├── .editorconfig ├── .flake8 ├── .github └── workflows │ ├── precommit_autoupdate.yaml │ ├── run_precommit.yaml │ ├── run_tests.yaml │ └── todo_to_issue.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── LICENSE ├── docker └── jupyter_omnipy │ ├── Dockerfile │ ├── README.md │ └── config │ ├── completion.jupyterlab-settings │ ├── manager.jupyterlab-settings │ ├── notification.jupyterlab-settings │ ├── plugin.jupyterlab-settings │ ├── pyright.json │ └── tracker.jupyterlab-settings ├── docs ├── contributing.md ├── data_models.md ├── examples │ └── dynamic_mixin_example.py ├── gen_ref_pages.py ├── graphs │ ├── top_level_modules │ │ ├── omnipy.dot │ │ └── omnipy.png │ └── two_level_modules │ │ ├── omnipy.dot │ │ └── omnipy.png ├── images │ ├── favicon.png │ ├── favicon │ │ ├── apple-touch-icon.png │ │ ├── favicon-96x96.png │ │ ├── favicon.ico │ │ ├── favicon.svg │ │ ├── favicon_html_links.txt │ │ ├── site.webmanifest │ │ ├── web-app-manifest-192x192.png │ │ └── web-app-manifest-512x512.png │ ├── omnipy-logo-180.png │ ├── omnipy-logo-320.png │ ├── omnipy-logo-640.png │ ├── omnipy-logo-white-180.png │ ├── omnipy-logo-white-320.png │ ├── omnipy-logo-white-640.png │ ├── omnipy-overview-comics-style.png │ ├── omnipy-puzzle-piece-favicon-dark.graffle │ ├── omnipy-puzzle-piece-favicon-dark.png │ ├── omnipy-puzzle-piece-favicon.graffle │ ├── omnipy-puzzle-piece-favicon.png │ ├── omnipy-puzzle-piece-logo-white.graffle │ ├── omnipy-puzzle-piece-logo-white.png │ ├── omnipy-puzzle-piece.graffle │ └── omnipy-puzzle-piece.png ├── index.md ├── notebooks │ ├── auto_complete.ipynb │ ├── ihec_encode.ipynb │ ├── isa_json_data_wrangling_example.ipynb │ ├── nobel_api_output_model.py │ └── nobel_idw2025.ipynb ├── old_readme.md ├── overrides │ ├── javascripts │ │ └── extra.js │ └── stylesheets │ │ └── extra.css ├── parse_dont_validate.md ├── python_typing.md ├── readme.md ├── release_notes.md └── use_cases.md ├── mkdocs.yml ├── pycharm-file-watchers.xml ├── pyproject.toml ├── scripts ├── import_performance.sh ├── isa_json_poster_example.py ├── json_types_import.py ├── omnipy_import.py ├── print_layout_panels.py ├── profile_module_as_script.py ├── pydeps_script.py ├── simple_print.py └── styles │ ├── donuts.json │ ├── export_to_styles.py │ └── get_all_tinted_style_names.py ├── src └── omnipy │ ├── __init__.py │ ├── _dynamic_all.py │ ├── components │ ├── __init__.py │ ├── _fairtracks │ │ ├── __init__.py │ │ ├── create_filter.py │ │ ├── functions.py │ │ ├── get_from_filter.py │ │ └── tasks.py │ ├── _frozen │ │ ├── __init__.py │ │ ├── datasets.py │ │ ├── models.py │ │ └── typedefs.py │ ├── general │ │ ├── __init__.py │ │ ├── models.py │ │ └── tasks.py │ ├── isa │ │ ├── __init__.py │ │ ├── datasets.py │ │ ├── flows.py │ │ └── models │ │ │ ├── __init__.py │ │ │ ├── assay_schema.py │ │ │ ├── comment_schema.py │ │ │ ├── data_schema.py │ │ │ ├── factor_schema.py │ │ │ ├── factor_value_schema.py │ │ │ ├── investigation_schema.py │ │ │ ├── material_attribute_schema.py │ │ │ ├── material_attribute_value_schema.py │ │ │ ├── material_schema.py │ │ │ ├── ontology_annotation_schema.py │ │ │ ├── ontology_source_reference_schema.py │ │ │ ├── organization_schema.py │ │ │ ├── person_schema.py │ │ │ ├── process_parameter_value_schema.py │ │ │ ├── process_schema.py │ │ │ ├── protocol_parameter_schema.py │ │ │ ├── protocol_schema.py │ │ │ ├── publication_schema.py │ │ │ ├── sample_schema.py │ │ │ ├── source_schema.py │ │ │ ├── study_group.py │ │ │ ├── study_schema.py │ │ │ └── validators.py │ ├── json │ │ ├── __init__.py │ │ ├── _functions.py │ │ ├── constants.py │ │ ├── datasets.py │ │ ├── flows.py │ │ ├── models.py │ │ ├── serializers.py │ │ ├── tasks.py │ │ └── typedefs.py │ ├── pandas │ │ ├── __init__.py │ │ ├── datasets.py │ │ ├── helpers.py │ │ ├── lazy_import.py │ │ ├── models.py │ │ ├── serializers.py │ │ └── tasks.py │ ├── prefect │ │ ├── __init__.py │ │ ├── engine │ │ │ ├── __init__.py │ │ │ └── prefect.py │ │ ├── lazy_import.py │ │ └── settings │ │ │ └── logging.yml │ ├── raw │ │ ├── __init__.py │ │ ├── datasets.py │ │ ├── models.py │ │ ├── protocols.py │ │ ├── serializers.py │ │ └── tasks.py │ ├── remote │ │ ├── __init__.py │ │ ├── constants.py │ │ ├── datasets.py │ │ ├── helpers.py │ │ ├── lazy_import.py │ │ ├── models.py │ │ └── tasks.py │ └── tables │ │ ├── __init__.py │ │ ├── datasets.py │ │ ├── models.py │ │ └── tasks.py │ ├── compute │ ├── __init__.py │ ├── _func_job.py │ ├── _job.py │ ├── _job_creator.py │ ├── _mixins │ │ ├── __init__.py │ │ ├── auto_async.py │ │ ├── flow_context.py │ │ ├── func_signature.py │ │ ├── iterate.py │ │ ├── name.py │ │ ├── params.py │ │ ├── result_key.py │ │ ├── serialize.py │ │ └── typedefs.py │ ├── _tasklist_job.py │ ├── flow.py │ └── task.py │ ├── config │ ├── __init__.py │ ├── data.py │ ├── engine.py │ ├── job.py │ └── root_log.py │ ├── data │ ├── __init__.py │ ├── _data_class_creator.py │ ├── _display │ │ ├── __init__.py │ │ ├── config.py │ │ ├── constraints.py │ │ ├── dimensions.py │ │ ├── frame.py │ │ ├── helpers.py │ │ ├── integrations │ │ │ ├── __init__.py │ │ │ ├── browser │ │ │ │ ├── __init__.py │ │ │ │ └── macosx.py │ │ │ └── jupyter │ │ │ │ ├── AvailableDisplayDimsDetector.vue │ │ │ │ ├── DimsCalculator.vue │ │ │ │ ├── ModelBrowser.vue │ │ │ │ ├── PageBgColorDetector.vue │ │ │ │ ├── __init__.py │ │ │ │ ├── components.py │ │ │ │ └── helpers.py │ │ ├── layout │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ └── flow │ │ │ │ ├── __init__.py │ │ │ │ ├── base.py │ │ │ │ └── helpers.py │ │ ├── panel │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── cropping.py │ │ │ ├── draft │ │ │ │ ├── __init__.py │ │ │ │ ├── base.py │ │ │ │ ├── layout.py │ │ │ │ ├── monospaced.py │ │ │ │ └── text.py │ │ │ ├── helpers.py │ │ │ ├── styling │ │ │ │ ├── __init__.py │ │ │ │ ├── base.py │ │ │ │ ├── layout.py │ │ │ │ ├── output.py │ │ │ │ └── text.py │ │ │ └── typedefs.py │ │ ├── styles │ │ │ ├── __init__.py │ │ │ ├── dynamic_styles.py │ │ │ ├── helpers.py │ │ │ └── omnipy_selenized.py │ │ └── text │ │ │ ├── __init__.py │ │ │ ├── pretty.py │ │ │ └── pretty_printer │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── bytes.py │ │ │ ├── compact_json.py │ │ │ ├── devtools.py │ │ │ ├── mixins.py │ │ │ ├── register.py │ │ │ ├── rich.py │ │ │ └── text.py │ ├── _mimic_models.py │ ├── _missing.py │ ├── _mixins │ │ ├── __init__.py │ │ ├── display.py │ │ └── task.py │ ├── _selector.py │ ├── _typedefs.py │ ├── dataset.py │ ├── helpers.py │ ├── model.py │ ├── param.py │ ├── serializer.py │ ├── snapshot.py │ └── typechecks.py │ ├── engine │ ├── __init__.py │ ├── _base.py │ ├── job_runner.py │ └── local.py │ ├── hub │ ├── __init__.py │ ├── _registry.py │ ├── log │ │ ├── __init__.py │ │ ├── _handlers.py │ │ ├── _root_log.py │ │ └── mixin.py │ ├── runtime.py │ └── ui.py │ ├── py.typed │ ├── shared │ ├── __init__.py │ ├── _typedefs.py │ ├── constants.py │ ├── enums │ │ ├── __init__.py │ │ ├── colorstyles.py │ │ ├── data.py │ │ ├── display.py │ │ ├── job.py │ │ └── ui.py │ ├── exceptions.py │ ├── protocols │ │ ├── __init__.py │ │ ├── _util.py │ │ ├── builtins.py │ │ ├── compute │ │ │ ├── __init__.py │ │ │ ├── _job.py │ │ │ ├── job.py │ │ │ ├── job_creator.py │ │ │ └── mixins.py │ │ ├── config.py │ │ ├── data.py │ │ ├── engine │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ └── job_runner.py │ │ ├── hub │ │ │ ├── __init__.py │ │ │ ├── log.py │ │ │ ├── registry.py │ │ │ └── runtime.py │ │ └── util.py │ └── typedefs.py │ └── util │ ├── __init__.py │ ├── _pydantic.py │ ├── callable_decorator.py │ ├── contexts.py │ ├── dataframe.py │ ├── decorators.py │ ├── helpers.py │ ├── literal_enum.py │ ├── literal_enum_generator.py │ ├── memo.py │ ├── mixin.py │ ├── param_key_mapper.py │ ├── publisher.py │ ├── range_lookup.py │ ├── setdeque.py │ └── weak.py └── tests ├── __init__.py ├── components ├── __init__.py ├── conftest.py ├── fairtracks │ └── __init__.py ├── frozen │ ├── __init__.py │ ├── cases │ │ ├── __init__.py │ │ ├── frozen_data.py │ │ └── raw │ │ │ ├── __init__.py │ │ │ └── examples.py │ ├── test_dataset.py │ ├── test_models.py │ └── test_types.py ├── general │ ├── __init__.py │ ├── helpers │ │ ├── __init__.py │ │ └── models.py │ ├── test_models.py │ └── test_tasks.py ├── helpers │ ├── __init__.py │ ├── classes.py │ └── remote │ │ └── __init__.py ├── json │ ├── __init__.py │ ├── cases │ │ ├── __init__.py │ │ ├── json_data.py │ │ └── raw │ │ │ ├── __init__.py │ │ │ └── examples.py │ ├── test_json.py │ ├── test_json_datasets.py │ ├── test_json_models.py │ ├── test_json_tasks.py │ ├── test_json_types.yml │ └── test_serialize_json.py ├── pandas │ ├── __init__.py │ ├── cases │ │ ├── __init__.py │ │ └── tablepairs.py │ ├── conftest.py │ ├── helpers │ │ ├── __init__.py │ │ ├── asserts.py │ │ └── functions.py │ ├── test_dataframe_merge.py │ ├── test_helpers.py │ ├── test_pandas_dataset.py │ ├── test_pandas_model.py │ └── test_serialize_pandas.py ├── prefect │ ├── __init__.py │ └── test_prefect.py ├── raw │ ├── __init__.py │ ├── test_datasets.py │ ├── test_models.py │ └── test_tasks.py ├── remote │ ├── __init__.py │ ├── cases │ │ ├── __init__.py │ │ └── request_types.py │ ├── conftest.py │ ├── helpers │ │ ├── __init__.py │ │ └── classes.py │ ├── test_datasets.py │ ├── test_helpers.py │ ├── test_models.py │ └── test_tasks.py └── tables │ ├── __init__.py │ ├── test_models.py │ └── test_tasks.py ├── compute ├── __init__.py ├── cases │ ├── __init__.py │ ├── decorators.py │ ├── flows.py │ ├── iterate_tasks.py │ ├── raw │ │ ├── __init__.py │ │ └── functions.py │ └── tasks.py ├── conftest.py ├── helpers │ ├── __init__.py │ ├── classes.py │ ├── functions.py │ └── mocks.py ├── mixins │ ├── __init__.py │ ├── test_auto_async.py │ ├── test_func_signature.py │ ├── test_iterate.py │ ├── test_mixin_integration.py │ ├── test_name.py │ ├── test_params.py │ └── test_result_key.py ├── test_decorators.py ├── test_flow.py ├── test_job.py ├── test_job_creator.py └── test_task.py ├── config ├── __init__.py └── test_display_config.py ├── conftest.py ├── data ├── __init__.py ├── conftest.py ├── display │ ├── __init__.py │ ├── conftest.py │ ├── helpers │ │ ├── __init__.py │ │ └── mocks.py │ ├── integrations │ │ ├── __init__.py │ │ └── jupyter │ │ │ ├── __init__.py │ │ │ └── test_helpers.py │ ├── layout │ │ ├── __init__.py │ │ ├── flow │ │ │ ├── __init__.py │ │ │ ├── cases │ │ │ │ ├── __init__.py │ │ │ │ └── layout_reflow.py │ │ │ ├── helpers │ │ │ │ └── mocks.py │ │ │ └── test_layout_flow.py │ │ └── test_layout.py │ ├── panel │ │ ├── __init__.py │ │ ├── bytes │ │ │ ├── __init__.py │ │ │ └── test_bytes_draft.py │ │ ├── conftest.py │ │ ├── helpers │ │ │ ├── __init__.py │ │ │ ├── case_setup.py │ │ │ ├── mocks.py │ │ │ └── panel_assert.py │ │ ├── layout │ │ │ ├── __init__.py │ │ │ ├── cases │ │ │ │ ├── __init__.py │ │ │ │ ├── layout_basics.py │ │ │ │ └── layout_styling.py │ │ │ ├── test_layout_draft.py │ │ │ └── test_layout_styling.py │ │ ├── test_draft.py │ │ ├── test_panel.py │ │ └── text │ │ │ ├── __init__.py │ │ │ ├── cases │ │ │ ├── __init__.py │ │ │ ├── text_basics.py │ │ │ └── text_styling.py │ │ │ ├── test_text_draft.py │ │ │ └── test_text_styling.py │ ├── styles │ │ ├── __init__.py │ │ └── test_styles.py │ ├── test_config.py │ ├── test_constraints.py │ ├── test_dimensions.py │ ├── test_frame.py │ ├── test_helpers.py │ └── text │ │ ├── __init__.py │ │ └── test_pretty.py ├── helpers │ ├── __init__.py │ ├── classes.py │ ├── datasets.py │ ├── functions.py │ ├── mocks.py │ └── models.py ├── test_data_class_creator.py ├── test_dataset.py ├── test_helpers.py ├── test_model.py ├── test_param.py ├── test_serializer.py └── test_snapshot.py ├── engine ├── __init__.py ├── cases │ ├── __init__.py │ ├── raw │ │ ├── __init__.py │ │ └── functions.py │ └── tasks.py ├── conftest.py ├── helpers │ ├── __init__.py │ ├── classes.py │ ├── functions.py │ └── mocks.py ├── test_all_engines.py ├── test_base.py └── test_job_runner.py ├── helpers ├── __init__.py ├── functions.py └── protocols.py ├── hub ├── __init__.py ├── helpers │ ├── __init__.py │ └── functions.py ├── log │ ├── __init__.py │ ├── test_log_mixin.py │ └── test_root_log.py ├── registry │ ├── __init__.py │ ├── conftest.py │ └── test_registry.py └── runtime │ ├── __init__.py │ ├── helpers │ ├── __init__.py │ └── mocks.py │ └── test_runtime.py ├── integration ├── __init__.py ├── conftest.py ├── novel │ ├── __init__.py │ ├── full │ │ ├── __init__.py │ │ ├── cases │ │ │ ├── __init__.py │ │ │ ├── flows.py │ │ │ └── raw │ │ │ │ ├── __init__.py │ │ │ │ ├── asserts.py │ │ │ │ ├── flows.py │ │ │ │ ├── tasks.py │ │ │ │ └── validators.py │ │ ├── helpers │ │ │ ├── __init__.py │ │ │ └── models.py │ │ ├── test_multi_model_dataset.py │ │ └── test_three_task_flow.py │ └── serialize │ │ ├── __init__.py │ │ ├── cases │ │ ├── __init__.py │ │ ├── datasets.py │ │ ├── functions.py │ │ └── jobs.py │ │ ├── conftest.py │ │ ├── test_serialize.py │ │ └── test_serializer_registry.py └── reused │ ├── __init__.py │ ├── compute │ ├── __init__.py │ ├── conftest.py │ ├── test_decorators_with_all_engines.py │ ├── test_flow_with_all_engines.py │ └── test_task_with_all_engines.py │ ├── conftest.py │ └── engine │ ├── __init__.py │ ├── conftest.py │ └── test_all_engines_with_real_jobs_and_registry.py ├── py.typed ├── test_omnipy.py └── util ├── __init__.py ├── conftest.py ├── helpers ├── __init__.py ├── classes.py ├── mocks.py └── other_module.py ├── test_callable_decorator_cls.py ├── test_contexts.py ├── test_data_publisher.py ├── test_decorators.py ├── test_dynamic_mixin.py ├── test_get_datetime_format.py ├── test_helpers.py ├── test_literal_enum.py ├── test_literal_enum_docs.py ├── test_literal_enum_generator.py ├── test_mako_helpers.py ├── test_memo.py ├── test_param_key_mapper.py ├── test_range_lookup.py ├── test_setdeque.py └── test_weak.py /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fairtracks/omnipy/HEAD/.editorconfig 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