Salish Sea Repos and Packages

Once you have your Mercurial Configuration set up and the Anaconda Python Distribution installed and activated you need to set up a working area, clone some Mercurial repositories, and install some Salish Sea MEOPAR project tools.

In the working environment on your Waterhole workstation you should create a work space on the /ocean/ partition:

mkdir -p /ocean/$USER/MEOPAR

On your own laptop, well, the choice of where you put files is up to you…

In the work space you need to clone a number of Salish Sea MEOPAR project repos from Bitbucket. The repos that you need depends whether the environment is for running the model, doing analysis, etc.; the Quick Start Guide provides guidance for the repos to install in model run environments. Here, we’ll assume that you are setting up your Waterhole machine working environment where you will be doing analysis, documentation, etc.

cd /ocean/$USER/MEOPAR/
hg clone ssh://hg@bitbucket.org/salishsea/docs
hg clone ssh://hg@bitbucket.org/salishsea/tools
hg clone ssh://hg@bitbucket.org/salishsea/nemo-cmd NEMO-Cmd
hg clone ssh://hg@bitbucket.org/salishsea/salishseacmd SalishSeaCmd

Next, install the SalishSeaTools Package and the Salish Sea NEMO Command Processor:

pip install --user --editable tools/SalishSeaTools
pip install --user --editable NEMO-Cmd
pip install --user --editable SalishSeaCmd

The links above contain information about the contents of those packages.

Next, you need a repo to store you analysis notebooks and other bits of code, text, etc. in. We used to all share a single analysis repo, but it got too big. So, we broke it up so that each team member has their own analysis repo, and there are a few special pupose analysis repos. You can find them all at https://bitbucket.org/account/user/salishsea/projects/SSM_ANALYSIS. The original analysis repo is now read-only.

If you are joining the team as a researcher there should be an analysis repo already set up for you. Its name will be something like analysis-james, but with your name. Go ahead and clone that repo too:

cd /ocean/$USER/MEOPAR/
hg clone ssh://hg@bitbucket.org/salishsea/analysis-james

If you are joining the team for a sprint, please clone the analysis-sprints repo:

cd /ocean/$USER/MEOPAR/
hg clone ssh://hg@bitbucket.org/salishsea/analysis-sprints

and create a directory in it named after yourself to work in.