Fixed Link Issues

theislab · Dec 2, 2024 · cb8596b · cb8596b
1 parent 2449053
commit cb8596b
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Showing 11 changed files with 344 additions and 332 deletions.
diff --git a/_config.yml b/_config.yml
@@ -1,35 +1,25 @@
 title: Transformers in Single-Cell Omics
 description: A curated collection of papers on transformers in single-cell analysis
-baseurl: ""
-url: "https://theislab.github.io/single-cell-transformer-papers"
+baseurl: "/single-cell-transformer-papers"
+url: "https://theislab.github.io"
 
 # Build settings
 markdown: kramdown
 plugins:
   - jekyll-feed
   - jekyll-seo-tag
 
-# Remove trailing slashes
-permalink: "/:title"
+# Explicitly remove trailing slashes
+permalink: /:title
 trailing_slash: false
 
 # Default layout settings
 defaults:
   -
     scope:
-      path: "" # Apply to all files
+      path: ""
     values:
       layout: "default"
-  -
-    scope:
-      path: "index.md"
-    values:
-      layout: "default"
-  - scope:
-      path: "assets/_data"
-      type: "yml"
-    values:
-      layout: null  # Prevent Jekyll from wrapping YAML files in the default layout
 
 # Collections
 collections:
@@ -40,9 +30,9 @@ collections:
 # Include directories and files
 include:
   - _pages
-  - _data
   - assets
   - assets/js/dist
+  - _data
 
 # Exclude from processing
 exclude:

diff --git a/_layouts/default.html b/_layouts/default.html
@@ -683,53 +683,50 @@
     </style>
 </head>
 <body>
-    <header class="fixed top-0 w-full bg-opacity-90 backdrop-filter backdrop-blur-lg z-50 flex items-center justify-between px-4 py-2 border-b border-gray-200">
-        <div class="flex items-center">
-            <button class="menu-button md:hidden" id="menu-toggle">
-                <i class="fas fa-bars"></i>
-            </button>
-            <a href="{{ '/single-cell-transformer-papers/' | absolute_url }}" class="text-xl font-semibold ml-2">
-                Transformers in Single-Cell Omics
+    <header class="fixed top-0 left-0 right-0 bg-white dark:bg-gray-900 shadow-md z-50">
+        <div class="flex items-center justify-between px-4 py-2">
+            <a href="{{ site.baseurl }}/" class="text-xl font-semibold ml-2">
+                {{ site.title }}
             </a>
-        </div>
 
-        <!-- Navigation Links -->
-        <div class="nav-links hidden md:flex items-center space-x-4" id="nav-links">
-            <a href="{{ '/single-cell-transformer-papers/single-cell-transformers/' | absolute_url }}" class="nav-link">Single Cell Transformers</a>
-            <a href="{{ '/single-cell-transformer-papers/transformer-llms/' | absolute_url }}" class="nav-link">Transformer LLMs</a>
-            <a href="{{ '/single-cell-transformer-papers/transformer-evaluation/' | absolute_url }}" class="nav-link">Transformer Evaluation</a>
-        </div>
+            <!-- Navigation Links -->
+            <div class="nav-links hidden md:flex items-center space-x-4" id="nav-links">
+                <a href="{{ site.baseurl }}/single-cell-transformers" class="nav-link">Single Cell Transformers</a>
+                <a href="{{ site.baseurl }}/transformer-llms" class="nav-link">Transformer LLMs</a>
+                <a href="{{ site.baseurl }}/transformer-evaluation" class="nav-link">Transformer Evaluation</a>
+            </div>
 
-        <div class="flex items-center space-x-6">
-            <!-- GitHub Dropdown -->
-            <div class="relative">
-                <button id="github-btn" class="text-gray-600 hover:text-gray-800 dark:text-gray-300 dark:hover:text-gray-100">
-                    <i class="fab fa-github text-xl"></i>
-                </button>
-                <div id="github-dropdown" class="dropdown right-0 mt-2 w-48">
-                    <a href="#" class="block px-4 py-2 hover:bg-gray-100 dark:hover:bg-gray-800">
-                        <i class="fas fa-code-branch mr-2"></i>Repository
-                    </a>
-                    <a href="#" class="block px-4 py-2 hover:bg-gray-100 dark:hover:bg-gray-800">
-                        <i class="fas fa-edit mr-2"></i>Suggest edit
-                    </a>
-                    <a href="#" class="block px-4 py-2 hover:bg-gray-100 dark:hover:bg-gray-800">
-                        <i class="fas fa-exclamation-circle mr-2"></i>Open issue
-                    </a>
+            <div class="flex items-center space-x-6">
+                <!-- GitHub Dropdown -->
+                <div class="relative">
+                    <button id="github-btn" class="text-gray-600 hover:text-gray-800 dark:text-gray-300 dark:hover:text-gray-100">
+                        <i class="fab fa-github text-xl"></i>
+                    </button>
+                    <div id="github-dropdown" class="dropdown right-0 mt-2 w-48">
+                        <a href="#" class="block px-4 py-2 hover:bg-gray-100 dark:hover:bg-gray-800">
+                            <i class="fas fa-code-branch mr-2"></i>Repository
+                        </a>
+                        <a href="#" class="block px-4 py-2 hover:bg-gray-100 dark:hover:bg-gray-800">
+                            <i class="fas fa-edit mr-2"></i>Suggest edit
+                        </a>
+                        <a href="#" class="block px-4 py-2 hover:bg-gray-100 dark:hover:bg-gray-800">
+                            <i class="fas fa-exclamation-circle mr-2"></i>Open issue
+                        </a>
+                    </div>
                 </div>
-            </div>
 
-            <!-- Download Button -->
-            <div class="relative" id="download-btn">
-                <button class="p-2 hover:bg-gray-100 dark:hover:bg-gray-800 rounded-lg">
-                    <i class="fas fa-download"></i>
+                <!-- Download Button -->
+                <div class="relative" id="download-btn">
+                    <button class="p-2 hover:bg-gray-100 dark:hover:bg-gray-800 rounded-lg">
+                        <i class="fas fa-download"></i>
+                    </button>
+                </div>
+
+                <!-- Theme Toggle -->
+                <button id="theme-toggle" class="text-gray-600 hover:text-gray-800 dark:text-gray-300 dark:hover:text-gray-100">
+                    <i class="fas fa-sun text-xl"></i>
                 </button>
             </div>
-
-            <!-- Theme Toggle -->
-            <button id="theme-toggle" class="text-gray-600 hover:text-gray-800 dark:text-gray-300 dark:hover:text-gray-100">
-                <i class="fas fa-sun text-xl"></i>
-            </button>
         </div>
     </header>
 
@@ -738,9 +735,9 @@
     <nav id="sidebar" class="sidebar fixed left-0 top-16 h-full text-white p-6"> <!-- increased padding -->
         <div class="space-y-6"> <!-- increased spacing -->
             <h2 class="text-2xl font-bold mb-8">Navigation</h2> <!-- larger text and margin -->
-            <a href="{{ '/single-cell-transformer-papers/single-cell-transformers/' | absolute_url }}" class="block py-3 hover:bg-opacity-20 hover:bg-white rounded">Single-cell transformers</a>
-            <a href="{{ '/single-cell-transformer-papers/transformer-llms/' | absolute_url }}" class="block py-3 hover:bg-opacity-20 hover:bg-white rounded">Transformer LLMs</a>
-            <a href="{{ '/single-cell-transformer-papers/transformer-evaluation/' | absolute_url }}" class="block py-3 hover:bg-opacity-20 hover:bg-white rounded">Transformer evaluation</a>
+            <a href="{{ site.baseurl }}/single-cell-transformers" class="block py-3 hover:bg-opacity-20 hover:bg-white rounded">Single-cell transformers</a>
+            <a href="{{ site.baseurl }}/transformer-llms" class="block py-3 hover:bg-opacity-20 hover:bg-white rounded">Transformer LLMs</a>
+            <a href="{{ site.baseurl }}/transformer-evaluation" class="block py-3 hover:bg-opacity-20 hover:bg-white rounded">Transformer evaluation</a>
         </div>
     </nav>
 
@@ -954,15 +951,10 @@ <h2 class="text-2xl font-bold mb-8">Navigation</h2> <!-- larger text and margin
         window.transformerEvaluation = {{ site.data.transformer-evaluation | jsonify }};
     </script>
 
-    <!-- Then load your bundles -->
-    <script src="{{ '/single-cell-transformer-papers/assets/js/dist/single-cell-transformers.bundle.js' | absolute_url }}"></script>
-    <script src="{{ '/single-cell-transformer-papers/assets/js/dist/transformer-llms.bundle.js' | absolute_url }}"></script>
-    <script src="{{ '/single-cell-transformer-papers/assets/js/dist/transformer-evaluation.bundle.js' | absolute_url }}"></script>
-
-    <!-- Add these divs where you want the tables to appear -->
-    <div id="single-cell-transformers"></div>
-    <div id="transformer-llms"></div>
-    <div id="transformer-evaluation"></div>
+    <!-- Load all bundles -->
+    <script src="{{ site.baseurl }}/assets/js/dist/single-cell-transformers.bundle.js"></script>
+    <script src="{{ site.baseurl }}/assets/js/dist/transformer-llms.bundle.js"></script>
+    <script src="{{ site.baseurl }}/assets/js/dist/transformer-evaluation.bundle.js"></script>
 </body>
 </html>
 
diff --git a/_pages/single-cell-transformers.md b/_pages/single-cell-transformers.md
@@ -1,15 +1,17 @@
 ---
 layout: default
-title: Single-cell Transformers
-permalink: /single-cell-transformer-papers/single-cell-transformers/
+title: Single Cell Transformers
+permalink: /single-cell-transformers
 ---
 
 <div id="single-cell-transformers-root"></div>
 
-<!-- Load React and ReactDOM from CDN -->
-<script crossorigin src="https://unpkg.com/react@18/umd/react.production.min.js"></script>
-<script crossorigin src="https://unpkg.com/react-dom@18/umd/react-dom.production.min.js"></script>
-
-<!-- Load your bundle with corrected path -->
-<script src="{{ '/assets/js/dist/single-cell-transformers.bundle.js' | absolute_url }}"></script>
+<script>
+    document.addEventListener('DOMContentLoaded', function() {
+        if (document.getElementById('single-cell-transformers-root')) {
+            const root = ReactDOM.createRoot(document.getElementById('single-cell-transformers-root'));
+            root.render(React.createElement(SingleCellTransformers));
+        }
+    });
+</script>
 
diff --git a/_pages/transformer-evaluation.md b/_pages/transformer-evaluation.md
@@ -1,14 +1,16 @@
 ---
 layout: default
 title: Transformer Evaluation
-permalink: /single-cell-transformer-papers/transformer-evaluation/
+permalink: /transformer-evaluation
 ---
 
 <div id="transformer-evaluation-root"></div>
 
-<!-- Load React and ReactDOM from CDN -->
-<script crossorigin src="https://unpkg.com/react@18/umd/react.production.min.js"></script>
-<script crossorigin src="https://unpkg.com/react-dom@18/umd/react-dom.production.min.js"></script>
-
-<!-- Load your bundle with corrected path -->
-<script src="{{ '/assets/js/dist/transformer-evaluation.bundle.js' | absolute_url }}"></script>
+<script>
+    document.addEventListener('DOMContentLoaded', function() {
+        if (document.getElementById('transformer-evaluation-root')) {
+            const root = ReactDOM.createRoot(document.getElementById('transformer-evaluation-root'));
+            root.render(React.createElement(TransformerEvaluation));
+        }
+    });
+</script>
diff --git a/_pages/transformer-llms.md b/_pages/transformer-llms.md
@@ -1,14 +1,16 @@
 ---
 layout: default
 title: Transformer LLMs
-permalink: /single-cell-transformer-papers/transformer-llms/
+permalink: /transformer-llms
 ---
 
 <div id="transformer-llms-root"></div>
 
-<!-- Load React and ReactDOM from CDN -->
-<script crossorigin src="https://unpkg.com/react@18/umd/react.production.min.js"></script>
-<script crossorigin src="https://unpkg.com/react-dom@18/umd/react-dom.production.min.js"></script>
-
-<!-- Load your bundle with corrected path -->
-<script src="{{ '/assets/js/dist/transformer-llms.bundle.js' | absolute_url }}"></script>
+<script>
+    document.addEventListener('DOMContentLoaded', function() {
+        if (document.getElementById('transformer-llms-root')) {
+            const root = ReactDOM.createRoot(document.getElementById('transformer-llms-root'));
+            root.render(React.createElement(TransformerLLMs));
+        }
+    });
+</script>
diff --git a/_site/LICENSE b/_site/LICENSE
@@ -0,0 +1,13 @@
+Copyright 2023 Theislab
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
diff --git a/_site/feed.xml b/_site/feed.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.3.4">Jekyll</generator><link href="http://localhost:4000/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/" rel="alternate" type="text/html" /><updated>2024-11-24T19:27:24+01:00</updated><id>http://localhost:4000/feed.xml</id><title type="html">Transformers in Single-Cell Omics</title><subtitle>A curated collection of papers on transformers in single-cell analysis</subtitle></feed>
+<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.3.4">Jekyll</generator><link href="http://localhost:4000/single-cell-transformer-papers/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/single-cell-transformer-papers/" rel="alternate" type="text/html" /><updated>2024-12-02T13:48:48+08:00</updated><id>http://localhost:4000/single-cell-transformer-papers/feed.xml</id><title type="html">Transformers in Single-Cell Omics</title><subtitle>A curated collection of papers on transformers in single-cell analysis</subtitle></feed>
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.3.4">Jekyll</generator><link href="http://localhost:4000/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/" rel="alternate" type="text/html" /><updated>2024-11-24T19:27:24+01:00</updated><id>http://localhost:4000/feed.xml</id><title type="html">Transformers in Single-Cell Omics</title><subtitle>A curated collection of papers on transformers in single-cell analysis</subtitle></feed>
		<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.3.4">Jekyll</generator><link href="http://localhost:4000/single-cell-transformer-papers/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/single-cell-transformer-papers/" rel="alternate" type="text/html" /><updated>2024-12-02T13:48:48+08:00</updated><id>http://localhost:4000/single-cell-transformer-papers/feed.xml</id><title type="html">Transformers in Single-Cell Omics</title><subtitle>A curated collection of papers on transformers in single-cell analysis</subtitle></feed>