Merge remote-tracking branch 'upstream/main' into multilevel_v4_update

Author: fonnesbeck

.jupytext.toml

@@ -1,3 +1,5 @@
+notebook_metadata_filter = "substitutions"
+
 [formats]
 "examples/" = "ipynb"
 "myst_nbs/" = ".myst.md:myst"

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
     files: ^examples/.+\.ipynb$
     args: ["--sync"]
 - repo: https://github.com/psf/black
-  rev: 22.1.0
+  rev: 22.3.0
   hooks:
     - id: black-jupyter
 - repo: https://github.com/nbQA-dev/nbQA
@@ -29,7 +29,6 @@ repos:
             |examples/gaussian_processes/GP-Latent\.ipynb$
             |examples/gaussian_processes/GP-MaunaLoa2\.ipynb$
             |examples/samplers/MLDA_gravity_surveying\.ipynb$
-            |examples/case_studies/putting_workflow\.ipynb$
             |examples/pymc3_howto/sampling_callback\.ipynb$
             |examples/case_studies/blackbox_external_likelihood\.ipynb$
             |examples/samplers/GLM-hierarchical-jax\.ipynb$
@@ -56,15 +55,6 @@ repos:
       minimum_pre_commit_version: 2.8.0
       name: Check notebooks have watermark (see Jupyter style guide from PyMC docs)
       types: [jupyter]
-    - id: add-tags
-      entry: python scripts/add_tags.py
-      language: python
-      name: Add PyMC3 classes used to tags
-      types: [jupyter]
-      additional_dependencies:
-         - nbqa==1.1.1
-         - beautifulsoup4==4.9.3
-         - myst_parser==0.13.7
 - repo: https://github.com/mwouts/jupytext
   rev: v1.13.7
   hooks:

README.rst

@@ -8,7 +8,7 @@ PyMC Examples
 
 Supporting examples and tutorials for PyMC, the Python package for Bayesian statistical modeling and Probabilistic Machine Learning!
 
-Check out the `getting started guide <http://docs.pymc.io/notebooks/getting_started>`__,  or
+Check out the `getting started guide <https://docs.pymc.io/en/latest/learning.html#learning>`__,  or
 interact with live examples using Binder! Each notebook in `PyMC examples gallery
 <https://pymc-examples.readthedocs.io>`__ has a binder badge.
 For questions on PyMC, head on over to our `PyMC Discourse <https://discourse.pymc.io/>`__ forum.

_templates/postcard_categories.html

@@ -50,14 +50,14 @@ <h3>
   <div class="container sd-fs-6 sd-font-weight-bold">
     <div class="row border-top border-bottom">
       {% set t_bool = "tutorial" in post.category|map('string') %}
-      <div class="col {{ setcolorclass(t_bool) }}"><a href="{{ pathtocategory('tutorial') }}">Tutorial</a></div>
+      <div class="col"><a class="{{ setcolorclass(t_bool) }}" href="{{ pathtocategory('tutorial') }}">Tutorial</a></div>
       {% set h_bool = "how-to" in post.category|map('string') %}
-      <div class="col {{ setcolorclass(h_bool) }}"><a href="{{ pathtocategory('how-to') }}">How-to</a></div>
+      <div class="col"><a class="{{ setcolorclass(h_bool) }}" href="{{ pathtocategory('how-to') }}">How-to</a></div>
       <div class="w-100"></div>
       {% set e_bool = "explanation" in post.category|map('string') %}
-      <div class="col {{ setcolorclass(e_bool) }}"><a href="{{ pathtocategory('explanation') }}">Explanation</a></div>
+      <div class="col"><a class="{{ setcolorclass(e_bool) }}" href="{{ pathtocategory('explanation') }}">Explanation</a></div>
       {% set r_bool = "reference" in post.category|map('string') %}
-      <div class="col {{ setcolorclass(r_bool) }}"><a href="{{ pathtocategory('reference') }}">Reference</a></div>
+      <div class="col"><a class="{{ setcolorclass(r_bool) }}" href="{{ pathtocategory('reference') }}">Reference</a></div>
     </div>
   </div>
 

examples/case_studies/LKJ.ipynb

@@ -69,6 +69,7 @@
         {"name": "API", "url": "https://docs.pymc.io/en/stable/api.html"},
     ],
     "page_sidebar_items": ["postcard", "page-toc", "edit-this-page"],
+    "google_analytics_id": "G-6KPRBTE6WV",
 }
 version = os.environ.get("READTHEDOCS_VERSION", "")
 version = version if "." in version else "main"
@@ -99,12 +100,11 @@
         # "sidebar-nav-bs.html",
         "postcard_categories.html",
         "tagcloud.html",
-        "sidebar-ethical-ads.html",
     ],
 }
 
 # ablog config
-blog_baseurl = "https://examples.pymc.io"
+blog_baseurl = "https://docs.pymc.io/projects/examples/en/latest/"
 blog_title = "PyMC Examples"
 blog_path = "blog"
 blog_authors = {
@@ -145,22 +145,8 @@
 bibtex_reference_style = "author_year"
 
 # OpenGraph config
-# ogp_site_url = "https://predictablynoisy.com"
-# ogp_image = "https://predictablynoisy.com/_static/profile-bw.png"
+# use default readthedocs integration aka no config here
 
-# codeautolink config
-from IPython.core.inputtransformer2 import TransformerManager
-
-
-def ipython_cell_transform(source):
-    out = TransformerManager().transform_cell(source)
-    return source, out
-
-
-# codeautolink
-codeautolink_custom_blocks = {
-    "ipython3": ipython_cell_transform,
-}
 codeautolink_autodoc_inject = False
 codeautolink_concat_default = True
 
@@ -169,10 +155,11 @@ def ipython_cell_transform(source):
     "aesara": ("https://aesara.readthedocs.io/en/latest/", None),
     "arviz": ("https://arviz-devs.github.io/arviz/", None),
     "bambi": ("https://bambinos.github.io/bambi/main", None),
+    "einstats": ("https://xarray-einstats.readthedocs.io/en/stable/", None),
     "mpl": ("https://matplotlib.org/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
-    "pymc": ("https://docs.pymc.io/en/stable/", None),
+    "pymc": ("https://docs.pymc.io/en/latest/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
     "xarray": ("http://xarray.pydata.org/en/stable/", None),
 }

examples/case_studies/factor_analysis.ipynb

@@ -955,7 +955,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.9"
   }
  },
  "nbformat": 4,

examples/case_studies/mediation_analysis.ipynb

@@ -76,4 +76,5 @@ has tags in its metadata they are listed on the right sidebar after the {fas}`ta
 :hidden:
 
 blog
+object_index/index
 :::

examples/case_studies/moderation_analysis.ipynb

@@ -0,0 +1,9 @@
+-------------
+Distributions
+-------------
+
+.. toctree::
+    :maxdepth: 2
+
+    distributions/continuous
+    distributions/discrete

examples/case_studies/putting_workflow.ipynb

@@ -0,0 +1,14 @@
+Continuous
+**********
+
+.. autolink-examples:: pymc.Beta
+   :type: class
+   :collapse:
+
+.. autolink-examples:: pymc.Exponential
+   :type: class
+   :collapse:
+
+.. autolink-examples:: pymc.Normal
+   :type: class
+   :collapse:

examples/case_studies/rugby_analytics.ipynb

@@ -0,0 +1,6 @@
+Discrete
+********
+
+.. autolink-examples:: pymc.Poisson
+   :type: class
+   :collapse:

examples/conf.py

@@ -0,0 +1,22 @@
+.. _object_index:
+
+================
+Object use index
+================
+
+This page is structured like the {ref}`PyMC API Reference page <pymc:api>` and
+for each function in the API it lists all the examples where that PyMC object
+is used.
+
+.. warning::
+
+   This page is still a proof of concept only. See
+   `pymc-examples#289 <https://github.com/pymc-devs/pymc-examples/issues/289>`_
+   for more details.
+
+.. toctree::
+    :maxdepth: 2
+
+    distributions
+    samplers
+

examples/generalized_linear_models/GLM-simpsons-paradox.ipynb

@@ -0,0 +1,31 @@
+------------------
+Sampling functions
+------------------
+
+.. autolink-examples:: pymc.sample
+   :type: func
+   :collapse:
+
+.. autolink-examples:: pymc.sample_posterior_predictive
+   :type: func
+   :collapse:
+
+.. autolink-examples:: pymc.sample_prior_predictive
+   :type: func
+   :collapse:
+
+--------
+Samplers
+--------
+
+.. autolink-examples:: pymc.NUTS
+   :type: class
+   :collapse:
+
+.. autolink-examples:: pymc.Metropolis
+   :type: class
+   :collapse:
+
+.. autolink-examples:: pymc.Slice
+   :type: class
+   :collapse: