_config.yml

# Welcome to Jekyll!
#
# This config file is meant for settings that affect your entire site, values
# which you are expected to set up once and rarely need to edit after that.
# For technical reasons, this file is *NOT* reloaded automatically when you use
# `jekyll serve`. If you change this file, please restart the server process.

# 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                    : #
title_separator          : "-"
subtitle                 : # site tagline that appears below site title in masthead
name                     : "USF Omics Hub"
description              : "We post our materials for our data-analysis workshops here, information for upcoming events, as well as the code we’ve developed for various other omics-related data analyses."
url                      : # the base hostname & protocol for your site e.g. "https://mmistakes.github.io"
baseurl                  : # the subpath of your site, e.g. "/blog"
repository               : # GitHub username/repo-name e.g. "mmistakes/minimal-mistakes"
teaser                   :  "/images/Hub_logo_2.0.png"
logo                     : /images/Hub_logo_2.0_small.PNG
masthead_title           : "USF Omics Hub"
#breadcrumbs              :  true #, false (default)
words_per_minute         : 200

# Analytics
analytics:
  provider               : false # false (default), "google", "google-universal", "google-gtag", "custom"
  google:
    tracking_id          :
    anonymize_ip         : # true, false (default)



# Reading Files
include:
  - .htaccess
  - _pages
  - /Cluster_Computing/FacilitiesResources/index.md # testing adding path directly to make into web page

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
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


# Plugins (previously gems:)
plugins:
  - jekyll-paginate
  - jekyll-sitemap
  - jekyll-gist
  - jekyll-feed
  - jekyll-include-cache
  - jekyll-relative-links # added to test if turning .md into html pages is easier

relative_links:
  enabled: true
  collections: true

# 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/


# HTML Compression
# - https://jch.penibelst.de/
compress_html:
  clippings: all
  ignore:
    envs: development


# Defaults
defaults:
  # _posts
  - scope:
      path: ""
      type: posts
    values:
      layout: single
      show_date: true # show dates on posts
      search: true # enable site-search
      author_profile: true
      read_time: true
      comments: # true
      share: true
      related: true




theme: jekyll-theme-minimal