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Switch to pydata sphinx theme (#4761)
* start changing theme * customize theme to match our needs * remove extra custom css from build * add github and twitter icons * move search bar to navbar * add version number * remove sidebars from home page left to do: * fix gallery generator -> stop using javascript * fix home page * move away from so much custom html -> myst markdown? * improve homepage layout * start using sphinx panels * convert learn page from html to myst
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‎conda-envs/environment-dev-py37.yml

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- numpydoc>=0.9
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- pandas=0.24
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- pre-commit>=2.8.0
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- pydata-sphinx-theme
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- pytest-cov>=2.5
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- pytest>=3.0
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- python-graphviz
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- python=3.7
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- recommonmark>=0.4
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- scipy>1.4.1
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- sphinx-autobuild>=0.7
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- sphinx-panels
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- sphinx>=1.5
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- typing-extensions
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- watermark

‎conda-envs/environment-dev-py38.yml

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- numpydoc>=0.9
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- pandas
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- pre-commit>=2.8.0
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- pydata-sphinx-theme
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- pytest-cov>=2.5
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- pytest>=3.0
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- python-graphviz
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- python=3.8
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- recommonmark>=0.4
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- scipy>1.4.1
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- sphinx-autobuild>=0.7
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- sphinx-panels
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- sphinx>=1.5
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- typing-extensions>=3.7.4
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- watermark

‎conda-envs/environment-dev-py39.yml

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- numpydoc>=0.9
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- pandas>=0.24.0
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- pre-commit>=2.8.0
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- pydata-sphinx-theme
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- pytest-cov>=2.5
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- pytest>=3.0
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- python-graphviz
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- python=3.9
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- recommonmark>=0.4
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- scipy>1.4.1
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- sphinx-autobuild>=0.7
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- sphinx-panels
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- sphinx>=1.5
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- typing-extensions>=3.7.4
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- watermark

‎docs/source/_templates/layout.html

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{% extends "!layout.html" %}
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<!-- Hide left sidebar in home page -->
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{% block docs_sidebar %}
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{% if pagename != 'index' %}
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{{ super() }}
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{% endif %}
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{% endblock %}
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<!-- Hide right sidebar in home page -->
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{% block docs_toc %}
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{% if pagename != 'index' %}
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{{ super() }}
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{% endif %}
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{% endblock %}
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<!-- Make body have full width in home page -->
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{% block docs_main %}
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{% if pagename == 'index' %}
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<main class="col-12 py-md-5 pl-md-5 pr-md-4 bd-content" role="main">
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{% block body %} {% endblock %}
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</main>
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{% else %}
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{{ super() }}
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{% endif %}
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{% endblock %}

‎docs/source/_templates/navbar-version.html

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{{ version }}

‎docs/source/conf.py

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"matplotlib.sphinxext.plot_directive",
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"sphinx.ext.autodoc",
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"sphinx.ext.autosummary",
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"sphinx.ext.viewcode",
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"sphinx.ext.mathjax",
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"sphinx.ext.intersphinx",
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"numpydoc",
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"sphinx.ext.napoleon",
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"gallery_generator",
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"myst_nb",
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"sphinx_panels",
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]
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# Don't auto-generate summary for class members.
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# directories to ignore when looking for source files.
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exclude_patterns = ["_build", "**.ipynb_checkpoints"]
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# myst and panels config
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jupyter_execute_notebooks = "off"
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myst_heading_anchors = 3
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myst_enable_extensions = [
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"colon_fence",
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]
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panels_add_bootstrap_css = False
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# The reST default role (used for this markup: `text`) to use for all
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# documents.
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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html_theme_path = ["."]
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html_theme = "semantic_sphinx"
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html_theme = "pydata_sphinx_theme"
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# Theme options are theme-specific and customize the look and feel of a theme
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# further. For a list of options available for each theme, see the
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# documentation.
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html_theme_options = {
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"navbar_links": [
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("Tutorials", "nb_tutorials/index"),
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("Examples", "nb_examples/index"),
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("Books + Videos", "learn"),
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("API", "api"),
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("Developer Guide", "developer_guide"),
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("About PyMC3", "about"),
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"icon_links": [
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{
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"name": "GitHub",
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"url": "https://github.com/pymc-devs/pymc3",
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"icon": "fab fa-github-square",
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},
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{
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"name": "Twitter",
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"url": "https://twitter.com/pymc_devs",
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"icon": "fab fa-twitter-square",
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},
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],
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# "fixed_sidebar": "false",
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# "description": "Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Aesara"
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"show_prev_next": False,
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"navbar_start": ["navbar-logo", "navbar-version"],
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"navbar_end": ["search-field.html", "navbar-icon-links.html"],
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"search_bar_text": "Search...",
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"use_edit_page_button": False, # TODO: see how to skip of fix for generated pages
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"google_analytics_id": "UA-176578023-1",
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}
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html_context = {
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"github_user": "pymc-devs",
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"github_repo": "pymc3",
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"github_version": "main",
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"doc_path": "docs/source/",
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}
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html_sidebars = {"learn": [], "**": ["sidebar-nav-bs.html", "sidebar-ethical-ads.html"]}
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# Add any paths that contain custom themes here, relative to this directory.
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# html_theme_path = []
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# html_use_smartypants = True
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# Custom sidebar templates, maps document names to template names.
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html_sidebars = {"**": ["about.html", "navigation.html", "searchbox.html"]}
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# html_sidebars = {"**": ["about.html", "navigation.html", "searchbox.html"]}
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# Additional templates that should be rendered to pages, maps page names to
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# template names.
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# texinfo_no_detailmenu = False
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def setup(app):
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app.add_css_file("https://cdn.jsdelivr.net/npm/semantic-ui@2.4.2/dist/semantic.min.css")
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app.add_css_file("default.css")
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# def setup(app):
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# app.add_css_file("https://cdn.jsdelivr.net/npm/semantic-ui@2.4.2/dist/semantic.min.css")
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# app.add_css_file("default.css")

‎docs/source/index.rst

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</div>
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<div class="eight wide right floated column">
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.. toctree::
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:maxdepth: 1
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:hidden:
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Tutorials<nb_tutorials/index>
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Examples<nb_examples/index>
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Books + Videos<learn>
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API<api>
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Developer Guide<developer_guide>
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About PyMC3<about>
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.. code-block:: python
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import pymc3 as pm

‎docs/source/learn.md

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

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