From 6f0199d2c41286a17acbc8cd51b464be1b014ca1 Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Mon, 2 Dec 2024 21:00:14 -0500
Subject: [PATCH] update workflow for readme

---
 .github/workflows/update_readme.yml | 15 ++++++++++++++-
 README.md                           | 15 ++++++---------
 docs/update_readme.py               |  2 --
 3 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/update_readme.yml b/.github/workflows/update_readme.yml
index eb9f6a4..50a89ff 100644
--- a/.github/workflows/update_readme.yml
+++ b/.github/workflows/update_readme.yml
@@ -21,14 +21,27 @@ jobs:
       with:
         python-version: '3.x'
 
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+
+
+    - name: "Set up Python"
+      uses: actions/setup-python@v5
+      with:
+        python-version-file: ".python-version"
+
+    - name: Install the project
+      run: uv sync --all-extras --dev
+
     - name: Install dependencies
       run: |
+        uv python install
         python -m pip install --upgrade pip
         pip install .
 
     - name: Update README
       run: |
-        python doc/update_readme.py
+        uv run docs/update_readme.py
 
     - name: Commit and push changes
       run: |
diff --git a/README.md b/README.md
index a2b1a4f..c4b3e3e 100644
--- a/README.md
+++ b/README.md
@@ -38,8 +38,8 @@ fig = plot_hipp_surf(label_gii.format(density=density), hemi=None, density=densi
 fig = plot_hipp_surf(label_gii.format(density=density), hemi=None, density=density, view='ventral')
 
 ```
-![png](doc/example1_0.png)
-![png](doc/example1_1.png)
+![png](docs/example1_0.png)
+![png](docs/example1_1.png)
     
 ### Example 2: Plot Left and Right Hemispheres Separately
 
@@ -59,8 +59,8 @@ fig = plot_hipp_surf(label_gii.format(density=density), hemi='right', density=de
 
 ```
     
-![png](doc/example2_0.png)
-![png](doc/example2_1.png)
+![png](docs/example2_0.png)
+![png](docs/example2_1.png)
 
 ### Example 3: Plot unfolded and canonical space separately
 
@@ -79,14 +79,13 @@ fig = plot_hipp_surf(label_gii.format(density=density), space='unfold', density=
 fig = plot_hipp_surf(label_gii.format(density=density), space='canonical', density=density, view='dorsal')
 ```
     
-![png](doc/example3_0.png)
-![png](doc/example3_1.png)
+![png](docs/example3_0.png)
+![png](docs/example3_1.png)
 
 ## 🛠️ Functions
 
 ### `plot_hipp_surf`
 
-```python
 Plot hippocampal surface map.
 
 This function plots a surface map of the hippocampus, which can be a label-hippdentate shape.gii, func.gii, or a Vx1 array 
@@ -141,8 +140,6 @@ can also be applied here, overriding the defaults set below.
 ###### Notes
 By default, this function will plot one hemisphere (left by default) in both canonical and unfolded space.
 Both surfaces can be plotted with hemi=None, but the same surf_map will be plotted on both.
-```
-
 ## 🧪 Testing
 
 To run the tests, including unit tests and docstring tests, use the following command:
diff --git a/docs/update_readme.py b/docs/update_readme.py
index 1af6cf5..19c3a7c 100644
--- a/docs/update_readme.py
+++ b/docs/update_readme.py
@@ -38,9 +38,7 @@ def update_readme(readme_path, docstrings):
     new_lines = lines[:start_functions + 2]
     for func_name, docstring in docstrings.items():
         new_lines.append(f"### `{func_name}`\n\n")
-        new_lines.append("```python\n")
         new_lines.append(f"{docstring}\n")
-        new_lines.append("```\n\n")
 
     new_lines.extend(lines[end_functions:])