datalog-theme 0.7.0 → 0.9.0

data/_includes/scripts.html

@@ -31,6 +31,55 @@
   {% assign academic_flag = 'false' %}
 {% endif %}
 
+{% if site.theme_options.reading_state.enabled == false %}
+  {% assign reading_state_flag = 'false' %}
+{% else %}
+  {% assign reading_state_flag = 'auto' %}
+{% endif %}
+
+{%- comment -%} The correction-report form needs a backend with the feature on (components/correction-report.html). {%- endcomment -%}
+{% assign corrections_flag = 'false' %}
+{% if site.dynamic_services.base_url and site.dynamic_services.base_url != '' and site.dynamic_services.features.corrections != false and site.corrections.enabled != false %}
+  {% assign corrections_flag = 'auto' %}
+{% endif %}
+
+{%- comment -%} The contact form likewise (components/contact-form.html). {%- endcomment -%}
+{% assign contact_flag = 'false' %}
+{% if site.dynamic_services.base_url and site.dynamic_services.base_url != '' and site.dynamic_services.features.contact != false and site.contact.enabled != false %}
+  {% assign contact_flag = 'auto' %}
+{% endif %}
+
+{%- comment -%} The comments thread of the api provider (components/comments-thread.html), site-wide or for this page. {%- endcomment -%}
+{% assign comments_flag = 'false' %}
+{% assign comments_options = site.datalog_plugins.options['datalog-comments'] %}
+{% if comments_options.provider == 'api' or page.datalog_comments.provider == 'api' %}
+  {% assign comments_flag = 'auto' %}
+{% endif %}
+
+{%- comment -%} "Was this useful?" needs a backend with the feature on (components/reactions.html). {%- endcomment -%}
+{% assign reactions_flag = 'false' %}
+{% if site.dynamic_services.base_url and site.dynamic_services.base_url != '' and site.dynamic_services.features.reactions != false and site.reactions.enabled != false %}
+  {% assign reactions_flag = 'auto' %}
+{% endif %}
+
+{%- comment -%} "Mentioned elsewhere" needs a backend with the feature on (components/webmentions.html). {%- endcomment -%}
+{% assign webmentions_flag = 'false' %}
+{% if site.dynamic_services.base_url and site.dynamic_services.base_url != '' and site.dynamic_services.features.webmentions != false and site.webmentions.enabled != false %}
+  {% assign webmentions_flag = 'auto' %}
+{% endif %}
+
+{%- comment -%} The newsletter form and its manage page need a backend with the feature on (components/subscribe-form.html). {%- endcomment -%}
+{% assign subscriptions_flag = 'false' %}
+{% if site.dynamic_services.base_url and site.dynamic_services.base_url != '' and site.dynamic_services.features.subscriptions != false and site.subscriptions.enabled != false %}
+  {% assign subscriptions_flag = 'auto' %}
+{% endif %}
+
+{%- comment -%} The moderation inbox is off unless the site turns it on (components/moderation-inbox.html). {%- endcomment -%}
+{% assign moderation_flag = 'false' %}
+{% if site.moderation.enabled == true %}
+  {% assign moderation_flag = 'auto' %}
+{% endif %}
+
 <script nonce="{{ page.csp_nonce }}">
   (function () {
     const body = document.body;
@@ -42,6 +91,14 @@
     body.dataset.featureMath = "{{ math_flag }}";
     body.dataset.featureNotebook = "{{ notebook_flag }}";
     body.dataset.featureAcademic = "{{ academic_flag }}";
+    body.dataset.featureReadingState = "{{ reading_state_flag }}";
+    body.dataset.featureCorrections = "{{ corrections_flag }}";
+    body.dataset.featureContact = "{{ contact_flag }}";
+    body.dataset.featureComments = "{{ comments_flag }}";
+    body.dataset.featureReactions = "{{ reactions_flag }}";
+    body.dataset.featureWebmentions = "{{ webmentions_flag }}";
+    body.dataset.featureSubscriptions = "{{ subscriptions_flag }}";
+    body.dataset.featureModeration = "{{ moderation_flag }}";
   })();
 </script>
 

data/_includes/search/index-data.json

@@ -2,6 +2,7 @@
   "generated_at": "{{ 'now' | date_to_xmlschema }}",
   "documents": [
     {% assign known_langs = 'python,r,sql,julia,javascript,scala,go,java,typescript,html,css' | split: ',' %}
+    {% assign no_code = '' | split: '' %}
     {% assign searchable = '' | split: '' %}
     {% for post in site.posts %}
       {% unless post.exclude_from_search %}
@@ -76,37 +77,19 @@
       {% capture doc_type %}
         {% if doc.collection == 'posts' %}post{% elsif doc.collection == 'portfolio' %}project{% elsif doc.collection == 'datasets' %}dataset{% elsif doc.layout == 'research' %}research{% elsif doc.layout == 'project' %}project{% elsif doc.layout == 'post' %}post{% else %}{{ doc.collection | default: doc.layout | default: 'page' }}{% endif %}
       {% endcapture %}
-      {% assign normalized_title = doc.title | default: doc.name | normalize_search %}
-      {% assign normalized_summary = summary | normalize_search %}
-      {% assign normalized_content = content_text | normalize_search %}
-      {% assign normalized_tags = tags | normalize_search_array %}
-      {% assign normalized_languages = languages | normalize_search_array %}
-      {% assign normalized_difficulty = doc.difficulty | default: doc.level | normalize_search | default: '' %}
+      {%- comment -%}
+      Each text field is written once. The search engine normalizes it in the browser with the
+      function it applies to queries; a precomputed normalized copy doubled the size of the file.
+      The code blocks come from the page's source, collected before rendering by
+      _plugins/search_code_blocks.rb: by the time this renders, a post's content is already HTML.
+      {%- endcomment %}
       {
         "title": {{ doc.title | default: doc.name | jsonify }},
         "url": {{ doc.url | relative_url | jsonify }},
         "type": {{ doc_type | strip | jsonify }},
         "summary": {{ summary | strip | jsonify }},
         "content": {{ content_text | jsonify }},
-        "code": [
-          {% assign raw_blocks = raw_content | split: '```' %}
-          {% assign code_counter = 0 %}
-          {% for block in raw_blocks %}
-            {% assign block_index = forloop.index0 | modulo: 2 %}
-            {% if block_index == 1 %}
-              {% assign lines = block | split: '\n' %}
-              {% assign first_line = lines[0] | default: '' %}
-              {% assign language_hint = first_line | strip | downcase | default: 'text' %}
-              {% assign code_body = block | remove_first: first_line | strip %}
-              {% if code_counter > 0 %},{% endif %}
-              {
-                "language": {{ language_hint | jsonify }},
-                "code": {{ code_body | jsonify }}
-              }
-              {% assign code_counter = code_counter | plus: 1 %}
-            {% endif %}
-          {% endfor %}
-        ],
+        "code": {{ doc.search_code | default: no_code | jsonify }},
         "math": [
           {% assign math_counter = 0 %}
           {% for piece in inline_math_segments %}
@@ -137,15 +120,7 @@
         "difficulty": {{ doc.difficulty | default: doc.level | default: '' | jsonify }},
         "topics": {{ doc.topics | default: tags | uniq | jsonify }},
         "date": {% if doc.date %}{{ doc.date | date_to_xmlschema | jsonify }}{% else %}null{% endif %},
-        "reading_time": {{ doc.reading_time | default: doc.time | default: '' | jsonify }},
-        "normalized": {
-          "title": {{ normalized_title | jsonify }},
-          "summary": {{ normalized_summary | jsonify }},
-          "content": {{ normalized_content | jsonify }},
-          "tags": {{ normalized_tags | uniq | jsonify }},
-          "languages": {{ normalized_languages | uniq | jsonify }},
-          "difficulty": {{ normalized_difficulty | jsonify }}
-        }
+        "reading_time": {{ doc.reading_time | default: doc.time | default: '' | jsonify }}
         {% assign search_extensions = doc.datalog_search_extensions %}
         {% if search_extensions and search_extensions != empty %}
         ,"extensions": {{ search_extensions | jsonify }}

data/_layouts/dataset.html

@@ -1,5 +1,6 @@
 ---
 layout: default
+show_title: false # this layout renders the page's <h1>
 ---
 {% assign localization_config = site.theme_options.localization %}
 {% assign date_format = page.date_format | default: localization_config.date_format | default: 'long' %}
@@ -7,7 +8,8 @@ layout: default
   <header class="dataset-header">
     <h1>{{ page.title }}</h1>
     {% if page.updated %}<p class="dataset-meta"><strong>{% t 'dataset.last_updated' %}</strong> {{ page.updated | localize_date: date_format }}</p>{% endif %}
-    {% if page.license %}<p class="dataset-meta"><strong>{% t 'dataset.license' %}</strong> {{ page.license }}</p>{% endif %}
+    {% assign dataset_license = page | page_license %}
+    {% if dataset_license %}<p class="dataset-meta"><strong>{% t 'dataset.license' %}</strong> {% include components/license-link.html license=dataset_license %}</p>{% endif %}
   </header>
   <div class="dataset-summary">
     {{ page.summary | default: page.excerpt }}
@@ -44,9 +46,9 @@ layout: default
     </section>
   {% endif %}
   {% assign citation_key = page.citation_key | default: page.slug | default: page.title | slugify %}
-  {% assign citation_authors = page.authors | default: page.author | default: site.author.name %}
+  {% assign citation_authors = page | page_authors %}
   {% assign citation_date = page.date | default: page.updated %}
   {% assign citation_url = page.url | absolute_url %}
-  {% include components/citation-tools.html title=page.title authors=citation_authors date=citation_date url=citation_url citation_key=citation_key publisher=site.author.affiliation citation_type='dataset' doi=page.doi %}
+  {% include components/citation-tools.html title=page.title authors=citation_authors date=citation_date url=citation_url citation_key=citation_key citation_type='dataset' doi=page.doi %}
   {% include components/open-science-badges.html %}
 </article>

data/_layouts/default.html

@@ -8,25 +8,33 @@
   <head>
     {% include head.html %}
     <meta name="twitter:creator" content="{{ site.author.twitter | default: site.social.twitter }}" />
-    {% if page.tags and page.tags.size > 0 %}
-      <meta name="keywords" content="{% include helpers/array-to-sentence.html items=page.tags conjunction='and' %}" />
-    {% endif %}
-    <meta name="format-detection" content="telephone=no" />
-    <link rel="preconnect" href="https://cdn.jsdelivr.net" crossorigin />
     {% include meta/schema.html page=page %}
-    {% include meta/scripts-loader.html location='head' %}
   </head>
   {% capture body_classes %}
     site-body{% if page.layout %} layout-{{ page.layout | replace: ' ', '-' }}{% endif %}{% if page.page_class %} page-{{ page.page_class | replace: ' ', '-' | downcase }}{% endif %}{% if page.classes %} {{ page.classes | join: ' ' }}{% endif %}{% if site.features.dark_mode_toggle %} has-dark-toggle{% endif %}{% if html_dir == 'rtl' %} rtl{% endif %}
   {% endcapture %}
   <body class="{{ body_classes | strip }}" data-theme="{{ page.theme | default: 'system' }}">
-    {% include skip-link.html %}
+    {%- comment -%}
+    Applies the saved or system color scheme before anything is drawn. core/dark-mode.js
+    applies the same rule, but only once the script bundles have loaded, so readers who
+    chose dark saw the light theme first; keep the two in step.
+    {%- endcomment %}
+    <script nonce="{{ page.csp_nonce }}">
+      try {
+        var mode = localStorage.getItem("datalog-color-mode");
+        if (mode === "dark" || (mode !== "light" && window.matchMedia("(prefers-color-scheme: dark)").matches)) {
+          document.body.classList.add("dark-mode");
+        }
+      } catch (error) {}
+    </script>
+    {%- comment -%} The skip link and the footer take nothing from the page, so each is rendered once per build (the skip link once per language). {%- endcomment -%}
+    {% include_cached skip-link.html lang=page.lang %}
     {% include header.html %}
     <main id="main-content" class="site-main container" role="main" tabindex="-1" aria-describedby="{{ math_status_id }}">
       {% include components/math-fallback.html expressions=page.math_expressions %}
       {% include layouts/default/article.html page=page content=content date_format=date_format %}
     </main>
-    {% include footer.html %}
+    {% include_cached footer.html lang=page.lang %}
     <div class="visually-hidden" aria-live="polite" id="{{ math_status_id }}">{% t 'global.math_loading' %}</div>
     {% include meta/scripts-loader.html location='body' %}
   </body>

data/_layouts/notebook.html

@@ -1,5 +1,6 @@
 ---
 layout: default
+show_title: false # this layout renders the page's <h1>
 ---
 
 {%- comment -%}

data/_layouts/package.html

@@ -1,5 +1,6 @@
 ---
 layout: default
+show_title: false # this layout renders the page's <h1>
 ---
 
 <div class="package-docs">
@@ -223,13 +224,14 @@ layout: default
     observer.observe(heading);
   });
 
-  // Smooth scroll for anchor links
+  // Scroll to anchor targets. The stylesheet's scroll-behavior decides whether
+  // the scroll is smooth, so reduced-motion preferences are respected.
   document.querySelectorAll('.package-nav__link[href^="#"]').forEach(link => {
     link.addEventListener('click', (e) => {
       e.preventDefault();
       const target = document.querySelector(link.getAttribute('href'));
       if (target) {
-        target.scrollIntoView({ behavior: 'smooth', block: 'start' });
+        target.scrollIntoView({ block: 'start' });
         history.pushState(null, null, link.getAttribute('href'));
       }
     });

data/_layouts/page.html

@@ -11,6 +11,21 @@ layout: default
     {% endif %}
     <div class="page-content">
       {{ content }}
+      {%- if page.contact_form %}
+      {%- comment -%} The contact and collaboration form, or the email address without a backend {%- endcomment %}
+      {% include components/contact-form.html %}
+      {%- endif %}
+      {%- if page.subscription_manage %}
+      {%- comment -%} Where the newsletter's emails lead: confirm, change topics, unsubscribe {%- endcomment %}
+      {% include components/subscription-manage.html %}
+      {%- endif %}
+      {%- if page.subscribe_form %}
+      {% include components/subscribe-form.html where='page' %}
+      {%- endif %}
+      {%- if page.moderation_inbox %}
+      {%- comment -%} The moderation inbox: a shell; the service authenticates every request {%- endcomment %}
+      {% include components/moderation-inbox.html %}
+      {%- endif %}
     </div>
   </div>
 </section>

data/_layouts/portfolio.html

@@ -1,5 +1,6 @@
 ---
 layout: default
+show_title: false # this layout renders the page's <h1>
 ---
 <article class="portfolio-item">
   <header class="portfolio-header">

data/_layouts/post.html

@@ -34,8 +34,8 @@ schema_type: TechnicalArticle
 
 {%- comment -%} Canonical URL & author info {%- endcomment -%}
 {% assign canonical_url = page.url | absolute_url %}
-{% assign author_name = page.author | default: site.author.name %}
-{% assign author_affiliation = page.author_affiliation | default: site.author.affiliation %}
+{% assign authors = page | page_authors %}
+{% assign contributors = page | page_contributors %}
 
 {%- comment -%} Tag/Category flags {%- endcomment -%}
 {% assign post_tags = page.tags %}
@@ -56,8 +56,8 @@ schema_type: TechnicalArticle
   {% if page.last_modified_at or page.updated %}
     <meta itemprop="dateModified" content="{{ page.last_modified_at | default: page.updated | date_to_xmlschema }}" />
   {% endif %}
-  <meta itemprop="author" content="{{ author_name }}" />
-  <meta itemprop="publisher" content="{{ site.author.affiliation | default: site.title }}" />
+  {% include meta/publisher.html %}
+  <meta itemprop="publisher" content="{{ publisher_name | escape }}" />
   <meta itemprop="timeRequired" content="{{ time_required }}" />
   {% if difficulty %}<meta itemprop="learningResourceType" content="{{ difficulty }}" />{% endif %}
   {% if has_tags %}<meta itemprop="keywords" content="{{ post_tags | join: ', ' }}" />{% endif %}
@@ -69,17 +69,28 @@ schema_type: TechnicalArticle
         <dt class="post-meta-term">{% t 'post.meta.published' %}</dt>
         <dd class="post-meta-definition">{{ page.date | localize_date: date_format }}</dd>
       </div>
+      {%- comment -%} The last change, when it fell on another day than the publication {%- endcomment -%}
+      {% assign modified = page.last_modified_at | default: page.updated %}
+      {% if modified %}
+        {% assign modified_day = modified | date: '%F' %}
+        {% assign published_day = page.date | date: '%F' %}
+        {% if modified_day != published_day %}
+          <div>
+            <dt class="post-meta-term">{% t 'post.meta.updated' %}</dt>
+            <dd class="post-meta-definition">{{ modified | localize_date: date_format }}</dd>
+          </div>
+        {% endif %}
+      {% endif %}
       <div>
-        <dt class="post-meta-term">{% t 'post.meta.author' %}</dt>
-        <dd class="post-meta-definition">
-          <span itemprop="author" itemscope itemtype="https://schema.org/Person">
-            <span itemprop="name">{{ author_name }}</span>
-            {% if author_affiliation %}
-              <span class="post-author-affiliation" itemprop="affiliation">{{ author_affiliation }}</span>
-            {% endif %}
-          </span>
-        </dd>
+        <dt class="post-meta-term">{% if authors.size > 1 %}{% t 'post.meta.authors' %}{% else %}{% t 'post.meta.author' %}{% endif %}</dt>
+        <dd class="post-meta-definition">{% include components/author-list.html people=authors %}</dd>
       </div>
+      {% if contributors.size > 0 %}
+        <div>
+          <dt class="post-meta-term">{% t 'post.meta.contributors' %}</dt>
+          <dd class="post-meta-definition">{% include components/author-list.html people=contributors property='contributor' %}</dd>
+        </div>
+      {% endif %}
       <div>
         <dt class="post-meta-term">{% t 'post.meta.reading_time' %}</dt>
         <dd class="post-meta-definition"><span data-reading-time>{{ reading_label }}</span></dd>
@@ -111,6 +122,16 @@ schema_type: TechnicalArticle
     </dl>
   </section>
 
+  {%- comment -%} The reader's tools: save for later and reading mode; and the article's address on paper {%- endcomment -%}
+  <div class="post-tools">
+    {% include components/reading-state-bookmark.html %}
+    {% include components/reading-mode-toggle.html %}
+  </div>
+  <p class="post-print-source print-only">{% t 'post.print.source' %} {{ canonical_url }}{% if page.doi %} · DOI {{ page.doi | escape }}{% endif %}</p>
+
+  {%- comment -%} The newest correction or update, with a link to the revision history {%- endcomment -%}
+  {% include components/revision-notice.html page=page date_format=date_format %}
+
   {% if has_tags or has_categories %}
     <section class="post-taxonomy" aria-labelledby="post-taxonomy-heading">
       <h2 id="post-taxonomy-heading" class="visually-hidden">{% t 'post.topics_heading' %}</h2>
@@ -134,6 +155,9 @@ schema_type: TechnicalArticle
   {%- comment -%} Editorial provenance (why_this_exists, evidence, methodology, reviewed_at) {%- endcomment -%}
   {% include components/content-provenance.html page=page date_format=date_format %}
 
+  {%- comment -%} The article's series: every part in order, and the previous and next ones {%- endcomment -%}
+  {% include components/series-nav.html page=page %}
+
   {%- comment -%} Enhanced social sharing {%- endcomment -%}
   {% include components/social-share.html url=canonical_url title=page.title description=page.excerpt %}
 
@@ -148,6 +172,24 @@ schema_type: TechnicalArticle
     </div>
   </div>
 
+  {%- comment -%} The previous and next parts of the series, for a reader who has finished this one {%- endcomment -%}
+  {% include components/series-nav.html page=page compact=true %}
+
+  {%- comment -%} Was this useful? A reaction without a comment, on a site with a backend {%- endcomment -%}
+  {% include components/reactions.html %}
+
+  {%- comment -%} The reader's own: resume prompt, highlights and notes, kept in the browser {%- endcomment -%}
+  {% include components/reading-state-panel.html %}
+
+  {%- comment -%} The code, data and environment behind the analysis {%- endcomment -%}
+  {% include components/reproducibility.html page=page %}
+
+  {%- comment -%} Report an error: structured feedback to the author, on a site with a backend {%- endcomment -%}
+  {% include components/correction-report.html %}
+
+  {%- comment -%} What changed since publication (revisions in front matter) {%- endcomment -%}
+  {% include components/revision-history.html page=page date_format=date_format %}
+
   <section class="post-interactive" aria-label="{% t 'post.interactive.label' %}">
     {% if page.interactive_components and page.interactive_components.size > 0 %}
       <ul class="post-interactive-list">
@@ -195,22 +237,44 @@ schema_type: TechnicalArticle
     </section>
   {% endif %}
 
+  {%- comment -%} What other websites said about this article, apart from the comments hosted here {%- endcomment -%}
+  {% include components/webmentions.html %}
+
+  {%- comment -%} Reuse terms: the licence of the text and figures, and of the code samples {%- endcomment -%}
+  {% include components/license-notice.html page=page %}
+
   {%- comment -%} ===== Citation tools & badges ===== {%- endcomment -%}
   {% assign citation_key = page.citation_key | default: page.slug | default: page.title | slugify %}
-  {% assign citation_authors = page.authors | default: page.author | default: author_name %}
   {% include components/citation-tools.html
        title=page.title
-       authors=citation_authors
+       authors=authors
        date=page.date
        url=canonical_url
        citation_key=citation_key
-       publisher=site.author.affiliation
        citation_type='article'
        doi=page.doi %}
   {% include components/open-science-badges.html %}
 
-  {%- comment -%} Author bio card {%- endcomment -%}
-  {% include components/author-bio.html author=author_name %}
+  {%- comment -%}
+    Author cards: a full card for a single author, or for each author with
+    `author_cards: detailed`; a compact card each for several authors;
+    none with `author_cards: false`.
+  {%- endcomment -%}
+  {% unless page.author_cards == false %}
+    {% assign detailed_cards = false %}
+    {% if authors.size == 1 or page.author_cards == 'detailed' %}{% assign detailed_cards = true %}{% endif %}
+    {% for author in authors %}
+      {% if detailed_cards %}
+        {% include components/author-bio.html person=author %}
+      {% else %}
+        {% include components/author-bio.html person=author compact=true %}
+      {% endif %}
+    {% endfor %}
+  {% endunless %}
+
+  {%- comment -%} The newsletter form at the end of the article, when subscriptions.placement says so {%- endcomment -%}
+  {% assign subscribe_placement = site.subscriptions.placement | default: 'footer' %}
+  {% if subscribe_placement contains 'post' %}{% include components/subscribe-form.html where='post' %}{% endif %}
 
   {%- comment -%} ===== Robust related posts (no where_exp, no nil sort) ===== {%- endcomment -%}
   {% include post/related-posts.html page=page date_format=date_format %}
@@ -272,7 +336,12 @@ schema_type: TechnicalArticle
       const metaBar = document.createElement('div');
       metaBar.className = 'code-block-meta';
 
-      const lang = codeBlock.getAttribute('class');
+      // Rouge puts the language on the block's wrapper rather than on the code.
+      // With line numbers on, the code is a table whose first column holds the
+      // numbers, and the copy leaves them out.
+      const langHolder = codeBlock.matches('[class*="language-"]') ? codeBlock : codeBlock.closest('.highlighter-rouge');
+      const lang = langHolder && langHolder.getAttribute('class');
+      const source = codeBlock.querySelector('.rouge-code') || codeBlock;
       if (lang) {
         const m = lang.match(/language-([a-z0-9+#]+)/i);
         if (m) {
@@ -291,7 +360,7 @@ schema_type: TechnicalArticle
 
       if (navigator.clipboard && navigator.clipboard.writeText) {
         button.addEventListener('click', function () {
-          navigator.clipboard.writeText(codeBlock.textContent).then(function () {
+          navigator.clipboard.writeText(source.textContent).then(function () {
             button.textContent = 'Copied!';
             button.classList.add('is-copied');
             setTimeout(function () {
@@ -311,9 +380,19 @@ schema_type: TechnicalArticle
       wrapper.insertBefore(metaBar, pre);
     });
 
-    // Make equation references focus their targets for accessibility.
-    if (window.MathJax && window.MathJax.startup) {
-      window.MathJax.startup.promise.then(function () {
+    // Make equation references focus their targets for accessibility. This runs
+    // on DOMContentLoaded, before MathJax has loaded, when window.MathJax is
+    // still the configuration object and has no startup.promise; reading it
+    // threw. The head's MathJax configuration announces typeset math instead.
+    const onMathReady = function (callback) {
+      if (document.body.classList.contains('math-ready') && document.querySelector('mjx-container')) {
+        callback();
+      } else {
+        document.addEventListener('datalog:math-ready', callback, { once: true });
+      }
+    };
+    if (window.MathJax) {
+      onMathReady(function () {
         const equations = document.querySelectorAll('.post-content mjx-container[display="true"]');
         let eqIndex = 1;
         equations.forEach(function (container) {

data/_layouts/project.html

@@ -1,5 +1,6 @@
 ---
 layout: default
+show_title: false # this layout renders the page's <h1>
 ---
 {% assign localization_config = site.theme_options.localization %}
 {% assign date_format = localization_config.date_format | default: 'long' %}
@@ -30,7 +31,7 @@ layout: default
       {% if page.github %}
       <section class="project-case__github" aria-labelledby="github-heading">
         <h2 id="github-heading">{% t 'project.header.github_repository' %}</h2>
-        <div class="project-case__github-card" data-github-repo="{{ page.github.repo }}" data-github-owner="{{ page.github.owner }}">
+        <div class="project-case__github-card" data-github-repo="{{ page.github.repo }}" data-github-owner="{{ page.github.owner }}" data-github-unavailable="{% t 'project.github.unavailable' %}">
           <div class="project-case__github-meta">
             <p class="project-case__github-name">
               <a href="https://github.com/{{ page.github.owner }}/{{ page.github.repo }}" itemprop="url">{{ page.github.owner }}/{{ page.github.repo }}</a>
@@ -208,10 +209,10 @@ layout: default
   {% endif %}
 
   {% assign citation_key = page.citation_key | default: page.slug | default: page.title | slugify %}
-  {% assign citation_authors = page.authors | default: page.author | default: site.author.name %}
+  {% assign citation_authors = page | page_authors %}
   {% assign citation_date = page.date | default: page.last_updated %}
   {% assign citation_url = page.url | absolute_url %}
-  {% include components/citation-tools.html title=page.title authors=citation_authors date=citation_date url=citation_url citation_key=citation_key publisher=site.author.affiliation citation_type='software' doi=page.doi %}
+  {% include components/citation-tools.html title=page.title authors=citation_authors date=citation_date url=citation_url citation_key=citation_key citation_type='software' doi=page.doi %}
 
   {% include components/open-science-badges.html %}
 

data/_layouts/research.html

@@ -3,8 +3,7 @@ layout: default
 schema_type: ScholarlyArticle
 ---
 {% assign date_format = site.date_format | default: '%B %-d, %Y' %}
-{% assign authors_source = page.authors | default: page.author | default: site.author %}
-{% assign authors = authors_source | arrayify %}
+{% assign authors = page | page_authors %}
 {% assign publication_name = page.publication | default: page.journal | default: page.conference %}
 {% assign publication_status = page.publication_status | default: page.status %}
 {% assign doi = page.doi %}
@@ -20,7 +19,13 @@ schema_type: ScholarlyArticle
 {% assign methodology_content = page.methodology %}
 {% assign results_content = page.results %}
 {% assign data_availability = page.data_availability %}
-{% assign reproducibility = page.reproducibility | default: page.reproducibility_notes %}
+{%- comment -%} `reproducibility` is free text here, or a map of artifacts for the panel (components/reproducibility.html). {%- endcomment -%}
+{% capture reproducibility_shape %}{{ page.reproducibility | jsonify | slice: 0, 1 }}{% endcapture %}
+{% if reproducibility_shape == '{' %}
+  {% assign reproducibility = page.reproducibility_notes %}
+{% else %}
+  {% assign reproducibility = page.reproducibility | default: page.reproducibility_notes %}
+{% endif %}
 {% assign peer_review = page.peer_review | default: page.peer_review_notes %}
 {% assign version_history = page.version_history %}
 {% assign appendices = page.appendices %}
@@ -28,8 +33,8 @@ schema_type: ScholarlyArticle
 {% assign references = page.references %}
 {% assign references_array = references | arrayify %}
 {% assign funding = page.funding %}
-{% assign rights = page.rights | default: page.license %}
-{% assign affiliation_default = site.author.affiliation %}
+{% assign rights = page.rights %}
+{% assign research_license = page | page_license %}
 {% assign show_publications = page.show_publications | default: false %}
 
 <div class="research-wrapper" itemscope itemtype="https://schema.org/ScholarlyArticle">
@@ -57,9 +62,9 @@ schema_type: ScholarlyArticle
       <h2 class="visually-hidden">Authors</h2>
       <ul class="research-author-list">
         {% for author in authors %}
-          {% assign author_name = author.name | default: author %}
-          {% assign author_affiliation = author.affiliation | default: author.institution | default: affiliation_default %}
-          {% assign author_orcid = author.orcid | default: site.author.orcid %}
+          {% assign author_name = author.name | escape %}
+          {% assign author_affiliation = author.affiliation | escape %}
+          {% assign author_orcid = author.orcid %}
           {% assign author_email = author.email | default: author.contact %}
           <li class="research-author" itemprop="author" itemscope itemtype="https://schema.org/Person">
             <span class="research-author-name" itemprop="name">{{ author_name }}</span>
@@ -125,6 +130,11 @@ schema_type: ScholarlyArticle
           <dt>Rights</dt>
           <dd>{{ rights }}</dd>
         </div>
+      {% elsif research_license %}
+        <div>
+          <dt>Rights</dt>
+          <dd>{% include components/license-link.html license=research_license %}</dd>
+        </div>
       {% endif %}
     </dl>
 
@@ -321,6 +331,8 @@ ER  -
     </section>
   {% endif %}
 
+  {% include components/reproducibility.html page=page %}
+
   {% if supplementary or appendices %}
     <section class="research-appendices" aria-labelledby="appendix-heading">
       <h2 id="appendix-heading">Appendix and supplementary materials</h2>

data/_plugins/analytics_dashboard.rb

@@ -31,7 +31,10 @@ module Datalog
 
       data = query_analytics(site)
       data["fetched_at"] = Time.now.utc.iso8601
-      write_cache(cache_path, data)
+      # Only a successful report is cached. A missing-configuration or error
+      # payload used to be kept for CACHE_TTL as well, so a site that had just
+      # set GA4_PROPERTY_ID went on reporting the old problem for a day.
+      write_cache(cache_path, data) if data["status"] == "ok"
       data
     rescue StandardError => e
       Jekyll.logger.warn("Analytics", "Falling back to cached analytics data: #{e.message}")
@@ -43,7 +46,7 @@ module Datalog
     end
 
     def fresh?(payload)
-      return false unless payload.is_a?(Hash)
+      return false unless payload.is_a?(Hash) && payload["status"] == "ok"
 
       fetched_at = payload["fetched_at"]
       return false if fetched_at.to_s.empty?
@@ -95,7 +98,10 @@ module Datalog
       results["status"] = "ok"
       results
     rescue LoadError => e
-      fallback_payload("missing_dependency", "Install googleauth to enable GA4 integration: #{e.message}")
+      # The theme does not depend on googleauth: only a site with a GA4 property
+      # configured needs it, and adds it to its own Gemfile.
+      fallback_payload("missing_dependency",
+                       "Add gem \"googleauth\" to the site's Gemfile to enable the GA4 integration: #{e.message}")
     rescue StandardError => e
       fallback_payload("error", e.message)
     end