.codespellrc
.gitignore
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.readthedocs.yaml
CHANGELOG.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
.github/workflows/ci.yml
.github/workflows/codespell.yml
.github/workflows/release.yml
_static/images/img.png
docs/Makefile
docs/application.rst
docs/architecture.md
docs/conf.py
docs/configuration.md
docs/index.rst
docs/journal.rst
docs/make.bat
docs/migration_guide.md
docs/readme.rst
docs/releasing.md
docs/tutorial.rst
docs/verification.md
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docs/example_models/new_syntax_examples.py
docs/example_models/application_models/AB_2CD.py
docs/example_models/application_models/AND_gate.py
docs/example_models/application_models/CRISPR_Oscillator.py
docs/example_models/application_models/For_The_Trees.py
docs/example_models/application_models/NOR_gate.py
docs/example_models/application_models/donor_receptor.py
docs/example_models/application_models/oscillator.py
docs/example_models/application_models/positive_phage_feedback_loop.py
docs/example_models/application_models/random_walk.py
docs/example_models/application_models/simple_infection.py
docs/example_models/application_models/simple_repressor.py
docs/example_models/application_models/simple_rule_based_and_gate.py
docs/example_models/comparisons/BioNetGen_multi_state.bngl
docs/example_models/comparisons/comparison_bioCRNpyler.py
docs/example_models/comparisons/hello_pysb.py
docs/example_models/comparisons/kappa_model.png
docs/example_models/images/Lysis_Clock/Lysis_Clock.pdf
docs/example_models/images/Mutual_Annihilation/Mutual_Annihilation.pdf
docs/example_models/images/Toggle_Switch/Toggle_Switch.pdf
docs/example_models/journal_models/Antimony_Comparison.py
docs/example_models/journal_models/BioCRNpyler_1.py
docs/example_models/journal_models/BioCRNpyler_2.py
docs/example_models/journal_models/BioNetGen_Comparison.py
docs/example_models/journal_models/Bistable_Gut_Inflammation.py
docs/example_models/journal_models/For_The_Trees.py
docs/example_models/journal_models/Kappa_comp_v1.py
docs/example_models/journal_models/Logical_XOR_Gate.py
docs/example_models/journal_models/Mutual_Annihilation.py
docs/example_models/journal_models/Phage_Transmission_System.py
docs/example_models/journal_models/PySB_Comparison.py
docs/example_models/journal_models/README.md
docs/example_models/journal_models/Synchronized_Cycles_of_Bacterial_Lysis.py
docs/example_models/tutorial_notebooks/01_Getting_Started.ipynb
docs/example_models/tutorial_notebooks/02_Characteristics.ipynb
docs/example_models/tutorial_notebooks/03_Inheritance.ipynb
docs/example_models/tutorial_notebooks/04_Initial_Conditions.ipynb
docs/example_models/tutorial_notebooks/05_Reaction_Order_and_Labels.ipynb
docs/example_models/tutorial_notebooks/06_Running_Simulations.ipynb
docs/example_models/tutorial_notebooks/07_Units.ipynb
docs/example_models/tutorial_notebooks/08_Reaction_Rates.ipynb
docs/example_models/tutorial_notebooks/09_Rev_All_and_Any.ipynb
docs/example_models/tutorial_notebooks/10_Events.ipynb
docs/example_models/tutorial_notebooks/11_Assignments.ipynb
docs/example_models/tutorial_notebooks/12_Composing_Simulations.ipynb
docs/example_models/tutorial_notebooks/13_Parameters_and_Sweeps.ipynb
docs/example_models/tutorial_notebooks/14_Exporting_Models.ipynb
docs/example_models/tutorial_notebooks/15_Plot_Configuration.ipynb
docs/example_models/tutorial_notebooks/16_Advanced_Topics.ipynb
mobspy/__init__.py
mobspy/compiled_state.py
mobspy/constants.py
mobspy/event_handling.py
mobspy/exceptions.py
mobspy/execution.py
mobspy/lazy_import.py
mobspy/mobspy_logging.py
mobspy/model.py
mobspy/model_generation.py
mobspy/plotting.py
mobspy/py.typed
mobspy/runtime.py
mobspy/simulation.py
mobspy/simulation_composition.py
mobspy/simulation_config.py
mobspy/types.py
mobspy.egg-info/PKG-INFO
mobspy.egg-info/SOURCES.txt
mobspy.egg-info/dependency_links.txt
mobspy.egg-info/requires.txt
mobspy.egg-info/top_level.txt
mobspy/compiler/__init__.py
mobspy/compiler/compiler.py
mobspy/compiler/expansion.py
mobspy/compiler/operators.py
mobspy/compiler/species_strings.py
mobspy/dsl/__init__.py
mobspy/dsl/any_species.py
mobspy/dsl/assignments_implementation.py
mobspy/dsl/declarations.py
mobspy/dsl/event_functions.py
mobspy/dsl/functions.py
mobspy/dsl/list_species.py
mobspy/dsl/logic_operators.py
mobspy/dsl/meta_class.py
mobspy/dsl/mobspy_parameters.py
mobspy/dsl/ode_operator.py
mobspy/dsl/order_operators.py
mobspy/dsl/reactions.py
mobspy/dsl/session_context.py
mobspy/dsl/set_counts_module.py
mobspy/dsl/species.py
mobspy/dsl/species_constructors.py
mobspy/dsl/species_operators.py
mobspy/dsl/species_utils.py
mobspy/expressions/__init__.py
mobspy/expressions/context.py
mobspy/expressions/evaluation.py
mobspy/expressions/nodes.py
mobspy/expressions/rate_builder.py
mobspy/expressions/rate_functions.py
mobspy/params/__init__.py
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mobspy/params/parametric_sweeps.py
mobspy/plot/__init__.py
mobspy/plot/default_plots.py
mobspy/plot/example_plot_reader.py
mobspy/plot/hierarchical_plot.py
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mobspy/results/__init__.py
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mobspy/results/estimation_loader.py
mobspy/results/io.py
mobspy/results/process_data.py
mobspy/results/processing.py
mobspy/results/time_series.py
mobspy/sbml/__init__.py
mobspy/sbml/backend.py
mobspy/sbml/builder.py
mobspy/sbml/runner.py
mobspy/sbml/writer.py
mobspy/units/__init__.py
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mobspy/units/model_context.py
mobspy/units/parameters.py
mobspy/units/registry.py
mobspy/units/transfer.py
mobspy/units/validation.py
scripts/check_release.py
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tests/__init__.py
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tests/test_birth_death_complex.py
tests/test_compilation.py
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tests/test_compiler_phases.py
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tests/test_dsl_operators.py
tests/test_events.py
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tests/test_examples.py
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tests/testconfig_units.yaml
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tests/plot_output/.gitkeep