How to (intermittently) skip certain cells when running IPython notebook?
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I usually have to rerun (most parts of) a notebook when reopen it, in order to get access to previously defined variables and go on working.
However, sometimes I'd like to skip some of the cells, which have no influence to subsequent cells (e.g., they might comprise a branch of analysis that is finished) and could take very long time to run. These cells can be scattered throughout the notebook, so that something like "Run All Below" won't help much.
Is there a way to achieve this?
Ideally, those cells could be tagged with some special flags, so that they could be "Run" manually, but would be skipped when "Run All".
%%cache (ipycache extension) as suggested by @Jakob solves the problem to some extent.
Actually, I don't even need to load any variables (which can be large but unnecessary for following cells) when re-run, only the stored output matters as analyzing results.
As a work-around, put
%%cache folder/unique_identifier to the beginning of the cell. The code will be executed only once and no variables will be loaded when re-run unless you delete the unique_identifier file.
Unfortunately, all the output results are lost when re-run with
EDIT II (Oct 14, 2013)
The master version of ipython+ipycache now pickles (and re-displays) the codecell output as well.
For rich display outputs including Latex, HTML(pandas DataFrame output), remember to use IPython's display() method, e.g.,
Magic or API to allow skipping of cells during run all? � Issue #175 , For reproducibility considerations, I usually rerun my notebook to make sure it However, there are cases that I would like to ignore certain cells during re- execution, for example, cells See also: ipython/ipython#11582� Phyton How to (intermittently) skip certain cells when running IPython notebook? Though this isn't exactly what you seem to be looking for, if you wish to entirely omit the execution of a cell (where no cached results are loaded), you can add the following hack at the beginning of a cell (assuming you are using a unix-based OS):
Though this isn't exactly what you seem to be looking for, if you wish to entirely omit the execution of a cell (where no cached results are loaded), you can add the following hack at the beginning of a cell (assuming you are using a unix-based OS):
or a variant (working as of early 2020 -- see here for explanation) :
%%script false --no-raise-error
Jupyter Notebook skipping cells after 'Restart & Run All' � Issue , The behavior appears non-deterministic: it doesn't always skip the same cell, and sometimes it doesn't skip any. Here's a screenshot of a simple� However, sometimes I'd like to skip some of the cells, which have no influence to subsequent cells (e.g., they might comprise a branch of analysis that is finished) and could take very long time to run. These cells can be scattered throughout the notebook, so that something like "Run All Below" won't help much. Is there a way to achieve this?
If no cached results are expected to be loaded, I find the
Freeze nbextension quite useful to this end.
Although unofficial, I strongly recommend to give these notebook extensions a try if you have never used them before.
To install the extension machinery,
$ pip install jupyter_contrib_nbextensions && jupyter contrib nbextension install
To enable the
Freeze extension, launch
jupyter notebook and open a new notebook, from the menu select
nbextensions config, and then check
How to (intermittently) skip certain cells when running IPython , These cells can be scattered throughout the notebook, so that something like " Run All Below" won't help much. Is there a way to achieve this? Ideally, those cells� How to (intermittently) skip certain cells when running IPython notebook? 18. IPython Notebook run all cells on open. 2. PuLP not printing output on IPython cell.
%%script false solution stopped working some time in 2019.
Here are some other available workarounds. These are based on programs ignoring their arguments when you tell them not to expect any. Here are some easy examples:
%%perl -e0 for i in range(10): print(i)
Here you're running:
perl -e '0' cellcontents
A more memorable version:
%%perl -eat for i in range(10): print(i)
Here you're running:
perl -e 'at' cellcontents
%%bash -c : for i in range(10): print(i)
':' is a noop in bash, so you're running:
bash -c : cellcontents
I haven't looked at the external magic implementation code, but I'm pretty sure "cellcontents" are passed as arguments and won't be interpreted by shell by mistake, say if you were to include ';' in them and accidentally inject some bad code. But I can't guarantee you that.
I'm sure you can come up with other creative solutions, by looking at the supported programs here: https://ipython.readthedocs.io/en/stable/interactive/magics.html#cell-magics
Table of Contents (2), Sections of currently selected/edited or running cells are highlighted in the toc. a configurable option to skip h1 headers from the ToC, to allow their use as a notebook title. It happens that the extension is sometimes loaded after this event. print - IPython Notebook output cell is truncating contents of my list pandas wrap text (4) I have a long list (about 4000 items) whose content is suppressed when I try to display it in an ipython notebook output cell.
Boosting Your Jupyter Notebook Productivity, Sometimes it is quite useful. NB. %run is not the same as importing python module. In : # this will execute all the code cells from different notebooks %run . Here's a way to display the whole list in the IPython output cell that doesn't require Pandas: from IPython.display import HTML x = range(4000) HTML('<br />'.join(str(y) for y in x)) It is also pretty easy to add additional HTML elements and get a more elaborate display.
How do you suppress output in IPython Notebook?, ipython-notebook. How can Answer. Add %%capture as the first line of the cell. eg How to (intermittently) skip certain cells when running IPython notebook? Run this cell (or simply run all cells). Note that the 2nd system call is simply pandoc -s paper.md -t docx -o paper.docx --filter pandoc-citeproc --bibliography=listb.bib --csl=apa.csl. I merely used paste0() to be able to spread this over multiple lines and make it nicer to read. The output is a word document.
- If you don't need to redisplay the output, you can define your own skip magic like I did here: stackoverflow.com/a/43584169/4098821
- Great to know about ipycache extension, which functions similarly to what I'm doing (manually) now, but only better! The
%%cachemagic effectively serves as the special flag when "Run All", and manual re-run requires simply cache file deletion. Brilliant! Thanks, Jakob~
- Indeed using %%cache is much more convenient than manually handling with %store. %store need to send one by one the variables to save, but can read all at time, little pointless. %%cache works perfect for whole cell, and %store works better for single variables.
ipycacheis no longer maintained- do you know any other solutions?
- @Chris_Rands currently I use the freeze extension. You might ask Rossant directly.
- Anyone know how to do this on Windows?
- It works perfectly on windows. The notebook output will be "Couldn't find program: 'false'".
- This stopped working some time in 2019. You can find new workarounds here.
- As a heads up, this gets rid of existing output. Not useful if you want to keep previous output of the cell.
- Here's another similar one (
%%script echo): stackoverflow.com/a/61544643/1090455
- Looks like the best solution. When hitting "Restart and Run All" or other commands, the frozen cells won't be re-executed but the cell outputs are still there.
- %%script false --no-raise-error works for the purpose on the Jupyter I tried today