├── .gitattributes ├── .github └── workflows │ ├── build_docs.yml │ ├── make_release.yml │ ├── regression_tests.yml │ ├── run_tutorials.yml │ └── tests.yml ├── .gitignore ├── .readthedocs.yaml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── README.md ├── _static │ └── custom.css ├── _templates │ └── autosummary │ │ └── class.rst ├── advanced_tutorials.rst ├── changelog.md ├── code_of_conduct.md ├── conf.py ├── contributing.md ├── contributor_guide.rst ├── credits.md ├── examples.rst ├── examples │ └── 00_l5pc_gradient_descent.ipynb ├── faq.rst ├── faq │ ├── question_01.md │ └── question_03.md ├── how_to_guide.rst ├── how_to_guide │ ├── choose_solver.ipynb │ ├── define_custom_stimuli.ipynb │ ├── edit_morphologies.ipynb │ ├── import_channels_from_neuron.ipynb │ ├── ion_diffusion.ipynb │ ├── save_and_load.ipynb │ └── set_ncomp.ipynb ├── index.rst ├── installation.md ├── jaxley.rst ├── logo.png ├── logo.svg ├── make.bat ├── tutorials.rst └── tutorials │ ├── 00_jaxley_api.ipynb │ ├── 01_morph_neurons.ipynb │ ├── 02_small_network.ipynb │ ├── 04_jit_and_vmap.ipynb │ ├── 05_channel_and_synapse_models.ipynb │ ├── 06_groups.ipynb │ ├── 07_gradient_descent.ipynb │ ├── 08_importing_morphologies.ipynb │ ├── 09_advanced_indexing.ipynb │ ├── 10_advanced_parameter_sharing.ipynb │ ├── 11_ion_dynamics.ipynb │ ├── 12_simplified_models.ipynb │ ├── 13_graph_backend.ipynb │ ├── data │ ├── example.swc │ └── morph.swc │ └── dev │ ├── graph_backend.ipynb │ └── indexing.ipynb ├── jaxley ├── __init__.py ├── __version__.py ├── channels │ ├── __init__.py │ ├── channel.py │ ├── hh.py │ ├── non_capacitive │ │ ├── __init__.py │ │ ├── izhikevich.py │ │ ├── rate.py │ │ └── spike.py │ └── pospischil.py ├── connect.py ├── integrate.py ├── io │ ├── __init__.py │ ├── graph.py │ └── swc.py ├── modules │ ├── __init__.py │ ├── base.py │ ├── branch.py │ ├── cell.py │ ├── compartment.py │ └── network.py ├── morphology │ ├── __init__.py │ ├── distance_utils.py │ └── morph_utils.py ├── optimize │ ├── __init__.py │ ├── optimizer.py │ ├── transforms.py │ └── utils.py ├── pumps │ ├── __init__.py │ ├── ca_pump.py │ ├── faraday_electrolysis.py │ ├── nernstreversal.py │ └── pump.py ├── solver_gate.py ├── solver_voltage.py ├── stimulus.py ├── synapses │ ├── __init__.py │ ├── ionotropic.py │ ├── synapse.py │ ├── tanh_conductance.py │ ├── tanh_rate.py │ └── test.py └── utils │ ├── __init__.py │ ├── cell_utils.py │ ├── colors.py │ ├── debug_solver.py │ ├── jax_utils.py │ ├── misc_utils.py │ ├── morph_attributes.py │ ├── plot_utils.py │ ├── solver_utils.py │ └── syn_utils.py ├── mkdocs ├── README.md ├── docs │ ├── index.md │ ├── logo.png │ └── logo_white.png ├── logo.png ├── logo_white.png ├── logo_white.svg └── mkdocs.yml ├── pyproject.toml └── tests ├── __init__.py ├── conftest.py ├── helpers.py ├── jaxley_identical ├── __init__.py ├── test_basic_modules.py ├── test_grad.py ├── test_radius_and_length.py └── test_swc.py ├── jaxley_vs_neuron ├── __init__.py ├── test_branch.py ├── test_cell.py ├── test_comp.py └── test_swc.py ├── nrn_mechanisms └── Ca_HVA.mod ├── swc_files ├── asc2swc.py ├── morph_3_types.swc ├── morph_3_types_single_point_soma.swc ├── morph_allen_485574832.swc ├── morph_ca1_n120.swc ├── morph_ca1_n120_250.swc ├── morph_ca1_n120_250_single_point_soma.swc ├── morph_ca1_n120_single_point_soma.swc ├── morph_flywire_t4_720575940626407426.swc ├── morph_interrupted_soma.swc ├── morph_l5pc_with_axon.swc ├── morph_minimal.swc ├── morph_multiple_roots.swc ├── morph_non_somatic_branchpoint.swc ├── morph_retina_20161028_1.swc ├── morph_single_branch.swc ├── morph_soma_both_ends.swc ├── morph_somatic_branchpoint.swc ├── morph_variable_radiuses_multi_branch.swc └── morph_variable_radiuses_within_branch.swc ├── test_api_equivalence.py ├── test_cell_matches_branch.py ├── test_channels.py ├── test_clamp.py ├── test_composability_of_modules.py ├── test_connection.py ├── test_data_feeding.py ├── 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