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Initialize standalone build (#218)
* Initialize standalone build * couple minor fixes to trigger readthedocs * extend contributing docs * review suggesions
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‎.gitignore

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*.pyc
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.ipynb_checkpoints
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.vscode/*
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_build
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jupyter_execute

‎.readthedocs.yml

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version: 2
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sphinx:
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configuration: examples/conf.py
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python:
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version: "3.8"
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install:
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- requirements: requirements-docs.txt
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- method: pip
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path: .

‎CONTRIBUTING.md

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* No `pre-commit` errors: see the [Jupyter Notebook style](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Jupyter-Notebook-Style-Guide) (and [Python code style](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Python-Code-Style)) page from our Wiki on how to install and run it.
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* Indicate how are you aiming to update the notebook (i.e. what is the target end column in the tracker). The pull request template has a template for this.
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## Contributor guide
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In order to work and run the example notebooks you need to install the packages in
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`requirements-write.txt`. To see how the notebook looks rendered, you can follow
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the instructions in the following paragraph or open a PR to see the preview in
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readthedocs.
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The markdown cells in the notebook can use MyST, a superset of CommonMark markdown. See
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https://myst-parser.readthedocs.io/en/latest/ and https://myst-nb.readthedocs.io/en/latest/
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for documentation on their features and syntax.
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To generate the draft standalone notebook gallery, you need to have installed all the packages in
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`requirements-docs.txt` and to run `sphinx-build examples/ _build -b html` from the repository
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home directory. After building, you can see the preview of the docs
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by opening `_build/index.html` file with your browser.

‎_static/PyMC3.ico

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‎examples/bibliography.md

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# General Bibliography
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:::{bibliography}
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:all:
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:::

‎examples/blog.md

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# Blog
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<!-- auto generated by ablog so it's empty -->

‎examples/case_studies/multilevel_modeling.ipynb

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# A Primer on Bayesian Methods for Multilevel Modeling"
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"# A Primer on Bayesian Methods for Multilevel Modeling\n",
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"\n",
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":::{post} 30 Aug, 2021\n",
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":tags: hierarchical\n",
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":category: intermediate\n",
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":::"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Example: Radon contamination (Gelman and Hill 2006)\n",
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"## Example: Radon contamination {cite:t}`gelman2006data`\n",
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"\n",
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"Radon is a radioactive gas that enters homes through contact points with the ground. It is a carcinogen that is the primary cause of lung cancer in non-smokers. Radon levels vary greatly from household to household.\n",
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"\n",
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"\n",
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"## References\n",
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"\n",
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"- Gelman, A., & Hill, J. (2006), *Data Analysis Using Regression and Multilevel/Hierarchical Models (1st ed.)*, Cambridge University Press.\n",
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"\n",
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"- Gelman, A. (2006), *Multilevel (Hierarchical) modeling: what it can and cannot do*, Technometrics, 48(3), 432–435.\n",
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":::{bibliography}\n",
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":filter: docname in docnames\n",
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"\n",
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"- McElreath, R. (2020), *Statistical Rethinking - A Bayesian Course with Examples in R and Stan (2nd ed.)*, CRC Press. "
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"gelman2006multilevel\n",
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"mcelreath2018statistical\n",
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":::"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Watermark"
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]
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},
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{
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"metadata": {
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"celltoolbar": "Raw Cell Format",
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.9"
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"version": "3.8.6"
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}
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},
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"nbformat": 4,

‎examples/case_studies/rugby_analytics.ipynb

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# A Hierarchical model for Rugby prediction"
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"# A Hierarchical model for Rugby prediction\n",
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"\n",
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":::{post} 30 Aug, 2021\n",
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":tags: hierarchical, sports\n",
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":category: intermediate\n",
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":::"
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]
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},
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{
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.2"
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"version": "3.8.6"
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}
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},
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"nbformat": 4,

‎examples/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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# import os
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# import sys
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# sys.path.insert(0, os.path.abspath('.'))
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# -- Project information -----------------------------------------------------
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project = "PyMC3"
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copyright = "2021, PyMC Community"
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author = "PyMC Community"
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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"sphinx.ext.intersphinx",
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"sphinx.ext.mathjax",
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"myst_nb",
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"ablog",
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"sphinx_design",
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"sphinxext.opengraph",
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"sphinx_copybutton",
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"sphinxcontrib.bibtex",
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]
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = [
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"_build",
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"Thumbs.db",
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".DS_Store",
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"*import_posts*",
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"**/.ipynb_checkpoints/*",
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]
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# -- Options for HTML output -------------------------------------------------
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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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# theme options
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html_theme = "pydata_sphinx_theme"
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html_theme_options = {
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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/pymc-examples",
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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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"name": "Discourse",
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"url": "https://discourse.pymc.io",
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"icon": "fab fa-discourse",
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},
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],
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"search_bar_text": "Search...",
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"navbar_end": ["search-field.html", "navbar-icon-links.html"],
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"external_links": [
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{"name": "Learning", "url": "https://pymc3.readthedocs.io/en/latest/learn.html"},
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{"name": "API", "url": "https://pymc3.readthedocs.io/en/latest/api.html"}
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]
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}
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html_favicon = "../_static/PyMC3.ico"
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ["../_static"]
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html_sidebars = {
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"**": ["sidebar-nav-bs.html", "tagcloud.html", "categories.html"],
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}
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# ablog config
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# blog_baseurl = "https://predictablynoisy.com"
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blog_title = "PyMC Examples"
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blog_path = "blog"
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# fontawesome_included = True
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# post_redirect_refresh = 1
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# post_auto_image = 1
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# post_auto_excerpt = 2
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# MyST config
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myst_enable_extensions = [
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"colon_fence",
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"deflist",
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"dollarmath",
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"amsmath"
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]
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# bibtex config
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bibtex_bibfiles = ['references.bib']
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bibtex_default_style = 'unsrt'
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bibtex_reference_style = "author_year"
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# OpenGraph config
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# ogp_site_url = "https://predictablynoisy.com"
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# ogp_image = "https://predictablynoisy.com/_static/profile-bw.png"
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# Temporarily stored as off until we fix it
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jupyter_execute_notebooks = "off"
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# intersphinx mappings
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intersphinx_mapping = {
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"aesara": ("https://aesara.readthedocs.io/en/latest/", None),
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"arviz": ("https://arviz-devs.github.io/arviz/", None),
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# "mpl": ("https://matplotlib.org/", None),
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# "numpy": ("https://numpy.org/doc/stable/", None),
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# "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
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"pymc3": ("https://docs.pymc.io/", None),
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# "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
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# "xarray": ("http://xarray.pydata.org/en/stable/", None),
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}

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