CHANGELOG.rst
CODE_OF_CONDUCT.rst
CONTRIBUTING.rst
LICENSE.txt
MANIFEST.in
README.rst
pyproject.toml
setup.py
docs/Makefile
docs/nitpick-exceptions
docs/source/conf.py
docs/source/glossary.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/_static/style.css
docs/source/_templates/layout.html
docs/source/api_reference/config_tree.rst
docs/source/api_reference/exceptions.rst
docs/source/api_reference/index.rst
docs/source/api_reference/interpolation.rst
docs/source/api_reference/testing_utilities.rst
docs/source/api_reference/framework/configuration.rst
docs/source/api_reference/framework/engine.rst
docs/source/api_reference/framework/event.rst
docs/source/api_reference/framework/index.rst
docs/source/api_reference/framework/lifecycle.rst
docs/source/api_reference/framework/lookup.rst
docs/source/api_reference/framework/metrics.rst
docs/source/api_reference/framework/plugins.rst
docs/source/api_reference/framework/randomness.rst
docs/source/api_reference/framework/resource.rst
docs/source/api_reference/framework/state_machine.rst
docs/source/api_reference/framework/time.rst
docs/source/api_reference/framework/utilities.rst
docs/source/api_reference/framework/values.rst
docs/source/api_reference/framework/artifact/artifact.rst
docs/source/api_reference/framework/artifact/hdf.rst
docs/source/api_reference/framework/artifact/index.rst
docs/source/api_reference/framework/artifact/manager.rst
docs/source/api_reference/framework/components/index.rst
docs/source/api_reference/framework/components/manager.rst
docs/source/api_reference/framework/components/parser.rst
docs/source/api_reference/framework/population/exceptions.rst
docs/source/api_reference/framework/population/index.rst
docs/source/api_reference/framework/population/manager.rst
docs/source/api_reference/framework/population/population_view.rst
docs/source/api_reference/interface/cli.rst
docs/source/api_reference/interface/index.rst
docs/source/api_reference/interface/interactive.rst
docs/source/api_reference/interface/utilities.rst
docs/source/concepts/builder.rst
docs/source/concepts/components.rst
docs/source/concepts/configuration.rst
docs/source/concepts/crn.rst
docs/source/concepts/data.rst
docs/source/concepts/entry_points.rst
docs/source/concepts/event.rst
docs/source/concepts/index.rst
docs/source/concepts/interpolation.rst
docs/source/concepts/lifecycle.rst
docs/source/concepts/lookup.rst
docs/source/concepts/population.rst
docs/source/concepts/resource.rst
docs/source/concepts/time.rst
docs/source/concepts/values.rst
docs/source/concepts/model_specification/index.rst
docs/source/concepts/model_specification/yaml_basics.rst
docs/source/images/crn_compare_cubes.jpg
docs/source/images/crn_cube.jpg
docs/source/images/crn_sim_alignment.jpg
docs/source/images/pipeline.jpg
docs/source/tutorials/artifact.rst
docs/source/tutorials/boids.rst
docs/source/tutorials/disease_model.rst
docs/source/tutorials/exploration.rst
docs/source/tutorials/getting_started.rst
docs/source/tutorials/index.rst
docs/source/tutorials/running_a_simulation/cli.rst
docs/source/tutorials/running_a_simulation/index.rst
docs/source/tutorials/running_a_simulation/interactive.rst
src/vivarium/__about__.py
src/vivarium/__init__.py
src/vivarium/config_tree.py
src/vivarium/exceptions.py
src/vivarium/interpolation.py
src/vivarium/testing_utilities.py
src/vivarium.egg-info/PKG-INFO
src/vivarium.egg-info/SOURCES.txt
src/vivarium.egg-info/dependency_links.txt
src/vivarium.egg-info/entry_points.txt
src/vivarium.egg-info/not-zip-safe
src/vivarium.egg-info/requires.txt
src/vivarium.egg-info/top_level.txt
src/vivarium/examples/__init__.py
src/vivarium/examples/boids/__init__.py
src/vivarium/examples/boids/location.py
src/vivarium/examples/boids/neighbors.py
src/vivarium/examples/boids/population.py
src/vivarium/examples/boids/visualization.py
src/vivarium/examples/disease_model/__init__.py
src/vivarium/examples/disease_model/disease.py
src/vivarium/examples/disease_model/disease_model.yaml
src/vivarium/examples/disease_model/intervention.py
src/vivarium/examples/disease_model/mortality.py
src/vivarium/examples/disease_model/observer.py
src/vivarium/examples/disease_model/population.py
src/vivarium/examples/disease_model/risk.py
src/vivarium/framework/__init__.py
src/vivarium/framework/configuration.py
src/vivarium/framework/engine.py
src/vivarium/framework/event.py
src/vivarium/framework/lifecycle.py
src/vivarium/framework/lookup.py
src/vivarium/framework/metrics.py
src/vivarium/framework/plugins.py
src/vivarium/framework/randomness.py
src/vivarium/framework/resource.py
src/vivarium/framework/state_machine.py
src/vivarium/framework/time.py
src/vivarium/framework/utilities.py
src/vivarium/framework/values.py
src/vivarium/framework/artifact/__init__.py
src/vivarium/framework/artifact/artifact.py
src/vivarium/framework/artifact/hdf.py
src/vivarium/framework/artifact/manager.py
src/vivarium/framework/components/__init__.py
src/vivarium/framework/components/manager.py
src/vivarium/framework/components/parser.py
src/vivarium/framework/population/__init__.py
src/vivarium/framework/population/exceptions.py
src/vivarium/framework/population/manager.py
src/vivarium/framework/population/population_view.py
src/vivarium/framework/results/__init__.py
src/vivarium/framework/results/manager.py
src/vivarium/interface/__init__.py
src/vivarium/interface/cli.py
src/vivarium/interface/interactive.py
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tests/__init__.py
tests/conftest.py
tests/test_interpolation.py
tests/config_tree/__init__.py
tests/config_tree/test_basic_functionality.py
tests/config_tree/test_ingestion.py
tests/framework/__init__.py
tests/framework/test_configuration.py
tests/framework/test_engine.py
tests/framework/test_event.py
tests/framework/test_lifecycle.py
tests/framework/test_lookup.py
tests/framework/test_plugins.py
tests/framework/test_randomness.py
tests/framework/test_randomness_index_map.py
tests/framework/test_resource.py
tests/framework/test_state_machine.py
tests/framework/test_utilities.py
tests/framework/test_values.py
tests/framework/artifact/test_artifact.py
tests/framework/artifact/test_hdf.py
tests/framework/artifact/test_manager.py
tests/framework/components/__init__.py
tests/framework/components/mocks.py
tests/framework/components/test_manager.py
tests/framework/components/test_parser.py
tests/framework/population/__init__.py
tests/framework/population/test_manager.py
tests/framework/population/test_population_view.py
tests/interface/__init__.py
tests/interface/test_utilities.py
tests/test_data/bad_model_specification.txt
tests/test_data/mock_model_specification.yaml
tests/test_data/mock_user_config.yaml