pymc-devs · michaelosthege · Jul 3, 2021 · Jun 25, 2021 · Jun 25, 2021 · Jun 27, 2021
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,16 @@
+version: 2
+
+sphinx:
+    configuration: docs/source/conf.py
+
+python:
+   version: 3.7
+   install:
+   - requirements: requirements-dev.txt
+   - method: pip
+     path: .
+
+
+submodules:
+    include: all
+    recursive: true
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -15,6 +15,8 @@
 import os
 import sys
 
+from pathlib import Path
+
 import pymc3
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -23,6 +25,8 @@
 sys.path.insert(0, os.path.abspath(os.path.join("..", "..")))
 sys.path.insert(0, os.path.abspath("sphinxext"))
 
+from gallery_generator import build_gallery
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -43,7 +47,6 @@
     "IPython.sphinxext.ipython_directive",
     "sphinx.ext.autosectionlabel",
     "sphinx.ext.napoleon",
-    "gallery_generator",
     "recommonmark",
 ]
 
@@ -330,3 +333,5 @@
 def setup(app):
     app.add_css_file("https://cdn.jsdelivr.net/npm/[email protected]/dist/semantic.min.css")
     app.add_css_file("default.css")
+    for gallery in ("tutorials", "examples"):
+        build_gallery(Path(__file__).parent, gallery)
diff --git a/docs/source/pymc-examples b/docs/source/pymc-examples
diff --git a/docs/source/sphinxext/gallery_generator.py b/docs/source/sphinxext/gallery_generator.py
@@ -200,12 +200,3 @@ def build_gallery(srcdir, gallery):
         )
 
     os.chdir(working_dir)
-
-
-def main(app):
-    for gallery in ("tutorials", "examples"):
-        build_gallery(app.builder.srcdir, gallery)
-
-
-def setup(app):
-    app.connect("builder-inited", main)
+5 −0		.github/ISSUE_TEMPLATE/bug-report.md
+39 −0		.github/ISSUE_TEMPLATE/tracker.md
+16 −0		.github/PULL_REQUEST_TEMPLATE.md
+1 −1		.github/workflows/pre-commit.yml
+1 −0		.gitignore
+11 −1		.pre-commit-config.yaml
+78 −0		CODE_OF_CONDUCT.md
+106 −0		CONTRIBUTING.md
+0 −2		README.md
+133 −0		README.rst
+92 −141		examples/case_studies/BEST.ipynb
+139 −96		examples/case_studies/LKJ.ipynb
+1,968 −0		examples/case_studies/bayesian_ab_testing.ipynb
+5 −5		examples/case_studies/blackbox_external_likelihood.ipynb
+5 −5		examples/case_studies/conditional-autoregressive-model.ipynb
+3 −3		examples/case_studies/disaster_model.py
+3 −3		examples/case_studies/disaster_model_theano_op.py
+333 −447		examples/case_studies/factor_analysis.ipynb
+2 −1		examples/case_studies/garch_example.py
+2 −1		examples/case_studies/gelman_schools.py
+25 −18		examples/case_studies/hierarchical_partial_pooling.ipynb
+2 −2		examples/case_studies/lightspeed_example.py
+124 −130		examples/case_studies/log-gaussian-cox-process.ipynb
+ −		examples/case_studies/mediation.png
+871 −0		examples/case_studies/mediation_analysis.ipynb
+920 −0		examples/case_studies/moderation_analysis.ipynb
+ −		examples/case_studies/moderation_figure.png
+263 −54		examples/case_studies/probabilistic_matrix_factorization.ipynb
+403 −520		examples/case_studies/putting_workflow.ipynb
+1,449 −524		examples/case_studies/rugby_analytics.ipynb
+65 −57		examples/case_studies/stochastic_volatility.ipynb
+1 −1		examples/data/mastectomy.csv
+244 −0		examples/data/muscle-percent-males-interaction.csv
+41 −34		examples/diagnostics_and_criticism/Bayes_factor.ipynb
+598 −566		examples/diagnostics_and_criticism/Diagnosing_biased_Inference_with_Divergences.ipynb
+132 −171		examples/diagnostics_and_criticism/model_averaging.ipynb
+77 −77		examples/diagnostics_and_criticism/model_comparison.ipynb
+66 −61		examples/diagnostics_and_criticism/posterior_predictive.ipynb
+1,346 −182		examples/diagnostics_and_criticism/sampler-stats.ipynb
+1,775 −0		examples/gaussian_processes/GP-Heteroskedastic.ipynb
+6 −8		examples/gaussian_processes/GP-Kron.ipynb
+5 −5		examples/gaussian_processes/GP-Latent.ipynb
+4 −4		examples/gaussian_processes/GP-Marginal.ipynb
+1,082 −310		examples/gaussian_processes/GP-MeansAndCovs.ipynb
+649 −0		examples/generalized_linear_models/GLM-binomial-regression.ipynb
+448 −59		examples/generalized_linear_models/GLM-hierarchical-binominal-model.ipynb
+3 −3		examples/generalized_linear_models/GLM-hierarchical.ipynb
+59 −56		examples/generalized_linear_models/GLM-linear.ipynb
+81 −64		examples/generalized_linear_models/GLM-logistic.ipynb
+561 −642		examples/generalized_linear_models/GLM-model-selection.ipynb
+655 −0		examples/generalized_linear_models/GLM-out-of-sample-predictions.ipynb
+760 −196		examples/generalized_linear_models/GLM-poisson-regression.ipynb
+258 −196		examples/generalized_linear_models/GLM-robust-with-outlier-detection.ipynb
+912 −0		examples/generalized_linear_models/GLM-truncated-censored-regression.ipynb
+2,686 −395		examples/generalized_linear_models/GLM.ipynb
+421 −384		examples/getting_started.ipynb
+1,930 −0		examples/mixture_models/dirichlet_mixture_of_multinomials.ipynb
+0 −4		examples/mixture_models/dp_mix.ipynb
+5 −5		examples/mixture_models/gaussian_mixture_model.ipynb
+7 −7		examples/ode_models/ODE_API_shapes_and_benchmarking.ipynb
+492 −176		examples/ode_models/ODE_with_manual_gradients.ipynb
+3 −3		examples/pymc3_howto/LKJ_correlation.py
+148 −159		examples/pymc3_howto/data_container.ipynb
+36 −24		examples/pymc3_howto/lasso_block_update.ipynb
+3 −2		examples/pymc3_howto/rankdata_ordered.py
+351 −58		examples/pymc3_howto/sampling_compound_step.ipynb
+27 −22		examples/pymc3_howto/sampling_conjugate_step.ipynb
+91 −83		examples/pymc3_howto/updating_priors.ipynb
+3 −7		examples/samplers/DEMetropolisZ_EfficiencyComparison.ipynb
+2 −11		examples/samplers/DEMetropolisZ_tune_drop_fraction.ipynb
+56 −56		examples/samplers/GLM-hierarchical-jax.ipynb
+711 −540		examples/samplers/MLDA_gravity_surveying.ipynb
+1 −1		examples/samplers/MLDA_introduction.ipynb
+62 −101		examples/samplers/MLDA_simple_linear_regression.ipynb
+212 −164		examples/samplers/MLDA_variance_reduction_linear_regression.ipynb
+5 −5		examples/samplers/SMC-ABC_Lotka-Volterra_example.ipynb
+1 −1		examples/samplers/SMC2_gaussians.ipynb
+6 −5		examples/samplers/samplers_mvnormal.py
+153 −207		examples/survival_analysis/bayes_param_survival_pymc3.ipynb
+290 −157		examples/survival_analysis/censored_data.ipynb
+58 −53		examples/survival_analysis/cox_model.ipynb
+684 −208		examples/survival_analysis/survival_analysis.ipynb
+8 −0		examples/table_of_contents_examples.js
+3 −2		examples/time_series/arma_example.py
+3 −2		examples/variational_inference/bayesian_neural_network_advi.ipynb
+84 −79		examples/variational_inference/empirical-approx-overview.ipynb
+1 −1		examples/variational_inference/normalizing_flows_overview.ipynb
+7 −6		examples/variational_inference/variational_api_quickstart.ipynb