From 48d1c67cff16282df59f1a114884cbfd75a768d1 Mon Sep 17 00:00:00 2001
From: Henrik Kjedsberg <henrik.kjeldsberg@live.no>
Date: Thu, 14 Mar 2024 11:12:51 +0100
Subject: [PATCH 1/3] Update docs and set docutils pin in requirements.txt

---
 .github/workflows/deploy_pages.yml | 14 +++++---------
 docs/api.rst                       |  2 +-
 docs/movingatrium.md               |  2 +-
 requirements.txt                   |  3 ++-
 4 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/deploy_pages.yml b/.github/workflows/deploy_pages.yml
index 4135a142..5a7b6f81 100644
--- a/.github/workflows/deploy_pages.yml
+++ b/.github/workflows/deploy_pages.yml
@@ -31,7 +31,7 @@ jobs:
       - name: Upgrade pip and setuptools
         run: |
           python3 -m pip install pip setuptools --upgrade
-          
+
       # See: https://github.com/marketplace/actions/setup-miniconda
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2
@@ -56,21 +56,17 @@ jobs:
         run: mamba env update -n vampy -f environment.yml
         if: steps.cache.outputs.cache-hit != 'true'
 
+      # Install requirements, with downgraded docutils to fix layout-bug
+      # https://github.com/executablebooks/jupyter-book/issues/1997
       - name: Install dependencies
-        run: |
-          pip install -r requirements.txt
+        run: pip install -r requirements.txt
 
       - name: Install VaMPy
         run: python3 -m pip install .[test]
 
-      # https://github.com/executablebooks/jupyter-book/issues/1997
-      - name: Downgrade docutils to fix layout-bug
-        run: python3 -m pip install docutils==0.17.1
-
         # Build the book
       - name: Build the book
-        run: |
-          jupyter-book build docs
+        run: jupyter-book build docs
 
       # Deploy the book's HTML to gh-pages branch
       - name: GitHub Pages action
diff --git a/docs/api.rst b/docs/api.rst
index 360d45b7..08bc421f 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -35,7 +35,7 @@ Pre-processing scripts
    :undoc-members:
    :show-inheritance:
 
-.. automodule:: vampy.automatedPreprocessing.ToolRepairSTL
+.. automodule:: vampy.automatedPreprocessing.repair_tools
    :members:
    :undoc-members:
    :show-inheritance:
diff --git a/docs/movingatrium.md b/docs/movingatrium.md
index abd0487f..142e1f3a 100644
--- a/docs/movingatrium.md
+++ b/docs/movingatrium.md
@@ -106,7 +106,7 @@ $ oasismove NSfracStepMove problem=MovingAtrium mesh_path=../../../models/moving
 
 Upon completion of the simulation, the results, along with the associated mesh, are stored in a concise HDF5 format.
 Additionally, the residence time $T_R$ and the velocity field are saved in the XDMF files `blood.xdmf`
-and `velocity.xdmf`, respectively, which includes the mesh deformation. {numref}`moving_results` presents the volumetric
+and `velocity.xdmf`, respectively, which includes the mesh deformation. The animation below presents the volumetric
 representation of the blood residence time and velocity field throughout the four cardiac cycles. It's noteworthy to
 observe the accumulating $T_R$ within the left atrial appendage over time.
 
diff --git a/requirements.txt b/requirements.txt
index 47eb2953..315d5e68 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,4 +3,5 @@ matplotlib
 numpy
 ghp-import
 cppimport
-scipy
\ No newline at end of file
+scipy
+docutils==0.17.1
\ No newline at end of file

From 8849f3d9af53cf0435e783fe4eab0f833b59395d Mon Sep 17 00:00:00 2001
From: Henrik Kjedsberg <henrik.kjeldsberg@live.no>
Date: Thu, 14 Mar 2024 11:30:12 +0100
Subject: [PATCH 2/3] Pin sphinx installation

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 315d5e68..5654fb47 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,4 +4,5 @@ numpy
 ghp-import
 cppimport
 scipy
+sphinx==5.3.0
 docutils==0.17.1
\ No newline at end of file

From 992bbd50a5ee9dd10e0cde8327a34401ded661d8 Mon Sep 17 00:00:00 2001
From: Henrik Kjedsberg <henrik.kjeldsberg@live.no>
Date: Thu, 14 Mar 2024 11:31:38 +0100
Subject: [PATCH 3/3] Add blank space

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 5654fb47..0bc22360 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,4 +5,4 @@ ghp-import
 cppimport
 scipy
 sphinx==5.3.0
-docutils==0.17.1
\ No newline at end of file
+docutils==0.17.1