CODEWITHSUNDEEP
python-3.xjupyter-notebookipython
BCArg
BCArg

Reputation: 2250

Fail to change directory (shell command) in jupyternotebook (or jupyterlab session)

I can run shell commands from an open jupyterlab (or jupyternotebook) session with an exclamation mark preprended to the shell command, as follows:

!mkdir /new_folder

This, as well as other commands such as ls and pwd work, though if I try to change directory with cd, as shown below

!cd /path/to/mydir

this does not work and I have noticed that the current working directory will always be the one where my jupyter notebook (.ipynb) is saved.

It is also odd that if I do: 

!cd /path/to/mydir && pwd

I will get /path/to/mydir printed out, though if, on the cell below I do

!pwd

I will get the current directory where my jupyternotebook is saved i.e. apparently I eventually cannot change the working directory with !cd in a jupyternotebook.

Does anyone know what the problem could be?

Upvotes: 15

Views: 7071

Answers (2)

Eduardo
Eduardo

Reputation: 1423

If you're writing bash scripts in Jupyter (i.e., don't have any Python code). You may consider using the bash kernel. Unlike using the typical Python kernel, this one keeps everything in the same session, meaning doing cd dir will be persistent across cells.

I use Jupyter to write tutorials for my open-source projects, and some of them are mainly command-line interfaces, so using the bash kernel simplifies things a lot: I no longer have to use the %%bash magic on each cell, the outputs are updated in real-time (when using %%bash then only show up when the command finishes), and I no longer have the cryptic traceback that is thrown when a command fails.

Upvotes: 0

swatchai
swatchai

Reputation: 18812

You cannot use !cd to navigate the filesystem from Jupyter notebook. The reason is that shell commands (preceding with ! symbol) in Jupyter notebook's code cells are executed in a temporary subshell. If you'd like to change the working directory, you can use the %cd magic command:

!pwd
/d/swatchai_works/tutorial/jupyter

%cd ..
/d/swatchai_works/tutorial

!pwd
/d/swatchai_works/tutorial

%cd jupyter
/d/swatchai_works/tutorial/jupyter

Edit Using magic command %cd to change working directory can cause problems to other code running on the jupyter notebook that rely on the directory at the startup of the notebook.

Using chaining bash commands with "&&" operator(s) may be better choice if you dont want to change the current working directory at the end of the process.

Upvotes: 23

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