_config.yml

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

title: Christian B. Macdonald, Ph.D. # the website title (if blank, full name will be used instead)
first_name: Christian
middle_name: B.
last_name: Macdonald
name: Christian B. Macdonald, Ph.D.
email: christian.macdonald at ucsf.edu
description: > # the ">" symbol means to ignore newlines until "footer_text:"
  Postdoctoral scholar at UCSF.

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>.

lang: en # the language of your site (for example: en, fr, cn, ru, etc.)

url: https://odcambc.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

cv_nav: true # set to true to have a link to a CV in the header

# -----------------------------------------------------------------------------
# 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: true

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

navbar_fixed: true
footer_fixed: true
search_enabled: true
socials_in_search: true

# Dimensions
max_width: 930px

# 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: odcambc
scholar_userid: pyTBwS0AAAAJ
orcid_id: 0000-0002-0201-8832
work_url: # work page URL

contact_note: >
  Email usually works best.

# -----------------------------------------------------------------------------
# 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: G-62JQ3VDEY8
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: # your google-site-verification ID (Google Search Console)
bing_site_verification: # out your bing-site-verification ID (Bing Webmaster)

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

blog_name: blog # blog_name will be displayed in your blog page
blog_description: basically notes
permalink: /blog/:year/:title/
lsi: false # produce an index for related posts

# Pagination
pagination:
  enabled: true

related_blog_posts:
  enabled: false
  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.

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

collections:
  news:
    defaults:
      layout: post
    output: true
    permalink: /news/:path/
  publications:
    output: true
    permalink: /publications/:path/
  research:
    output: true
    permalink: /research/:path/
  reviews:
    output: true
    permalink: /reviews/:path/
  projects:
    output: false
    permalink: /projects/:path/

announcements:
  enabled: true
  scrollable: true # adds a vertical scroll bar if there are more than 3 news items
  limit: 5 # leave blank to include all the news in the `_news` folder

latest_posts:
  enabled: true
  scrollable: true # adds a vertical scroll bar if there are more than 3 new posts items
  limit: 3 # 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
  - Dockerfile
  - docker-compose.yml
  - docker-compose-slim.yml
  - FAQ.md
  - Gemfile
  - Gemfile.lock
  - INSTALL.md
  - LICENSE
  - lighthouse_results/
  - package.json
  - package-lock.json
  - _pages/about_einstein.md
  - purgecss.config.js
  - README.md
  - readme_preview/
  - 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-tabs
  - 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", "assets/js/search/*.js"]
  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: Macdonald
  first_name: Christian B.

  style: genome-biology-and-evolution
  locale: en

  sort_by: year, month
  order: descending

  source: /_bibliography/
  bibliography: papers.bib
  bibliography_template: bib

  replace_strings: true
  join_strings: true

  details_dir: bibliography
  details_layout: bibtex.html
  details_link: Details

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

# Display different badges withs stats for your publications
enable_publication_badges:
  altmetric: true # Altmetric badge (https://www.altmetric.com/products/altmetric-badges/)
  dimensions: true # Dimensions badge (https://badge.dimensions.ai/)
  google_scholar: true # 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,
    additional_info,
    altmetric,
    arxiv,
    award,
    award_name,
    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: 3 # 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: false # 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: true # enables categorization of projects 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
enable_video_embedding: false # enables video embedding for bibtex entries. If false, the button opens the video link in a new window.

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

# Add the url, version and integrity hash of the libraries you use in your site.
# The integrity hash is used to ensure that the library is not tampered with.
# Integrity hashes not provided by the libraries were generated using https://www.srihash.org/
third_party_libraries:
  download: false # if true, download the versions of the libraries specified below and use the downloaded files
  bootstrap-table:
    integrity:
      css: "sha256-uRX+PiRTR4ysKFRCykT8HLuRCub26LgXJZym3Yeom1c="
      js: "sha256-4rppopQE9POKfukn2kEvhJ9Um25Cf6+IDVkARD0xh78="
    url:
      css: "https://cdn.jsdelivr.net/npm/bootstrap-table@{{version}}/dist/bootstrap-table.min.css"
      js: "https://cdn.jsdelivr.net/npm/bootstrap-table@{{version}}/dist/bootstrap-table.min.js"
    version: "1.22.4"
  chartjs:
    integrity:
      js: "sha256-0q+JdOlScWOHcunpUk21uab1jW7C1deBQARHtKMcaB4="
    url:
      js: "https://cdn.jsdelivr.net/npm/chart.js@{{version}}/dist/chart.umd.min.js"
    version: "4.4.1"
  d3:
    integrity:
      js: "sha256-1rA678n2xEx7x4cTZ5x4wpUCj6kUMZEZ5cxLSVSFWxw="
    url:
      js: "https://cdn.jsdelivr.net/npm/d3@{{version}}/dist/d3.min.js"
    version: "7.8.5"
  diff2html:
    integrity:
      css: "sha256-IMBK4VNZp0ivwefSn51bswdsrhk0HoMTLc2GqFHFBXg="
      js: "sha256-eU2TVHX633T1o/bTQp6iIJByYJEtZThhF9bKz/DcbbY="
    url:
      css: "https://cdn.jsdelivr.net/npm/diff2html@{{version}}/bundles/css/diff2html.min.css"
      js: "https://cdn.jsdelivr.net/npm/diff2html@{{version}}/bundles/js/diff2html-ui.min.js"
    version: "3.4.47"
  echarts:
    integrity:
      js:
        library: "sha256-QvgynZibb2U53SsVu98NggJXYqwRL7tg3FeyfXvPOUY="
        dark_theme: "sha256-sm6Ui9w41++ZCWmIWDLC18a6ki72FQpWDiYTDxEPXwU="
    url:
      js:
        library: "https://cdn.jsdelivr.net/npm/echarts@{{version}}/dist/echarts.min.js"
        dark_theme: "https://cdn.jsdelivr.net/npm/echarts@{{version}}/theme/dark-fresh-cut.js"
    version: "5.5.0"
  google_fonts:
    url:
      fonts: "https://fonts.googleapis.com/css?family=Roboto:300,400,500,700|Roboto+Slab:100,300,400,500,700|Material+Icons&display=swap"
  highlightjs:
    integrity:
      css:
        light: "sha256-Oppd74ucMR5a5Dq96FxjEzGF7tTw2fZ/6ksAqDCM8GY="
        dark: "sha256-nyCNAiECsdDHrr/s2OQsp5l9XeY2ZJ0rMepjCT2AkBk="
    url:
      css:
        light: "https://cdn.jsdelivr.net/npm/highlight.js@{{version}}/styles/github.min.css"
        dark: "https://cdn.jsdelivr.net/npm/highlight.js@{{version}}/styles/github-dark.min.css"
    version: "11.9.0"
  imagesloaded:
    integrity:
      js: "sha256-htrLFfZJ6v5udOG+3kNLINIKh2gvoKqwEhHYfTTMICc="
    url:
      js: https://cdn.jsdelivr.net/npm/imagesloaded@{{version}}/imagesloaded.pkgd.min.js
    version: "5.0.0"
  img-comparison-slider:
    integrity:
      css: "sha256-3qTIuuUWIFnnU3LpQMjqiXc0p09rvd0dmj+WkpQXSR8="
      js: "sha256-EXHg3x1K4oIWdyohPeKX2ZS++Wxt/FRPH7Nl01nat1o="
      map: "sha256-3wfqS2WU5kGA/ePcgFzJXl5oSN1QsgZI4/edprTgX8w="
    url:
      css: "https://cdn.jsdelivr.net/npm/img-comparison-slider@{{version}}/dist/styles.min.css"
      js: "https://cdn.jsdelivr.net/npm/img-comparison-slider@{{version}}/dist/index.min.js"
      map: "https://cdn.jsdelivr.net/npm/img-comparison-slider@{{version}}/dist/index.js.map"
    version: "8.0.6"
  jquery:
    integrity:
      js: "sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4="
    url:
      js: "https://cdn.jsdelivr.net/npm/jquery@{{version}}/dist/jquery.min.js"
    version: "3.6.0"
  leaflet:
    integrity:
      css: "sha256-q9ba7o845pMPFU+zcAll8rv+gC+fSovKsOoNQ6cynuQ="
      js: "sha256-MgH13bFTTNqsnuEoqNPBLDaqxjGH+lCpqrukmXc8Ppg="
      js_map: "sha256-YAoQ3FzREN4GmVENMir8vgHHypC0xfSK3CAxTHCqx1M="
    local:
      images: "images/"
    url:
      css: "https://cdn.jsdelivr.net/npm/leaflet@{{version}}/dist/leaflet.min.css"
      images: "https://cdn.jsdelivr.net/npm/leaflet@{{version}}/dist/images/"
      js: "https://cdn.jsdelivr.net/npm/leaflet@{{version}}/dist/leaflet.min.js"
      js_map: "https://cdn.jsdelivr.net/npm/leaflet@{{version}}/dist/leaflet.js.map"
    version: "1.9.4"
  mathjax:
    integrity:
      js: "sha256-rjmgmaB99riUNcdlrDtcAiwtLIojSxNyUFdl+Qh+rB4="
    local:
      fonts: "output/chtml/fonts/woff-v2/"
    url:
      fonts: "https://cdn.jsdelivr.net/npm/mathjax@{{version}}/es5/output/chtml/fonts/woff-v2/"
      js: "https://cdn.jsdelivr.net/npm/mathjax@{{version}}/es5/tex-mml-chtml.min.js"
    version: "3.2.0"
  masonry:
    integrity:
      js: "sha256-Nn1q/fx0H7SNLZMQ5Hw5JLaTRZp0yILA/FRexe19VdI="
    url:
      js: "https://cdn.jsdelivr.net/npm/masonry-layout@{{version}}/dist/masonry.pkgd.min.js"
    version: "4.2.2"
  mdb:
    integrity:
      css: "sha256-jpjYvU3G3N6nrrBwXJoVEYI/0zw8htfFnhT9ljN3JJw="
      css_map: "sha256-iYYMNfsJdVZjvsebJulg09miBXM4/GMTJgv1u5EZFFM="
      js: "sha256-NdbiivsvWt7VYCt6hYNT3h/th9vSTL4EDWeGs5SN3DA="
      js_map: "sha256-UPgyn4YNsT0khkBK5553QwhnlbTlU0aa+igyc6qP1bE="
    url:
      css: "https://cdn.jsdelivr.net/npm/mdbootstrap@{{version}}/css/mdb.min.css"
      css_map: "https://cdn.jsdelivr.net/npm/mdbootstrap@{{version}}/css/mdb.min.css.map"
      js: "https://cdn.jsdelivr.net/npm/mdbootstrap@{{version}}/js/mdb.min.js"
      js_map: "https://cdn.jsdelivr.net/npm/mdbootstrap@{{version}}/js/mdb.min.js.map"
    version: "4.20.0"
  medium_zoom:
    integrity:
      js: "sha256-ZgMyDAIYDYGxbcpJcfUnYwNevG/xi9OHKaR/8GK+jWc="
    url:
      js: "https://cdn.jsdelivr.net/npm/medium-zoom@{{version}}/dist/medium-zoom.min.js"
    version: "1.1.0"
  mermaid:
    integrity:
      js: "sha256-TtLOdUA8mstPoO6sGvHIGx2ceXrrX4KgIItO06XOn8A="
    url:
      js: "https://cdn.jsdelivr.net/npm/mermaid@{{version}}/dist/mermaid.min.js"
    version: "10.7.0"
  polyfill:
    url:
      js: "https://cdnjs.cloudflare.com/polyfill/v{{version}}/polyfill.min.js?features=es6"
    version: "3"
  pseudocode:
    integrity:
      css: "sha256-VwMV//xgBPDyRFVSOshhRhzJRDyBmIACniLPpeXNUdc="
      js: "sha256-aVkDxqyzrB+ExUsOY9PdyelkDhn/DfrjWu08aVpqNlo="
    url:
      css: "https://cdn.jsdelivr.net/npm/pseudocode@{{version}}/build/pseudocode.min.css"
      js: "https://cdn.jsdelivr.net/npm/pseudocode@{{version}}/build/pseudocode.min.js"
    version: "2.4.1"
  swiper:
    integrity:
      css: "sha256-yUoNxsvX+Vo8Trj3lZ/Y5ZBf8HlBFsB6Xwm7rH75/9E="
      js: "sha256-BPrwikijIybg9OQC5SYFFqhBjERYOn97tCureFgYH1E="
      map: "sha256-lbF5CsospW93otqvWOIbbhj80CjazrZXvamD7nC7TBI="
    url:
      css: "https://cdn.jsdelivr.net/npm/swiper@{{version}}/swiper-bundle.min.css"
      js: "https://cdn.jsdelivr.net/npm/swiper@{{version}}/swiper-element-bundle.min.js"
      map: "https://cdn.jsdelivr.net/npm/swiper@{{version}}/swiper-element-bundle.min.js.map"
    version: "11.0.5"
  swiper-map:
    integrity:
      js: "sha256-hlZaH8ySXX97bZaetnrtYlKuhx3oEXFz/s2IXchu6vk="
    url:
      js: "https://cdn.jsdelivr.net/npm/swiper@11.1.0/swiper-element-bundle.min.js.map"
    version: "11.0.5"
  vega:
    integrity:
      js: "sha256-Yot/cfgMMMpFwkp/5azR20Tfkt24PFqQ6IQS+80HIZs="
      js_map: "sha256-z0x9ICA65dPkZ0JVa9wTImfF6n7AJsKc6WlFE96/wNA="
    url:
      js: "https://cdn.jsdelivr.net/npm/vega@{{version}}/build/vega.min.js"
      js_map: "https://cdn.jsdelivr.net/npm/vega@{{version}}/build/vega.min.js.map"
    version: "5.27.0"
  vega-embed:
    integrity:
      js: "sha256-FPCJ9JYCC9AZSpvC/t/wHBX7ybueZhIqOMjpWqfl3DU="
      js_map: "sha256-VBbfSEFYSMdX/rTdGrONEHNP6BprCB7H/LpMMNt/cPA="
    url:
      js: "https://cdn.jsdelivr.net/npm/vega-embed@{{version}}/build/vega-embed.min.js"
      js_map: "https://cdn.jsdelivr.net/npm/vega-embed@{{version}}/build/vega-embed.min.js.map"
    version: "6.24.0"
  vega-lite:
    integrity:
      js: "sha256-TvBvIS5jUN4BSy009usRjNzjI1qRrHPYv7xVLJyjUyw="
      js_map: "sha256-l2I4D5JC23Ulsu6e3sKVe5AJ+r+DFkzkKnZS8nUGz28="
    url:
      js: "https://cdn.jsdelivr.net/npm/vega-lite@{{version}}/build/vega-lite.min.js"
      js_map: "https://cdn.jsdelivr.net/npm/vega-lite@{{version}}/build/vega-lite.min.js.map"
    version: "5.16.3"

# -----------------------------------------------------------------------------
# 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