Jonathan Barnoud

The code tries to follow the gromacs code as much as possible. It is a good place to start to understand.

There used to be a single exposed function and it was documented in the readme 😛

I'll have a look at the pickling, see if I can recall how it works. But I never really needed to use it. @mnmelo is probably one who knows the...

I think a CC license would be the most appropriate. However, the user guide is backed quite a bit by docstring and those have been contributed under GPL. That may...

While I am not opposed to having the developer guide be completely split in an other repo / separate URL, I do see a drawback that should be considered. By...

On 04/05/15 17:01, Hub wrote: > ``` > The critical point of going to Python (scipy or scikit-learn) is > to have the same results as in R for the...

Cool ! I added scipy to the notebook and it gives the same clusters as the others for 3 clusters. For 4 clusters, however, scipy and scikit-learn agree with each...

I updated my notebook to include your medoid function. I also increased the number of requested clusters to 5, showing more discrepancy between scipy and scikit-learn on one side, and...

I updated my notebook again to use the newest version of R (3.2.0 (2015-04-16)). The 'ward.D2' method gives an even more different result. Also, I encounter issue #66.

Great test! I am quite disappointed about scipy but there are other options to use ward with python outside of scipy. The question now would be what criterion should we...