pymc-devs · michaelosthege · Jul 3, 2021 · Jun 25, 2021 · Jun 25, 2021 · Jun 27, 2021
diff --git a/.github/workflows/arviz_compat.yml b/.github/workflows/arviz_compat.yml
@@ -1,7 +1,7 @@
 name: arviz-compatibility
 
 on:
-  pull_request:
+  # pull_request:
   push:
     branches: [v3]
 

diff --git a/.github/workflows/jaxtests.yml b/.github/workflows/jaxtests.yml
@@ -1,7 +1,7 @@
 name: jax-sampling
 
 on:
-  pull_request:
+  # pull_request:
   push:
     branches: [v3]
 

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -1,7 +1,7 @@
 name: pre-commit
 
 on:
-  pull_request:
+  # pull_request:
   push:
     branches: [v3]
 

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -1,7 +1,7 @@
 name: pytest
 
 on:
-  pull_request:
+  # pull_request:
   push:
     branches: [v3]
 

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -1,7 +1,7 @@
 name: windows
 
 on:
-  pull_request:
+  # pull_request:
   push:
     branches: [v3]
 

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/RELEASE-NOTES.md b/RELEASE-NOTES.md
@@ -6,6 +6,7 @@
 + `theano.printing.pydotprint` is now hotfixed upon import (see [#4594](https://github.com/pymc-devs/pymc3/pull/4594)).
 + Fix bug in the computation of the log pseudolikelihood values (SMC-ABC). (see [#4672](https://github.com/pymc-devs/pymc3/pull/4672)).
 + Fix `LKJCorr.random` method to work with `pm.sample_prior_predictive`. (see [#4780](https://github.com/pymc-devs/pymc3/pull/4780))
++ Enable documentation generation via ReadTheDocs for upcoming v3 releases. (see [#4805](https://github.com/pymc-devs/pymc3/pull/4805)).
 
 ### New Features
 + Generalized BART, bounded distributions like Binomial and Poisson can now be used as likelihoods (see [#4675](https://github.com/pymc-devs/pymc3/pull/4675), [#4709](https://github.com/pymc-devs/pymc3/pull/4709) and

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,
@@ -330,3 +332,6 @@
 def setup(app):
     app.add_css_file("https://cdn.jsdelivr.net/npm/[email protected]/dist/semantic.min.css")
     app.add_css_file("default.css")
+    dir_root = Path(__file__).parent
+    for directory in html_static_path:
+        os.makedirs(str(dir_root / directory), exist_ok=True)
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -44,28 +44,28 @@
 
         <div class="ui container">
 
-        <h2 class="ui dividing header">Installation</h2>
-
-            <div class="row">
-                <div class="ui text container">
-                    <h3 class="ui header">Via conda-forge:</h3>
-
-.. code-block:: bash
-
-    conda install -c conda-forge pymc3
-
-
-.. raw:: html
-
-                    <h3 class="ui header">Latest (unstable):</h3>
+        <div class="ui vertical segment">
+            <h2 class="ui dividing header">Installation</h2>
+            <div class="ui three stackable cards">
 
-.. code-block:: bash
+                <a class="ui link card" href="https://github.com/pymc-devs/pymc3/wiki/Installation-Guide-(Linux)">
+                    <div class="content">
+                        <div class="header">Instructions for Linux</div>
+                    </div>
+                </a>
 
-    pip install git+https://github.com/pymc-devs/pymc3
+                <a class="ui link card" href="https://github.com/pymc-devs/pymc3/wiki/Installation-Guide-(MacOS)">
+                    <div class="content">
+                        <div class="header">Instructions for MacOS</div>
+                    </div>
+                </a>
 
-.. raw:: html
+                <a class="ui link card" href="https://github.com/pymc-devs/pymc3/wiki/Installation-Guide-(Windows)">
+                    <div class="content">
+                        <div class="header">Instructions for Windows</div>
+                    </div>
+                </a>
 
-                </div>
             </div>
         </div>
 

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
@@ -170,16 +170,23 @@ def build_gallery(srcdir, gallery):
         if basename.find(".rst") < 1:
             filename = os.path.join(source_dir, basename + ".ipynb")
             ex = NotebookGenerator(filename, target_dir)
+            url = Path(os.path.join(os.sep, gallery, ex.output_html))
+            # Need to chop off "/${gallery}/../" so as redirection works in multi versioned docs.
+            url = str(Path("..", *url.parts[3:]))
             data[basename] = {
                 "title": ex.pagetitle,
-                "url": os.path.join(os.sep, gallery, ex.output_html),
+                "url": url,
                 "thumb": os.path.basename(ex.png_path),
             }
+
         else:
             filename = basename.split(".")[0]
+            url = Path(os.path.join(os.sep, gallery, "../" + filename + ".html"))
+            # Need to chop off "/${gallery}/../" so as redirection works in multi versioned docs.
+            url = str(Path("..", *url.parts[3:]))
             data[basename] = {
                 "title": " ".join(filename.split("_")),
-                "url": os.path.join(os.sep, gallery, "../" + filename + ".html"),
+                "url": url,
                 "thumb": os.path.basename(default_png_path),
             }
+22 −0		.github/ISSUE_TEMPLATE/bug-report.md
+8 −0		.github/ISSUE_TEMPLATE/config.yml
+20 −0		.github/ISSUE_TEMPLATE/notebook-proposal.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
+108 −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
+145 −0		examples/data/AirPassengers.csv
+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
+647 −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
+426 −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
+9 −0		examples/table_of_contents_examples.js
+1,165 −0		examples/time_series/Air_passengers-Prophet_with_Bayesian_workflow.ipynb
+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