Merge branch 'master' into release

.github/workflows/broken-links.yml

@@ -46,4 +46,4 @@ jobs:
         with:
           fail: true
           # removed md files that include liquid tags
-          args: --user-agent 'curl/7.54' --exclude-path README.md --exclude-path _pages/404.md --exclude-path _pages/blog.md --exclude-path _posts/2018-12-22-distill.md --verbose --no-progress './**/*.md' './**/*.html'
+          args: --user-agent 'curl/7.54' --exclude-path README.md --exclude-path _pages/404.md --exclude-path _pages/blog.md --exclude-path _posts/2018-12-22-distill.md --exclude-path _posts/2023-04-24-videos.md --verbose --no-progress './**/*.md' './**/*.html'

.github/workflows/deploy.yml

@@ -6,6 +6,7 @@ on:
       - release
     paths:
       - "assets/**"
+      - "**.bib"
       - "**.html"
       - "**.js"
       - "**.liquid"
@@ -28,6 +29,7 @@ on:
       - release
     paths:
       - "assets/**"
+      - "**.bib"
       - "**.html"
       - "**.js"
       - "**.liquid"

CUSTOMIZE.md

@@ -80,7 +80,7 @@ You can easily create your own collections, apps, short stories, courses, or wha
 
 To add publications create a new entry in the [\_bibliography/papers.bib](_bibliography/papers.bib) file. You can find the BibTeX entry of a publication in Google Scholar by clicking on the quotation marks below the publication title, then clicking on "BibTeX", or also in the conference page itself. By default, the publications will be sorted by year and the most recent will be displayed first. You can change this behavior and more in the `Jekyll Scholar` section in [\_config.yml](_config.yml) file.
 
-You can add extra information to a publication, like a PDF file in the `assets/pdfs/` directory and add the path to the PDF file in the BibTeX entry with the `pdf` field. Some of the supported fields are: `abstract`, `altmetric`, `arxiv`, `bibtex_show`, `blog`, `code`, `dimensions`, `doi`, `eprint`, `html`, `isbn`, `pdf`, `pmid`, `poster`, `slides`, `supp`, `video`, and `website`.
+You can add extra information to a publication, like a PDF file in the `assets/pdfs/` directory and add the path to the PDF file in the BibTeX entry with the `pdf` field. Some of the supported fields are: `abstract`, `altmetric`, `annotation`, `arxiv`, `bibtex_show`, `blog`, `code`, `dimensions`, `doi`, `eprint`, `html`, `isbn`, `pdf`, `pmid`, `poster`, `slides`, `supp`, `video`, and `website`.
 
 ### Author annotation
 
@@ -124,6 +124,7 @@ There are several custom bibtex keywords that you can use to affect how the entr
 - `abbr`: Adds an abbreviation to the left of the entry. You can add links to these by creating a venue.yaml-file in the \_data folder and adding entries that match.
 - `abstract`: Adds an "Abs" button that expands a hidden text field when clicked to show the abstract text
 - `altmetric`: Adds an [Altmetric](https://www.altmetric.com/) badge (Note: if DOI is provided just use `true`, otherwise only add the altmetric identifier here - the link is generated automatically)
+- `annotation`: Adds a popover info message to the end of the author list that can potentially be used to clarify superscripts. HTML is allowed.
 - `arxiv`: Adds a link to the Arxiv website (Note: only add the arxiv identifier here - the link is generated automatically)
 - `bibtex_show`: Adds a "Bib" button that expands a hidden text field with the full bibliography entry
 - `blog`: Adds a "Blog" button redirecting to the specified link
@@ -145,3 +146,9 @@ A variety of beautiful theme colors have been selected for you to choose from. T
 ## Adding social media information
 
 You can add your social media links by adding the specified information at the `Social integration` section in the [\_config.yml](_config.yml) file. This information will appear at the bottom of the `About` page.
+
+## Adding a newsletter
+
+You can add a newsletter subscription form by adding the specified information at the `newsletter` section in the [\_config.yml](_config.yml) file. To set up a newsletter, you can use a service like [Loops.so](https://loops.so/), which is the current supported solution. Once you have set up your newsletter, you can add the form [endpoint](https://loops.so/docs/forms/custom-form) to the `endpoint` field in the `newsletter` section of the [\_config.yml](_config.yml) file.
+
+Depending on your specified footer behavior, the sign up form either will appear at the bottom of the `About` page and at the bottom of blogposts if `related_posts` are enabled, or in the footer at the bottom of each page.

Gemfile

@@ -11,6 +11,7 @@ group :jekyll_plugins do
     gem 'jekyll-link-attributes'
     gem 'jekyll-minifier'
     gem 'jekyll-paginate-v2'
+    gem 'jekyll-regex-replace'
     gem 'jekyll-scholar'
     gem 'jekyll-sitemap'
     gem 'jekyll-tabs'

Gemfile.lock

@@ -1,7 +1,7 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (7.1.3.2)
+    activesupport (7.1.3.4)
       base64
       bigdecimal
       concurrent-ruby (~> 1.0, >= 1.0.2)
@@ -11,8 +11,8 @@ GEM
       minitest (>= 5.1)
       mutex_m
       tzinfo (~> 2.0)
-    addressable (2.8.6)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     base64 (0.2.0)
     bibtex-ruby (6.1.0)
       latex-decode (~> 0.0)
@@ -27,7 +27,7 @@ GEM
       fast-stemmer (~> 1.0)
       matrix (~> 0.4)
     colorator (1.1.0)
-    concurrent-ruby (1.2.3)
+    concurrent-ruby (1.3.3)
     connection_pool (2.4.1)
     crass (1.0.6)
     csl (1.6.0)
@@ -50,13 +50,15 @@ GEM
     feedjira (3.2.3)
       loofah (>= 2.3.1, < 3)
       sax-machine (>= 1.0, < 2)
-    ffi (1.16.3)
+    ffi (1.17.0)
+    ffi (1.17.0-arm64-darwin)
+    ffi (1.17.0-x86_64-darwin)
     forwardable-extended (2.6.0)
     gemoji (4.1.0)
-    google-protobuf (4.26.1-aarch64-linux)
-      rake (>= 13)
-    google-protobuf (4.26.1-x86_64-linux)
-      rake (>= 13)
+    google-protobuf (3.25.3-aarch64-linux)
+    google-protobuf (3.25.3-arm64-darwin)
+    google-protobuf (3.25.3-x86_64-darwin)
+    google-protobuf (3.25.3-x86_64-linux)
     html-pipeline (2.14.3)
       activesupport (>= 2)
       nokogiri (>= 1.4)
@@ -105,6 +107,7 @@ GEM
       uglifier (~> 4.1)
     jekyll-paginate-v2 (3.0.0)
       jekyll (>= 3.0, < 5.0)
+    jekyll-regex-replace (1.1.0)
     jekyll-sass-converter (3.0.0)
       sass-embedded (~> 1.54)
     jekyll-scholar (7.1.3)
@@ -116,7 +119,7 @@ GEM
       jekyll (>= 3.7, < 5.0)
     jekyll-tabs (1.2.1)
       jekyll (>= 3.0, < 5.0)
-    jekyll-toc (0.18.0)
+    jekyll-toc (0.19.0)
       jekyll (>= 3.9)
       nokogiri (~> 1.12)
     jekyll-twitter-plugin (2.1.0)
@@ -135,6 +138,8 @@ GEM
       kramdown (~> 2.0)
     latex-decode (0.4.0)
     libv8-node (21.7.2.0-aarch64-linux)
+    libv8-node (21.7.2.0-arm64-darwin)
+    libv8-node (21.7.2.0-x86_64-darwin)
     libv8-node (21.7.2.0-x86_64-linux)
     liquid (4.0.4)
     listen (3.9.0)
@@ -148,32 +153,38 @@ GEM
     mini_mime (1.1.5)
     mini_racer (0.12.0)
       libv8-node (~> 21.7.2.0)
-    minitest (5.22.3)
-    multi_xml (0.7.1)
-      bigdecimal (~> 3.1)
+    minitest (5.24.1)
+    multi_xml (0.6.0)
     mutex_m (0.2.0)
     namae (1.2.0)
       racc (~> 1.7)
-    nokogiri (1.16.5-aarch64-linux)
+    nokogiri (1.16.6-aarch64-linux)
       racc (~> 1.4)
-    nokogiri (1.16.5-x86_64-linux)
+    nokogiri (1.16.6-arm64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.16.6-x86_64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.16.6-x86_64-linux)
       racc (~> 1.4)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (5.0.5)
-    racc (1.7.3)
+    public_suffix (6.0.0)
+    racc (1.8.0)
     rake (13.2.1)
     rb-fsevent (0.11.2)
-    rb-inotify (0.10.1)
+    rb-inotify (0.11.1)
       ffi (~> 1.0)
-    rexml (3.2.8)
-      strscan (>= 3.0.9)
-    rouge (4.2.1)
+    rexml (3.3.1)
+      strscan
+    rouge (4.3.0)
     safe_yaml (1.0.5)
-    sass-embedded (1.77.0-aarch64-linux-gnu)
-      google-protobuf (>= 3.25, < 5.0)
-    sass-embedded (1.77.0-x86_64-linux-gnu)
-      google-protobuf (>= 3.25, < 5.0)
+    sass-embedded (1.69.5)
+      google-protobuf (~> 3.23)
+      rake (>= 13.0.0)
+    sass-embedded (1.69.5-arm64-darwin)
+      google-protobuf (~> 3.23)
+    sass-embedded (1.69.5-x86_64-darwin)
+      google-protobuf (~> 3.23)
     sax-machine (1.3.2)
     strscan (3.1.0)
     terminal-table (3.0.2)
@@ -188,7 +199,9 @@ GEM
 
 PLATFORMS
   aarch64-linux
-  x86_64-linux-gnu
+  arm64-darwin
+  x86_64-darwin
+  x86_64-linux
 
 DEPENDENCIES
   classifier-reborn
@@ -205,6 +218,7 @@ DEPENDENCIES
   jekyll-link-attributes
   jekyll-minifier
   jekyll-paginate-v2
+  jekyll-regex-replace
   jekyll-scholar
   jekyll-sitemap
   jekyll-tabs

README.md

@@ -141,6 +141,8 @@ Feel free to add your own page(s) by sending a PR.
 <a href="https://abhilesh.github.io/" target="_blank">★</a>
 <a href="https://jackjburnett.github.io/" target="_blank">★</a>
 <a href="https://physics-morris.github.io/" target="_blank">★</a>
+<a href="https://sraf.ir" target="_blank">★</a>
+<a href="https://acad.garywei.dev/" target="_blank">★</a>
 </td>
 </tr>
 <tr>
@@ -180,7 +182,8 @@ Score Based Methods (NeurIPS: <a href="https://score-based-methods-workshop.gith
 Images2Symbols (CogSci: <a href="https://images2symbols.github.io/" target="_blank"> 2022</a>) <br>
 Medical Robotics Junior Faculty Forum (ISMR: <a href="https://junior-forum-ismr.github.io/" target="_blank"> 2023</a>)<br>
 Beyond Vision: Physics meets AI (ICIAP: <a href="https://physicsmeetsai.github.io/beyond-vision/" target="_blank">2023</a>) <br>
-Workshop on Diffusion Models (NeurIPS: <a href="https://diffusionworkshop.github.io/" target="_blank">2023</a>)
+Workshop on Diffusion Models (NeurIPS: <a href="https://diffusionworkshop.github.io/" target="_blank">2023</a>) <br>
+Workshop on Structured Probabilistic Inference & Generative Modeling (ICML: <a href="https://spigmworkshop.github.io/" target="_blank">2023</a>, <a href="https://spigmworkshop2024.github.io/" target="_blank">2024</a>)
 </td>
 </tr>
 </table>

_bibliography/papers.bib

@@ -36,7 +36,7 @@ @article{einstein1950meaning
 @article{PhysRev.47.777,
   abbr={PhysRev},
   title={Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?},
-  author={Einstein, A. and Podolsky, B. and Rosen, N.},
+  author={Einstein*†, A. and Podolsky*, B. and Rosen*, N.},
   abstract={In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.},
   journal={Phys. Rev.},
   location={New Jersey},
@@ -56,6 +56,7 @@ @article{PhysRev.47.777
   google_scholar_id={qyhmnyLat1gC},
   video={https://www.youtube-nocookie.com/embed/aqz-KE-bpKQ},
   additional_info={. *More Information* can be [found here](https://github.com/alshedivat/al-folio/)},
+  annotation={* Example use of superscripts<br>† Albert Einstein},
   selected={true}
 }
 

_config.yml

@@ -50,6 +50,7 @@ navbar_fixed: true
 footer_fixed: false
 search_enabled: true
 socials_in_search: true
+bib_search: true
 
 # Dimensions
 max_width: 930px
@@ -120,6 +121,7 @@ contact_note: >
 # 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)
+pirsch_analytics: # your Pirsch analytics site ID (length 32 characters)
 
 # 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)
@@ -172,6 +174,15 @@ disqus_shortname: al-folio # put your disqus shortname
 #       - url: https://blog.google/technology/ai/google-gemini-update-flash-ai-assistant-io-2024/
 #         published_date: 2024-05-14
 
+# -----------------------------------------------------------------------------
+# Newsletter
+# -----------------------------------------------------------------------------
+
+newsletter:
+  enabled: false
+  endpoint: # your loops endpoint (e.g., https://app.loops.so/api/newsletter-form/YOUR-ENDPOINT)
+  # https://loops.so/docs/forms/custom-form
+
 # -----------------------------------------------------------------------------
 # Collections
 # -----------------------------------------------------------------------------
@@ -250,6 +261,7 @@ plugins:
   - jekyll-link-attributes
   - jekyll-minifier
   - jekyll-paginate-v2
+  - jekyll-regex-replace
   - jekyll/scholar
   - jekyll-sitemap
   - jekyll-tabs
@@ -337,6 +349,7 @@ filtered_bibtex_keywords:
     abstract,
     additional_info,
     altmetric,
+    annotation,
     arxiv,
     award,
     award_name,
@@ -409,6 +422,7 @@ lazy_loading_images: true # enables lazy loading of images (recommended)
 
 enable_google_analytics: false # enables google analytics
 enable_cronitor_analytics: false # enables cronitor RUM analytics
+enable_pirsch_analytics: false # enables Pirsch analytics (https://pirsch.io/)
 enable_google_verification: false # enables google site verification
 enable_bing_verification: false # enables bing site verification
 enable_masonry: true # enables automatic project cards arrangement
@@ -518,13 +532,13 @@ third_party_libraries:
     version: "1.9.4"
   mathjax:
     integrity:
-      js: "sha256-rjmgmaB99riUNcdlrDtcAiwtLIojSxNyUFdl+Qh+rB4="
+      js: "sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI="
     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"
+      js: "https://cdn.jsdelivr.net/npm/mathjax@{{version}}/es5/tex-mml-chtml.js"
+    version: "3.2.2"
   masonry:
     integrity:
       js: "sha256-Nn1q/fx0H7SNLZMQ5Hw5JLaTRZp0yILA/FRexe19VdI="

_data/repositories.yml

@@ -1,6 +1,8 @@
 github_users:
   - ajyey
 
+repo_description_lines_max: 2
+
 github_repos:
   - ajyey/fastmail-masked-email
   - ajyey/masked-email-manager

_includes/footer.liquid

@@ -15,6 +15,10 @@
   </footer>
 {% else %}
   <footer class="sticky-bottom mt-5" role="contentinfo">
+    {% if site.newsletter.enabled %}
+      {% include scripts/newsletter.liquid %}
+    {% endif %}
+
     <div class="container">
       &copy; Copyright {{ site.time | date: '%Y' }}
       {{ site.first_name }}

_includes/header.liquid

@@ -95,7 +95,8 @@
                   </div>
                 </li>
               {% else %}
-                <li class="nav-item {% if page.url contains p.permalink %}active{% endif %}">
+                {% assign parent_link = p.permalink | remove: 'index.html' %}
+                <li class="nav-item {% if page.url contains parent_link %}active{% endif %}">
                   {% if p.permalink contains '/blog/' %}{% assign url = '/blog/' %} {% else %}{% assign url = p.url %}{% endif %}
                   <a class="nav-link" href="{{ url | relative_url }}">
                     {{- p.title }}

_includes/related_posts.liquid

@@ -16,3 +16,7 @@
     <a class="text-pink-700 underline font-semibold hover:text-pink-800" href="{{ site.baseurl }}{{ post.url }}">{{ post.title }}</a>
   </li>
 {% endfor %}
+{% if site.newsletter.enabled and site.footer_fixed %}
+  <p class="mb-2" style="margin-top: 1.5rem !important">Subscribe to be notified of future articles:</p>
+  {% include scripts/newsletter.liquid left=true %}
+{% endif %}

_includes/repository/repo.liquid

@@ -5,17 +5,23 @@
   {% assign show_owner = true %}
 {% endif %}
 
+{% if site.data.repositories.repo_description_lines_max %}
+  {% assign max_lines = site.data.repositories.repo_description_lines_max %}
+{% else %}
+  {% assign max_lines = 2 %}
+{% endif %}
+
 <div class="repo p-2 text-center">
   <a href="https://github.com/{{ include.repository }}">
     <img
       class="repo-img-light w-100"
       alt="{{ include.repository }}"
-      src="https://github-readme-stats.vercel.app/api/pin/?username={{ repo_url[0] }}&repo={{ repo_url[1] }}&theme={{ site.repo_theme_light }}&show_owner={{ show_owner }}"
+      src="https://github-readme-stats.vercel.app/api/pin/?username={{ repo_url[0] }}&repo={{ repo_url[1] }}&theme={{ site.repo_theme_light }}&show_owner={{ show_owner }}&description_lines_count={{ max_lines }}"
     >
     <img
       class="repo-img-dark w-100"
       alt="{{ include.repository }}"
-      src="https://github-readme-stats.vercel.app/api/pin/?username={{ repo_url[0] }}&repo={{ repo_url[1] }}&theme={{ site.repo_theme_dark }}&show_owner={{ show_owner }}"
+      src="https://github-readme-stats.vercel.app/api/pin/?username={{ repo_url[0] }}&repo={{ repo_url[1] }}&theme={{ site.repo_theme_dark }}&show_owner={{ show_owner }}&description_lines_count={{ max_lines }}"
     >
   </a>
 </div>

_includes/scripts/analytics.liquid

@@ -22,3 +22,11 @@
     cronitor('config', { clientKey: '{{site.cronitor_analytics}}' });
   </script>
 {% endif %}
+{% if site.enable_pirsch_analytics %}
+  <script
+    defer
+    src="https://api.pirsch.io/pa.js"
+    id="pianjs"
+    data-code="{{ site.pirsch_analytics }}"
+  ></script>
+{% endif %}