Merge .py and notebook examples in the same directory structure

Sriatunckfbs · Dec 18, 2020 · b3d66ba · b3d66ba
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Showing 104 changed files with 3 additions and 30 deletions.
diff --git a/examples/__init__.py b/examples/__init__.py
diff --git a/notebooks/case_studies/BEST.ipynb → examples/case_studies/BEST.ipynb b/notebooks/case_studies/BEST.ipynb → examples/case_studies/BEST.ipynb
diff --git a/examples/GHME_2013.py → examples/case_studies/GHME_2013.py b/examples/GHME_2013.py → examples/case_studies/GHME_2013.py
diff --git a/notebooks/case_studies/LKJ.ipynb → examples/case_studies/LKJ.ipynb b/notebooks/case_studies/LKJ.ipynb → examples/case_studies/LKJ.ipynb
diff --git a/examples/baseball.py → examples/case_studies/baseball.py b/examples/baseball.py → examples/case_studies/baseball.py
diff --git a/...tudies/blackbox_external_likelihood.ipynb → ...tudies/blackbox_external_likelihood.ipynb b/...tudies/blackbox_external_likelihood.ipynb → ...tudies/blackbox_external_likelihood.ipynb
diff --git a/...es/conditional-autoregressive-model.ipynb → ...es/conditional-autoregressive-model.ipynb b/...es/conditional-autoregressive-model.ipynb → ...es/conditional-autoregressive-model.ipynb
diff --git a/examples/disaster_model.py → examples/case_studies/disaster_model.py b/examples/disaster_model.py → examples/case_studies/disaster_model.py
diff --git a/examples/disaster_model_theano_op.py → .../case_studies/disaster_model_theano_op.py b/examples/disaster_model_theano_op.py → .../case_studies/disaster_model_theano_op.py
diff --git a/notebooks/case_studies/factor_analysis.ipynb → examples/case_studies/factor_analysis.ipynb b/notebooks/case_studies/factor_analysis.ipynb → examples/case_studies/factor_analysis.ipynb
diff --git a/examples/garch_example.py → examples/case_studies/garch_example.py b/examples/garch_example.py → examples/case_studies/garch_example.py
diff --git a/examples/gelman_bioassay.py → examples/case_studies/gelman_bioassay.py b/examples/gelman_bioassay.py → examples/case_studies/gelman_bioassay.py
diff --git a/examples/gelman_schools.py → examples/case_studies/gelman_schools.py b/examples/gelman_schools.py → examples/case_studies/gelman_schools.py
diff --git a/...tudies/hierarchical_partial_pooling.ipynb → ...tudies/hierarchical_partial_pooling.ipynb b/...tudies/hierarchical_partial_pooling.ipynb → ...tudies/hierarchical_partial_pooling.ipynb
diff --git a/examples/lasso_missing.py → examples/case_studies/lasso_missing.py b/examples/lasso_missing.py → examples/case_studies/lasso_missing.py
diff --git a/examples/lightspeed_example.py → examples/case_studies/lightspeed_example.py b/examples/lightspeed_example.py → examples/case_studies/lightspeed_example.py
diff --git a/...se_studies/log-gaussian-cox-process.ipynb → ...se_studies/log-gaussian-cox-process.ipynb b/...se_studies/log-gaussian-cox-process.ipynb → ...se_studies/log-gaussian-cox-process.ipynb
diff --git a/...ks/case_studies/multilevel_modeling.ipynb → ...es/case_studies/multilevel_modeling.ipynb b/...ks/case_studies/multilevel_modeling.ipynb → ...es/case_studies/multilevel_modeling.ipynb
diff --git a/.../probabilistic_matrix_factorization.ipynb → .../probabilistic_matrix_factorization.ipynb b/.../probabilistic_matrix_factorization.ipynb → .../probabilistic_matrix_factorization.ipynb
diff --git a/...books/case_studies/putting_workflow.ipynb → examples/case_studies/putting_workflow.ipynb b/...books/case_studies/putting_workflow.ipynb → examples/case_studies/putting_workflow.ipynb
diff --git a/notebooks/case_studies/rugby_analytics.ipynb → examples/case_studies/rugby_analytics.ipynb b/notebooks/case_studies/rugby_analytics.ipynb → examples/case_studies/rugby_analytics.ipynb
diff --git a/.../case_studies/stochastic_volatility.ipynb → .../case_studies/stochastic_volatility.ipynb b/.../case_studies/stochastic_volatility.ipynb → .../case_studies/stochastic_volatility.ipynb
diff --git a/...gnostics_and_criticism/Bayes_factor.ipynb → ...gnostics_and_criticism/Bayes_factor.ipynb b/...gnostics_and_criticism/Bayes_factor.ipynb → ...gnostics_and_criticism/Bayes_factor.ipynb
diff --git a/...g_biased_Inference_with_Divergences.ipynb → ...g_biased_Inference_with_Divergences.ipynb b/...g_biased_Inference_with_Divergences.ipynb → ...g_biased_Inference_with_Divergences.ipynb
diff --git a/...stics_and_criticism/model_averaging.ipynb → ...stics_and_criticism/model_averaging.ipynb b/...stics_and_criticism/model_averaging.ipynb → ...stics_and_criticism/model_averaging.ipynb
diff --git a/...tics_and_criticism/model_comparison.ipynb → ...tics_and_criticism/model_comparison.ipynb b/...tics_and_criticism/model_comparison.ipynb → ...tics_and_criticism/model_comparison.ipynb
diff --git a/..._and_criticism/posterior_predictive.ipynb → ..._and_criticism/posterior_predictive.ipynb b/..._and_criticism/posterior_predictive.ipynb → ..._and_criticism/posterior_predictive.ipynb
diff --git a/...nostics_and_criticism/sampler-stats.ipynb → ...nostics_and_criticism/sampler-stats.ipynb b/...nostics_and_criticism/sampler-stats.ipynb → ...nostics_and_criticism/sampler-stats.ipynb
diff --git a/...ooks/gaussian_processes/GP-Circular.ipynb → ...ples/gaussian_processes/GP-Circular.ipynb b/...ooks/gaussian_processes/GP-Circular.ipynb → ...ples/gaussian_processes/GP-Circular.ipynb
diff --git a/notebooks/gaussian_processes/GP-Kron.ipynb → examples/gaussian_processes/GP-Kron.ipynb b/notebooks/gaussian_processes/GP-Kron.ipynb → examples/gaussian_processes/GP-Kron.ipynb
diff --git a/notebooks/gaussian_processes/GP-Latent.ipynb → examples/gaussian_processes/GP-Latent.ipynb b/notebooks/gaussian_processes/GP-Latent.ipynb → examples/gaussian_processes/GP-Latent.ipynb
diff --git a/...ooks/gaussian_processes/GP-Marginal.ipynb → ...ples/gaussian_processes/GP-Marginal.ipynb b/...ooks/gaussian_processes/GP-Marginal.ipynb → ...ples/gaussian_processes/GP-Marginal.ipynb
diff --git a/...ooks/gaussian_processes/GP-MaunaLoa.ipynb → ...ples/gaussian_processes/GP-MaunaLoa.ipynb b/...ooks/gaussian_processes/GP-MaunaLoa.ipynb → ...ples/gaussian_processes/GP-MaunaLoa.ipynb
diff --git a/...oks/gaussian_processes/GP-MaunaLoa2.ipynb → ...les/gaussian_processes/GP-MaunaLoa2.ipynb b/...oks/gaussian_processes/GP-MaunaLoa2.ipynb → ...les/gaussian_processes/GP-MaunaLoa2.ipynb
diff --git a/.../gaussian_processes/GP-MeansAndCovs.ipynb → .../gaussian_processes/GP-MeansAndCovs.ipynb b/.../gaussian_processes/GP-MeansAndCovs.ipynb → .../gaussian_processes/GP-MeansAndCovs.ipynb
diff --git a/.../gaussian_processes/GP-SparseApprox.ipynb → .../gaussian_processes/GP-SparseApprox.ipynb b/.../gaussian_processes/GP-SparseApprox.ipynb → .../gaussian_processes/GP-SparseApprox.ipynb
diff --git a/...ooks/gaussian_processes/GP-TProcess.ipynb → ...ples/gaussian_processes/GP-TProcess.ipynb b/...ooks/gaussian_processes/GP-TProcess.ipynb → ...ples/gaussian_processes/GP-TProcess.ipynb
diff --git a/...oks/gaussian_processes/GP-smoothing.ipynb → ...les/gaussian_processes/GP-smoothing.ipynb b/...oks/gaussian_processes/GP-smoothing.ipynb → ...les/gaussian_processes/GP-smoothing.ipynb
diff --git a/...gaussian_processes/gaussian_process.ipynb → ...gaussian_processes/gaussian_process.ipynb b/...gaussian_processes/gaussian_process.ipynb → ...gaussian_processes/gaussian_process.ipynb
diff --git a/...ls/GLM-hierarchical-binominal-model.ipynb → ...ls/GLM-hierarchical-binominal-model.ipynb b/...ls/GLM-hierarchical-binominal-model.ipynb → ...ls/GLM-hierarchical-binominal-model.ipynb
diff --git a/...ized_linear_models/GLM-hierarchical.ipynb → ...ized_linear_models/GLM-hierarchical.ipynb b/...ized_linear_models/GLM-hierarchical.ipynb → ...ized_linear_models/GLM-hierarchical.ipynb
diff --git a/...eneralized_linear_models/GLM-linear.ipynb → ...eneralized_linear_models/GLM-linear.ipynb b/...eneralized_linear_models/GLM-linear.ipynb → ...eneralized_linear_models/GLM-linear.ipynb
diff --git a/...eralized_linear_models/GLM-logistic.ipynb → ...eralized_linear_models/GLM-logistic.ipynb b/...eralized_linear_models/GLM-logistic.ipynb → ...eralized_linear_models/GLM-logistic.ipynb
diff --git a/...d_linear_models/GLM-model-selection.ipynb → ...d_linear_models/GLM-model-selection.ipynb b/...d_linear_models/GLM-model-selection.ipynb → ...d_linear_models/GLM-model-selection.ipynb
diff --git a/...ls/GLM-negative-binomial-regression.ipynb → ...ls/GLM-negative-binomial-regression.ipynb b/...ls/GLM-negative-binomial-regression.ipynb → ...ls/GLM-negative-binomial-regression.ipynb
diff --git a/...inear_models/GLM-poisson-regression.ipynb → ...inear_models/GLM-poisson-regression.ipynb b/...inear_models/GLM-poisson-regression.ipynb → ...inear_models/GLM-poisson-regression.ipynb
diff --git a/...s/GLM-robust-with-outlier-detection.ipynb → ...s/GLM-robust-with-outlier-detection.ipynb b/...s/GLM-robust-with-outlier-detection.ipynb → ...s/GLM-robust-with-outlier-detection.ipynb
diff --git a/...eneralized_linear_models/GLM-robust.ipynb → ...eneralized_linear_models/GLM-robust.ipynb b/...eneralized_linear_models/GLM-robust.ipynb → ...eneralized_linear_models/GLM-robust.ipynb
diff --git a/...inear_models/GLM-rolling-regression.ipynb → ...inear_models/GLM-rolling-regression.ipynb b/...inear_models/GLM-rolling-regression.ipynb → ...inear_models/GLM-rolling-regression.ipynb
diff --git a/...books/generalized_linear_models/GLM.ipynb → examples/generalized_linear_models/GLM.ipynb b/...books/generalized_linear_models/GLM.ipynb → examples/generalized_linear_models/GLM.ipynb
diff --git a/notebooks/getting_started.ipynb → examples/getting_started.ipynb b/notebooks/getting_started.ipynb → examples/getting_started.ipynb
diff --git a/...models/dependent_density_regression.ipynb → ...models/dependent_density_regression.ipynb b/...models/dependent_density_regression.ipynb → ...models/dependent_density_regression.ipynb
diff --git a/notebooks/mixture_models/dp_mix.ipynb → examples/mixture_models/dp_mix.ipynb b/notebooks/mixture_models/dp_mix.ipynb → examples/mixture_models/dp_mix.ipynb
diff --git a/...xture_models/gaussian_mixture_model.ipynb → ...xture_models/gaussian_mixture_model.ipynb b/...xture_models/gaussian_mixture_model.ipynb → ...xture_models/gaussian_mixture_model.ipynb
diff --git a/...marginalized_gaussian_mixture_model.ipynb → ...marginalized_gaussian_mixture_model.ipynb b/...marginalized_gaussian_mixture_model.ipynb → ...marginalized_gaussian_mixture_model.ipynb
diff --git a/...oks/ode_models/ODE_API_introduction.ipynb → ...les/ode_models/ODE_API_introduction.ipynb b/...oks/ode_models/ODE_API_introduction.ipynb → ...les/ode_models/ODE_API_introduction.ipynb
diff --git a/...els/ODE_API_shapes_and_benchmarking.ipynb → ...els/ODE_API_shapes_and_benchmarking.ipynb b/...els/ODE_API_shapes_and_benchmarking.ipynb → ...els/ODE_API_shapes_and_benchmarking.ipynb
diff --git a/...de_models/ODE_with_manual_gradients.ipynb → ...de_models/ODE_with_manual_gradients.ipynb b/...de_models/ODE_with_manual_gradients.ipynb → ...de_models/ODE_with_manual_gradients.ipynb
diff --git a/examples/LKJ_correlation.py → examples/pymc3_howto/LKJ_correlation.py b/examples/LKJ_correlation.py → examples/pymc3_howto/LKJ_correlation.py
diff --git a/notebooks/pymc3_howto/api_quickstart.ipynb → examples/pymc3_howto/api_quickstart.ipynb b/notebooks/pymc3_howto/api_quickstart.ipynb → examples/pymc3_howto/api_quickstart.ipynb
diff --git a/examples/arbitrary_stochastic.py → examples/pymc3_howto/arbitrary_stochastic.py b/examples/arbitrary_stochastic.py → examples/pymc3_howto/arbitrary_stochastic.py
diff --git a/examples/custom_dists.py → examples/pymc3_howto/custom_dists.py b/examples/custom_dists.py → examples/pymc3_howto/custom_dists.py
diff --git a/notebooks/pymc3_howto/data_container.ipynb → examples/pymc3_howto/data_container.ipynb b/notebooks/pymc3_howto/data_container.ipynb → examples/pymc3_howto/data_container.ipynb
diff --git a/examples/factor_potential.py → examples/pymc3_howto/factor_potential.py b/examples/factor_potential.py → examples/pymc3_howto/factor_potential.py
diff --git a/notebooks/pymc3_howto/howto_debugging.ipynb → examples/pymc3_howto/howto_debugging.ipynb b/notebooks/pymc3_howto/howto_debugging.ipynb → examples/pymc3_howto/howto_debugging.ipynb
diff --git a/...ooks/pymc3_howto/lasso_block_update.ipynb → ...ples/pymc3_howto/lasso_block_update.ipynb b/...ooks/pymc3_howto/lasso_block_update.ipynb → ...ples/pymc3_howto/lasso_block_update.ipynb
diff --git a/notebooks/pymc3_howto/profiling.ipynb → examples/pymc3_howto/profiling.ipynb b/notebooks/pymc3_howto/profiling.ipynb → examples/pymc3_howto/profiling.ipynb
diff --git a/examples/rankdata_ordered.py → examples/pymc3_howto/rankdata_ordered.py b/examples/rankdata_ordered.py → examples/pymc3_howto/rankdata_ordered.py
diff --git a/...books/pymc3_howto/sampling_callback.ipynb → examples/pymc3_howto/sampling_callback.ipynb b/...books/pymc3_howto/sampling_callback.ipynb → examples/pymc3_howto/sampling_callback.ipynb
diff --git a/.../pymc3_howto/sampling_compound_step.ipynb → .../pymc3_howto/sampling_compound_step.ipynb b/.../pymc3_howto/sampling_compound_step.ipynb → .../pymc3_howto/sampling_compound_step.ipynb
diff --git a/...pymc3_howto/sampling_conjugate_step.ipynb → ...pymc3_howto/sampling_conjugate_step.ipynb b/...pymc3_howto/sampling_conjugate_step.ipynb → ...pymc3_howto/sampling_conjugate_step.ipynb
diff --git a/notebooks/pymc3_howto/updating_priors.ipynb → examples/pymc3_howto/updating_priors.ipynb b/notebooks/pymc3_howto/updating_priors.ipynb → examples/pymc3_howto/updating_priors.ipynb
diff --git a/.../DEMetropolisZ_EfficiencyComparison.ipynb → .../DEMetropolisZ_EfficiencyComparison.ipynb b/.../DEMetropolisZ_EfficiencyComparison.ipynb → .../DEMetropolisZ_EfficiencyComparison.ipynb
diff --git a/...rs/DEMetropolisZ_tune_drop_fraction.ipynb → ...rs/DEMetropolisZ_tune_drop_fraction.ipynb b/...rs/DEMetropolisZ_tune_drop_fraction.ipynb → ...rs/DEMetropolisZ_tune_drop_fraction.ipynb
diff --git a/...books/samplers/GLM-hierarchical-jax.ipynb → examples/samplers/GLM-hierarchical-jax.ipynb b/...books/samplers/GLM-hierarchical-jax.ipynb → examples/samplers/GLM-hierarchical-jax.ipynb
diff --git a/...oks/samplers/MLDA_gravity_surveying.ipynb → ...les/samplers/MLDA_gravity_surveying.ipynb b/...oks/samplers/MLDA_gravity_surveying.ipynb → ...les/samplers/MLDA_gravity_surveying.ipynb
diff --git a/notebooks/samplers/MLDA_introduction.ipynb → examples/samplers/MLDA_introduction.ipynb b/notebooks/samplers/MLDA_introduction.ipynb → examples/samplers/MLDA_introduction.ipynb
diff --git a/...plers/MLDA_simple_linear_regression.ipynb → ...plers/MLDA_simple_linear_regression.ipynb b/...plers/MLDA_simple_linear_regression.ipynb → ...plers/MLDA_simple_linear_regression.ipynb
diff --git a/...ariance_reduction_linear_regression.ipynb → ...ariance_reduction_linear_regression.ipynb b/...ariance_reduction_linear_regression.ipynb → ...ariance_reduction_linear_regression.ipynb
diff --git a/...lers/SMC-ABC_Lotka-Volterra_example.ipynb → ...lers/SMC-ABC_Lotka-Volterra_example.ipynb b/...lers/SMC-ABC_Lotka-Volterra_example.ipynb → ...lers/SMC-ABC_Lotka-Volterra_example.ipynb
diff --git a/notebooks/samplers/SMC2_gaussians.ipynb → examples/samplers/SMC2_gaussians.ipynb b/notebooks/samplers/SMC2_gaussians.ipynb → examples/samplers/SMC2_gaussians.ipynb
diff --git a/examples/samplers_mvnormal.py → examples/samplers/samplers_mvnormal.py b/examples/samplers_mvnormal.py → examples/samplers/samplers_mvnormal.py
diff --git a/notebooks/samplers/smc.png → examples/samplers/smc.png b/notebooks/samplers/smc.png → examples/samplers/smc.png
diff --git a/examples/simpletest.py b/examples/simpletest.py
diff --git a/...analysis/bayes_param_survival_pymc3.ipynb → ...analysis/bayes_param_survival_pymc3.ipynb b/...analysis/bayes_param_survival_pymc3.ipynb → ...analysis/bayes_param_survival_pymc3.ipynb
diff --git a/...oks/survival_analysis/censored_data.ipynb → ...les/survival_analysis/censored_data.ipynb b/...oks/survival_analysis/censored_data.ipynb → ...les/survival_analysis/censored_data.ipynb
diff --git a/notebooks/survival_analysis/cox_model.ipynb → examples/survival_analysis/cox_model.ipynb b/notebooks/survival_analysis/cox_model.ipynb → examples/survival_analysis/cox_model.ipynb
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diff --git a/...books/survival_analysis/weibull_aft.ipynb → examples/survival_analysis/weibull_aft.ipynb b/...books/survival_analysis/weibull_aft.ipynb → examples/survival_analysis/weibull_aft.ipynb
diff --git a/notebooks/table_of_contents_examples.js → examples/table_of_contents_examples.js b/notebooks/table_of_contents_examples.js → examples/table_of_contents_examples.js
diff --git a/notebooks/table_of_contents_tutorials.js → examples/table_of_contents_tutorials.js b/notebooks/table_of_contents_tutorials.js → examples/table_of_contents_tutorials.js
diff --git a/notebooks/time_series/AR.ipynb → examples/time_series/AR.ipynb b/notebooks/time_series/AR.ipynb → examples/time_series/AR.ipynb
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diff --git a/...me_series/MvGaussianRandomWalk_demo.ipynb → ...me_series/MvGaussianRandomWalk_demo.ipynb b/...me_series/MvGaussianRandomWalk_demo.ipynb → ...me_series/MvGaussianRandomWalk_demo.ipynb
diff --git a/examples/arma_example.py → examples/time_series/arma_example.py b/examples/arma_example.py → examples/time_series/arma_example.py
diff --git a/...nce/GLM-hierarchical-advi-minibatch.ipynb → ...nce/GLM-hierarchical-advi-minibatch.ipynb b/...nce/GLM-hierarchical-advi-minibatch.ipynb → ...nce/GLM-hierarchical-advi-minibatch.ipynb
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diff --git a/...inference/empirical-approx-overview.ipynb → ...inference/empirical-approx-overview.ipynb b/...inference/empirical-approx-overview.ipynb → ...inference/empirical-approx-overview.ipynb
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diff --git a/...variational_inference/lda-advi-aevb.ipynb → ...variational_inference/lda-advi-aevb.ipynb b/...variational_inference/lda-advi-aevb.ipynb → ...variational_inference/lda-advi-aevb.ipynb
diff --git a/...nference/normalizing_flows_overview.ipynb → ...nference/normalizing_flows_overview.ipynb b/...nference/normalizing_flows_overview.ipynb → ...nference/normalizing_flows_overview.ipynb
diff --git a/...nference/variational_api_quickstart.ipynb → ...nference/variational_api_quickstart.ipynb b/...nference/variational_api_quickstart.ipynb → ...nference/variational_api_quickstart.ipynb
diff --git a/scripts/check_toc_is_complete.py b/scripts/check_toc_is_complete.py