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Running Scripts from IPython

IPython has a %%script cell magic, which lets you run a cell in a subprocess of any interpreter on your system, such as: bash, ruby, perl, zsh, R, etc.

It can even be a script of your own, which expects input on stdin.

In [1]:
import sys

Basic usage

To use it, simply pass a path or shell command to the program you want to run on the %%script line, and the rest of the cell will be run by that script, and stdout/err from the subprocess are captured and displayed.

In [2]:
%%script python2
import sys
print 'hello from Python %s' % sys.version

hello from Python 2.7.9 (default, Jan 29 2015, 06:27:40) 
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)]
In [3]:
%%script python3
import sys
print('hello from Python: %s' % sys.version)

hello from Python: 3.4.2 |Continuum Analytics, Inc.| (default, Oct 21 2014, 17:42:20) 
[GCC 4.2.1 (Apple Inc. build 5577)]

IPython also creates aliases for a few common interpreters, such as bash, ruby, perl, etc.

These are all equivalent to %%script <name>

In [4]:
%%ruby
puts "Hello from Ruby #{RUBY_VERSION}"

Hello from Ruby 2.0.0
In [5]:
%%bash
echo "hello from $BASH"

hello from /usr/local/bin/bash

Capturing output

You can also capture stdout/err from these subprocesses into Python variables, instead of letting them go directly to stdout/err

In [6]:
%%bash
echo "hi, stdout"
echo "hello, stderr" >&2

hi, stdout

hello, stderr
In [7]:
%%bash --out output --err error
echo "hi, stdout"
echo "hello, stderr" >&2
In [8]:
print(error)
print(output)

hello, stderr

hi, stdout

Background Scripts

These scripts can be run in the background, by adding the --bg flag.

When you do this, output is discarded unless you use the --out/err flags to store output as above.

In [9]:
%%ruby --bg --out ruby_lines
for n in 1...10
    sleep 1
    puts "line #{n}"
    STDOUT.flush
end

Starting job # 0 in a separate thread.

When you do store output of a background thread, these are the stdout/err pipes, rather than the text of the output.

In [10]:
ruby_lines
Out[10]:
<open file '<fdopen>', mode 'rb' at 0x10a4be660>
In [11]:
print(ruby_lines.read())

line 1
line 2
line 3
line 4
line 5
line 6
line 7
line 8
line 9

Arguments to subcommand

You can pass arguments the subcommand as well, such as this example instructing Python to use integer division from Python 3:

In [12]:
%%script python2 -Qnew
print 1/3

0.333333333333

You can really specify any program for %%script, for instance here is a 'program' that echos the lines of stdin, with delays between each line.

In [13]:
%%script --bg --out bashout bash -c "while read line; do echo $line; sleep 1; done"
line 1
line 2
line 3
line 4
line 5

Starting job # 2 in a separate thread.

Remember, since the output of a background script is just the stdout pipe, you can read it as lines become available:

In [14]:
import time
tic = time.time()
line = True
while True:
    line = bashout.readline()
    if not line:
        break
    sys.stdout.write("%.1fs: %s" %(time.time()-tic, line))
    sys.stdout.flush()

0.0s: line 1
1.0s: line 2
2.0s: line 3
3.0s: line 4
4.0s: line 5

Configuring the default ScriptMagics

The list of aliased script magics is configurable.

The default is to pick from a few common interpreters, and use them if found, but you can specify your own in ipython_config.py:

c.ScriptMagics.scripts = ['R', 'pypy', 'myprogram']

And if any of these programs do not appear on your default PATH, then you would also need to specify their location with:

c.ScriptMagics.script_paths = {'myprogram': '/opt/path/to/myprogram'}