Getting docs ready for v4

example doc restructure working and hopefully illustrative doc skeleton update requirements WIP Change log: - Upload new PyMC logo - Updated conf.py to pymc instead of pymc3 - Start configuring and populating index page - Start configuring and populating learning page - Start configuring and populating api page - Updated API to follow the docs/Architecture.png layout - Start configuring and populating learning page - Fix typo in filename of "index legacy" add community page, other minor changes Continue restructuring the API Delete conflicting files example doc restructure update requirements update requirements and gitignore some fixes add changes introduced by pre-commit checks fix community page title update api for distributions update gaussian process api fix end of file more changes sponsor logos sponsor logos cleanup, other changes changes to satisfy pre-commit checks requirements changes minor changes Add testimonials to docs homepage remove sphinx panels and other changes center buttons add explanation of MAP to glassor minor change fix typo minor changes put content in videos and podcasts section. Change formatting of testimonials (width of 2 cards for better formating in narrow screens) add code example to front page revise some definitions (#5126) minor changes minor changes WIP: organizing notebooks into learning section
pymc-devs · Nov 13, 2021 · 2c65116 · 2c65116
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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/_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:
diff --git a/docs/source/api/distributions/transforms.rst b/docs/source/api/distributions/transforms.rst
@@ -1,10 +1,10 @@
 ****************************************************************
-Transformations of a random variable from one space to another.
+Transformations of a random variable from one space to another
 ****************************************************************
 
 Note that for convenience these entities can be addressed as
 ``pm.transforms.``\ *X* for any name *X*, although they are actually
-implemented as ``pm.distributions.transforms.``\*X*.
+implemented as ``pm.distributions.transforms.``\ *X*.
 
 .. currentmodule:: pymc.distributions.transforms
 
@@ -14,13 +14,11 @@ implemented as ``pm.distributions.transforms.``\*X*.
 ..
    .. autosummary::
 
-   transform
+   Transform
    stick_breaking
    logodds
    interval
    log_exp_m1
-   lowerbound
-   upperbound
    ordered
    log
    sum_to_1