.gitignore
.pre-commit-config.yaml
CLAUDE.md
LICENSE
Makefile
README.md
pyproject.toml
uv.lock
.claude/agents/api-archaeologist.md
.claude/agents/bench-scientist.md
.claude/agents/mathematician.md
.claude/agents/performance-engineer.md
.claude/agents/physicist.md
.claude/agents/silent-failure-hunter.md
.claude/agents/systems-biologist.md
.github/workflows/basic_CI_linux.yaml
.github/workflows/release.yaml
configs/alt_cell_config.json
configs/bench_population.json
configs/bench_population_dallepezze.json
configs/default_cell_config.json
configs/eriq_config.json
configs/saturating_removal_config.json
demos/__init__.py
demos/bench_dispatch.py
demos/bench_gradient.py
demos/bench_population.py
demos/clamp_setpoint.py
demos/composite_population.py
demos/dp14_published_fit.py
demos/gerard2014_xpp.py
demos/gz06_damage_channel_scan.py
demos/gz06_oscillator.py
demos/gz06_population.py
demos/hallmark_levers.py
demos/multi_hallmark_calibrate.py
demos/multi_hallmark_figures.py
demos/multi_hallmark_hybrid.py
demos/multi_hallmark_ssa.py
demos/multiscale_coupling_demo.py
demos/proctor2007_ssa.py
demos/regulon_readout.py
demos/run_all_sivakumar.py
demos/subsystem_diagnostics.py
demos/validate_sivakumar.py
demos/assets/buck-logo.webp
demos/assets/furmanlab.svg
demos/models/__init__.py
demos/models/eriq.py
demos/models/hallmarks.py
demos/models/mitochondrial_aging.py
demos/models/multi_hallmark.py
demos/models/stem_cell_niche.py
demos/models/sbml/__init__.py
demos/models/sbml/dallepezze2014/dallepezze2014_BIOMD0000000582.xml
demos/models/sbml/hoffmann2002/hoffmann2002_BIOMD0000000140.xml
demos/models/sbml/ihekwaba2004/ihekwaba2004_BIOMD0000000230.xml
demos/models/sbml/kallenberger2014/kallenberger2014_BIOMD0000000524.xml
demos/models/sbml/kowald2006/kowald2006_BIOMD0000000108.xml
demos/models/sbml/nazaret2009/README.md
demos/models/sbml/nazaret2009/nazaret2009_BIOMD0000000232.xml
demos/models/sbml/proctor2007/proctor2007_BIOMD0000000105.xml
demos/models/sbml/proctor2008/proctor2008_BIOMD0000000188.xml
demos/models/sbml/sivakumar2011/README.md
demos/models/sbml/sivakumar2011/crosstalk_BIOMD0000000398.xml
demos/models/sbml/sivakumar2011/egf_BIOMD0000000394.xml
demos/models/sbml/sivakumar2011/notch_BIOMD0000000396.xml
demos/models/sbml/sivakumar2011/shh_BIOMD0000000395.xml
demos/models/sbml/sivakumar2011/wnt_BIOMD0000000397.xml
demos/models/sbml/zatorsky2006/zatorsky2006_BIOMD0000000157.xml
docs/architecture.md
docs/benchmarks.md
docs/calibration.md
docs/fixed-problems.md
docs/known-problems.md
docs/rejections.md
docs/roadmap.md
docs/assets/hallsim_architecture.png
hallsim.egg-info/PKG-INFO
hallsim.egg-info/SOURCES.txt
hallsim.egg-info/dependency_links.txt
hallsim.egg-info/entry_points.txt
hallsim.egg-info/requires.txt
hallsim.egg-info/scm_file_list.json
hallsim.egg-info/scm_version.json
hallsim.egg-info/top_level.txt
scripts/bench.py
scripts/bench_field.py
scripts/bench_scheduler.py
scripts/build_jacobian_corpus.py
scripts/build_reference_tables.py
scripts/check_no_registry_ids.py
scripts/check_prose_ratio.py
scripts/compare_abscissa_methods.py
scripts/conformance.py
src/hallsim/__init__.py
src/hallsim/ablation.py
src/hallsim/attenuation.py
src/hallsim/bifurcation.py
src/hallsim/calibration.py
src/hallsim/calibration_report.py
src/hallsim/census.py
src/hallsim/cli.py
src/hallsim/composite.py
src/hallsim/config.py
src/hallsim/coupling_wiring.py
src/hallsim/cps_import.py
src/hallsim/dataset_census.py
src/hallsim/datasets.py
src/hallsim/diagnostics.py
src/hallsim/discovery.py
src/hallsim/gene_reporters.py
src/hallsim/hallmarks.py
src/hallsim/handles.py
src/hallsim/identifiability.py
src/hallsim/imported.py
src/hallsim/intake.py
src/hallsim/io.py
src/hallsim/kinetics.py
src/hallsim/literature.py
src/hallsim/plotting.py
src/hallsim/process.py
src/hallsim/py.typed
src/hallsim/regulon.py
src/hallsim/rejections.py
src/hallsim/reporter_wiring.py
src/hallsim/root_finders.py
src/hallsim/sbml_core.py
src/hallsim/sbml_events.py
src/hallsim/sbml_export.py
src/hallsim/sbml_import.py
src/hallsim/sbml_math.py
src/hallsim/scheduler.py
src/hallsim/steady_state.py
src/hallsim/stiffness.py
src/hallsim/stochastic.py
src/hallsim/store.py
src/hallsim/structure.py
src/hallsim/tracing.py
src/hallsim/units.py
src/hallsim/validation.py
src/hallsim/web_discovery.py
src/hallsim/xpp_import.py
src/hallsim/models/__init__.py
src/hallsim/models/bistable_latch.py
src/hallsim/models/clamp_edge.py
src/hallsim/models/forcing.py
src/hallsim/models/gain_edge.py
src/hallsim/models/gated_removal.py
src/hallsim/models/hill_edge.py
src/hallsim/models/kick_event.py
src/hallsim/models/neuralode.py
src/hallsim/models/observer.py
src/hallsim/models/running_integral.py
src/hallsim/models/saturating_removal.py
src/hallsim/reference/collectri/PROVENANCE.md
src/hallsim/reference/collectri/collectri_human.tsv
src/hallsim/reference/ontology/go_aspect.tsv
src/hallsim/reference/ontology/ortholog_mouse_human.tsv
src/hallsim/reference/ontology/uniprot_symbol.tsv
src/hallsim/view/__init__.py
src/hallsim/view/_app.py
src/hallsim/view/_bake.py
src/hallsim/view/_fit.py
src/hallsim/view/_graph.py
src/hallsim/view/_levers.py
src/hallsim/view/_model.py
src/hallsim/view/_page.py
src/hallsim/view/_theme.py
src/hallsim/view/bake.html
src/hallsim/view/bake.js
src/hallsim/view/hallsim.css
tests/conftest.py
tests/fixtures/refdata/collectri/collectri_human.tsv
tests/fixtures/refdata/ontology/go_aspect.tsv
tests/fixtures/refdata/ontology/ortholog_mouse_human.tsv
tests/fixtures/refdata/ontology/uniprot_symbol.tsv
tests/integration/test_doc_examples.py
tests/integration/test_eriq_composable.py
tests/unit/test_ablation.py
tests/unit/test_assignment_pass.py
tests/unit/test_attenuation.py
tests/unit/test_bifurcation.py
tests/unit/test_calibration.py
tests/unit/test_calibration_report.py
tests/unit/test_census.py
tests/unit/test_clamp_edge.py
tests/unit/test_cli.py
tests/unit/test_composition.py
tests/unit/test_coupling_loop.py
tests/unit/test_coupling_wiring.py
tests/unit/test_cps_import.py
tests/unit/test_dataset_census.py
tests/unit/test_datasets.py
tests/unit/test_diagnostics.py
tests/unit/test_discovery.py
tests/unit/test_fit_param_validation.py
tests/unit/test_fit_set.py
tests/unit/test_forward_mode_after_eager.py
tests/unit/test_gain_edge.py
tests/unit/test_gain_placement.py
tests/unit/test_gated_removal.py
tests/unit/test_gene_reporters.py
tests/unit/test_hallmark_levers.py
tests/unit/test_handles_under_jit.py
tests/unit/test_hill_edge.py
tests/unit/test_identifiability.py
tests/unit/test_initial_step.py
tests/unit/test_io.py
tests/unit/test_kinetics.py
tests/unit/test_known_problems.py
tests/unit/test_literature.py
tests/unit/test_macro_loop_compiles_once.py
tests/unit/test_models.py
tests/unit/test_multiscale.py
tests/unit/test_null_baseline.py
tests/unit/test_performance.py
tests/unit/test_port_binding.py
tests/unit/test_propensity_scan.py
tests/unit/test_published_fit.py
tests/unit/test_rejections.py
tests/unit/test_reporter_wiring.py
tests/unit/test_reused_scheduler_hybrid_lane.py
tests/unit/test_root_finders.py
tests/unit/test_run_config.py
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tests/unit/test_sbml_events.py
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tests/unit/test_sbml_import.py
tests/unit/test_sbml_math.py
tests/unit/test_steady_state.py
tests/unit/test_stiffness_large_group.py
tests/unit/test_stiffness_routing.py
tests/unit/test_stochastic.py
tests/unit/test_structure.py
tests/unit/test_suggest_handles.py
tests/unit/test_sum_observer.py
tests/unit/test_symbolic_boundary_rules.py
tests/unit/test_symbolic_forms.py
tests/unit/test_trace_safety.py
tests/unit/test_untimed_grouping.py
tests/unit/test_validation.py
tests/unit/test_view.py
tests/unit/test_web_discovery.py
tests/unit/test_xpp_import.py
tests/unit/test_xpp_robustness.py