Preview publications redesign

.github/workflows/on-pull-request.yaml

@@ -14,9 +14,5 @@ permissions:
   pull-requests: write
 
 jobs:
-  update-citations:
-    uses: ./.github/workflows/update-citations.yaml
-
   build-preview:
-    needs: update-citations
     uses: ./.github/workflows/build-preview.yaml

.github/workflows/on-push.yaml

@@ -14,11 +14,5 @@ permissions:
   pull-requests: write
 
 jobs:
-  update-citations:
-    # skip first run because nothing enabled or setup yet
-    if: github.run_number != 1
-    uses: ./.github/workflows/update-citations.yaml
-
   build-site:
-    needs: update-citations
     uses: ./.github/workflows/build-site.yaml

.gitignore

@@ -1,4 +1,5 @@
 _site
+.bundle
 .sass-cache
 .jekyll-cache
 .jekyll-metadata

Gemfile

@@ -4,8 +4,18 @@ source "https://rubygems.org"
 gem "jekyll", "~> 4.3"
 gem "webrick", "~> 1.7"
 
+# stdlib gems no longer bundled with Ruby >= 3.4
+gem "logger"
+gem "csv"
+gem "base64"
+gem "bigdecimal"
+gem "ostruct"
+
 gem "html-proofer", "~> 5.0"
 
+# bibtex parsing for the publications page (see _plugins/bibtex.rb)
+gem "bibtex-ruby"
+
 # plugins
 group :jekyll_plugins do
   gem "jekyll-spaceship"

Gemfile.lock

@@ -10,31 +10,36 @@ GEM
       fiber-annotation
       io-event (~> 1.1)
       timers (~> 4.1)
+    base64 (0.3.0)
+    benchmark (0.5.0)
+    bibtex-ruby (6.0.0)
+      latex-decode (~> 0.0)
+    bigdecimal (4.1.2)
     colorator (1.1.0)
     concurrent-ruby (1.2.2)
     console (1.23.4)
       fiber-annotation
       fiber-local
       json
+    csv (3.3.5)
     em-websocket (0.5.3)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0)
     ethon (0.16.0)
       ffi (>= 1.15.0)
     eventmachine (1.2.7)
+    eventmachine (1.2.7-x64-mingw32)
     ffi (1.15.5)
-    ffi (1.15.5-x64-mingw-ucrt)
     fiber-annotation (0.2.0)
     fiber-local (1.0.0)
     forwardable-extended (2.6.0)
     gemoji (3.0.1)
     google-protobuf (3.22.0)
-    google-protobuf (3.22.0-arm64-darwin)
-    google-protobuf (3.22.0-x64-mingw-ucrt)
     hashery (2.1.2)
-    html-proofer (5.0.8)
+    html-proofer (5.2.1)
       addressable (~> 2.3)
       async (~> 2.1)
+      benchmark (~> 0.5)
       nokogiri (~> 1.13)
       pdf-reader (~> 2.11)
       rainbow (~> 3.0)
@@ -84,17 +89,18 @@ GEM
       rexml
     kramdown-parser-gfm (1.1.0)
       kramdown (~> 2.0)
+    latex-decode (0.4.2)
     liquid (4.0.4)
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
+    logger (1.7.0)
     mercenary (0.4.0)
     mini_portile2 (2.8.1)
     nokogiri (1.13.10)
       mini_portile2 (~> 2.8.0)
       racc (~> 1.4)
-    nokogiri (1.13.10-arm64-darwin)
-      racc (~> 1.4)
+    ostruct (0.6.3)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
     pdf-reader (2.12.0)
@@ -118,10 +124,20 @@ GEM
     sass-embedded (1.58.3)
       google-protobuf (~> 3.21)
       rake (>= 10.0.0)
+    sass-embedded (1.58.3-aarch64-linux-gnu)
+      google-protobuf (~> 3.21)
+    sass-embedded (1.58.3-arm-linux-gnueabihf)
+      google-protobuf (~> 3.21)
     sass-embedded (1.58.3-arm64-darwin)
       google-protobuf (~> 3.21)
     sass-embedded (1.58.3-x64-mingw-ucrt)
       google-protobuf (~> 3.21)
+    sass-embedded (1.58.3-x64-mingw32)
+      google-protobuf (~> 3.21)
+    sass-embedded (1.58.3-x86-linux-gnu)
+      google-protobuf (~> 3.21)
+    sass-embedded (1.58.3-x86_64-linux-gnu)
+      google-protobuf (~> 3.21)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
     timers (4.3.5)
@@ -135,6 +151,7 @@ GEM
 
 PLATFORMS
   aarch64-linux
+  arm64-darwin-25
   linux
   universal-darwin-21
   universal-darwin-22
@@ -144,13 +161,19 @@ PLATFORMS
   x86_64-linux
 
 DEPENDENCIES
+  base64
+  bibtex-ruby
+  bigdecimal
+  csv
   html-proofer (~> 5.0)
   jekyll (~> 4.3)
   jekyll-feed
   jekyll-last-modified-at
   jekyll-redirect-from
   jekyll-sitemap
   jekyll-spaceship
+  logger
+  ostruct
   webrick (~> 1.7)
 
 BUNDLED WITH

README.md

@@ -8,3 +8,32 @@
   Visit **[cosilab.github.io](https://cosilab.github.io)** 🚀
 
   _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
+
+  ## Contributing
+
+  ### Run the site locally
+
+  Install the Ruby dependencies, then start the local Jekyll server:
+
+  ```bash
+  bundle install
+  bundle exec jekyll serve
+  ```
+
+  Open [http://127.0.0.1:4000](http://127.0.0.1:4000) to preview the site.
+
+  ### Update a biography
+
+  Edit the relevant Markdown file in `_members/`. Member portraits should be
+  square 300 × 300 pixel images stored in `images/members/`.
+
+  ### Add a publication
+
+  Add or update the publication entry in `_bibliography/papers.bib`. The site
+  generates the publications list from this file.
+
+  ### Open a pull request
+
+  Preview and build the site locally before opening a pull request. Keep
+  binary asset changes focused, and squash commits when merging to avoid
+  unnecessary image files in the commit history.