Python Command Line Arguments

It is often useful to pass certain parameters to a python script. For example: if you need a batch job to run on a desired queue, if want to specify desired memory allocation, or if you simply need to define the name of a file being generated by the script. A quick and easy solution to handle changing parameters is to include code that accepts user-defined input.

Example code: command-line-arguments-example.py

import argparse

def parse_args():

    parser = argparse.ArgumentParser(add_help=False)

    # arguments that provide script information
    parser.add_argument(
        '-v', 
        '--version', 
        action='version',
        version='%(prog)s 1.0', 
        help="Show program's version number and exit."
    )
    
    parser.add_argument(
        '-h',
        '--help', 
        action='help', 
        default=argparse.SUPPRESS,
        help='Show this help message and exit.'
    )

    # required arguments
    parser.add_argument(
        "-m",
        "--memory",
        type=int,
        metavar="",
        required=True,
        help="""Memory allocated to job."""
    )

    parser.add_argument(
        "-q",
        "--jobQueue",
        type=str,
        metavar="",
        required=True,
        choices=["analysis-queue-1", "analysis-queue-2"],
        help="""Batch queue. Select from: analysis-queue-1, analysis-queue-2"""
    )

    # optional argument with default value set
    parser.add_argument(
        "-n",
        "--jobName",
        type=str,
        metavar="",
        default="analysis-job",
        help="""AWS Batch job name. Default value: analysis-job."""
    )

    return parser.parse_args()

def main():
    args = parse_args()
    mem = args.memory
    queue= args.jobQueue
    jobName = args.jobName

    print("Memory:",mem)
    print("Queue:",queue)
    print("Job Name:",jobName)

if __name__ == "__main__":
    main()

Example usage:

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Let’s break down the elements:

• Import the argparse module, which allows users to input data, provides help messages, and shows errors if arguments are invalid.

import argparse

• Provide a version for your script. Generally, this is a good programming practice. If you need guidance for versioning, visit this blog post. Note that a ‘help’ message in included for this argument all subsequent arguments. Use this to describe the basic function of the argument.

    parser.add_argument(
        '-v', 
        '--version', 
        action='version',
        version='%(prog)s 1.0', 
        help="Show program's version number and exit."
    )

• Describe the purpose of the python script. What does this program accomplish? This text is shown when the user enters help mode. The help message for each command-line argument is also displayed.

    parser.add_argument(
        '-h',
        '--help', 
        action='help', 
        default=argparse.SUPPRESS,
        help='Show this help message and exit.'
    )

• Add required arguments with required set to True. These arguments can passed to the script using either the shorthand or long version, ie. -m 400 and --memory 400 are programmatically equivalent. Include the variable type, such as int or str. Note that the job name argument only accepts 2 values. Use this feature to control what users can enter for arguments. Finally, metavar is used a placeholder for the help message display.

    # required argument
    parser.add_argument(
        "-m",
        "--memory",
        type=int,
        metavar="",
        required=True,
        help="""Memory allocated to job.""",
    )

    parser.add_argument(
        "-q",
        "--jobQueue",
        type=str,
        metavar="",
        required=True,
        choices=["analysis-queue-1", "analysis-queue-2"],
        help="""Batch queue. Select from: analysis-queue-1, analysis-queue-2"""
    )

• Add optional requirements and set a default value. Notice that the required parameter is not set because the default value is False.

    parser.add_argument(
        "-n",
        "--jobName",
        type=str,
        metavar="",
        default="analysis-job",
        help="""AWS Batch job name. Default value: analysis-job."""
    )

• Close out the parse_args() function by returning all of the arguments.

    return parser.parse_args()

• Access user-defined command input in your script by calling the parse_args function.

def main():
    args = parse_args()
    mem = args.memory
    queue= args.jobQueue
    jobName = args.jobName

    print("Memory:",mem)
    print("Queue:",queue)
    print("Job Name:",jobName)

if __name__ == "__main__":
    main()

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Additional Helpful Resources:

1. https://docs.python.org/3/library/argparse.html

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