Nick Youngblut

Is it actually possible to read in a non-ultrametric tree and then convert it to ultrametric? The package docs make a lot of statements about how ultrametric trees are needed...

I guess that the user can just make the symmetric matrix via: ``` taxa = t.taxon_namespace np.array([pdc(t1,t2) for t2 in taxa for t1 in taxa]).reshape(len(taxa), len(taxa)) ``` ...but it would...

hmm... without the numpy requirement, the user would have to convert to an array, such as via: ``` numpy.array([numpy.array(xi) for xi in x]) ``` ...which is nearly as much work...

Sorry for not specifying that in my initial comment. I was trying to push to GitHub, so I'm guessing that history-rewriting is not the issue.

I repeated twice before I posted the original comment. The commands in my original comment pasted from my history (with file names changed).

Are there any plans to implement this? One of snakemake's best features is that it can resubmit jobs with increased user-defined resources (eg., `mem = attempt ** 3 + 10`,...

This happened to me also. Why can't batchtools provide an error if the registry is not accessible from a node? Shouldn't there at least be a check for the registry...

Another, likely better option, would be to just create a new subdirectory within the user-specified directory for each run. A UUID could be used for the subdirectory name

Also, it appears that `makeRegistry()` doesn't use `recursive = TRUE` for `dir.create`

That would require one to always create the function or source it. Optional parameters provide the user with the option to select one subjective choice or another. It was just...