Fix broken build and add back news section

.github/workflows/build-preview.yaml

@@ -26,7 +26,7 @@ jobs:
         uses: crazy-max/ghaction-dump-context@v1
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.head_ref }}
@@ -35,13 +35,13 @@ jobs:
         if: github.event.action != 'closed'
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: "3.0"
+          ruby-version: "3.1"
           bundler-cache: true
 
       - name: Get Pages url
         if: github.event.action != 'closed'
         id: pages
-        uses: actions/configure-pages@v2
+        uses: actions/configure-pages@v5
         with:
           enablement: false
 

.github/workflows/build-site.yaml

@@ -25,17 +25,17 @@ jobs:
         uses: crazy-max/ghaction-dump-context@v1
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
 
       - name: Install Ruby packages
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: "3.0"
+          ruby-version: "3.1"
           bundler-cache: true
 
       - name: Get Pages url
         id: pages
-        uses: actions/configure-pages@v2
+        uses: actions/configure-pages@v5
         with:
           enablement: false
 

.github/workflows/first-time-setup.yaml

@@ -25,7 +25,7 @@ jobs:
           branch: "gh-pages"
 
       - name: Checkout Pages branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
           ref: gh-pages
 
@@ -41,13 +41,13 @@ jobs:
         run: echo "Placeholder homepage" > index.html
 
       - name: Commit changes to Pages branch
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v7
         with:
           branch: gh-pages
           commit_message: "Clear branch"
 
       - name: Checkout main branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
 
       - name: Remove files user doesn't need
         run: |
@@ -80,7 +80,7 @@ jobs:
           " > README.md
 
       - name: Personalize Jekyll config for user
-        uses: actions/github-script@v6
+        uses: actions/github-script@v8
         with:
           script: |
             const { readFileSync, writeFileSync } = require("fs");
@@ -97,7 +97,7 @@ jobs:
             writeFileSync(file, contents);
 
       - name: Personalize homepage for user
-        uses: actions/github-script@v6
+        uses: actions/github-script@v8
         with:
           script: |
             const { readFileSync, writeFileSync } = require("fs");
@@ -109,6 +109,6 @@ jobs:
             writeFileSync(file, contents);
 
       - name: Commit changed files
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v7
         with:
           commit_message: "Setup repo"

.github/workflows/update-citations.yaml

@@ -33,13 +33,13 @@ jobs:
         uses: crazy-max/ghaction-dump-context@v1
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.head_ref }}
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
           cache: "pip"
@@ -55,7 +55,7 @@ jobs:
 
       - name: Check if citations changed
         id: changed
-        uses: tj-actions/verify-changed-files@v17
+        uses: tj-actions/verify-changed-files@v20
         with:
           files: |
             _data/citations.yaml
@@ -64,15 +64,15 @@ jobs:
         if: |
           steps.changed.outputs.files_changed == 'true' &&
           inputs.open-pr != true
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v7
         with:
           commit_message: "Update citations"
 
       - name: Open pull request with updated citations
         if: |
           steps.changed.outputs.files_changed == 'true' &&
           inputs.open-pr == true
-        uses: peter-evans/create-pull-request@v4
+        uses: peter-evans/create-pull-request@v8
         with:
           branch: citation-update
           title: Periodic citation update

.github/workflows/update-url.yaml

@@ -25,16 +25,16 @@ jobs:
 
       - name: Get Pages url
         id: pages
-        uses: actions/configure-pages@v2
+        uses: actions/configure-pages@v5
         with:
           enablement: false
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
 
       # update link to site in readme
       - name: Update readme
-        uses: actions/github-script@v6
+        uses: actions/github-script@v8
         with:
           script: |
             const { readFileSync, writeFileSync } = require("fs");
@@ -53,14 +53,14 @@ jobs:
 
       - name: Check if readme changed
         id: changed
-        uses: tj-actions/verify-changed-files@v13
+        uses: tj-actions/verify-changed-files@v20
         with:
           files: |
             README.md
 
       - name: Commit changed files
         if: steps.changed.outputs.files_changed == 'true'
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v7
         with:
           commit_message: "Update url"
 

_data/citations.yaml

@@ -11,7 +11,7 @@
   - Nicholas R. Howe
   - Halie M. Rando
   publisher: American Journal of Veterinary Research
-  date: '2025-02-21'
+  date: '2025-03-01'
   link: https://doi.org/g85s7s
   type: journal paper
   tags:
@@ -479,7 +479,7 @@
   - Anupam Sule
   - Umit Topaloglu
   - Melissa A. Haendel
-  publisher: Cold Spring Harbor Laboratory
+  publisher: openRxiv
   date: '2021-03-26'
   link: https://doi.org/gjk3ng
   image: https://user-images.githubusercontent.com/8975841/112666874-013a3400-8e33-11eb-9be9-5c74f3e397ea.png

_includes/post-info.html

@@ -33,5 +33,5 @@
 </div>
 
 {% if include.tags %}
-  {% include tags.html tags=include.tags link="blog" %}
+  {% include tags.html tags=include.tags link="news" %}
 {% endif %}

_layouts/member.html

@@ -39,13 +39,17 @@
 </p>
 
 {% capture search -%}
-  blog/?search={{ page.name }}
+  news/?search={{ page.name }}
 {%- endcapture %}
 
-<!--
+{% assign authored_posts = site.posts
+  | where_exp: "post", "post.author == page.slug"
+%}
+
+{% if authored_posts.size > 0 %}
 <p class="center">
   <a href="{{ search | relative_url }}">
-    See {{ page.name | default: page.title }}'s posts on the Blog page
+    See {{ page.name | default: page.title }}'s news posts on the News page
   </a>
 </p>
--->
+{% endif %}

_members/Zihan_Lyu.md

@@ -2,7 +2,7 @@
 name: Zihan Lyu '25
 image: images/ZihanLyu.jpg
 description: Undergraduate Researcher
-role: undergrad
+role: alum
 aliases:
   - Zihan Lyu
 links:
@@ -11,4 +11,4 @@ links:
   LinkedIn: https://www.linkedin.com/in/zihan-lyu/
 ---
 
-I am a senior at Smith College, double majoring in Computer Science and Neuroscience. I plan to pursue further education and apply my skills in medical technology, focusing on rehabilitation and neural interfaces. In my free time, I enjoy cooking, crocheting, and ceramics. 
+Zihan graduated from Smith College in 2025 with a double major in Computer Science and Neuroscience. She is now pursuing her interest in medical technology, focusing on rehabilitation and neural interfaces, at the graduate level: she is now pursuing an M.S. in Engineering at Johns Hopkins University, focusing on sensory feedback and functional restoration in upper-limb amputations in the [Neuroengineering and Biomedical Instrumentation Lab led by Prof. Nitish Thakor](https://neuroengineering.bme.jhu.edu/people). In her free time, she enjoys cooking, crocheting, and ceramics. 

_members/hildana_shiferaw.md

@@ -2,7 +2,7 @@
 name: Hildana Shiferaw '25
 image: images/hildana_shiferaw.jpg 
 description: Undergraduate Researcher
-role: undergrad
+role: alum
 links:
 ---
-
+Hildana graduate from Smith in 2025 with B.A. in Biological Sciences and a B.S. in Engineering Science. She completed the VBIL's first honors thesis, where she assessed the viability of miRNA markers for assessing ovarian cancer risk, with the goal of developing point of care diagnostic testing. After graduating from Smith, she went on to pursue a [Ph.D. in  Computational Biology and Biomedical Informatics at Yale University](https://cbb.yale.edu/students).

_members/xinran_bi.md

@@ -8,3 +8,5 @@ links:
 ---
 
 Xinran completed majors in Mathematical Statistics and Computer Science as a 2024J graduate. Her current research interest lies in the intersection of artificial intelligence and biomedicine. She is originally from Shanghai, China. Outside of academics, she enjoys listening to audio books, learning languages, and cooking.
+
+After graduating from Smith, Xinran continued her work in bioinformatics while pursuing an [M.S. in Computer Science](https://www.cs.princeton.edu/people/grad) in the [Pritykin Lab at Princeton University](https://pritykinlab.github.io/).

_posts/.gitkeep

@@ -0,0 +1 @@
+

index.md

@@ -7,6 +7,27 @@ Here in the VBIL within the Computer Science Department at Smith, we are interes
 
 {% include section.html %}
 
+## Latest News
+
+{% if site.posts.size > 0 %}
+{% for post in site.posts limit: 3 %}
+{% include post-excerpt.html lookup=post.slug %}
+{% endfor %}
+{% else %}
+Future lab announcements, milestones, publications, and event updates will appear here.
+{% endif %}
+
+{%
+  include button.html
+  link="news"
+  text="View all news"
+  icon="fa-solid fa-arrow-right"
+  flip=true
+  style="bare"
+%}
+
+{% include section.html %}
+
 ## Highlights
 
 {% capture text %}

news/index.md

@@ -0,0 +1,40 @@
+---
+title: News
+nav:
+  order: 4
+  tooltip: Lab updates and announcements
+redirect_from:
+  - /blog
+  - /blog/
+---
+
+# {% include icon.html icon="fa-regular fa-newspaper" %}News
+
+Use this page for lab updates, student milestones, publications, talks, and other announcements from the VBIL.
+
+{% if site.posts.size > 0 %}
+
+{% include search-box.html %}
+
+{% include search-info.html %}
+
+{% assign posts_by_year = site.posts
+  | group_by_exp: "post", "post.date | date: '%Y'"
+%}
+
+{% for year in posts_by_year %}
+## {{ year.name }}
+
+{% for post in year.items %}
+{% include post-excerpt.html lookup=post.slug %}
+{% endfor %}
+
+{% endfor %}
+
+{% else %}
+
+No news posts have been published yet.
+
+To publish one, add a Markdown file to `_posts/` using the filename format `YYYY-MM-DD-title.md`.
+
+{% endif %}