pymc-devs · twiecki · Jun 18, 2021 · Jun 8, 2021 · Jun 10, 2021 · Jun 11, 2021
diff --git a/conda-envs/environment-dev-py37.yml b/conda-envs/environment-dev-py37.yml
@@ -12,11 +12,13 @@ dependencies:
 - numpydoc>=0.9
 - pandas=0.24
 - pre-commit>=2.8.0
+- pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.7
 - scipy=1.2
 - sphinx-autobuild>=0.7
+- sphinx-panels
 - sphinx>=1.5
 - watermark
diff --git a/conda-envs/environment-dev-py38.yml b/conda-envs/environment-dev-py38.yml
@@ -10,10 +10,12 @@ dependencies:
 - myst-nb
 - numpydoc>=0.9
 - pre-commit>=2.8.0
+- pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.8
 - sphinx-autobuild>=0.7
+- sphinx-panels
 - sphinx>=1.5
 - watermark
diff --git a/conda-envs/environment-dev-py39.yml b/conda-envs/environment-dev-py39.yml
@@ -10,10 +10,12 @@ dependencies:
 - myst-nb
 - numpydoc>=0.9
 - pre-commit>=2.8.0
+- pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.9
 - sphinx-autobuild>=0.7
+- sphinx-panels
 - sphinx>=1.5
 - watermark
diff --git a/docs/source/_templates/layout.html b/docs/source/_templates/layout.html
@@ -0,0 +1,26 @@
+{% extends "!layout.html" %}
+
+<!-- Hide left sidebar in home page -->
+{% block docs_sidebar %}
+  {% if pagename != 'index' %}
+    {{ super() }}
+  {% endif %}
+{% endblock %}
+
+<!-- Hide right sidebar in home page -->
+{% block docs_toc %}
+  {% 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 %}
+{% endblock %}
diff --git a/docs/source/_templates/navbar-version.html b/docs/source/_templates/navbar-version.html
@@ -0,0 +1 @@
+{{ version }}
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -39,6 +39,7 @@
     "matplotlib.sphinxext.plot_directive",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
     "sphinx.ext.mathjax",
     "sphinx.ext.intersphinx",
     "numpydoc",
@@ -48,6 +49,7 @@
     "sphinx.ext.napoleon",
     "gallery_generator",
     "myst_nb",
+    "sphinx_panels",
 ]
 
 # Don't auto-generate summary for class members.
@@ -104,7 +106,13 @@
 # directories to ignore when looking for source files.
 exclude_patterns = ["_build", "**.ipynb_checkpoints"]
 
+# myst and panels config
 jupyter_execute_notebooks = "off"
+myst_heading_anchors = 3
+myst_enable_extensions = [
+    "colon_fence",
+]
+panels_add_bootstrap_css = False
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -143,26 +151,40 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme_path = ["."]
-html_theme = "semantic_sphinx"
+html_theme = "pydata_sphinx_theme"
 
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 
 html_theme_options = {
-    "navbar_links": [
-        ("Tutorials", "nb_tutorials/index"),
-        ("Examples", "nb_examples/index"),
-        ("Books + Videos", "learn"),
-        ("API", "api"),
-        ("Developer Guide", "developer_guide"),
-        ("About PyMC3", "about"),
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/pymc-devs/pymc3",
+            "icon": "fab fa-github-square",
+        },
+        {
+            "name": "Twitter",
+            "url": "https://twitter.com/pymc_devs",
+            "icon": "fab fa-twitter-square",
+        },
     ],
-    #     "fixed_sidebar": "false",
-    #     "description": "Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Aesara"
+    "show_prev_next": False,
+    "navbar_start": ["navbar-logo", "navbar-version"],
+    "navbar_end": ["search-field.html", "navbar-icon-links.html"],
+    "search_bar_text": "Search...",
+    "use_edit_page_button": False,  # TODO: see how to skip of fix for generated pages
+    "google_analytics_id": "UA-176578023-1",
+}
+html_context = {
+    "github_user": "pymc-devs",
+    "github_repo": "pymc3",
+    "github_version": "main",
+    "doc_path": "docs/source/",
 }
+html_sidebars = {"learn": [], "**": ["sidebar-nav-bs.html", "sidebar-ethical-ads.html"]}
 
 # Add any paths that contain custom themes here, relative to this directory.
 # html_theme_path = []
@@ -202,7 +224,7 @@
 # html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {"**": ["about.html", "navigation.html", "searchbox.html"]}
+# html_sidebars = {"**": ["about.html", "navigation.html", "searchbox.html"]}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
@@ -330,6 +352,6 @@
 # texinfo_no_detailmenu = False
 
 
-def setup(app):
-    app.add_css_file("https://cdn.jsdelivr.net/npm/semantic-ui@2.4.2/dist/semantic.min.css")
-    app.add_css_file("default.css")
+# def setup(app):
+#     app.add_css_file("https://cdn.jsdelivr.net/npm/semantic-ui@2.4.2/dist/semantic.min.css")
+#     app.add_css_file("default.css")
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -17,6 +17,17 @@
                 </div>
                 <div class="eight wide right floated column">
 
+.. toctree::
+  :maxdepth: 1
+  :hidden:
+
+  Tutorials<nb_tutorials/index>
+  Examples<nb_examples/index>
+  Books + Videos<learn>
+  API<api>
+  Developer Guide<developer_guide>
+  About PyMC3<about>
+
 .. code-block:: python
 
     import pymc3 as pm

diff --git a/docs/source/learn.md b/docs/source/learn.md
@@ -0,0 +1,182 @@
+# Learn Bayesian statistics
+
+## ...with others!
+
+:::{list-table}
+:header-rows: 0
+:widths: 10 150
+
+* - {fa}`discourse,fa-2x,style=fab`
+  - [Discourse Forum](https://discourse.pymc.io/)
+
+    The PyMC3 discourse forum is a great place to ask general questions about Bayesian statistics, or more specific ones about PyMC3 usage.
+* - {fa}`meetup,fa-2x,style=fab`
+  - Conferences
+
+    PyMC3 talks have been given at a number of conferences, including [PyCon](https://us.pycon.org/),
+    [PyData](https://pydata.org/events/), and [ODSC](https://odsc.com/) events.
+* - {fa}`python,fa-2x,style=fab`
+  - [Meetup Groups](https://www.meetup.com/)
+
+    Many areas have an local Bayesian, PyData, or Stan meetup.
+:::
+
+## ...with a video!
+
+:::{list-table}
+:header-rows: 0
+:widths: 10 150
+
+* - {fa}`youtube,fa-2x,style=fab`
+  - [YouTube Playlist](https://www.youtube.com/playlist?list=PL1Ma_1DBbE82OVW8Fz_6Ts1oOeyOAiovy)
+
+    There is an actively curated playlist of PyMC3 talks on YouTube.
+* - {fa}`youtube,fa-2x,style=fab`
+  - [Advance Bayesian Modelling with PyMC3](https://github.com/junpenglao/advance-bayesian-modelling-with-PyMC3)
+
+    A two days advance workshop in May 2018 @CEAi in the Czech Republic.
+:::
+
+## ...with a book!
+
+::::{panels}
+:column: col-lg-4 col-md-4
+
+---
+:img-top: https://camo.githubusercontent.com/4a0aca82ca82efab71747d00db30f3a68de98e82/687474703a2f2f692e696d6775722e636f6d2f36444b596250622e706e673f31
+
+Bayesian Methods for Hackers
+
+*Cameron Davidson-Pilon*
+^^^^^^^^
+
+Fantastic book with many applied code examples.
+
+:::{list-table}
+:header-rows: 0
+:widths: 4 60
+
+* - [{fa}`link`][hackers source]
+  - [Github Repo][hackers source]
+* - [{fa}`link`][hackers homepage]
+  - [Project Homepage][hackers homepage]
+:::
+
+---
+:img-top: https://lh3.googleusercontent.com/qU5yWpiVSkujyCnRZhQo8cBUrW_3e_7Cx4jEs5yfpmMbEEuDnxTGOELhy2x7F7qkwFwQJ4pFYNszZhNpN1jCSdrdHsVUHtf1Mg6F8qwb3SQe1TDE=w1280
+
+Doing Bayesian Data Analysis
+
+*John Kruschke*
+^^^^^^^^
+
+Principled introduction to Bayesian data analysis.
+
+:::{list-table}
+:header-rows: 0
+:widths: 4 60
+
+* - [{fa}`link`][dbda website]
+  - [Book Website][dbda website]
+* - [{fa}`link`][dbda 1st ed nb]
+  - [PyMC3 notebooks for *first edition*][dbda 1st ed nb]
+* - [{fa}`link`][dbda 2nd ed nb]
+  - [PyMC3 notebooks for *second edition*][dbda 2nd ed nb]
+:::
+
+---
+:img-top: http://xcelab.net/rm/wp-content/uploads/2012/01/9781482253443-191x300.jpg
+
+Statistical Rethingking
+
+*Richard McElreath*
+^^^^^^^^
+
+A Bayesian Course with Examples in R and Stan.
+
+:::{list-table}
+:header-rows: 0
+:widths: 4 60
+
+* - [{fa}`link`][rethinking website]
+  - [Book Website][rethinking website]
+* - [{fa}`link`][rethinking port]
+  - [PyMC3 port of the code][rethinking port]
+:::
+
+---
+:img-top: https://raw.githubusercontent.com/aloctavodia/BAP/master/Cover.png
+
+Bayesian Analysis with Python
+
+*Osvaldo Martin*
+^^^^^^^^
+
+A great introductory book written by a maintainer of PyMC3.
+
+:::{list-table}
+:header-rows: 0
+:widths: 4 60
+
+* - [{fa}`link`][bap website]
+  - [Book Website][bap website]
+* - [{fa}`link`][bap code]
+  - [Code and errata in PyMC3][bap code]
+:::
+
+---
+:img-top: https://images-na.ssl-images-amazon.com/images/I/51K33XI2I8L._SX330_BO1,204,203,200_.jpg
+
+Bayesian Cognitive Modeling: A Practical Course
+
+*Michael Lee and Eric-Jan Wagenmakers*
+^^^^^^^^
+
+Focused on using Bayesian statistics in cognitive modeling.
+
+:::{list-table}
+:header-rows: 0
+:widths: 4 60
+
+* - [{fa}`link`][bcm website]
+  - [Book Website][bcm website]
+* - [{fa}`link`][bcm code]
+  - [PyMC3 implementation][bcm code]
+:::
+
+---
+:img-top: http://www.stat.columbia.edu/~gelman/book/bda_cover.png
+
+Bayesian Data Analysis
+
+*Andrew Gelman, John Carlin, Hal Stern, David Dunson, Aki Vehtari, and Donald Rubin*
+^^^^^^^^
+
+A comprehensive, standard, and wonderful textbook on Bayesian methods.
+
+:::{list-table}
+:header-rows: 0
+:widths: 4 60
+
+* - [{fa}`link`][bda3 website]
+  - [Book Website][bda3 website]
+* - [{fa}`link`][bda3 port]
+  - [Examples and exercises implemented in PyMC3][bda3 port]
+:::
+
+::::
+
+
+[hackers source]: https://github.com/CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
+[hackers homepage]: http://camdavidsonpilon.github.io/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers/
+[dbda website]: https://sites.google.com/site/doingbayesiandataanalysis/home
+[dbda 1st ed nb]: https://github.com/aloctavodia/Doing_bayesian_data_analysis
+[dbda 2nd ed nb]: https://github.com/JWarmenhoven/DBDA-python
+[rethinking website]: http://xcelab.net/rm/statistical-rethinking/
+[rethinking port]: https://github.com/pymc-devs/resources/tree/master/Rethinking
+[bap website]: https://www.packtpub.com/big-data-and-business-intelligence/bayesian-analysis-python-second-edition
+[bap code]: https://github.com/aloctavodia/BAP
+[bcm website]: https://bayesmodels.com/
+[bcm code]: https://github.com/pymc-devs/resources/tree/master/BCM
+[bda3 website]: https://www.stat.columbia.edu/~gelman/book/
+[bda3 port]: https://github.com/pymc-devs/resources/tree/master/BDA3