test json-tree-cpg

[matsen]

And, I'll take you up on your previous offer: I would like to test
json-tree-cpg in a similar way to json-cpg; could you add that in? I
would, but it isn't as straightforward as adding another file to
nestly/models/, as some of the calls and options are different:
fit-tree-model.R rather than fit-model.R, and make-genmat takes no -o
flag, as the location of the genmats is specified in the config file.

[matsen]

Hello Peter--

It seems to me that this is the first instance of a path being specified in a config file. It seems to me good to keep it that way unless there is a solid reason to change this and the CLI of all of the tools to accomodate several genmats. What if I changed things to save the several genmats into one .RData file, such that we could keep things as they are?

Thanks!

[petrelharp]

Hm, so: changing make-genmat.R to store in a single file everything needed
for the tree? That sounds like a good idea. Perhaps it should also do the
setup done by peel.transmat, since that is shared in common by anything
with the same tree as well; then the thing that is being stored is still a
single object.

-p

On Sat, Feb 7, 2015 at 11:54 AM, Erick Matsen notifications@github.com
wrote:

Hello Peter--

It seems to me that this is the first instance of a path being specified
in a config file. It seems to me good to keep it that way unless there is a
solid reason to change this and the CLI of all of the tools to accomodate
several genmats. What if I changed things to save the several genmats into
one .RData file, such that we could keep things as they are?

Thanks!

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