_config.yml

plugins:
  - jekyll-glossary_tooltip
  - jekyll-remote-theme
  - jekyll-paginate
  - jekyll-sitemap
  - jekyll-gist
  - jemoji
  - jekyll-include-cache
  - jekyll-archives

# mimic GitHub Pages with --safe
whitelist:
  - jekyll-sitemap
  - jekyll-gist
  - jemoji
  - jekyll-include-cache


remote_theme: mmistakes/minimal-mistakes@4.24.0
### https://github.com/mmistakes/minimal-mistakes
### REMEMBER TO OCCASIONALLY TEST THE NEWER VERSIONS FOR NEW GOODIES!!!!!
minimal_mistakes_skin: contrast

# Site Settings
locale: en-US
title: "Fred Hutch Biomedical Data Science Wiki"
description: "Collective documentation for Data Science, Bioinformatics and Scientific Computing at the Fred Hutch"
url                      : https://sciwiki.fredhutch.org
baseurl                  : ""
repository               : "FredHutch/wiki"
logo                     : "/images/biomedical-wiki-2023.png"


collections:
  datascience:
    output: true
    permalink: /:collection/:path/
  dasldemos:
    output: true
    permalink: /:collection/:path/
  scicomputing:
    output: true
    permalink: /:collection/:path/
  pathways:
    output: true
    permalink: /:collection/:path/
  hdc:
    output: true
    permalink: /:collection/:path/
  contributors:
    output: true
    permalink: /:collection/:path/
  compdemos:
    output: true
    permalink: /:collection/:path/
  scicompannounce:
    output: true
    permalink: /:collection/:path/
  pythonModules:
    output: true
    permalink: /:collection/:path/
  rModules:
    output: true
    permalink: /:collection/:path/


atom_feed:
  path                   :  # blank (default) uses feed.xml
  hide: true
search                   :  false #, false (default)
search_full_content      :  false #, false (default)
#Note: Only the first 50 words of a post or page’s body content is added to the Lunr search index. Setting search_full_content to true in your _config.yml will override this and could impact page load performance.
# search_provider          :  google #(default), algolia
# Can use google search, here are instructions: https://mmistakes.github.io/minimal-mistakes/docs/configuration/
google:
  search_engine_id: 008250600098126702450:xciawyvddl8

# Analytics
analytics:
  provider               : "google-gtag" # false (default), "google", "google-universal", "custom"
  google:
    tracking_id          : "G-FXHRYCV6VK" # UA-123256805-1

# New as of 8/2019
footer:
  links:
    - label: "See our GitHub Repo"
      icon: "fab fa-fw fa-github"
      url: "https://github.com/FredHutch/wiki"
    - label: "Join the Conversation on Slack"
      icon: "fab fa-fw fa-slack"
      url: "https://hutchdatascience.org/joinslack/"
    - label: "See our Contributors"
      icon: "fas fa-user-edit"
      url: /contributors/
    - label: "About this Resource"
      icon: "fas fa-landmark"
      url: /about/



# Reading Files
include:
  - _data
  - assets
  - _layouts
exclude:
  - archive



# Outputting
permalink: /:categories/:title/
paginate: 5 # amount of posts to show
paginate_path: /page:num/
timezone: America/Los_Angeles # https://en.wikipedia.org/wiki/List_of_tz_database_time_zones



# Defaults
###NOTE:  for sciwiki, share: true will turn on the "Edit this page" function at the bottom of the pages
defaults:
  # _datascience
  - scope:
      path: ""
      type: datascience
    values:
      layout: single
      toc: true
      toc_label: "On This Page"
      toc_sticky: true
      share: true
      sidebar:
        nav: "datascience"

  # _dasldemos
  - scope:
      path: ""
      type: dasldemos
    values:
      layout: single
      toc: true
      toc_label: "On This Page"
      toc_sticky: true
      share: true
      sidebar:
        nav: "datascience"

# _compdemos
  - scope:
      path: ""
      type: compdemos
    values:
      layout: single
      toc: true
      toc_label: "On This Page"
      toc_sticky: true
      share: true
      sidebar:
        nav: "scicomputing"

  # _scicomputing
  - scope:
      path: ""
      type: scicomputing
    values:
      layout: single
      toc: true
      toc_label: "On This Page"
      toc_sticky: true
      share: true
      sidebar:
        nav: "scicomputing"
# _pathways
  - scope:
      path: ""
      type: pathways
    values:
      layout: single
      toc: true
      toc_sticky: true
      toc_label: "On This Page"
      share: true
      sidebar:
        nav: "generic"

  # _hdc
  - scope:
      path: ""
      type: hdc
    values:
      layout: single
      toc: true
      toc_label: "On This Page"
      toc_sticky: true
      share: true
      sidebar:
        nav: "hdc"

# _contributors
  - scope:
      path: ""
      type: contributors
    values:
      layout: single
      share: false

# _scicompannounce
  - scope:
      path: ""
      type: scicompannounce
    values:
      layout: single
      share: true
      sidebar:
        nav: "scicomputing"

  # _posts
  - scope:
      path: ""
      type: posts
    values:
      layout: single
      author_profile: true
      read_time: true
      share: true
      sidebar:
        nav: "scicomputing"
# _rModules
  - scope:
      path: ""
      type: rModules
    values:
      layout: single
      share: true
      sidebar:
        nav: "scicomputing"
# _pythonModules
  - scope:
      path: ""
      type: pythonModules
    values:
      layout: single
      share: true
      sidebar:
        nav: "scicomputing"

exclude:
  - ".gitignore"
  - ".gitlab-ci.yml"
  - "elasticsearch"
  - "tmp"
  - "*.py"
  - "*.yml"
  - "Rakefile"
  - "*.gz"
  - "rancher-v0.6.2"
  - "*.sh"
  - "Dockerfile"
  - "Gemfile*"


#
tag_archive:
  type: liquid
  path: /tags/

webrick:
  headers:
    Access-Control-Allow-Origin: "*"
    access-control-allow-origin: "*"
    Access-Control-Allow_Credentials: "true"
    Access-Control-Allow-Headers: "Authorization,Accept,Origin,DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range"
    Access-Control-Allow-Methods: "GET,POST,OPTIONS,PUT,DELETE,PATCH"