Python Functions defined for computational ION
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README.md

ION Functions

Functions for utilization in the ION Parameter Function framework

Reference Information: add link

#Prerequisites

This assumes basic development environment setup (git, directory structure). Please follow the "New Developers Tutorial" for basic steps.

Install the following if not yet present:

Install git 1.7.7: Download the Mac or Linux installer and run it

OS Packages and package management: For Mac, use homebrew

/usr/bin/ruby -e "$(curl -fsSL https://raw.github.com/gist/323731)"
  • python 2.7

Install python, hdf5 and netcdf with Homebrew

brew install python

You can even reinstall git using brew to clean up your /usr/local directory Be sure to read the pyon README for platform specific guidance to installing dependent libraries and packages. Linux: Note that many installs have much older versions installed by default. You will need to upgrade couchdb to at least 1.1.0.

##libgswteos Dependency

A very important component is the libgswteos-10 library. Installation is quite straightforward on Mac OSX and a little more hairy on Linux.

On OSX

The libgswteos dependency is brew installable:

brew tap lukecampbell/homebrew-libgswteos
brew install libgswteos-10
brew test -v libgswteos-10

On Linux

The dependencies for building/installing the library are: autoconf, automake, & libtool

  1. Obtain the tarball from: https://github.com/lukecampbell/gsw-teos/tarball/v3.0r4

    • sha1: 6ae190b7da78d6aff7859e7d1a3bb027ce6cc5f3
  2. Build Procedure

     bash ./autogen.sh  
     ./configure --prefix=/usr/local/libgswteos-10  
     make  
     sudo make install  
    
  3. Linking Procedure:

     sudo ln -s /usr/local/libgswteos-10/lib/libgswteos-10.la /usr/local/lib/  
     sudo ln -s /usr/local/libgswteos-10/lib/libgswteos-10.so.3 /usr/local/lib/  
     sudo ln -s /usr/local/libgswteos-10/lib/libgswteos-10.so.3.0.0 /usr/local/lib/  
     sudo ln -s /usr/local/libgswteos-10/lib/libgswteos-10.so /usr/local/lib/  
     sudo ln -s /usr/local/libgswteos-10/include/gswteos-10.h /usr/local/include/  
    
  4. Ensure that the global C_INCLUDE_PATH and LD_LIBRARY_PATH includes /usr/local/lib in all profiles otherwise python won't run correctly:

     export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib  
     export C_INCLUDE_PATH=$C_INCLUDE_PATH:/usr/local/include  
    

Python packages and environment management:

Install pip

easy_install pip

Install virtualenv and virtualenvwrapper modules for your python 2.7 installation Note: This may require Mac's XCode (use XCode 3.3 free version

easy_install --upgrade virtualenv
easy_install --upgrade virtualenvwrapper

Setup a virtualenv to run ion-functions (use any name you like):

mkvirtualenv --python=python2.7 ion_functions
workon ion_functions
pip install numpy==1.6.2

#Source

To obtain the ion-functions project, begin by forking the GitHub repository. Next, clone your fork of the repository to your local machine (replace your_name with the name of your github account:

git clone git@github.com:your_name/ion-functions.git
cd ion-functions

#Installation Ensure you are in a virtualenv prior to running the steps below

From the ion-functions directory, run the following commands:

python bootstrap.py -v 1.7
bin/buildout

Once those steps complete, you should be able to run the unit tests

#Running unit tests (via nose)

From the coverage-model directory, run the following command:

bin/nosetests -v

This will run all tests in the ion-functions repository. The -v flag denotes verbose output (the name of each test prints as it runs). For more nose options, refer to the nose documentation

Running C-Extension Unit Tests

From the ion-functions directory, run the following command:

make

This will compile the C-extension unit tests. To run the tests:

extensions/test

You should see something of the like:

test_spike_simple... ok
test_spike_l simple... ok
test_spike_long... ok

#Libraries Currently Included

  • Numpy – array manipulation
    • import numpy as np
  • Numexpr – relatively trivial "one line" expressions
    • import numexpr
      • vals = umexpr.evaluate('sin(x)**10 – y', local_dict={'x': x_vals, 'y': y_vals})
  • Gibbs Seawater equations – from TEOS-10 (Contact Luke Campbell if you notice something's missing)
    • from pygsw import vectors as gsw
      • vals = gsw.sp_from_sa(input_1, …)
  • GeoMag python library