Running the basic tutorial

[NoraLoose]

• [x] Starting from the "default" constants.hpp, I modified variables as in the documentation, but in addition needed to make the following modification:

EXTEND_DOMAIN_TO_POLES = false

I think it would be useful to include this in the docs too.

• [ ] It would be nice if the tutorial included the required python dependencies, e.g., for example by providing an environment.yml file to set up a conda environment.
• [ ] How about including a jupyter notebook that executes the steps done with python? Could be a great way to make the tutorial more interactive, and give the user some nice figures to look at and reproduce! It would only take a few lines of code to get started, e.g.,

  import xarray as xr
  ds = xr.open_dataset('/glade/u/home/noraloose/FlowSieve/Tutorial/Basic/velocity_sample.nc')
  ds.uo.plot()

  but you could also consider to make the 2 python scripts more interactive and step through them in the notebook.

This issue is part of the JOSS review process over at https://github.com/openjournals/joss-reviews/issues/4277.

[bastorer]

Making notebook versions of the tutorial python scripts is a good idea!

I'm not very familiar with conda, but agree that giving explicit library dependencies would be helpful. I'll look into those this week.

[NoraLoose]

Let's try to work toward closing this issue.

• [ ] I'll leave it up to you if you want to include a jupyter notebook for this tutorial or not.
• [ ] But I think providing an environment.yml for the required python dependencies (for all tutorials together, so I would place it here with some instructions) would be very helpful - then I can also tick off the following reviewer box :)

  Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

[bastorer]

Notebook added :-)

I've added an environment file listing the versions that I used why I ran the tutorials. I'm not very familiar with .yml files, but I think I've got it formatted correctly.

[NoraLoose]

You can check whether your conda environment works correctly by following the steps here.

• A quick test tells me that cmocean is missing in the environment.yml file. There may be other packages missing. Could you check if all tutorials are running after activating the FlowSieve-tutorial-env environment? Thanks!
• It would be great if you could add instructions to https://github.com/husseinaluie/FlowSieve/blob/master/Tutorial/TUTORIAL.md on how to create and activate the conda environment before running any of the tutorials.

[bastorer]

I'm running into permissions issues with conda env. I'll try switching to a different server to see if I can test the environment there :-)

[bastorer]

I've got the conda environment working on the other server :-) I'm having some trouble getting it to play nice when I try to activate the environment inside of submitted jobs, but otherwise running in command-line in the activated environment reproduces the tutorial figures

[bastorer]

Hi Nora,

With the environment.yml and jupyter notebooks set up, is there anything else that you think needs to be addressed for this ticket?

Thanks!

[NoraLoose]

Cool, I just tested the conda environment, and am able to run all python scripts. Closing this issue!