Improved version of sbliven/d413c2f2f4af3bf56e13d1f8656751b1 using configparser

mysettings.ini

[nlsa]                                                                                                                 |~
name = Custom Settings                                                                                                 |~
x = 4                                                                                                                  |~

read_settings_ini.py

"""main module

usage: python read_settings_ini.py mysettings.ini

This will import settings from mysettings.ini
"""
import argparse
import importlib

try:
    import configparser
except ImportError:
    # Python 2. Note that the python 3 syntax is much nicer
    import ConfigParser as configparser


def load_config(filename):
    config = configparser.ConfigParser()
    # set defaults
    config.add_section("nlsa")
    config.set("nlsa", "x", 0)
    config.set("nlsa", "y", 0)

    # load actual file
    config.read(filename)

    return config


def main(args=None):
    parser = argparse.ArgumentParser(description="")
    parser.add_argument("settings", help="settings ini file")
    args = parser.parse_args(args)

    config = load_config(args.settings)

    print("Name: %s" % config.get("nlsa", "name"))
    print("Coords: %d,%d" % (config.getint("nlsa", "x"), config.getint("nlsa", "y")))


if __name__ == "__main__":
    main()

submit_ini.sh

#!/bin/bash
# Slurm submission script
# usage: sbatch submit_ini.sh mysettings.ini

#SBATCH -p hourly
#SBATCH -n 1
#SBATCH --account=merlin

module purge
module load anaconda
conda activate dev27

# pass sbatch arguments to python
python read_settings_ini.py "$@"

This improves on the previous version by using ini files to store the settings rather than python modules.

• Call sbatch submit_ini.sh mysettings.ini
• Inside submit_ini.sh, "mysettings.ini" is stored as $@ (standard bash argument handling)
• On the compute node, submit_ini.sh calls python read_settings_ini.py mysettings.ini
• read_settings_ini.py gets "mysettings.ini" passed as sys.argv[1]. This is parsed by the cli library (here the built-in argparse, but click is nicer) and stored as args.settings
• The config file is loaded

This file is python 2.7 compatible. Unfortunately the 2.7 ConfigParser lacks many features available in python 3 (e.g. accessing values like config["nlsa"]["x"])