Update Ruby to 3.3 and fix dependencies accordingly

Starting with version 3.19.3, html-proofer removes its dependency
on the end-of-life nokogumbo library and replaces it with nokogirl.
gjtorikian/html-proofer#660

Front_matter_parser 1.0.1 fixes an error with newer versios of Ruby
https://github.com/waiting-for-dev/front_matter_parser/blob/main/CHANGELOG.md#101---2021-07-20

The base64 and csv gems will no longer be included with Ruby, so add to Gemfile
to ensure they will be installed

Update bundler to fix up some warnings/errors and update the rest of the packages

Update to Ruby 3.3

Ruby 3.0 will no longer be supported as of 2024-03-31, so let's get
it upgraded.

research.rb and teaching.rb are included in this changeset because
they were using File.exists, which is invalid syntax as of Ruby 3.2

ignore env helper files

Author: bsweger

.github/workflows/build-site.yml

@@ -18,7 +18,7 @@ jobs:
     - name: install ruby
       uses: ruby/setup-ruby@v1
       with:
-        ruby-version: '3.0'
+        ruby-version: '3.3.0'
         bundler-cache: true
     - name: run deploy script
       env:

.gitignore

@@ -6,3 +6,6 @@
 *.Rproj
 *.Rhistory
 .DS_Store
+
+.envrc
+.env

.ruby-version

@@ -0,0 +1 @@
+3.3.0

Gemfile

@@ -1,9 +1,11 @@
 source "https://rubygems.org"
-ruby RUBY_VERSION
+ruby file: ".ruby-version"
 
+gem "base64"
+gem "csv"
 gem "jekyll", ">=3.3.1"
-gem "html-proofer"
-gem "front_matter_parser"
+gem "html-proofer", ">=3.19.3"
+gem "front_matter_parser", ">=1.0.1"
 gem "kramdown"
 gem "kramdown-parser-gfm"
 gem "rake"

Gemfile.lock

@@ -1,112 +1,153 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.7.0)
-      public_suffix (>= 2.0.2, < 5.0)
+    Ascii85 (1.1.0)
+    addressable (2.8.6)
+      public_suffix (>= 2.0.2, < 6.0)
+    afm (0.2.2)
+    async (2.10.1)
+      console (~> 1.10)
+      fiber-annotation
+      io-event (~> 1.5, >= 1.5.1)
+      timers (~> 4.1)
+    base64 (0.2.0)
+    bigdecimal (3.1.7)
     colorator (1.1.0)
-    concurrent-ruby (1.1.8)
-    em-websocket (0.5.2)
+    concurrent-ruby (1.2.3)
+    console (1.23.6)
+      fiber-annotation
+      fiber-local
+      json
+    csv (3.3.0)
+    em-websocket (0.5.3)
       eventmachine (>= 0.12.9)
-      http_parser.rb (~> 0.6.0)
-    ethon (0.14.0)
+      http_parser.rb (~> 0)
+    ethon (0.16.0)
       ffi (>= 1.15.0)
     eventmachine (1.2.7)
-    faraday (1.4.1)
-      faraday-excon (~> 1.1)
-      faraday-net_http (~> 1.0)
-      faraday-net_http_persistent (~> 1.1)
-      multipart-post (>= 1.2, < 3)
-      ruby2_keywords (>= 0.0.4)
-    faraday-excon (1.1.0)
-    faraday-net_http (1.0.1)
-    faraday-net_http_persistent (1.1.0)
-    ffi (1.15.0)
+    faraday (2.9.0)
+      faraday-net_http (>= 2.0, < 3.2)
+    faraday-net_http (3.1.0)
+      net-http
+    ffi (1.16.3)
+    fiber-annotation (0.2.0)
+    fiber-local (1.0.0)
     forwardable-extended (2.6.0)
-    front_matter_parser (1.0.0)
-    html-proofer (3.19.1)
+    front_matter_parser (1.0.1)
+    google-protobuf (4.26.1-arm64-darwin)
+      rake (>= 13)
+    google-protobuf (4.26.1-x86_64-darwin)
+      rake (>= 13)
+    google-protobuf (4.26.1-x86_64-linux)
+      rake (>= 13)
+    hashery (2.1.2)
+    html-proofer (5.0.8)
       addressable (~> 2.3)
-      mercenary (~> 0.3)
-      nokogumbo (~> 2.0)
-      parallel (~> 1.3)
+      async (~> 2.1)
+      nokogiri (~> 1.13)
+      pdf-reader (~> 2.11)
       rainbow (~> 3.0)
       typhoeus (~> 1.3)
       yell (~> 2.0)
-    http_parser.rb (0.6.0)
-    i18n (1.8.10)
+      zeitwerk (~> 2.5)
+    http_parser.rb (0.8.0)
+    i18n (1.14.4)
       concurrent-ruby (~> 1.0)
-    jekyll (4.2.0)
+    io-event (1.5.1)
+    jekyll (4.3.3)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
       i18n (~> 1.0)
-      jekyll-sass-converter (~> 2.0)
+      jekyll-sass-converter (>= 2.0, < 4.0)
       jekyll-watch (~> 2.0)
-      kramdown (~> 2.3)
+      kramdown (~> 2.3, >= 2.3.1)
       kramdown-parser-gfm (~> 1.0)
       liquid (~> 4.0)
-      mercenary (~> 0.4.0)
+      mercenary (>= 0.3.6, < 0.5)
       pathutil (~> 0.9)
-      rouge (~> 3.0)
+      rouge (>= 3.0, < 5.0)
       safe_yaml (~> 1.0)
-      terminal-table (~> 2.0)
+      terminal-table (>= 1.8, < 4.0)
+      webrick (~> 1.7)
     jekyll-paginate (1.1.0)
-    jekyll-sass-converter (2.1.0)
-      sassc (> 2.0.1, < 3.0)
+    jekyll-sass-converter (3.0.0)
+      sass-embedded (~> 1.54)
     jekyll-watch (2.2.1)
       listen (~> 3.0)
-    kramdown (2.3.1)
+    json (2.7.1)
+    kramdown (2.4.0)
       rexml
     kramdown-parser-gfm (1.1.0)
       kramdown (~> 2.0)
-    liquid (4.0.3)
-    listen (3.5.1)
+    liquid (4.0.4)
+    listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.4.0)
-    multipart-post (2.1.1)
-    nokogiri (1.11.3-x86_64-darwin)
+    net-http (0.4.1)
+      uri
+    nokogiri (1.16.3-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.11.3-x86_64-linux)
+    nokogiri (1.16.3-x86_64-darwin)
       racc (~> 1.4)
-    nokogumbo (2.0.5)
-      nokogiri (~> 1.8, >= 1.8.4)
-    octokit (4.21.0)
-      faraday (>= 0.9)
-      sawyer (~> 0.8.0, >= 0.5.3)
-    parallel (1.20.1)
+    nokogiri (1.16.3-x86_64-linux)
+      racc (~> 1.4)
+    octokit (8.1.0)
+      base64
+      faraday (>= 1, < 3)
+      sawyer (~> 0.9)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (4.0.6)
-    racc (1.5.2)
-    rainbow (3.0.0)
-    rake (13.0.3)
-    rb-fsevent (0.10.4)
+    pdf-reader (2.12.0)
+      Ascii85 (~> 1.0)
+      afm (~> 0.2.1)
+      hashery (~> 2.0)
+      ruby-rc4
+      ttfunk
+    public_suffix (5.0.4)
+    racc (1.7.3)
+    rainbow (3.1.1)
+    rake (13.1.0)
+    rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rexml (3.2.5)
-    rouge (3.26.0)
-    ruby2_keywords (0.0.4)
+    rexml (3.2.6)
+    rouge (4.2.1)
+    ruby-rc4 (0.1.5)
     safe_yaml (1.0.5)
-    sassc (2.4.0)
-      ffi (~> 1.9)
-    sawyer (0.8.2)
+    sass-embedded (1.72.0-arm64-darwin)
+      google-protobuf (>= 3.25, < 5.0)
+    sass-embedded (1.72.0-x86_64-darwin)
+      google-protobuf (>= 3.25, < 5.0)
+    sass-embedded (1.72.0-x86_64-linux-gnu)
+      google-protobuf (>= 3.25, < 5.0)
+    sawyer (0.9.2)
       addressable (>= 2.3.5)
-      faraday (> 0.8, < 2.0)
-    terminal-table (2.0.0)
-      unicode-display_width (~> 1.1, >= 1.1.1)
-    typhoeus (1.4.0)
+      faraday (>= 0.17.3, < 3)
+    terminal-table (3.0.2)
+      unicode-display_width (>= 1.1.1, < 3)
+    timers (4.3.5)
+    ttfunk (1.8.0)
+      bigdecimal (~> 3.1)
+    typhoeus (1.4.1)
       ethon (>= 0.9.0)
-    unicode-display_width (1.7.0)
-    webrick (1.7.0)
+    unicode-display_width (2.5.0)
+    uri (0.13.0)
+    webrick (1.8.1)
     yell (2.2.2)
+    zeitwerk (2.6.13)
 
 PLATFORMS
+  arm64-darwin-23
   x86_64-darwin-20
   x86_64-linux
 
 DEPENDENCIES
-  front_matter_parser
-  html-proofer
+  base64
+  csv
+  front_matter_parser (>= 1.0.1)
+  html-proofer (>= 3.19.3)
   jekyll (>= 3.3.1)
   jekyll-paginate
   kramdown
@@ -116,7 +157,7 @@ DEPENDENCIES
   webrick (~> 1.7)
 
 RUBY VERSION
-   ruby 3.0.2p107
+   ruby 3.3.0p0
 
 BUNDLED WITH
-   2.2.17
+   2.5.7

_plugins/research.rb

@@ -8,7 +8,7 @@ class ResearchGen < Jekyll::Generator
     def generate(site)
       repo_data = {}
       data_file = File.join('_data', 'repositories.yml')
-      if File.exists? data_file
+      if File.exist? data_file
         repo_data = YAML.load_file(data_file)
       end
       research_files = Dir.glob(File.join('_research', '*.md'))

_plugins/teaching.rb

@@ -8,7 +8,7 @@ class TeachingGen < Jekyll::Generator
     def generate(site)
       repo_data = {}
       data_file = File.join('_data', 'repositories.yml')
-      if File.exists? data_file
+      if File.exist? data_file
         repo_data = YAML.load_file(data_file)
       end
       teaching_files = Dir.glob(File.join('_teaching', '*.md'))