.gitignore
LICENSE
MANIFEST.in
README.md
pyproject.toml
.github/workflows/publish.yml
.github/workflows/tests.yml
.vscode/launch.json
PyAntiGen.egg-info/PKG-INFO
PyAntiGen.egg-info/SOURCES.txt
PyAntiGen.egg-info/dependency_links.txt
PyAntiGen.egg-info/entry_points.txt
PyAntiGen.egg-info/requires.txt
PyAntiGen.egg-info/scm_file_list.json
PyAntiGen.egg-info/scm_version.json
PyAntiGen.egg-info/top_level.txt
docs/MULTISTART.md
docs/PROTOCOL_LAYER.md
docs/V2_DESIGN.md
pyantigen/.gitignore
pyantigen/__init__.py
pyantigen/_version.py
pyantigen/cli.py
pyantigen/.agents/skills/module_generation/SKILL.md
pyantigen/.agents/skills/ode_conversion_antimony/SKILL.md
pyantigen/.agents/skills/ode_extraction_pipeline/SKILL.md
pyantigen/engine/Anchor_cache.py
pyantigen/engine/Deadline.py
pyantigen/engine/Differential_evolution.py
pyantigen/engine/Evaluator.py
pyantigen/engine/Event_times.py
pyantigen/engine/Fast_profile.py
pyantigen/engine/Fit_cache.py
pyantigen/engine/Identifiability.py
pyantigen/engine/Model_cache.py
pyantigen/engine/Model_optimize.py
pyantigen/engine/Model_simulate.py
pyantigen/engine/Multistart.py
pyantigen/engine/Nelder_mead.py
pyantigen/engine/Noise_floor.py
pyantigen/engine/Optimize.py
pyantigen/engine/Petab_export.py
pyantigen/engine/Preequil_cache.py
pyantigen/engine/Profile_checkpoint.py
pyantigen/engine/Profile_plan.py
pyantigen/engine/README.md
pyantigen/engine/Results.py
pyantigen/engine/Sensitivity_analysis.py
pyantigen/engine/Simulate.py
pyantigen/engine/Stop_rules.py
pyantigen/engine/__init__.py
pyantigen/generate/AntimonyGen.py
pyantigen/generate/RxnDict_to_antimony.py
pyantigen/generate/TelluriumGen.py
pyantigen/generate/__init__.py
pyantigen/generate/antimony_utils.py
pyantigen/generate/data_interpolation.py
pyantigen/generate/isotopomer_tools.py
pyantigen/generate/model_generation.py
pyantigen/generate/models.py
pyantigen/generate/module_base.py
pyantigen/generate/pyantigen.py
pyantigen/generate/rate_laws.py
pyantigen/generate/reaction_creation.py
pyantigen/study/__init__.py
pyantigen/study/assay.py
pyantigen/study/describe.py
pyantigen/study/design.py
pyantigen/study/lower_v1.py
pyantigen/study/optimization.py
pyantigen/study/params.py
pyantigen/study/quantity.py
pyantigen/study/reagent.py
pyantigen/study/refs.py
pyantigen/study/remarks.py
pyantigen/study/serialize.py
pyantigen/study/validate.py
pyantigen/template/Example/AntiGen_paths.py
pyantigen/template/Example/Flipflop_reference.py
pyantigen/template/Example/Model_generate.py
pyantigen/template/Example/Model_run.py
pyantigen/template/Example/Modules/Data.py
pyantigen/template/Example/Modules/Events.py
pyantigen/template/Example/Modules/Experiment.py
pyantigen/template/Example/Modules/Loss_config.py
pyantigen/template/Example/Modules/Observed_species.py
pyantigen/template/Example/Modules/Optimizer_settings.py
pyantigen/template/Example/Modules/Plots.py
pyantigen/template/Example/Modules/Solver_settings.py
pyantigen/template/Example/Modules/Update_opt_parameters.py
pyantigen/template/Example/Modules/Update_parameters.py
pyantigen/template/Example/optimizations/Example1_ADneg.json
pyantigen/template/Example/optimizations/Example1_ADpos.json
pyantigen/template/Example/optimizations/Example3_joint.json
pyantigen/template/Example/optimizations/Example4_flipflop.json
pyantigen/template/Example/optimizations/example.py
pyantigen/template/Example/studies/example.json
pyantigen/template/Example/studies/example.py
pyantigen/template/Example/studies/flipflop.json
pyantigen/template/data/ADneg.csv
pyantigen/template/data/ADpos.csv
pyantigen/template/data/Flipflop.csv
pyantigen/template/data/make_flipflop_data.py