added recipe to install PyNEMO

README.md

@@ -6,6 +6,48 @@ To be udated soon. This work springboards from the [PyNEMO](http://pynemo.readth
 
 ## 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 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 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**  
+- 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
+
+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 lest)
+	$ pynemo -s /path/to/namelist/file (e.g. PyNEMO/inputs/namelist_remote.bdy)
+
+**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 ##

environment_pynemo.yml

+name: pynemo_env
+channels:
+  - conda-forge
+  - anaconda
+  - srikanthnagella
+  - defaults
+dependencies:
+  - alabaster=0.7.12=py27_0
+  - appnope=0.1.0=py27hb466136_0
+  - asn1crypto=1.0.1=py27_0
+  - astroid=1.6.5=py27_0
+  - attrs=19.2.0=py_0
+  - babel=2.7.0=py_0
+  - backports=1.0=py_2
+  - backports.functools_lru_cache=1.5=py_2
+  - backports.shutil_get_terminal_size=1.0.0=py27_2
+  - backports_abc=0.5=py27h6972548_0
+  - basemap=1.2.0=py27h0acbc05_0
+  - blas=1.0=mkl
+  - bleach=3.1.0=py27_0
+  - bzip2=1.0.8=h1de35cc_0
+  - ca-certificates=2019.10.16=0
+  - cartopy=0.16.0=py27h9263bd1_0
+  - certifi=2019.9.11=py27_0
+  - cffi=1.12.3=py27hb5b8e2f_0
+  - cftime=1.0.3.4=py27h1d22016_1001
+  - chardet=3.0.4=py27_1003
+  - cloudpickle=1.2.2=py_0
+  - configparser=4.0.2=py27_0
+  - cryptography=2.7=py27ha12b0ac_0
+  - curl=7.65.3=ha441bb4_0
+  - cycler=0.10.0=py27hfc73c78_0
+  - cython=0.29.13=py27h0a44026_0
+  - dbus=1.13.6=h90a0687_0
+  - decorator=4.4.0=py27_1
+  - defusedxml=0.6.0=py_0
+  - docutils=0.15.2=py27_0
+  - entrypoints=0.3=py27_0
+  - enum34=1.1.6=py27_1
+  - expat=2.2.6=h0a44026_0
+  - freetype=2.9.1=hb4e5f40_0
+  - functools32=3.2.3.2=py27_1
+  - futures=3.3.0=py27_0
+  - geos=3.6.2=h5470d99_2
+  - gettext=0.19.8.1=h15daf44_3
+  - glib=2.56.2=hd9629dc_0
+  - hdf4=4.2.13=h39711bb_2
+  - hdf5=1.10.1=ha036c08_1
+  - icu=58.2=h4b95b61_1
+  - idna=2.8=py27_0
+  - imagesize=1.1.0=py27_0
+  - intel-openmp=2019.4=233
+  - ipaddress=1.0.22=py27_0
+  - ipykernel=4.10.0=py27_0
+  - ipython=5.8.0=py27_0
+  - ipython_genutils=0.2.0=py27h8b9a179_0
+  - ipywidgets=7.5.1=py_0
+  - isort=4.3.21=py27_0
+  - jedi=0.15.1=py27_0
+  - jinja2=2.10.3=py_0
+  - jpeg=9b=he5867d9_2
+  - jsonschema=3.0.2=py27_0
+  - jupyter=1.0.0=py27_7
+  - jupyter_client=5.3.3=py27_1
+  - jupyter_console=5.2.0=py27_1
+  - jupyter_core=4.5.0=py_0
+  - keyring=18.0.0=py27_0
+  - kiwisolver=1.1.0=py27h0a44026_0
+  - krb5=1.16.1=hddcf347_7
+  - lazy-object-proxy=1.4.2=py27h1de35cc_0
+  - libcurl=7.65.3=h051b688_0
+  - libcxx=4.0.1=hcfea43d_1
+  - libcxxabi=4.0.1=hcfea43d_1
+  - libedit=3.1.20181209=hb402a30_0
+  - libffi=3.2.1=h475c297_4
+  - libgfortran=3.0.1=h93005f0_2
+  - libiconv=1.15=hdd342a3_7
+  - libnetcdf=4.5.0=h42fd751_7
+  - libpng=1.6.37=ha441bb4_0
+  - libsodium=1.0.16=h3efe00b_0
+  - libssh2=1.8.2=ha12b0ac_0
+  - libtiff=4.0.10=hcb84e12_2
+  - libxml2=2.9.9=hf6e021a_1
+  - libxslt=1.1.33=h33a18ac_0
+  - lxml=4.4.1=py27hef8c89e_0
+  - markupsafe=1.1.1=py27h1de35cc_0
+  - matplotlib=2.2.3=py27h54f8f79_0
+  - mccabe=0.6.1=py27_1
+  - mistune=0.8.4=py27h1de35cc_0
+  - mkl=2019.4=233
+  - mkl-service=2.3.0=py27hfbe908c_0
+  - mkl_fft=1.0.14=py27h5e564d8_0
+  - mkl_random=1.1.0=py27ha771720_0
+  - nbconvert=5.6.0=py27_1
+  - nbformat=4.4.0=py27hddc86d0_0
+  - ncurses=6.1=h0a44026_1
+  - netcdf4=1.3.1=py27he3ffdca_2
+  - notebook=5.7.8=py27_0
+  - numpy=1.16.5=py27hacdab7b_0
+  - numpy-base=1.16.5=py27h6575580_0
+  - numpydoc=0.9.1=py_0
+  - olefile=0.46=py27_0
+  - openssl=1.1.1d=h1de35cc_3
+  - owslib=0.18.0=py_0
+  - packaging=19.2=py_0
+  - pandoc=2.2.3.2=0
+  - pandocfilters=1.4.2=py27_1
+  - parso=0.5.1=py_0
+  - pathlib2=2.3.5=py27_0
+  - pcre=8.43=h0a44026_0
+  - pexpect=4.7.0=py27_0
+  - pickleshare=0.7.5=py27_0
+  - pillow=6.2.0=py27hb68e598_0
+  - pip=19.2.3=py27_0
+  - proj4=5.0.1=h1de35cc_0
+  - prometheus_client=0.7.1=py_0
+  - prompt_toolkit=1.0.15=py27h4a7b9c2_0
+  - psutil=5.6.3=py27h1de35cc_0
+  - ptyprocess=0.6.0=py27_0
+  - pycodestyle=2.5.0=py27_0
+  - pycparser=2.19=py27_0
+  - pyepsg=0.4.0=py27_0
+  - pyflakes=2.1.1=py27_0
+  - pygments=2.4.2=py_0
+  - pyjnius=1.4=py27_0
+  - pylint=1.9.2=py27_0
+  - pyopenssl=19.0.0=py27_0
+  - pyparsing=2.4.2=py_0
+  - pyproj=1.9.5.1=py27h833a5d7_1
+  - pyqt=4.11.4=py27_4
+  - pyrsistent=0.15.4=py27h1de35cc_0
+  - pyshp=2.1.0=py_0
+  - pysocks=1.7.1=py27_0
+  - python=2.7.16=h97142e2_7
+  - python-dateutil=2.8.0=py27_0
+  - python.app=2=py27_9
+  - pytz=2019.3=py_0
+  - pyzmq=18.1.0=py27h0a44026_0
+  - qt=4.8.7=1
+  - qtawesome=0.6.0=py_0
+  - qtconsole=4.5.5=py_0
+  - qtpy=1.9.0=py_0
+  - readline=7.0=h1de35cc_5
+  - requests=2.22.0=py27_0
+  - rope=0.14.0=py_0
+  - scandir=1.10.0=py27h1de35cc_0
+  - scipy=1.2.1=py27h1410ff5_0
+  - seawater=3.3.4=py_1
+  - send2trash=1.5.0=py27_0
+  - setuptools=41.4.0=py27_0
+  - shapely=1.6.4=py27h20de77a_0
+  - simplegeneric=0.8.1=py27_2
+  - singledispatch=3.4.0.3=py27he22c18d_0
+  - sip=4.18=py27_0
+  - six=1.12.0=py27_0
+  - snowballstemmer=2.0.0=py_0
+  - sphinx=1.8.5=py27_0
+  - sphinxcontrib=1.0=py27_1
+  - sphinxcontrib-websupport=1.1.2=py_0
+  - spyder=3.2.8=py27_0
+  - spyder-kernels=1.4.0=py27_0
+  - sqlite=3.30.0=ha441bb4_0
+  - subprocess32=3.5.4=py27h1de35cc_0
+  - terminado=0.8.2=py27_0
+  - testpath=0.4.2=py27_0
+  - thredds_crawler=1.0.0=py27_0
+  - tk=8.6.8=ha441bb4_0
+  - tornado=5.1.1=py27h1de35cc_0
+  - traitlets=4.3.3=py27_0
+  - typing=3.7.4.1=py27_0
+  - urllib3=1.24.2=py27_0
+  - wcwidth=0.1.7=py27h817c265_0
+  - webencodings=0.5.1=py27_1
+  - wheel=0.33.6=py27_0
+  - widgetsnbextension=3.5.1=py27_0
+  - wrapt=1.11.2=py27h1de35cc_0
+  - wurlitzer=1.0.3=py27_0
+  - xz=5.2.4=h1de35cc_4
+  - zeromq=4.3.1=h0a44026_3
+  - zlib=1.2.11=h1de35cc_3
+  - zstd=1.3.7=h5bba6e5_0
+  - pip:
+    - pynemo==0.1.0
+prefix: /Users/thopri/anaconda3/envs/pynemo_env
+