Gallery

.pre-commit-config.yaml

@@ -45,7 +45,6 @@ repos:
     - id: bibtex-tidy
       files: examples/references.bib
       args: ["--sort=key", --quiet]
-      language_version: 15.14.0
 - repo: local
   hooks:
     - id: watermark

examples/conf.py

@@ -1,12 +1,15 @@
-import os
+import os, sys
+from sphinx.application import Sphinx
 
 # -- Project information -----------------------------------------------------
 project = "PyMC"
-copyright = "2021, PyMC Community"
+copyright = "2022, PyMC Community"
 author = "PyMC Community"
 
 # -- General configuration ---------------------------------------------------
 
+sys.path.insert(0, os.path.abspath("../sphinxext"))
+
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
@@ -21,6 +24,8 @@
     "sphinxcontrib.bibtex",
     "sphinx_codeautolink",
     "notfound.extension",
+    "sphinx_gallery.load_style",
+    "gallery_generator",
 ]
 
 # List of patterns, relative to source directory, that match files and
@@ -37,6 +42,96 @@
 ]
 
 
+def hack_nbsphinx(app: Sphinx) -> None:
+    from nbsphinx import (
+        depart_gallery_html,
+        doctree_resolved,
+        GalleryNode,
+        NbGallery,
+        patched_toctree_resolve,
+        NotebookParser,
+        NbInput,
+        NbOutput,
+        NbInfo,
+        NbWarning,
+        CodeAreaNode,
+        depart_codearea_html,
+        visit_codearea_latex,
+        depart_codearea_latex,
+        GetSizeFromImages,
+    )
+    from sphinx.environment.adapters import toctree
+
+    nbsphinx_thumbnails = {
+        "case_studies/stochastic_volatility": "_static/stochastic_volatility.png",
+    }
+
+    def builder_inited(app: Sphinx):
+        if not hasattr(app.env, "nbsphinx_thumbnails"):
+            app.env.nbsphinx_thumbnails = {}
+
+    def do_nothing(*node):
+        pass
+
+    app.add_source_parser(NotebookParser)
+    # app.add_config_value('nbsphinx_execute', 'auto', rebuild='env')
+    app.add_config_value("nbsphinx_kernel_name", "", rebuild="env")
+    app.add_config_value("nbsphinx_execute_arguments", [], rebuild="env")
+    app.add_config_value("nbsphinx_allow_errors", False, rebuild="")
+    app.add_config_value("nbsphinx_timeout", None, rebuild="")
+    app.add_config_value("nbsphinx_codecell_lexer", "none", rebuild="env")
+    app.add_config_value("nbsphinx_prompt_width", "4.5ex", rebuild="html")
+    app.add_config_value("nbsphinx_responsive_width", "540px", rebuild="html")
+    app.add_config_value("nbsphinx_prolog", None, rebuild="env")
+    app.add_config_value("nbsphinx_epilog", None, rebuild="env")
+    app.add_config_value("nbsphinx_input_prompt", "[%s]:", rebuild="env")
+    app.add_config_value("nbsphinx_output_prompt", "[%s]:", rebuild="env")
+    app.add_config_value("nbsphinx_custom_formats", {}, rebuild="env")
+    # Default value is set in config_inited():
+    app.add_config_value("nbsphinx_requirejs_path", None, rebuild="html")
+    # Default value is set in config_inited():
+    app.add_config_value("nbsphinx_requirejs_options", None, rebuild="html")
+    # This will be updated in env_updated():
+    app.add_config_value("nbsphinx_widgets_path", None, rebuild="html")
+    app.add_config_value("nbsphinx_widgets_options", {}, rebuild="html")
+    # app.add_config_value('nbsphinx_thumbnails', {}, rebuild='html')
+    app.add_config_value("nbsphinx_assume_equations", True, rebuild="env")
+
+    app.add_directive("nbinput", NbInput)
+    app.add_directive("nboutput", NbOutput)
+    app.add_directive("nbinfo", NbInfo)
+    app.add_directive("nbwarning", NbWarning)
+    app.add_directive("nbgallery", NbGallery)
+    app.add_node(
+        CodeAreaNode,
+        html=(do_nothing, depart_codearea_html),
+        latex=(visit_codearea_latex, depart_codearea_latex),
+        text=(do_nothing, do_nothing),
+    )
+    app.connect("builder-inited", builder_inited)
+    app.connect("doctree-resolved", doctree_resolved)
+    app.add_post_transform(GetSizeFromImages)
+
+    app.add_config_value("nbsphinx_execute", "auto", rebuild="env")
+    app.add_config_value("nbsphinx_thumbnails", nbsphinx_thumbnails, rebuild="html")
+    app.add_directive("nbgallery", NbGallery)
+    app.add_node(
+        GalleryNode,
+        html=(do_nothing, depart_gallery_html),
+        latex=(do_nothing, do_nothing),
+        text=(do_nothing, do_nothing),
+    )
+    app.connect("builder-inited", builder_inited)
+    app.connect("doctree-resolved", doctree_resolved)
+
+    # Monkey-patch Sphinx TocTree adapter
+    toctree.TocTree.resolve = patched_toctree_resolve
+
+
+def setup(app: Sphinx):
+    hack_nbsphinx(app)
+
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -93,7 +188,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["../_static"]
+html_static_path = ["../_static", "../thumbnails"]
 html_css_files = ["custom.css"]
 templates_path = ["../_templates"]
 html_sidebars = {

examples/gallery.rst

@@ -0,0 +1,115 @@
+Gallery
+=======
+
+
+(Generalized) Linear and Hierarchical Linear Models
+-------------------------
+
+.. nbgallery::
+    :caption: This is a thumbnail gallery:
+    :name: generalized_linear_models
+    :glob:
+    :reversed:
+
+    generalized_linear_models/*
+
+
+Case Studies
+------------
+
+.. nbgallery::
+    :caption: This is a thumbnail gallery:
+    :name: case_studies
+    :glob:
+    :reversed:
+
+    case_studies/*
+
+Diagnostics and Model Criticism
+-------------------------------
+
+.. nbgallery::
+    :caption: This is a thumbnail gallery:
+    :name: diagnostics_and_criticism
+    :glob:
+    :reversed:
+
+    diagnostics_and_criticism/*
+
+
+Gaussian Processes
+------------------
+
+.. nbgallery::
+    :caption: This is a thumbnail gallery:
+    :name: gaussian_processes
+    :glob:
+    :reversed:
+
+    gaussian_processes/*
+
+Inference in ODE models
+-----------------------
+
+.. nbgallery::
+    :caption: This is a thumbnail gallery:
+    :name: ode_models
+    :glob:
+    :reversed:
+
+    ode_models/*
+
+MCMC
+----
+
+.. nbgallery::
+    :caption: This is a thumbnail gallery:
+    :name: samplers
+    :glob:
+    :reversed:
+
+    samplers/*
+
+Mixture Models
+--------------
+
+.. nbgallery::
+    :caption: This is a thumbnail gallery:
+    :name: mixture_models
+    :glob:
+    :reversed:
+
+    mixture_models/*
+
+Survival Analysis
+-----------------
+
+.. nbgallery::
+    :caption: This is a thumbnail gallery:
+    :name: survival_analysis
+    :glob:
+    :reversed:
+
+    survival_analysis/*
+
+Time Series
+-----------
+
+.. nbgallery::
+    :caption: This is a thumbnail gallery:
+    :name: time_series
+    :glob:
+    :reversed:
+
+    time_series/*
+
+Variational Inference
+---------------------
+
+.. nbgallery::
+    :caption: This is a thumbnail gallery:
+    :name: variational_inference
+    :glob:
+    :reversed:
+
+    variational_inference/*

examples/index.md

@@ -74,7 +74,7 @@ has tags in its metadata they are listed on the right sidebar after the {fas}`ta
 :::{toctree}
 :maxdepth: 1
 :hidden:
-
+gallery
 blog
 object_index/index
 :::

requirements-docs.txt

@@ -8,3 +8,5 @@ ablog
 sphinxext-opengraph
 sphinx-codeautolink
 sphinx-notfound-page
+nbsphinx
+sphinx-gallery