Add web interface (#49)

* Initial commit with cleaned history * Adding necessary files for subsides * README.md * Adding index.html to create subsides with Jekyll * Change to the Structure of the Site s.t. the subsides are laoding properly. * Further changes to make the subsides appear * Update _config.yml * Update _config.yml * Update _config.yml * Update single-cell-transformers.md * Update transformer-evaluation.md * Update transformer-llms.md * Update index.md * Update _config.yml * Update index.html * Update _config.yml * Changing layout and making side functioning * Made some working changes * New Layout; Icons are working now * Adding Filter function and API connecetd towards YAML Files * Add mobile responsiveness * Initial Commit * Mobile responsiveness added and issues fixed with dark mode * Remove _site directory from git tracking * Hello * Final Changes * New Document-Generation * New Document-Generation.yml * Link for Issues was broken * Files and Folder for the Website * Update _config.yml Changed website title to Theislab/single-cell-transformer-papers * fix link issues * fix link issues * fix link issues * Fixed Link Issues * Updated Mobile Responsiveness --------- Co-authored-by: Paul O.-P <[email protected]> Co-authored-by: Paul <[email protected]>
theislab · Dec 2, 2024 · 0ae6bd1 · 0ae6bd1
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diff --git a/.babelrc b/.babelrc
@@ -0,0 +1,15 @@
+{
+  "presets": [
+    ["@babel/preset-env", {
+      "targets": {
+        "browsers": ["last 2 versions"]
+      }
+    }],
+    ["@babel/preset-react", {
+      "runtime": "automatic"
+    }]
+  ],
+  "plugins": [
+    "@babel/plugin-transform-runtime"
+  ]
+}
diff --git a/.github/workflows/document-generation.yml b/.github/workflows/document-generation.yml
@@ -0,0 +1,66 @@
+name: Document Generation
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  convert:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      # Setup Python for notebook conversion
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install jupytext nbconvert WeasyPrint markdown
+          
+      # Convert Markdown to Notebook
+      - name: Convert to Notebook
+        run: |
+          for f in _pages/*.md; do
+            jupytext --to notebook "${f}" -o "${f%.md}.ipynb"
+          done
+          
+      # Generate PDF
+      - name: Create conversion script
+        run: |
+          cat > convert.py << 'EOF'
+          import os
+          import markdown
+          import weasyprint
+          
+          for filename in os.listdir('_pages'):
+              if filename.endswith('.md'):
+                  md_path = os.path.join('_pages', filename)
+                  pdf_path = md_path.replace('.md', '.pdf')
+                  
+                  with open(md_path, 'r', encoding='utf-8') as md_file:
+                      html = markdown.markdown(md_file.read())
+                  weasyprint.HTML(string=html).write_pdf(pdf_path)
+          EOF
+
+      - name: Generate PDF
+        run: python convert.py
+
+      # Upload artifacts
+      - name: Upload PDF artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: pdfs
+          path: _pages/*.pdf
+
+      - name: Upload Notebook artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: notebooks
+          path: _pages/*.ipynb
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,11 @@
+<<<<<<< HEAD
 .idea
-.DS_Store
+.DS_Store
+=======
+# ignore everything in this directory
+node_modules/
+.env
+.env.local
+*.log
+.cache/_site/
+>>>>>>> main
diff --git a/.htaccess b/.htaccess
@@ -0,0 +1,8 @@
+RewriteEngine On
+RewriteCond %{REQUEST_FILENAME} !-d
+RewriteRule ^(.*)/$ /$1 [L,R=301]
+
+RewriteCond %{REQUEST_FILENAME} !-f
+RewriteCond %{REQUEST_FILENAME} !-d
+RewriteCond %{REQUEST_FILENAME}.html -f
+RewriteRule ^(.*)$ $1.html [L]
diff --git a/Gemfile b/Gemfile
@@ -0,0 +1,17 @@
+source "https://rubygems.org"
+
+gem "jekyll", "~> 4.3.4"
+gem "webrick", "~> 1.7"
+
+group :jekyll_plugins do
+  gem "jekyll-feed", "~> 0.12"
+  gem "jekyll-seo-tag", "~> 2.6"
+  gem 'jekyll-default-layout'
+end
+
+# Explicitly include standard library gems to suppress deprecation warnings
+gem 'bigdecimal'
+gem 'logger'
+gem 'csv'
+gem 'ostruct'
+gem 'base64'
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -0,0 +1,93 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
+    base64 (0.2.0)
+    bigdecimal (3.1.8)
+    colorator (1.1.0)
+    concurrent-ruby (1.3.4)
+    csv (3.3.0)
+    em-websocket (0.5.3)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0)
+    eventmachine (1.2.7)
+    ffi (1.17.0-x86_64-darwin)
+    forwardable-extended (2.6.0)
+    google-protobuf (4.28.3-x86_64-darwin)
+      bigdecimal
+      rake (>= 13)
+    http_parser.rb (0.8.0)
+    i18n (1.14.6)
+      concurrent-ruby (~> 1.0)
+    jekyll (4.3.4)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      em-websocket (~> 0.5)
+      i18n (~> 1.0)
+      jekyll-sass-converter (>= 2.0, < 4.0)
+      jekyll-watch (~> 2.0)
+      kramdown (~> 2.3, >= 2.3.1)
+      kramdown-parser-gfm (~> 1.0)
+      liquid (~> 4.0)
+      mercenary (>= 0.3.6, < 0.5)
+      pathutil (~> 0.9)
+      rouge (>= 3.0, < 5.0)
+      safe_yaml (~> 1.0)
+      terminal-table (>= 1.8, < 4.0)
+      webrick (~> 1.7)
+    jekyll-default-layout (0.1.5)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-feed (0.17.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-sass-converter (3.0.0)
+      sass-embedded (~> 1.54)
+    jekyll-seo-tag (2.8.0)
+      jekyll (>= 3.8, < 5.0)
+    jekyll-watch (2.2.1)
+      listen (~> 3.0)
+    kramdown (2.4.0)
+      rexml
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    liquid (4.0.4)
+    listen (3.9.0)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    logger (1.6.1)
+    mercenary (0.4.0)
+    ostruct (0.6.1)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    public_suffix (6.0.1)
+    rake (13.2.1)
+    rb-fsevent (0.11.2)
+    rb-inotify (0.11.1)
+      ffi (~> 1.0)
+    rexml (3.3.9)
+    rouge (4.5.1)
+    safe_yaml (1.0.5)
+    sass-embedded (1.80.6-x86_64-darwin)
+      google-protobuf (~> 4.28)
+    terminal-table (3.0.2)
+      unicode-display_width (>= 1.1.1, < 3)
+    unicode-display_width (2.6.0)
+    webrick (1.9.0)
+
+PLATFORMS
+  x86_64-darwin
+
+DEPENDENCIES
+  base64
+  bigdecimal
+  csv
+  jekyll (~> 4.3.4)
+  jekyll-default-layout
+  jekyll-feed (~> 0.12)
+  jekyll-seo-tag (~> 2.6)
+  logger
+  ostruct
+  webrick (~> 1.7)
+
+BUNDLED WITH
+   2.5.23
diff --git a/_config.yml b/_config.yml
@@ -0,0 +1,48 @@
+title: Transformers in Single-Cell Omics
+description: A curated collection of papers on transformers in single-cell analysis
+baseurl: "/single-cell-transformer-papers"
+url: "https://theislab.github.io"
+
+# Build settings
+markdown: kramdown
+plugins:
+  - jekyll-feed
+  - jekyll-seo-tag
+
+# Explicitly remove trailing slashes
+permalink: /:title
+trailing_slash: false
+
+# Default layout settings
+defaults:
+  -
+    scope:
+      path: ""
+    values:
+      layout: "default"
+
+# Collections
+collections:
+  pages:
+    output: true
+    permalink: /:title
+
+# Include directories and files
+include:
+  - _pages
+  - assets
+  - assets/js/dist
+  - _data
+
+# Exclude from processing
+exclude:
+  - node_modules
+  - webpack.config.js
+  - package.json
+  - package-lock.json
+  - README.md
+  - Gemfile
+  - Gemfile.lock
+
+# Explicitly set data directory
+data_dir: _data