Merge pull request #2 from CompuCell3D/fix/intro_funding_pages

Fixed broken funding and introduction pages; also a few minor edits
CompuCell3D · Feb 21, 2020 · 4c3ddc3 · 4c3ddc3
2 parents 7ea9e02 + b48eae0
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diff --git a/docs/funding.rst b/docs/funding.rst
@@ -1,5 +1,5 @@
 Funding
-=======
+#######
 
 From early days CompuCell3D was funded by science grants. The list of funding entities include
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -8,8 +8,21 @@ The focus of this manual is to teach you how to use CC3DML (XML-based syntax) to
 multi-cell tissue simulations. We will assume that you have a working knowledge of XML.
 You do not have to be an XML guru but you should know how to write simple XML documents
 
-funding
-introduction
+.. toctree::
+   :maxdepth: 1
+   :hidden:
+   :caption: Funding
+
+   funding
+
+
+.. toctree::
+   :maxdepth: 1
+   :hidden:
+   :caption: Introduction
+
+   introduction
+
 
 .. toctree::
    :maxdepth: 1

diff --git a/docs/introduction.rst b/docs/introduction.rst
@@ -1,9 +1,9 @@
 Introduction to CompuCell3D Modules CC3DML Syntax
-=====================================================
+###################################################
 
-This CompuCell3D reference material provides users with fairly detaild
+This CompuCell3D reference material provides users with fairly detailed
 description of CC3DML syntax (CC3DML is XML-based model description
-format) of CC3D modules. The presented material is indended for users
+format) of CC3D modules. The presented material is intended for users
 who are already familiar with CompuCell3D basics and know how to build
 and run simple simulations such as cell-sorting, bacterium macrophage or
 cell-type-oscillator. Since we often show CC3DML syntax and accompanying

diff --git a/docs/mitosis.rst b/docs/mitosis.rst
@@ -1,5 +1,5 @@
 Mitosis Steppable.
------------------
+------------------
 
 Mitosis steppable is described in great detail in "Python Scripting Manual" - see for example
  https://pythonscriptingmanual.readthedocs.io/en/latest/mitosis.html?highlight=mitosis

diff --git a/docs/potts.rst b/docs/potts.rst
@@ -54,7 +54,7 @@ type we use the following syntax:
     <FluctuationAmplitude>
         <FluctuationAmplitudeParameters CellType="Condensing"\
         FluctuationAmplitude="10"/>
-        <FluctuationAmplitudeParameters CellType="NonCondensing”\
+        <FluctuationAmplitudeParameters CellType="NonCondensing"\
         FluctuationAmplitude="5"/>
     </FluctuationAmplitude>
 
@@ -85,17 +85,17 @@ users defined fluctuation amplitude for cell types using expanded CC3DML
 definition and if so it will use those values as fluctuation amplitudes.
 Lastly, it will resort to globally defined fluctuation amplitude
 (``Temperature``). Thus, it is perfectly fine to use ``FluctuationAmplitude``
-CC3DML tags and set ``fluctAmp``l for certain cells. In such a case
-CompuCell3D will use ``fluctAmp``l for cells for which users defined it and
+CC3DML tags and set ``fluctAmpl`` for certain cells. In such a case
+CompuCell3D will use ``fluctAmpl`` for cells for which users defined it and
 for all other cells it will use values defined in the CC3DML.
 
 In GGH model, the fluctuation amplitude is determined taking into
-account fluctuation amplitude of *“source”* (expanding) cell and
-*“destination”* (being overwritten) cell. Currently CompuCell3D supports 3
+account fluctuation amplitude of *"source"* (expanding) cell and
+*"destination"* (being overwritten) cell. Currently CompuCell3D supports 3
 type functions used to calculate resultant fluctuation amplitude (those
-functions take as argument fluctuation amplitude of “source” and
-*“destination”* cells and return fluctuation amplitude that is used in
-calculation of pixel-copy acceptance). The 3 functions are`` Min``, ``Max``, and
+functions take as argument fluctuation amplitude of "source" and
+*"destination"* cells and return fluctuation amplitude that is used in
+calculation of pixel-copy acceptance). The 3 functions are ``Min``, ``Max``, and
 ``ArithmeticAverage`` and we can set them using the following option of the
 Potts section:
 
@@ -106,10 +106,10 @@ Potts section:
          …
     </Potts>
 
-By default we use``Min`` function. Notice, that if you use global
+By default we use ``Min`` function. Notice, that if you use global
 fluctuation amplitude definition ``Temperature`` it does not really matter
-which function you use. The differences arise when *“source*” and
-*“destination”* cells have different fluctuation amplitudes.
+which function you use. The differences arise when *"source"* and
+*"destination"* cells have different fluctuation amplitudes.
 
 The above concepts are best illustrated by the following example:
 
@@ -160,7 +160,7 @@ membrane fluctuations:
 
 
 
-Assigning negative``fluctuationAmplitude`` ``cell.fluctAmpl = -1`` is interpreted
+Assigning negative ``fluctuationAmplitude``, ``cell.fluctAmpl = -1`` is interpreted
 by CompuCell3D as a hint to use fluctuation amplitude defined in the
 CC3DML.
 
@@ -186,7 +186,7 @@ Let us revisit our original example of the ``Potts`` section CC3DML:
         </Potts>
 
 Based on discussion about the difference between pixel-flip attempts and
-MCS (see “Introduction to CompuCell3D”) we can specify how many pixel
+MCS (see "Introduction to CompuCell3D") we can specify how many pixel
 copies should be attempted in every MCS. We specify this number
 indirectly by specifying the ``Flip2DimRatio``  by using
 
@@ -287,8 +287,8 @@ system are accepted with probability
    \end{eqnarray}
 
 
-where ``δ`` and ``*k``* are specified by ``Offset`` and ``KBoltzman`` tags respectively.
-By default ``δ=``0 and ``*k=1*``.
+where ``δ`` and ``*k*`` are specified by ``Offset`` and ``KBoltzman`` tags respectively.
+By default ``δ=0`` and ``*k=1*``.
 
 As an alternative to exponential acceptance function you may use a
 simplified version which is essentially 1 order expansion of the

diff --git a/docs/steppable_section.rst b/docs/steppable_section.rst
@@ -8,7 +8,7 @@ Steppable Section
 Steppables are CompuCell modules that are called every Monte Carlo Step
 (MCS). More precisely, they are called after all the pixel copy attempts
 in a given MCS have been carried out. Steppables may have various
-functions - for example solving PDE's, checking if critical
+functions - for example solving PDEs, checking if critical
 concentration threshold have been reached, updating target volume or
 target surface given the concentration of come growth factor,
 initializing cell field, writing numerical results to a file, *etc...* In
@@ -21,7 +21,7 @@ currently available in the CompuCell3D and describe their usage.
     It is most convenient to implement Steppables in Python. However, in certain situations
     where code performance is an issue users can implement steppables in C++
 
-This section "off-the-shelf" steppables that are availab e in CC3D and were implemented using C++
+This section "off-the-shelf" steppables that are available in CC3D and were implemented using C++
 
 * :doc:`uniform_initializer`
 * :doc:`blob_initializer`