First major version

Author: duncanwp

.DS_Store

@@ -15,3 +15,5 @@ group :jekyll_plugins do
   gem "jekyll-include-cache"
   gem "jekyll-algolia"
 end
+
+gem "webrick", "~> 1.8"

Gemfile

@@ -8,68 +8,305 @@
 # For technical reasons, this file is *NOT* reloaded automatically when you use
 # 'bundle exec jekyll serve'. If you change this file, please restart the server process.
 
-# Site settings
-# These are used to personalize your new site. If you look in the HTML files,
-# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
-# You can create any custom variable you would like, and they will be accessible
-# in the templates via {{ site.myvariable }}.
-title: Climate Analytics Lab
-email: dwatsonparris@ucsd.edu
-description: >- # this means to ignore newlines until "baseurl:"
-  The Climate Analytics Lab aims to reduce uncertainty in the role of anthropogenic aerosol 
-  on the climate by exploiting recent advances in machine learning to enable improved 
-  projections and gain new insights from observations.
-twitter_username: dwatsonparris
-github_username: climate-analytics-lab
-minimal_mistakes_skin: default
-search: true
-
-# Build settings
+# Theme Settings
+#
+# Review documentation to determine if you should use `theme` or `remote_theme`
+# https://mmistakes.github.io/minimal-mistakes/docs/quick-start-guide/#installing-the-theme
+
+# theme                  : "minimal-mistakes-jekyll"
+# remote_theme           : "mmistakes/minimal-mistakes"
+minimal_mistakes_skin    : "default" # "air", "aqua", "contrast", "dark", "dirt", "neon", "mint", "plum", "sunrise"
+
+
+# Site Settings
+locale                   : "en-US"
+title                    : "Climate Analytics Lab"
+title_separator          : "-"
+subtitle                 : # site tagline that appears below site title in masthead
+name                     : "CAL"
+description              : >- # this means to ignore newlines until "baseurl:"
+                              The Climate Analytics Lab aims to reduce uncertainty in the role of anthropogenic aerosol 
+                              on the climate by exploiting recent advances in machine learning to enable improved 
+                              projections and gain new insights from observations.
+url                      : "https://climate-analytics-lab.github.io" # the base hostname & protocol for your site e.g. "https://mmistakes.github.io"
+# baseurl                  : "/ccog.github.io" # the subpath of your site, e.g. "/blog"
+repository               : "climate-analytics-lab/climate-analytics-lab.github.io" # GitHub username/repo-name e.g. "mmistakes/minimal-mistakes"
+teaser                   : # path of fallback teaser image, e.g. "/assets/images/500x300.png"
+logo                     : "/assets/images/logo.svg"
+masthead_title           : "CAL" # overrides the website title displayed in the masthead, use " " for no title
+# breadcrumbs            : false # true, false (default)
+words_per_minute         : 200
+comments:
+  provider               : # false (default), "disqus", "discourse", "facebook", "staticman", "staticman_v2", "utterances", "giscus", "custom"
+  disqus:
+    shortname            : # https://help.disqus.com/customer/portal/articles/466208-what-s-a-shortname-
+  discourse:
+    server               : # https://meta.discourse.org/t/embedding-discourse-comments-via-javascript/31963 , e.g.: meta.discourse.org
+  facebook:
+    # https://developers.facebook.com/docs/plugins/comments
+    appid                :
+    num_posts            : # 5 (default)
+    colorscheme          : # "light" (default), "dark"
+  utterances:
+    theme                : # "github-light" (default), "github-dark"
+    issue_term           : # "pathname" (default)
+  giscus:
+    repo_id              : # Shown during giscus setup at https://giscus.app
+    category_name        : # Full text name of the category
+    category_id          : # Shown during giscus setup at https://giscus.app
+    discussion_term      : # "pathname" (default), "url", "title", "og:title"
+    reactions_enabled    : # '1' for enabled (default), '0' for disabled
+    theme                : # "light" (default), "dark", "dark_dimmed", "transparent_dark", "preferred_color_scheme"
+  staticman:
+    branch               : # "master"
+    endpoint             : # "https://{your Staticman v3 API}/v3/entry/github/"
+reCaptcha:
+  siteKey                :
+  secret                 :
+atom_feed:
+  path                   : # blank (default) uses feed.xml
+  hide                   : true # true, false (default)
+search                   : # true, false (default)
+search_full_content      : # true, false (default)
+search_provider          : # lunr (default), algolia, google
+lunr:
+  search_within_pages    : # true, false (default)
+algolia:
+  application_id         : # YOUR_APPLICATION_ID
+  index_name             : # YOUR_INDEX_NAME
+  search_only_api_key    : # YOUR_SEARCH_ONLY_API_KEY
+  powered_by             : # true (default), false
+google:
+  search_engine_id       : # YOUR_SEARCH_ENGINE_ID
+  instant_search         : # false (default), true
+# SEO Related
+google_site_verification :
+bing_site_verification   :
+naver_site_verification  :
+yandex_site_verification :
+baidu_site_verification  :
+
+
+# Social Sharing
+twitter:
+  username               : dwatsonparris
+facebook:
+  username               :
+  app_id                 :
+  publisher              :
+og_image                 : # Open Graph/Twitter default site image
+# For specifying social profiles
+# - https://developers.google.com/structured-data/customize/social-profiles
+social:
+  type                   : # Person or Organization (defaults to Person)
+  name                   : # If the user or organization name differs from the site's name
+  links: # An array of links to social media profiles
+
+# Analytics
+analytics:
+  provider               : false # false (default), "google", "google-universal", "google-gtag", "custom"
+  google:
+    tracking_id          :
+    anonymize_ip         : # true, false (default)
+
+
+# Site Author
+author:
+  name             : "Climate Analytics Lab"
+  avatar           : "/assets/images/logo.svg" # path of avatar image, e.g. "/assets/images/bio-photo.jpg"
+  bio              : "Improving climate projections with machine learning"
+  location         : "UC San Diego"
+  email            : "dwatsonparris@ucsd.edu"
+  links:
+    - label: "Email"
+      icon: "fas fa-fw fa-envelope-square"
+      # url: "mailto:sonnewald@ucdavis.edu"
+    - label: "Website"
+      icon: "fas fa-fw fa-link"
+      # url: "https://your-website.com"
+    - label: "Twitter"
+      icon: "fab fa-fw fa-twitter-square"
+      url: "https://twitter.com/dwatsonparris"
+    - label: "Facebook"
+      icon: "fab fa-fw fa-facebook-square"
+      # url: "https://facebook.com/"
+    - label: "GitHub"
+      icon: "fab fa-fw fa-github"
+      url: "https://github.com/climate-analytics-lab"
+    - label: "Instagram"
+      icon: "fab fa-fw fa-instagram"
+      # url: "https://instagram.com/"
+
+# Site Footer
+footer:
+  links:
+    - label: "Twitter"
+      icon: "fab fa-fw fa-twitter-square"
+      # url:
+    - label: "Facebook"
+      icon: "fab fa-fw fa-facebook-square"
+      # url:
+    - label: "GitHub"
+      icon: "fab fa-fw fa-github"
+      url: "https://github.com/CompClimate"
+    - label: "GitLab"
+      icon: "fab fa-fw fa-gitlab"
+      # url:
+    - label: "Bitbucket"
+      icon: "fab fa-fw fa-bitbucket"
+      # url:
+    - label: "Instagram"
+      icon: "fab fa-fw fa-instagram"
+      # url:
+
+
+# Reading Files
+include:
+  - .htaccess
+  - _pages
+exclude:
+  - "*.sublime-project"
+  - "*.sublime-workspace"
+  - vendor
+  - .asset-cache
+  - .bundle
+  - .jekyll-assets-cache
+  - .sass-cache
+  - assets/js/plugins
+  - assets/js/_main.js
+  - assets/js/vendor
+  - Capfile
+  - CHANGELOG
+  - config
+  - Gemfile
+  - Gruntfile.js
+  - gulpfile.js
+  - LICENSE
+  - log
+  - node_modules
+  - package.json
+  - package-lock.json
+  - Rakefile
+  - README
+  - tmp
+  - /docs # ignore Minimal Mistakes /docs
+  - /test # ignore Minimal Mistakes /test
+keep_files:
+  - .git
+  - .svn
+encoding: "utf-8"
+markdown_ext: "markdown,mkdown,mkdn,mkd,md"
+
+
+# Conversion
 markdown: kramdown
-remote_theme: mmistakes/minimal-mistakes
+highlighter: rouge
+lsi: false
+excerpt_separator: "\n\n"
+incremental: false
+
+
+# Markdown Processing
+kramdown:
+  input: GFM
+  hard_wrap: false
+  auto_ids: true
+  footnote_nr: 1
+  entity_output: as_char
+  toc_levels: 1..6
+  smart_quotes: lsquo,rsquo,ldquo,rdquo
+  enable_coderay: false
+
+
+# Sass/SCSS
+sass:
+  sass_dir: _sass
+  style: compressed # https://sass-lang.com/documentation/file.SASS_REFERENCE.html#output_style
+
+
 # Outputting
 permalink: /:categories/:title/
 paginate: 5 # amount of posts to show
 paginate_path: /page:num/
 timezone: # https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
 
-include:
-  - _pages
-
-# Exclude from processing.
-# The following items will not be processed, by default. Create a custom list
-# to override the default setting.
-# exclude:
-#   - Gemfile
-#   - Gemfile.lock
-#   - node_modules
-#   - vendor/bundle/
-#   - vendor/cache/
-#   - vendor/gems/
-#   - vendor/ruby/
 
 # Plugins (previously gems:)
 plugins:
   - jekyll-paginate
   - jekyll-sitemap
   - jekyll-gist
   - jekyll-feed
-  - jemoji
   - jekyll-include-cache
 
+# mimic GitHub Pages with --safe
+whitelist:
+  - jekyll-paginate
+  - jekyll-sitemap
+  - jekyll-gist
+  - jekyll-feed
+  - jekyll-include-cache
+
+
+# Archives
+#  Type
+#  - GitHub Pages compatible archive pages built with Liquid ~> type: liquid (default)
+#  - Jekyll Archives plugin archive pages ~> type: jekyll-archives
+#  Path (examples)
+#  - Archive page should exist at path when using Liquid method or you can
+#    expect broken links (especially with breadcrumbs enabled)
+#  - <base_path>/tags/my-awesome-tag/index.html ~> path: /tags/
+#  - <base_path>/categories/my-awesome-category/index.html ~> path: /categories/
+#  - <base_path>/my-awesome-category/index.html ~> path: /
+# category_archive:
+#   type: liquid
+#   path: /categories/
+tag_archive:
+  type: liquid
+  path: /tags/
+# https://github.com/jekyll/jekyll-archives
+# jekyll-archives:
+#   enabled:
+#     - categories
+#     - tags
+#   layouts:
+#     category: archive-taxonomy
+#     tag: archive-taxonomy
+#   permalinks:
+#     category: /categories/:name/
+#     tag: /tags/:name/
 
-footer:
-  links:
-    - label: "Twitter"
-      icon: "fab fa-fw fa-twitter-square"
-      url: "https://twitter.com/dwatsonparris"
-    - label: "GitHub"
-      icon: "fab fa-fw fa-github"
-      url: "https://github.com/duncanwp"
-    - label: "Instagram"
-      icon: "fab fa-fw fa-instagram"
-      url: "https://instagram.com/"
 
+# HTML Compression
+# - https://jch.penibelst.de/
+compress_html:
+  clippings: all
+  ignore:
+    envs: development
+
+
+# jekyll-scholar
+# https://pages.lip6.fr/Pascal.Poizat/blog/posts/2016/02/01/jekyll-and-bibtex/
+scholar:
+  style: "nature-publishing-group-vancouver"
+  locale: en
+
+  source: ./_data
+  bibliography: publications.bib
+  bibliography_template: "bibtemplate"
+
+  sort_by: year, month
+  order: descending
+
+
+# Collections
+collections:
+  news:
+    output: true
+  people:
+    output: true
+
+# Defaults
 defaults:
   # _posts
   - scope:
@@ -78,21 +315,22 @@ defaults:
     values:
       layout: single
       author_profile: true
-      read_time: true
-      comments: true
-      share: true
+      read_time: false
+      comments: # true
+      share: false
       related: true
   # _pages
   - scope:
       path: "_pages"
       type: pages
     values:
-      layout: single
-      author_profile: false
-
-category_archive:
-  type: liquid
-  path: /categories/
-tag_archive:
-  type: liquid
-  path: /tags/
+      layout: splash
+      author_profile: true
+  # _projects
+  - scope:
+      path: "projects"
+      type: posts
+    values:
+      layout: projects
+      author_profile: true
+      share: true