diff --git a/.github/DISCUSSION_TEMPLATE/general.yaml b/.github/DISCUSSION_TEMPLATE/general.yaml deleted file mode 100644 index 66b2c49..0000000 --- a/.github/DISCUSSION_TEMPLATE/general.yaml +++ /dev/null @@ -1,35 +0,0 @@ -body: - - type: checkboxes - attributes: - label: Checks - options: - - label: I have searched **[the docs](https://greene-lab.gitbook.io/lab-website-template-docs)**, [existing issues](https://github.com/greenelab/lab-website-template/issues), and [existing discussions](https://github.com/greenelab/lab-website-template/discussions) for answers first. - required: true - - - type: input - id: repo - attributes: - label: Link to your website repo - description: "In almost all cases, **we cannot help you if you don't provide this**." - placeholder: ex. https://github.com/greenelab/greenelab.com - validations: - required: true - - - type: input - id: version - attributes: - label: Version of Lab Website Template you are using - description: See your `CITATION.cff` file. - placeholder: ex. 1.0.0 - validations: - required: true - - - type: textarea - id: description - attributes: - label: Description - description: | - Describe your issue in as much detail as possible. For example: What happened? What did you expect to happen? How can we reproduce the problem? What browser are you seeing the problem in? - placeholder: Description - validations: - required: true diff --git a/.github/DISCUSSION_TEMPLATE/q-a.yaml b/.github/DISCUSSION_TEMPLATE/q-a.yaml deleted file mode 100644 index 66b2c49..0000000 --- a/.github/DISCUSSION_TEMPLATE/q-a.yaml +++ /dev/null @@ -1,35 +0,0 @@ -body: - - type: checkboxes - attributes: - label: Checks - options: - - label: I have searched **[the docs](https://greene-lab.gitbook.io/lab-website-template-docs)**, [existing issues](https://github.com/greenelab/lab-website-template/issues), and [existing discussions](https://github.com/greenelab/lab-website-template/discussions) for answers first. - required: true - - - type: input - id: repo - attributes: - label: Link to your website repo - description: "In almost all cases, **we cannot help you if you don't provide this**." - placeholder: ex. https://github.com/greenelab/greenelab.com - validations: - required: true - - - type: input - id: version - attributes: - label: Version of Lab Website Template you are using - description: See your `CITATION.cff` file. - placeholder: ex. 1.0.0 - validations: - required: true - - - type: textarea - id: description - attributes: - label: Description - description: | - Describe your issue in as much detail as possible. For example: What happened? What did you expect to happen? How can we reproduce the problem? What browser are you seeing the problem in? - placeholder: Description - validations: - required: true diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml deleted file mode 100644 index 7d0b7de..0000000 --- a/.github/ISSUE_TEMPLATE/config.yml +++ /dev/null @@ -1,8 +0,0 @@ -blank_issues_enabled: true -contact_links: - - name: 💬 Start a discussion - url: https://github.com/greenelab/lab-website-template/discussions - about: I need help, I have a question, or other discussion. - - name: 📚 Docs issue - url: https://github.com/greenelab/lab-website-template-docs/issues - about: I have a question or issue related to the template documentation. diff --git a/.github/ISSUE_TEMPLATE/issue.yaml b/.github/ISSUE_TEMPLATE/issue.yaml deleted file mode 100644 index d812555..0000000 --- a/.github/ISSUE_TEMPLATE/issue.yaml +++ /dev/null @@ -1,38 +0,0 @@ -name: 🐞 Create an issue -description: I think I've discovered a bug, I want to request a feature/change, or other issue. - -body: - - type: checkboxes - attributes: - label: Checks - options: - - label: I have searched **[the docs](https://greene-lab.gitbook.io/lab-website-template-docs)**, [existing issues](https://github.com/greenelab/lab-website-template/issues), and [existing discussions](https://github.com/greenelab/lab-website-template/discussions) for answers first. - required: true - - - type: input - id: repo - attributes: - label: Link to your website repo - description: "In almost all cases, **we cannot help you if you don't provide this**." - placeholder: ex. https://github.com/greenelab/greenelab.com - validations: - required: true - - - type: input - id: version - attributes: - label: Version of Lab Website Template you are using - description: See your `CITATION.cff` file. - placeholder: ex. 1.0.0 - validations: - required: true - - - type: textarea - id: description - attributes: - label: Description - description: | - Describe your issue in as much detail as possible. For example: What happened? What did you expect to happen? How can we reproduce the problem? What browser are you seeing the problem in? - placeholder: Description - validations: - required: true diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 6aaf76b..00a0e71 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,13 +1,4 @@ -STOP!!! +This website is based on the Lab Website Template. +See its documentation for working with this site: -You are about to open this pull request against THE TEMPLATE ITSELF. You probably meant to open it against your own website repo. - ---- - -FOR THE TEMPLATE MAINTAINER(S) - -New template version checklist: - -- [ ] I have updated CITATION and CHANGELOG as appropriate. -- [ ] I have updated lab-website-template-docs as appropriate. -- [ ] I have checked the testbed as appropriate. +https://greene-lab.gitbook.io/lab-website-template-docs diff --git a/.github/user_pull_request_template.md b/.github/user_pull_request_template.md deleted file mode 100644 index 00a0e71..0000000 --- a/.github/user_pull_request_template.md +++ /dev/null @@ -1,4 +0,0 @@ -This website is based on the Lab Website Template. -See its documentation for working with this site: - -https://greene-lab.gitbook.io/lab-website-template-docs diff --git a/.github/workflows/versioning.yaml b/.github/workflows/versioning.yaml deleted file mode 100644 index e148f36..0000000 --- a/.github/workflows/versioning.yaml +++ /dev/null @@ -1,135 +0,0 @@ -name: versioning -run-name: versioning tasks - -on: - pull_request: - branches: - - main - push: - branches: - - main - -permissions: - contents: write - -jobs: - pull-request: - # only run on template itself, not user instance of template - if: | - github.repository == 'greenelab/lab-website-template' && - github.event_name == 'pull_request' - runs-on: ubuntu-latest - steps: - # for debugging - - uses: crazy-max/ghaction-dump-context@v2 - - if: runner.debug == '1' - uses: mxschmitt/action-tmate@v3 - - - name: Checkout base branch contents - uses: actions/checkout@v4 - with: - ref: main - path: base - - - name: Checkout pr branch contents - uses: actions/checkout@v4 - with: - path: pr - - - name: Install packages - run: npm install yaml semver - - - name: Check version, date, changelog - uses: actions/github-script@v7 - with: - script: | - const { readFileSync } = require("fs"); - const { lte, valid } = require("semver"); - const { parse } = require("yaml"); - - // load and parse file contents - const { version: oldVersion, "date-released": oldDate } = parse( - readFileSync("base/CITATION.cff").toString() - ); - const { version: newVersion, "date-released": newDate } = parse( - readFileSync("pr/CITATION.cff").toString() - ); - const changelog = readFileSync("pr/CHANGELOG.md") - .toString() - .split(/^## /m) - .map((section) => { - const [heading, ...body] = section.split("\n"); - return [heading.trim(), body.join("\n").trim()]; - }); - - // check version - if (!valid(newVersion)) throw Error("Version not valid"); - if (lte(newVersion, oldVersion)) throw Error("Version not updated"); - - // check date - if (new Date(newDate).toISOString().split("T")[0] !== newDate) - throw Error("Date not valid"); - if (new Date(newDate) <= new Date(oldDate)) throw Error("Date not updated"); - - // check changelog - const newSection = changelog.find( - ([heading, body]) => - heading.includes(newVersion) && heading.includes(newDate) && body - ); - if (!newSection) throw Error("Changelog not updated or not valid"); - - push: - # only run on template itself, not user instance of template - if: | - github.repository == 'greenelab/lab-website-template' && - github.event_name == 'push' - runs-on: ubuntu-latest - steps: - # for debugging - - uses: crazy-max/ghaction-dump-context@v2 - - - name: Checkout branch contents - uses: actions/checkout@v4 - - - name: Install packages - run: npm install yaml semver - - # for debugging - - if: runner.debug == '1' - uses: mxschmitt/action-tmate@v3 - - - name: Get version and body - id: version - uses: actions/github-script@v7 - with: - script: | - const { readFileSync } = require("fs"); - const { parse } = require("yaml"); - - // load and parse file contents - const { version, "date-released": date } = parse( - readFileSync("CITATION.cff").toString() - ); - const changelog = readFileSync("CHANGELOG.md") - .toString() - .split(/^## /m) - .map((section) => { - const [heading, ...body] = section.split("\n"); - return [heading.trim(), body.join("\n").trim()]; - }); - - // find changelog body for version - const [, body = ""] = - changelog.find( - ([heading]) => heading.includes(version) && heading.includes(date) - ) || []; - - return { version, body }; - - - name: Create GitHub release - uses: ncipollo/release-action@v1.14.0 - with: - commit: ${{ github.ref }} - tag: v${{ fromJson(steps.version.outputs.result).version }} - name: v${{ fromJson(steps.version.outputs.result).version }} - body: ${{ fromJson(steps.version.outputs.result).body }} diff --git a/CHANGELOG.md b/CHANGELOG.md deleted file mode 100644 index d702c3e..0000000 --- a/CHANGELOG.md +++ /dev/null @@ -1,146 +0,0 @@ -# Changelog - -Reference: common-changelog.org - -## 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. diff --git a/README.md b/README.md index 29bf9a2..adc2c25 100644 --- a/README.md +++ b/README.md @@ -1,30 +1,7 @@ -
- -
-Lab Website Template (LWT) is an easy-to-use, flexible website template for labs. -Spend less time worrying about managing a website and citations, and more time running your lab. +# wu-tecon's Website -👇👇 **Get Started** 👇👇 +Visit **[website url](#)** 🚀 -[**Documentation**](https://greene-lab.gitbook.io/lab-website-template-docs) +_Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_ -## Key Features - -- 🤖 Based on Git, GitHub, and Jekyll. -- 📜 Automatically generated citations from simple identifiers (DOI, PubMed, ORCID, and many more) using Manubot. E.g. `doi:1234/5678` -> `title`, `authors`, `publisher`, `date`, etc. -- 🧱 A comprehensive and flexible suite of pre-made components (building blocks) for structuring and styling your website: - - Formatted tables, code blocks, figures, and other basic elements. - - Citations with thumbnails and other rich details. - - List large sets of data with flexible filters and components. - - ...many more -- 👁️ Automatic pull request previews. -- ⚙️ Easy and automated configuration. -- 👥 Team member pages with bios, roles, and social media links. -- 🖋️ Blog posts with tags and rich content. -- 📱 Works and looks good on desktop and mobile. -- 🤝 Great documentation and support (if we do say so ourselves). -- ... and much more! - -![GitHub last commit](https://img.shields.io/github/last-commit/greenelab/lab-website-template) diff --git a/_config.yaml b/_config.yaml index 1c6b790..7579484 100644 --- a/_config.yaml +++ b/_config.yaml @@ -1,19 +1,19 @@ # site properties and page defaults -title: Lab Website Template -subtitle: by the Greene Lab -description: An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more. +title: wu-tecon +subtitle: +description: An engaging 1-3 sentence description of your lab. header: images/background.jpg footer: images/background.jpg proofer: false # site social media and other links links: - email: contact@your-lab.com + email: contact@wu-tecon.com orcid: 0000-0001-8713-9213 google-scholar: ETJoidYAAAAJ - github: your-lab - twitter: YourLabHandle - youtube: YourLabChannel + github: wu-tecon + twitter: wu-tecon + youtube: wu-tecon ### jekyll settings diff --git a/index.md b/index.md index bea6980..5ea9e0f 100644 --- a/index.md +++ b/index.md @@ -1,22 +1,9 @@ --- --- -# Lab Website Template +# wu-tecon's Website -[Lab Website Template](https://github.com/greenelab/lab-website-template) is an easy-to-use, flexible website template for [labs](https://www.greenelab.com/). -Spend less time worrying about managing a website and citations, and more time running your lab. - -{% - include button.html - type="docs" - link="https://greene-lab.gitbook.io/lab-website-template-docs" -%} -{% - include button.html - type="github" - text="On GitHub" - link="greenelab/lab-website-template" -%} +An engaging 1-3 sentence description of your lab. {% include section.html %} diff --git a/testbed.md b/testbed.md deleted file mode 100644 index 6b343a5..0000000 --- a/testbed.md +++ /dev/null @@ -1,437 +0,0 @@ ---- -title: Testbed -header: https://upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg/1024px-Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg -footer: https://upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg/1024px-Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg -header-dark: false -footer-dark: false ---- - -# Testbed - -{% include section.html %} - -# Basic formatting - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. -Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. -Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. - -[External link](https://some-website.org/) - -[Internal link](team) - -_italic text_ - -**bold text** - -~~strike-through text~~ - -