_config.yml

# -----------------------------------------------------------------------------
# Site settings
# -----------------------------------------------------------------------------

title: Biomedical Computation Group # the website title (if blank, full name will be used instead)
first_name: Andrea
middle_name: Yeong
last_name: Weisse
email:
description: > # the ">" symbol means to ignore newlines until "footer_text:"
  The Biomedical Computation Group led by Dr. Andrea Weisse at the University of Edinburgh.
footer_text: >
  Powered by <a href="https://jekyllrb.com/" target="_blank">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio">al-folio</a> theme.
  Hosted by <a href="https://pages.github.com/" target="_blank">GitHub Pages</a>.
keywords: > 
  biomedical computation group, andrea weisse, mechanistic, computation, amr, antimicrobial resistance, biology, 
  biochemistry, bioinformatics, mathematics, machine learning, university of edinburgh, engineering biology, bacterial 
  growth, synthetic biology, health data science, research
lang: en # the language of your site (for example: en, fr, cn, ru, etc.)
icon: "favicon.ico" # the emoji used as the favicon (alternatively, provide image name in /assets/img/)

url: https://chwag.github.io # the base hostname & protocol for your site
baseurl: # the subpath of your site, e.g. /blog/
last_updated: true # set to true if you want to display last updated in the footer
impressum_path: # set to path to include impressum link in the footer, use the same path as permalink in a page, helps to conform with EU GDPR

# -----------------------------------------------------------------------------
# Theme
# -----------------------------------------------------------------------------

# repo color theme
repo_theme_light: default # https://github.com/anuraghazra/github-readme-stats/blob/master/themes/README.md
repo_theme_dark: dark # https://github.com/anuraghazra/github-readme-stats/blob/master/themes/README.md
repo_trophies:
  enabled: true
  theme_light: flat # https://github.com/ryo-ma/github-profile-trophy
  theme_dark: gitdimmed # https://github.com/ryo-ma/github-profile-trophy

# -----------------------------------------------------------------------------
# RSS Feed
# -----------------------------------------------------------------------------
# will use title and url fields
# Take a look to https://github.com/jekyll/jekyll-feed for more customization

rss_icon: false

# -----------------------------------------------------------------------------
# Layout
# -----------------------------------------------------------------------------

navbar_fixed: true
footer_fixed: false

# Dimensions
max_width: 800px

# TODO: add layout settings (single page vs. multi-page)

# -----------------------------------------------------------------------------
# Open Graph & Schema.org
# -----------------------------------------------------------------------------
# Display links to the page with a preview object on social media.
# see https://schema.org/docs/faq.html for more information
serve_og_meta: false # Include Open Graph meta tags in the HTML head
serve_schema_org: false # Include Schema.org in the HTML head
og_image: # The site-wide (default for all links) Open Graph preview image

# -----------------------------------------------------------------------------
# Social integration
# -----------------------------------------------------------------------------

github_username: # your GitHub user name
gitlab_username: # your GitLab user name
x_username: # your X handle
mastodon_username: # your mastodon instance+username in the format instance.tld/@username
linkedin_username: # your LinkedIn user name
telegram_username: # your Telegram user name
scholar_userid: # your Google Scholar ID
semanticscholar_id: # your Semantic Scholar ID
whatsapp_number: # your WhatsApp number (full phone number in international format. Omit any zeroes, brackets, or dashes when adding the phone number in international format.)
orcid_id: # your ORCID ID
medium_username: # your Medium username
quora_username: # your Quora username
publons_id: # your ID on Publons
lattes_id: # your ID on Lattes (Brazilian Lattes CV)
osf_id: # your OSF ID
research_gate_profile: # your profile on ResearchGate
scopus_id: # your profile on Scopus
blogger_url: # your blogger URL
work_url: # work page URL
keybase_username: # your keybase user name
wikidata_id: # your wikidata id
wikipedia_id: # your wikipedia id (Case sensitive)
dblp_url: # your DBLP profile url
stackoverflow_id: # your stackoverflow id
kaggle_id: # your kaggle id
lastfm_id: # your lastfm id
spotify_id: # your spotify id
pinterest_id: # your pinterest id
unsplash_id: # your unsplash id
instagram_id: # your instagram id
facebook_id: # your facebook id
youtube_id: # your youtube channel id (youtube.com/@<youtube_id>)
discord_id: # your discord id (18-digit unique numerical identifier)
zotero_username: # your zotero username
wechat_qr: # filename of your wechat qr-code saved as an image (e.g., wechat-qr.png if saved to assets/img/wechat-qr.png)

contact_note: >
  For any enquiries, please reach out by e-mail at andrea[dot]weisse[at]ed.ac.uk

# -----------------------------------------------------------------------------
# Analytics and search engine verification
# -----------------------------------------------------------------------------

# For Google Analytics, see https://support.google.com/analytics/answer/10447272?hl=en&ref_topic=14088998&sjid=5129943941510317771-SA#zippy=%2Cgoogle-sites
# and follow the instructions for Google Sites. You will need to create a Google Analytics property and copy the Google tag ID.
google_analytics: # your Google Analytics measurement ID (format: G-XXXXXXXXXX)
cronitor_analytics: # cronitor RUM analytics site ID (format: XXXXXXXXX)

# For Google Search Console, see https://support.google.com/webmasters/answer/9008080?hl=en#meta_tag_verification&zippy=%2Chtml-tag
google_site_verification: K6i_ICGHYk30gcMZ37na3VpTYtWUej7KSMgSjUeXDdY # your google-site-verification ID (Google Search Console)
bing_site_verification: # out your bing-site-verification ID (Bing Webmaster)

# -----------------------------------------------------------------------------
# Blog
# -----------------------------------------------------------------------------

blog_name: # blog_name will be displayed in your blog page
blog_nav_title: # your blog must have a title for it to be displayed in the nav bar
blog_description: a simple whitespace theme for academics
permalink: /blog/:year/:title/

# Pagination
pagination:
  enabled: true

related_blog_posts:
  enabled: true
  max_related: 5

# Giscus comments (RECOMMENDED)
# Follow instructions on https://giscus.app/ to setup for your repo to fill out the information below.
giscus:
  repo: # <your-github-user-name>/<your-github-repo-name>
  repo_id: # leave empty or specify your repo_id (see https://giscus.app/)
  category: Comments # name of the category under which discussions will be created
  category_id: # leave empty or specify your category_id (see https://giscus.app/)
  mapping: title # identify discussions by post title
  strict: 1 # use strict identification mode
  reactions_enabled: 1 # enable (1) or disable (0) emoji reactions
  input_position: bottom # whether to display input form below (bottom) or above (top) the comments
  theme: preferred_color_scheme # name of the color scheme (preferred works well with al-folio light/dark mode)
  emit_metadata: 0
  lang: en

# Disqus comments (DEPRECATED)
disqus_shortname: al-folio # put your disqus shortname
# https://help.disqus.com/en/articles/1717111-what-s-a-shortname

# External sources.
# If you have blog posts published on medium.com or other external sources,
# you can display them in your blog by adding a link to the RSS feed.
external_sources:
  - name: medium.com
    rss_url: https://medium.com/@al-folio/feed

# -----------------------------------------------------------------------------
# Collections
# -----------------------------------------------------------------------------

collections:
  news:
    defaults:
      layout: post
    output: true
    permalink: /news/:path/
  projects:
    output: true
    permalink: /projects/:path/
  people:
    output: true
    permalink: /people/:path/
  alumni:
    output: false
    permalink: /alumni/:path/

announcements:
  enabled: true
  scrollable: true # adds a vertical scroll bar if there are more than 3 news items
  limit: # leave blank to include all the news in the `_news` folder

latest_posts:
  enabled: false
  scrollable: true # adds a vertical scroll bar if there are more than 3 new posts items
  limit: # leave blank to include all the blog posts

# -----------------------------------------------------------------------------
# Jekyll settings
# -----------------------------------------------------------------------------

# Markdown and syntax highlight
markdown: kramdown
highlighter: rouge
kramdown:
  input: GFM
  syntax_highlighter_opts:
    css_class: "highlight"
    span:
      line_numbers: false
    block:
      line_numbers: false
      start_line: 1

# Includes & excludes
include: ["_pages"]
exclude:
  - bin
  - CONTRIBUTING.md
  - CUSTOMIZE.md
  - docker-compose.yml
  - Dockerfile
  - FAQ.md
  - Gemfile
  - Gemfile.lock
  - INSTALL.md
  - LICENSE
  - package.json
  - package-lock.json
  - purgecss.config.js
  - README.md
  - vendor
keep_files:
  - CNAME
  - .nojekyll

# Plug-ins
plugins:
  - jekyll-archives
  - jekyll-email-protect
  - jekyll-feed
  - jekyll-get-json
  - jekyll-imagemagick
  - jekyll-jupyter-notebook
  - jekyll-link-attributes
  - jekyll-minifier
  - jekyll-paginate-v2
  - jekyll/scholar
  - jekyll-sitemap
  - jekyll-toc
  - jekyll-twitter-plugin
  - jemoji

# Sitemap settings
defaults:
  - scope:
      path: "assets"
    values:
      sitemap: false

sass:
  style: compressed

# -----------------------------------------------------------------------------
# Jekyll Minifier
# -----------------------------------------------------------------------------

jekyll-minifier:
  exclude: ["robots.txt"]
  uglifier_args:
    harmony: true

# -----------------------------------------------------------------------------
# Jekyll Archives
# -----------------------------------------------------------------------------

jekyll-archives:
  enabled: [year, tags, categories] # enables year, tag and category archives (remove if you need to disable one of them).
  layouts:
    year: archive-year
    tag: archive-tag
    category: archive-category
  permalinks:
    year: "/blog/:year/"
    tag: "/blog/tag/:name/"
    category: "/blog/category/:name/"

display_tags: ["formatting", "images", "links", "math", "code"] # these tags will be displayed on the front page of your blog
display_categories: ["blockquotes"] # these categories will be displayed on the front page of your blog

# -----------------------------------------------------------------------------
# Jekyll Scholar
# -----------------------------------------------------------------------------

scholar:
  last_name:
  first_name:

  style: apa
  locale: en

  source: /_bibliography/
  bibliography: papers.bib
  bibliography_template: bib
  # Note: if you have latex math in your bibtex, the latex filter
  # preprocessing may conflict with MathJAX if the latter is enabled.
  # See https://github.com/alshedivat/al-folio/issues/357.
  bibtex_filters: [latex, smallcaps, superscript]

  replace_strings: true
  join_strings: true

  details_dir: bibliography
  details_link: Details

  query: "@*"
  group_by: year
  group_order: descending

# Display different badges withs stats for your publications
enable_publication_badges:
  altmetric: false # Altmetric badge (https://www.altmetric.com/products/altmetric-badges/)
  dimensions: false # Dimensions badge (https://badge.dimensions.ai/)
  google_scholar: false # Google Scholar badge (https://scholar.google.com/intl/en/scholar/citations.html)

# Filter out certain bibtex entry keywords used internally from the bib output
filtered_bibtex_keywords:
  [abbr, abstract, altmetric, arxiv, bibtex_show, blog, code, html, pdf, poster, preview, selected, slides, supp, video, website]

# Maximum number of authors to be shown for each publication (more authors are visible on click)
max_author_limit: 5 # leave blank to always show all authors
more_authors_animation_delay: 10 # more authors are revealed on click using animation; smaller delay means faster animation

# Enables publication thumbnails. If disabled, none of the publications will display thumbnails, even if specified in the bib entry.
enable_publication_thumbnails: true

# -----------------------------------------------------------------------------
# Jekyll Link Attributes
# -----------------------------------------------------------------------------

# These are the defaults
external_links:
  enabled: true
  rel: external nofollow noopener
  target: _blank
  exclude:

# -----------------------------------------------------------------------------
# Responsive WebP Images
# -----------------------------------------------------------------------------

# MAKE SURE imagemagick is installed and on your PATH before enabling imagemagick. In a terminal, run:
#   convert -version
imagemagick:
  enabled: true # enables responsive images for your site (recommended, see https://github.com/alshedivat/al-folio/issues/537)
  widths:
    - 480
    - 800
    - 1400
  input_directories:
    - assets/img/
  input_formats:
    - ".jpg"
    - ".jpeg"
    - ".png"
    - ".tiff"
    - ".gif"
  output_formats:
    webp: "-quality 85"

# Lazy loading images
#   If you enable lazy loading, all images will add the loading="lazy" attribute.
#   This will make your site load faster, but it may not be supported in all browsers.
#   You can also set loading="" to other values for specific images to override the default behavior.
#   Options: "auto", "eager", "lazy"
#   See https://web.dev/browser-level-image-lazy-loading/ for more information.
lazy_loading_images: true # enables lazy loading of images (recommended)

# -----------------------------------------------------------------------------
# Optional Features
# -----------------------------------------------------------------------------

enable_google_analytics: false # enables google analytics
enable_cronitor_analytics: false # enables cronitor RUM analytics
enable_google_verification: true # enables google site verification
enable_bing_verification: false # enables bing site verification
enable_masonry: true # enables automatic project cards arrangement
enable_math: true # enables math typesetting (uses MathJax)
enable_tooltips: false # enables automatic tooltip links generated for each section titles on pages and posts
enable_darkmode: true # enables switching between light/dark modes
enable_navbar_social: false # enables displaying social links in the navbar on the about page
enable_project_categories: false # enables categorization of projects into multiple categories
enable_people_categories: false # enables categorization of people into multiple categories
enable_medium_zoom: true # enables image zoom feature (as on medium.com)
enable_progressbar: true # enables a horizontal progress bar linked to the vertical scroll position

# -----------------------------------------------------------------------------
# Library versions
# -----------------------------------------------------------------------------

bootstrap-table:
  version: "1.22.1"
chartjs:
  version: "4.4.1"
d3:
  version: "7.8.5"
  integrity: "sha256-1rA678n2xEx7x4cTZ5x4wpUCj6kUMZEZ5cxLSVSFWxw="
diff2html:
  version: "3.4.47"
  integrity:
    css: "sha256-IMBK4VNZp0ivwefSn51bswdsrhk0HoMTLc2GqFHFBXg="
    js: "sha256-eU2TVHX633T1o/bTQp6iIJByYJEtZThhF9bKz/DcbbY="
echarts:
  version: "5.4.3"
  integrity:
    library: "sha256-EVZCmhajjLhgTcxlGMGUBtQiYULZCPjt0uNTFEPFTRk="
    dark_theme: "sha256-UmFIP/4VvOqBDIl2QWl1HBuAJ1XWs/iFZxT5yJRZOKo="
highlightjs:
  version: "11.9.0"
  integrity:
    css:
      light: "sha256-Oppd74ucMR5a5Dq96FxjEzGF7tTw2fZ/6ksAqDCM8GY="
      dark: "sha256-nyCNAiECsdDHrr/s2OQsp5l9XeY2ZJ0rMepjCT2AkBk="
imagesloaded:
  version: "5.0.0"
  integrity: "sha256-htrLFfZJ6v5udOG+3kNLINIKh2gvoKqwEhHYfTTMICc="
img-comparison-slider:
  version: "8.0.6"
jquery:
  version: "3.6.0"
  integrity: "sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4="
leaflet:
  version: "1.9.4"
  integrity:
    css: "sha256-p4NxAoJBhIIN+hmNHrzRCf9tD/miZyoHS5obTRR9BMY="
    js: "sha256-20nQCchB9co0qIjJZRGuk2/Z9VM+kNiyxNV1lvTlZBo="
mathjax:
  version: "3.2.0"
masonry:
  version: "4.2.2"
  integrity: "sha256-Nn1q/fx0H7SNLZMQ5Hw5JLaTRZp0yILA/FRexe19VdI="
mdb:
  version: "4.20.0"
  integrity:
    css: "sha256-jpjYvU3G3N6nrrBwXJoVEYI/0zw8htfFnhT9ljN3JJw="
    js: "sha256-NdbiivsvWt7VYCt6hYNT3h/th9vSTL4EDWeGs5SN3DA="
medium_zoom:
  version: "1.1.0"
  integrity: "sha256-ZgMyDAIYDYGxbcpJcfUnYwNevG/xi9OHKaR/8GK+jWc="
mermaid:
  version: "10.7.0"
  integrity: "sha256-TtLOdUA8mstPoO6sGvHIGx2ceXrrX4KgIItO06XOn8A="
swiper:
  version: "11.0.5"
  integrity:
    css: "sha256-yUoNxsvX+Vo8Trj3lZ/Y5ZBf8HlBFsB6Xwm7rH75/9E="
    js: "sha256-BPrwikijIybg9OQC5SYFFqhBjERYOn97tCureFgYH1E="
vega:
  version: "5.27.0"
  integrity: "sha256-Yot/cfgMMMpFwkp/5azR20Tfkt24PFqQ6IQS+80HIZs="
vega-embed:
  version: "6.24.0"
  integrity: "sha256-FPCJ9JYCC9AZSpvC/t/wHBX7ybueZhIqOMjpWqfl3DU="
vega-lite:
  version: "5.16.3"
  integrity: "sha256-TvBvIS5jUN4BSy009usRjNzjI1qRrHPYv7xVLJyjUyw="

# -----------------------------------------------------------------------------
# Get external JSON data
# -----------------------------------------------------------------------------

jekyll_get_json:
  - data: resume
    json: assets/json/resume.json # it can also be an url
jsonresume:
  - basics
  - work
  - education
  - publications
  - projects
  - volunteer
  - awards
  - certificates
  - skills
  - languages
  - interests
  - references