I run the command in IPython
cd $cs<TAB>
but it does not allow me to expand the path.
How can you make IPython to read shell variables?
If i understand correctly what you mean by 'shell variables'. If you mean variables set in the shell ('environment variables'): you can read them with os.environ...
import os
cs = os.environ.get('cs')
runstring = "cd %s" (cs)
...
Related
Question is in the title.
I know that % usually denotes a "magic variable" in IPython. That's not a concept I'm terribly familiar with yet, but I have read about it.
However, today I saw a tutorial where someone was using it to run a shell command. Normally I have seen and used !.
Is there a difference? Both seem to be doing the same thing when I try them.
The difference is this:
When you run a command with !, it directly executes a bash command in a subshell.
When you run a command with %, it executes one of the magic commands defined in IPython.
Some of the magic commands defined by IPython deliberately mirror bash commands, but they differ in the implementation details.
For example, running the !cd bash command does not persistently change your directory, because it runs in a temporary subshell. However, running the %cd magic command will persistently change your directory:
!pwd
# /content
!cd sample_data/
!pwd
# /content
%cd sample_data/
!pwd
# /content/sample_data
Read more in IPython: Built-in Magic Commands.
I use the system/unix command on Matlab in order to run an external program via the command line. I want to execute it via an alias define in .zshrc on my computer. Unfortunately, the alias seems to be not available.
Example with ll
on a terminal: which ll gives ll: aliased to ls -lh
on Matlab: unix('ll') gives zsh:1: command not found: ll
I check if I used the right shell: unix('echo $SHELL') gives /usr/local/bin/zsh.
I have add setopt aliases in my .zshrc but it changes nothing. Is it possible to check which startup files is used when you open a non interactive shell?
The ~/.zshrc seems to be not loaded in the non interactive case. The solution consists in loaded aliases and added setopt aliases in ~/.zshenv. See this for instance.
I'm relatively new to NumPy/SciPy and IPython.
To execute a python script in the python interactive mode, we may use the following commands.
>>> import os
>>> os.system('executable.py')
Then the print outputs can be seen from the python prompt.
But the same idea doesn't work with IPython notebook.
In [64]:
import os
os.system('executable.py')
Out[64]:
0
In this case, I cannot see any print outputs. The notebook only tells weather execution was successful or not. Are there any ways to see the outputs when I use IPython notebook?
Use the magic function %run:
%run executable.py
This properly redirects stdout to the browser and you will see the output from the program in the notebook.
It gives you both, the typical features of running from command line plus Python tracebacks if there is exception.
Parameters after the filename are passed as command-line arguments to
the program (put in sys.argv). Then, control returns to IPython's
prompt.
This is similar to running at a system prompt python file args,
but with the advantage of giving you IPython's tracebacks, and of
loading all variables into your interactive namespace for further use
(unless -p is used, see below).
The option -t times your script. With -d it runs in the debugger pdb. More nice options to explore.
I want to accomplish a loop over R code within an IPython notebook. What is the best way to do this?
l = []
for i in range(10):
# execute R script
%%R -i i -o result #some arbitrary R code
# and use the output
l.append(result)
Can this be done inside a notebook (Looping over next cell)?
Have you looked into rmagic and rpy2 module?
If you have R scripts, then you can call them and assign their output to a variable using the shell command notation:
var=!R_script arguments....
The above does not need you need you to install rpy2 since ! shell command execution is basic in ipython. You can pass values of variables from ipython notebook by using $var in the arg list.
I was hoping it would be easy to rewrite a few bash scripts using ipython by using the "!" command. Unfortunately if I try to run ipython in non-interactive mode like so:
ipython -p sh myipythonscript.py
where myipythonscript.py contains commands like:
env=%env
d=!ls
This doesn't work. I get SyntaxError.
Is there an option which allows ipython to be run in non-interactive mode?
Python also has modules which makes it easy to completely replace bash calls. these are easier to debug and give better error handling.
for example instead of ls you can use glob, it supports the same syntax:
files=glob.glob('myfiles*.txt')
for environment variables:
env = os.environ
for path related functions:
os.path
for common operations, os.mkdir, os.chmod, os.getcwd [same as pwd]