.gitignore
CHANGELOG.md
LICENSE
README.md
cha_kinetics_analysis.png
cha_kinetics_species.png
cliff.toml
mkdocs.yml
pyproject.toml
releases.md
.github/workflows/docs.yml
.github/workflows/publish.yml
.github/workflows/test.yml
docs/api.md
docs/index.md
docs/assets/banner.png
examples/01_simple_reversible.py
examples/02_michaelis_menten.py
examples/03_brusselator.py
examples/04_cha_cascade.py
examples/05_brusselator_chemostatted.py
examples/06_goldbeter_koshland.py
examples/brusselator_combined.png
examples/brusselator_oscillations.png
examples/brusselator_stable.png
examples/cha_bifurcation.png
examples/cha_kinetics_analysis.png
examples/cha_kinetics_species.png
examples/cha_reaction_graph.png
examples/gk_switch_dose_response.png
examples/michaelis_menten.png
mantis/__init__.py
mantis/analysis.py
mantis/crnt.py
mantis/network.py
mantis/parsing.py
mantis/plot.py
mantis/stoichiometry.py
mantis/symbolic.py
mantis_delta.egg-info/PKG-INFO
mantis_delta.egg-info/SOURCES.txt
mantis_delta.egg-info/dependency_links.txt
mantis_delta.egg-info/requires.txt
mantis_delta.egg-info/top_level.txt
paper/.gitignore
paper/README.md
paper/mantis_preprint.pdf
paper/mantis_preprint.qmd
paper/paper.md
paper/references.bib
scripts/release.sh
tests/test_analysis.py
tests/test_cha.py
tests/test_chemostatted.py
tests/test_crnt.py
tests/test_gk_switch.py
tests/test_parsing.py
tests/test_stochastic.py
tests/test_symbolic.py
tests/test_tau_leap.py