OSIPI · RohanKrMahato · Aug 21, 2025 · Aug 21, 2025 · Aug 21, 2025 · Aug 21, 2025
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -20,7 +20,7 @@ jobs:
         cache: 'pip'
         cache-dependency-path: |
           setup.py
-          notebooks/requirements.txt
+          docs/notebooks/requirements.txt
     - name: Install dependencies
       run: |
         pip install wheel pytest
@@ -46,26 +46,26 @@ jobs:
     - name: Convert contributors csv to md
       if: env.CONTINUE == 'true'
       run: |
-        pip install -r notebooks/requirements.txt
+        pip install -r docs/notebooks/requirements.txt
         python doc/convert_to_md.py
     - name: Build the book
       if: env.CONTINUE == 'true'
       run: |
-        jupyter-book build notebooks/
-        touch notebooks/_build/html/.nojekyll
+        jupyter-book build docs/notebooks/
+        touch docs/notebooks/_build/html/.nojekyll
     - name: Re-organize files
       if: env.CONTINUE == 'true'
       run: |
         mkdir out
-        mv notebooks/_build/html out/docs
+        mv docs/notebooks/_build/html out/docs
         mv test out/test
-    - name: Deploy notebook's html to DCE-DSC-MRI_TestResults repository
-      if: env.CONTINUE == 'true'
-      uses: cpina/github-action-push-to-another-repository@master
-      env:
-        API_TOKEN_GITHUB: ${{ secrets.DEMO_TOKEN }}
-      with:
-        source-directory: 'out'
-        destination-github-username: 'OSIPI'
-        destination-repository-name: 'DCE-DSC-MRI_TestResults'
-        user-email: zaki@live.ca
+    # - name: Deploy notebook's html to DCE-DSC-MRI_TestResults repository
+    #   if: env.CONTINUE == 'true'
+    #   uses: cpina/github-action-push-to-another-repository@master
+    #   env:
+    #     API_TOKEN_GITHUB: ${{ secrets.DEMO_TOKEN }}
+    #   with:
+    #     source-directory: 'out'
+    #     destination-github-username: 'OSIPI'
+    #     destination-repository-name: 'DCE-DSC-MRI_TestResults'
+    #     user-email: zaki@live.ca
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -0,0 +1,40 @@
+name: Deploy MkDocs to GitHub Pages
+
+on:
+  push:
+    branches:
+      - feat/mkdocs-migration
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout source code
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.8'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip 
+          pip install -r requirements.txt 
+          pip install .
+
+      - name: Test with pytest
+        run: |
+          pytest .
+
+      - name: Execute notebooks before building docs
+        run: |
+          find docs/notebooks -type f -name "*.ipynb" ! -path "*/old_nb/*" | while read nb; do
+            echo "Executing $nb"
+            jupyter nbconvert --to notebook --execute --inplace "$nb"
+          done
+
+      - name: Deploy to GitHub Pages
+        run: |
+          mkdocs gh-deploy --force
diff --git a/.gitignore b/.gitignore
@@ -150,8 +150,8 @@ cython_debug/
 test/results-old
 
 # notebook data
-notebooks/data
-notebooks/_build
+docs/notebooks/data
+docs/notebooks/_build
 
 # test results (these are commited to separate repository)
 /results

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 
 
 - [code database with links to source code](https://osipi.github.io/DCE-DSC-MRI_TestResults/overview_of_code_collection.html)
-- [test-results website](https://osipi.github.io/DCE-DSC-MRI_TestResults/intro.html)
+- [test-results website](https://osipi.github.io/DCE-DSC-MRI_TestResults/index.html)
 
 The ISMRM Open Science Initiative for Perfusion Imaging ([OSIPI](https://osipi.ismrm.org)) aims to promote the sharing of perfusion imaging software in order to reduce duplication, improve reproducibility and speed up translation. This **DCE-DSC-MRI_CodeCollection** code library is maintained by [Taskforce 2.3](https://osipi.github.io/task-force-2-3/) of OSIPI and aims to collect, test and share open-source perfusion imaging code for use in research and software development. Code contributions can include modules covering one or more steps within the image processing pipeline, for example T1 mapping, converting signal to concentration and pharmacokinetic modelling. A further aim of OSIPI is to develop a fully tested and harmonised code library, drawing on the contributions within this repository.
 
@@ -39,8 +39,9 @@ Wiki                                   # Information and guidelines
 Click [here](https://osipi.github.io/DCE-DSC-MRI_TestResults/overview_of_code_collection.html) for 
 database of code available with links to code. 
 
-The results of the validated code are published on the [test-results website](https://osipi.github.io/DCE-DSC-MRI_TestResults/intro.html), which is hosted via a separate [repository](https://github.com/OSIPI/DCE-DSC-MRI_TestResults).
+The results of the validated code are published on the [test-results website](https://osipi.github.io/DCE-DSC-MRI_TestResults/index.html), which is hosted via a separate [repository](https://github.com/OSIPI/DCE-DSC-MRI_TestResults).
 
 
 
 This is an ongoing project, we welcome new contributions. If you would like to contribute to the OSIPI initiative please email the contacts listed on our [website](https://osipi.github.io/task-force-2-3/).
+
diff --git a/doc/convert_to_md.py b/doc/convert_to_md.py
@@ -2,6 +2,6 @@
 
 df = pd.read_csv('doc/code_contributions_record.csv')
 md = df.to_markdown(index=False).replace("(../", "(https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/tree/develop/")
-with open('notebooks/overview_of_code_collection.md', 'w') as f:
+with open('docs/notebooks/overview_of_code_collection.md', 'w') as f:
     f.write("# Overview of code collection\n\n")
     f.write(md)
diff --git a/docs/assets/osipiImgs/OSIPI_logo.png b/docs/assets/osipiImgs/OSIPI_logo.png
diff --git a/docs/assets/osipiImgs/OSIPI_logo_only_square.png b/docs/assets/osipiImgs/OSIPI_logo_only_square.png
diff --git a/notebooks/logo.png → docs/assets/osipiImgs/OsipiBanner.png b/notebooks/logo.png → docs/assets/osipiImgs/OsipiBanner.png
diff --git a/docs/assets/osipiImgs/osipi_logo.ico b/docs/assets/osipiImgs/osipi_logo.ico
diff --git a/docs/assets/stylesheets/extra.css b/docs/assets/stylesheets/extra.css
@@ -0,0 +1,8 @@
+.md-grid {
+    max-width: 90vw;
+}
+
+.md-header__button.md-logo{
+    padding-bottom: 18px;
+    scale: 1.2;
+}
diff --git a/notebooks/intro.md → docs/index.md b/notebooks/intro.md → docs/index.md
diff --git a/docs/js/mathjax-config.js b/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']
+    }
+  };
+
diff --git a/docs/notebooks/2CUM.ipynb b/docs/notebooks/2CUM.ipynb
diff --git a/docs/notebooks/2CXM.ipynb b/docs/notebooks/2CXM.ipynb
diff --git a/notebooks/Acknowledgements.ipynb → docs/notebooks/Acknowledgements.ipynb b/notebooks/Acknowledgements.ipynb → docs/notebooks/Acknowledgements.ipynb
diff --git a/notebooks/DCE.md → docs/notebooks/DCE.md b/notebooks/DCE.md → docs/notebooks/DCE.md
diff --git a/notebooks/DCEmodels.md → docs/notebooks/DCEmodels.md b/notebooks/DCEmodels.md → docs/notebooks/DCEmodels.md
@@ -2,12 +2,14 @@ DCE models
 ====================
 
 Several perfusion models are currently available in the code respository:
+
 - Tofts model
 - extended Tofts model
 - Patlak model
 - 2-compartment exchange model
 - 2-compartment uptake model
 
 Not tested yet:
+
 - dual inlet models
 - [to be extended]
diff --git a/notebooks/DSC.md → docs/notebooks/DSC.md b/notebooks/DSC.md → docs/notebooks/DSC.md
diff --git a/docs/notebooks/DSC_pars.ipynb b/docs/notebooks/DSC_pars.ipynb
diff --git a/docs/notebooks/ExtendedToftsModel.ipynb b/docs/notebooks/ExtendedToftsModel.ipynb
diff --git a/docs/notebooks/GeorgiouAIF.ipynb b/docs/notebooks/GeorgiouAIF.ipynb
diff --git a/docs/notebooks/ParkerAIF.ipynb b/docs/notebooks/ParkerAIF.ipynb
diff --git a/docs/notebooks/PatlakModel.ipynb b/docs/notebooks/PatlakModel.ipynb
diff --git a/notebooks/PopulationAIF.md → docs/notebooks/PopulationAIF.md b/notebooks/PopulationAIF.md → docs/notebooks/PopulationAIF.md
@@ -2,6 +2,7 @@ Population arterial Input function
 ====================
 
 This part describes the results for the population arterial input functions:
+
 - Parker AIF
 - Georgiou AIF
 - preclinical AIF
diff --git a/docs/notebooks/PreclinicalAIF.ipynb b/docs/notebooks/PreclinicalAIF.ipynb