#57 adjust tutorial heading levels

Author: kwabenantim

test/python/cell_based/tutorials/TestCellSortingTutorial.py

@@ -33,13 +33,13 @@
 #ifndef
 #define TRIGGER_WIKI
 
-## # 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
 
 import unittest # Python testing framework
 import matplotlib.pyplot as plt # Plotting
@@ -52,7 +52,7 @@
 
 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.
 

test/python/cell_based/tutorials/TestMeshBasedCellSimulationsPythonTutorial.py

@@ -33,11 +33,11 @@
 #ifndef
 #define TRIGGER_WIKI
 
-## # 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
 
 import unittest  # Python testing framework
 import matplotlib.pyplot as plt  # Plotting
@@ -51,7 +51,7 @@
 
 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.
 
@@ -136,7 +136,7 @@ def test_monolayer(self):
 
         ## 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.
 

test/python/cell_based/tutorials/TestNodeBasedCellSimulationsPythonTutorial.py

@@ -33,11 +33,11 @@
 #ifndef
 #define TRIGGER_WIKI
 
-## # 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
 
 import unittest  # Python testing framework
 import numpy as np  # Matrix tools
@@ -49,7 +49,7 @@
 
 
 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.
 
@@ -131,7 +131,7 @@ def test_monolayer(self):
 
         # 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.
 
@@ -209,7 +209,7 @@ def test_spheroid(self):
 
         # 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.
 

test/python/cell_based/tutorials/TestPottsBasedCellSimulationsPythonTutorial.py

@@ -33,11 +33,11 @@
 #ifndef
 #define TRIGGER_WIKI
 
-## # 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
 
 import unittest  # Python testing framework
 import chaste  # The PyChaste module
@@ -48,7 +48,7 @@
 
 
 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.
 
@@ -159,7 +159,7 @@ def test_monolayer(self):
 
         # 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.
 
@@ -239,7 +239,7 @@ def test_potts_monolayer_cell_sorting(self):
 
         # JUPYTER_TEARDOWN 
 
-    ## ## Test 3 - 3D Cell Sorting
+    ## ### Test 3 - 3D Cell Sorting
     ## The next test extends the previous example to three dimensions.
 
     def test_potts_spheroid_cell_sorting(self):

test/python/cell_based/tutorials/TestScratchAssayTutorial.py

@@ -33,7 +33,7 @@
 #ifndef
 #define TRIGGER_WIKI
 
-## # 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:
 ##
@@ -56,7 +56,7 @@
 
 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).
     ## 

test/python/cell_based/tutorials/TestSpheroidTutorial.py

@@ -33,14 +33,14 @@
 #ifndef
 #define TRIGGER_WIKI
 
-## # 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
 
 import unittest # Python testing framework
 import matplotlib.pyplot as plt # Plotting
@@ -55,7 +55,7 @@
 
 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.
 

test/python/cell_based/tutorials/TestTensileTestTutorial.py

@@ -33,14 +33,14 @@
 #ifndef
 #define TRIGGER_WIKI
 
-## # 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
 
 import unittest  # Python testing framework
 import numpy as np  # Matrix tools
@@ -53,7 +53,7 @@
 
 class TestTensileTestTutorial(chaste.cell_based.AbstractCellBasedTestSuite):
 
-    ## ## Test 1 - A 2d test
+    ## ### Test 1 - A 2D test
 
     def test_monolayer(self):
 

test/python/cell_based/tutorials/TestVertexBasedCellSimulationsPythonTutorial.py

@@ -33,12 +33,12 @@
 #ifndef
 #define TRIGGER_WIKI
 
-## # Introduction
+## ## Introduction
 ## In this tutorial we show how Chaste can be used to create, run and visualize vertex-based simulations. 
 ## 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
 
 import unittest  # Python testing framework
 import matplotlib.pyplot as plt  # Plotting
@@ -50,7 +50,7 @@
 chaste.init()  # Set up MPI
 
 class TestRunningVertexBasedSimulationsTutorial(chaste.cell_based.AbstractCellBasedTestSuite):
-    ## ## Test 1 - A basic vertex-based simulation
+    ## ### Test 1 - A basic vertex-based simulation
     ## In the first test, we run a simple vertex-based simulation, in which we create a monolayer of cells, 
     ## using a mutable vertex mesh. Each cell is assigned a stochastic cell-cycle model.
 
@@ -140,7 +140,7 @@ def test_monolayer(self):
 
         # JUPYTER_TEARDOWN
 
-    ## ## Test 2 - introducing periodicity, boundaries and cell killers
+    ## ### Test 2 - introducing periodicity, boundaries and cell killers
     ## In the second test, we run a simple vertex-based simulation, in which we create a monolayer of cells in a periodic geometry, 
     ## using a cylindrical vertex mesh. We also include a fixed boundary which cells can't pass through and a cell killer which removes
     ## cells once they leave a region. As before each cell is assigned a stochastic cell-cycle model.