Bad file extensions in cluster.py's --center-features don't error

[justinrporter]

cluster.py, if you pass a path with a weird file extension for --center-features, doesn't warn you. For example, if you're doing rmsd clustering, and you give xxx.npy, it will save that, even if it's a pickle.

[arudzinska]

Hi, is this issue still up? I understand the problem is in this file. I see some warnings related to file extensions already there though.

[justinrporter]

Yes, I think so. There are two related things going on here:

1. If you use --trajectories instead of --features (they are mutually exclusive), there are two types of files you can get for the output of --center-features. One is an h5, and this is if you pass --topology and --trajectories only once and the other is a pickle, and that's if you pass them more than once.
2. I think there might actually be some sort of bug where the warning is triggered incorrectly. I'll have to poke around on this a bit more, though.