hcluster -> scipy?

[mszep]

I ran into some problems during the install of crosscat where it tries to install the hcluster package (see my comment on closed issue #8). I looked into why a simple pip install hcluster wouldn't work, and found that hcluster has been incorporated into scipy.

Specifically, these are the hcluster functions that I can see used in crosscat, and their scipy counterparts:

hcluster	scipy
pdist	spatial.distance.pdist
linkage	cluster.hierarchy.linkage
dendrogram	cluster.hierarchy.dendrogram

Note that I haven't compared them in detail, but I presume they haven't changed much, if at all; their docstrings look very similar.

It seems that a niggly dependency could be eliminated by switching to the scipy versions, so I'm wondering whether you'd accept pull requests implementing that (if so, are there any tests I should run), or have you considered all this and is there a good reason for using the original hcluster versions?

[jbaxter]

Hi @mszep,

Thanks! Yes, a few people been running into trouble installing hcluster, so I agree with you that we should just switch to scipy. I just did it in this commit here: b36cc04

[mszep]

👍

Although I guess the install scripts should be changed as well, to skip the installing of hcluster?

[jbaxter]

Good catch, thank you. Removed from the scripts here: 5c62662