pysh

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pysh is a syntax that transpiles to Python. It allows you to embed shell scripts into your Python code for syntactic sugar.

Check the wiki for detailed documentation.

Syntax

pysh has the following major syntax additions to Python:

• Inline evaluations: These allow you to write single-line shell commands whose outputs are returned.

Suppose you need to count the number of iterations a program has run in a file, and the program outputs lines starting with iter i. You could then do

iterations = int`grep "^iter" | wc -l`

The int formatter is a built-in function that specifies that the result of the shell command must be an integer. If this is not satisfied, it raises a TypeError.

Another example involves cut. To extract the second field from each line of a |-delimited file, one could use the pysh syntax as follows:

favorite_colors = list.str`cut -d '|' -f2 input.txt`

Here, we use the list.str formatter, since cut returns multiple lines of output, that we wish to be formatted into a list, each element of which we want to be a str. One could also use the list formatter itself, and the .str is implicitly assumed, but the former is a clearer syntax.

• Inline Python code: You can use pysh to run commands that either return no output, or whose output you wish to ignore.

The following example runs 20 jobs in slurm, waiting 3 seconds after each to ensure there was no error (which would stop the slurm job).

import time

for i in range(20):
    output = str`sbatch run.sh`  # output is "Submitted job <job-id>
    job_id = output.split()[-1]

    time.sleep(3)
    job_running = int`squeue | grep -c {{job_id}} | wc -l` > 0
    if not job_running:
        print("Job", job_id, "is not running!")

In this code, we use the double bracket syntax to use a Python variable in a shell command.