Merge branch 'master' of https://github.com/alshedivat/al-folio

* 'master' of https://github.com/alshedivat/al-folio: (35 commits)
  Fixes alshedivat#304. Fix bad horizontal template include (alshedivat#305)
  Adds support for image zoom (alshedivat#296)
  Fix project page colors (alshedivat#295)
  Added BibTeX hidden block (alshedivat#293)
  add dblp to social links (alshedivat#270)
  Fix for images (alshedivat#271)
  Added proper instructions in personal webpages (alshedivat#261)
  Added the Programming Group at HSG to labs (alshedivat#254)
  Categories for projects and an optional horizontal project card style (alshedivat#224)
  Change gitcdn link (alshedivat#234)
  Issue 183 (alshedivat#192)
  Update Gemfile (alshedivat#230)
  Add gitlab to social (alshedivat#229)
  Update stale.yml
  Create stale.yml
  Switch favicon to emoji (alshedivat#217)
  Update README.md (alshedivat#216)
  Update README.md
  Update README.md
  Fix titles and headings (alshedivat#204)
  ...

# Conflicts:
#	_bibliography/papers.bib
#	_config.yml
#	_data/coauthors.yml
#	_includes/head.html
#	_layouts/about.html
#	_layouts/bib.html
#	_pages/projects.md
#	_projects/mali.markdown
#	_sass/_base.scss
#	_sass/_themes.scss
#	_sass/_variables.scss
#	_software/feddlib.markdown
#	_teaching/ss20-scientific-machine-learning.markdown
#	_teaching/ws1516-seminar-numII.markdown

.github/stale.yml

@@ -0,0 +1,18 @@
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 60
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 7
+# Issues with these labels will never be considered stale
+exemptLabels:
+  - pinned
+  - security
+  - enhancement
+# Label to use when marking an issue as stale
+staleLabel: wontfix
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. Thank you
+  for your contributions.
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: false

.github/workflows/deploy.yml

@@ -0,0 +1,54 @@
+name: Deploy
+
+on:
+  push:
+    branches:
+      - master
+      - source
+  pull_request:
+    branches:
+      - master
+      - source
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+    - name: Setup Ruby
+      uses: actions/setup-ruby@v1
+      with:
+        ruby-version: '2.7'
+    - name: Enable bundler cache
+      uses: actions/cache@v2
+      with:
+        path: vendor/bundle
+        key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}
+        restore-keys: |
+          ${{ runner.os }}-gems-
+    - name: Install deps
+      run: |
+        gem install bundler
+        bundle config path vendor/bundle
+        bundle install --jobs 4 --retry 3
+    - name: Setup deploy options
+      id: setup
+      run: |
+        git config --global user.name "GitHub Action"
+        git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+        if [[ ${GITHUB_REF} = refs/pull/*/merge ]]; then # pull request
+          echo "::set-output name=SRC_BRANCH::${GITHUB_HEAD_REF}"
+          echo "::set-output name=NO_PUSH::--no-push"
+        elif [[ ${GITHUB_REF} = refs/heads/* ]]; then # branch, e.g. master, source etc
+          echo "::set-output name=SRC_BRANCH::${GITHUB_REF#refs/heads/}"
+        fi
+        if [[ ${{ github.repository }} = *.github.io ]]; then # user/org repo
+          echo "::set-output name=DEPLOY_BRANCH::master"
+        else
+          echo "::set-output name=DEPLOY_BRANCH::gh-pages"
+        fi
+    - name: Deploy website 
+      run:  yes | bin/deploy --verbose ${{ steps.setup.outputs.NO_PUSH }}
+                    --src ${{ steps.setup.outputs.SRC_BRANCH }} 
+                    --deploy ${{ steps.setup.outputs.DEPLOY_BRANCH }} 

.gitignore

@@ -1,7 +1,10 @@
 _site
+.bundle
 .sass-cache
+.jekyll-cache
 .jekyll-metadata
 .DS_store
 .ruby-version
-.tweet-cache/
+.tweet-cache
 Gemfile.lock
+vendor

Gemfile

@@ -1,12 +1,13 @@
 source 'https://rubygems.org'
 group :jekyll_plugins do
-    gem 'github-pages'
     gem 'jekyll'
     gem 'jekyll-email-protect'
     gem 'jekyll-github-metadata'
     gem 'jekyll-paginate-v2'
     gem 'jekyll-scholar'
     gem 'jekyll-twitter-plugin'
     gem 'jemoji'
+    gem 'kramdown-parser-gfm'
     gem 'unicode_utils'
+    gem 'webrick'
 end

_config.yml

@@ -16,9 +16,11 @@ footer_text:
   Hosted by <a href="https://pages.github.com/" target="_blank">GitHub Pages</a>.
 # Photos from <a href="https://unsplash.com" target="_blank">Unsplash</a>.
 
+icon:  # the emoji used as the favicon
 url:  # the base hostname & protocol for your site
 baseurl: #/al-folio # 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
 
 # -----------------------------------------------------------------------------
 # Layout
@@ -44,21 +46,26 @@ og_image: # The site-wide (default for all links) Open Graph preview image
 # -----------------------------------------------------------------------------
 
 github_username: searhein # your GitHub user name
+gitlab_username: # your GitLab user name
 twitter_username: # your Twitter handle
-linkedin_username: # your LinkedIn user name
+linkedin_username: alexander-heinlein-9b569380 # your LinkedIn user name
 scholar_userid: Pb5ZhSIAAAAJ # your Google Scholar ID
 orcid_id: 0000-0003-1578-8104 # your ORCID ID
 medium_username: # your Medium username
 quora_username: # your Quora username
 publons_id: # your ID on Publons
 research_gate_profile: Alexander_Heinlein # your profile on ResearchGate
+arxiv: a/heinlein_a_1.html
 blogger_url: # your blogger URL
+work_url: # work page URL
 keybase_username: # your keybase user name
+wikidata_id: # your wikidata id
 
 contact_note: >
 #  You can even add a little note about which of these is the best way to reach you.
 
 google_analytics: UA-XXXXXXXXX # out your google-analytics code
+panelbear_analytics: XXXXXXXXX # panelbear analytics site ID
 
 # -----------------------------------------------------------------------------
 # Blog
@@ -120,7 +127,15 @@ kramdown:
 
 # Includes & excludes
 include: ['_pages']
-exclude: [vendor]
+exclude:
+  - bin
+  - Gemfile
+  - Gemfile.lock
+  - vendor
+keep_files:
+  - CNAME
+  - .nojekyll
+  - .git
 
 # Plug-ins
 plugins:
@@ -130,8 +145,9 @@ plugins:
   - jekyll/scholar
   - jekyll-twitter-plugin
   - jemoji
-  # - bootstrap
-  # - material-sass
+
+# Extras
+github: [metadata]
 
 # -----------------------------------------------------------------------------
 # Jekyll Scholar
@@ -162,12 +178,18 @@ scholar:
 # Optional Features
 # -----------------------------------------------------------------------------
 
-enable_google_analytics:  false
-enable_mansory:           true
-enable_math:              true
-enable_tooltips:          false
-enable_darkmode:          true
-show_social_icons:        true
+enable_google_analytics:    false  # enables google analytics
+enable_panelbear_analytics: false  # enables panelbear analytics
+enable_mansory:             true   # enables automatic project cards arangement
+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:       true   # 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)
 
 # -----------------------------------------------------------------------------
 # Library versions
@@ -200,3 +222,6 @@ mdb:
 popper:
   version: "2.4.4"
   integrity: "sha512-eUQ9hGdLjBjY3F41CScH3UX+4JDSI9zXeroz7hJ+RteoCaY+GP/LDoM8AO+Pt+DRFw3nXqsjh9Zsts8hnYv8/A=="
+medium_zoom:
+  version: "1.0.6"
+  integrity: "sha256-EdPgYcPk/IIrw7FYeuJQexva49pVRZNmt3LculEr7zM="

_data/coauthors.yml

@@ -1,59 +1,79 @@
 Balzani:
+  - firstname: ["Daniel", "D."]
     url: http://www.lkm.rub.de/institut/team/Balzani.html
 
 Deparis:
+  - firstname: ["Simone", "S."]
     url: https://people.epfl.ch/Simone.Deparis?lang=en
 
 Frei:
+  - firstname: ["Stefan", "S."]
     url: https://www.math.uni-konstanz.de/~frei/
 
 Grimm:
+  - firstname: ["Viktor", "V."]
     url: https://numerik.uni-koeln.de/arbeitsgruppe/v-grimm-m-sc
 
 Hochmuth:
+  - firstname: ["Christian", "C."]
     url: https://numerik.uni-koeln.de/arbeitsgruppe/dr-c-hochmuth
 
 Lanser:
+  - firstname: ["Martin", "M."]
     url: https://numerik.uni-koeln.de/arbeitsgruppe/dr-m-lanser
 
 Klawonn:
+  - firstname: ["Axel", "A."]
     url: https://numerik.uni-koeln.de
 
 Knepper:
+  - firstname: ["Jascha", "J."]
     url: https://numerik.uni-koeln.de/arbeitsgruppe/j-knepper-m-sc
 
 Kühn:
+  - firstname: ["Martin", "M."]
     url: https://www.dlr.de/sc/desktopdefault.aspx/tabid-1192/1635_read-38447/sortby-b_city/
 
 Perego:
+  - firstname: ["Mauro", "M."]
     url: https://cfwebprod.sandia.gov/cfdocs/CompResearch/templates/insert/profile.cfm?mperego
 
 Quarteroni:
+  - firstname: ["Alfio", "A."]
     url: https://mox.polimi.it/people/alfio-quarteroni/
 
 Rajamanickam:
+  - firstname: ["Sivasankaran", "Siva", "S."]
     url: https://www.sandia.gov/~srajama/index.html
 
 Rheinbach:
+  - firstname: ["Oliver", "O."]
     url: https://tu-freiberg.de/fakult1/nmo/rheinbach
 
 Richter:
+  - firstname: ["Thomas", "T."]
     url: https://www.math.uni-magdeburg.de/~richter/
 
 Röver:
+  - firstname: ["Friederike", "F."]
     url: https://tu-freiberg.de/fakult1/nmo/roever
 
 Sandfeld:
+  - firstname: ["Stefan", "S."]
     url: https://tu-freiberg.de/fakult4/imfd/mimm/mitarbeiter/stefan-sandfeld
 
 Schröder:
+  - firstname: ["Jörg", "J."]
     url: https://www.uni-due.de/mechanika/index.php
 
 Steinberger:
+  - firstname: ["Daniel", "D."]
     url: https://tu-freiberg.de/fakult4/imfd/mimm/mitarbeiter/dominik-steinberger
 
 Weber:
+  - firstname: ["Janine", "J."]
     url: https://numerik.uni-koeln.de/arbeitsgruppe/j-weber-m-sc
 
 Widlund:
+  - firstname: ["Olof B.", "Olof B.", "O. B.", "O."]
     url: https://cs.nyu.edu/widlund/

_includes/footer.html

@@ -3,6 +3,9 @@
   <div class="container mt-0">
     &copy; Copyright {{ site.time | date: '%Y' }} {{ site.first_name }} {{ site.middle_name }} {{ site.last_name }}.
     {{ site.footer_text }}
+    {% if site.impressum_path %}
+    <a href="{{ site.url }}{{ site.baseurl }}{{ site.impressum_path }}">Impressum</a>.
+    {% endif %}
     {% if site.last_updated %}
     Last updated: {{ "now" | date: '%B %d, %Y' }}.
     {% endif %}
@@ -13,6 +16,9 @@
   <div class="container">
     &copy; Copyright {{ site.time | date: '%Y' }} {{ site.first_name }} {{ site.middle_name }} {{ site.last_name }}.
     {{ site.footer_text }}
+    {% if site.impressum_path %}
+    <a href="{{ site.url }}{{ site.baseurl }}{{ site.impressum_path }}">Impressum</a>.
+    {% endif %}
     {% if site.last_updated %}
     Last updated: {{ "now" | date: '%B %d, %Y' }}.
     {% endif %}

_includes/head.html

@@ -2,7 +2,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 
-<title>{% if site.title == blank %}{{ site.title }}{% else %}{{ site.first_name }} {{ site.middle_name }} {{ site.last_name }}{% endif %}{% if page.title and page.url != "/" %} | {{ page.title }}{% endif %}</title>
+<title>{% if site.title == "blank" %}{{ site.first_name }} {{ site.middle_name }} {{ site.last_name }}{% else %}{{ site.title }}{% endif %}{% if page.title and page.url != "/" %} | {{ page.title }}{% endif %}</title>
 <meta name="description" content="{{ site.description }}">
 
 <!-- Open Graph -->
@@ -25,27 +25,43 @@
 <link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto:300,400,500,700|Roboto+Slab:100,300,400,500,700|Material+Icons">
 
 <!-- Code Syntax Highlighting -->
-<link rel="stylesheet" href="https://gitcdn.link/repo/jwarby/jekyll-pygments-themes/master/{{ site.highlight_theme }}.css" />
+<link rel="stylesheet" href="https://gitcdn.xyz/repo/jwarby/jekyll-pygments-themes/master/{{ site.highlight_theme }}.css" />
 
 <!-- Styles -->
+{% if site.icon != empty %}
+<link rel="icon" href="data:image/svg+xml,<svg xmlns=%22http://www.w3.org/2000/svg%22 viewBox=%220 0 100 100%22><text y=%22.9em%22 font-size=%2290%22>{{ site.icon }}</text></svg>">
+{% else %}
 <link rel="shortcut icon" href="{{ '/assets/img/favicon.ico' | relative_url }}?">
+{% endif %}
 <link rel="stylesheet" href="{{ '/assets/css/main.css' | relative_url }}">
-
 <link rel="canonical" href="{{ page.url | replace:'index.html','' | relative_url }}">
 
+<!-- JQuery -->
+{% include scripts/jquery.html %}
+
 <!-- Theming-->
 {% if site.enable_darkmode %}
-  <script src="{{ '/assets/js/theme.js' | relative_url }}"></script>
+<script src="{{ '/assets/js/theme.js' | relative_url }}"></script>
+<script src="{{ '/assets/js/dark_mode.js' | relative_url }}"></script>
 {% endif %}
 
 {% if site.enable_google_analytics %}
-  <!-- Global site tag (gtag.js) - Google Analytics -->
-  <script async src="https://www.googletagmanager.com/gtag/js?id={{ site.google_analytics }}"></script>
-  <script>
-    window.dataLayer = window.dataLayer || [];
-    function gtag() { dataLayer.push(arguments); }
-    gtag('js', new Date());
-
-    gtag('config', '{{ site.google_analytics }}');
-  </script>
+<!-- Global site tag (gtag.js) - Google Analytics -->
+<script async src="https://www.googletagmanager.com/gtag/js?id={{ site.google_analytics }}"></script>
+<script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag() { dataLayer.push(arguments); }
+  gtag('js', new Date());
+
+  gtag('config', '{{ site.google_analytics }}');
+</script>
+{% endif %}
+
+{% if site.enable_panelbear_analytics %}
+<!-- Panelbear Analytics - We respect your privacy -->
+<script async src="https://cdn.panelbear.com/analytics.js?site={{site.panelbear_analytics}}"></script>
+<script>
+    window.panelbear = window.panelbear || function() { (window.panelbear.q = window.panelbear.q || []).push(arguments); };
+    panelbear('config', { site: '{{site.panelbear_analytics}}' });
+</script>
 {% endif %}

_includes/header.html

@@ -5,15 +5,15 @@
     <div class="container">
       {% if page.title != "about" %}
       <a class="navbar-brand title font-weight-lighter" href="{{ site.baseurl | prepend: site.url }}/">
-       {% if site.title == blank %}{{ site.title }}{% else %}<span class="font-weight-bold">{{ site.first_name }}</span> {{ site.middle_name }}  {{ site.last_name }}{% endif %}
+       {% if site.title == "blank" %}<span class="font-weight-bold">{{ site.first_name }}</span> {{ site.middle_name }}  {{ site.last_name }}{% else %}{{ site.title }}{% endif %}
       </a>
-      {% elsif site.show_social_icons %}
+      {% elsif site.enable_navbar_social %}
         <!-- Social Icons -->
-        <div class="row ml-1 ml-sm-0">
+        <div class="navbar-brand social">
           {% include social.html %}
         </div>
       {% endif %}
-      <!-- Navbar Toogle -->
+      <!-- Navbar Toggle -->
       <button class="navbar-toggler collapsed ml-auto" type="button" data-toggle="collapse" data-target="#navbarNav" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation">
         <span class="sr-only">Toggle navigation</span>
         <span class="icon-bar top-bar"></span>