Ocean Observatories Initiative Cyber Infrastructure (OOI CI)
Integrated Observatory Network (ION) - OOINet

Marine Integration source code repository.

(C) The Regents of the University of California, 2010-2014
See LICENSE.txt for license.

This is the repository that contains the implemention for all marine integrations
including drivers and transforms. 

Get the code!

Clone this repository

Read only checkout

$ git clone git://github.com/oceanobservatories/mi-instrument

Read / write checkout

$ git clone [email protected]:<your_github_uname>/mi-instrument

OSX/Homebrew Instructions

INSTALL prerequisite software

Install homebrew

https://brew.sh/
brew tap homebrew/science

Install python 2.7

brew install python --framework --universal

Install git

brew install git

Install libraries

brew install libevent libyaml zeromq rabbitmq hdf5 pkg-config netcdf freetype spatialindex udunits

Install pip/virtualenv

pip install -U pip
pip install virtualenv virtualenvwrapper

Modify ~/.bash_profile

add this to the end:
   export WORKON_HOME=$HOME/virtenvs
   . /usr/local/bin/virtualenvwrapper.sh
   
source ~/.bash_profile

Create a virtualenv

mkvirtualenv --no-site-packages --python=python2.7 ooi

Install requirements

workon ooi
pip install numpy cython
pip install -r requirements.txt

OSX/Anaconda Instructions

Install Anaconda/Miniconda 2

https://conda.io/miniconda.html

Create conda env

cd into mi-instrument and then type the command below:
conda env create -f conda_env_other.yml
source activate mi

Linux/Anaconda Instructions

Install Anaconda/Miniconda 2

https://conda.io/miniconda.html

Create conda env

conda env create -f conda_env_linux64.yml
source activate mi

Run the tests

nosetests -a UNIT --processes=4 --process-timeout=360

Table of Contents

Source code is organized in directories by instrument vendor. The following is a listing of currently deployed instruments by make.

Instrument	  location
----------------------------------------------
ADCP          teledyne.workhorse.adcp
ADCPS         teledyne.workhorse.adcp
BOTPT         noaa.botpt.ooicore
CAMDS         kml.cam.camds
CAMHD         subc_control.onecam.ooicore
CTDBP-NO      seabird.sbe16plus_v2.ctdbp_no
CTDPF-Optode  seabird.sbe16plus_v2.ctdpf_jb
CTDPF-SBE43   seabird.sbe16plus_v2.ctdpf_sbe43
D1000         mclane.ras.d1000
FLOR          wetlabs.fluorometer.flort_d
HPIES         uw.hpies.ooicore
MASSP         harvard.massp.mcu
NUTNR         satlantic.suna_deep.ooicore
OPTAA         wetlabs.ac_s.ooicore
PARAD         satlantic.par_ser_600m
PCO2W-A       sunburst.sami2_pco2.pco2a
PCO2W-B       sunburst.sami2_pco2.pco2b
PHSEN         sunburst.sami2_ph.ooicore
PPSDN         mclane.ras.ppsdn
PREST         seabird.sbe54tps
RASFL         mclane.ras.rasfl
SPKIR         satlantic.ocr_507_icsw.ooicore
THSPH         um.thsph.ooicore
TMPSF         rbr.xr_420_thermistor_24.ooicore
TRHPH         uw.bars.ooicore
VADCP         teledyne.workhorse.vadcp
VEL3D-B       nobska.mavs4.ooicore
VEL3D_B       nobska.mavs4.ooicore
VEL3D-C       nortek.vector.ooicore
VEL3D_C       nortek.vector.ooicore
VELPT         nortek.aquadopp.ooicore
ZPLSC         kut.ek60.ooicore

Release Instructions

Deploying a release of the mi-instrument package involves the following steppes:

1. update version
2. push changes to repository (mi-instrument)
3. tag release
4. build anaconda package

Update Version

Release notes (RELEASE_NOTES) should include the Version and number on a line by itself, followed by a list of issues with a brief description. Prepend updates to the beginning of the file. E.g.:

Version 1.2.3

* Issue #12345 - Fix ctdbp parser to read new format xyz

The setup file (setup.py) must be updated with the appropriate version:

version = '1.2.3'

Tag Release

Set the new tag:

git tag -a v0.4.0
git push upstream master --tags

Get the current tags from remote repository (to see the currently available tags):

git fetch upstream --tags

Build Anaconda Package

See the ooi-config repository for instructions.

Tools

The following tools are available in the project (WORK IN PROGRESS):

Name	Description
zplsc_echogram_generator	Generates echograms from raw sensor data files.