Spot the difference: Immerse --> master

.gitignore

@@ -7,6 +7,11 @@ __pycache__/
 *.so
 *.nc
 *.xml
+
+# CMEMS creditial file
+CMEMS_cred.py
+motu_config.ini
+
 # Distribution / packaging
 .Python
 build/
@@ -28,6 +33,8 @@ wheels/
 MANIFEST
 outputs
 .DS_Store
+DATA
+SSW_FVCOM
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

README.rst

@@ -1,10 +1,11 @@
 PyNEMO
 ======
 
-To be updated soon. This work springboards from the `PyNEMO Project <http://pynemo.readthedocs.io/en/latest/index.html/>`_.
+Full documentation here.
 
 What is this repository for?
 ----------------------------
+PyNEMO boundary generation toolbox for NEMO ocean model.
 
 How do I get set up?
 --------------------
@@ -20,16 +21,16 @@ Steps to take to install PyNEMO, creating a specific conda virtual environment i
 - 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
+    $ cd PyNEMO
+    $ conda env create -f pynemo_37.yml
 
 - Activate the new virtual environment::
 
-   $ source activate pynemo_env
+   $ source activate pynemo3
 
-- Install Jave JRE (outside scope of this readme) and link libjvm.dylib to LD_LIBRARY_PATH variable::
+- Install Jave JDK (outside scope of this readme) and link Java Home to conda environment::
 
-    $ export LD_LIBRARY_PATH=/path/to/java/library/folder/containing/libjvm.dylib:$LD_LIBARY_PATH # see notes below
+    $ export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-13.0.2.jdk/Contents/Home # see notes below
 
 - Install PyNEMO::
 
@@ -39,45 +40,54 @@ Steps to take to install PyNEMO, creating a specific conda virtual environment i
 
 This should result in PyNEMO being installed in the virtual environment, and can be checked by entering::  
 
-    $ pynemo -v
+    $ pynemo -h
 
 Resulting in a help usage prompt::
 
-    $ usage: pynemo -g -s <namelist.bdy> 
+    $ usage: pynemo [-g] -s -d <namelist.bdy>
+       -g (optional) will open settings editor before extracting the data
+       -s <bdy filename> file to use
+       -d (optional) will download CMEMS data using provided bdy file
 
 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::
+    $ conda deactivate
 
-    $ source activate pynemo_env
+To reactivate, the following needs to be typed::
 
+    $ source activate pynemo3
 
 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** 
+Other commands include -d which downloads the specified CMEMS data in the namelist bdy file.::
 
-For Macbook Pro 2015, macOS Mojave and Java SDK 13 and JRE 8 the following path for the libjvm library should be correct:: 
+    $ pynemo -d /PyNEMO/inputs/namelist_cmems.bdy
 
-    /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/lib/server
+To use the CMEMS download service an account needs to be created at http://marine.copernicus.eu/services-portfolio/access-to-products/
+Once created the user name and password need to be added to PyNEMO. To do this a file with the name CMEMS_cred.py in the utils folder
+needs to be created with two defined strings one called user and the other called pwd to define the user name and password.::
 
-Resulting in the following command: (this will be different for different java versions and operating systems)::
+    $ touch pynemo/utils/CMEMS_cred.py
+    $ vim pynemo/utils/CMEMS_cred.py
+    press i
+    user='username'
+    pwd='password'
+    press esc and then :q
 
-    $ export LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/lib/server:$LD_LIBRARY_PATH
+**IMPORTANT** This will create a py file in the right place with the parameters required to download CMEMS, the password is stored as plain text so please
+do not reuse any existing password!
 
-For an iMac 2013, macOS Catalina and JRE 8 only the followinng path was found to be correct::
-
-   /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/server
-
-With the following command being required to set the environment variable::
+PyNEMO creates a log file be default, this provided info, warning and error messages. By default this is called nrct.log and is saved in the directory where pynemo is run from. (usually /PyNEMO)
+New runs are appended onto the end of the log file so it will periodically need to be delelted to reduce the size of the log.
 
-    $ export LD_LIBRARY_PATH=/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/server:$LD_LIBRARY_PATH
+**Additional NOTES**
 
-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!)
+The above path for Java Home was valid for a Macbook Pro 2015 with macOS Catalina and Java SDK 13.0.2
+however for different java versions, operating systems etc this may be different
 
-**Update** conda environment yaml file has been tested (and works!) on a Macbook Pro 2015 and iMac 2013 running Anaconda 3.7 and Miniconda 3.7 respectively. 
+The conda environment yaml file has been tested with miniconda 3.7 and found to install the environment correctly.
 
 Contribution guidelines
 -----------------------
@@ -101,6 +111,19 @@ The PyNEMO module can be tested using the bench marking namelist bdy file in the
   :width: 800
   :alt: Example BDY coords output
 
+Unit Tests
+-------------------
+
+To test operation of the PyNEMO module, running the PyTest script in the unit tests folder will perform a range of tests on different child grids,
+e.g. checking the interpolation of the source data on to the child grid. To do this the following command is required::
+
+    $ pytest -v pynemo/pynemo_unit_test.py
+
+The results of the test will show if all tests pass or the errors that result from failed tests.
+
+Currently **(26/03/2020)** there are 7 tests that cover checking the interpolation results of different child grids. The input data is generated as part of the
+test and is removed afterwards. The number of tests will be increased in the future to cover more PyNEMO functionality.
+
 Who do I talk to?
 -----------------
 
@@ -110,5 +133,6 @@ Who do I talk to?
 
 * Other community or team contact
 
+  thopri
 
 For more information regarding the use and development of PyNEMO see: [PyNEMO Wiki](https://github.com/jdha/PyNEMO/wiki)