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Deploy preview for PR 257 🛫
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vincerubinetti committed Apr 22, 2024
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706 changes: 706 additions & 0 deletions preview/pr-257/2019/01/07/example-post-1.html

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163 changes: 163 additions & 0 deletions preview/pr-257/CHANGELOG.md
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# Changelog

Reference: common-changelog.org

## 1.2.2 - 2024-04-24

### Added

- Add `affiliation` member portrait field.

### Changed

- 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.
47 changes: 47 additions & 0 deletions preview/pr-257/_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);
}
25 changes: 25 additions & 0 deletions preview/pr-257/_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);
};
}
67 changes: 67 additions & 0 deletions preview/pr-257/_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 [];
}
};
}
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