如何从Jupyter Notebook中的Python字符串执行bash脚本？

Question

I am using Jupyter Notebook and would like to execute a bash script from a python string. I have a python cell creating the bash script which then I need to print, copy to another cell, and then run it. Is it possible to use something like exec('print('hello world!')') ?

Here is an example of my bash script:

%%bash -s "$folder_dir" "$name_0" "$name_1" "$name_2" "$name_3" "$name_4" "$name_5" "$name_6" "$name_7" "$name_8" "$name_9" "$name_10" "$name_11"

cd $1

ds9 ${2} ${3} ${4} ${5} ${6} ${7} ${8} ${9} ${10} ${11} ${12} ${13}

If not possible, then how can I go to a different directory, and run

ds9 dir1 dir2 dir3 ...

within my Jupyter Notebook since I only can initialize dir's using python. Note that the number of dir's is not fixed every time I run my code. ds9 is just a command to open multiple astronomical images at the same time.

I know I can save my bash script to a .sh file and execute that, but I am looking for a classier solution.

Answer 1

The subprocess module is the Right Thing for invoking external software -- in a shell or otherwise -- from Python.

import subprocess

folder_dir="/" # your directory
names=["name_one", "name_two"]   # this is your list of names you want to open

subprocess.check_call(
    ['cd "$1" || exit; shift; exec ds9 "$@"', "_", folder_dir] + names,
    shell=True)

---

How it works (Python)

When passing a Python list with shell=True , the first item in that list is the script to run; the second is the value of $0 when that script is running, and subsequent items are values for $1 and onward.

Note that this runs sh -c '...' with your command. sh is not bash, but (in modern systems) a POSIX sh interpreter. It's thus important not to use bash-only syntax in this context.

How it works (Shell)

Let's go over this line-by-line:

cd "$1" || exit # try to cd to the directory passed as $1; abort if that fails
shift           # remove $1 from our argument list; the old $2 is now $1, &c.
exec ds9 "$@"   # replace the shell in memory with the "ds9" program (as an efficiency
                # ...measure), with our argument list appended to it.

Note that "$1" and "$@" are quoted. Any unquoted expansion will be string-split and glob-expanded; without this change, you won't be able to open files with spaces in their names.