Deploy preview for PR 289 🛫

preview/pr-289/CHANGELOG.md

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+# Changelog
+
+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
+
+- List component `filters` parameter changed to `filter` and now takes any Ruby expression instead of the existing custom syntax.
+  Example: `filters="publisher: bioRxiv, date: ^2020"` becomes `filter="publisher == 'bioRxiv' and date =~ /^2020/"`.
+  See docs for more info.
+- Fix rare bug where data (e.g. a paper title) containing certain characters (e.g. a double quote) can mess up HTML rendering.
+- Fix "first time setup" workflow bug.
+- Tweak GitHub Actions debugging/logging.
+
+### Added
+
+- Styling for `<details>` HTML element.
+
+## 1.2.2 - 2024-06-05
+
+### Added
+
+- Add `affiliation` member portrait field.
+
+### Changed
+
+- Change order and type of preferred ids from ORCID API.
+- Expand list of supported Manubot identifiers and thus keep ORCID API details less often.
+- Simplify portrait component under-the-hood.
+- Make tag component de-duplication consistent with search plugin de-duplication.
+
+## 1.2.1 - 2024-04-01
+
+### Changed
+
+- Minor bug fixes in cite process and sitemap generation.
+
+## 1.2.0 - 2024-03-08
+
+### Changed
+
+- Update all GitHub Actions to fix "Node v16 deprecated" warnings.
+- Sources that Manubot doesn't know how to cite (e.g. wosuid:12345) are now ignored by default if they're from metasources.
+- Fix bug where passing tags to tags component manually doesn't work.
+- Fix bug in citation (and other) components when `lookup` is blank.
+- Fix nested tables bug.
+- Dark mode tweaks.
+- Various CSS tweaks and fixes.
+
+### Added
+
+- Add `image` param to support blog post thumbnails.
+- Add `html-proofer` plugin that checks for broken images/links/etc.
+- Add `remove` flag to remove a source from a metasource.
+
+## 1.1.6 - 2023-10-06
+
+### Changed
+
+- Use latest minor versions of Python packages in auto-cite script.
+
+## 1.1.5 - 2023-05-19
+
+### Changed
+
+- Fix ORCID plugin bug and other cite process tweaks.
+
+## 1.1.4 - 2023-04-28
+
+### Changed
+
+- Fix ORCID plugin and other cite process bugs.
+
+## 1.1.3 - 2023-04-20
+
+### Changed
+
+- Fix first-time-setup mv bug.
+- Fix citation, float, and portrait component CSS.
+- Filter and trim citation info fields.
+
+## 1.1.2 - 2023-04-11
+
+### Changed
+
+- Fix first-time-setup rm bug.
+
+## 1.1.1 - 2023-04-06
+
+### Changed
+
+- Change member profile page from col layout to float.
+- Fix first time setup. Preserve config formatting and comments.
+- Improve Docker cite process behavior.
+- Fix post excerpt component start/end markers and special search attr chars.
+- Fix misc CSS.
+
+### Added
+
+- Add show-title and show-subtitle site config options.
+- Include site subtitle in description meta tag.
+- Add user pull request template.
+- Add title and link fallbacks to citation component.
+
+## 1.1.0 - 2023-03-17
+
+Add alert component, Docker support, accessibility fixes.
+
+### Changed
+
+- Fix Lighthouse accessibility issues.
+- De-href components when link isn't provided (no hand cursor icon on hover or nav on click).
+- In search script, limit highlights by total count instead of char length.
+- Grid and link style tweaks.
+- Take ORCID icon from Font Awesome.
+- Misc bug fixes in tags script, float component.
+
+### Added
+
+- Add Docker configuration and scripts for local previewing.
+- Add alert component and types.
+- Role icon in portrait component hoisted to top left.
+
+## 1.0.0 - 2023-02-28
+
+First official release.
+
+High-level comparison with pre-releases:
+
+- Simpler configuration.
+- More automation, less setup.
+- More customization and flexibility.
+- Redesigned components.
+- New docs.
+- Complete rewrite.
+- Culmination of years of feedback.
+
+### Changed
+
+- Template is no longer limited to GitHub Pages white-listed Jekyll plugins. Any plugins possible.
+- Pull request previews happen right within GitHub instead of needing Netlify.
+- Better versioning. `CITATION.cff` file now source of truth for version, and tags/releases enforced.
+- Citation-related files in `/_data` must now be named prefixed with the cite plugin they are to be run with, e.g. `sources-2020.yaml` or `orcid-students.yaml`.
+- Folder renames for clarity and for better separation of template and user content: `/auto-cite` → `/_cite`, `/css` → `/_styles`, `/js` → `/_scripts`.
+- Rename "Tools" page to "Projects" to be more clear and general purpose.
+- Rename `extra-links` to `buttons` in `sources.yaml` files.
+- Rename `theme.scss` to `-theme.scss`.
+- Rename/repurpose components: link → button, two-col → cols, gallery → grid.
+- Combine "link" and "role" data lists into single `types.yaml` map.
+- Redesign components, change parameters and behavior.
+- Update Font Awesome icon names from v5 to v6.
+- Change placeholder text, images, and other images.
+- Use CSS variables instead of Sass variables.
+- Simplify caching method in cite process.
+- Simplify Liquid code by including custom Ruby plugins.
+- Simplify styles and scripts.
+
+### Added
+
+- New docs at greene-lab.gitbook.io/lab-website-template-docs.
+- Add automations for first time setup and URL change.
+- Write PubMed and Google Scholar automatic citation plugins.
+- Automatic citations through GitHub Actions should now work from (most) forks.
+- Add optional description and type params for citations.
+- Add periodic cite process run that opens a pull request.
+- List component filters can now accept arbitrary regex.
+- Add light/dark mode toggle.
+- Pre-install selection of useful Jekyll plugins, namely Jekyll Spaceship.
+- Add author portrait and updated date for blog posts.
+- Add richer metadata for SEO.
+- Google Fonts link determined automatically from theme file.
+
+### Removed
+
+- Remove options from `_config.yaml` to simplify configuration: `baseurl`, `auto-cite`, `logo`.
+- Remove `/favicons` folder, hardcode files for logo, icon, and share in `/images`.
+- Remove `palettes.scss` and `mixins.scss`.
+- Remove banner component (same thing can be achieved with full width section and figure components).
+- Remove role component. Combine with portrait component.

preview/pr-289/_scripts/anchors.js

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+/*
+  creates link next to each heading that links to that section.
+*/
+
+{
+  const onLoad = () => {
+    // for each heading
+    const headings = document.querySelectorAll(
+      "h1[id], h2[id], h3[id], h4[id], h5[id], h6[id]"
+    );
+    for (const heading of headings) {
+      // create anchor link
+      const link = document.createElement("a");
+      link.classList.add("icon", "fa-solid", "fa-link", "anchor");
+      link.href = "#" + heading.id;
+      link.setAttribute("aria-label", "link to this section");
+      heading.append(link);
+
+      // if first heading in the section, move id to parent section
+      if (heading.matches("section > :first-child")) {
+        heading.parentElement.id = heading.id;
+        heading.removeAttribute("id");
+      }
+    }
+  };
+
+  // scroll to target of url hash
+  const scrollToTarget = () => {
+    const id = window.location.hash.replace("#", "");
+    const target = document.getElementById(id);
+
+    if (!target) return;
+    const offset = document.querySelector("header").clientHeight || 0;
+    window.scrollTo({
+      top: target.getBoundingClientRect().top + window.scrollY - offset,
+      behavior: "smooth",
+    });
+  };
+
+  // after page loads
+  window.addEventListener("load", onLoad);
+  window.addEventListener("load", scrollToTarget);
+  window.addEventListener("tagsfetched", scrollToTarget);
+
+  // when hash nav happens
+  window.addEventListener("hashchange", scrollToTarget);
+}

preview/pr-289/_scripts/dark-mode.js

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+/*
+  manages light/dark mode.
+*/
+
+{
+  // immediately load saved (or default) mode before page renders
+  document.documentElement.dataset.dark =
+    window.localStorage.getItem("dark-mode") ?? "false";
+
+  const onLoad = () => {
+    // update toggle button to match loaded mode
+    document.querySelector(".dark-toggle").checked =
+      document.documentElement.dataset.dark === "true";
+  };
+
+  // after page loads
+  window.addEventListener("load", onLoad);
+
+  // when user toggles mode button
+  window.onDarkToggleChange = (event) => {
+    const value = event.target.checked;
+    document.documentElement.dataset.dark = value;
+    window.localStorage.setItem("dark-mode", value);
+  };
+}

preview/pr-289/_scripts/fetch-tags.js

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+/*
+  fetches tags (aka "topics") from a given GitHub repo and adds them to row of
+  tag buttons. specify repo in data-repo attribute on row.
+*/
+
+{
+  const onLoad = async () => {
+    // get tag rows with specified repos
+    const rows = document.querySelectorAll("[data-repo]");
+
+    // for each repo
+    for (const row of rows) {
+      // get props from tag row
+      const repo = row.dataset.repo.trim();
+      const link = row.dataset.link.trim();
+
+      // get tags from github
+      if (!repo) continue;
+      let tags = await fetchTags(repo);
+
+      // filter out tags already present in row
+      let existing = [...row.querySelectorAll(".tag")].map((tag) =>
+        window.normalizeTag(tag.innerText)
+      );
+      tags = tags.filter((tag) => !existing.includes(normalizeTag(tag)));
+
+      // add tags to row
+      for (const tag of tags) {
+        const a = document.createElement("a");
+        a.classList.add("tag");
+        a.innerHTML = tag;
+        a.href = `${link}?search="tag: ${tag}"`;
+        a.dataset.tooltip = `Show items with the tag "${tag}"`;
+        row.append(a);
+      }
+
+      // delete tags container if empty
+      if (!row.innerText.trim()) row.remove();
+    }
+
+    // emit "tags done" event for other scripts to listen for
+    window.dispatchEvent(new Event("tagsfetched"));
+  };
+
+  // after page loads
+  window.addEventListener("load", onLoad);
+
+  // GitHub topics endpoint
+  const api = "https://api.github.com/repos/REPO/topics";
+  const headers = new Headers();
+  headers.set("Accept", "application/vnd.github+json");
+
+  // get tags from GitHub based on repo name
+  const fetchTags = async (repo) => {
+    const url = api.replace("REPO", repo);
+    try {
+      const response = await (await fetch(url)).json();
+      if (response.names) return response.names;
+      else throw new Error(JSON.stringify(response));
+    } catch (error) {
+      console.groupCollapsed("GitHub fetch tags error");
+      console.log(error);
+      console.groupEnd();
+      return [];
+    }
+  };
+}