├── .flake8 ├── .github ├── FUNDING.yml ├── ISSUE_TEMPLATE.md ├── PULL_REQUEST_TEMPLATE.md ├── codecov.yml ├── dependabot.yml └── workflows │ ├── main.yml │ └── release.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .pylintrc ├── .readthedocs.yml ├── CONTRIBUTING.md ├── LICENSE.md ├── MANIFEST.in ├── README.md ├── cmdstanpy ├── __init__.py ├── _version.py ├── cmdstan_args.py ├── compilation.py ├── install_cmdstan.py ├── install_cxx_toolchain.py ├── model.py ├── progress.py ├── py.typed ├── stanfit │ ├── __init__.py │ ├── gq.py │ ├── laplace.py │ ├── mcmc.py │ ├── metadata.py │ ├── mle.py │ ├── pathfinder.py │ ├── runset.py │ └── vb.py └── utils │ ├── __init__.py │ ├── cmdstan.py │ ├── command.py │ ├── data_munging.py │ ├── filesystem.py │ ├── json.py │ ├── logging.py │ └── stancsv.py ├── cmdstanpy_tutorial.ipynb ├── cmdstanpy_tutorial.py ├── docs ├── .buildinfo ├── .nojekyll ├── _modules │ ├── cmdstanpy │ │ ├── cmdstan_args.html │ │ ├── compilation.html │ │ ├── install_cmdstan.html │ │ ├── model.html │ │ ├── stanfit.html │ │ ├── stanfit │ │ │ ├── gq.html │ │ │ ├── laplace.html │ │ │ ├── mcmc.html │ │ │ ├── metadata.html │ │ │ ├── mle.html │ │ │ ├── pathfinder.html │ │ │ ├── runset.html │ │ │ └── vb.html │ │ ├── utils.html │ │ └── utils │ │ │ ├── cmdstan.html │ │ │ └── logging.html │ ├── index.html │ └── stanio │ │ └── json.html ├── _sources │ ├── api.rst.txt │ ├── changes.rst.txt │ ├── community.rst.txt │ ├── index.rst.txt │ ├── installation.rst.txt │ ├── internal_api.rst.txt │ ├── users-guide.rst.txt │ └── users-guide │ │ ├── examples.rst.txt │ │ ├── examples │ │ ├── MCMC Sampling.ipynb.txt │ │ ├── Maximum Likelihood Estimation.ipynb.txt │ │ ├── Pathfinder.ipynb.txt │ │ ├── Run Generated Quantities.ipynb.txt │ │ ├── Using External C++.ipynb.txt │ │ ├── VI as Sampler Inits.ipynb.txt │ │ └── Variational Inference.ipynb.txt │ │ ├── hello_world.rst.txt │ │ ├── outputs.rst.txt │ │ ├── overview.rst.txt │ │ └── workflow.rst.txt ├── _static │ ├── _sphinx_javascript_frameworks_compat.js │ ├── basic.css │ ├── check-solid.svg │ ├── clipboard.min.js │ ├── copy-button.svg │ ├── copybutton.css │ ├── copybutton.js │ ├── copybutton_funcs.js │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── images │ │ ├── logo_icon.png │ │ └── logo_tm.png │ ├── jquery-3.6.0.js │ ├── jquery.js │ ├── language_data.js │ ├── logo_icon.png │ ├── minus.png │ ├── nbsphinx-broken-thumbnail.svg │ ├── nbsphinx-code-cells.css │ ├── nbsphinx-gallery.css │ ├── nbsphinx-no-thumbnail.svg │ ├── plus.png │ ├── pygments.css │ ├── scripts │ │ └── pydata-sphinx-theme.js │ ├── searchtools.js │ ├── sphinx_highlight.js │ ├── styles │ │ ├── pydata-sphinx-theme.css │ │ └── theme.css │ ├── underscore-1.13.1.js │ ├── underscore.js │ ├── vendor │ │ └── fontawesome │ │ │ └── 5.13.0 │ │ │ ├── LICENSE.txt │ │ │ ├── css │ │ │ └── all.min.css │ │ │ └── webfonts │ │ │ ├── fa-brands-400.eot │ │ │ ├── fa-brands-400.svg │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.eot │ │ │ ├── fa-regular-400.svg │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.eot │ │ │ ├── fa-solid-900.svg │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff │ │ │ └── fa-solid-900.woff2 │ └── webpack-macros.html ├── api.html ├── changes.html ├── community.html ├── genindex.html ├── index.html ├── installation.html ├── internal_api.html ├── objects.inv ├── py-modindex.html ├── search.html ├── searchindex.js ├── users-guide.html └── users-guide │ ├── examples.html │ ├── examples │ ├── MCMC Sampling.html │ ├── MCMC Sampling.ipynb │ ├── Maximum Likelihood Estimation.html │ ├── Maximum Likelihood Estimation.ipynb │ ├── Pathfinder.html │ ├── Pathfinder.ipynb │ ├── Run Generated Quantities.html │ ├── Run Generated Quantities.ipynb │ ├── Using External C++.html │ ├── Using External C++.ipynb │ ├── VI as Sampler Inits.html │ ├── VI as Sampler Inits.ipynb │ ├── Variational Inference.html │ └── Variational Inference.ipynb │ ├── hello_world.html │ ├── outputs.html │ ├── overview.html │ └── workflow.html ├── docsrc ├── Makefile ├── _static │ ├── css │ │ └── custom.css │ └── images │ │ ├── logo_icon.png │ │ └── logo_tm.png ├── api.rst ├── changes.rst ├── community.rst ├── conf.py ├── env.yml ├── index.rst ├── installation.rst ├── internal_api.rst ├── make.bat ├── numpydoc_docstring.py ├── users-guide.rst └── users-guide │ ├── examples.rst │ ├── examples │ ├── .gitignore │ ├── MCMC Sampling.ipynb │ ├── Maximum Likelihood Estimation.ipynb │ ├── Pathfinder.ipynb │ ├── Run Generated Quantities.ipynb │ ├── Using External C++.ipynb │ ├── VI as Sampler Inits.ipynb │ ├── Variational Inference.ipynb │ ├── bernoulli.data.json │ ├── bernoulli.stan │ ├── bernoulli_datagen.stan │ ├── bernoulli_external.stan │ ├── bernoulli_ppc.stan │ ├── blr.stan │ ├── eight_schools.data.json │ ├── eight_schools.stan │ ├── eta_should_fail.stan │ ├── make_odds.hpp │ ├── redcard.json │ ├── redcard_reduce_sum.stan │ └── sblri.json │ ├── hello_world.rst │ ├── outputs.rst │ ├── overview.rst │ └── workflow.rst ├── pyproject.toml └── test ├── __init__.py ├── conftest.py ├── data ├── .gitignore ├── add_one_model.stan ├── bad_syntax.stan ├── bernoulli with space in name.stan ├── bernoulli.data.R ├── bernoulli.data.json ├── bernoulli.init.json ├── bernoulli.init_1.json ├── bernoulli.init_2.json ├── bernoulli.metric-2.json ├── bernoulli.metric.json ├── bernoulli.stan ├── bernoulli_array.stan ├── bernoulli_datagen.data.json ├── bernoulli_datagen.stan ├── bernoulli_include.stan ├── bernoulli_output_1.csv ├── bernoulli_pedantic.stan ├── bernoulli_ppc.stan ├── bernoulli_ppc_dup.stan ├── chain-1-missing-data-stderr.txt ├── chain-1-missing-data-stdout.txt ├── chain-2-missing-data-stderr.txt ├── chain-2-missing-data-stdout.txt ├── chain-3-missing-data-stderr.txt ├── chain-3-missing-data-stdout.txt ├── complex_var.stan ├── container_vars.stan ├── data-test.stan ├── datagen_poisson_glm.stan ├── diagnose-good │ └── corr_gauss_depth8-1.csv ├── divide_real_by_two.stan ├── eight_schools.data.R ├── eight_schools.data.json ├── eight_schools.stan ├── external.stan ├── fixed_param_sample.csv ├── format_me.stan ├── format_me_deprecations.stan ├── from_csv │ └── wrong_header_method.csv ├── include-path │ └── add_one_function.stan ├── linear_regression.data.json ├── linear_regression.stan ├── logistic.data.R ├── logistic.missing_data.R ├── logistic.stan ├── logistic_output_1.csv ├── logistic_output_2.csv ├── logistic_output_3.csv ├── logistic_output_4.csv ├── lotka-volterra.csv ├── lotka-volterra.data.json ├── matrix_var.stan ├── metric_bad.data.json ├── metric_bad_1.data.R ├── metric_bad_2.data.R ├── metric_dense.data.R ├── metric_dense.data.json ├── metric_diag.data.R ├── metric_diag.data.json ├── multidim_vars.csv ├── multidim_vars.stan ├── named_output.stan ├── no_param_hmc_sample.csv ├── normal-rng.stan ├── optimize │ ├── eight_schools_mle_iters.csv │ ├── exponential_boundary.stan │ ├── no_data.stan │ ├── rosenbrock.stan │ ├── rosenbrock_mle.csv │ └── rosenbrock_mle_iters.csv ├── out_of_bounds.stan ├── output_bad_cols.csv ├── output_bad_metric_1.csv ├── output_bad_metric_2.csv ├── output_bad_metric_3.csv ├── output_bad_metric_4.csv ├── output_bad_rows.csv ├── path with space │ └── bernoulli_path_with_space.stan ├── pathfinder │ └── bernoulli-pathfinder.csv ├── path~with~tilde │ └── bernoulli_path_with_tilde.stan ├── profile_likelihood.stan ├── rdump_array.data.R ├── rdump_bad_1.data.R ├── rdump_bad_2.data.R ├── rdump_bad_3.data.R ├── rdump_jags.data.R ├── rdump_test.data.R ├── redcard.json ├── redcard_reduce_sum.stan ├── return_one.hpp ├── runset-bad │ ├── bad-cols-bern-1.csv │ ├── bad-cols-bern-2.csv │ ├── bad-cols-bern-3.csv │ ├── bad-cols-bern-4.csv │ ├── bad-draws-bern-1.csv │ ├── bad-draws-bern-2.csv │ ├── bad-draws-bern-3.csv │ ├── bad-draws-bern-4.csv │ ├── bad-hdr-bern-1.csv │ ├── bad-hdr-bern-2.csv │ ├── bad-hdr-bern-3.csv │ ├── bad-hdr-bern-4.csv │ ├── bad-transcript-bern-1.txt │ ├── bad-transcript-bern-2.txt │ ├── bad-transcript-bern-3.txt │ └── bad-transcript-bern-4.txt ├── runset-big │ ├── output_icar_nyc-1.csv │ └── output_icar_nyc-2.csv ├── runset-good │ ├── bern-1.csv │ ├── bern-1.txt │ ├── bern-2.csv │ ├── bern-2.txt │ ├── bern-3.csv │ ├── bern-3.txt │ ├── bern-4.csv │ └── bern-4.txt ├── sampling_output.csv ├── timeout.stan ├── tuple_data.stan └── variational │ ├── eta_big_output.csv │ ├── eta_should_be_big.stan │ ├── eta_should_be_small.stan │ └── eta_should_fail.stan ├── test_cmdstan_args.py ├── test_compilation.py ├── test_compliance.py ├── test_cxx_installation.py ├── test_generate_quantities.py ├── test_install_cmdstan.py ├── test_laplace.py ├── test_log_prob.py ├── test_logging.py ├── test_metadata.py ├── test_model.py ├── test_optimize.py ├── test_pathfinder.py ├── test_runset.py ├── test_sample.py ├── test_stancsv.py ├── test_utils.py └── 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