From fcd6857376c198b6481c7b8a2aff3a1c6f7a29d4 Mon Sep 17 00:00:00 2001 From: Alexius Wadell Date: Wed, 8 Nov 2023 11:17:35 -0500 Subject: [PATCH 1/2] add ci --- .github/workflows/jekyll-gh-pages.yml | 4 ++- .pre-commit-config.yaml | 15 --------- Gemfile | 2 ++ Gemfile.lock | 45 +++++++++++++++++++++++++++ Makefile | 10 ++++++ _config.yml | 6 +--- _includes/head.html | 2 +- _includes/news-item.html | 3 +- _includes/project-card.html | 15 +++++---- _projects/catalyst.md | 2 +- _projects/pde.md | 4 +-- _pages/about.md => about.md | 0 assets/css/main.scss | 6 ++++ 13 files changed, 80 insertions(+), 34 deletions(-) create mode 100644 Makefile rename _pages/about.md => about.md (100%) diff --git a/.github/workflows/jekyll-gh-pages.yml b/.github/workflows/jekyll-gh-pages.yml index b7fed2f..f087455 100644 --- a/.github/workflows/jekyll-gh-pages.yml +++ b/.github/workflows/jekyll-gh-pages.yml @@ -37,9 +37,11 @@ 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: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5394b4b..a6236ba 100644 --- a/.pre-commit-config.yaml +++ b/.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" diff --git a/Gemfile b/Gemfile index f9f388a..14e2974 100644 --- a/Gemfile +++ b/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" diff --git a/Gemfile.lock b/Gemfile.lock index bcf1e78..c169d34 100644 --- a/Gemfile.lock +++ b/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) @@ -49,14 +74,27 @@ 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) @@ -64,14 +102,21 @@ GEM 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) diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..d91f323 --- /dev/null +++ b/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 diff --git a/_config.yml b/_config.yml index 08ec55a..bb1c3aa 100644 --- a/_config.yml +++ b/_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 diff --git a/_includes/head.html b/_includes/head.html index e96f5da..482124b 100644 --- a/_includes/head.html +++ b/_includes/head.html @@ -8,7 +8,7 @@ - + diff --git a/_includes/news-item.html b/_includes/news-item.html index c5a17fd..23de835 100644 --- a/_includes/news-item.html +++ b/_includes/news-item.html @@ -28,7 +28,8 @@
{{ post.title }}
{% if post.image %} {% capture img %} - + {{ post.image_alt }} {% endcapture %}
diff --git a/_includes/project-card.html b/_includes/project-card.html index 33ba324..113df4e 100644 --- a/_includes/project-card.html +++ b/_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 @@
-

{{ card-title }}

-

{{ project.card-content }}

+

{{ card-title }}

+

{{ project.card-content }}

- Learn More! + Learn More!
diff --git a/_projects/catalyst.md b/_projects/catalyst.md index 76bc039..71ed16c 100644 --- a/_projects/catalyst.md +++ b/_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. diff --git a/_projects/pde.md b/_projects/pde.md index 1663add..a1476f1 100644 --- a/_projects/pde.md +++ b/_projects/pde.md @@ -9,7 +9,7 @@ people: card-image: assets/img/FFM.png --- - +![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. @@ -17,5 +17,5 @@ Most physical systems of interests share common physics between them. The goal i 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) diff --git a/_pages/about.md b/about.md similarity index 100% rename from _pages/about.md rename to about.md diff --git a/assets/css/main.scss b/assets/css/main.scss index 921ee50..f38716f 100644 --- a/assets/css/main.scss +++ b/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"; From 717299aad0ca8791d61c296cf6e655d8b3c0f2aa Mon Sep 17 00:00:00 2001 From: Alexius Wadell Date: Wed, 8 Nov 2023 11:09:50 -0500 Subject: [PATCH 2/2] always run ci --- .github/workflows/jekyll-gh-pages.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/jekyll-gh-pages.yml b/.github/workflows/jekyll-gh-pages.yml index f087455..4ab9837 100644 --- a/.github/workflows/jekyll-gh-pages.yml +++ b/.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: @@ -49,6 +48,7 @@ jobs: # Deployment job deploy: + if: ${{ github.ref == 'refs/heads/main' }} environment: name: github-pages url: ${{ steps.deployment.outputs.page_url }}