reformatted to rst rather than markdown

README.rst

+PyNEMO
+======
+
+To be updated soon. This work springboards from the [PyNEMO](http://pynemo.readthedocs.io/en/latest/index.html) Project.
+
+What is this repository for?
+----------------------------
+
+How do I get set up?
+--------------------
+
+Steps to take to install PyNEMO, creating a specific conda virtual environment is highly recommended. 
+`click here for more about virtual enviroments <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html/>`_
+
+- Install Conda, either Anaconda or Miniconda (outside scope of this readme)
+- Create conda environment for PyNEMO::
+
+    $ cd to/PyNEMO/directory
+    $ conda env create -f environment_pynemo.yml
+
+- Activate the new virtual environment::
+
+   $ source activate pynemo_env
+
+- Install Jave JRE (outside scope of this readme) and link libjvm.dylib to LD_LIBRARY_PATH variable::
+
+    $ export LD_LIBRARY_PATH=/path/to/java/library/folder/containing/libjvm.dylib:$LD_LIBARY_PATH # see notes below
+
+- Install Git (outside scope of this readme)::
+
+   $ git clone https://github.com/NOC-MSM/PyNEMO.git
+
+- Install PyNEMO::
+  
+    $ cd /location/of/pynemo/repo 
+    $ python setup.py build
+    $ python setup.py install
+
+This should result in PyNEMO being installed in the virtual environment, and can be checked by entering::  
+
+    $ pynemo -v
+
+Resulting in a help usage prompt::
+ 
+    $ usage: pynemo -g -s <namelist.bdy> 
+
+The virtual environment can be deactivated to return you to the normal prompt by typing::  
+    
+$ conda deactivate
+To reactivate, the following needs to be typed::
+
+    $ source activate pynemo_env
+
+
+To use PyNEMO, the following command is entered: (the example will run an benchmarking test)::
+
+    $ pynemo -s /path/to/namelist/file (e.g. PyNEMO/inputs/namelist_remote.bdy)
+
+**Additional NOTES** 
+
+for MacOs and Java SDK 13 and JRE 8 the following path should be correct:: 
+
+    /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/lib/server
+
+Resulting in the following command: (this will be different for different java versions and operating systems)::
+
+    $ export LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/lib/server:$LD_LIBRARY_PATH
+
+The conda environment creation command has not yet been tested. The yml document (can be opened using text editor) gives a list of all the modules and their versions that are required for PyNEMO so a environment can be constructed using this document as reference (or if you use pip!)
+
+Contribution guidelines
+-----------------------
+
+Bench Marking Tests
+-------------------
+
+The PyNEMO module can be tested using the bench marking namelist bdy file in the inputs folder. To check the outputs of the benchmark test, these can be visualised using the plotting script within the test_scripts folder. The following steps are required,
+
+- Run PyNEMO using the namelist file in the inputs folder (namelist_remote.bdy) e.g.::
+
+    $ pynemo -s /path/to/namelist/file
+
+- This will create two output files coordinates.bdy.nc and NNA_R12_bdyT_y1979)m11.nc in an outputs folder
+
+- To check the coordinates.bdy.nc has the correct boundary points, the script bdy_coords_plot.py will plot the domain boundaries and shown the different locations of the rim width (increasing number should go inwards) This script is located in the test_scripts folder.
+
+- The result should look like this (if using the current benchmark data)
+
+.. image:: /screenshots/example_bdy_coords.png
+  :width: 800
+  :alt: Example BDY coords output
+
+Who do I talk to?
+-----------------
+
+* Repo owner or admin
+
+  jdha
+
+* Other community or team contact
+
+
+For more information regarding the use and development of PyNEMO see: [PyNEMO Wiki](https://github.com/jdha/PyNEMO/wiki)