No hard rules, but two guidelines:
- Small (ie. single file) scripts/programs that may or may not be used frequently
- Series of tools which aren't used frequently, but important to keep track of
The utilities are split between machine specific and general utilities.
These are some general guidelines for the creation of utility scripts that can be added here.
A simple example of this in a bash script is:
#!/bin/bash
HELPMSG="Here is a helpful message about how to use this utility.
You can even break it into multiple lines if you want."
if [ "$1" == "-h" ] || [ "$1" = "--help" ]; then
echo $HELPMSG
fi
In python, you can use something like argparse
if you have more complicated
options overview, or just want to have the help documentation generated
automagically.
As these are utilities developed for research tasks, they are probably going to be built for a specific task. If someone (or yourself) wants to adapt it to do something slightly different, comments help tremendously.