Scripting in Bash is a pain. Bash can do almost anything, and is unbeatable for small scripts, but it struggles when scaling up to doing anything close to a real world scripting problem. Python is a natural choice, especially for the scientist who already is using it for analysis. But, it’s much harder to do basic tasks in Python. So you are left with scripts starting out as Bash scripts, and then becoming a mess, then being (usually poorly) ported to Python, or even worse, being run by a Python script. I’ve seen countless Python scripts that run Bash scripts that run real programs. I’ve even written one or two. It’s not pretty.
I recently came (back) across a really powerful library for doing efficient command line scripts in Python. It contains a set of tools that makes the four (five with color) main tasks of command line scripts simple and powerful. I will also go over the one main drawback of the library (and the possible enhancement!).