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.
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.
Related
I am using pycodestyle_magic as a linter in Jupyter. I am following the instructions at
https://github.com/mattijn/pycodestyle_magic
But I get error with 1-cell checking be it '%%pycodestyle' or '%%flake8'.
1st ERROR
# 1st CELL
%load_ext pycodestyle_magic
# 2nd CELL
%%pycodestyle
a=1
print(a)
2nd ERROR
# 1st CELL
%load_ext pycodestyle_magic
# 2nd CELL
%%flake8
a=1
print(a)
1st ERROR
I'm basing this on your image you posted for '1st error' and not the inaccurate code you posted:
Note that the error in your first error was saying line magic and not cell magic because it was not looking for cell magic anymore. You can see it will look for cell magic on the first line of a cell by putting in %%fake_magic as a first line and then 2 + 2 as a second line of cell. Running that you'll see UsageError: Cell magic %%fake_magic not found.
Hence, your first 'error' is that you are missing that the first line of the cell where you want to use cell magic becomes special. You cannot have something else on the first line where you want to use cell magic, even if it is commented out. In the image, you have #%%flake8 above %%pycodestyle. If you remove that line, it should work.
2nd ERROR
I'm basing this on your image you posted for '2nd ERROR' and not the inaccurate code you posted:
You've stumbled upon a bug currently involving flake8. (Maybe same or more bugs seem to prevent the %%flake8 magic from working at all for now, see comments.)
The solution/workaround is very similar to the '1st ERROR'. Remove the line you were trying to comment out because it being there is causing an issue.
The reasoning appears to be complex about the way the %%flake8 cell magic appears to work behind the scenes so that you cannot have comments in the code content at this time or it won't work. (And the second time it sees that comment symbol, it throws the error you see.) This bug has been reported here.
But the solution/work-around for now is straightforward. Remove the complexity you added, and see if it works.
In case of the %%flake8 magic, running the demo notebook as shown there doesn't work as shown, and so there is indeed a bug in the current version that was introduced by actually a bug in flake8 that the extension uses, see the specific comment here and the link to the underlying issue over at the flake8 repo. (In fact the extent that it doesn't work may be greater than the notebook reflects because as discussed in the comments, even cells without commented lines fail to report any formatting issues. The demo actually doesn't have any without and so I got distracted noting it only didn't show the buffer error for the first one in the demo notebook but since it had a commented line I thought it was still related.)The other way to workaround it at present is to install an older version of flake8 as pointed out here. The solution was merged though and should be available soon, and so just avoiding the triggering code in simple cases like yours is probably easier.
Note about the inaccurate code:
Post code for what gave you the issue, not what you think gave you the issue. Part of why you are asked to provide code as text the way you ran it, it is so those looking into it can run it the same way. Plus they don't have to type and can easily run it as you did. Beyond that, there's more reason behind it: you can try to see if what you observed originally matches what you are seeing now.
If you had run what you posted under the heading '1st ERROR' as the code block text, you would have seen it without the error you showed in your image. Usually you'd then discern the error/difference yourself. In other words, starball's comment was trying to point you to why you should be doing that, and sorted that 1st error out yourself. That would ultimately make your point about the fragile nature of %%flake8 magic have more impact because it isn't diluted by report of an error that isn't really an error. Plus, you may have realized what was necessary to avoid '2nd ERROR' because that code block works without error no matter how many times you run it.
Technical notes:
Anyone wishing to try out pycodestyle_magic with some of this code and the demo notebooks can click here to launch such a session served via the mybinder.org. service with most things necessary already set up. Once the session starts up in the classic Jupyter notebook interface, you need to do some further preparation to use pycodestyle_magic. As detailed here, you can install it with pip install flake8 pycodestyle_magic. So open a new notebook with the Python kernel backing it using New drop down on the upper right side and then choose the Python3 kernel. When it opens, make a cell that has %pip install flake8 pycodestyle_magic and run it. Then put %load_ext pycodestyle_magic as a cell and run that. You can now try the magic with code or pull the demo notebooks over and run those.
I'm not sure I can include reproducible code on this, given there's 4,000 lines of code and that may be part of the problem, but let me try to explain my question the best I can:
I love using beepr to play an audible sound when a bunch of code is done processing. If my computer is taking a while to run it, I'll go look at a different screen or do something else in the room when its thinking.
I have a large .rmd file. Its 4187 lines long and beep() is on line 4185. I made sure it was nowhere else in the document using ctrl+f. When I "run all", the beep goes off when I'm about this far through the document:
And then it'll continue thinking for another few minutes before its done. This defeats the entire purpose of beepr().
So I guess my question is: is this a known problem? Is there anything particular to a .rmd document that does this? Any known fixes?
{knitr} manpage says:
This function takes an input file, extracts the R code in it according to a list of patterns, evaluates the code and writes the output in another file.
So the thing you are observing is due to the fact all R code in the .rmd gets evaluated before the whole process is finished. The sound plays when the beepr line is executed, since this will happen (rcode chunk) before the document is processed by pandoc (or similar) i would just advise you to put the beeper outside of the .rmd itself to trigger it after the process finished. write a 3 line r sript:
knit("my.rmd")
Sys.sleep(1)
beepr()
This makes sure the beep will only start after the document is created (Sys.sleep just to make sure and prob. not necessary)
I, an R user, decided recently to try using Emacs-ESS combo. So far I have been work in a single-window mode (C-x 1) just for text highlighting.
Now I am trying split it in two windows (C-x 3) to work on an .R file in the left window, and have R execute the commands in the right window. Something like this:
After selecting sections of code on the left, how can I "send" it as a command to the right? Essentially, I want the input to remain on on the left (so that I can incrementally build the code up) and the actual R output on (including error messages) the right.
Two good options:
ess-eval-region-or-function-or-paragraph vis
(C-M-x): Sends the current selected region or function or paragraph.
ess-eval-region-or-function-or-paragraph-and-step (C-c C-c): Like ess-eval-region-or-function-or-paragraph but steps to next line of code.
Source: ESS manual.
You can also use:
C-c-p to send a paragraph or region between two empty lines
C-c-r to send a region that has been selected and is highlighted
I prefer this way because you only need to press the Ctrl key
there are normally many ways to send code to the R console. It will take you time to realize what is best for you, or you may eventually change the key bindings.
Is there a way to write your own macro in R(studio). Many times in my code i need to comment out a line/piece of code, run it, and then comment it in again.
I know that a shortcut to comment in a line/piece of code is ctrl+shift+c, so I would like to create a shortcut e.g. ctrl+alt+c to comment in/out+run+comment in/out
You can create an Addins doing exactly what you want and assign a shortcut to it.
For exemple, that Addin is used to create upgraded shortcut for pipe.
To do what you want, a solution may be possible but require a few constrain.
Three, at least:
First, you need to select the code you want to comment
Secondly, in the same time you use the shortcut, the file should be saved.
Thirdly in your file, you can't have two time the same selected piece of code.
The commented code will be the input of the Addins.
The code is as simple as read your file, replace the code by commented code, then run the modified code.
It is different in what you want to achieve in the sense of in that case, it is more create a temporary copy of the code, comment the undesirable code, run the temporary modified code.
For shortcuts see here. Macros might be found here.
E.g. commenting in/out = Ctrl +Shift + C (Both)
If you want a to have a new shortcut, you have to ask RStudio. For an example, where it was already solved, see here. From the list of available shortcuts it is clear that "your" shortcut does not exist.
I have Julia code edited in Juno, which contains a very simple code block with a calculation at each line. When I select it all and execute it, only the result for the last line is displayed:
I'd like to execute the block, but have the results for each line, like this (image obtained executing line by line):
Is it possible (via some shortcut or option)?
There's no way to do this yet, although it's something we'd like to see in future. I opened an issue to track the feature.
One thing that might help is the Shift-Enter command, which is the same as C-Enter but skips to the next code block. If you repeatedly Shift-Enter from the beginning of that block of code you'll get all of the results very quickly, if not quite instantaneously.