.coveragerc
.gitignore
.readthedocs.yaml
LICENSE
README.md
pyproject.toml
pytest.ini
.github/workflows/build.yml
.github/workflows/lint.yml
.github/workflows/pypi-deploy.yml
.github/workflows/test.yml
.vscode/settings.json
autoreduce/__init__.py
autoreduce/_version.py
autoreduce.egg-info/PKG-INFO
autoreduce.egg-info/SOURCES.txt
autoreduce.egg-info/dependency_links.txt
autoreduce.egg-info/requires.txt
autoreduce.egg-info/scm_file_list.json
autoreduce.egg-info/scm_version.json
autoreduce.egg-info/top_level.txt
autoreduce/reductions/__init__.py
autoreduce/reductions/abundance.py
autoreduce/reductions/conservation.py
autoreduce/reductions/core.py
autoreduce/reductions/timescale.py
autoreduce/reductions/utils.py
autoreduce/reductions/projection/__init__.py
autoreduce/reductions/projection/dmd.py
autoreduce/solvers/__init__.py
autoreduce/solvers/ode.py
autoreduce/solvers/ssm.py
autoreduce/solvers/utils.py
autoreduce/system/__init__.py
autoreduce/system/control.py
autoreduce/system/pydmd.py
autoreduce/system/system.py
autoreduce/utils/__init__.py
autoreduce/utils/converters.py
autoreduce/utils/sbml.py
docs/Makefile
docs/conf.py
docs/contributing.rst
docs/develop.rst
docs/examples.rst
docs/generate_library_docs.py
docs/index.rst
docs/installation.rst
docs/introduction.rst
docs/library.rst
docs/reductions.rst
docs/requirements.txt
docs/solvers.rst
docs/systems.rst
docs/usage.rst
docs/_static/css/custom.css
docs/notebooks/bacterial_population_control.nblink
docs/notebooks/biocrnpyler_interface.nblink
docs/notebooks/gene_expression_analysis.nblink
docs/notebooks/hill_function_derivation.nblink
docs/notebooks/michaelis_menten.nblink
docs/notebooks/motor_control.nblink
docs/notebooks/parameter_sensitivity.nblink
docs/notebooks/qss_with_python_control.nblink
docs/notebooks/toggle_switch.nblink
docs/notebooks/viral_spread.nblink
examples/biological/Bacterial population control.ipynb
examples/biological/BioCRNPyler interface.ipynb
examples/biological/Derivation of Hill functions.ipynb
examples/biological/Exploration of gene expression models.ipynb
examples/biological/Toggle switch.ipynb
examples/biological/default_parameters.txt
examples/biological/models/biocrnpyler_gene_expression.xml
examples/biological/models/design1_parameters.tsv
examples/biological/models/design1_regulated_promoter.xml
examples/biological/models/example1.xml
examples/biological/models/example_1.xml
examples/biological/models/reduced_gene_expression.xml
examples/canonical/Michaelis Menten.ipynb
examples/canonical/Parameter sensitivity.ipynb
examples/canonical/QSS with python-control.ipynb
examples/cyber-physical/Motor control.ipynb
examples/ecological/Viral spread.ipynb
graphics/autoreduce_banner.png
tests/README.md
tests/conftest.py
tests/test_auto_reduce.py
tests/test_conservation.py
tests/test_converters.py
tests/test_jupyter_notebooks.py
tests/test_objects.py
tests/test_ode.py
tests/test_optional_integrations.py
tests/test_system.py
tests/test_time_scale_separation.py
tests/models/example_1.xml