#57 update generated markdown tutorials

Author: kwabenantim

doc/tutorials/TestCellSortingTutorial.md

@@ -8,18 +8,17 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from the file ../test/python/cell_based/tutorials/TestCellSortingTutorial.py .
+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).
 Note that the code is given in full at the bottom of the page.
 
 
-
-# Introduction
+## Introduction
 This test is a demonstration of cell sorting using a Cellular Potts based framework.
 It shows:
  * How to set up a Potts simulation
  * Working with labels
 
-## The Test
+### The Test
 
 ```python
 import unittest # Python testing framework
@@ -34,7 +33,7 @@ import chaste.visualization # Visualization tools
 class TestCellSortingTutorial(chaste.cell_based.AbstractCellBasedTestSuite):
 
 ```
-## Test 1 - Cell sorting
+### Test 1 - Cell sorting
 The next test generates a collection of cells, there are two types of cells, labelled ones and non labelled ones,
 there is differential adhesion between the cell types. For the parameters specified, the cells sort into separate types.
 
@@ -150,11 +149,11 @@ if __name__ == '__main__':
 ```
 
 
-# Code 
+## Code 
 The full code is given below
 
 
-## File name `TestCellSortingTutorial.py` 
+### File name TestCellSortingTutorial.py 
 
 ```python
 import unittest # Python testing framework

doc/tutorials/TestMeshBasedCellSimulationsPythonTutorial.md

@@ -8,16 +8,15 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from the file ../test/python/cell_based/tutorials/TestMeshBasedCellSimulationsPythonTutorial.py .
+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).
 Note that the code is given in full at the bottom of the page.
 
 
-
-# Introduction
+## 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
+### Imports and Setup
 
 ```python
 import unittest  # Python testing framework
@@ -32,7 +31,7 @@ import chaste.visualization  # Visualization tools
 class TestRunningMeshBasedSimulationsTutorial(chaste.cell_based.AbstractCellBasedTestSuite):
 
 ```
-## Test 1 - a basic mesh-based simulation
+### Test 1 - a basic mesh-based simulation
 In the first test, we run a simple mesh-based simulation,
 in which we create a monolayer of cells, using a mutable mesh. Each cell is assigned a stochastic cell-cycle model.
 
@@ -139,7 +138,7 @@ To run the simulation, we call `Solve()`. We can again do a quick rendering of t
 ```
 Full results can be visualized in Paraview from the `file_handler.GetOutputDirectoryFullPath()` directory.
 
-## Test 2 -  a basic mesh-based simulation with ghost nodes
+### Test 2 -  a basic mesh-based simulation with ghost nodes
 In the second test, we run a simple mesh-based simulation with ghost nodes, in which we create a monolayer of cells, using a mutable mesh.
 Each cell is assigned a stochastic cell-cycle model.
 
@@ -256,11 +255,11 @@ if __name__ == '__main__':
 ```
 
 
-# Code 
+## Code 
 The full code is given below
 
 
-## File name `TestMeshBasedCellSimulationsPythonTutorial.py` 
+### File name TestMeshBasedCellSimulationsPythonTutorial.py 
 
 ```python
 import unittest  # Python testing framework

doc/tutorials/TestNodeBasedCellSimulationsPythonTutorial.md

@@ -8,16 +8,15 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from the file ../test/python/cell_based/tutorials/TestNodeBasedCellSimulationsPythonTutorial.py .
+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).
 Note that the code is given in full at the bottom of the page.
 
 
-
-# Introduction
+## 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
@@ -30,7 +29,7 @@ chaste.init()  # Set up MPI
 
 class TestRunningNodeBasedSimulationsTutorial(chaste.cell_based.AbstractCellBasedTestSuite):
 ```
-## Test 1 - A basic node-based simulation
+### Test 1 - A basic node-based simulation
 In the first test, we run a simple node-based simulation, in which we create a monolayer of cells,
 using a nodes only mesh. Each cell is assigned a uniform cell-cycle model.
 
@@ -136,7 +135,7 @@ If different simulation input parameters are being explored the lines should be
         # JUPYTER_TEARDOWN
 
 ```
-## Test 2 - a basic node-based simulation in 3D
+### Test 2 - a basic node-based simulation in 3D
 In the second test we run a simple node-based simulation in 3D. This is very similar to the 2D test with the dimension changed from 2 to 3 and
 instead of using a mesh generator we generate the nodes directly.
 
@@ -238,7 +237,7 @@ If different simulation input parameters are being explored the lines should be
         # JUPYTER_TEARDOWN
 
 ```
-## Test 3 - a node-based simulation on a restricted geometry
+### Test 3 - a node-based simulation on a restricted geometry
 In the second test we run a simple node-based simulation in 3D. This is very similar to the 2D test with the dimension changed from 2 to 3 and
 instead of using a mesh generator we generate the nodes directly.
 
@@ -339,11 +338,11 @@ if __name__ == '__main__':
 ```
 
 
-# Code 
+## Code 
 The full code is given below
 
 
-## File name `TestNodeBasedCellSimulationsPythonTutorial.py` 
+### File name TestNodeBasedCellSimulationsPythonTutorial.py 
 
 ```python
 import unittest  # Python testing framework

doc/tutorials/TestPottsBasedCellSimulationsPythonTutorial.md

@@ -8,16 +8,15 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from the file ../test/python/cell_based/tutorials/TestPottsBasedCellSimulationsPythonTutorial.py .
+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).
 Note that the code is given in full at the bottom of the page.
 
 
-
-# Introduction
+## 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
@@ -29,7 +28,7 @@ chaste.init()  # Set up MPI
 
 class TestRunningPottsBasedSimulationsTutorial(chaste.cell_based.AbstractCellBasedTestSuite):
 ```
-## Test 1 - A basic node-based simulation
+### Test 1 - A basic node-based simulation
 In the first test, we run a simple Potts-based simulation, in which we create a monolayer of cells, using a Potts mesh.
 Each cell is assigned a stochastic cell-cycle model.
 
@@ -174,7 +173,7 @@ If different simulation input parameters are being explored the lines should be
         # JUPYTER_TEARDOWN
 
 ```
-## Test 2 - Cell sorting
+### Test 2 - Cell sorting
 The next test generates a collection of cells, there are two types of cells, labelled ones and non labelled ones,
 there is differential adhesion between the cell types. For the parameters specified, the cells sort into separate types.
 
@@ -276,7 +275,7 @@ If different simulation input parameters are being explored the lines should be
         # JUPYTER_TEARDOWN
 
 ```
-## Test 3 - 3D Cell Sorting
+### Test 3 - 3D Cell Sorting
 The next test extends the previous example to three dimensions.
 
 ```python
@@ -384,11 +383,11 @@ if __name__ == '__main__':
 ```
 
 
-# Code 
+## Code 
 The full code is given below
 
 
-## File name `TestPottsBasedCellSimulationsPythonTutorial.py` 
+### File name TestPottsBasedCellSimulationsPythonTutorial.py 
 
 ```python
 import unittest  # Python testing framework

doc/tutorials/TestScratchAssayTutorial.md

@@ -8,12 +8,11 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from the file ../test/python/cell_based/tutorials/TestScratchAssayTutorial.py .
+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).
 Note that the code is given in full at the bottom of the page.
 
 
-
-# Introduction
+## Introduction
 This tutorial is an example of modelling a scratch assay using a simple cellular automaton
 representation of cells. It will cover the following techniques:
 
@@ -37,7 +36,7 @@ import chaste.visualization # Visualization tools
 class TestScratchAssayTutorial(chaste.cell_based.AbstractCellBasedTestSuite):
 
 ```
-## Test 1 - Scratch Assay
+### Test 1 - Scratch Assay
 In this test we will create a scratch along the middle of a domain and quantify the migration
 of cells into the region. Cells will migrate by random walk on the their regular mesh  (lattice).
 
@@ -227,11 +226,11 @@ if __name__ == '__main__':
 ```
 
 
-# Code 
+## Code 
 The full code is given below
 
 
-## File name `TestScratchAssayTutorial.py` 
+### File name TestScratchAssayTutorial.py 
 
 ```python
 import unittest # Python testing framework

doc/tutorials/TestSpheroidTutorial.md

@@ -8,19 +8,18 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from the file ../test/python/cell_based/tutorials/TestSpheroidTutorial.py .
+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).
 Note that the code is given in full at the bottom of the page.
 
 
-
-# Introduction
+## Introduction
 This tutorial is an example of modelling spheroid growth with a nutrient.
 It covers:
  * Setting up an off-lattice cell population
  * 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
+ ### Imports and Setup
 
 ```python
 import unittest # Python testing framework
@@ -36,7 +35,7 @@ chaste.init() # Set up MPI
 class TestSpheroidTutorial(chaste.cell_based.AbstractCellBasedTestSuite):
 
 ```
-## Test 1 - a 2D mesh-based spheroid
+### Test 1 - a 2D mesh-based spheroid
 In this test we set up a spheroid with a plentiful supply of oxygen on the boundary and watch it grow
 over time. Cells can gradually become apoptotic if the oxygen tension is too low.
 
@@ -184,11 +183,11 @@ if __name__ == '__main__':
 ```
 
 
-# Code 
+## Code 
 The full code is given below
 
 
-## File name `TestSpheroidTutorial.py` 
+### File name TestSpheroidTutorial.py 
 
 ```python
 import unittest # Python testing framework

doc/tutorials/TestTensileTestTutorial.md

@@ -8,19 +8,18 @@ toc: true
 layout: "single"
 ---
 
-This tutorial is automatically generated from the file ../test/python/cell_based/tutorials/TestTensileTestTutorial.py .
+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).
 Note that the code is given in full at the bottom of the page.
 
 
-
-# Introduction
+## Introduction
 In this tutorial we will demonstrate a simulated tensile test on an epithelial sheet. This test
 demonstrates:
  * Working with vertex based off lattice populations
  * Applying boundary conditions
  * Working with forces
 
-## The Test
+### The Test
 
 ```python
 import unittest  # Python testing framework
@@ -34,7 +33,7 @@ chaste.init()  # Set up MPI
 class TestTensileTestTutorial(chaste.cell_based.AbstractCellBasedTestSuite):
 
 ```
-## Test 1 - A 2d test
+### Test 1 - A 2D test
 
 ```python
     def test_monolayer(self):
@@ -169,11 +168,11 @@ if __name__ == '__main__':
 ```
 
 
-# Code 
+## Code 
 The full code is given below
 
 
-## File name `TestTensileTestTutorial.py` 
+### File name TestTensileTestTutorial.py 
 
 ```python
 import unittest  # Python testing framework