v1.3.1 (greenelab#289)

Closes greenelab#288 Closes greenelab#287 Closes greenelab#285 New template version checklist: - [x] I have updated CITATION and CHANGELOG as appropriate. - [x] I have updated lab-website-template-docs as appropriate. - [x] I have checked the testbed as appropriate. --- - use latest major version of setup-ruby gh-action - run "commit cache" step if citations step fails so that progress (successful citations) will be saved - replace xml_escape filter with appropriate escapes for each situation, and slightly modify regex_strip filter to allow some basic punctuation
stajichlab · Nov 13, 2024 · 2849c60 · 2849c60
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commit 2849c60
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diff --git a/.github/workflows/build-preview.yaml b/.github/workflows/build-preview.yaml
@@ -32,7 +32,7 @@ jobs:
 
       - name: Install Ruby packages
         if: github.event.action != 'closed'
-        uses: ruby/setup-ruby@v1.172.0
+        uses: ruby/setup-ruby@v1
         with:
           ruby-version: "3.1"
           bundler-cache: true

diff --git a/.github/workflows/build-site.yaml b/.github/workflows/build-site.yaml
@@ -27,7 +27,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Install Ruby packages
-        uses: ruby/setup-ruby@v1.172.0
+        uses: ruby/setup-ruby@v1
         with:
           ruby-version: "3.1"
           bundler-cache: true

diff --git a/.github/workflows/update-citations.yaml b/.github/workflows/update-citations.yaml
@@ -60,6 +60,13 @@ jobs:
         run: python _cite/cite.py
         timeout-minutes: 15
 
+      - name: Commit cache
+        if: failure()
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          file_pattern: "**/.cache/**"
+          commit_message: "Commit cache"
+
       - name: Check if citations changed
         if: github.event.action != 'closed'
         id: changed

diff --git a/.gitignore b/.gitignore
@@ -5,8 +5,6 @@ _site
 vendor
 debug.log
 __pycache__
-.cache
-!cache.db
 .DS_STORE
 .env*
 package.json

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,13 @@
 
 Reference: common-changelog.org
 
+## 1.3.1 - 2024-11-11
+
+### Changed
+
+- Update and improve workflows for building site and citations
+- Escape user inputs better in rare edge cases
+
 ## 1.3.0 - 2024-08-16
 
 ### Changed

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,8 +1,8 @@
 # citation metadata for the template itself
 
 title: "Lab Website Template"
-version: 1.3.0
-date-released: 2024-08-16
+version: 1.3.1
+date-released: 2024-11-11
 url: "https://github.com/greenelab/lab-website-template"
 authors:
   - family-names: "Rubinetti"

diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db
diff --git a/_includes/button.html b/_includes/button.html
@@ -13,7 +13,7 @@
       {% if include.flip %}
         data-flip
       {% endif %}
-      aria-label="{{ button.tooltip | default: button.icon | default: "button" | xml_escape }}"
+      aria-label="{{ button.tooltip | default: button.icon | default: "button" | regex_strip }}"
     >
       {% include icon.html icon=button.icon %}
       {% if button.text and button.text != "" %}

diff --git a/_includes/card.html b/_includes/card.html
@@ -2,14 +2,14 @@
 <div class="card" data-style="{{ include.style }}">
   <a
     {% if include.link %}
-      href="{{ include.link | relative_url | xml_escape }}"
+      href="{{ include.link | relative_url | uri_escape }}"
     {% endif %}
-    aria-label="{{ include.title | default: "card link" | xml_escape }}"
+    aria-label="{{ include.title | default: "card link" | regex_strip }}"
     class="card-image"
   >
     <img
-      src="{{ include.image | relative_url | xml_escape }}"
-      alt="{{ include.title | default: "card image" | xml_escape }}"
+      src="{{ include.image | relative_url | uri_escape }}"
+      alt="{{ include.title | default: "card image" | regex_strip }}"
       loading="lazy"
       {% include fallback.html %}
     >
@@ -19,7 +19,7 @@
     {% if include.title %}
       <a
         {% if include.link %}
-          href="{{ include.link | relative_url | xml_escape }}"
+          href="{{ include.link | relative_url | uri_escape }}"
         {% endif %}
         {% if include.tooltip %}
           data-tooltip="{{ include.tooltip | xml_escape }}"

diff --git a/_includes/citation.html b/_includes/citation.html
@@ -13,14 +13,14 @@
     {% if include.style == "rich" %}
       <a
         {% if citation.link %}
-          href="{{ citation.link | relative_url | xml_escape }}"
+          href="{{ citation.link | relative_url | uri_escape }}"
         {% endif %}
         class="citation-image"
-        aria-label="{{ citation.title | default: "citation link" | xml_escape }}"
+        aria-label="{{ citation.title | default: "citation link" | regex_strip }}"
       >
         <img
-          src="{{ citation.image | relative_url | xml_escape }}"
-          alt="{{ citation.title | default: "citation image" | xml_escape }}"
+          src="{{ citation.image | relative_url | uri_escape }}"
+          alt="{{ citation.title | default: "citation image" | regex_strip }}"
           loading="lazy"
           {% include fallback.html %}
         >

diff --git a/_includes/content.html b/_includes/content.html
@@ -24,7 +24,7 @@
       data-dark="{{ dark }}"
     {% endif %}
     {% if background %}
-      style="--image: url('{{ image | relative_url | xml_escape }}')"
+      style="--image: url('{{ image | relative_url | uri_escape }}')"
     {% endif %}
   >
     {{ section }}

diff --git a/_includes/feature.html b/_includes/feature.html
@@ -6,15 +6,15 @@
 >
   <a
     {% if include.link %}
-      href="{{ include.link | relative_url | xml_escape }}"
+      href="{{ include.link | relative_url | uri_escape }}"
     {% endif %}
     class="feature-image"
-    aria-label="{{ include.title | default: "feature link" | xml_escape }}"
+    aria-label="{{ include.title | default: "feature link" | regex_strip }}"
   >
     <img
-      src="{{ include.image | relative_url | xml_escape }}"
+      src="{{ include.image | relative_url | uri_escape }}"
       loading="lazy"
-      alt="{{ include.title | default: "feature image" | xml_escape }}"
+      alt="{{ include.title | default: "feature image" | regex_strip }}"
       {% include fallback.html %}
     >
   </a>

diff --git a/_includes/figure.html b/_includes/figure.html
@@ -1,18 +1,18 @@
 <figure class="figure">
   <a
     {% if include.link %}
-      href="{{ include.link | relative_url | xml_escape }}"
+      href="{{ include.link | relative_url | uri_escape }}"
     {% endif %}
     class="figure-image"
-    aria-label="{{ include.caption | default: "figure link" | xml_escape }}"
+    aria-label="{{ include.caption | default: "figure link" | regex_strip }}"
   >
     <img
-      src="{{ include.image | relative_url | xml_escape }}"
+      src="{{ include.image | relative_url | uri_escape }}"
       style="
         width: {{ include.width | default: "auto" }};
         max-height: {{ include.height | default: "unset" }};
       "
-      alt="{{ include.caption | default: "figure image" | xml_escape }}"
+      alt="{{ include.caption | default: "figure image" | regex_strip }}"
       loading="lazy"
       {% include fallback.html %}
     >

diff --git a/_includes/footer.html b/_includes/footer.html
@@ -3,7 +3,7 @@
 
 <footer
   class="background"
-  style="--image: url('{{ image | relative_url | xml_escape }}')"
+  style="--image: url('{{ image | relative_url | uri_escape }}')"
   {% if dark == true or dark == false %}
     data-dark="{{ dark }}"
   {% endif %}

diff --git a/_includes/header.html b/_includes/header.html
@@ -8,7 +8,7 @@
 
 <header
   class="background"
-  style="--image: url('{{ image | relative_url | xml_escape }}')"
+  style="--image: url('{{ image | relative_url | uri_escape }}')"
   {% if dark == true or dark == false %}
     data-dark="{{ dark }}"
   {% endif %}
@@ -22,7 +22,7 @@
         {% if svg %}
           {{ svg | file_read }}
         {% else %}
-          <img src="{{ logo | relative_url | xml_escape }}" alt="logo">
+          <img src="{{ logo | relative_url | uri_escape }}" alt="logo">
         {% endif %}
       </span>
     {% endif %}
@@ -48,7 +48,7 @@
     {% for page in pages %}
       {% if page.nav %}
         <a
-          href="{{ page.dir | relative_url | xml_escape }}"
+          href="{{ page.dir | relative_url | uri_escape }}"
           data-tooltip="{{ page.nav.tooltip | xml_escape }}"
         >
           {{ page.title }}

diff --git a/_includes/meta.html b/_includes/meta.html
@@ -1,8 +1,8 @@
 {% assign filename = page.path | split: "/" | last %}
 {% if page.name and page.name != filename %}
-  {% assign title = page.name | xml_escape %}
+  {% assign title = page.name %}
 {% elsif page.title %}
-  {% assign title = page.title | xml_escape %}
+  {% assign title = page.title %}
 {% else %}
   {% assign title = nil %}
 {% endif %}
@@ -14,11 +14,11 @@
 {% if site.title %}
   {% assign fulltitle = fulltitle | push: site.title %}
 {% endif %}
-{% assign fulltitle = fulltitle | join: " | " | xml_escape %}
+{% assign fulltitle = fulltitle | join: " | " %}
 
-{% assign subtitle = site.subtitle | xml_escape %}
+{% assign subtitle = site.subtitle %}
 
-{% assign description = page.description | default: site.description | xml_escape %}
+{% assign description = page.description | default: site.description %}
 {% if site.subtitle %}
   {% capture description -%}
     {{ site.subtitle }}. {{ description }}
@@ -47,24 +47,24 @@
 
 <link rel="icon" href="{{ icon }}">
 
-<meta name="title" content="{{ title }}">
-<meta name="description" content="{{ description }}">
+<meta name="title" content="{{ title | xml_escape }}">
+<meta name="description" content="{{ description | xml_escape }}">
 
-<meta property="og:title" content="{{ title }}">
-<meta property="og:site_title" content="{{ site.title }}">
-<meta property="og:description" content="{{ description }}">
+<meta property="og:title" content="{{ title | xml_escape }}">
+<meta property="og:site_title" content="{{ site.title | xml_escape }}">
+<meta property="og:description" content="{{ description | xml_escape }}">
 <meta property="og:url" content="{{ url }}">
 <meta property="og:image" content="{{ share }}">
 <meta property="og:locale" content="en_US">
 
-<meta property="twitter:title" content="{{ title }}">
-<meta property="twitter:description" content="{{ description }}">
+<meta property="twitter:title" content="{{ title | xml_escape }}">
+<meta property="twitter:description" content="{{ description | xml_escape }}">
 <meta property="twitter:url" content="{{ url }}">
 <meta property="twitter:card" content="summary_large_image">
 <meta property="twitter:image" content="{{ share }}">
 
 {% if page.author %}
-  <meta name="author" content="{{ page.author }}">
+  <meta name="author" content="{{ page | xml_escape.author }}">
   <meta property="og:type" content="article">
   <meta property="og:updated_time" content="{{ updated }}">
   <meta property="article:published_time" content="{{ published }}">

diff --git a/_includes/portrait.html b/_includes/portrait.html
@@ -12,18 +12,18 @@
 <div class="portrait-wrapper">
   <a
     {% if page.slug != member.slug %}
-      href="{{ member.url | relative_url | xml_escape }}"
+      href="{{ member.url | relative_url | uri_escape }}"
     {% endif %}
     class="portrait"
     data-style="{{ include.style }}"
-    aria-label="{{ member.name | default: "member link" | xml_escape }}"
+    aria-label="{{ member.name | default: "member link" | regex_strip }}"
   >
     {% if type %}
       {% include icon.html icon=type.icon %}
     {% endif %}
 
     <img
-      src="{{ member.image | relative_url | xml_escape }}"
+      src="{{ member.image | relative_url | uri_escape }}"
       class="portrait-image"
       alt="member portrait"
       loading="lazy"

diff --git a/_includes/post-excerpt.html b/_includes/post-excerpt.html
@@ -16,21 +16,21 @@
 
     {% if image %}
       <a
-        href="{{ url | relative_url | xml_escape }}"
+        href="{{ url | relative_url | uri_escape }}"
         class="post-excerpt-image"
-        aria-label="{{ title | default: "excerpt link" | xml_escape }}"
+        aria-label="{{ title | default: "excerpt link" | regex_strip }}"
       >
         <img
-          src="{{ image | relative_url | xml_escape }}"
-          alt="{{ title | default: "excerpt image" | xml_escape }}"
+          src="{{ image | relative_url | uri_escape }}"
+          alt="{{ title | default: "excerpt image" | regex_strip }}"
           loading="lazy"
           {% include fallback.html %}
         >
       </a>
     {% endif %}
 
     <div class="post-excerpt-text">
-      <a href="{{ url | relative_url | xml_escape }}">{{ title }}</a>
+      <a href="{{ url | relative_url | uri_escape }}">{{ title }}</a>
 
       {%
         include post-info.html
@@ -48,11 +48,10 @@
         | strip_html
       %}
       {% assign search = post.content
-        | strip_html 
         | strip_newlines
         | regex_strip
       %}
-      <p data-search="{{ search | xml_escape }}">
+      <p data-search="{{ search }}">
         {{ excerpt }}
       </p>
     </div>

diff --git a/_includes/post-nav.html b/_includes/post-nav.html
@@ -2,15 +2,15 @@
   <span>
     {% if include.post.previous %}
       {% include icon.html icon="fa-solid fa-angle-left" %} Previous post<br>
-      <a href="{{ include.post.previous.url | relative_url | xml_escape }}">
+      <a href="{{ include.post.previous.url | relative_url }}">
         {{ include.post.previous.title }}
       </a>
     {% endif %}
   </span>
   <span>
     {% if include.post.next %}
       Next post {% include icon.html icon="fa-solid fa-angle-right" %}<br>
-      <a href="{{ include.post.next.url | relative_url | xml_escape }}">
+      <a href="{{ include.post.next.url | relative_url }}">
         {{ include.post.next.title }}
       </a>
     {% endif %}

diff --git a/_layouts/member.html b/_layouts/member.html
@@ -33,7 +33,7 @@
 {%- endcapture %}
 
 <p class="center">
-  <a href="{{ search | relative_url | xml_escape }}">
+  <a href="{{ search | relative_url | uri_escape }}">
     Search for {{ page.name | default: page.title }}'s papers on the Research page
   </a>
 </p>
@@ -44,7 +44,7 @@
 
 <!--
 <p class="center">
-  <a href="{{ search | relative_url | xml_escape }}">
+  <a href="{{ search | relative_url | uri_escape }}">
     See {{ page.name | default: page.title }}'s posts on the Blog page
   </a>
 </p>

diff --git a/_plugins/regex.rb b/_plugins/regex.rb
@@ -20,7 +20,7 @@ def regex_replace(string, search, replace)
 
     # strip all non-letter and non-number characters from string
     def regex_strip(string)
-      return string.gsub(/[^\p{L}\p{N}]/u, " ")
+      return string.gsub(/[^\p{L}\p{N}.,;:-]/u, " ").gsub(/\s+/, " ").strip
     end
   end
 end