From f795cbe6279e4bce8f4c95eacb7a30ac2b6efe56 Mon Sep 17 00:00:00 2001
From: Thomas Wiecki <thomas.wiecki@gmail.com>
Date: Mon, 18 Jul 2016 10:25:50 +0200
Subject: [PATCH 1/4] BLD Add build_shinx.

---
 setup.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index acfe76eb423..70604a15e48 100755
--- a/setup.py
+++ b/setup.py
@@ -54,4 +54,9 @@
           classifiers=classifiers,
           install_requires=install_reqs,
           tests_require=test_reqs,
-          test_suite='nose.collector')
+          test_suite='nose.collector',
+          command_options={
+              'build_sphinx': {
+                  'project': ('setup.py', DISTNAME),
+                  'version': ('setup.py', VERSION)}},
+)

From f5a3e98cfd4eb7089bc1e3b8317496057d6398e6 Mon Sep 17 00:00:00 2001
From: Thomas Wiecki <thomas.wiecki@gmail.com>
Date: Mon, 18 Jul 2016 10:26:14 +0200
Subject: [PATCH 2/4] MAINT Move notebooks dir back to examples dir.

---
 pymc3/examples/notebooks                                         | 1 -
 {docs/source => pymc3/examples}/notebooks/BEST.ipynb             | 0
 .../examples}/notebooks/GLM-hierarchical-ADVI.ipynb              | 0
 .../examples}/notebooks/GLM-hierarchical-advi-minibatch.ipynb    | 0
 {docs/source => pymc3/examples}/notebooks/GLM-hierarchical.ipynb | 0
 {docs/source => pymc3/examples}/notebooks/GLM-linear.ipynb       | 0
 {docs/source => pymc3/examples}/notebooks/GLM-logistic.ipynb     | 0
 .../examples}/notebooks/GLM-model-selection.ipynb                | 0
 .../examples}/notebooks/GLM-poisson-regression.ipynb             | 0
 .../examples}/notebooks/GLM-robust-with-outlier-detection.ipynb  | 0
 {docs/source => pymc3/examples}/notebooks/GLM-robust.ipynb       | 0
 {docs/source => pymc3/examples}/notebooks/GLM.ipynb              | 0
 {docs/source => pymc3/examples}/notebooks/GP-smoothing.ipynb     | 0
 {docs/source => pymc3/examples}/notebooks/Model Comparison.ipynb | 0
 {docs/source => pymc3/examples}/notebooks/advi.ipynb             | 0
 .../examples}/notebooks/bayesian_neural_network_advi.ipynb       | 0
 {docs/source => pymc3/examples}/notebooks/cox_model.ipynb        | 0
 {docs/source => pymc3/examples}/notebooks/disaster_model.ipynb   | 0
 .../source => pymc3/examples}/notebooks/discrete_find_MAP.ipynb  | 0
 {docs/source => pymc3/examples}/notebooks/dp_mix.ipynb           | 0
 .../examples}/notebooks/gaussian-mixture-model-advi.ipynb        | 0
 .../examples}/notebooks/gaussian_mixture_model.ipynb             | 0
 {docs/source => pymc3/examples}/notebooks/getting_started.ipynb  | 0
 {docs/source => pymc3/examples}/notebooks/hierarchical.ipynb     | 0
 {docs/source => pymc3/examples}/notebooks/howto_debugging.ipynb  | 0
 .../source => pymc3/examples}/notebooks/lasso_block_update.ipynb | 0
 {docs/source => pymc3/examples}/notebooks/pmf-pymc.ipynb         | 0
 .../examples}/notebooks/posterior_predictive.ipynb               | 0
 {docs/source => pymc3/examples}/notebooks/profiling.ipynb        | 0
 .../source => pymc3/examples}/notebooks/rolling_regression.ipynb | 0
 {docs/source => pymc3/examples}/notebooks/rugby_analytics.ipynb  | 0
 .../examples}/notebooks/stochastic_volatility.ipynb              | 0
 .../source => pymc3/examples}/notebooks/survival_analysis.ipynb  | 0
 {docs/source => pymc3/examples}/notebooks/tutorial.ipynb         | 0
 34 files changed, 1 deletion(-)
 delete mode 120000 pymc3/examples/notebooks
 rename {docs/source => pymc3/examples}/notebooks/BEST.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/GLM-hierarchical-ADVI.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/GLM-hierarchical-advi-minibatch.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/GLM-hierarchical.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/GLM-linear.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/GLM-logistic.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/GLM-model-selection.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/GLM-poisson-regression.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/GLM-robust-with-outlier-detection.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/GLM-robust.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/GLM.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/GP-smoothing.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/Model Comparison.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/advi.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/bayesian_neural_network_advi.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/cox_model.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/disaster_model.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/discrete_find_MAP.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/dp_mix.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/gaussian-mixture-model-advi.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/gaussian_mixture_model.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/getting_started.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/hierarchical.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/howto_debugging.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/lasso_block_update.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/pmf-pymc.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/posterior_predictive.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/profiling.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/rolling_regression.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/rugby_analytics.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/stochastic_volatility.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/survival_analysis.ipynb (100%)
 rename {docs/source => pymc3/examples}/notebooks/tutorial.ipynb (100%)

diff --git a/pymc3/examples/notebooks b/pymc3/examples/notebooks
deleted file mode 120000
index 8cab85b4d51..00000000000
--- a/pymc3/examples/notebooks
+++ /dev/null
@@ -1 +0,0 @@
-../../docs/source/notebooks
\ No newline at end of file
diff --git a/docs/source/notebooks/BEST.ipynb b/pymc3/examples/notebooks/BEST.ipynb
similarity index 100%
rename from docs/source/notebooks/BEST.ipynb
rename to pymc3/examples/notebooks/BEST.ipynb
diff --git a/docs/source/notebooks/GLM-hierarchical-ADVI.ipynb b/pymc3/examples/notebooks/GLM-hierarchical-ADVI.ipynb
similarity index 100%
rename from docs/source/notebooks/GLM-hierarchical-ADVI.ipynb
rename to pymc3/examples/notebooks/GLM-hierarchical-ADVI.ipynb
diff --git a/docs/source/notebooks/GLM-hierarchical-advi-minibatch.ipynb b/pymc3/examples/notebooks/GLM-hierarchical-advi-minibatch.ipynb
similarity index 100%
rename from docs/source/notebooks/GLM-hierarchical-advi-minibatch.ipynb
rename to pymc3/examples/notebooks/GLM-hierarchical-advi-minibatch.ipynb
diff --git a/docs/source/notebooks/GLM-hierarchical.ipynb b/pymc3/examples/notebooks/GLM-hierarchical.ipynb
similarity index 100%
rename from docs/source/notebooks/GLM-hierarchical.ipynb
rename to pymc3/examples/notebooks/GLM-hierarchical.ipynb
diff --git a/docs/source/notebooks/GLM-linear.ipynb b/pymc3/examples/notebooks/GLM-linear.ipynb
similarity index 100%
rename from docs/source/notebooks/GLM-linear.ipynb
rename to pymc3/examples/notebooks/GLM-linear.ipynb
diff --git a/docs/source/notebooks/GLM-logistic.ipynb b/pymc3/examples/notebooks/GLM-logistic.ipynb
similarity index 100%
rename from docs/source/notebooks/GLM-logistic.ipynb
rename to pymc3/examples/notebooks/GLM-logistic.ipynb
diff --git a/docs/source/notebooks/GLM-model-selection.ipynb b/pymc3/examples/notebooks/GLM-model-selection.ipynb
similarity index 100%
rename from docs/source/notebooks/GLM-model-selection.ipynb
rename to pymc3/examples/notebooks/GLM-model-selection.ipynb
diff --git a/docs/source/notebooks/GLM-poisson-regression.ipynb b/pymc3/examples/notebooks/GLM-poisson-regression.ipynb
similarity index 100%
rename from docs/source/notebooks/GLM-poisson-regression.ipynb
rename to pymc3/examples/notebooks/GLM-poisson-regression.ipynb
diff --git a/docs/source/notebooks/GLM-robust-with-outlier-detection.ipynb b/pymc3/examples/notebooks/GLM-robust-with-outlier-detection.ipynb
similarity index 100%
rename from docs/source/notebooks/GLM-robust-with-outlier-detection.ipynb
rename to pymc3/examples/notebooks/GLM-robust-with-outlier-detection.ipynb
diff --git a/docs/source/notebooks/GLM-robust.ipynb b/pymc3/examples/notebooks/GLM-robust.ipynb
similarity index 100%
rename from docs/source/notebooks/GLM-robust.ipynb
rename to pymc3/examples/notebooks/GLM-robust.ipynb
diff --git a/docs/source/notebooks/GLM.ipynb b/pymc3/examples/notebooks/GLM.ipynb
similarity index 100%
rename from docs/source/notebooks/GLM.ipynb
rename to pymc3/examples/notebooks/GLM.ipynb
diff --git a/docs/source/notebooks/GP-smoothing.ipynb b/pymc3/examples/notebooks/GP-smoothing.ipynb
similarity index 100%
rename from docs/source/notebooks/GP-smoothing.ipynb
rename to pymc3/examples/notebooks/GP-smoothing.ipynb
diff --git a/docs/source/notebooks/Model Comparison.ipynb b/pymc3/examples/notebooks/Model Comparison.ipynb
similarity index 100%
rename from docs/source/notebooks/Model Comparison.ipynb
rename to pymc3/examples/notebooks/Model Comparison.ipynb
diff --git a/docs/source/notebooks/advi.ipynb b/pymc3/examples/notebooks/advi.ipynb
similarity index 100%
rename from docs/source/notebooks/advi.ipynb
rename to pymc3/examples/notebooks/advi.ipynb
diff --git a/docs/source/notebooks/bayesian_neural_network_advi.ipynb b/pymc3/examples/notebooks/bayesian_neural_network_advi.ipynb
similarity index 100%
rename from docs/source/notebooks/bayesian_neural_network_advi.ipynb
rename to pymc3/examples/notebooks/bayesian_neural_network_advi.ipynb
diff --git a/docs/source/notebooks/cox_model.ipynb b/pymc3/examples/notebooks/cox_model.ipynb
similarity index 100%
rename from docs/source/notebooks/cox_model.ipynb
rename to pymc3/examples/notebooks/cox_model.ipynb
diff --git a/docs/source/notebooks/disaster_model.ipynb b/pymc3/examples/notebooks/disaster_model.ipynb
similarity index 100%
rename from docs/source/notebooks/disaster_model.ipynb
rename to pymc3/examples/notebooks/disaster_model.ipynb
diff --git a/docs/source/notebooks/discrete_find_MAP.ipynb b/pymc3/examples/notebooks/discrete_find_MAP.ipynb
similarity index 100%
rename from docs/source/notebooks/discrete_find_MAP.ipynb
rename to pymc3/examples/notebooks/discrete_find_MAP.ipynb
diff --git a/docs/source/notebooks/dp_mix.ipynb b/pymc3/examples/notebooks/dp_mix.ipynb
similarity index 100%
rename from docs/source/notebooks/dp_mix.ipynb
rename to pymc3/examples/notebooks/dp_mix.ipynb
diff --git a/docs/source/notebooks/gaussian-mixture-model-advi.ipynb b/pymc3/examples/notebooks/gaussian-mixture-model-advi.ipynb
similarity index 100%
rename from docs/source/notebooks/gaussian-mixture-model-advi.ipynb
rename to pymc3/examples/notebooks/gaussian-mixture-model-advi.ipynb
diff --git a/docs/source/notebooks/gaussian_mixture_model.ipynb b/pymc3/examples/notebooks/gaussian_mixture_model.ipynb
similarity index 100%
rename from docs/source/notebooks/gaussian_mixture_model.ipynb
rename to pymc3/examples/notebooks/gaussian_mixture_model.ipynb
diff --git a/docs/source/notebooks/getting_started.ipynb b/pymc3/examples/notebooks/getting_started.ipynb
similarity index 100%
rename from docs/source/notebooks/getting_started.ipynb
rename to pymc3/examples/notebooks/getting_started.ipynb
diff --git a/docs/source/notebooks/hierarchical.ipynb b/pymc3/examples/notebooks/hierarchical.ipynb
similarity index 100%
rename from docs/source/notebooks/hierarchical.ipynb
rename to pymc3/examples/notebooks/hierarchical.ipynb
diff --git a/docs/source/notebooks/howto_debugging.ipynb b/pymc3/examples/notebooks/howto_debugging.ipynb
similarity index 100%
rename from docs/source/notebooks/howto_debugging.ipynb
rename to pymc3/examples/notebooks/howto_debugging.ipynb
diff --git a/docs/source/notebooks/lasso_block_update.ipynb b/pymc3/examples/notebooks/lasso_block_update.ipynb
similarity index 100%
rename from docs/source/notebooks/lasso_block_update.ipynb
rename to pymc3/examples/notebooks/lasso_block_update.ipynb
diff --git a/docs/source/notebooks/pmf-pymc.ipynb b/pymc3/examples/notebooks/pmf-pymc.ipynb
similarity index 100%
rename from docs/source/notebooks/pmf-pymc.ipynb
rename to pymc3/examples/notebooks/pmf-pymc.ipynb
diff --git a/docs/source/notebooks/posterior_predictive.ipynb b/pymc3/examples/notebooks/posterior_predictive.ipynb
similarity index 100%
rename from docs/source/notebooks/posterior_predictive.ipynb
rename to pymc3/examples/notebooks/posterior_predictive.ipynb
diff --git a/docs/source/notebooks/profiling.ipynb b/pymc3/examples/notebooks/profiling.ipynb
similarity index 100%
rename from docs/source/notebooks/profiling.ipynb
rename to pymc3/examples/notebooks/profiling.ipynb
diff --git a/docs/source/notebooks/rolling_regression.ipynb b/pymc3/examples/notebooks/rolling_regression.ipynb
similarity index 100%
rename from docs/source/notebooks/rolling_regression.ipynb
rename to pymc3/examples/notebooks/rolling_regression.ipynb
diff --git a/docs/source/notebooks/rugby_analytics.ipynb b/pymc3/examples/notebooks/rugby_analytics.ipynb
similarity index 100%
rename from docs/source/notebooks/rugby_analytics.ipynb
rename to pymc3/examples/notebooks/rugby_analytics.ipynb
diff --git a/docs/source/notebooks/stochastic_volatility.ipynb b/pymc3/examples/notebooks/stochastic_volatility.ipynb
similarity index 100%
rename from docs/source/notebooks/stochastic_volatility.ipynb
rename to pymc3/examples/notebooks/stochastic_volatility.ipynb
diff --git a/docs/source/notebooks/survival_analysis.ipynb b/pymc3/examples/notebooks/survival_analysis.ipynb
similarity index 100%
rename from docs/source/notebooks/survival_analysis.ipynb
rename to pymc3/examples/notebooks/survival_analysis.ipynb
diff --git a/docs/source/notebooks/tutorial.ipynb b/pymc3/examples/notebooks/tutorial.ipynb
similarity index 100%
rename from docs/source/notebooks/tutorial.ipynb
rename to pymc3/examples/notebooks/tutorial.ipynb

From 531638b612acd7309c67036ce225c0ba73d0170d Mon Sep 17 00:00:00 2001
From: Thomas Wiecki <thomas.wiecki@gmail.com>
Date: Mon, 18 Jul 2016 10:46:43 +0200
Subject: [PATCH 3/4] DOC Fix links.

---
 docs/source/conf.py => conf.py  |  2 +-
 docs/source/examples.rst        | 36 ++++++++++++++++-----------------
 docs/source/getting_started.rst |  2 +-
 3 files changed, 20 insertions(+), 20 deletions(-)
 rename docs/source/conf.py => conf.py (99%)

diff --git a/docs/source/conf.py b/conf.py
similarity index 99%
rename from docs/source/conf.py
rename to conf.py
index a6d1903a0ba..fc6fc6561cc 100755
--- a/docs/source/conf.py
+++ b/conf.py
@@ -58,7 +58,7 @@
 #source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = 'docs/source/index'
 
 # General information about the project.
 project = 'PyMC3'
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
index 06859f216c1..050f92fff8c 100644
--- a/docs/source/examples.rst
+++ b/docs/source/examples.rst
@@ -5,21 +5,21 @@ Examples
 ********
 
 .. toctree::
-   notebooks/BEST.ipynb
-   notebooks/stochastic_volatility.ipynb
-   notebooks/GLM-linear.ipynb
-   notebooks/GLM-robust.ipynb
-   notebooks/GLM-robust-with-outlier-detection.ipynb
-   notebooks/GLM-model-selection.ipynb
-   notebooks/rolling_regression.ipynb
-   notebooks/GLM-logistic.ipynb
-   notebooks/GLM-hierarchical.ipynb
-   notebooks/pmf-pymc.ipynb
-   notebooks/rugby_analytics.ipynb
-   notebooks/posterior_predictive.ipynb
-   notebooks/survival_analysis.ipynb
-   notebooks/GP-smoothing.ipynb
-   notebooks/Bayesian_LogReg.ipynb
-   notebooks/dp_mix.ipynb
-   notebooks/bayesian_neural_network_advi.ipynb
-   notebooks/howto_debugging.ipynb
+   ../../pymc3/examples/notebooks/BEST.ipynb
+   ../../pymc3/examples/notebooks/stochastic_volatility.ipynb
+   ../../pymc3/examples/notebooks/GLM-linear.ipynb
+   ../../pymc3/examples/notebooks/GLM-robust.ipynb
+   ../../pymc3/examples/notebooks/GLM-robust-with-outlier-detection.ipynb
+   ../../pymc3/examples/notebooks/GLM-model-selection.ipynb
+   ../../pymc3/examples/notebooks/rolling_regression.ipynb
+   ../../pymc3/examples/notebooks/GLM-logistic.ipynb
+   ../../pymc3/examples/notebooks/GLM-hierarchical.ipynb
+   ../../pymc3/examples/notebooks/pmf-pymc.ipynb
+   ../../pymc3/examples/notebooks/rugby_analytics.ipynb
+   ../../pymc3/examples/notebooks/posterior_predictive.ipynb
+   ../../pymc3/examples/notebooks/survival_analysis.ipynb
+   ../../pymc3/examples/notebooks/GP-smoothing.ipynb
+   ../../pymc3/examples/notebooks/Bayesian_LogReg.ipynb
+   ../../pymc3/examples/notebooks/dp_mix.ipynb
+   ../../pymc3/examples/notebooks/bayesian_neural_network_advi.ipynb
+   ../../pymc3/examples/notebooks/howto_debugging.ipynb
diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
index 38c54f0e992..a5fc702bbbd 100644
--- a/docs/source/getting_started.rst
+++ b/docs/source/getting_started.rst
@@ -5,4 +5,4 @@ Getting started
 ***************
 
 .. toctree::
-   notebooks/getting_started.ipynb
+   ../../pymc3/examples/notebooks/getting_started.ipynb

From f18edb2fa58ba6421c6084ba184e26faad0caf5c Mon Sep 17 00:00:00 2001
From: Thomas Wiecki <thomas.wiecki@gmail.com>
Date: Mon, 18 Jul 2016 10:48:54 +0200
Subject: [PATCH 4/4] DOC Fix data link in getting started guide.

---
 docs/source/data                               | 1 -
 pymc3/examples/notebooks/getting_started.ipynb | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)
 delete mode 120000 docs/source/data

diff --git a/docs/source/data b/docs/source/data
deleted file mode 120000
index 58d2de77be5..00000000000
--- a/docs/source/data
+++ /dev/null
@@ -1 +0,0 @@
-../../pymc3/examples/data
\ No newline at end of file
diff --git a/pymc3/examples/notebooks/getting_started.ipynb b/pymc3/examples/notebooks/getting_started.ipynb
index f2ab9518cf8..6658e8dfd8f 100644
--- a/pymc3/examples/notebooks/getting_started.ipynb
+++ b/pymc3/examples/notebooks/getting_started.ipynb
@@ -1492,5 +1492,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 0
 }