Started work on new command line infastructure. I looked around a lot, and couldn't find any 'command line framework' that was simple and did what I want, so I implemented the minimal version of the IPython-like system. It's a little less magical though. Subcommands are classes, and they pack their arguments as class attributes which get pased to argparse.ArgumentParser.add_argument, and then they define a start(self, args) method that receives the argparse.Namespace when they get started.
Slightly simpler
Got the parsers working for fit-em. Haven't implemented the actual main() function yet
comment
atomindices script
typo
Typo fixes
Add inspect command
Merge pull request #15 from rmcgibbo/cmdline

[WIP] New command line interface