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Sciunit testing


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Created: Jan 18, 2022 at 12:38 a.m.
Last updated: Feb 15, 2022 at 8:22 p.m.
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Abstract

Illustration of General idea of use case for sciunit container.
1. User creates sciunit (sciunit create Project1)
2. User initiates interactive capturing (sciunit exec -i)
3. User does their work. For now assume this is a series of shell commands
4. User saves or copies the sciunit
5. User opens the sciunit on a new computer and can re-execute the commands exactly as they would have on the old computer, from command line, from bash shell escapes or python in Jupyter
6. User sees a list of the commands that were in the sciunit and could use editing of them to reproduce

The setup.
On CUAHSI JupyterHub the user has a resource (the one above) with some code that is a simple example for modeling the relationship between streamflow and snow

There is a python "dependency" GetDatafunctions.py in a folder on CUAHSI JupyterHub. This is not part of the directory where the user is working. It is added to the python path for the programs to execute. This is a simple example of what could be a dependency the user may not exactly be aware of (e.g. if it is part of the CUAHSI JupyterHub platform, but not part of other platforms).

An export PYTHONPATH command is used to add the dependency to the python path.

Then the analysis is illustrated outside of sciunit.

Then sciunit is installed and the analysis repeated using sciunit exec.

Finally sciunit copy copies the sciunit to the sciunit repository

Then on a new computer

Sciunit open retrieves the sciunit

After repeating one of the executions, the sciunit directory has the dependency container unpacked

Setting the PYTHONPATH to the unpacked dependency allows the commands to be run on the new computer, just as they were on the old computer.

This is the vision - running on the new computer with dependencies from the old computer resolved.

Would like the dependencies to be “installed” on the new computer so that they work with Jupyter and Jupyter escape bash commands.

All is done from the command line - the Jupyter Notebook is just used as a convenient notepad.

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How to Cite

Tarboton, D. (2022). Sciunit testing, HydroShare, http://www.hydroshare.org/resource/7c7048c648794f5da8df79966377b448

This resource is shared under the Creative Commons Attribution CC BY.

http://creativecommons.org/licenses/by/4.0/
CC-BY

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