├── .coveragerc ├── .gitattributes ├── .github └── workflows │ ├── build.yml │ ├── keep-alive.yml │ ├── mirror-ebrains.yml │ └── test.yml ├── .gitignore ├── .readthedocs.yaml ├── .zenodo.json ├── AUTHORS.txt ├── COPYING ├── COPYING.lesser ├── Dockerfile ├── LICENSE.txt ├── MANIFEST.in ├── Makefile ├── README.rst ├── bluepyopt ├── __init__.py ├── api.py ├── deapext │ ├── CMA_MO.py │ ├── CMA_SO.py │ ├── __init__.py │ ├── algorithms.py │ ├── hype.py │ ├── optimisations.py │ ├── optimisationsCMA.py │ ├── stoppingCriteria.py │ ├── tools │ │ ├── __init__.py │ │ └── selIBEA.py │ └── utils.py ├── ephys │ ├── __init__.py │ ├── acc.py │ ├── base.py │ ├── create_acc.py │ ├── create_hoc.py │ ├── efeatures.py │ ├── evaluators.py │ ├── examples │ │ ├── __init__.py │ │ └── simplecell │ │ │ ├── __init__.py │ │ │ ├── simple.swc │ │ │ └── simplecell.py │ ├── extra_features_utils.py │ ├── locations.py │ ├── mechanisms.py │ ├── models.py │ ├── morphologies.py │ ├── objectives.py │ ├── objectivescalculators.py │ ├── parameters.py │ ├── parameterscalers │ │ ├── __init__.py │ │ ├── acc_iexpr.py │ │ └── parameterscalers.py │ ├── protocols.py │ ├── recordings.py │ ├── responses.py │ ├── serializer.py │ ├── simulators.py │ ├── static │ │ └── arbor_mechanisms.json │ ├── stimuli.py │ └── templates │ │ ├── acc │ │ ├── _json_template.jinja2 │ │ ├── decor_acc_template.jinja2 │ │ └── label_dict_acc_template.jinja2 │ │ └── cell_template.jinja2 ├── evaluators.py ├── ipyp │ ├── __init__.py │ └── bpopt_tasksdb.py ├── neuroml │ ├── NeuroML2_mechanisms │ │ ├── Ca.channel.nml │ │ ├── Ca_HVA.channel.nml │ │ ├── Ca_LVAst.channel.nml │ │ ├── Ih.channel.nml │ │ ├── Im.channel.nml │ │ ├── K_Pst.channel.nml │ │ ├── K_Tst.channel.nml │ │ ├── KdShu2007.channel.nml │ │ ├── NaTa_t.channel.nml │ │ ├── NaTs2_t.channel.nml │ │ ├── Nap_Et2.channel.nml │ │ ├── SK_E2.channel.nml │ │ ├── SKv3_1.channel.nml │ │ ├── StochKv_deterministic.channel.nml │ │ ├── baseCaDynamics_E2_NML2.nml │ │ └── pas.channel.nml │ ├── __init__.py │ ├── biophys.py │ ├── cell.py │ ├── morphology.py │ └── simulation.py ├── objectives.py ├── optimisations.py ├── parameters.py ├── stoppingCriteria.py ├── tests │ ├── .gitignore │ ├── __init__.py │ ├── disable_simplecell_scoop.py │ ├── expected_results.json │ ├── test_bluepyopt.py │ ├── test_deapext │ │ ├── __init__.py │ │ ├── deapext_test_utils.py │ │ ├── test_algorithms.py │ │ ├── test_hype.py │ │ ├── test_optimisations.py │ │ ├── test_optimisationsCMA.py │ │ ├── test_selIBEA.py │ │ ├── test_stoppingCriteria.py │ │ └── test_utils.py │ ├── test_ephys │ │ ├── __init__.py │ │ ├── test_acc.py │ │ ├── test_create_acc.py │ │ ├── test_create_hoc.py │ │ ├── test_evaluators.py │ │ ├── test_extra_features_utils.py │ │ ├── test_features.py │ │ ├── test_init.py │ │ ├── test_locations.py │ │ ├── test_mechanisms.py │ │ ├── test_models.py │ │ ├── test_morphologies.py │ │ ├── test_objectives.py │ │ ├── test_parameters.py │ │ ├── test_parameterscalers.py │ │ ├── test_protocols.py │ │ ├── test_recordings.py │ │ ├── test_serializer.py │ │ ├── test_simulators.py │ │ ├── test_stimuli.py │ │ ├── testdata │ │ │ ├── TimeVoltageResponse.csv │ │ │ ├── acc │ │ │ │ ├── CCell │ │ │ │ │ ├── CCell.json │ │ │ │ │ ├── CCell_decor.acc │ │ │ │ │ ├── CCell_label_dict.acc │ │ │ │ │ └── simple_axon_replacement.acc │ │ │ │ ├── expsyn │ │ │ │ │ ├── simple.swc │ │ │ │ │ ├── simple_cell.json │ │ │ │ │ ├── simple_cell_decor.acc │ │ │ │ │ └── simple_cell_label_dict.acc │ │ │ │ ├── l5pc │ │ │ │ │ ├── C060114A7.asc │ │ │ │ │ ├── C060114A7_axon_replacement.acc │ │ │ │ │ ├── C060114A7_modified.acc │ │ │ │ │ ├── l5pc.json │ │ │ │ │ ├── l5pc_decor.acc │ │ │ │ │ └── l5pc_label_dict.acc │ │ │ │ ├── l5pc_py37 │ │ │ │ │ └── l5pc_decor.acc │ │ │ │ ├── simplecell │ │ │ │ │ ├── simple.swc │ │ │ │ │ ├── simple_axon_replacement.acc │ │ │ │ │ ├── simple_cell.json │ │ │ │ │ ├── simple_cell_decor.acc │ │ │ │ │ ├── simple_cell_label_dict.acc │ │ │ │ │ └── simple_modified.acc │ │ │ │ └── templates │ │ │ │ │ ├── cell_json_template.jinja2 │ │ │ │ │ ├── decor_acc_template.jinja2 │ │ │ │ │ └── label_dict_acc_template.jinja2 │ │ │ ├── apic.swc │ │ │ ├── lfpy_soma_time.npy │ │ │ ├── lfpy_soma_voltage.npy │ │ │ ├── lfpy_time.npy │ │ │ ├── lfpy_voltage.npy │ │ │ ├── mean_waveforms.dat │ │ │ ├── simple.swc │ │ │ ├── simple.wrong │ │ │ ├── simple_ax1.swc │ │ │ ├── simple_ax2.asc │ │ │ ├── simple_ax2.swc │ │ │ └── test.jinja2 │ │ ├── testmodels │ │ │ ├── __init__.py │ │ │ └── dummycells.py │ │ └── utils.py │ ├── test_evaluators.py │ ├── test_l5pc.py │ ├── test_lfpy.py │ ├── test_neuroml_fcts.py │ ├── test_parameters.py │ ├── test_simplecell.py │ ├── test_stochkv.py │ ├── test_tools.py │ └── testdata │ │ └── l5pc_validate_neuron_arbor │ │ └── param_values.json └── tools.py ├── cloud-config ├── README.md ├── config │ ├── amazon │ │ ├── README.md │ │ ├── ansible.cfg │ │ ├── create_instance.yaml │ │ ├── gather_config.py │ │ ├── site.yaml │ │ └── vars.yaml │ ├── cluster-user │ │ ├── README.md │ │ ├── ansible.cfg │ │ ├── hosts │ │ ├── site.yaml │ │ └── vars.yaml │ └── vagrant │ │ ├── README.md │ │ ├── Vagrantfile │ │ ├── ansible.cfg │ │ ├── hosts │ │ ├── site.yaml │ │ └── vars.yaml └── roles │ ├── base │ └── tasks │ │ └── main.yaml │ ├── deap │ └── tasks │ │ └── main.yaml │ ├── granule-example │ └── tasks │ │ └── main.yaml │ ├── neuron │ └── tasks │ │ ├── main.yaml │ │ └── python27.yaml │ └── scoop-master │ └── tasks │ └── main.yaml ├── codecov.yml ├── docs ├── .gitignore ├── Makefile └── source │ ├── .gitignore │ ├── _static │ └── bbp.jpg │ ├── _templates │ └── module.rst │ ├── api.rst │ ├── conf.py │ ├── deapext.rst │ ├── ephys.rst │ ├── index.rst │ ├── logo │ ├── BluePyOptBanner.png │ └── BluePyOptLogo.png │ └── optimisations.rst ├── examples ├── BluePyOpt-ipyparallel.md ├── README.md ├── __init__.py ├── cma_strategy │ └── cma.ipynb ├── expsyn │ ├── .gitignore │ ├── ExpSyn.ipynb │ ├── ExpSyn_arbor.ipynb │ ├── expsyn.py │ ├── generate_acc.py │ └── simple.swc ├── graupnerbrunelstdp │ ├── checkpoints │ │ └── .gitignore │ ├── figures │ │ └── .gitignore │ ├── gbevaluator.py │ ├── graupnerbrunelstdp.ipynb │ ├── run_fit.py │ ├── stdputil.py │ └── test_stdputil.py ├── l5pc │ ├── .gitignore │ ├── L5PC.ipynb │ ├── L5PC_arbor.ipynb │ ├── benchmark │ │ ├── get_stats.py │ │ ├── l5pc_benchmark.sbatch │ │ ├── logs │ │ │ └── .gitignore │ │ ├── run_benchmark.sh │ │ ├── start.sh │ │ └── task_stats.py │ ├── cADpyr_76.hoc │ ├── checkpoints │ │ └── .gitignore │ ├── config │ │ ├── features.json │ │ ├── fixed_params.json │ │ ├── mechanisms.json │ │ ├── parameters.json │ │ ├── params.json │ │ └── protocols.json │ ├── convert_noise_exp.py │ ├── convert_params.py │ ├── create_tables.py │ ├── exp_data │ │ ├── .gitignore │ │ └── noise_i.txt │ ├── figures │ │ └── .gitignore │ ├── generate_acc.py │ ├── generate_hoc.py │ ├── hocmodel.py │ ├── l5_config.zip │ ├── l5pc_analysis.py │ ├── l5pc_evaluator.py │ ├── l5pc_model.py │ ├── l5pc_validate_neuron_arbor.ipynb │ ├── l5pc_validate_neuron_arbor_pm.py │ ├── mechanisms │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_HVA.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── LICENSE │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── SK_E2.mod │ │ ├── SKv3_1.mod │ │ └── dummy.inc │ ├── morphology │ │ ├── C060114A7.asc │ │ └── LICENSE │ ├── nsg │ │ ├── .gitignore │ │ ├── Makefile │ │ └── init.py │ ├── opt_l5pc.py │ ├── opt_l5pc.sh │ ├── tables │ │ └── .gitignore │ └── tasks2dataframe.py ├── l5pc_lfpy │ ├── L5PC_LFPy.ipynb │ ├── __init__.py │ ├── extra_features.json │ ├── generate_extra_features.py │ ├── l5pc_lfpy_evaluator.py │ └── l5pc_lfpy_model.py ├── metaparameters │ ├── .gitignore │ ├── metaparameters.ipynb │ └── twocompartment.swc ├── neuroml │ └── neuroml.ipynb ├── simplecell │ ├── .gitignore │ ├── checkpoints │ │ └── .gitignore │ ├── figures │ │ ├── .gitignore │ │ └── landscape_example.png │ ├── generate_acc.py │ ├── generate_hoc.py │ ├── responses.pkl │ ├── simple.swc │ ├── simplecell-paperfig.ipynb │ ├── simplecell.ipynb │ ├── simplecell_arbor.ipynb │ └── simplecell_model.py ├── stochkv │ ├── .gitignore │ ├── mechanisms │ │ ├── StochKv.mod │ │ ├── StochKv3.mod │ │ └── dummy.inc │ ├── morphology │ │ └── simple.swc │ ├── stochkv3cell.hoc │ ├── stochkv3cell.py │ ├── stochkv3cell_det.hoc │ ├── stochkvcell.hoc │ ├── stochkvcell.py │ └── stochkvcell_det.hoc ├── thalamocortical-cell │ ├── CellEvalSetup │ │ ├── __init__.py │ │ ├── evaluator.py │ │ ├── protocols.py │ │ ├── template.py │ │ └── tools.py │ ├── LICENSE.txt │ ├── checkpoints │ │ └── checkpoint.pkl │ ├── config │ │ ├── features │ │ │ ├── cAD_ltb.json │ │ │ └── cNAD_ltb.json │ │ ├── params │ │ │ └── TC.json │ │ ├── protocols │ │ │ ├── cAD_ltb.json │ │ │ └── cNAD_ltb.json │ │ └── recipes.json │ ├── mechanisms │ │ ├── SK_E2.mod │ │ ├── TC_HH.mod │ │ ├── TC_ITGHK_Des98.mod │ │ ├── TC_Ih_Bud97.mod │ │ ├── TC_Nap_Et2.mod │ │ ├── TC_cadecay.mod │ │ ├── TC_iA.mod │ │ └── TC_iL.mod │ ├── morphologies │ │ ├── jy160728_A_idA.asc │ │ └── jy170517_A_idA.asc │ ├── results │ │ ├── cAD_ltb_params.csv │ │ └── cNAD_ltb_params.csv │ └── thalamocortical-cell_opt.ipynb └── tsodyksmarkramstp │ ├── AUTHORS.txt │ ├── README.md │ ├── amps.pkl │ ├── tmevaluator.py │ ├── tmevaluator_multiplefreqs.py │ ├── tmodeint.py │ ├── tmodesolve.py │ ├── trace.pkl │ ├── tsodyksmarkramstp.ipynb │ └── tsodyksmarkramstp_multiplefreqs.ipynb ├── misc ├── github_wiki │ ├── bibtex │ │ ├── mentions_BPO.bib │ │ ├── mentions_BPO_extra.bib │ │ ├── poster_uses_BPO.bib │ │ ├── thesis_mentions_BPO.bib │ │ ├── thesis_uses_BPO.bib │ │ ├── uses_BPO.bib │ │ └── uses_BPO_extra.bib │ └── creates_publication_list_markdown.py └── pytest_migration │ └── convert_pytest.sh ├── package.json ├── pyproject.toml ├── pytest.ini ├── requirements.txt ├── requirements_docs.txt └── tox.ini /.coveragerc: -------------------------------------------------------------------------------- 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