├── .flake8 ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── user-story.md ├── copilot-instructions.md └── workflows │ ├── publish_dev.yml │ ├── run_dev_tests.yml │ ├── run_main_tests.yml │ ├── tag_and_publish_main.yml │ └── update_docs.yml ├── .gitignore ├── .readthedocs.yaml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── base │ └── core │ │ ├── acquisition.md │ │ ├── data_description.md │ │ ├── instrument.md │ │ ├── metadata.md │ │ ├── model.md │ │ ├── procedures.md │ │ ├── processing.md │ │ ├── quality_control.md │ │ └── subject.md ├── make.bat └── source │ ├── _static │ ├── bregma_and_lambda2.png │ ├── coordinates2.png │ ├── coordinates2_original.png │ ├── custom.css │ ├── dark-logo.svg │ ├── favicon.ico │ ├── light-logo.svg │ ├── session_image_1.png │ ├── session_image_2.png │ └── session_image_3.png │ ├── acquisition.md │ ├── aind_data_schema_models │ ├── atlas.md │ ├── brain_atlas.md │ ├── coordinates.md │ ├── data_name_patterns.md │ ├── devices.md │ ├── external.md │ ├── harp_types.md │ ├── licenses.md │ ├── modalities.md │ ├── organizations.md │ ├── pid_names.md │ ├── process_names.md │ ├── reagent.md │ ├── registries.md │ ├── species.md │ ├── specimen_procedure_types.md │ ├── stimulus_modality.md │ ├── system_architecture.md │ └── units.md │ ├── components.rst │ ├── components │ ├── configs.md │ ├── connections.md │ ├── coordinates.md │ ├── devices.md │ ├── identifiers.md │ ├── injection_procedures.md │ ├── measurements.md │ ├── reagent.md │ ├── specimen_procedures.md │ ├── stimulus.md │ ├── subject_procedures.md │ ├── subjects.md │ └── surgery_procedures.md │ ├── conf.py │ ├── coordinate_systems.md │ ├── data_description.md │ ├── example_workflow │ ├── example_workflow.md │ ├── example_workflow.py │ └── example_workflow.xlsx │ ├── general.md │ ├── index.rst │ ├── instrument.md │ ├── metadata.md │ ├── model.md │ ├── procedures.md │ ├── processing.md │ ├── quality_control.md │ ├── registries.rst │ ├── related_standards.md │ ├── subject.md │ └── validation.md ├── examples ├── __init__.py ├── aibs_smartspim_instrument.py ├── aibs_smartspim_procedures.py ├── aind_smartspim_instrument.py ├── bergamo_ophys_acquisition.py ├── data_description.py ├── ephys_acquisition.py ├── ephys_instrument.py ├── exaspim_acquisition.py ├── exaspim_instrument.py ├── exaspim_quality_control.py ├── fip_behavior_instrument.py ├── fip_ophys_acquisition.py ├── fip_ophys_instrument.py ├── model.py ├── mri_acquisition.py ├── multiplane_ophys_acquisition.py ├── multiplane_ophys_instrument.py ├── ophys_acquisition.py ├── ophys_procedures.py ├── procedures.py ├── processing.py ├── quality_control.py └── subject.py ├── pyproject.toml ├── schemas ├── acquisition_schema.json ├── data_description_schema.json ├── instrument_schema.json ├── metadata_schema.json ├── model_schema.json ├── procedures_schema.json ├── processing_schema.json ├── quality_control_schema.json └── subject_schema.json ├── setup.py ├── src └── aind_data_schema │ ├── __init__.py │ ├── base.py │ ├── components │ ├── __init__.py │ ├── configs.py │ ├── connections.py │ ├── coordinates.py │ ├── devices.py │ ├── identifiers.py │ ├── injection_procedures.py │ ├── measurements.py │ ├── reagent.py │ ├── specimen_procedures.py │ ├── stimulus.py │ ├── subject_procedures.py │ ├── subjects.py │ ├── surgery_procedures.py │ └── wrappers.py │ ├── core │ ├── __init__.py │ ├── acquisition.py │ ├── data_description.py │ ├── instrument.py │ ├── metadata.py │ ├── model.py │ ├── procedures.py │ ├── processing.py │ ├── quality_control.py │ └── subject.py │ └── utils │ ├── __init__.py │ ├── compatibility_check.py │ ├── docs │ ├── doc_generator.py │ ├── model_generator.py │ ├── registries_generator.py │ └── utils.py │ ├── examples_generator.py │ ├── exceptions.py │ ├── json_writer.py │ ├── merge.py │ ├── schema_version_bump.py │ └── validators.py └── tests ├── __init__.py ├── test_acquisition.py ├── test_acquisition_configs.py ├── test_aind_generic.py ├── test_base.py ├── test_bump_schema_versions.py ├── test_compatibility_check.py ├── test_composability_merge.py ├── test_configs.py ├── test_coordinates.py ├── test_data_description.py ├── test_device.py ├── test_examples.py ├── test_examples_generator.py ├── test_identifiers.py ├── test_imaging.py ├── test_inst_acq_compatibility.py ├── test_instrument.py ├── test_json_writer.py ├── test_measurements.py ├── test_metadata.py ├── test_model.py ├── test_procedures.py ├── test_processing.py ├── test_quality_control.py ├── test_stimulus.py ├── test_subject.py ├── test_subjects.py ├── test_utils_merge.py ├── test_utils_validators.py └── test_wrappers.py /.flake8: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/HEAD/.flake8 -------------------------------------------------------------------------------- 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