mspass-team / mspass-team/mspass_tutorial

Error in use of "Raw" boxes in tutorials

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Dominant language
Jupyter Notebook
Stars
9
Forks
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PR merge metrics
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Description

I discovered that I (@pavlis ) had a misunderstanding on the purpose of a "Raw" box selection in jupyter notebooks. When run under jupyter lab/notebook servers Raw boxes are ignored and more-or-less treated as being commented out. The issue here is that if notebook file is converted to a python script with this kind of command:

jupyter nbconvert --to script notebook.ipynb

boxes marked "Raw" are converted directly. That means any notebooks in this tutorial with raw boxes (there are some in the Earthscope short course directories for example and probably others) will behave differently if converted to a script and run in batch on HPC. This issue won't bite anyone unless you use use these notebooks as template and try to run them on an HPC system in the batch mode using the mspass_launcher or with variations of the hpc shell scripts found in the mspass repository and the "--batch" option.

I will try to resolve this issue as soon as possible, but that could be weeks as this isn't a high priority.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by inventorying the notebooks in the Earthscope short course directories and other tutorial directories that contain Raw boxes. Run jupyter nbconvert --to script notebook.ipynb and compare the result with execution in Jupyter and with the mspass_launcher or referenced HPC shell scripts using --batch. Done means the affected tutorials have consistent, documented behavior in interactive and batch execution.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook
Domain
documentation, hpc
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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