sync with upstream (#3)

* Increase font size in code blocks

See academicpages#59

* Adds missing semi-colon

* fix font awesome code icon in syntax box

* Fix encoding issue with bib files

* add goodreads to site

* change orcid color

* add medium icon

* add medium profile

* Resolve Google Scholar link not displayed

There was as slight typo in the logic due to which the google scholar link for the respective author's profile set in Config was not being displayed.

* Adding pronouns field to author profile

* Add Google Analytics 4 Support

* fix: Remove deprecated JavaScript to avoid load error from 404 page

* Update files to be ignored

* + webrick to gem file

* academicpages#1902 RM excerpt in pages

* Start updating the README

* academicpages#456 Use real Google Scholar link as an example

* Update issue templates

* RM minimal mistakes changelog

* academicpages#1906

* Edit readme

* + Syntax highlighting example

* Update README.md

* Update README

* Correct syntax

* Streamline config organization for new users

* Add Mastodon to social media

* Closes academicpages#696 with new Kaggle link

* Adjustments to Kaggle link

* Closes academicpages#271 with addition of arXiv

* academicpages#244, academicpages#1600, academicpages#1917 update font awesome to v6, add icons

* Closes academicpages#1911 with update to Academicons

* Closes academicpages#1671 with a new favicon

* academicpages#462 update inline documentation

* academicpages#1041 allow links to wrap

* Closes academicpages#1773 with update to HTML

* Closes academicpages#45 with an update to the CV generator

* academicpages#33, academicpages#1919 Possible missing template fix, bump MathJax to 3.0

* academicpages#1153 add Zhihu

* Closes academicpages#1905 with updates to documentation

* Closes academicpages#693 with updates to documentation and location of citation

* Closes academicpages#820 with updated style

* added missing spanish translations and updated some of the previous ones on ui-text-yml

* Replace `polyfill.io`

* Closes academicpages#1972, update Markdown documentation

* Closes academicpages#1936 with setting to hide RSS feed

* academicpages#1935 clean-up the footer follow a bit

* RM old development override

* Make it clearer where the footnotes are

* academicpages#1975 ignore files created by npm

* Closes academicpages#339 with a fixed masthead

* academicpages#1975 version updates, manage jQuery from npm

* Closes academicpages#1970 with responsive element

* Fix typo

* Closes academicpages#1999

* scroll in sidebar

* scroll in sidebar

* Add scroll to sidebar and adjust media query for screen adaptability

* Closes academicpages#2029 with update to sidebar

* Closes academicpages#1917 with with icon, FA bump to 6.5.2

* academicpages#2061 Update README with note on dependencies

* Closes academicpages#2055 with adjustment to masthead-height

* Adjust variable name to prevent confusion

* Update casing of template name

* Fix typo in build-essential package name.

The package which is required for this installation is named `build-essential`, not `build-essentials`.

* Fix academicpages#1920 by allowing text to wrap

* Add support to semantic scholar in author profile

* Support for displaying slides on publication pages

* Addressed PR academicpages#2126 review comments

* Fix typo, modifications to style

* Update _config.yml

Make claimed default and actual default consistent

* Add Chinese (both simplified and traditional) to ui-text.yml

Simplified Chinese:
  zh
  zh-CN

Traditional Chinese:
  zh-HK
  zh-TW

* Adds commands for MacOS

* Update README.md

* academicpages#2316 update padding

* academicpages#2318 updating documentation a bit

* Alphabetize the excludes

* Closes academicpages#48 with a more general and customizable approach

* fix: lastfm url

* Update README.md

* Fixing YouTube URL generation in author-profile.html

YouTube does not use /user/username at the moment. If a person has a YouTube handle, the URL is:
www.youtube.com/@HANDLE

The fix is very minimal but I needed it for my website so I've also added it here.

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* academicpages#1975 cleaning up the gem files a bit

* academicpages#1975 update fitvids to NPM

* academicpages#1975 update magnific-popup to NPM

* academicpages#1975 update smooth scroll to NPM

* Closes academicpages#1975 RM stickyfill in favor of native browser support

* Closes academicpages#2287, academicpages#534 with updates to documentation, better emoji generation

* Add a dockerfile

* Update README.md

* bug: comments appear at bottom of page

* Closes academicpages#146 with information the details HTML tag

* Minor formatting

* Closes academicpages#828 with update to put the pages last update in the footer.

* academicpages#828 different format string

* academicpages#828 adjustments to account for GitHub Pages limitations

* Fix toc crop (academicpages#221)

Fix by @qhuang-math. I have also removed underlining of toc links, which was being overridden by post body css.

* Reduce excessive footer padding

* Fix misalignment of navigation bar with post body

There was a regression in the template updates where the navigation bar no longer aligns with the post left margin at normal viewport.

* Add notebook to fetch publication information from orcid

* Update author-profile.html

improve alignment of "employer" sidebar

* Closes academicpages#2469 with update to only use username

* academicpages#1093 MV notebook to generator directory

* Update Dockerfile

---------

Co-authored-by: Steve <sbitner@uwf.edu>
Co-authored-by: Rob Williams <jayrobwilliams@gmail.com>
Co-authored-by: sigma67 <benedikt.putz@wiwi.uni-regensburg.de>
Co-authored-by: naveenarun <notatroll.troll@gmail.com>
Co-authored-by: Mohit_Gupta <52665879+Mohit-15@users.noreply.github.com>
Co-authored-by: Bhavish Pahwa <53102161+bp-high@users.noreply.github.com>
Co-authored-by: amyzlc <6166519+amyzlc@users.noreply.github.com>
Co-authored-by: Sonny Arora <sonnyarora@Sonnys-MacBook-Air.local>
Co-authored-by: Bhav Beri <43399374+bhavberi@users.noreply.github.com>
Co-authored-by: rjzupkoii <rjzii@yahoo.com>
Co-authored-by: johnhandleyd <translatjohn@gmail.com>
Co-authored-by: SukkaW <isukkaw@gmail.com>
Co-authored-by: Maximiliano <maximilianogalindo7@gmail.com>
Co-authored-by: Dan Grahn <dgrahn@users.noreply.github.com>
Co-authored-by: Dan Grahn <dan.grahn@altamiracorp.com>
Co-authored-by: thiagorr162 <thiagorr162@gmail.com>
Co-authored-by: Saravanan D. <saravananinca@gmail.com>
Co-authored-by: Manuel Haussmann <manuel.haussmann@mailbox.org>
Co-authored-by: Yuhang YAN (Henry) <96647290+YanY-Henry@users.noreply.github.com>
Co-authored-by: Zarela <zarelavp@yahoo.com>
Co-authored-by: Yanchen Huang <90331527+02hyc@users.noreply.github.com>
Co-authored-by: edbrito-swdev <90706749+edbrito-swdev@users.noreply.github.com>
Co-authored-by: Alberto Barradas <abcsds@gmail.com>
Co-authored-by: Samir Rashid <Samir-Rashid@godsped.com>
Co-authored-by: Carlos Martinez <neocarlitos@gmail.com>
Co-authored-by: Xiaofei (Carl) Zang <xbz5174@psu.edu>
Co-authored-by: Zoe <60870971+zoelesv@users.noreply.github.com>

.gitignore

@@ -1,5 +1,6 @@
-# Ignore the contents of the _site directory
+# Ignore the contents of the _site directory and other cache directories
 _site/
+.sass-cache/
 
 # Ignore the directory for local files during development
 local/

Dockerfile

@@ -0,0 +1,24 @@
+# Base image: Ruby with necessary dependencies for Jekyll
+FROM ruby:3.2
+
+# Install dependencies
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    nodejs \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set the working directory inside the container
+WORKDIR /usr/src/app
+
+# Copy Gemfile into the container (necessary for `bundle install`)
+COPY Gemfile ./
+
+# Install bundler and dependencies
+RUN gem install bundler:2.3.26 && bundle install
+
+# Expose port 4000 for Jekyll server
+EXPOSE 4000
+
+# Command to serve the Jekyll site
+CMD ["bundle", "exec", "jekyll", "serve", "--host", "0.0.0.0", "--watch"]
+

Gemfile

@@ -1,28 +1,11 @@
-source "https://rubygems.org"
+source 'https://rubygems.org'
 
-# Hello! This is where you manage which Jekyll version is used to run.
-# When you want to use a different version, change it below, save the
-# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
-#
-#     bundle exec jekyll serve
-#
-# This will help ensure the proper Jekyll version is running.
-# Happy Jekylling!
-
-gem "github-pages", group: :jekyll_plugins
-
-# If you want to use Jekyll native, uncomment the line below.
-# To upgrade, run `bundle update`.
-
-# gem "jekyll"
-
-gem "wdm", "~> 0.1.0" if Gem.win_platform?
-
-# If you have any plugins, put them here!
 group :jekyll_plugins do
-  # gem "jekyll-archives"
-  gem "jekyll-feed"
+  gem 'jekyll'
+  gem 'jekyll-feed'
   gem 'jekyll-sitemap'
-  gem 'hawkins'
-  gem "webrick", "~> 1.8"
+  gem 'jemoji'
+  gem 'webrick', '~> 1.8'
 end
+
+gem 'github-pages'

README.md

@@ -1,8 +1,5 @@
 # Academic Pages
-
-![pages-build-deployment](https://github.com/academicpages/academicpages.github.io/actions/workflows/pages/pages-build-deployment/badge.svg)
-
-Academic Pages is a Github Pages template for academic websites.
+**Academic Pages is a Github Pages template for academic websites.**
 
 # Getting Started
 
@@ -16,7 +13,7 @@ Academic Pages is a Github Pages template for academic websites.
 
 See more info at https://academicpages.github.io/
 
-## Running Locally
+## Running locally
 
 When you are initially working your website, it is very useful to be able to preview the changes locally before pushing them to GitHub. To work locally you will need to:
 
@@ -38,6 +35,21 @@ When you are initially working your website, it is very useful to be able to pre
 
 If you are running on Linux it may be necessary to install some additional dependencies prior to being able to run locally: `sudo apt install build-essential gcc make`
 
+## Using Docker
+
+Working from a different OS, or just want to avoid installing dependencies? You can use the provided `Dockerfile` to build a container that will run the site for you if you have [Docker](https://www.docker.com/) installed.
+
+Start by build the container:
+
+```bash
+docker build -t jekyll-site .
+```
+
+Next, run the container:
+```bash
+docker run -p 4000:4000 --rm -v $(pwd):/usr/src/app jekyll-site
+```
+
 # Maintenance
 
 Bug reports and feature requests to the template should be [submitted via GitHub](https://github.com/academicpages/academicpages.github.io/issues/new/choose). For questions concerning how to style the template, please feel free to start a [new discussion on GitHub](https://github.com/academicpages/academicpages.github.io/discussions).
@@ -49,3 +61,15 @@ This repository was forked (then detached) by [Stuart Geiger](https://github.com
 If you have bugfixes and enhancements that you would like to submit as a pull request, you will need to [fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo) this repository as opposed to using it as a template. This will also allow you to [synchronize your copy](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork) of template to your fork as well.
 
 Unfortunately, one logistical issue with a template theme like Academic Pages that makes it a little tricky to get bug fixes and updates to the core theme. If you use this template and customize it, you will probably get merge conflicts if you attempt to synchronize. If you want to save your various .yml configuration files and markdown files, you can delete the repository and fork it again. Or you can manually patch.
+
+---
+<div align="center">
+
+![pages-build-deployment](https://github.com/academicpages/academicpages.github.io/actions/workflows/pages/pages-build-deployment/badge.svg)
+[![GitHub contributors](https://img.shields.io/github/contributors/academicpages/academicpages.github.io.svg)](https://github.com/academicpages/academicpages.github.io/graphs/contributors)
+[![GitHub release](https://img.shields.io/github/v/release/academicpages/academicpages.github.io)](https://github.com/academicpages/academicpages.github.io/releases/latest)
+[![GitHub license](https://img.shields.io/github/license/academicpages/academicpages.github.io?color=blue)](https://github.com/academicpages/academicpages.github.io/blob/master/LICENSE)
+
+[![GitHub stars](https://img.shields.io/github/stars/academicpages/academicpages.github.io)](https://github.com/academicpages/academicpages.github.io)
+[![GitHub forks](https://img.shields.io/github/forks/academicpages/academicpages.github.io)](https://github.com/academicpages/academicpages.github.io/fork)
+</div>

_config.yml

@@ -148,23 +148,26 @@ exclude:
   - "*.sublime-workspace"
   - .asset-cache
   - .bundle
+  - .github
   - .jekyll-assets-cache
   - .sass-cache
-  - CHANGELOG
-  - Capfile
-  - Gemfile
-  - Gruntfile.js
-  - LICENSE
-  - README
-  - Rakefile
   - assets/js/_main.js
   - assets/js/plugins
   - assets/js/vendor
+  - CHANGELOG
+  - Capfile
   - config
+  - Dockerfile
+  - Gemfile
+  - Gruntfile.js
   - gulpfile.js
+  - LICENSE
+  - local
   - log
   - node_modules
-  - package.json
+  - package.json*
+  - Rakefile
+  - README
   - tmp
   - vendor
 keep_files:
@@ -287,17 +290,18 @@ timezone: America/Los_Angeles # http://en.wikipedia.org/wiki/List_of_tz_database
 
 # Plugins
 plugins:
+  - jekyll-feed
+  - jekyll-gist
   - jekyll-paginate
   - jekyll-sitemap
-  - jekyll-gist
-  - jekyll-feed
-  - jekyll-redirect-from
-# mimic GitHub Pages with --safe
+  - jemoji
+
+# Mimic GitHub Pages with --safe
 whitelist:
+  - jekyll-feed
+  - jekyll-gist
   - jekyll-paginate
   - jekyll-sitemap
-  - jekyll-gist
-  - jekyll-feed
   - jemoji
 
 # Archives

_data/navigation.yml

@@ -1,4 +1,9 @@
-# main links links
+# The following is the order of the links in the header of the website.
+#
+# Changing the order here will adjust the order and you can also add additional
+# links. Removing a link prevents it from showing in the header, but does not
+# prevent it from being included in the site.
+
 main:
   - title: "Publications"
     url: /publications/