Comments (8)
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.
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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.
from flowsieve.
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.
from flowsieve.
You can check whether your conda environment works correctly by following the steps here.
- A quick test tells me that
cmocean
is missing in theenvironment.yml
file. There may be other packages missing. Could you check if all tutorials are running after activating theFlowSieve-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.
from flowsieve.
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 :-)
from flowsieve.
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
from flowsieve.
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!
from flowsieve.
Cool, I just tested the conda environment, and am able to run all python scripts. Closing this issue!
from flowsieve.
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