Toni G

Perhaps the version change can be done with bump2version and a post commit hook?

Maybe a continuous version of this criterion? http://mdtraj.org/1.6.2/api/generated/mdtraj.wernet_nilsson.html This has the advantage of requiring only one threshold with respect to other angle/distance combinations.

Not trivial but should be available in the next major release. In the meantime, as a possible workaround, consider repeating the alignment multiple times with several subsets (possibly overlapping) of...

It is intended. `jmax` is the **index to** the element containing the last aligned point. It may differ from N-1 for `open_end=True` alignments.

I think you rather want either the `.index1` or `.index2` properties in the result. `jmax` is just an index. They will be of the same length and be correct for...

Thanks for the added details. I'll have a look. The R `warp` function should be correct.

Sorry for the delay. I still haven't had the time to carefully check the fix and think about the corner cases, but in the meantime, it sounds good for people...

Python version's `warp` function relies on scipy interpolation, which is different from R's. This should be fixed in the future. So, even with the fix there still can be discrepancies.

Hit this too. Perhaps there could be an option which causes file names to be rewritten (say, appending an underscore after each capital letter)?

Actually, I was able to regenerate them with minor changes to your script. In particular, got the file [ALL variant-disease associations](http://www.disgenet.org/ds/DisGeNET/results/all_variant_disease_associations.tsv.gz) and changed `inst/extdata/build_DGN_Anno.R` as follows ``` x