Merge branch 'ci' into updates

.github/workflows/jekyll-gh-pages.yml

@@ -4,8 +4,7 @@ name: Deploy Jekyll with GitHub Pages dependencies preinstalled
 on:
   # Runs on pushes targeting the default branch
   push:
-    branches:
-    - main
+  pull_request:
 
   # Release new blog posts daily at 9am EST
   schedule:
@@ -37,16 +36,19 @@ jobs:
         with:
           bundler-cache: true
       - name: Build with Jekyll
-        run: bundle exec jekyll build
+        run: make build
         env:
           JEKYLL_ENV: production
+      - name: Check Site
+        run: make test
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v2
         with:
           path: _site/
 
   # Deployment job
   deploy:
+    if: ${{ github.ref == 'refs/heads/main' }}
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}

.pre-commit-config.yaml

@@ -3,10 +3,6 @@ repos:
     rev: v4.0.1
     hooks:
       - id: trailing-whitespace
-        args: [--markdown-linebreak-ext=md]
-      - id: check-added-large-files
-        args: ['--maxkb=100', '--enforce-all']
-        types: ['image']
       - id: check-yaml
       - id: check-xml
       - id: end-of-file-fixer
@@ -23,17 +19,6 @@ repos:
       - id: check-github-workflows
   - repo: local
     hooks:
-      - id: images-in-img
-        name: Check for images outside of img/
-        entry: Images go in /img
-        language: fail
-        exclude: ^assets/img/
-        types: ['image']
-      - id: no-binary-files
-        name: Check for binary files
-        entry: Binary files are not allowed, please remove them
-        language: fail
-        exclude_types: ['image', 'text']
       - id: valid-post-filename
         name: Checks that post have valid filenames
         entry: "Files in _posts/ must be named: YYYY-MM-DD-name_with_underscore.md"

Gemfile

@@ -9,3 +9,5 @@ gem "jekyll", "~> 4.3"
 gem "jekyll-sitemap", "~> 1.4"
 
 gem "jekyll-seo-tag", "~> 2.8"
+
+gem "html-proofer", "~> 5.0"

Gemfile.lock

@@ -1,21 +1,46 @@
 GEM
   remote: https://rubygems.org/
   specs:
+    Ascii85 (1.1.0)
     addressable (2.8.5)
       public_suffix (>= 2.0.2, < 6.0)
+    afm (0.2.2)
+    async (2.6.5)
+      console (~> 1.10)
+      fiber-annotation
+      io-event (~> 1.1)
+      timers (~> 4.1)
     colorator (1.1.0)
     concurrent-ruby (1.2.2)
+    console (1.23.2)
+      fiber-annotation
+      fiber-local
     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)
     ffi (1.16.3)
+    fiber-annotation (0.2.0)
+    fiber-local (1.0.0)
     forwardable-extended (2.6.0)
     google-protobuf (3.25.0-arm64-darwin)
     google-protobuf (3.25.0-x86_64-linux)
+    hashery (2.1.2)
+    html-proofer (5.0.8)
+      addressable (~> 2.3)
+      async (~> 2.1)
+      nokogiri (~> 1.13)
+      pdf-reader (~> 2.11)
+      rainbow (~> 3.0)
+      typhoeus (~> 1.3)
+      yell (~> 2.0)
+      zeitwerk (~> 2.5)
     http_parser.rb (0.8.0)
     i18n (1.14.1)
       concurrent-ruby (~> 1.0)
+    io-event (1.3.3)
     jekyll (4.3.2)
       addressable (~> 2.4)
       colorator (~> 1.0)
@@ -49,29 +74,49 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.4.0)
+    nokogiri (1.15.4-arm64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.15.4-x86_64-linux)
+      racc (~> 1.4)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
+    pdf-reader (2.11.0)
+      Ascii85 (~> 1.0)
+      afm (~> 0.2.1)
+      hashery (~> 2.0)
+      ruby-rc4
+      ttfunk
     public_suffix (5.0.3)
+    racc (1.7.3)
+    rainbow (3.1.1)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rexml (3.2.6)
     rouge (4.2.0)
+    ruby-rc4 (0.1.5)
     safe_yaml (1.0.5)
     sass-embedded (1.69.5-arm64-darwin)
       google-protobuf (~> 3.23)
     sass-embedded (1.69.5-x86_64-linux-gnu)
       google-protobuf (~> 3.23)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
+    timers (4.3.5)
+    ttfunk (1.7.0)
+    typhoeus (1.4.0)
+      ethon (>= 0.9.0)
     unicode-display_width (2.5.0)
     webrick (1.8.1)
+    yell (2.2.2)
+    zeitwerk (2.6.12)
 
 PLATFORMS
   arm64-darwin-22
   x86_64-linux
 
 DEPENDENCIES
+  html-proofer (~> 5.0)
   jekyll (~> 4.3)
   jekyll-seo-tag (~> 2.8)
   jekyll-sitemap (~> 1.4)

Makefile

@@ -0,0 +1,10 @@
+all: install build test
+
+install:
+	bundle install
+
+build:
+	bundle exec jekyll build
+
+test: build
+	bundle exec htmlproofer --disable-external --ignore-missing-alt _site

_config.yml

@@ -1,6 +1,6 @@
 title: Scientific Foundation Models
 navtitle: Scientific Foundation Models
-description: |
+url: scifm.ai
 
 plugins:
 - jekyll-seo-tag
@@ -13,10 +13,6 @@ sass:
   sass_dir: /assets/css/_sass
   style: compressed
 
-include:
-  - _pages
-  - _projects
-
 exclude:
   - .sass-cache
 

_includes/head.html

@@ -8,7 +8,7 @@
 
     <!-- Bootstrap core CSS -->
     <link href="{{ site.baseurl }}/assets/css/main.css" rel="stylesheet" />
-    <link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
+    <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
 
     <!-- Favicon -->
     <link rel="apple-touch-icon" sizes="180x180" href="/assets/favicon/apple-touch-icon.png">

_includes/news-item.html

@@ -28,7 +28,8 @@ <h5> <a href="{{ site.baseurl }}{{ post.url }}"> {{ post.title }} </a> </h5>
     {% if post.image %}
 
     {% capture img %}
-    <img class="img-fluid d-block mx-auto" style="{{ post.image_style }}" src="{{ post.image }}">
+    <img class="img-fluid d-block mx-auto" style="{{ post.image_style }}" alt="{{ post.image_alt }}"
+        src="{{ post.image }}">
     {% endcapture %}
 
     <div class="row">

_includes/project-card.html

@@ -1,16 +1,15 @@
-
 {% assign project = include.project %}
 
 {% if project.link %}
-    {% assign proj-url = project.link %}
+{% assign proj-url = project.link %}
 {% else %}
-    {% capture proj-url %}{{site.baseurl}}{{project.url}}{% endcapture %}
+{% capture proj-url %}{{site.baseurl}}{{project.url}}{% endcapture %}
 {% endif %}
 
 {% if project.card-image %}
-    {% assign card-image = project.card-image %}
+{% assign card-image = project.card-image %}
 {% else %}
-    {% assign card-image = "http://placeholder.pics/svg/400x300/3cb371-3cb371/3cb371-3cb371" %}
+{% assign card-image = "http://placeholder.pics/svg/400x300/3cb371-3cb371/3cb371-3cb371" %}
 {% endif %}
 
 {% if project.card-title %}
@@ -23,11 +22,11 @@
     <div class="card border-0 shadow h-100">
         <img class="card-img-top" width=400 height=200 src="{{ card-image }}" alt="" />
         <div class="card-body">
-        <h4 class="card-title"> {{ card-title }}</h4>
-        <p class="card-text">{{ project.card-content }}</p>
+            <h4 class="card-title"> {{ card-title }}</h4>
+            <p class="card-text">{{ project.card-content }}</p>
         </div>
         <div class="card-footer">
-        <a href="{{ proj-url }}" class="btn btn-primary">Learn More!</a>
+            <a href="{{ proj-url }}" class="btn btn-primary">Learn More!</a>
         </div>
     </div>
 </div>

_projects/catalyst.md

@@ -13,7 +13,7 @@ people:
 
 ## Traversing High Dimensional Chemical Design Space with Foundation Models
 
-![]({% link assets/img/incite_image_mb.png %})
+![Flowchart of our proposed workflow]({% link assets/img/incite_image_mb.png %})
 
 Current energy storage materials development is hindered by expensive experiments that limit exploration to the vast space of known synthesizable materials. Therefore, current research has only focused on a very limited design space space hindering the effective development of batteries for electric vehicles, grid storage, and electric aircraft applications. To address the unique demands of these applications, such as high energy density, safety, scalability, and power density, it is essential to explore a much larger chemical space than the few hundred that are currently considered due to the high cost of experiments and physics simulations.
 

_projects/pde.md

@@ -9,13 +9,13 @@ people:
 card-image: assets/img/FFM.png
 ---
 
-<img src="../assets/img/FFM.png" width="800"/>
+![Diagram of a Fluid Foundation Model]({% link assets/img/FFM.png %})
 
 Creating machine learning surrogate models that capture the dynamics of physical systems is a field that has seen rapid development in recent years. However, creating these models from scratch are both time consuming and data intensive. Foundation models for PDEs that can be finetuned to specific systems of interest offer a solution to this problem.
 
 Most physical systems of interests share common physics between them. The goal is to create a model that is trained on multiple physics from diverse datasets, that is able to capture these common features and understand behavior of these systems across different scales. While efforts have started in this direction [^1]<sup>,</sup>[^2] , there are many questions to be explored regarding choice of model architecture, creation of larger and more diverse datasets, training strategies, and the effects of boundary conditions and geometries.
 
 We can currently working on building a Vision Transformer that generalizes across the parameter space of a given PDE. Expect to see the paper on ArXiv soon.
 
-[^1]: [Shashank Subramanian, Peter Harrington, Kurt Keutzer, Wahid Bhimji, Dmitriy Morozov, Michael Mahoney, & Amir Gholami. (2023). Towards Foundation Models for Scientific Machine Learning: Characterizing Scaling and Transfer Behavior.](https://arxiv.org/abs/2306.00258) 
+[^1]: [Shashank Subramanian, Peter Harrington, Kurt Keutzer, Wahid Bhimji, Dmitriy Morozov, Michael Mahoney, & Amir Gholami. (2023). Towards Foundation Models for Scientific Machine Learning: Characterizing Scaling and Transfer Behavior.](https://arxiv.org/abs/2306.00258)
 [^2]: [Michael McCabe, Bruno Régaldo-Saint Blancard, Liam Holden Parker, Ruben Ohana, Miles Cranmer, Alberto Bietti, Michael Eickenberg, Siavash Golkar, Geraud Krawezik, Francois Lanusse, Mariel Pettee, Tiberiu Tesileanu, Kyunghyun Cho, & Shirley Ho. (2023). Multiple Physics Pretraining for Physical Surrogate Models.](https://arxiv.org/abs/2310.02994)

assets/css/main.scss

@@ -99,6 +99,12 @@ div#news {
     justify-content: space-evenly;
 }
 
+.row{
+    img{
+        max-width: 100%;
+    }
+}
+
 //@import "bootstrap/bootstrap/bootstrap.css";
 @import "bootstrap/functions";
 @import "bootstrap/variables";