#57 update generated tutorials

kwabenantim · kwabenantim · commit 650bfd8e2176 · 2024-02-23T11:52:30.000Z
diff --git a/doc/tutorials/TestCellSortingTutorial.md b/doc/tutorials/TestCellSortingTutorial.md
@@ -8,7 +8,7 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from [TestCellSortingTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestCellSortingTutorial.py) at revision [be59762f](https://github.com/Chaste/PyChaste/commit/be59762fe3e4709aa796fb442199fd23cadfd269).
+This tutorial is automatically generated from [TestCellSortingTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestCellSortingTutorial.py) at revision [f810861a](https://github.com/Chaste/PyChaste/commit/f810861afe376ba19bd791e14e85f29583993205).
 Note that the code is given in full at the bottom of the page.
 
 
@@ -18,7 +18,7 @@ It shows:
  * How to set up a Potts simulation
  * Working with labels
  
-### The Test
+## The Test
 
 ```python
 import unittest # Python testing framework
@@ -149,11 +149,10 @@ if __name__ == '__main__':
 ```
 
 
-## Code 
-The full code is given below
+## Full code 
 
 
-### File name TestCellSortingTutorial.py 
+**File name:** `TestCellSortingTutorial.py` 
 
 ```python
 import unittest # Python testing framework
diff --git a/doc/tutorials/TestMeshBasedCellSimulationsPythonTutorial.md b/doc/tutorials/TestMeshBasedCellSimulationsPythonTutorial.md
@@ -8,15 +8,15 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from [TestMeshBasedCellSimulationsPythonTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestMeshBasedCellSimulationsPythonTutorial.py) at revision [be59762f](https://github.com/Chaste/PyChaste/commit/be59762fe3e4709aa796fb442199fd23cadfd269).
+This tutorial is automatically generated from [TestMeshBasedCellSimulationsPythonTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestMeshBasedCellSimulationsPythonTutorial.py) at revision [f810861a](https://github.com/Chaste/PyChaste/commit/f810861afe376ba19bd791e14e85f29583993205).
 Note that the code is given in full at the bottom of the page.
 
 
 ## Introduction
 In this tutorial we show how Chaste can be used to create, run and visualize mesh-based simulations.
 Full details of the mathematical model can be found in van Leeuwen et al. (2009) [doi:10.1111/j.1365-2184.2009.00627.x].
 
-### Imports and Setup
+## The Test
 
 ```python
 import unittest  # Python testing framework
@@ -255,11 +255,10 @@ if __name__ == '__main__':
 ```
 
 
-## Code 
-The full code is given below
+## Full code 
 
 
-### File name TestMeshBasedCellSimulationsPythonTutorial.py 
+**File name:** `TestMeshBasedCellSimulationsPythonTutorial.py` 
 
 ```python
 import unittest  # Python testing framework
diff --git a/doc/tutorials/TestNodeBasedCellSimulationsPythonTutorial.md b/doc/tutorials/TestNodeBasedCellSimulationsPythonTutorial.md
@@ -8,15 +8,15 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from [TestNodeBasedCellSimulationsPythonTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestNodeBasedCellSimulationsPythonTutorial.py) at revision [be59762f](https://github.com/Chaste/PyChaste/commit/be59762fe3e4709aa796fb442199fd23cadfd269).
+This tutorial is automatically generated from [TestNodeBasedCellSimulationsPythonTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestNodeBasedCellSimulationsPythonTutorial.py) at revision [f810861a](https://github.com/Chaste/PyChaste/commit/f810861afe376ba19bd791e14e85f29583993205).
 Note that the code is given in full at the bottom of the page.
 
 
 ## Introduction
 In this tutorial we show how Chaste can be used to create, run and visualize node-based simulations. Full details of the mechanical model can be found in Pathamathan et
 al "A computational study of discrete mechanical tissue models", Physical Biology. Vol. 6. No. 3. 2009.. DOI (10.1088/1478-3975/6/3/036001).
 
-### The Test
+## The Test
 
 ```python
 import unittest  # Python testing framework
@@ -338,11 +338,10 @@ if __name__ == '__main__':
 ```
 
 
-## Code 
-The full code is given below
+## Full code 
 
 
-### File name TestNodeBasedCellSimulationsPythonTutorial.py 
+**File name:** `TestNodeBasedCellSimulationsPythonTutorial.py` 
 
 ```python
 import unittest  # Python testing framework
diff --git a/doc/tutorials/TestPottsBasedCellSimulationsPythonTutorial.md b/doc/tutorials/TestPottsBasedCellSimulationsPythonTutorial.md
@@ -8,15 +8,15 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from [TestPottsBasedCellSimulationsPythonTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestPottsBasedCellSimulationsPythonTutorial.py) at revision [be59762f](https://github.com/Chaste/PyChaste/commit/be59762fe3e4709aa796fb442199fd23cadfd269).
+This tutorial is automatically generated from [TestPottsBasedCellSimulationsPythonTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestPottsBasedCellSimulationsPythonTutorial.py) at revision [f810861a](https://github.com/Chaste/PyChaste/commit/f810861afe376ba19bd791e14e85f29583993205).
 Note that the code is given in full at the bottom of the page.
 
 
 ## Introduction
 In this tutorial we show how Chaste can be used to create, run and visualize Potts-based simulations.
 Full details of the mathematical model can be found in Graner, F. and Glazier, J. A. (1992).
 
-### The Test
+## The Test
 
 ```python
 import unittest  # Python testing framework
@@ -383,11 +383,10 @@ if __name__ == '__main__':
 ```
 
 
-## Code 
-The full code is given below
+## Full code 
 
 
-### File name TestPottsBasedCellSimulationsPythonTutorial.py 
+**File name:** `TestPottsBasedCellSimulationsPythonTutorial.py` 
 
 ```python
 import unittest  # Python testing framework
diff --git a/doc/tutorials/TestScratchAssayTutorial.md b/doc/tutorials/TestScratchAssayTutorial.md
@@ -8,7 +8,7 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from [TestScratchAssayTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestScratchAssayTutorial.py) at revision [be59762f](https://github.com/Chaste/PyChaste/commit/be59762fe3e4709aa796fb442199fd23cadfd269).
+This tutorial is automatically generated from [TestScratchAssayTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestScratchAssayTutorial.py) at revision [f810861a](https://github.com/Chaste/PyChaste/commit/f810861afe376ba19bd791e14e85f29583993205).
 Note that the code is given in full at the bottom of the page.
 
 
@@ -23,6 +23,8 @@ representation of cells. It will cover the following techniques:
  * Simulating cell migration on the mesh
  * Real-time visualization of the cell population and plotting of population statistics
  
+## The Test
+
 ```python
 import unittest # Python testing framework
 import matplotlib.pyplot as plt # Plotting
@@ -226,11 +228,10 @@ if __name__ == '__main__':
 ```
 
 
-## Code 
-The full code is given below
+## Full code 
 
 
-### File name TestScratchAssayTutorial.py 
+**File name:** `TestScratchAssayTutorial.py` 
 
 ```python
 import unittest # Python testing framework
diff --git a/doc/tutorials/TestSpheroidTutorial.md b/doc/tutorials/TestSpheroidTutorial.md
@@ -8,7 +8,7 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from [TestSpheroidTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestSpheroidTutorial.py) at revision [be59762f](https://github.com/Chaste/PyChaste/commit/be59762fe3e4709aa796fb442199fd23cadfd269).
+This tutorial is automatically generated from [TestSpheroidTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestSpheroidTutorial.py) at revision [f810861a](https://github.com/Chaste/PyChaste/commit/f810861afe376ba19bd791e14e85f29583993205).
 Note that the code is given in full at the bottom of the page.
 
 
@@ -19,7 +19,8 @@ It covers:
  * Setting up a cell cycle model with oxygen dependence
  * Setting up and solving an oxygen transport PDE
  * Setting up a cell killer
- ### Imports and Setup
+ 
+## The Test
 
 ```python
 import unittest # Python testing framework
@@ -183,11 +184,10 @@ if __name__ == '__main__':
 ```
 
 
-## Code 
-The full code is given below
+## Full code 
 
 
-### File name TestSpheroidTutorial.py 
+**File name:** `TestSpheroidTutorial.py` 
 
 ```python
 import unittest # Python testing framework
diff --git a/doc/tutorials/TestTensileTestTutorial.md b/doc/tutorials/TestTensileTestTutorial.md
@@ -8,7 +8,7 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from [TestTensileTestTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestTensileTestTutorial.py) at revision [be59762f](https://github.com/Chaste/PyChaste/commit/be59762fe3e4709aa796fb442199fd23cadfd269).
+This tutorial is automatically generated from [TestTensileTestTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestTensileTestTutorial.py) at revision [f810861a](https://github.com/Chaste/PyChaste/commit/f810861afe376ba19bd791e14e85f29583993205).
 Note that the code is given in full at the bottom of the page.
 
 
@@ -19,7 +19,7 @@ demonstrates:
  * Applying boundary conditions
  * Working with forces
  
-### The Test
+## The Test
 
 ```python
 import unittest  # Python testing framework
@@ -168,11 +168,10 @@ if __name__ == '__main__':
 ```
 
 
-## Code 
-The full code is given below
+## Full code 
 
 
-### File name TestTensileTestTutorial.py 
+**File name:** `TestTensileTestTutorial.py` 
 
 ```python
 import unittest  # Python testing framework
diff --git a/doc/tutorials/TestVertexBasedCellSimulationsPythonTutorial.md b/doc/tutorials/TestVertexBasedCellSimulationsPythonTutorial.md
@@ -8,7 +8,7 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from [TestVertexBasedCellSimulationsPythonTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestVertexBasedCellSimulationsPythonTutorial.py) at revision [be59762f](https://github.com/Chaste/PyChaste/commit/be59762fe3e4709aa796fb442199fd23cadfd269).
+This tutorial is automatically generated from [TestVertexBasedCellSimulationsPythonTutorial](https://github.com/Chaste/PyChaste/blob/develop/test/python/cell_based/tutorials/TestVertexBasedCellSimulationsPythonTutorial.py) at revision [f810861a](https://github.com/Chaste/PyChaste/commit/f810861afe376ba19bd791e14e85f29583993205).
 Note that the code is given in full at the bottom of the page.
 
 
@@ -17,7 +17,7 @@ In this tutorial we show how Chaste can be used to create, run and visualize ver
 Full details of the mechanical model proposed by T. Nagai and H. Honda ("A dynamic cell model for the formation of epithelial tissues",
 Philosophical Magazine Part B 81:699-719).
 
-### The Test
+## The Test
 
 ```python
 import unittest  # Python testing framework
@@ -255,11 +255,10 @@ if __name__ == '__main__':
 ```
 
 
-## Code 
-The full code is given below
+## Full code 
 
 
-### File name TestVertexBasedCellSimulationsPythonTutorial.py 
+**File name:** `TestVertexBasedCellSimulationsPythonTutorial.py` 
 
 ```python
 import unittest  # Python testing framework
