Init sources

Gemfile

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+source 'https://rubygems.org'
+gem 'github-pages'
+gem 'jekyll-scholar'

Gemfile.lock

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+GEM
+  remote: https://rubygems.org/
+  specs:
+    RedCloth (4.2.9)
+    activesupport (4.2.4)
+      i18n (~> 0.7)
+      json (~> 1.7, >= 1.7.7)
+      minitest (~> 5.1)
+      thread_safe (~> 0.3, >= 0.3.4)
+      tzinfo (~> 1.1)
+    addressable (2.3.8)
+    bibtex-ruby (4.0.14)
+      latex-decode (~> 0.0)
+    blankslate (2.1.2.4)
+    citeproc (1.0.2)
+      namae (~> 0.8)
+    citeproc-ruby (1.1.0)
+      citeproc (>= 1.0.2, < 2.0)
+      csl (~> 1.4)
+    classifier-reborn (2.0.3)
+      fast-stemmer (~> 1.0)
+    coffee-script (2.4.1)
+      coffee-script-source
+      execjs
+    coffee-script-source (1.9.1.1)
+    colorator (0.1)
+    csl (1.4.3)
+      namae (~> 0.7)
+    csl-styles (1.0.1.6)
+      csl (~> 1.0)
+    ethon (0.8.0)
+      ffi (>= 1.3.0)
+    execjs (2.6.0)
+    fast-stemmer (1.0.2)
+    ffi (1.9.10)
+    gemoji (2.1.0)
+    github-pages (39)
+      RedCloth (= 4.2.9)
+      github-pages-health-check (~> 0.2)
+      jekyll (= 2.4.0)
+      jekyll-coffeescript (= 1.0.1)
+      jekyll-feed (= 0.3.1)
+      jekyll-mentions (= 0.2.1)
+      jekyll-redirect-from (= 0.8.0)
+      jekyll-sass-converter (= 1.3.0)
+      jekyll-sitemap (= 0.8.1)
+      jemoji (= 0.5.0)
+      kramdown (= 1.5.0)
+      liquid (= 2.6.2)
+      maruku (= 0.7.0)
+      mercenary (~> 0.3)
+      pygments.rb (= 0.6.3)
+      rdiscount (= 2.1.7)
+      redcarpet (= 3.3.2)
+      terminal-table (~> 1.4)
+    github-pages-health-check (0.5.3)
+      addressable (~> 2.3)
+      net-dns (~> 0.8)
+      public_suffix (~> 1.4)
+      typhoeus (~> 0.7)
+    html-pipeline (1.9.0)
+      activesupport (>= 2)
+      nokogiri (~> 1.4)
+    i18n (0.7.0)
+    jekyll (2.4.0)
+      classifier-reborn (~> 2.0)
+      colorator (~> 0.1)
+      jekyll-coffeescript (~> 1.0)
+      jekyll-gist (~> 1.0)
+      jekyll-paginate (~> 1.0)
+      jekyll-sass-converter (~> 1.0)
+      jekyll-watch (~> 1.1)
+      kramdown (~> 1.3)
+      liquid (~> 2.6.1)
+      mercenary (~> 0.3.3)
+      pygments.rb (~> 0.6.0)
+      redcarpet (~> 3.1)
+      safe_yaml (~> 1.0)
+      toml (~> 0.1.0)
+    jekyll-coffeescript (1.0.1)
+      coffee-script (~> 2.2)
+    jekyll-feed (0.3.1)
+    jekyll-gist (1.3.4)
+    jekyll-mentions (0.2.1)
+      html-pipeline (~> 1.9.0)
+      jekyll (~> 2.0)
+    jekyll-paginate (1.1.0)
+    jekyll-redirect-from (0.8.0)
+      jekyll (>= 2.0)
+    jekyll-sass-converter (1.3.0)
+      sass (~> 3.2)
+    jekyll-scholar (4.5.0)
+      bibtex-ruby (~> 4.0, >= 4.0.13)
+      citeproc-ruby (~> 1.0)
+      csl-styles (~> 1.0)
+      jekyll (~> 2.0)
+    jekyll-sitemap (0.8.1)
+    jekyll-watch (1.3.0)
+      listen (~> 3.0)
+    jemoji (0.5.0)
+      gemoji (~> 2.0)
+      html-pipeline (~> 1.9)
+      jekyll (>= 2.0)
+    json (1.8.3)
+    kramdown (1.5.0)
+    latex-decode (0.2.2)
+      unicode (~> 0.4)
+    liquid (2.6.2)
+    listen (3.0.3)
+      rb-fsevent (>= 0.9.3)
+      rb-inotify (>= 0.9)
+    maruku (0.7.0)
+    mercenary (0.3.5)
+    mini_portile (0.6.2)
+    minitest (5.8.1)
+    namae (0.10.1)
+    net-dns (0.8.0)
+    nokogiri (1.6.6.2)
+      mini_portile (~> 0.6.0)
+    parslet (1.5.0)
+      blankslate (~> 2.0)
+    posix-spawn (0.3.11)
+    public_suffix (1.5.1)
+    pygments.rb (0.6.3)
+      posix-spawn (~> 0.3.6)
+      yajl-ruby (~> 1.2.0)
+    rb-fsevent (0.9.6)
+    rb-inotify (0.9.5)
+      ffi (>= 0.5.0)
+    rdiscount (2.1.7)
+    redcarpet (3.3.2)
+    safe_yaml (1.0.4)
+    sass (3.4.18)
+    terminal-table (1.5.2)
+    thread_safe (0.3.5)
+    toml (0.1.2)
+      parslet (~> 1.5.0)
+    typhoeus (0.8.0)
+      ethon (>= 0.8.0)
+    tzinfo (1.2.2)
+      thread_safe (~> 0.1)
+    unicode (0.4.4.2)
+    yajl-ruby (1.2.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  github-pages
+  jekyll-scholar
+
+BUNDLED WITH
+   1.10.6

README.md

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+# Biome website

_config.yml

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+# Site settings
+title: Theoretical Ecosystem Ecology lab
+email: [email protected]
+description: > # this means to ignore newlines until "baseurl:"
+  Write an awesome description for your new site here. You can edit this
+  line in _config.yml. It will appear in your document head meta (for
+  Google search results) and in your feed.xml site description.
+baseurl: "" # the subpath of your site, e.g. /blog/
+url: "http://yourdomain.com" # the base hostname & protocol for your site
+twitter_username: jekyllrb
+github_username:  jekyll
+
+# Build settings
+markdown: kramdown
+
+scholar:
+  style: ieee
+  locale: en
+  repository: assets/pdf
+  sort_by: year
+  order: reverse
+
+  source: _bibliography
+  bibliography: publi_lab.bib
+  bibliography_template: bib
+
+  replace_strings: true
+  join_strings:    false
+
+  bibliography_list_tag: p
+  bibliography_item_tag: p
+
+  query: "@*"

_data/members.yml

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+- Name: Dominique
+  LastName: Gravel
+  Status: Principal investigator
+  Github: DominiqueGravel
+  Email: [email protected]
+  Image: Photo_Gravel.jpg
+
+- Name: Steve
+  LastName: Vissault
+  Status: M.Sc. Student
+  Year_start: 2013
+  Year_finish: 2015
+  Supervisor: Dominique Gravel
+  CoSupervisor: Isabelle Boulangeat & Matt Talluto
+  Title: Simulate the Eastern Boreal-Temperate forests ecotone under Climate Change
+  Abstract_fr: Fr - Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+  Abstract_en: En - Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+  Website: www.steve-vissault.me
+  Github: SteveViss
+  Email: [email protected]
+  Image: steve.png
+
+
+- Name: Amael
+  LastName: Lesquin
+  Status: Ph.D. Student
+  Year_start: 2014
+  Year_finish: 2018
+  Supervisor: Dominique Gravel
+  CoSupervisor: Isabelle Boulangeat
+  Title: Development of diffusion model to understand tree species migration under climate change constraints.
+  Abstract_fr: Fr - Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+  Abstract_en: En - Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+  Email: [email protected]
+  Image: amael.png
+
+- Name: Claire
+  LastName: Jacquet
+  Status: Ph.D. Student
+  Year_start: 2012
+  Year_finish: 2016
+  Supervisor: Dominique Gravel
+  CoSupervisor: David Moulliot
+  Title: Theoretical integration of biogeography and ecosystem functioning.
+  Abstract_fr: Fr - Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+  Abstract_en: En - Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+  Email: [email protected]
+  Image: claire.png
+
+- Name: Philippe
+  LastName: Desjardins-Proulx
+  Status: Ph.D. Student
+  Year_start: 2012
+  Year_finish: 2016
+  Supervisor: Dominique Gravel
+  CoSupervisor: Timothée Poisot
+  Title: Deep transfer learning in complex ecosystems
+  Abstract_fr: Fr - Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+  Abstract_en: En - Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+  Email: [email protected]
+  Image: phdp.jpg
+
+- Name: Timothée
+  LastName: Poisot
+  Status: Post-Doc
+  Position: Assistant professor at the University of Montreal
+  Year_start: 2011
+  Year_finish: 2013
+  Supervisor: Dominique Gravel
+  Website: timotheepoisot.fr
+  Github: tpoisot
+  Email: [email protected]
+  Image: tim.jpg

_includes/footer.html

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+<footer>
+
+<div class="row" style="padding-top:10px;">
+<div class="large-6 columns">
+  <h5 style='color:white;margin-bottom:0px;font-weight:500;'>Follow us on   <a href="https://github.com/TheoreticalEcosystemEcology"><i class="step fi-social-github" style="font-size: 40px;"></i></a> </h5>
+  As a contribution to the Society, all code developed within the lab are available on Github
+</div>
+<div class="large-6 columns">
+  <h5 style='color:white;margin-bottom:5px;font-weight:500;'>Contact us</h5>
+  <b>Dominique Gravel</b> </br>
+  Canada Research Chair on Biogeography and metacommunity ecology </br>
+  Département de biologie, Université du Québec à Rimouski </br>
+  300, Allée des Ursulines, Rimouski, Qc, G5L 3A1. Canada. </br>
+  418.723.1986 #1752 </br>
+  <a href="mailto:[email protected]">[email protected]</a>
+</div>
+
+<div class="large-12 columns text-left" style="margin-top:20px;margin-bottom:20px">
+  Made with <i class="fi-heart"></i> and <a href="https://jekyllrb.com/">Jekyll</a> by [Biome]
+</div>
+</div>
+<script src="/js/vendor/jquery.js"></script>
+<script src="/js/foundation/foundation.js"></script>
+<script src="/js/foundation/foundation.topbar.js"></script>
+<script src="/js/foundation/foundation.accordion.js"></script>
+<!-- Other JS plugins can be included here -->
+
+<script>
+  $(document).foundation({
+    accordion: {
+      // specify the class used for accordion panels
+      content_class: 'content',
+      // specify the class used for active (or open) accordion panels
+      active_class: 'active',
+      // allow multiple accordion panels to be active at the same time
+      multi_expand: true,
+      // allow accordion panels to be closed by clicking on their headers
+      // setting to false only closes accordion panels when another is opened
+      toggleable: true
+    }
+  });
+</script>
+</footer>

_includes/head.html

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+<head>
+  <meta charset="utf-8">
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+
+  <title>{% if page.title %}{{ page.title }}{% else %}{{ site.title }}{% endif %}</title>
+  <meta name="description" content="{% if page.excerpt %}{{ page.excerpt | strip_html | strip_newlines | truncate: 160 }}{% else %}{{ site.description }}{% endif %}">
+
+  <link rel="stylesheet" href="/css/foundation.css"/>
+  <link rel="stylesheet" href="/css/foundation-icons.css" />
+  <!-- This is how you would link your custom stylesheet -->
+  <link rel="stylesheet" href="/css/app.css"/>
+
+
+  <script src="/js/vendor/modernizr.js"></script>
+
+  <link rel="alternate" type="application/rss+xml" title="{{ site.title }}" href="{{ "/feed.xml" | prepend: site.baseurl | prepend: site.url }}" />
+</head>

_includes/header.html

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+
+<div class="contain-to-grid sticky">
+<nav class="top-bar" data-topbar role="navigation">
+  <ul class="title-area">
+    <li class="name">
+            <h1><a href="/home/"> <span style="  font-family: 'Raleway', sans-serif;font-weight: 300;font-size:18px;">[Biome]</span> Lab</a></h1>
+    </li>
+  </ul>
+  <section class="top-bar-section">
+    <!-- Right Nav Section -->
+    <ul class="right">
+      {% assign pages = site.pages | sort:"weight"  %}
+      {% for node in pages %}
+        {% if page.url == node.url %}
+          <li class="active"><a href="{{node.url}}" class="active">{{node.title}}</a></li>
+        {% else %}
+          <li><a href="{{node.url}}">{{node.title}}</a></li>
+        {% endif %}
+      {% endfor %}
+    </ul>
+
+  </section>
+</nav>
+</div>