updated recipe and markdown formating

README.md

@@ -10,42 +10,68 @@ Steps to take to install PyNEMO, creating a specific conda virtual environment i
 
 - Install Conda, either Anaconda or Miniconda (outside of this readme)
 - Create conda environment for PyNEMO
-    - $ cd to/PyNEMO/directory
-    - $ conda env create -f environment_pynemo.yml
+```
+$ cd to/PyNEMO/directory
+```
+```
+$ conda env create -f environment_pynemo.yml
+```
 - Activate the new virtual environment
-    - $ source activate pynemo_env
+```
+$ source activate pynemo_env
+```
 - Install Jave JRE (outside this readme) and link libjvm.dylib to LD_LIBRARY_PATH variable
-    - $ export LD_LIBRARY_PATH=/path/to/java/library/folder/containing/libjvm.dylib:$LD_LIBARY_PATH **SEE NOTES**  
+```
+$ export LD_LIBRARY_PATH=/path/to/java/library/folder/containing/libjvm.dylib:$LD_LIBARY_PATH # see notes below
+```
 - Install Git (outside 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
+```
+$ 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> 
+``` 
+$ usage: pynemo -g -s <namelist.bdy> 
+```
 
-The virtual environment can be deactivated to return you to the normal prompt by typing:
-	$ conda deactivate
+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
+```
+$ source activate pynemo_env
+```
 
-To use PyNEMO, the following command is entered: (the example will run an benchmarking lest)
-	$ pynemo -s /path/to/namelist/file (e.g. PyNEMO/inputs/namelist_remote.bdy)
+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)
+```
 
-**NOTES** 
+**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
+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:$LD_LIBRARY_PATH
-
+```
+$ 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 ##
@@ -56,7 +82,7 @@ The PyNEMO module can be tested using the bench marking namelist bdy file in the
 
 - Run PyNEMO using the namelist file in the inputs folder (namelist_remote.bdy) e.g.
 
-	-	$ pynemo -s /path/to/namelist/file
+    -   $ 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