feat: created the landing page for OSIPI documentation hub

Readme.md

@@ -1,72 +1,56 @@
-## 🛠️ Setup and Run Instructions
+# Guide to run this documentation locally
 
-Follow these steps to set up and run the project:
+## 1. Create a Virtual Environment
 
----
-
-### 1. ✅ Prerequisites
-
-Make sure **Python** is installed on your system. You can verify it by running:
+Run the following command in your project directory:
 
 ```bash
-python --version
+python -m venv venv
 ```
 
----
-
-### 2. 📦 Initialize the Virtual Environment
-
-Set up your environment and install dependencies with:
-
-```bash
-python setup_env.py initialize
-```
-
-This will:
-
-* Create a virtual environment (default: `venv`)
-* Install all packages listed in `requirements.txt`
-* Output the command to activate the virtual environment
+This will create a folder named **`venv`** containing the virtual environment.
 
 ---
 
-### 3. 🚀 Activate the Virtual Environment
+## 2. Activate the Virtual Environment
 
-Use the command printed after initialization to activate the environment:
+To start using the virtual environment:
 
-* On **Windows** (use **Git Bash** for compatibility — PowerShell/CMD may not work):
+* **On macOS/Linux:**
 
   ```bash
-  source venv/Scripts/activate
+  source venv/bin/activate
   ```
 
-* On **macOS/Linux**:
+* **On Windows (Git Bash):**
 
-  ```bash
-  source venv/bin/activate
+  ```powershell
+  source venv/Scripts/activate
   ```
 
 ---
 
-### 4. 🔧 Start the Development Server
+## 3. Install Dependencies
 
-Once the virtual environment is active, start the MkDocs server:
+If you have a `requirements.txt` file in your project:
 
 ```bash
-mkdocs serve
+pip install -r requirements.txt
 ```
 
-This will launch a local server at:
-👉 `http://127.0.0.1:8000`
-
 ---
 
-### 5. 🧹 Clean Up (Optional)
-
-To remove the virtual environment and temporary files, run:
+## 4. Serve the Mkdocs locally
 
-```bash
-python setup_env.py clean
 ```
+mkdocs serve
+```
+This will start the mkdocs server
 
-This will delete the environment and clean the project directory.
+## 5 ( Optional ). Deactivate the Virtual Environment
+
+When finished working, you can exit the environment with:
+
+```bash
+deactivate
+```

docs/assets/stylesheets/extra.css

@@ -1,5 +1,5 @@
 .md-grid {
-    max-width: 85vw;
+    max-width: 90vw;
 }
 
 .md-header__button.md-logo{

docs/js/mathjax-config.js

@@ -0,0 +1,12 @@
+window.MathJax = {
+    tex: {
+      inlineMath: [['$', '$'], ['\\(', '\\)']],
+      displayMath: [['$$', '$$'], ['\\[', '\\]']],
+      processEscapes: true,
+      processEnvironments: true
+    },
+    options: {
+      skipHtmlTags: ['script', 'noscript', 'style', 'textarea', 'pre']
+    }
+  };
+

docs/lexicons.md

@@ -2,14 +2,13 @@
 
 OSIPI develops standardized lexicons to improve consistency and interoperability in perfusion MRI research.
 
-!!! abstract "CAPLEX (TF4.2)"
-    A curated lexicon of definitions for quantities, models, and analysis methods used in **contrast-agent based perfusion MRI** (DCE and DSC).
-
-    📘 [CAPLEX Documentation](https://osipi.github.io/OSIPI_CAPLEX/)  
-    🧪 [GitHub Repository](https://github.com/OSIPI/OSIPI_CAPLEX)
-
 !!! abstract "ASL Lexicon (TF4.1)"
     A community-driven terminology guide for **Arterial Spin Labeling (ASL)** imaging, providing standardized parameter definitions and reporting recommendations.
 
     📘 [ASL Lexicon Documentation](https://osipi.github.io/ASL-Lexicon/)  
     🧪 [GitHub Repository](https://github.com/osipi/ASL-Lexicon/)
+!!! abstract "CAPLEX (TF4.2)"
+    A curated lexicon of definitions for quantities, models, and analysis methods used in **contrast-agent based perfusion MRI** (DCE and DSC).
+
+    📘 [CAPLEX Documentation](https://osipi.github.io/OSIPI_CAPLEX/)  
+    🧪 [GitHub Repository](https://github.com/OSIPI/OSIPI_CAPLEX)

docs/overrides/main.html

@@ -22,3 +22,6 @@
   {{ super() }}
   <script src="{{ 'assets/javascripts/custom.9e5da760.min.js' | url }}"></script>
 {% endblock %}
+{% block htmltitle %}
+  <title>{{ config.site_name }}</title>
+{% endblock %}

mkdocs.yml

@@ -82,6 +82,9 @@ plugins:
           imports: [
             docs/index.md,docs/user-guide/*,docs/about/index.md, docs/contribution/index.md
           ]
+  - open-in-new-tab
+  - mkdocs-jupyter
+  # - mknotebooks
 # Additional configuration
 extra:
   social:
@@ -92,12 +95,17 @@ extra:
 
 extra_css:
     - assets/stylesheets/extra.css
+extra_javascript:
+  - js/mathjax-config.js
+  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
+
 
 # Extensions
 markdown_extensions:
   - abbr
   - admonition
   - attr_list
+  - codehilite
   - def_list
   - footnotes
   - md_in_html
@@ -177,11 +185,10 @@ nav:
         - References: https://osipi.github.io/osipi/references/
         - Examples: https://osipi.github.io/osipi/generated/gallery/
 
-
       - "(TF2.2) ASL repository":
         - Documentation: https://github.com/OSIPI/TF2.2_OSIPI-ASL-toolbox/blob/main/ASL_functionalities_test_report_Github.docx
       - "(TF2.3) DCE/DSC repository":
-        - Documentation: https://osipi.github.io/DCE-DSC-MRI_TestResults/intro.html
+        - Documentation: https://rohankrmahato.github.io/DCE-DSC-MRI_CodeCollection/
       - "(TF2.4) IVIM repository": 
         - Documentation: https://osipi.github.io/TF2.4_IVIM-MRI_CodeCollection/
 

requirements.txt

@@ -2,4 +2,10 @@ mkdocs
 mkdocs-multirepo-plugin
 mkdocs-material
 mkdocs-material-extensions
-mkdocs-minify-plugin
+mkdocs-minify-plugin
+mkdocs-jupyter
+Pygments
+jupyter-book
+pytest
+wheel
+mkdocs-open-in-new-tab