Change command-line options and add feature specification

[jchodera]

This changes to use optparse for command-line option parsing, and adds a --features featname specification as in #29.

An example command-line is now:

msm-pipeline --trajectories "alanine_*.h5" --name "alanine" --nclusters 50 --features backbone-dihedrals

Help is now:

[LSKI1497:choderalab/msm-pipeline/msm-pipeline.choderalab] choderaj% msm-pipeline --help
Usage: msm-pipeline [options]

Options:
  -h, --help            show this help message and exit
  -t PATH_TO_TRAJS, --trajectories=PATH_TO_TRAJS
                        path to trajectories (must be quoted if wildcards are
                        used)
  -n PROJECT_NAME, --name=PROJECT_NAME
                        don't print status messages to stdout
  -c N_CLUSTERS, --nclusters=N_CLUSTERS
                        number of clusters
  -f FEATURE_SELECTION, --features=FEATURE_SELECTION
                        choice of features: ['backbone-dihedrals']

Hopefully

[jchodera]

This doesn't actually add any new featurizer options---it just makes it easy for us to add the framework to do that.

[maxentile]

Thanks, John!

I added a few lines to parallelize the find_respairs_that_changed function, and included it as a --features option.

[maxentile]

Can I go ahead and merge this, @sonyahanson , @jchodera ?

[jchodera]

Made a couple of comments, but otherwise looks great!

[sonyahanson]

Looks good to me!

[maxentile]

Thanks! Merging.