Add progress bar to encoder with `tqdm`

[cthoyt]

I'm encoding the Rhea reactions with drfp right now and it's taking more than 10 seconds, so naturally I'd like to see how much longer it will take using a progress bar. This PR adds a progress bar with tqdm.

There was a strange bit of code before that I changed for _, x in enumerate(X): that didn't actually take advantage of the enumeration itself. This could have been replaced with iter(X) if the goal was just to turn it into an iterator, but also using tqdm gets the job done the same.

[daenuprobst]

Hey, I'm keeping the repo as-is until peer-review is done. (Yes, it's been a while ;-))

[cthoyt]

@daenuprobst friendly reminder :) this is a short PR with nothing controversial

[cthoyt]

@daenuprobst any chance of merging this now?

[daenuprobst]

Hey, I've added it to the latest release with other things I did. Finally ;-)