Maintenance of Conda environment, Gemfile and Gemfile.lock

Gemfile

@@ -1,5 +1,8 @@
 source "https://rubygems.org"
 
+ruby "~> 3.2"
+gem "rubygems-update", "~> 3.4"
+
 # 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:
@@ -8,7 +11,7 @@ source "https://rubygems.org"
 #
 # This will help ensure the proper Jekyll version is running.
 # Happy Jekylling!
-gem "jekyll", ">= 4"
+gem "jekyll", "~> 4.0"
 
 # This is the default theme for new Jekyll sites. You may change this to anything you like.
 #gem "minima", "~> 2.0"
@@ -20,13 +23,15 @@ gem "jekyll", ">= 4"
 # If you have any plugins, put them here!
 group :jekyll_plugins do
    gem "jekyll-feed", "~> 0.6"
+   gem "jekyll-compose"
+   gem "jekyll-scholar", "~> 7.1"
+   gem "jekyll-twitter-plugin"
 end
 
 # Windows does not include zoneinfo files, so bundle the tzinfo-data gem
-gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]
-gem 'jekyll-compose', group: [:jekyll_plugins]
-gem 'jekyll-scholar'
-gem 'html-proofer'
-gem 'jekyll-twitter-plugin'
+gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
+
+# Other gems.
+gem "html-proofer"
 gem "nokogiri", ">= 1.10.8"
-gem "bibtex-ruby", ">= 5.1.0"
+gem "bibtex-ruby", ">= 5.1.1"

Gemfile.lock

@@ -1,118 +1,149 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.7.0)
-      public_suffix (>= 2.0.2, < 5.0)
-    bibtex-ruby (5.1.1)
+    Ascii85 (1.1.0)
+    addressable (2.8.4)
+      public_suffix (>= 2.0.2, < 6.0)
+    afm (0.2.2)
+    async (2.6.2)
+      console (~> 1.10)
+      fiber-annotation
+      io-event (~> 1.1)
+      timers (~> 4.1)
+    bibtex-ruby (6.0.0)
       latex-decode (~> 0.0)
-    citeproc (1.0.9)
+    citeproc (1.0.10)
       namae (~> 1.0)
-    citeproc-ruby (1.1.10)
+    citeproc-ruby (1.1.14)
       citeproc (~> 1.0, >= 1.0.9)
-      csl (~> 1.5)
+      csl (~> 1.6)
     colorator (1.1.0)
-    concurrent-ruby (1.1.5)
-    csl (1.5.0)
+    concurrent-ruby (1.2.2)
+    console (1.17.2)
+      fiber-annotation
+      fiber-local
+    csl (1.6.0)
       namae (~> 1.0)
-    csl-styles (1.0.1.9)
+      rexml
+    csl-styles (1.0.1.11)
       csl (~> 1.0)
-    em-websocket (0.5.1)
+    em-websocket (0.5.3)
       eventmachine (>= 0.12.9)
-      http_parser.rb (~> 0.6.0)
-    ethon (0.9.1)
-      ffi (>= 1.3.0)
+      http_parser.rb (~> 0)
+    ethon (0.16.0)
+      ffi (>= 1.15.0)
     eventmachine (1.2.7)
-    ffi (1.11.1)
+    ffi (1.15.5)
+    fiber-annotation (0.2.0)
+    fiber-local (1.0.0)
     forwardable-extended (2.6.0)
-    html-proofer (3.13.0)
+    google-protobuf (3.23.4-x86_64-linux)
+    hashery (2.1.2)
+    html-proofer (5.0.7)
       addressable (~> 2.3)
-      mercenary (~> 0.3)
-      nokogiri (~> 1.10)
-      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 (0.9.5)
+      zeitwerk (~> 2.5)
+    http_parser.rb (0.8.0)
+    i18n (1.14.1)
       concurrent-ruby (~> 1.0)
-    jekyll (4.0.0)
+    io-event (1.2.2)
+    jekyll (4.3.2)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
-      i18n (>= 0.9.5, < 2)
-      jekyll-sass-converter (~> 2.0)
+      i18n (~> 1.0)
+      jekyll-sass-converter (>= 2.0, < 4.0)
       jekyll-watch (~> 2.0)
-      kramdown (~> 2.1)
+      kramdown (~> 2.3, >= 2.3.1)
       kramdown-parser-gfm (~> 1.0)
       liquid (~> 4.0)
-      mercenary (~> 0.3.3)
+      mercenary (>= 0.3.6, < 0.5)
       pathutil (~> 0.9)
-      rouge (~> 3.0)
+      rouge (>= 3.0, < 5.0)
       safe_yaml (~> 1.0)
-      terminal-table (~> 1.8)
-    jekyll-compose (0.11.0)
+      terminal-table (>= 1.8, < 4.0)
+      webrick (~> 1.7)
+    jekyll-compose (0.12.0)
       jekyll (>= 3.7, < 5.0)
-    jekyll-feed (0.12.1)
+    jekyll-feed (0.17.0)
       jekyll (>= 3.7, < 5.0)
-    jekyll-sass-converter (2.0.1)
-      sassc (> 2.0.1, < 3.0)
-    jekyll-scholar (6.8.0)
-      bibtex-ruby (~> 5.0)
+    jekyll-sass-converter (3.0.0)
+      sass-embedded (~> 1.54)
+    jekyll-scholar (7.1.3)
+      bibtex-ruby (~> 6.0)
       citeproc-ruby (~> 1.0)
       csl-styles (~> 1.0)
       jekyll (~> 4.0)
     jekyll-twitter-plugin (2.1.0)
     jekyll-watch (2.2.1)
       listen (~> 3.0)
-    kramdown (2.3.1)
+    kramdown (2.4.0)
       rexml
     kramdown-parser-gfm (1.1.0)
       kramdown (~> 2.0)
-    latex-decode (0.3.1)
-    liquid (4.0.3)
-    listen (3.2.0)
+    latex-decode (0.4.0)
+    liquid (4.0.4)
+    listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    mercenary (0.3.6)
-    mini_portile2 (2.5.0)
-    namae (1.0.1)
-    nokogiri (1.11.0)
-      mini_portile2 (~> 2.5.0)
+    mercenary (0.4.0)
+    namae (1.1.1)
+    nokogiri (1.15.3-x86_64-linux)
       racc (~> 1.4)
-    parallel (1.18.0)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (4.0.6)
-    racc (1.5.2)
-    rainbow (3.0.0)
-    rb-fsevent (0.10.3)
-    rb-inotify (0.10.0)
+    pdf-reader (2.11.0)
+      Ascii85 (~> 1.0)
+      afm (~> 0.2.1)
+      hashery (~> 2.0)
+      ruby-rc4
+      ttfunk
+    public_suffix (5.0.3)
+    racc (1.7.1)
+    rainbow (3.1.1)
+    rb-fsevent (0.11.2)
+    rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rexml (3.2.4)
-    rouge (3.12.0)
+    rexml (3.2.5)
+    rouge (4.1.2)
+    ruby-rc4 (0.1.5)
+    rubygems-update (3.4.16)
     safe_yaml (1.0.5)
-    sassc (2.3.0)
-      ffi (~> 1.9)
-    terminal-table (1.8.0)
-      unicode-display_width (~> 1.1, >= 1.1.1)
-    typhoeus (1.3.1)
+    sass-embedded (1.63.6-x86_64-linux-gnu)
+      google-protobuf (~> 3.23)
+    terminal-table (3.0.2)
+      unicode-display_width (>= 1.1.1, < 3)
+    timers (4.3.5)
+    ttfunk (1.7.0)
+    typhoeus (1.4.0)
       ethon (>= 0.9.0)
-    unicode-display_width (1.6.0)
+    unicode-display_width (2.4.2)
+    webrick (1.8.1)
     yell (2.2.2)
+    zeitwerk (2.6.8)
 
 PLATFORMS
-  ruby
+  x86_64-linux
 
 DEPENDENCIES
-  bibtex-ruby (>= 5.1.0)
+  bibtex-ruby (>= 5.1.1)
   html-proofer
-  jekyll (>= 4)
+  jekyll (~> 4.0)
   jekyll-compose
   jekyll-feed (~> 0.6)
-  jekyll-scholar
+  jekyll-scholar (~> 7.1)
   jekyll-twitter-plugin
   nokogiri (>= 1.10.8)
+  rubygems-update (~> 3.4)
   tzinfo-data
 
+RUBY VERSION
+   ruby 3.2.2p53
+
 BUNDLED WITH
-   1.17.2
+   2.4.10

environment.yml

@@ -5,74 +5,10 @@ channels:
   - defaults
 dependencies:
   - ca-certificates
-  - pyzotero
-  - bibtexparser
-  - gdbm=1.18
-  - gmp=6.2.0
-  - icu=64.2
-  - libffi=3.2.1
-  - libiconv=1.15
-  - libxml2=2.9.10
-  - libxslt=1.1.33
-  - ncurses=6.1
-  - openssl=1.1.1d
-  - rb-activesupport=4.2.11.1
-  - rb-addressable=2.7.0
-  - rb-bibtex-ruby=5.1.1
-  - rb-citeproc=1.0.9
-  - rb-citeproc-ruby=1.1.10
-  - rb-colorator=1.1.0
-  - rb-concurrent-ruby=1.1.5
-  - rb-csl=1.5.0
-  - rb-csl-styles=1.0.1.9
-  - rb-em-websocket=0.5.1
-  - rb-ethon=0.9.1
-  - rb-eventmachine=1.2.7
-  - rb-ffi=1.11.1
-  - rb-forwardable-extended=2.6.0
-  - rb-html-proofer=3.13.0
-  - rb-http_parser.rb=0.6.0
-  - rb-i18n=0.9.5
-  - rb-jekyll=4.0.0
-  - rb-jekyll-compose=0.11.0
-  - rb-jekyll-feed=0.12.1
-  - rb-jekyll-sass-converter=2.0.1
-  - rb-jekyll-scholar=6.8.0
-  - rb-jekyll-twitter-plugin=2.1.0
-  - rb-jekyll-watch=2.2.1
-  - rb-kramdown=2.3.0
-  - rb-kramdown-parser-gfm=1.1.0
-  - rb-latex-decode=0.3.1
-  - rb-liquid=4.0.3
-  - rb-listen=3.2.0
-  - rb-mercenary=0.3.6
-  - rb-mini_portile2=2.4.0
-  - rb-minitest=5.12.2
-  - rb-namae=1.0.1
-  - rb-nokogiri=1.10.8
-  - rb-parallel=1.18.0
-  - rb-pathutil=0.16.2
-  - rb-public_suffix=4.0.6
-  - rb-rainbow=3.0.0
-  - rb-rb-fsevent=0.10.3
-  - rb-rb-inotify=0.10.0
-  - rb-rouge=3.12.0
-  - rb-ruby_dep=1.5.0
-  - rb-safe_yaml=1.0.5
-  - rb-sass=3.7.4
-  - rb-sass-listen=4.0.0
-  - rb-sassc=2.3.0
-  - rb-terminal-table=1.8.0
-  - rb-thread_safe=0.3.6
-  - rb-typhoeus=1.3.1
-  - rb-tzinfo=1.2.5
-  - rb-tzinfo-data=1.2019.3
-  - rb-unicode-display_width=1.6.0
-  - rb-yell=2.2.2
-  - readline=8
-  - ruby=2.6
-  - tk
-  - xz
-  - yaml
-  - zlib
+  - pyzotero=1
+  - bibtexparser=1
+  - ruby>=3.2,<4
+  - python-frontmatter=1
+  - pandas=2
+  - requests=2