page_0_Picture_2.jpeg │ │ ├── _page_10_Figure_2.jpeg │ │ ├── _page_11_Figure_2.jpeg │ │ ├── _page_1_Figure_2.jpeg │ │ ├── _page_2_Figure_2.jpeg │ │ ├── _page_3_Figure_2.jpeg │ │ ├── _page_4_Figure_2.jpeg │ │ ├── _page_5_Figure_2.jpeg │ │ ├── _page_6_Figure_2.jpeg │ │ ├── _page_7_Figure_2.jpeg │ │ ├── _page_8_Figure_2.jpeg │ │ ├── _page_9_Figure_2.jpeg │ │ └── yasa-figures.md │ └── yasa │ │ ├── _page_0_Picture_0.jpeg │ │ ├── _page_4_Figure_2.jpeg │ │ ├── _page_5_Figure_8.jpeg │ │ ├── _page_9_Figure_2.jpeg │ │ └── yasa.md ├── pdf_to_markdown.py └── pdfs │ └── EEGPT.pdf ├── mkdocs.yml ├── mypy-fast.ini ├── mypy.ini ├── pyproject.toml ├── pytest.ini ├── scripts ├── README.md ├── data │ ├── TRANSFER_TO_REFERENCE_REPO.md │ ├── compare_tuev_versions.py │ ├── download_datasets.py │ ├── download_tuev_for_reference.sh │ ├── download_tusz.sh │ ├── download_tusz_auto.py │ ├── monitor_tusz_download.sh │ ├── verify_tuab_dataset.py │ └── verify_tuev_dataset.py ├── download_tusz.sh ├── evaluate_seizure_transformer.py ├── guard_no_oz.sh ├── testing │ ├── benchmark_end_to_end.py │ ├── debug_tuev_training.py │ ├── quick_api_test.py │ ├── run_benchmarks.py │ └── test_sleep_analysis.py ├── tools │ ├── coverage_report.py │ ├── fix_pass_statements.py │ ├── mypy_daemon.sh │ ├── run_green_baseline.sh │ ├── run_nightly_tests.sh │ └── verify_no_skips.sh ├── validate_before_push.sh └── validate_tuev_cache.py ├── src └── brain_go_brrr │ ├── __init__.py │ ├── __main__.py │ ├── _typing.py │ ├── api │ ├── __init__.py │ ├── app.py │ ├── auth.py │ ├── cache.py │ ├── dependencies.py │ ├── deps.py │ ├── job_store.py │ ├── main.py │ ├── models.py │ ├── py.typed │ ├── routers │ │ ├── __init__.py │ │ ├── cache.py │ │ ├── channel_router.py │ │ ├── eegpt.py │ │ ├── health.py │ │ ├── jobs.py │ │ ├── qc.py │ │ ├── queue.py │ │ ├── resources.py │ │ └── sleep.py │ ├── routes.py │ ├── schemas.py │ └── settings.py │ ├── application │ ├── __init__.py │ ├── async_base.py │ ├── config │ │ ├── __init__.py │ │ ├── abnormality_config.py │ │ └── base.py │ ├── factories.py │ ├── factories │ │ ├── detector.py │ │ ├── extractor.py │ │ └── qc.py │ ├── factories_types.py │ ├── jobs │ │ ├── __init__.py │ │ ├── models.py │ │ └── store.py │ ├── pipeline │ │ ├── __init__.py │ │ ├── eegpt_orchestration.py │ │ ├── hierarchical_pipeline.py │ │ └── parallel.py │ ├── training │ │ ├── __init__.py │ │ └── sleep_probe_trainer.py │ └── use_cases │ │ └── tasks │ │ ├── __init__.py │ │ ├── abnormality_detection.py │ │ └── enhanced_abnormality_detection.py │ ├── cli.py │ ├── config │ └── __init__.py │ ├── domain │ ├── __init__.py │ ├── abnormal │ │ ├── __init__.py │ │ ├── detector.py │ │ ├── ports.py │ │ └── settings.py │ ├── channels.py │ ├── constants.py │ ├── constraints.py │ ├── exceptions.py │ ├── ports │ │ ├── __init__.py │ │ ├── base.py │ │ └── cache.py │ ├── preprocessing │ │ ├── __init__.py │ │ ├── basic.py │ │ ├── core_logic.py │ │ ├── eegpt_preprocessing.py │ │ ├── features │ │ │ ├── __init__.py │ │ │ └── extractor.py │ │ ├── nan_policy.py │ │ ├── sleep_preprocessor.py │ │ └── window_extractor.py │ ├── protocols │ │ ├── __init__.py │ │ └── logger.py │ ├── quality │ │ ├── __init__.py │ │ └── controller.py │ └── sleep │ │ ├── __init__.py │ │ ├── analyzer.py │ │ └── analyzer_enhanced.py │ ├── infra │ ├── __init__.py │ ├── adapters │ │ ├── autoreject_adapter.py │ │ ├── logger_adapter.py │ │ ├── model_adapter.py │ │ └── preprocessor_flexible.py │ ├── cache.py │ ├── cache_factory.py │ ├── data │ │ ├── __init__.py │ │ ├── channels.py │ │ ├── edf_loader.py │ │ ├── edf_streaming.py │ │ ├── edf_validator.py │ │ ├── tuab_cached_dataset.py │ │ ├── tuab_dataset.py │ │ ├── tuab_enhanced_dataset.py │ │ ├── tuev_dataset.py │ │ ├── tuev_event_dataset.py │ │ ├── tusz_detection_dataset.py │ │ └── tusz_labels.py │ ├── eval │ │ ├── nedc_wrapper.py │ │ └── post_processing.py │ ├── external │ │ └── yasa_adapter.py │ ├── logger.py │ ├── ml_models │ │ ├── __init__.py │ │ ├── channel_mapper.py │ │ ├── eegpt_architecture.py │ │ ├── eegpt_compat.py │ │ ├── eegpt_probe_unified.py │ │ ├── eegpt_wrapper.py │ │ ├── linear_probe.py │ │ ├── probe_factory.py │ │ ├── seizure_transformer_utils.py │ │ ├── seizure_transformer_wrapper.py │ │ └── seizure_transformer_wu2025.py │ ├── preprocessing │ │ ├── __init__.py │ │ ├── autoreject_adapter.py │ │ ├── channel_utils.py │ │ ├── chunked_autoreject.py │ │ ├── eeg_preprocessor.py │ │ ├── flexible_preprocessor.py │ │ ├── mne_preprocessor.py │ │ ├── snippets │ │ │ ├── __init__.py │ │ │ └── maker.py │ │ ├── tuev_event_extractor.py │ │ └── tuev_preprocessor.py │ ├── py.typed │ ├── redis │ │ ├── __init__.py │ │ ├── pool.py │ │ └── redis_migration.md │ ├── safe_load.py │ ├── serialization.py │ └── training │ │ └── losses.py │ ├── mne_compat.py │ ├── models │ └── __init__.py │ ├── preprocessing │ └── __init__.py │ ├── presentation │ ├── __init__.py │ └── visualization │ │ ├── __init__.py │ │ ├── markdown_report.py │ │ └── pdf_report.py │ ├── py.typed │ ├── services │ ├── __init__.py │ └── hierarchical_pipeline.py │ ├── utils │ ├── __init__.py │ ├── collate_tuab.py │ ├── collate_tuev.py │ ├── collate_tuev_parity.py │ ├── deprecated_redirect.py │ ├── logging_utils.py │ ├── probe_utils.py │ ├── sampling.py │ └── time.py │ └── visualization │ └── __init__.py ├── stubs ├── GPUtil.pyi ├── autoreject.pyi ├── tsfresh.pyi └── yasa.pyi ├── tests ├── README.md ├── __init__.py ├── _mocks.py ├── _test_utils.py ├── benchmarks │ ├── benchmark_config.py │ ├── conftest.py │ ├── test_eegpt_microbench.py │ ├── test_eegpt_performance.py │ ├── test_performance.py │ └── test_smoke.py ├── conftest.py ├── fakes.py ├── fixtures │ ├── __init__.py │ ├── benchmark_data.py │ ├── cache_fixtures.py │ ├── deterministic_fixtures.py │ ├── eeg │ │ ├── README.md │ │ ├── labels.json │ │ ├── tuab_001_norm_30s.fif │ │ ├── tuab_001_norm_5s.fif │ │ ├── tuab_002_norm_30s.fif │ │ ├── tuab_002_norm_5s.fif │ │ ├── tuab_003_abnorm_30s.fif │ │ ├── tuab_003_abnorm_5s.fif │ │ ├── tuab_004_abnorm_30s.fif │ │ ├── tuab_004_abnorm_5s.fif │ │ └── tuab_005_short_10s.fif │ ├── mock_eeg_generator.py │ ├── mock_eegpt.py │ ├── simple_mock_eegpt.py │ ├── synthetic_data.py │ └── tuab_fixtures.py ├── import_mapping.md ├── integration │ ├── api │ │ ├── test_api.py │ │ ├── test_api_auth.py │ │ ├── test_api_endpoints.py │ │ ├── test_api_linear_probe.py │ │ ├── test_api_root.py │ │ ├── test_api_sleep_edf.py │ │ ├── test_job_queue_api.py │ │ └── test_sleep_analysis_api.py │ ├── conftest.py │ ├── infra │ │ ├── data │ │ │ └── test_tusz_dataset_integration.py │ │ └── ml_models │ │ │ └── test_seizure_transformer_integration.py │ ├── test_abnormality_real.py │ ├── test_classifier_compatibility.py │ ├── test_data_pipeline_integration.py │ ├── test_data_pipeline_real.py │ ├── test_eegpt_integration.py │ ├── test_eegpt_real_inference.py │ ├── test_eegpt_streaming_integration.py │ ├── test_end_to_end.py │ ├── test_hierarchical_pipeline.py │ ├── test_parallel_pipeline.py │ ├── test_pdf_report_integration.py │ ├── test_preprocessing_real.py │ ├── test_sleep_enhanced.py │ ├── test_train_sleep_probe.py │ ├── test_tuab_normalized.py │ ├── test_tuab_real_data.py │ ├── test_tuab_smoke.py │ ├── test_tuev_event_pipeline.py │ ├── test_tuev_paper_parity.py │ ├── test_tuev_real_data.py │ ├── test_tuev_smoke.py │ ├── test_yasa_channel_aliasing.py │ └── test_yasa_integration.py ├── quality │ └── test_code_quality.py ├── smoke │ ├── test_api_contract.py │ ├── test_cli_and_version.py │ ├── test_e2e_pipeline_synthetic.py │ ├── test_end_to_end_wiring.py │ ├── test_factories_contract.py │ └── test_imports.py └── unit │ ├── api │ ├── routers │ │ ├── test_cache.py │ │ ├── test_eegpt.py │ │ ├── test_eegpt_p0_green.py │ │ ├── test_resources.py │ │ └── test_resources_clean.py │ ├── test_app.py │ ├── test_cache.py │ ├── test_channel_router.py │ ├── test_dependencies.py │ ├── test_legitimate_api.py │ ├── test_models.py │ ├── test_p0_regression_guard.py │ ├── test_routes.py │ └── test_schemas.py │ ├── application │ ├── config │ │ ├── test_config.py │ │ └── test_defaults.py │ ├── jobs │ │ ├── test_serialization.py │ │ └── test_store_behavior.py │ ├── pipeline │ │ └── test_orchestration.py │ ├── test_abnormality_probe_checkpoint_loading.py │ ├── test_async_base.py │ └── test_threadsafe_job_store.py │ ├── cli │ ├── test_cli.py │ ├── test_commands.py │ └── test_streaming.py │ ├── data │ ├── test_edf_loader_unit.py │ └── test_edf_streaming_edges.py │ ├── domain │ ├── abnormal │ │ ├── test_accuracy.py │ │ ├── test_enhanced.py │ │ ├── test_metrics.py │ │ └── test_preprocessor.py │ ├── ports │ │ └── test_behavior.py │ ├── preprocessing │ │ ├── test_core.py │ │ ├── test_flexible.py │ │ ├── test_nan_policy.py │ │ ├── test_pipeline.py │ │ ├── test_window_extractor.py │ │ ├── test_window_extractor_edges.py │ │ └── test_window_tail.py │ ├── quality │ │ └── test_controller.py │ ├── sleep │ │ ├── test_analysis.py │ │ ├── test_enhanced_analyzer.py │ │ ├── test_montage_detection.py │ │ └── test_preprocessor.py │ ├── test_channel_mapper.py │ ├── test_channels.py │ ├── test_constants.py │ ├── test_constraints_layers.py │ ├── test_exceptions.py │ ├── test_exceptions_hierarchy.py │ ├── test_ports_cache_contract.py │ └── test_settings.py │ ├── infra │ ├── adapters │ │ └── test_autoreject.py │ ├── cache │ │ └── test_factory.py │ ├── data │ │ ├── test_edf_loader.py │ │ ├── test_edf_streaming.py │ │ └── test_edf_validator.py │ ├── eval │ │ ├── test_nedc_wrapper.py │ │ └── test_post_processing.py │ ├── external │ │ ├── test_yasa_adapter.py │ │ ├── test_yasa_compliance.py │ │ └── test_yasa_smoothing.py │ ├── ml_models │ │ ├── test_channel_mapper.py │ │ ├── test_checkpoint_loading.py │ │ ├── test_compat_coverage.py │ │ ├── test_compat_strict.py │ │ ├── test_contract_fuzzer.py │ │ ├── test_discrimination.py │ │ ├── test_encoder_output.py │ │ ├── test_feature_extractor.py │ │ ├── test_linear_probe.py │ │ ├── test_model_loading.py │ │ ├── test_pipeline.py │ │ ├── test_preprocessing.py │ │ ├── test_probe.py │ │ ├── test_probe_head.py │ │ ├── test_probe_unified.py │ │ ├── test_robust_probe.py │ │ ├── test_rotary_embedding.py │ │ ├── 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