From 5d36eb6510d896796677e1d1fd9faf2ab4104991 Mon Sep 17 00:00:00 2001 From: Chris Fonnesbeck Date: Wed, 16 Dec 2020 10:54:56 -0600 Subject: [PATCH 1/4] Assigned notebooks to subfolders --- notebooks/{ => case_studies}/BEST.ipynb | 0 notebooks/{ => case_studies}/LKJ.ipynb | 0 .../blackbox_external_likelihood.ipynb | 0 .../conditional-autoregressive-model.ipynb | 0 notebooks/{ => case_studies}/factor_analysis.ipynb | 0 .../hierarchical_partial_pooling.ipynb | 0 .../log-gaussian-cox-process.ipynb | 0 .../{ => case_studies}/multilevel_modeling.ipynb | 0 .../probabilistic_matrix_factorization.ipynb | 0 notebooks/{ => case_studies}/putting_workflow.ipynb | 0 notebooks/{ => case_studies}/rugby_analytics.ipynb | 0 .../{ => case_studies}/stochastic_volatility.ipynb | 0 .../Bayes_factor.ipynb | 0 ...agnosing_biased_Inference_with_Divergences.ipynb | 0 .../model_averaging.ipynb | 0 .../model_comparison.ipynb | 0 .../posterior_predictive.ipynb | 0 .../sampler-stats.ipynb | 0 .../{ => gaussian_processes}/GP-Circular.ipynb | 0 notebooks/{ => gaussian_processes}/GP-Kron.ipynb | 0 notebooks/{ => gaussian_processes}/GP-Latent.ipynb | 0 .../{ => gaussian_processes}/GP-Marginal.ipynb | 0 .../{ => gaussian_processes}/GP-MaunaLoa.ipynb | 0 .../{ => gaussian_processes}/GP-MaunaLoa2.ipynb | 0 .../{ => gaussian_processes}/GP-MeansAndCovs.ipynb | 0 .../{ => gaussian_processes}/GP-SparseApprox.ipynb | 0 .../{ => gaussian_processes}/GP-TProcess.ipynb | 0 .../{ => gaussian_processes}/GP-smoothing.ipynb | 0 .../{ => gaussian_processes}/gaussian_process.ipynb | 0 .../GLM-hierarchical-binominal-model.ipynb | 0 .../GLM-hierarchical-jax.ipynb | 0 .../GLM-hierarchical.ipynb | 0 .../GLM-linear.ipynb | 0 .../GLM-logistic.ipynb | 0 .../GLM-model-selection.ipynb | 0 .../GLM-negative-binomial-regression.ipynb | 0 .../GLM-poisson-regression.ipynb | 0 .../GLM-robust-with-outlier-detection.ipynb | 0 .../GLM-robust.ipynb | 0 .../GLM-rolling-regression.ipynb | 0 notebooks/{ => 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from notebooks/empirical-approx-overview.ipynb rename to notebooks/variational_inference/empirical-approx-overview.ipynb diff --git a/notebooks/gaussian-mixture-model-advi.ipynb b/notebooks/variational_inference/gaussian-mixture-model-advi.ipynb similarity index 100% rename from notebooks/gaussian-mixture-model-advi.ipynb rename to notebooks/variational_inference/gaussian-mixture-model-advi.ipynb diff --git a/notebooks/lda-advi-aevb.ipynb b/notebooks/variational_inference/lda-advi-aevb.ipynb similarity index 100% rename from notebooks/lda-advi-aevb.ipynb rename to notebooks/variational_inference/lda-advi-aevb.ipynb diff --git a/notebooks/normalizing_flows_overview.ipynb b/notebooks/variational_inference/normalizing_flows_overview.ipynb similarity index 100% rename from notebooks/normalizing_flows_overview.ipynb rename to notebooks/variational_inference/normalizing_flows_overview.ipynb diff --git a/notebooks/variational_api_quickstart.ipynb b/notebooks/variational_inference/variational_api_quickstart.ipynb similarity index 100% rename from notebooks/variational_api_quickstart.ipynb rename to notebooks/variational_inference/variational_api_quickstart.ipynb From fca998c50cabc31d14ee5e1f6acaeb5d4f98e1a8 Mon Sep 17 00:00:00 2001 From: Chris Fonnesbeck Date: Wed, 16 Dec 2020 11:03:45 -0600 Subject: [PATCH 2/4] Swapped api_quickstert and getting_started locations --- notebooks/{pymc3_howto => }/getting_started.ipynb | 0 notebooks/{ => pymc3_howto}/api_quickstart.ipynb | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename notebooks/{pymc3_howto => }/getting_started.ipynb (100%) rename notebooks/{ => pymc3_howto}/api_quickstart.ipynb (100%) diff --git a/notebooks/pymc3_howto/getting_started.ipynb b/notebooks/getting_started.ipynb similarity index 100% rename from notebooks/pymc3_howto/getting_started.ipynb rename to notebooks/getting_started.ipynb diff --git a/notebooks/api_quickstart.ipynb b/notebooks/pymc3_howto/api_quickstart.ipynb similarity index 100% rename from notebooks/api_quickstart.ipynb rename to notebooks/pymc3_howto/api_quickstart.ipynb From 022e55f53046d7f8362b9889b7108ff7f78eb65d Mon Sep 17 00:00:00 2001 From: Chris Fonnesbeck Date: Wed, 16 Dec 2020 11:27:13 -0600 Subject: [PATCH 3/4] Added subdirs to index --- .../GLM-hierarchical-jax.ipynb | 0 .../SMC-ABC_Lotka-Volterra_example.ipynb | 0 .../SMC2_gaussians.ipynb | 0 .../smc.png | Bin notebooks/table_of_contents_examples.js | 132 +++++++++--------- notebooks/table_of_contents_tutorials.js | 34 ++--- 6 files changed, 83 insertions(+), 83 deletions(-) rename notebooks/{generalized_linear_models => samplers}/GLM-hierarchical-jax.ipynb (100%) rename notebooks/{simulation_based_inference => samplers}/SMC-ABC_Lotka-Volterra_example.ipynb (100%) rename notebooks/{simulation_based_inference => samplers}/SMC2_gaussians.ipynb (100%) rename notebooks/{simulation_based_inference => samplers}/smc.png (100%) diff --git a/notebooks/generalized_linear_models/GLM-hierarchical-jax.ipynb b/notebooks/samplers/GLM-hierarchical-jax.ipynb similarity index 100% rename from notebooks/generalized_linear_models/GLM-hierarchical-jax.ipynb rename to notebooks/samplers/GLM-hierarchical-jax.ipynb diff --git a/notebooks/simulation_based_inference/SMC-ABC_Lotka-Volterra_example.ipynb b/notebooks/samplers/SMC-ABC_Lotka-Volterra_example.ipynb similarity index 100% rename from notebooks/simulation_based_inference/SMC-ABC_Lotka-Volterra_example.ipynb rename to notebooks/samplers/SMC-ABC_Lotka-Volterra_example.ipynb diff --git a/notebooks/simulation_based_inference/SMC2_gaussians.ipynb b/notebooks/samplers/SMC2_gaussians.ipynb similarity index 100% rename from notebooks/simulation_based_inference/SMC2_gaussians.ipynb rename to notebooks/samplers/SMC2_gaussians.ipynb diff --git a/notebooks/simulation_based_inference/smc.png b/notebooks/samplers/smc.png similarity index 100% rename from notebooks/simulation_based_inference/smc.png rename to notebooks/samplers/smc.png diff --git a/notebooks/table_of_contents_examples.js b/notebooks/table_of_contents_examples.js index 77a714bf7..ed760392f 100644 --- a/notebooks/table_of_contents_examples.js +++ b/notebooks/table_of_contents_examples.js @@ -1,69 +1,69 @@ Gallery.contents = { - "BEST": "Case Studies", - "LKJ": "Case Studies", - "stochastic_volatility": "Case Studies", - "rugby_analytics": "Case Studies", - "multilevel_modeling": "Case Studies", - "putting_workflow": "Case Studies", - "Diagnosing_biased_Inference_with_Divergences": "Diagnostics and Model Criticism", - "model_comparison": "Diagnostics and Model Criticism", - "posterior_predictive": "Diagnostics and Model Criticism", - "Bayes_factor": "Diagnostics and Model Criticism", - "GLM": "(Generalized) Linear and Hierarchical Linear Models", - "GLM-linear": "(Generalized) Linear and Hierarchical Linear Models", - "GLM-logistic": "(Generalized) Linear and Hierarchical Linear Models", - "GLM-hierarchical-binominal-model": "(Generalized) Linear and Hierarchical Linear Models", - "GLM-hierarchical": "(Generalized) Linear and Hierarchical Linear Models", - "hierarchical_partial_pooling": "(Generalized) Linear and Hierarchical Linear Models", - "GLM-model-selection": "(Generalized) Linear and Hierarchical Linear Models", - "GLM-negative-binomial-regression": "(Generalized) Linear and Hierarchical Linear Models", - "GLM-poisson-regression": "(Generalized) Linear and Hierarchical Linear Models", - "GLM-robust-with-outlier-detection": "(Generalized) Linear and Hierarchical Linear Models", - "GLM-robust": "(Generalized) Linear and Hierarchical Linear Models", - "GLM-rolling-regression": "(Generalized) Linear and Hierarchical Linear Models", - "GLM-hierarchical-advi-minibatch": "(Generalized) Linear and Hierarchical Linear Models", - "GP-Kron": "Gaussian Processes", - "GP-Latent": "Gaussian Processes", - "GP-Marginal": "Gaussian Processes", - "GP-MaunaLoa": "Gaussian Processes", - "GP-MaunaLoa2": "Gaussian Processes", - "GP-MeansAndCovs": "Gaussian Processes", - "GP-SparseApprox": "Gaussian Processes", - "GP-TProcess": "Gaussian Processes", - "GP-smoothing": "Gaussian Processes", - "gaussian_process": "Gaussian Processes", - "conditional-autoregressive-model": "Gaussian Processes", - "log-gaussian-cox-process":"Gaussian Processes", - "GP-Circular": "Gaussian Processes", - "dependent_density_regression": "Mixture Models", - "dp_mix": "Mixture Models", - "gaussian-mixture-model-advi": "Mixture Models", - "gaussian_mixture_model": "Mixture Models", + "case_studies/BEST": "Case Studies", + "case_studies/LKJ": "Case Studies", + "case_studies/stochastic_volatility": "Case Studies", + "case_studies/rugby_analytics": "Case Studies", + "case_studies/multilevel_modeling": "Case Studies", + "case_studies/putting_workflow": "Case Studies", + "diagnostics_and_criticism/Diagnosing_biased_Inference_with_Divergences": "Diagnostics and Model Criticism", + "diagnostics_and_criticism/model_comparison": "Diagnostics and Model Criticism", + "diagnostics_and_criticism/posterior_predictive": "Diagnostics and Model Criticism", + "diagnostics_and_criticism/Bayes_factor": "Diagnostics and Model Criticism", + "generalized_linear_models/GLM": "(Generalized) Linear and Hierarchical Linear Models", + "generalized_linear_models/GLM-linear": "(Generalized) Linear and Hierarchical Linear Models", + "generalized_linear_models/GLM-logistic": "(Generalized) Linear and Hierarchical Linear Models", + "generalized_linear_models/GLM-hierarchical-binominal-model": "(Generalized) Linear and Hierarchical Linear Models", + "generalized_linear_models/GLM-hierarchical": "(Generalized) Linear and Hierarchical Linear Models", + "case/studies/hierarchical_partial_pooling": "(Generalized) Linear and Hierarchical Linear Models", + "generalized_linear_models/GLM-model-selection": "(Generalized) Linear and Hierarchical Linear Models", + "generalized_linear_models/GLM-negative-binomial-regression": "(Generalized) Linear and Hierarchical Linear Models", + "generalized_linear_models/GLM-poisson-regression": "(Generalized) Linear and Hierarchical Linear Models", + "generalized_linear_models/GLM-robust-with-outlier-detection": "(Generalized) Linear and Hierarchical Linear Models", + "generalized_linear_models/GLM-robust": "(Generalized) Linear and Hierarchical Linear Models", + "generalized_linear_models/GLM-rolling-regression": "(Generalized) Linear and Hierarchical Linear Models", + "generalized_linear_models/GLM-hierarchical-advi-minibatch": "(Generalized) Linear and Hierarchical Linear Models", + "gaussian_processes/GP-Kron": "Gaussian Processes", + "gaussian_processes/GP-Latent": "Gaussian Processes", + "gaussian_processes/GP-Marginal": "Gaussian Processes", + "gaussian_processes/GP-MaunaLoa": "Gaussian Processes", + "gaussian_processes/GP-MaunaLoa2": "Gaussian Processes", + "gaussian_processes/GP-MeansAndCovs": "Gaussian Processes", + "gaussian_processes/GP-SparseApprox": "Gaussian Processes", + "gaussian_processes/GP-TProcess": "Gaussian Processes", + "gaussian_processes/GP-smoothing": "Gaussian Processes", + "gaussian_processes/gaussian_process": "Gaussian Processes", + "case_studies/conditional-autoregressive-model": "Gaussian Processes", + "case_studies/log-gaussian-cox-process":"Gaussian Processes", + "gaussian_processes/GP-Circular": "Gaussian Processes", + "mixture_models/dependent_density_regression": "Mixture Models", + "mixture_models/dp_mix": "Mixture Models", + "variational_inference/gaussian-mixture-model-advi": "Mixture Models", + "mixture_models/gaussian_mixture_model": "Mixture Models", "marginalized_gaussian_mixture_model": "Mixture Models", - "SMC2_gaussians": "Simulation-based Inference", - "SMC-ABC_Lotka-Volterra_example": "Simulation-based Inference", - "bayes_param_survival_pymc3": "Survival Analysis", - "censored_data": "Survival Analysis", - "survival_analysis": "Survival Analysis", - "weibull_aft": "Survival Analysis", - "cox_model": "Survival Analysis", - "MvGaussianRandomWalk_demo": "Time Series", - "AR": "Time Series", - "Euler-Maruyama_and_SDEs": "Time Series", - "bayesian_neural_network_advi": "Variational Inference", - "convolutional_vae_keras_advi": "Variational Inference", - "empirical-approx-overview": "Variational Inference", - "lda-advi-aevb": "Variational Inference", - "normalizing_flows_overview": "Variational Inference", - "gaussian-mixture-model-advi": "Variational Inference", - "GLM-hierarchical-advi-minibatch": "Variational Inference", - "ODE_with_manual_gradients": "Inference in ODE models", - "ODE_API_introduction": "Inference in ODE models", - "probabilistic_matrix_factorization": "Case Studies", - "sampling_conjugate_step":"MCMC", - "MLDA_introduction": "MCMC", - "MLDA_simple_linear_regression": "MCMC", - "MLDA_gravity_surveying": "MCMC", - "MLDA_variance_reduction_linear_regression": "MCMC", - "GLM-hierarchical-jax": "MCMC" + "samplers/SMC2_gaussians": "Simulation-based Inference", + "samplers/SMC-ABC_Lotka-Volterra_example": "Simulation-based Inference", + "survival_analysis/bayes_param_survival_pymc3": "Survival Analysis", + "survival_analysis/censored_data": "Survival Analysis", + "survival_analysis/survival_analysis": "Survival Analysis", + "survival_analysis/weibull_aft": "Survival Analysis", + "survival_analysis/cox_model": "Survival Analysis", + "time_series/MvGaussianRandomWalk_demo": "Time Series", + "time_series/R": "Time Series", + "time_series/Euler-Maruyama_and_SDEs": "Time Series", + "variational_inference/bayesian_neural_network_advi": "Variational Inference", + "variational_inference/convolutional_vae_keras_advi": "Variational Inference", + "variational_inference/empirical-approx-overview": "Variational Inference", + "variational_inference/lda-advi-aevb": "Variational Inference", + "variational_inference/normalizing_flows_overview": "Variational Inference", + "variational_inference/gaussian-mixture-model-advi": "Variational Inference", + "variational_inference/GLM-hierarchical-advi-minibatch": "Variational Inference", + "ode_models/ODE_with_manual_gradients": "Inference in ODE models", + "ode_models/ODE_API_introduction": "Inference in ODE models", + "case_studies/probabilistic_matrix_factorization": "Case Studies", + "pymc3_howto/sampling_conjugate_step":"MCMC", + "samplers/MLDA_introduction": "MCMC", + "samplers/MLDA_simple_linear_regression": "MCMC", + "samplers/MLDA_gravity_surveying": "MCMC", + "samplers/MLDA_variance_reduction_linear_regression": "MCMC", + "samplers/GLM-hierarchical-jax": "MCMC" } diff --git a/notebooks/table_of_contents_tutorials.js b/notebooks/table_of_contents_tutorials.js index bfaadab4b..94b74990d 100644 --- a/notebooks/table_of_contents_tutorials.js +++ b/notebooks/table_of_contents_tutorials.js @@ -1,24 +1,24 @@ Gallery.contents = { - "api_quickstart": "Basics", - "variational_api_quickstart": "Basics", + "pymc3_howto/api_quickstart": "Basics", + "variational_inference/variational_api_quickstart": "Basics", "PyMC3_and_Theano.rst": "Basics", "Probability_Distributions.rst": "Basics", "Gaussian_Processes.rst": "Basics", - "data_container": "Basics", - "sampling_compound_step": "Deep dives", - "sampling_callback": "Deep dives", - "sampler-stats": "Deep dives", - "Diagnosing_biased_Inference_with_Divergences": "Deep dives", + "pymc3_howto/data_container": "Basics", + "pymc3_howto/sampling_compound_step": "Deep dives", + "pymc3_howto/sampling_callback": "Deep dives", + "diagnostics_and_criticism/sampler-stats": "Deep dives", + "diagnostics_and_criticism/Diagnosing_biased_Inference_with_Divergences": "Deep dives", "Advanced_usage_of_Theano_in_PyMC3.rst": "Deep dives", "getting_started": "Deep dives", - "ODE_API_shapes_and_benchmarking": "Deep dives", - "DEMetropolisZ_EfficiencyComparison": "Deep dives", - "DEMetropolisZ_tune_drop_fraction": "Deep dives", - "factor_analysis": "Deep dives", - "blackbox_external_likelihood": "How-To", - "profiling": "How-To", - "howto_debugging": "How-To", - "model_averaging": "How-To", - "updating_priors": "How-To", - "lasso_block_update": "How-To" + "ode_models/ODE_API_shapes_and_benchmarking": "Deep dives", + "samplers/DEMetropolisZ_EfficiencyComparison": "Deep dives", + "samplers/DEMetropolisZ_tune_drop_fraction": "Deep dives", + "case_studies/factor_analysis": "Deep dives", + "case_studies/blackbox_external_likelihood": "How-To", + "pymc3_howto/profiling": "How-To", + "pymc3_howto/howto_debugging": "How-To", + "diagnostics_and_criticism/model_averaging": "How-To", + "pymc3_howto/updating_priors": "How-To", + "pymc3_howto/lasso_block_update": "How-To" } From 86796bde79c65ea195cd352f43dab0390969fc70 Mon Sep 17 00:00:00 2001 From: Marco Gorelli Date: Wed, 16 Dec 2020 18:06:16 +0000 Subject: [PATCH 4/4] fixup incorrect table of content entries (thanks pre-commit hook) --- notebooks/table_of_contents_examples.js | 6 +++--- scripts/check_toc_is_complete.py | 25 +++++++++++++++++++++++++ 2 files changed, 28 insertions(+), 3 deletions(-) create mode 100644 scripts/check_toc_is_complete.py diff --git a/notebooks/table_of_contents_examples.js b/notebooks/table_of_contents_examples.js index ed760392f..af30b6a86 100644 --- a/notebooks/table_of_contents_examples.js +++ b/notebooks/table_of_contents_examples.js @@ -14,7 +14,7 @@ Gallery.contents = { "generalized_linear_models/GLM-logistic": "(Generalized) Linear and Hierarchical Linear Models", "generalized_linear_models/GLM-hierarchical-binominal-model": "(Generalized) Linear and Hierarchical Linear Models", "generalized_linear_models/GLM-hierarchical": "(Generalized) Linear and Hierarchical Linear Models", - "case/studies/hierarchical_partial_pooling": "(Generalized) Linear and Hierarchical Linear Models", + "case_studies/hierarchical_partial_pooling": "(Generalized) Linear and Hierarchical Linear Models", "generalized_linear_models/GLM-model-selection": "(Generalized) Linear and Hierarchical Linear Models", "generalized_linear_models/GLM-negative-binomial-regression": "(Generalized) Linear and Hierarchical Linear Models", "generalized_linear_models/GLM-poisson-regression": "(Generalized) Linear and Hierarchical Linear Models", @@ -39,7 +39,7 @@ Gallery.contents = { "mixture_models/dp_mix": "Mixture Models", "variational_inference/gaussian-mixture-model-advi": "Mixture Models", "mixture_models/gaussian_mixture_model": "Mixture Models", - "marginalized_gaussian_mixture_model": "Mixture Models", + "mixture_models/marginalized_gaussian_mixture_model": "Mixture Models", "samplers/SMC2_gaussians": "Simulation-based Inference", "samplers/SMC-ABC_Lotka-Volterra_example": "Simulation-based Inference", "survival_analysis/bayes_param_survival_pymc3": "Survival Analysis", @@ -48,7 +48,7 @@ Gallery.contents = { "survival_analysis/weibull_aft": "Survival Analysis", "survival_analysis/cox_model": "Survival Analysis", "time_series/MvGaussianRandomWalk_demo": "Time Series", - "time_series/R": "Time Series", + "time_series/AR": "Time Series", "time_series/Euler-Maruyama_and_SDEs": "Time Series", "variational_inference/bayesian_neural_network_advi": "Variational Inference", "variational_inference/convolutional_vae_keras_advi": "Variational Inference", diff --git a/scripts/check_toc_is_complete.py b/scripts/check_toc_is_complete.py new file mode 100644 index 000000000..f2d2219af --- /dev/null +++ b/scripts/check_toc_is_complete.py @@ -0,0 +1,25 @@ +""" +Check that given Jupyter notebooks all appear in the table of contents. + +This is intended to be used as a pre-commit hook, see `.pre-commit-config.yaml`. +You can run it manually with `pre-commit run check-toc --all`. +""" + +import argparse +import ast + +from pathlib import Path + +if __name__ == "__main__": + toc_examples = (Path("notebooks") / "table_of_contents_examples.js").read_text() + toc_tutorials = (Path("notebooks") / "table_of_contents_tutorials.js").read_text() + toc_keys = { + **ast.literal_eval(toc_examples[toc_examples.find("{") :]), + **ast.literal_eval(toc_tutorials[toc_tutorials.find("{") :]), + }.keys() + parser = argparse.ArgumentParser() + parser.add_argument("paths", nargs="*", type=Path) + args = parser.parse_args() + for path in args.paths: + notebook_name = path.relative_to('notebooks').with_suffix('').as_posix() + assert notebook_name in toc_keys, f"Notebook '{notebook_name}' not added to table of contents!"