Major updates to be compatible with al-folio changes

+ add updated gemfile and purgecss
+ add back remote theme
+ add _plugins
+ add README to _plugins and remove cache-bust
+ remove dockerfile
+ update _pages/publications.md and include blog.md
+ remove old blog dir
+ pin remote theme to specific version
+ update libraries for third-party-plugin
+ remover terser because it isn't working

Author: nicholasphair

Dockerfile

@@ -1,28 +1,41 @@
 source 'https://rubygems.org'
+
+gem 'jekyll'
+
+# Core plugins that directly affect site building
 group :jekyll_plugins do
     gem "jekyll-remote-theme"
-    gem 'classifier-reborn'
-    gem 'jekyll'
     gem 'jekyll-archives'
-    gem 'jekyll-diagrams'
     gem 'jekyll-email-protect'
     gem 'jekyll-feed'
     gem 'jekyll-get-json'
     gem 'jekyll-imagemagick'
+    # NB (nphair): Don't want.
     #gem 'jekyll-jupyter-notebook'
     gem 'jekyll-link-attributes'
     gem 'jekyll-minifier'
     gem 'jekyll-paginate-v2'
+    gem 'jekyll-regex-replace'
     gem 'jekyll-scholar'
     gem 'jekyll-sitemap'
+    gem 'jekyll-tabs'
+    # NB (nphair): Remove for now, causing issues.
+    #gem 'jekyll-terser', :git => "https://github.com/RobertoJBeltran/jekyll-terser.git"
     gem 'jekyll-toc'
     gem 'jekyll-twitter-plugin'
     gem 'jemoji'
-    gem 'mini_racer'
-    gem 'unicode_utils'
-    gem 'webrick'
+
+    gem 'classifier-reborn'  # used for content categorization during the build
 end
+
+# Gems for development or external data fetching (outside :jekyll_plugins)
 group :other_plugins do
+    gem 'css_parser'
     gem 'feedjira'
     gem 'httparty'
+    gem 'observer'       # used by jekyll-scholar
+    gem 'ostruct'        # used by jekyll-twitter-plugin
+    gem 'terser'         # used by jekyll-terser
+    # gem 'unicode_utils' -- should be already installed by jekyll
+    # gem 'webrick' -- should be already installed by jekyll
 end

Gemfile

@@ -2,7 +2,7 @@
 # Site settings
 # -----------------------------------------------------------------------------
 
-remote_theme: alshedivat/al-folio
+remote_theme: alshedivat/al-folio@v0.13.4
 
 title: blank # the website title (if blank, full name will be used instead)
 first_name: Nicholas
@@ -131,7 +131,6 @@ keep_files:
 plugins:
   - jekyll-remote-theme
   - jekyll-archives
-  - jekyll-diagrams
   - jekyll-email-protect
   - jekyll-feed
   - jekyll-get-json
@@ -202,30 +201,221 @@ enable_project_categories:  true   # enables categorization of projects into
 # Library versions
 # -----------------------------------------------------------------------------
 
-academicons:
-  version: "1.9.0"
-  integrity: "sha512-W4yqoT1+8NLkinBLBZko+dFB2ZbHsYLDdr50VElllRcNt2Q4/GSs6u71UHKxB7S6JEMCp5Ve4xjh3eGQl/HRvg=="
-bootstrap:
-  version: "4.5.2"
-  integrity:
-    css: "sha512-MoRNloxbStBcD8z3M/2BmnT+rg4IsMxPkXaGh2zD6LGNNFE80W3onsAhRcMAMrSoyWL9xD7Ert0men7vR8LUZg=="
-    js: "sha512-M5KW3ztuIICmVIhjSqXe01oV2bpe248gOxqmlcYrEzAvws7Pw3z6BK0iGbrwvdrUQUhi3eXgtxp5I8PDo9YfjQ=="
-fontawesome:
-  version: "5.14.0"
-  integrity: "sha512-1PKOgIY59xJ8Co8+NE6FZ+LOAZKjy+KY8iq0G4B3CyeY6wYHN3yt9PW0XpSriVlkMXe40PTKnXrLnZ9+fkDaog=="
-jquery:
-  version: "3.5.1"
-  integrity: "sha512-bLT0Qm9VnAYZDflyKcBaQ2gg0hSYNQrJ8RilYldYQ1FxQYoCLtUjuuRuZo+fjqhx/qtq/1itJ0C2ejDxltZVFg=="
-mathjax:
-  version: "3.1.2"
-mansory:
-  version: "4.2.2"
-  integrity: "sha256-Nn1q/fx0H7SNLZMQ5Hw5JLaTRZp0yILA/FRexe19VdI="
-mdb:
-  version: "4.19.1"
-  integrity:
-    css: "sha512-RO38pBRxYH3SoOprtPTD86JFOclM51/XTIdEPh5j8sj4tp8jmQIx26twG52UaLi//hQldfrh7e51WzP9wuP32Q=="
-    js: "sha512-Mug9KHKmroQFMLm93zGrjhibM2z2Obg9l6qFG2qKjXEXkMp/VDkI4uju9m4QKPjWSwQ6O2qzZEnJDEeCw0Blcw=="
-popper:
-  version: "2.4.4"
-  integrity: "sha512-eUQ9hGdLjBjY3F41CScH3UX+4JDSI9zXeroz7hJ+RteoCaY+GP/LDoM8AO+Pt+DRFw3nXqsjh9Zsts8hnYv8/A=="
+# Add the url, version and integrity hash of the libraries you use in your site.
+# The integrity hash is used to ensure that the library is not tampered with.
+# Integrity hashes not provided by the libraries were generated using https://www.srihash.org/
+third_party_libraries:
+  download: false # if true, download the versions of the libraries specified below and use the downloaded files
+  bootstrap-table:
+    integrity:
+      css: "sha256-uRX+PiRTR4ysKFRCykT8HLuRCub26LgXJZym3Yeom1c="
+      js: "sha256-4rppopQE9POKfukn2kEvhJ9Um25Cf6+IDVkARD0xh78="
+    url:
+      css: "https://cdn.jsdelivr.net/npm/bootstrap-table@{{version}}/dist/bootstrap-table.min.css"
+      js: "https://cdn.jsdelivr.net/npm/bootstrap-table@{{version}}/dist/bootstrap-table.min.js"
+    version: "1.22.4"
+  chartjs:
+    integrity:
+      js: "sha256-0q+JdOlScWOHcunpUk21uab1jW7C1deBQARHtKMcaB4="
+    url:
+      js: "https://cdn.jsdelivr.net/npm/chart.js@{{version}}/dist/chart.umd.min.js"
+    version: "4.4.1"
+  d3:
+    integrity:
+      js: "sha256-1rA678n2xEx7x4cTZ5x4wpUCj6kUMZEZ5cxLSVSFWxw="
+    url:
+      js: "https://cdn.jsdelivr.net/npm/d3@{{version}}/dist/d3.min.js"
+    version: "7.8.5"
+  diff2html:
+    integrity:
+      css: "sha256-IMBK4VNZp0ivwefSn51bswdsrhk0HoMTLc2GqFHFBXg="
+      js: "sha256-eU2TVHX633T1o/bTQp6iIJByYJEtZThhF9bKz/DcbbY="
+    url:
+      css: "https://cdn.jsdelivr.net/npm/diff2html@{{version}}/bundles/css/diff2html.min.css"
+      js: "https://cdn.jsdelivr.net/npm/diff2html@{{version}}/bundles/js/diff2html-ui.min.js"
+    version: "3.4.47"
+  echarts:
+    integrity:
+      js:
+        library: "sha256-QvgynZibb2U53SsVu98NggJXYqwRL7tg3FeyfXvPOUY="
+        dark_theme: "sha256-sm6Ui9w41++ZCWmIWDLC18a6ki72FQpWDiYTDxEPXwU="
+    url:
+      js:
+        library: "https://cdn.jsdelivr.net/npm/echarts@{{version}}/dist/echarts.min.js"
+        dark_theme: "https://cdn.jsdelivr.net/npm/echarts@{{version}}/theme/dark-fresh-cut.js"
+    version: "5.5.0"
+  google_fonts:
+    url:
+      fonts: "https://fonts.googleapis.com/css?family=Roboto:300,400,500,700|Roboto+Slab:100,300,400,500,700|Material+Icons&display=swap"
+  highlightjs:
+    integrity:
+      css:
+        light: "sha256-Oppd74ucMR5a5Dq96FxjEzGF7tTw2fZ/6ksAqDCM8GY="
+        dark: "sha256-nyCNAiECsdDHrr/s2OQsp5l9XeY2ZJ0rMepjCT2AkBk="
+    url:
+      css:
+        light: "https://cdn.jsdelivr.net/npm/highlight.js@{{version}}/styles/github.min.css"
+        dark: "https://cdn.jsdelivr.net/npm/highlight.js@{{version}}/styles/github-dark.min.css"
+    version: "11.9.0"
+  imagesloaded:
+    integrity:
+      js: "sha256-htrLFfZJ6v5udOG+3kNLINIKh2gvoKqwEhHYfTTMICc="
+    url:
+      js: https://cdn.jsdelivr.net/npm/imagesloaded@{{version}}/imagesloaded.pkgd.min.js
+    version: "5.0.0"
+  img-comparison-slider:
+    integrity:
+      css: "sha256-3qTIuuUWIFnnU3LpQMjqiXc0p09rvd0dmj+WkpQXSR8="
+      js: "sha256-EXHg3x1K4oIWdyohPeKX2ZS++Wxt/FRPH7Nl01nat1o="
+      map: "sha256-3wfqS2WU5kGA/ePcgFzJXl5oSN1QsgZI4/edprTgX8w="
+    url:
+      css: "https://cdn.jsdelivr.net/npm/img-comparison-slider@{{version}}/dist/styles.min.css"
+      js: "https://cdn.jsdelivr.net/npm/img-comparison-slider@{{version}}/dist/index.min.js"
+      map: "https://cdn.jsdelivr.net/npm/img-comparison-slider@{{version}}/dist/index.js.map"
+    version: "8.0.6"
+  jquery:
+    integrity:
+      js: "sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4="
+    url:
+      js: "https://cdn.jsdelivr.net/npm/jquery@{{version}}/dist/jquery.min.js"
+    version: "3.6.0"
+  leaflet:
+    integrity:
+      css: "sha256-q9ba7o845pMPFU+zcAll8rv+gC+fSovKsOoNQ6cynuQ="
+      js: "sha256-MgH13bFTTNqsnuEoqNPBLDaqxjGH+lCpqrukmXc8Ppg="
+      js_map: "sha256-YAoQ3FzREN4GmVENMir8vgHHypC0xfSK3CAxTHCqx1M="
+    local:
+      images: "images/"
+    url:
+      css: "https://cdn.jsdelivr.net/npm/leaflet@{{version}}/dist/leaflet.min.css"
+      images: "https://cdn.jsdelivr.net/npm/leaflet@{{version}}/dist/images/"
+      js: "https://cdn.jsdelivr.net/npm/leaflet@{{version}}/dist/leaflet.min.js"
+      js_map: "https://cdn.jsdelivr.net/npm/leaflet@{{version}}/dist/leaflet.js.map"
+    version: "1.9.4"
+  lightbox2:
+    integrity:
+      css: "sha256-uypRbsAiJcFInM/ndyI/JHpzNe6DtUNXaWEUWEPfMGo="
+      js: "sha256-A6jI5V9s1JznkWwsBaRK8kSeXLgIqQfxfnvdDOZEURY="
+    url:
+      css: "https://cdn.jsdelivr.net/npm/lightbox2@{{version}}/dist/css/lightbox.min.css"
+      js: "https://cdn.jsdelivr.net/npm/lightbox2@{{version}}/dist/js/lightbox.min.js"
+    version: "2.11.5"
+  mathjax:
+    integrity:
+      js: "sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI="
+    local:
+      fonts: "output/chtml/fonts/woff-v2/"
+    url:
+      fonts: "https://cdn.jsdelivr.net/npm/mathjax@{{version}}/es5/output/chtml/fonts/woff-v2/"
+      js: "https://cdn.jsdelivr.net/npm/mathjax@{{version}}/es5/tex-mml-chtml.js"
+    version: "3.2.2"
+  masonry:
+    integrity:
+      js: "sha256-Nn1q/fx0H7SNLZMQ5Hw5JLaTRZp0yILA/FRexe19VdI="
+    url:
+      js: "https://cdn.jsdelivr.net/npm/masonry-layout@{{version}}/dist/masonry.pkgd.min.js"
+    version: "4.2.2"
+  mdb:
+    integrity:
+      css: "sha256-jpjYvU3G3N6nrrBwXJoVEYI/0zw8htfFnhT9ljN3JJw="
+      css_map: "sha256-iYYMNfsJdVZjvsebJulg09miBXM4/GMTJgv1u5EZFFM="
+      js: "sha256-NdbiivsvWt7VYCt6hYNT3h/th9vSTL4EDWeGs5SN3DA="
+      js_map: "sha256-UPgyn4YNsT0khkBK5553QwhnlbTlU0aa+igyc6qP1bE="
+    url:
+      css: "https://cdn.jsdelivr.net/npm/mdbootstrap@{{version}}/css/mdb.min.css"
+      css_map: "https://cdn.jsdelivr.net/npm/mdbootstrap@{{version}}/css/mdb.min.css.map"
+      js: "https://cdn.jsdelivr.net/npm/mdbootstrap@{{version}}/js/mdb.min.js"
+      js_map: "https://cdn.jsdelivr.net/npm/mdbootstrap@{{version}}/js/mdb.min.js.map"
+    version: "4.20.0"
+  medium_zoom:
+    integrity:
+      js: "sha256-ZgMyDAIYDYGxbcpJcfUnYwNevG/xi9OHKaR/8GK+jWc="
+    url:
+      js: "https://cdn.jsdelivr.net/npm/medium-zoom@{{version}}/dist/medium-zoom.min.js"
+    version: "1.1.0"
+  mermaid:
+    integrity:
+      js: "sha256-TtLOdUA8mstPoO6sGvHIGx2ceXrrX4KgIItO06XOn8A="
+    url:
+      js: "https://cdn.jsdelivr.net/npm/mermaid@{{version}}/dist/mermaid.min.js"
+    version: "10.7.0"
+  photoswipe:
+    integrity:
+      js: "sha256-VCBpdxvrNNxGHNuTdNqK9kPFkev2XY7DYzHdmgaB69Q="
+    url:
+      css: "https://cdn.jsdelivr.net/npm/photoswipe@{{version}}/dist/photoswipe.min.css"
+      js: "https://cdn.jsdelivr.net/npm/photoswipe@{{version}}/dist/photoswipe.esm.min.js"
+    version: "5.4.4"
+  photoswipe-lightbox:
+    integrity:
+      js: "sha256-uCw4VgT5DMdwgtjhvU9e98nT2mLZXcw/8WkaTrDd3RI="
+    url:
+      js: "https://cdn.jsdelivr.net/npm/photoswipe@{{version}}/dist/photoswipe-lightbox.esm.min.js"
+    version: "5.4.4"
+  polyfill:
+    url:
+      js: "https://cdnjs.cloudflare.com/polyfill/v{{version}}/polyfill.min.js?features=es6"
+    version: "3"
+  pseudocode:
+    integrity:
+      css: "sha256-VwMV//xgBPDyRFVSOshhRhzJRDyBmIACniLPpeXNUdc="
+      js: "sha256-aVkDxqyzrB+ExUsOY9PdyelkDhn/DfrjWu08aVpqNlo="
+    url:
+      css: "https://cdn.jsdelivr.net/npm/pseudocode@{{version}}/build/pseudocode.min.css"
+      js: "https://cdn.jsdelivr.net/npm/pseudocode@{{version}}/build/pseudocode.min.js"
+    version: "2.4.1"
+  spotlight:
+    integrity:
+      css: "sha256-Dsvkx8BU8ntk9Iv+4sCkgHRynYSQQFP6gJfBN5STFLY="
+    url:
+      css: "https://cdn.jsdelivr.net/npm/spotlight.js@{{version}}/dist/css/spotlight.min.css"
+      js: "https://cdn.jsdelivr.net/npm/spotlight.js@{{version}}/dist/spotlight.bundle.min.js"
+    version: "0.7.8"
+  swiper:
+    integrity:
+      css: "sha256-yUoNxsvX+Vo8Trj3lZ/Y5ZBf8HlBFsB6Xwm7rH75/9E="
+      js: "sha256-BPrwikijIybg9OQC5SYFFqhBjERYOn97tCureFgYH1E="
+      map: "sha256-lbF5CsospW93otqvWOIbbhj80CjazrZXvamD7nC7TBI="
+    url:
+      css: "https://cdn.jsdelivr.net/npm/swiper@{{version}}/swiper-bundle.min.css"
+      js: "https://cdn.jsdelivr.net/npm/swiper@{{version}}/swiper-element-bundle.min.js"
+      map: "https://cdn.jsdelivr.net/npm/swiper@{{version}}/swiper-element-bundle.min.js.map"
+    version: "11.0.5"
+  swiper-map:
+    integrity:
+      js: "sha256-hlZaH8ySXX97bZaetnrtYlKuhx3oEXFz/s2IXchu6vk="
+    url:
+      js: "https://cdn.jsdelivr.net/npm/[email protected]/swiper-element-bundle.min.js.map"
+    version: "11.0.5"
+  vega:
+    integrity:
+      js: "sha256-Yot/cfgMMMpFwkp/5azR20Tfkt24PFqQ6IQS+80HIZs="
+      js_map: "sha256-z0x9ICA65dPkZ0JVa9wTImfF6n7AJsKc6WlFE96/wNA="
+    url:
+      js: "https://cdn.jsdelivr.net/npm/vega@{{version}}/build/vega.min.js"
+      js_map: "https://cdn.jsdelivr.net/npm/vega@{{version}}/build/vega.min.js.map"
+    version: "5.27.0"
+  vega-embed:
+    integrity:
+      js: "sha256-FPCJ9JYCC9AZSpvC/t/wHBX7ybueZhIqOMjpWqfl3DU="
+      js_map: "sha256-VBbfSEFYSMdX/rTdGrONEHNP6BprCB7H/LpMMNt/cPA="
+    url:
+      js: "https://cdn.jsdelivr.net/npm/vega-embed@{{version}}/build/vega-embed.min.js"
+      js_map: "https://cdn.jsdelivr.net/npm/vega-embed@{{version}}/build/vega-embed.min.js.map"
+    version: "6.24.0"
+  vega-lite:
+    integrity:
+      js: "sha256-TvBvIS5jUN4BSy009usRjNzjI1qRrHPYv7xVLJyjUyw="
+      js_map: "sha256-l2I4D5JC23Ulsu6e3sKVe5AJ+r+DFkzkKnZS8nUGz28="
+    url:
+      js: "https://cdn.jsdelivr.net/npm/vega-lite@{{version}}/build/vega-lite.min.js"
+      js_map: "https://cdn.jsdelivr.net/npm/vega-lite@{{version}}/build/vega-lite.min.js.map"
+    version: "5.16.3"
+  venobox:
+    integrity:
+      css: "sha256-ohJEB0/WsBOdBD+gQO/MGfyJSbTUI8OOLbQGdkxD6Cg="
+      js: "sha256-LsGXHsHMMmTcz3KqTaWvLv6ome+7pRiic2LPnzTfiSo="
+    url:
+      css: "https://cdn.jsdelivr.net/npm/venobox@{{version}}/dist/venobox.min.css"
+      js: "https://cdn.jsdelivr.net/npm/venobox@{{version}}/dist/venobox.min.js"
+    version: "2.1.8"