Merge remote-tracking branch 'upstream/main'

Author: Chris Fonnesbeck

.gitignore

@@ -5,3 +5,4 @@
 
 _build
 jupyter_execute
+_thumbnails

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
             |examples/gaussian_processes/GP-Latent\.ipynb$
             |examples/gaussian_processes/GP-MaunaLoa2\.ipynb$
             |examples/samplers/MLDA_gravity_surveying\.ipynb$
-            |examples/pymc3_howto/sampling_callback\.ipynb$
+            |examples/howto/sampling_callback\.ipynb$
             |examples/case_studies/blackbox_external_likelihood\.ipynb$
             |examples/samplers/GLM-hierarchical-jax\.ipynb$
             |examples/variational_inference/convolutional_vae_keras_advi\.ipynb$
@@ -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
@@ -69,7 +68,6 @@ repos:
                examples/case_studies/blackbox_external_likelihood.ipynb|
                examples/case_studies/blackbox_external_likelihood_numpy.ipynb|
                examples/case_studies/item_response_nba.ipynb|
-               examples/case_studies/multilevel_modeling.ipynb|
                examples/diagnostics_and_criticism/sampler-stats.ipynb|
                examples/gaussian_processes/GP-MaunaLoa2.ipynb|
                examples/generalized_linear_models/GLM-logistic.ipynb|
@@ -78,7 +76,7 @@ repos:
                examples/generalized_linear_models/GLM-robust.ipynb|
                examples/generalized_linear_models/GLM-rolling-regression.ipynb|
                examples/generalized_linear_models/GLM-simpsons-paradox.ipynb|
-               examples/pymc3_howto/api_quickstart.ipynb|
+               examples/howto/api_quickstart.ipynb|
                examples/samplers/MLDA_gravity_surveying.ipynb|
                examples/samplers/MLDA_simple_linear_regression.ipynb|
                examples/samplers/SMC-ABC_Lotka-Volterra_example.ipynb|
@@ -105,3 +103,9 @@ repos:
   - id: jupytext
     files: ^examples/.+\.ipynb$
     args: ["--sync"]
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.1.0
+  hooks:
+  - id: codespell
+    files: myst_nbs/
+    args: ["--write-changes", "--ignore-words-list", "hist,fpr,fro,lik", "--uri-ignore-words-list", "*"]

.readthedocs.yml

@@ -7,5 +7,3 @@ python:
    version: "3.8"
    install:
    - requirements: requirements-docs.txt
-   - method: pip
-     path: .

_static/custom.css

@@ -11,3 +11,11 @@
 .bd-sidebar {
   overflow-y: auto;
 }
+
+.navbar-brand {
+  display: inline-block !important;
+}
+
+.supportbutton a {
+ color: var(--pst-color-sidebar-link-active);
+}

_templates/donate.html

@@ -0,0 +1,9 @@
+{% if "generated" in sourcename %}
+<div class="tocsection editthispage">
+{% else %}
+<div class="tocsection supportbutton">
+{% endif %}
+    <a href="https://numfocus.org/donate-to-pymc3">
+      <i class="far fa-heart"></i> {{ _("Support PyMC") }}
+    </a>
+</div>

_templates/search-field.html

@@ -0,0 +1,4 @@
+<form class="bd-search d-flex align-items-center" action="https://www.pymc.io/search.html" method="get">
+  <i class="icon fas fa-search"></i>
+  <input type="search" class="form-control" name="q" id="search-input" placeholder="{{ _(theme_search_bar_text) }}" aria-label="{{ theme_search_bar_text }}" autocomplete="off" >
+</form>

_thumbnails/thumbnails/README.txt

@@ -0,0 +1 @@
+Thumbnails will automatically be generated an placed in this directory by the thumbnail_extractor.py script.

examples/404.md

@@ -6,39 +6,9 @@ orphan: true
 
 **Sorry, we could not find this page**
 
-We are working on the next major release for PyMC,
-which will come with faster sampling, more flexible
-model building, multiple computational backends...
+Click on the navigation bar on top of the page to go to the right section
+of the default docs, or alternatively:
 
-::::{grid} 3
-:::{grid-item}
-![old banner](https://raw.githubusercontent.com/pymc-devs/pymc/v3/docs/logos/svg/PyMC3_banner.svg)
-:::
-:::{grid-item}
-:class: text-center
-{fas}`arrow-alt-circle-right;fa-5x`
-:::
-:::{grid-item}
-![new banner](https://raw.githubusercontent.com/pymc-devs/pymc/main/docs/logos/svg/PyMC_banner.svg)
-:::
-::::
-
-...and much better documentation too! However, to
-do so we have moved some files around and we have
-modified the base url in order to support multi version docs
-and better rendering and cross-referencing for notebooks.
-
-::::{grid} 3
-:::{grid-item}
-:::
-:::{grid-item}
-```{button-link} https://docs.pymc.io/projects/examples/en/latest/
-:color: primary
-:expand:
-
-Back to example gallery homepage
-```
-:::
-:::{grid-item}
-:::
-::::
+* Go to the current [PyMC example gallery homepage](https://www.pymc.io/projects/examples/en/latest/)
+* Go to the PyMC3 3.x snapshot of the [PyMC example gallery](https://www.pymc.io/projects/examples/en/2022.01.0/)
+  (also available for each page from the version switcher at the bottom right of the page)

examples/BART/BART_introduction.ipynb

@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 # Recent updates
 
 <!-- auto generated by ablog so it's empty -->