steshinoki
diff --git a/‎.github/workflows/scrape_talks.yml
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diff --git a/‎.gitignore
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diff --git a/‎Dockerfile
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diff --git a/‎Gemfile
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diff --git a/‎README.md
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diff --git a/‎_config.yml
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diff --git a/‎_config_docker.yml
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diff --git a/‎_data/navigation.yml
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diff --git a/‎_includes/archive-single-cv.html
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diff --git a/‎_includes/archive-single-talk-cv.html
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diff --git a/‎_includes/archive-single-talk.html
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diff --git a/‎_includes/archive-single.html
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diff --git a/‎_includes/author-profile.html
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diff --git a/‎_includes/comments.html
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diff --git a/‎_includes/footer.html
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diff --git a/‎_includes/head/custom.html
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diff --git a/‎_includes/page__hero.html
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diff --git a/‎_includes/page__taxonomy.html
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@@ -0,0 +1,36 @@
+name: Scrape Talk Locations
+
+on:
+  push:
+    paths:
+      - 'talks/**'
+      - 'talkmap.ipynb'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.9'  # Specify the Python version you need
+
+    - name: Install dependencies
+      run: |
+        pip install jupyter pandas requests beautifulsoup4 geopy  # Add other dependencies as needed
+        pip install getorg --upgrade
+
+    - name: Run Jupyter Notebook
+      run: |
+        jupyter nbconvert --to notebook --execute talkmap.ipynb --output talkmap_out.ipynb
+
+    - name: Commit changes
+      run: |
+        git config user.name "github-actions[bot]"
+        git config user.email "github-actions[bot]@users.noreply.github.com"
+        git add .
+        git commit -m "Automated update of talk locations" || echo "No changes to commit"
+        git push
@@ -1,5 +1,6 @@
-# Ignore the contents of the _site directory
+# Ignore the contents of the _site directory and other cache directories
 _site/
+.sass-cache/
 
 # Ignore the directory for local files during development
 local/
 
@@ -0,0 +1,21 @@
+# Base image: Ruby with necessary dependencies for Jekyll
+FROM ruby:3.2
+
+# Install dependencies
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    nodejs \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set the working directory inside the container
+WORKDIR /usr/src/app
+
+# Copy Gemfile into the container (necessary for `bundle install`)
+COPY Gemfile ./
+
+# Install bundler and dependencies
+RUN gem install bundler:2.3.26 && bundle install
+
+# Command to serve the Jekyll site
+CMD ["jekyll", "serve", "-H", "0.0.0.0", "-w", "--config", "_config.yml,_config_docker.yml"]
+
@@ -1,28 +1,12 @@
-source "https://rubygems.org"
+source 'https://rubygems.org'
 
-# Hello! This is where you manage which Jekyll version is used to run.
-# When you want to use a different version, change it below, save the
-# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
-#
-#     bundle exec jekyll serve
-#
-# This will help ensure the proper Jekyll version is running.
-# Happy Jekylling!
-
-gem "github-pages", group: :jekyll_plugins
-
-# If you want to use Jekyll native, uncomment the line below.
-# To upgrade, run `bundle update`.
-
-# gem "jekyll"
-
-gem "wdm", "~> 0.1.0" if Gem.win_platform?
-
-# If you have any plugins, put them here!
 group :jekyll_plugins do
-  # gem "jekyll-archives"
-  gem "jekyll-feed"
+  gem 'jekyll'
+  gem 'jekyll-feed'
   gem 'jekyll-sitemap'
-  gem 'hawkins'
-  gem "webrick", "~> 1.8"
+  gem 'jekyll-redirect-from'
+  gem 'jemoji'
+  gem 'webrick', '~> 1.8'
 end
+
+gem 'github-pages'
@@ -1,3 +1,3 @@
 Personal website for Stéphanie.
 
-Based on [https://academicpages.github.io/](https://academicpages.github.io/)
+Based on [https://academicpages.github.io/](https://academicpages.github.io/)
@@ -8,6 +8,7 @@
 
 # Basic Site Settings
 locale                   : "en-US"
+site_theme               : "default"
 title                    : "Stéphanie Tramontin Shinoki"
 title_separator          : "-"
 name                     : &name "Stéphanie T. Shinoki"
@@ -38,6 +39,7 @@ author:
   semantic         : # URL
   pubmed           : #"https://www.ncbi.nlm.nih.gov/pubmed/?term=john+snow"
   researchgate     : # URL
+  scopus           : # URL
 
   # Repositories and software development
   bitbucket        : # Username - Update with your username on the site
@@ -71,16 +73,24 @@ author:
   wikipedia        : # Username
   xing             : # Username
   youtube          : # Username
-  zhihu            : # URL
+  zhihu            : # Username
 
+# Publication Category - The following the list of publication categories and their headings
+publication_category:
+  books:
+    title: 'Books'
+  manuscripts:
+    title: 'Journal Articles'    
+  conferences:
+    title: 'Conference Papers'
 
 # Site Settings
 teaser                   :  # filename of teaser fallback teaser image placed in /images/, .e.g. "500x300.png"
 breadcrumbs              : false # true, false (default)
 words_per_minute         : 160
 future                   : true
 read_more                : "disabled" # if enabled, adds "Read more" links to excerpts
-talkmap_link             : false #change to true to add link to talkmap on talks page
+talkmap_link             : false      #change to true to add link to talkmap on talks page
 comments:
   provider               : # false (default), "disqus", "discourse", "facebook", "google-plus", "staticman", "custom"
   disqus:
@@ -152,23 +162,26 @@ exclude:
   - "*.sublime-workspace"
   - .asset-cache
   - .bundle
+  - .github
   - .jekyll-assets-cache
   - .sass-cache
-  - CHANGELOG
-  - Capfile
-  - Gemfile
-  - Gruntfile.js
-  - LICENSE
-  - README
-  - Rakefile
   - assets/js/_main.js
   - assets/js/plugins
   - assets/js/vendor
+  - CHANGELOG
+  - Capfile
   - config
+  - Dockerfile
+  - Gemfile
+  - Gruntfile.js
   - gulpfile.js
+  - LICENSE
+  - local
   - log
   - node_modules
-  - package.json
+  - package.json*
+  - Rakefile
+  - README
   - tmp
   - vendor
 keep_files:
@@ -198,7 +211,7 @@ kramdown:
   enable_coderay: false
 
 
-# Collections
+# These settings control the types of collections used by the template
 collections:
   teaching:
     output: true
@@ -217,7 +230,7 @@ collections:
     permalink: /:collection/:path/
 
 
-# Defaults
+# These settings control how pages and collections are included in the site
 defaults:
   # _posts
   - scope:
@@ -298,17 +311,20 @@ timezone: America/Sao_Paulo # http://en.wikipedia.org/wiki/List_of_tz_database_t
 
 # Plugins
 plugins:
+  - jekyll-feed
+  - jekyll-gist
   - jekyll-paginate
   - jekyll-sitemap
-  - jekyll-gist
-  - jekyll-feed
   - jekyll-redirect-from
-# mimic GitHub Pages with --safe
+  - jemoji
+
+# Mimic GitHub Pages with --safe
 whitelist:
+  - jekyll-feed
+  - jekyll-gist
   - jekyll-paginate
   - jekyll-sitemap
-  - jekyll-gist
-  - jekyll-feed
+  - jekyll-redirect-from
   - jemoji
 
 
 
@@ -0,0 +1 @@
+url: ""
@@ -1,4 +1,9 @@
-# main links links
+# The following is the order of the links in the header of the website.
+#
+# Changing the order here will adjust the order and you can also add additional
+# links. Removing a link prevents it from showing in the header, but does not
+# prevent it from being included in the site.
+
 main:
   - title: "Research"
     url: /research/
 
@@ -34,7 +34,7 @@ <h3 class="archive__item-title" itemprop="headline">
       {% endif %}
     </h3>
     {% if post.read_time %}
-      <p class="page__meta"><i class="fa fa-clock-o" aria-hidden="true"></i> {% include read-time.html %}</p>
+      <p class="page__meta"><i class="fa fa-clock" aria-hidden="true"></i> {% include read-time.html %}</p>
     {% endif %}
     {% if post.venue%}<p class="archive__item-excerpt" itemprop="description">{{ post.citation }}</p> {% endif %}
     </li>
 
@@ -33,7 +33,7 @@ <h3 class="archive__item-title" itemprop="headline">
         <a href="{{ base_path }}{{ post.url }}" rel="permalink">{{ title }}</a>
       {% endif %}
     </h3>
-    {% if post.date %}<p class="page__meta"><i class="fa fa-clock-o" aria-hidden="true"></i> {{ post.date | date: '%B %d, %Y' }}</p>{% endif %}
+    {% if post.date %}<p class="page__meta"><i class="fa fa-clock" aria-hidden="true"></i> {{ post.date | date: '%B %d, %Y' }}</p>{% endif %}
     {% if post.venue%}<p class="archive__item-excerpt" itemprop="description">{{post.type}} at {{ post.venue }},  {{post.location}}</p>{% endif %}
     </li>
   </article>
 
@@ -33,9 +33,9 @@ <h2 class="archive__item-title" itemprop="headline">
       {% endif %}
     </h2>
     {% if post.read_time %}
-      <p class="page__meta"><i class="fa fa-clock-o" aria-hidden="true"></i> {% include read-time.html %}</p>
+      <p class="page__meta"><i class="fa fa-clock" aria-hidden="true"></i> {% include read-time.html %}</p>
     {% endif %}
-    {% if post.date %}<p class="page__meta"><i class="fa fa-clock-o" aria-hidden="true"></i> {{ post.date | date: '%B %d, %Y' }}</p>{% endif %}
+    {% if post.date %}<p class="page__meta"><i class="fa fa-clock" aria-hidden="true"></i> {{ post.date | date: '%B %d, %Y' }}</p>{% endif %}
     {% if post.venue %}<p class="archive__item-excerpt" itemprop="description">{{post.type}}, {{ post.venue }},  {{post.location}} {% endif %}
     {% if post.excerpt %}<p class="archive__item-excerpt" itemprop="description">{{ post.excerpt | markdownify }}</p>{% endif %}
   </article>
 
@@ -36,7 +36,7 @@ <h3 class="archive__item-title" itemprop="headline">
     </h3>
 
     {% if post.read_time %}
-      <p class="page__meta"><i class="fa fa-clock-o" aria-hidden="true"></i> {% include read-time.html %}</p>
+      <p class="page__meta"><i class="fa fa-clock" aria-hidden="true"></i> {% include read-time.html %}</p>
     {% endif %}
 
         {% if post.coauthors %}
@@ -89,6 +89,10 @@ <h3 class="archive__item-title" itemprop="headline">
 
     {% if post.citation %}
       <p>Recommended citation: {{ post.citation }}</p>
+    {% elsif post.paperurl %}
+      <p><a href=" {{ post.paperurl }} ">Download Paper</a></p>
+    {% elsif post.slidesurl %}
+      <p><a href="{{ post.slidesurl }}">Download Slides</a></p>
     {% endif %}
 
   </article>
 
@@ -28,7 +28,7 @@ <h3 class="author__name">{{ author.name }}</h3>
         <li class="author__desktop"><i class="fa-solid fa-location-dot icon-pad-right" aria-hidden="true"></i>{{ author.location }}</li>
       {% endif %}
       {% if author.employer %}
-        <li class="author__desktop"><i class="fa fa-solid fa-building-columns icon-pad-right" aria-hidden="true"></i>{{ author.employer }}</li>
+        <li class="author__desktop"><i class="fas fa-fw fa-building-columns icon-pad-right" aria-hidden="true"></i>{{ author.employer }}</li>
       {% endif %}
       {% if author.uri %}
         <li><a href="{{ author.uri }}"><i class="fas fa-fw fa-link icon-pad-right" aria-hidden="true"></i>{{ site.data.ui-text[site.locale].website_label | default: "Website" }}</a></li>
@@ -59,6 +59,9 @@ <h3 class="author__name">{{ author.name }}</h3>
       {% if author.researchgate %}
         <li><a href="{{ author.researchgate }}"><i class="fab fa-fw fa-researchgate icon-pad-right" aria-hidden="true"></i>ResearchGate</a></li>
       {% endif %}
+      {% if author.scopus %}
+        <li><a href="{{ author.scopus }}"><i class="ai ai-scopus icon-pad-right"></i>Scopus</a></li>
+      {% endif %}
 
       <!-- Font Awesome icons / Repositories and software development -->
       {% if author.bitbucket %}
@@ -71,7 +74,7 @@ <h3 class="author__name">{{ author.name }}</h3>
         <li><a href="https://dribbble.com/{{ author.dribbble }}"><i class="fab fa-fw fa-dribbble icon-pad-right" aria-hidden="true"></i>Dribbble</a></li>
       {% endif %}      
       {% if author.github %}
-        <li><a href="https://github.com/{{ author.github }}"><i class="fab fa-fw fa-github icon-pad-right" aria-hidden="true"></i>Github</a></li>
+        <li><a href="https://github.com/{{ author.github }}"><i class="fab fa-fw fa-github icon-pad-right" aria-hidden="true"></i>GitHub</a></li>
       {% endif %}
       {% if author.kaggle %}
         <li><a href="https://kaggle.com/{{ author.kaggle }}"><i class="fab fa-fw fa-kaggle icon-pad-right" aria-hidden="true"></i>Kaggle</a></li>
@@ -106,7 +109,7 @@ <h3 class="author__name">{{ author.name }}</h3>
         <li><a href="https://instagram.com/{{ author.instagram }}"><i class="fab fa-fw fa-instagram icon-pad-right" aria-hidden="true"></i>Instagram</a></li>
       {% endif %}      
       {% if author.lastfm %}
-        <li><a href="https://lastfm.com/user/{{ author.lastfm }}"><i class="fab fa-fw fa-lastfm icon-pad-right" aria-hidden="true"></i>Last.fm</a></li>
+        <li><a href="https://last.fm/user/{{ author.lastfm }}"><i class="fab fa-fw fa-lastfm icon-pad-right" aria-hidden="true"></i>Last.fm</a></li>
       {% endif %}      
       {% if author.linkedin %}
         <li><a href="https://www.linkedin.com/in/{{ author.linkedin }}"><i class="fab fa-fw fa-linkedin icon-pad-right" aria-hidden="true"></i>LinkedIn</a></li>
@@ -148,10 +151,10 @@ <h3 class="author__name">{{ author.name }}</h3>
         <li><a href="https://www.xing.com/profile/{{ author.xing }}"><i class="fab fa-fw fa-xing icon-pad-right" aria-hidden="true"></i>XING</a></li>
       {% endif %}
       {% if author.youtube %}
-        <li><a href="https://www.youtube.com/user/{{ author.youtube }}"><i class="fab fa-fw fa-youtube icon-pad-right" aria-hidden="true"></i>YouTube</a></li>
+        <li><a href="https://www.youtube.com/@{{ author.youtube }}"><i class="fab fa-fw fa-youtube icon-pad-right" aria-hidden="true"></i>YouTube</a></li>
       {% endif %}
       {% if author.zhihu %}
-      <li><a href="{{ author.zhihu }}"><i class="fab fa-fw fa-zhihu icon-pad-right" aria-hidden="true"></i>Zhihu</a></li>
+      <li><a href="https://www.zhihu.com/people/{{ author.zhihu }}"><i class="fab fa-fw fa-zhihu icon-pad-right" aria-hidden="true"></i>Zhihu</a></li>
       {% endif %}      
     </ul>
   </div>
 
@@ -76,6 +76,8 @@ <h4 class="page__comments-title">{{ site.data.ui-text[site.locale].comments_labe
       {% endif %}
     </section>
   {% when "custom" %}
+    <h4 class="page__comments-title">{{ comments_label }}</h4>
     <section id="comments"></section>
+    {% include /comments-providers/scripts.html %}
   {% endcase %}
 </div>
@@ -19,4 +19,7 @@
 </div>
 {% endif %}
 
-<div class="page__footer-copyright">&copy; {{ site.time | date: '%Y' }} {{ site.name | default: site.title }}. {{ site.data.ui-text[site.locale].powered_by | default: "Powered by" }} <a href="http://jekyllrb.com" rel="nofollow">Jekyll</a> &amp; <a href="https://github.com/academicpages/academicpages.github.io">AcademicPages</a>, a fork of <a href="https://mademistakes.com/work/minimal-mistakes-jekyll-theme/" rel="nofollow">Minimal Mistakes</a>.</div>
+<div class="page__footer-copyright">
+  &copy; {{ site.time | date: '%Y' }} {{ site.name | default: site.title }}, {{ site.data.ui-text[site.locale].powered_by | default: "Powered by" }} <a href="http://jekyllrb.com" rel="nofollow">Jekyll</a> &amp; <a href="https://github.com/academicpages/academicpages.github.io">AcademicPages</a>, a fork of <a href="https://mademistakes.com/work/minimal-mistakes-jekyll-theme/" rel="nofollow">Minimal Mistakes</a>.<br />
+  Site last updated {{ "now" | date: '%Y-%m-%d' %}}
+</div>
@@ -2,6 +2,16 @@
 
 <!-- start custom head snippets -->
 
+<!-- favicon from https://commons.wikimedia.org/wiki/File:OOjs_UI_icon_academic-progressive.svg -->
+<link rel="apple-touch-icon" sizes="180x180" href="{{ base_path }}/images/apple-touch-icon-180x180.png"/>
+<link rel="icon" type="image/svg+xml" href="{{ base_path }}/images/favicon.svg"/>
+<link rel="icon" type="image/png" href="{{ base_path }}/images/favicon-32x32.png" sizes="32x32"/>
+<link rel="icon" type="image/png" href="{{ base_path }}/images/favicon-192x192.png" sizes="192x192"/>
+<link rel="manifest" href="{{ base_path }}/images/manifest.json"/>
+<link rel="icon" href="/images/favicon.ico"/>
+<meta name="theme-color" content="#ffffff"/>
+<link rel="stylesheet" href="{{ base_path }}/assets/css/academicons.css"/>
+
 
 <!-- Support for MatJax -->
 
 
@@ -40,7 +40,7 @@ <h1 class="page__title" itemprop="headline">
         <p class="page__lead">{{ page.excerpt | markdownify | remove: "<p>" | remove: "</p>" }}</p>
       {% endif %}
       {% if site.read_time and page.read_time %}
-        <p class="page__meta"><i class="fa fa-clock-o" aria-hidden="true"></i> {% include read-time.html %}</p>
+        <p class="page__meta"><i class="fa fa-clock" aria-hidden="true"></i> {% include read-time.html %}</p>
       {% endif %}
       {% if page.header.cta_url %}
         <p><a href="{{ cta_path }}" class="btn btn--light-outline btn--large">{{ page.header.cta_label | default: site.data.ui-text[site.locale].more_label | default: "Learn More" }}</a></p>
 
@@ -4,6 +4,6 @@
   {% include tag-list.html %}
 {% endif %}
 
-{% if site.category_archive.type and page.categories[0] %}
+{% if site.category_archive.type and page.categories[0] and page.collection != 'publications' %}
   {% include category-list.html %}
 {% endif %}
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,3 @@`
`1`	`1`	`Personal website for Stéphanie.`
`2`	`2`
`3`		`-Based on [https://academicpages.github.io/](https://academicpages.github.io/)`
	`3`	`+Based on [https://academicpages.github.io/](https://academicpages.github.io/)`