Use variables

FAQ.qmd

@@ -10,6 +10,6 @@ This notebook publication (or "notebook pub") is an experimental format we're te
 
 There is a comment section at the bottom of the [pub](index.ipynb), where you can read and contribute to any community discussion. Note that commenting requires a GitHub account and authorizing Giscus, a GitHub Discussions widget.
 
-## 3. Can I join?
+## 3. How can I contribute?
 
 We welcome improvements to this publication! Please see our guide for [contributing](CONTRIBUTING.qmd).

_quarto.yml

@@ -8,15 +8,14 @@ website:
   favicon: assets/logo_white.png # https://quarto.org/docs/websites/website-tools.html#favicon
   twitter-card: true # https://quarto.org/docs/websites/website-tools.html#twitter-cards
   open-graph: true # https://quarto.org/docs/websites/website-tools.html#open-graph
-  title: "Arcadia Science"
   navbar:
     title: false
     left:
       - text: "{{< iconify qlementine-icons:version-control-16 >}}"
         menu:
           - text: latest
             href: index.ipynb
-      - text: Paired residue prediction dependencies in ESM2
+      - text: "{{< var pub.title >}}"
         href: index.ipynb
     right:
       - text: FAQ
@@ -27,7 +26,7 @@ website:
       - icon: twitter-x
         href: https://twitter.com/arcadiascience
       - icon: github
-        href: https://github.com/Arcadia-Science/notebook-pub-template
+        href: https://github.com/{{< var pub.repo >}}
     logo: assets/logo_text.png
     logo-href: https://www.arcadiascience.com/
     background: white
@@ -42,7 +41,7 @@ website:
       - icon: twitter-x
         href: https://twitter.com/arcadiascience
       - icon: github
-        href: https://github.com/Arcadia-Science/notebook-pub-template
+        href: https://github.com/{{< var pub.repo >}}
 format:
   html:
     include-in-header:
@@ -53,5 +52,5 @@ format:
     toc: true
 comments:
   giscus:
-    repo: Arcadia-Science/notebook-pub-template
+    repo: "{{< var pub.repo >}}"
     input-position: top

_variables.yml

@@ -0,0 +1,3 @@
+pub:
+  repo: "Arcadia-Science/notebook-pub-template"
+  title: "Notebook pub template demo"

assets/logo-animation.html

@@ -10,7 +10,7 @@
     video.muted = true;
     video.playsInline = true;
     video.loop = false;
-    video.playbackRate = 0.8;
+    video.playbackRate = 1.0;
 
     const source = document.createElement("source");
 

index.ipynb

@@ -10,13 +10,13 @@
    },
    "source": [
     "---\n",
-    "title: Paired residue prediction dependencies in ESM2\n",
+    "title: \"{{< var pub.title >}}\"\n",
     "author:\n",
     "  - name: Evan Kiefl\n",
     "    orcid: 0000-0002-6473-0921\n",
     "    corresponding: true\n",
     "    email: evan.kiefl@arcadiascience.com\n",
-    "date: 'December 17, 2024'\n",
+    "date: 'January 1, 2025'\n",
     "reference-location: margin\n",
     "bibliography: ref.bib\n",
     "csl: assets/arcadia.csl\n",
@@ -31,6 +31,35 @@
    "source": [
     "## Introduction\n",
     "\n",
+    "This is a template notebook that once edited by you, will become your publication.\n",
+    "\n",
+    "To see how a live preview of how the notebook renders into a publication, follow the instructions in the `README.md` (spoiler: `make preview`). And to view the published version of this template see [here](https://arcadia-science.github.io/notebook-pub-template/).\n",
+    "\n",
+    "## Getting started\n",
+    "\n",
+    "If you already have a notebook, replace this file with it. While a this will properly render (`make preview`)\n",
+    "\n",
+    "## Quarto Resources\n",
+    "\n",
+    "\n",
+    "\n",
+    "## Examples\n",
+    "\n",
+    "\n",
+    "\n",
+    "If you already have a notebook, you . Follow the instructions\n",
+    "\n",
+    "See the [README.md](https://github.com/Arcadia-Science/notebook-pub-template/blob/main/index.ipynb)\n",
+    "\n",
+    "The Arcadia template.\n",
+    "\n",
+    "[Quarto](https://quarto.org/) is a technical publishing system that can render Jupyter notebooks, R Markdown documents, and other file formats into stylistically rendered documents render for publication.\n",
+    "\n",
+    "\n",
+    "This short demo examples some of the features at your disposal. You can see how it's published here: [https://arcadia-science.github.io/notebook-pub-template/](https://arcadia-science.github.io/notebook-pub-template/).\n",
+    "\n",
+    "\n",
+    "\n",
     "This notebook details a quick analysis we performed on the ESM2 (Evolutionary Scale Modeling) model for masked token prediction. We stumbled upon a counter-intuitive result related to the effect that masking one residue has on the distribution of another.\n",
     "\n",
     "Before jumping into our results, let's first establish what masked token prediction is, how it works, and our consequent motivation for this analysis.\n",