fix website rendering (#540)

* update conf.py to updated versions

* update rtd config

* Use older versions

* fix requirements

* try newer versions with older ablog

Author: OriolAbril

.readthedocs.yml

@@ -3,7 +3,11 @@ version: 2
 sphinx:
     configuration: examples/conf.py
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 python:
-   version: "3.8"
    install:
    - requirements: requirements-docs.txt

_templates/nb-badges.html

@@ -1,9 +1,11 @@
+{% if pagename in ablog %}
+
 <!-- Generate correct links and render github/binder/colab badges -->
 {% set gh_basepath =  github_user + '/' + github_repo + '/blob/' + github_version + '/' %}
 {% set encoded_base =  github_user + '%252F' + github_repo  %}
 {% set gh_binder = github_user + '/' + github_repo + '/' + github_version %}
 {% set doc_path_aux = doc_path | trim('/') %}
-{% set file_path = doc_path_aux + '/' + pagename + page_source_suffix %}
+{% set file_path = doc_path_aux + '/' + pagename + ".ipynb" %}
 {% set encoded_path = file_path | replace("/", "%252F") %}
 
 
@@ -19,3 +21,4 @@
     <img src="{{ pathto('_static/colab.svg', 1) }}" alt="Open In Colab"/></a>
   </p>
 </div>
+{% endif %}

_templates/page.html

@@ -0,0 +1,13 @@
+<!-- continuation of examples/page_footer.md -->
+{% if pagename in ablog %}
+  {% set post = ablog[pagename] %}
+    {% for coll in post.author %}
+      {% if coll|length %}
+        {{ coll }}
+        {% if loop.index < post.author | length %},{% endif %}
+      {% else %}
+        {{ coll }}
+        {% if loop.index < post.author | length %},{% endif %}
+      {% endif %}
+    {% endfor %}. "{{ title.split(' — ')[0] }}". In: <i>PyMC Examples</i>. Ed. by PyMC Team. DOI: <a href={{ doi_url }}>{{ doi_code }}</a>
+{% endif %}

_templates/rendered_citation.html

@@ -1,7 +1,6 @@
 {
  "cells": [
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "domestic-remove",
    "metadata": {},
@@ -10,14 +9,13 @@
     "# Modeling Heteroscedasticity with BART\n",
     "\n",
     ":::{post} January, 2023\n",
-    ":tags: bart regression \n",
+    ":tags: BART, regression\n",
     ":category: beginner, reference\n",
-    ":author: [Juan Orduz](https://juanitorduz.github.io/)\n",
+    ":author: Juan Orduz\n",
     ":::"
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "72588976-efc3-4adc-bec2-bc5b6ac4b7e1",
    "metadata": {},
@@ -60,7 +58,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "4cae4407",
    "metadata": {},
@@ -167,7 +164,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "6d6364a9",
    "metadata": {},
@@ -206,7 +202,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "5c3971f2",
    "metadata": {},
@@ -215,7 +210,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "e8a3ce48",
    "metadata": {},
@@ -237,7 +231,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "a29b706c",
    "metadata": {},
@@ -253,7 +246,52 @@
    "outputs": [
     {
      "data": {
-      "image/svg+xml": "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n<!-- Generated by graphviz version 2.50.0 (0)\n -->\n<!-- Pages: 1 -->\n<svg width=\"138pt\" height=\"260pt\"\n viewBox=\"0.00 0.00 138.00 259.91\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n<g id=\"graph0\" class=\"graph\" transform=\"scale(1 1) rotate(0) translate(4 255.91)\">\n<polygon fill=\"white\" stroke=\"transparent\" points=\"-4,4 -4,-255.91 134,-255.91 134,4 -4,4\"/>\n<g id=\"clust1\" class=\"cluster\">\n<title>cluster2 x 200</title>\n<path fill=\"none\" stroke=\"black\" d=\"M20,-129.95C20,-129.95 110,-129.95 110,-129.95 116,-129.95 122,-135.95 122,-141.95 122,-141.95 122,-231.91 122,-231.91 122,-237.91 116,-243.91 110,-243.91 110,-243.91 20,-243.91 20,-243.91 14,-243.91 8,-237.91 8,-231.91 8,-231.91 8,-141.95 8,-141.95 8,-135.95 14,-129.95 20,-129.95\"/>\n<text text-anchor=\"middle\" x=\"93\" y=\"-137.75\" font-family=\"Times,serif\" font-size=\"14.00\">2 x 200</text>\n</g>\n<g id=\"clust2\" class=\"cluster\">\n<title>cluster200</title>\n<path fill=\"none\" stroke=\"black\" d=\"M26,-8C26,-8 104,-8 104,-8 110,-8 116,-14 116,-20 116,-20 116,-109.95 116,-109.95 116,-115.95 110,-121.95 104,-121.95 104,-121.95 26,-121.95 26,-121.95 20,-121.95 14,-115.95 14,-109.95 14,-109.95 14,-20 14,-20 14,-14 20,-8 26,-8\"/>\n<text text-anchor=\"middle\" x=\"97.5\" y=\"-15.8\" font-family=\"Times,serif\" font-size=\"14.00\">200</text>\n</g>\n<!-- w -->\n<g id=\"node1\" class=\"node\">\n<title>w</title>\n<ellipse fill=\"none\" stroke=\"black\" cx=\"65\" cy=\"-198.43\" rx=\"48.58\" ry=\"37.45\"/>\n<text text-anchor=\"middle\" x=\"65\" y=\"-209.73\" font-family=\"Times,serif\" font-size=\"14.00\">w</text>\n<text text-anchor=\"middle\" x=\"65\" y=\"-194.73\" font-family=\"Times,serif\" font-size=\"14.00\">~</text>\n<text text-anchor=\"middle\" x=\"65\" y=\"-179.73\" font-family=\"Times,serif\" font-size=\"14.00\">BART_w</text>\n</g>\n<!-- y -->\n<g id=\"node2\" class=\"node\">\n<title>y</title>\n<ellipse fill=\"lightgrey\" stroke=\"black\" cx=\"65\" cy=\"-76.48\" rx=\"43.27\" ry=\"37.45\"/>\n<text text-anchor=\"middle\" x=\"65\" y=\"-87.78\" font-family=\"Times,serif\" font-size=\"14.00\">y</text>\n<text text-anchor=\"middle\" x=\"65\" y=\"-72.78\" font-family=\"Times,serif\" font-size=\"14.00\">~</text>\n<text text-anchor=\"middle\" x=\"65\" y=\"-57.78\" font-family=\"Times,serif\" font-size=\"14.00\">Gamma</text>\n</g>\n<!-- w&#45;&gt;y -->\n<g id=\"edge1\" class=\"edge\">\n<title>w&#45;&gt;y</title>\n<path fill=\"none\" stroke=\"black\" d=\"M65,-160.79C65,-149.38 65,-136.65 65,-124.63\"/>\n<polygon fill=\"black\" stroke=\"black\" points=\"68.5,-124.31 65,-114.31 61.5,-124.31 68.5,-124.31\"/>\n</g>\n</g>\n</svg>\n",
+      "image/svg+xml": [
+       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
+       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
+       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
+       "<!-- Generated by graphviz version 2.50.0 (0)\n",
+       " -->\n",
+       "<!-- Pages: 1 -->\n",
+       "<svg width=\"138pt\" height=\"260pt\"\n",
+       " viewBox=\"0.00 0.00 138.00 259.91\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
+       "<g id=\"graph0\" class=\"graph\" transform=\"scale(1 1) rotate(0) translate(4 255.91)\">\n",
+       "<polygon fill=\"white\" stroke=\"transparent\" points=\"-4,4 -4,-255.91 134,-255.91 134,4 -4,4\"/>\n",
+       "<g id=\"clust1\" class=\"cluster\">\n",
+       "<title>cluster2 x 200</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M20,-129.95C20,-129.95 110,-129.95 110,-129.95 116,-129.95 122,-135.95 122,-141.95 122,-141.95 122,-231.91 122,-231.91 122,-237.91 116,-243.91 110,-243.91 110,-243.91 20,-243.91 20,-243.91 14,-243.91 8,-237.91 8,-231.91 8,-231.91 8,-141.95 8,-141.95 8,-135.95 14,-129.95 20,-129.95\"/>\n",
+       "<text text-anchor=\"middle\" x=\"93\" y=\"-137.75\" font-family=\"Times,serif\" font-size=\"14.00\">2 x 200</text>\n",
+       "</g>\n",
+       "<g id=\"clust2\" class=\"cluster\">\n",
+       "<title>cluster200</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M26,-8C26,-8 104,-8 104,-8 110,-8 116,-14 116,-20 116,-20 116,-109.95 116,-109.95 116,-115.95 110,-121.95 104,-121.95 104,-121.95 26,-121.95 26,-121.95 20,-121.95 14,-115.95 14,-109.95 14,-109.95 14,-20 14,-20 14,-14 20,-8 26,-8\"/>\n",
+       "<text text-anchor=\"middle\" x=\"97.5\" y=\"-15.8\" font-family=\"Times,serif\" font-size=\"14.00\">200</text>\n",
+       "</g>\n",
+       "<!-- w -->\n",
+       "<g id=\"node1\" class=\"node\">\n",
+       "<title>w</title>\n",
+       "<ellipse fill=\"none\" stroke=\"black\" cx=\"65\" cy=\"-198.43\" rx=\"48.58\" ry=\"37.45\"/>\n",
+       "<text text-anchor=\"middle\" x=\"65\" y=\"-209.73\" font-family=\"Times,serif\" font-size=\"14.00\">w</text>\n",
+       "<text text-anchor=\"middle\" x=\"65\" y=\"-194.73\" font-family=\"Times,serif\" font-size=\"14.00\">~</text>\n",
+       "<text text-anchor=\"middle\" x=\"65\" y=\"-179.73\" font-family=\"Times,serif\" font-size=\"14.00\">BART_w</text>\n",
+       "</g>\n",
+       "<!-- y -->\n",
+       "<g id=\"node2\" class=\"node\">\n",
+       "<title>y</title>\n",
+       "<ellipse fill=\"lightgrey\" stroke=\"black\" cx=\"65\" cy=\"-76.48\" rx=\"43.27\" ry=\"37.45\"/>\n",
+       "<text text-anchor=\"middle\" x=\"65\" y=\"-87.78\" font-family=\"Times,serif\" font-size=\"14.00\">y</text>\n",
+       "<text text-anchor=\"middle\" x=\"65\" y=\"-72.78\" font-family=\"Times,serif\" font-size=\"14.00\">~</text>\n",
+       "<text text-anchor=\"middle\" x=\"65\" y=\"-57.78\" font-family=\"Times,serif\" font-size=\"14.00\">Gamma</text>\n",
+       "</g>\n",
+       "<!-- w&#45;&gt;y -->\n",
+       "<g id=\"edge1\" class=\"edge\">\n",
+       "<title>w&#45;&gt;y</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M65,-160.79C65,-149.38 65,-136.65 65,-124.63\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"68.5,-124.31 65,-114.31 61.5,-124.31 68.5,-124.31\"/>\n",
+       "</g>\n",
+       "</g>\n",
+       "</svg>\n"
+      ],
       "text/plain": [
        "<graphviz.graphs.Digraph at 0x7f31ae9c47f0>"
       ]
@@ -272,7 +310,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "9aa885a3",
    "metadata": {},
@@ -292,13 +329,7 @@
      "text": [
       "Multiprocess sampling (4 chains in 4 jobs)\n",
       "PGBART: [w]\n",
-      "PGBART: [w]\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
+      "PGBART: [w]\n",
       "Sampling 4 chains for 1_000 tune and 1_000 draw iterations (4_000 + 4_000 draws total) took 136 seconds.\n",
       "The rhat statistic is larger than 1.01 for some parameters. This indicates problems during sampling. See https://arxiv.org/abs/1903.08008 for details\n"
      ]
@@ -313,7 +344,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "eba7cee5",
    "metadata": {},
@@ -392,7 +422,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "d1775acb",
    "metadata": {},
@@ -401,7 +430,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "b743d58b-2678-4e17-9947-a8fe4ed03e21",
    "metadata": {},
@@ -479,7 +507,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "pymc-examples-env",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -493,7 +521,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.10.0"
   },
   "vscode": {
    "interpreter": {

examples/case_studies/bart_heteroscedasticity.ipynb

@@ -5,7 +5,7 @@ jupytext:
     format_name: myst
     format_version: 0.13
 kernelspec:
-  display_name: pymc-examples-env
+  display_name: Python 3 (ipykernel)
   language: python
   name: python3
 ---
@@ -14,9 +14,9 @@ kernelspec:
 # Modeling Heteroscedasticity with BART
 
 :::{post} January, 2023
-:tags: bart regression 
+:tags: BART, regression
 :category: beginner, reference
-:author: [Juan Orduz](https://juanitorduz.github.io/)
+:author: Juan Orduz
 :::
 
 +++

examples/case_studies/bart_heteroscedasticity.myst.md

@@ -75,6 +75,9 @@ def setup(app: Sphinx):
     "logo": {
         "link": "https://www.pymc.io",
     },
+    "article_header_end": ["nb-badges"],
+    "show_prev_next": True,
+    "article_footer_items": ["rendered_citation.html"],
 }
 version = os.environ.get("READTHEDOCS_VERSION", "")
 version = version if "." in version else "main"
@@ -118,6 +121,7 @@ def setup(app: Sphinx):
     "contributors": ("PyMC Contributors", "https://docs.pymc.io"),
 }
 blog_default_author = "contributors"
+post_show_prev_next = False
 fontawesome_included = True
 # post_redirect_refresh = 1
 # post_auto_image = 1

examples/conf.py

@@ -4,7 +4,7 @@ pymc-sphinx-theme==0.13
 sphinx-design
 sphinx-copybutton
 sphinxcontrib-bibtex
-ablog
+ablog<0.11
 sphinxext-opengraph
 sphinx-codeautolink
 sphinx-notfound-page