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I am using JupyterLab to build a bioinformatics pipeline that uses both bash and python scripts. The first bash script results gives a lot of feedback on every step of the process. However, this feedback is not helpful (unless there was an error) and makes the document less readable.

I would like to be able to hide this cell's output by default, but also to be able to open it when necessary to troubleshoot. I know it's possible to click 3 times on the output to collapse it; I was just wondering whether there is a way to do so by default.

I tried to add the tag specified on here (https://jupyterbook.org/features/hiding.html#Hiding-outputs) to the cell, but it does not seem to work for me.

Thanks for your help.

jordimaggi
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1 Answers1

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You may just want to suppress the output using %%capture cell magic as illustrated here. Then you simply remove that magic command from the first line of the cell for times you want to see the output, such as when troubleshooting.

If you want to make it so every time you run the cell, you can later decide to review what was captured you can use the %%capture magic command more as it was meant to be used. By assigning what is captured you can also do something like what the %%bash cell magic allows with handling output streams (see here), too. As described and illustrated here using the utils object you can easily get the stdout and/or stderr as a string, see http://ipython.readthedocs.io/en/stable/api/generated/IPython.utils.capture.html.

So say you put the following at the top of you cell to assign what was captured to out:

%%capture out

You can review the stdout stream later with the following:

print(out.stdout)

Or if you just want part of it, something like print(out.stdout[1:500]). I have some fancier handling illustrated in some blocks of code here.

Wayne
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