pymc-devs · OriolAbril · Nov 24, 2021 · Sep 5, 2021 · Nov 13, 2021 · Nov 14, 2021
diff --git a/.gitignore b/.gitignore
@@ -17,6 +17,7 @@ tags
 
 # Sphinx
 _build
+docs/jupyter_execute
 
 # Merge tool
 *.orig

diff --git a/.gitmodules b/.gitmodules
diff --git a/conda-envs/environment-dev-py37.yml b/conda-envs/environment-dev-py37.yml
@@ -23,9 +23,8 @@ dependencies:
 - python-graphviz
 - python=3.7
 - scipy>1.4.1
-- sphinx-autobuild>=0.7
+- sphinx-copybutton
 - sphinx-notfound-page
-- sphinx-panels
 - sphinx>=1.5
 - typing-extensions
 - pip:

diff --git a/conda-envs/environment-dev-py38.yml b/conda-envs/environment-dev-py38.yml
@@ -23,9 +23,8 @@ dependencies:
 - python-graphviz
 - python=3.8
 - scipy>1.4.1
-- sphinx-autobuild>=0.7
+- sphinx-copybutton
 - sphinx-notfound-page
-- sphinx-panels
 - sphinx>=1.5
 - typing-extensions>=3.7.4
 - pip:

diff --git a/conda-envs/environment-dev-py39.yml b/conda-envs/environment-dev-py39.yml
@@ -23,9 +23,8 @@ dependencies:
 - python-graphviz
 - python=3.9
 - scipy>1.4.1
-- sphinx-autobuild>=0.7
+- sphinx-copybutton
 - sphinx-notfound-page
-- sphinx-panels
 - sphinx>=1.5
 - typing-extensions>=3.7.4
 - pip:

diff --git a/conda-envs/windows-environment-dev-py38.yml b/conda-envs/windows-environment-dev-py38.yml
@@ -27,8 +27,8 @@ dependencies:
 - pytest-cov>=2.5
 - pytest>=3.0
 - sphinx-autobuild>=0.7
+- sphinx-copybutton
 - sphinx-notfound-page
-- sphinx-panels
 - sphinx>=1.5
 - watermark
 - pip:

diff --git a/docs/logos/sponsors/numfocus.png b/docs/logos/sponsors/numfocus.png
diff --git a/docs/pymc-labs-logo.png → docs/logos/sponsors/pymc-labs.png b/docs/pymc-labs-logo.png → docs/logos/sponsors/pymc-labs.png
diff --git a/docs/pymc_logo.jpg b/docs/pymc_logo.jpg
diff --git a/docs/source/Advanced_usage_of_Aesara_in_PyMC.rst b/docs/source/Advanced_usage_of_Aesara_in_PyMC.rst
@@ -1,5 +1,5 @@
 :orphan:
-
+(Advanced_usage_of_Aesara_in_PyMC)
 ..
     _referenced in docs/source/notebooks/table_of_contents_tutorials.js
 

diff --git a/docs/source/_templates/footer.html b/docs/source/_templates/footer.html
@@ -0,0 +1,9 @@
+<footer class="footer mt-5 mt-md-0">
+  <div class="container">
+    {% for footer_item in theme_footer_items %}
+    <div class="footer-item">
+      {% include footer_item %}
+    </div>
+    {% endfor %}
+  </div>
+</footer>
diff --git a/docs/source/_templates/layout.html b/docs/source/_templates/layout.html
@@ -2,25 +2,25 @@
 
 <!-- Hide left sidebar in home page -->
 {% block docs_sidebar %}
-  {% if pagename != 'index' %}
-    {{ super() }}
-  {% endif %}
+{% if pagename != 'index' %}
+{{ super() }}
+{% endif %}
 {% endblock %}
 
 <!-- Hide right sidebar in home page -->
 {% block docs_toc %}
-  {% if pagename != 'index' %}
-    {{ super() }}
-  {% endif %}
+{% if pagename != 'index' %}
+{{ super() }}
+{% endif %}
 {% endblock %}
 
 <!-- Make body have full width in home page -->
 {% block docs_main %}
-  {% if pagename == 'index' %}
-    <main class="col-12 py-md-5 pl-md-5 pr-md-4 bd-content" role="main">
-      {% block body %} {% endblock %}
-    </main>
-  {% else %}
-    {{ super() }}
-  {% endif %}
+{% if pagename == 'index' %}
+<main class="col-12 py-md-5 pl-md-5 pr-md-4 bd-content" role="main">
+  {% block body %} {% endblock %}
+</main>
+{% else %}
+{{ super() }}
+{% endif %}
 {% endblock %}
diff --git a/docs/source/about.rst b/docs/source/about.rst
@@ -1,8 +1,3 @@
-:orphan:
-
-..
-    _href from docs/source/index.rst
-
 .. _about:
 
 **********
@@ -41,10 +36,18 @@ PyMC strives to make Bayesian modeling as simple and painless as possible,  allo
 * Bayesian models can be embedded in larger programs, and results can be analyzed
   with the full power of Python.
 
+What's new in version 4
+=======================
+
+:bdg-warning:`TODO`
+Add text
 
 What's new in version 3
 =======================
 
+:bdg-warning:`TODO`
+Move this section to a different place
+
 The third major version of PyMC has benefitted from being re-written from scratch. Substantial improvements in the user interface and performance have resulted from this. While PyMC2 relied on Fortran extensions (via f2py) for most of the computational heavy-lifting, PyMC leverages Aesara, a fork of the Theano library from the Montréal Institute for Learning Algorithms (MILA), for array-based expression evaluation, to perform its computation. What this provides, above all else, is fast automatic differentiation, which is at the heart of the gradient-based sampling and optimization methods currently providing inference for probabilistic programming.
 
 Major changes from previous versions:

diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -1,8 +1,3 @@
-:orphan:
-
-..
-    _"api" is referenced in html_theme_options docs/source/conf.py
-
 .. _api:
 
 *************
@@ -13,20 +8,14 @@ API Reference
    :maxdepth: 2
 
    api/distributions
-   api/bounds
-   api/inference
-   api/glm
    api/gp
-   api/plots
-   api/stats
-   api/backends
-   api/math
-   api/data
    api/model
-   api/model_graph
-   api/variables
-   api/shape_utils
    api/ode
+   api/samplers
+   api/smc
+   api/step_methods
+   api/inference
+   api/plots
 
 Indices and tables
 ===================

diff --git a/docs/source/api/backends.rst b/docs/source/api/backends.rst
diff --git a/docs/source/api/bounds.rst b/docs/source/api/bounds.rst
diff --git a/docs/source/api/data.rst b/docs/source/api/data.rst
diff --git a/docs/source/api/distributions.rst b/docs/source/api/distributions.rst
@@ -6,6 +6,7 @@ Distributions
 
    distributions/continuous
    distributions/discrete
+   distributions/logprob
    distributions/multivariate
    distributions/mixture
    distributions/simulator

diff --git a/docs/source/api/distributions/continuous.rst b/docs/source/api/distributions/continuous.rst
@@ -10,32 +10,33 @@ Continuous
    HalfFlat
    Normal
    TruncatedNormal
-   HalfNormal
-   SkewNormal
    Beta
    Kumaraswamy
    Exponential
    Laplace
-   AsymmetricLaplace
    StudentT
-   HalfStudentT
    Cauchy
    HalfCauchy
    Gamma
-   InverseGamma
    Weibull
+   HalfStudentT
    LogNormal
    ChiSquared
+   HalfNormal
    Wald
    Pareto
+   InverseGamma
    ExGaussian
    VonMises
+   SkewNormal
    Triangular
    Gumbel
-   Rice
    Logistic
    LogitNormal
    Interpolated
+   Rice
+   Moyal
+   AsymmetricLaplace
    PolyaGamma
 
 .. automodule:: pymc.distributions.continuous

diff --git a/docs/source/api/distributions/discrete.rst b/docs/source/api/distributions/discrete.rst
@@ -6,19 +6,19 @@ Discrete
 .. autosummary::
 
    Binomial
-   ZeroInflatedBinomial
    BetaBinomial
    Bernoulli
+   DiscreteWeibull
    Poisson
-   ZeroInflatedPoisson
    NegativeBinomial
+   Constant
+   ZeroInflatedPoisson
+   ZeroInflatedBinomial
    ZeroInflatedNegativeBinomial
    DiscreteUniform
    Geometric
    HyperGeometric
    Categorical
-   DiscreteWeibull
-   Constant
    OrderedLogistic
    OrderedProbit
 

diff --git a/docs/source/api/distributions/multivariate.rst b/docs/source/api/distributions/multivariate.rst
@@ -6,16 +6,17 @@ Multivariate
 .. autosummary::
 
    MvNormal
-   MatrixNormal
-   KroneckerNormal
    MvStudentT
-   Wishart
-   LKJCholeskyCov
-   LKJCorr
-   Multinomial
-   OrderedMultinomial
    Dirichlet
+   Multinomial
    DirichletMultinomial
+   OrderedMultinomial
+   Wishart
+   WishartBartlett
+   LKJCorr
+   LKJCholeskyCov
+   MatrixNormal
+   KroneckerNormal
    CAR
 
 .. automodule:: pymc.distributions.multivariate

diff --git a/docs/source/api/distributions/simulator.rst b/docs/source/api/distributions/simulator.rst
@@ -5,7 +5,9 @@ Simulator
 .. currentmodule:: pymc.distributions.simulator
 .. autosummary::
 
+   SimulatorRV
    Simulator
+   KullbackLiebler
 
 .. automodule:: pymc.distributions.simulator
    :members:
-Original file line number
+Diff line change
@@ Expand Up / @@ -17,6 +17,7 @@ tags @@
     # Sphinx
     _build
+    docs/jupyter_execute
     # Merge tool
     *.orig
@@ Expand Down @@