Apply suggestions from code review

Thanks for the review! These were all reasonable suggestions. Most of the text in "introduction.md" actually came from the referenced paper, so the text fixes should be in there. For me this is a placeholder anyway, as I think Eva and/or Bandan should write these parts. For now i just accepted your contributions, which made it more readable.

Co-authored-by: Alexander Hadjiivanov <43831101+cantordust@users.noreply.github.com>

Author: JaroCamphuijsen

README.dev.md

@@ -3,14 +3,14 @@
 
 ## Note
 
-Testing and contributing is very welcome, especially if you can contribute with new algorithms and features.
+Testing and contributing is very welcome, especially if you can contribute new algorithms and features.
 
 
 # Development
 
 ## Building the documentation locally
 
-Documentation is generated with [Sphinx](https://www.sphinx-doc.org/) and [Doxygen](https://www.doxygen.nl/) (for automatically generating the technical documentation) with [Breathe](https://breathe.readthedocs.io/) providing a bridge between the Sphinx and Doxygen documentation systems. To build the documentation locally follow these steps:
+Documentation is generated with [Sphinx](https://www.sphinx-doc.org/) and [Doxygen](https://www.doxygen.nl/) (for automatically generating the technical documentation), with [Breathe](https://breathe.readthedocs.io/) providing a bridge between the Sphinx and Doxygen documentation systems. To build the documentation locally, follow these steps:
 
 ### Linux
 Install doxygen:
@@ -19,19 +19,19 @@ Install doxygen:
 sudo apt install doxygen
 ```
 
-Then, from the root of the repository install Sphinx and the other Python dependencies:
+Then, install Sphinx and the other Python dependencies from the root of the repository:
 
 ```
 python -m venv .venv
 source .venv/bin/activate
 pip install -r doc/requirements.txt
 ```
 
-Then we generate the doxygen technical documentation xml files and use Sphinx to generate the html files with the full documentation:
+Then we generate the Doxygen technical documentation XML files and use Sphinx to generate the HTML files with the full documentation:
 
 ```
 doxygen doc/Doxyfile
 sphinx-build doc doc/build
 ```
 
-And we can view the generated documentation by opening `doc/build/index.md` in a browser.
+And we can view the generated documentation by opening `doc/build/index.html` in a browser.

doc/conf.py

@@ -8,7 +8,7 @@
 
 project = 'CorticalSim3D'
 copyright = '2017-%Y'
-author = 'Eva Deinum, Bandan Chakrabortty, Simon Tindemans, Jaro Camphuijsen, Alex Hadjiivanov'
+author = 'Eva Deinum, Bandan Chakrabortty, Simon Tindemans, Jaro Camphuijsen, Alexander Hadjiivanov'
 release = ''
 
 # -- General configuration ---------------------------------------------------

doc/introduction.md

@@ -1,11 +1,11 @@
 # Introduction
 Plant morphogenesis is strongly dependent on the directional growth and the subsequent oriented division of individual cells.
-It has been shown that the plant cortical microtubule array plays a key role in controlling both these processes.
+It has been shown that the plant cortical microtubule array plays a key role in controlling both of these processes.
 This ordered structure emerges as the collective result of stochastic interactions between large numbers of dynamic microtubules.
-To elucidate this complex self-organization process a number of analytical and computational approaches to study the dynamics of cortical microtubules have been proposed.
-To date, however, these models have been restricted to two dimensional planes or geometrically simple surfaces in three dimensions, which strongly limits their applicability as plant cells display a wide variety of shapes.
+A number of analytical and computational approaches to studying the dynamics of cortical microtubules have been proposed in order to elucidate this complex self-organization process.
+To date, however, these models have been restricted to two-dimensional planes or geometrically simple surfaces in three dimensions, which strongly limits their applicability as plant cells display a wide variety of shapes.
 This limitation is even more acute, as both local as well as global geometrical features of cells are expected to influence the overall organization of the array.
-CorticalSim3D is a framework for efficiently simulating microtubule dynamics on triangulated approximations of arbitrary three dimensional surfaces.
+CorticalSim3D is a framework for efficiently simulating microtubule dynamics on triangulated approximations of arbitrary three-dimensional surfaces.
 This allows the study of microtubule array organization on realistic cell surfaces obtained by segmentation of microscopic images.