How to (intermittently) skip certain cells when running IPython notebook?

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Question :

How to (intermittently) skip certain cells when running IPython notebook?

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”.

EDIT

%%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 %%cache

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., display(Latex(r'$alpha_1$'))

Answer #1:

Currently, there is no such feature included in the IPython notebook.
Nevertheless, there are some possibilities to make your life easier, like:

  • use the %store or maybe better the %%cache magic (extension) to store the results of these intermittently cells, so they don’t have to be recomputed (see https://github.com/rossant/ipycache)

  • add a if==0: before the cells you don’t want to execute

  • convert these cells to raw cells (but you will loose the already stored output!)

(see discussion at https://github.com/ipython/ipython/issues/2125)

Jakob

Answered By: herrlich10

Answer #2:

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):

%%script false 

or a variant (working as of early 2020 — see here for explanation) :

%%script false --no-raise-error
Answered By: Jakob

Answer #3:

If no cached results are expected to be loaded, I find the Freeze nbextension quite useful to this end.

enter image description here

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 Edit > nbextensions config, and then check Freeze.

Answered By: Mark

Answer #4:

This question is a bit older, but the most convenient answer seems to be missing. You can use the ‘initialization cells’ from the NBextensions. Once installed/activated, you can in any notebook mark cells as ‘initialization cells’ which can then be run with a specific button.

  • Install NBextensions:here
  • Activate ‘initialization cells’ when you launch the jupyter dashboard

  • In your notebook, in the ‘view’ menu choose ‘cell toolbar’ then ‘initialization cell’

  • Next to each cell there is now a checkbox. Mark all the cells you want to run for initialization
  • When reopening a notebook, click the button that looks like a pocket calculator to run all the initialization cells.
Answered By: herrlich10

Answer #5:

The simplest way to skip python code in jupyter notebook cell from running, I temporarily convert those cells to markdown.

Answered By: timmey

Answer #6:

The %%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:

%%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:

%%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

Answered By: Aarvy

Answer #7:

Here’s a simple and universal solution without the need for workarounds:
Simply type this as the top line of the cell to skip the cell:

%%script echo skipping

It’s tested on Windows and Mac with recent Jupyter, and I think it should work on other Unix-like platforms as well because they also have an echo command. Some of the other proposed solutions are more platform-specific.

Of course you can put what ever text you like instead of “skipping”. When you execute the cell, it will merely print this text instead of executing the code in the cell.

Answered By: stason

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