Matthew Andres Moreno

This would be a good target for function logging: https://github.com/devosoft/Empirical/blob/0ef98e967984a6b8d47dcf9a588b220050c9c138/source/hardware/EventDrivenGP.h#L1305

here's some emp::data examples https://github.com/devosoft/Empirical/tree/master/examples/data

conversation RE macros on slack #empirical Emily Dolson Apr 11th at 12:35 Or, should we have a convention where each part of Empirical has its own verbose flag (e.g. EMP_VERBOSE_SIGNALGP...

I think that would make a lot of sense. Especially because Python2 has been EOL'ed for 3 years now and users will still be able to access previous versions (just...

Python2.7 support will be dropped in Dendropy 5.

Able to reproduce, `tree.txt` ``` ((1_Species+1_sp,1_Species2_sp),1-Species+sp); ``` `python3 applications/sumtrees/sumtrees.py tree.txt` produces ``` ... BEGIN TAXA; DIMENSIONS NTAX=3; TAXLABELS '1 Species+1 sp' 1_Species2_sp '1-Species+sp' ; END; BEGIN TREES; TREE 1 =...

**edit:** this is not the case, disabling these lines does not affect outcome Suspect culprit is interaction of one of these lines with library deserialization logic that assumes `preserve_underscores` is...

Actual explanation (I think): 1. when deserializing, all underscores are ripped out - if `preserve_underscores=False`, as is the case for `sumtrees.py` 2. internal representation with and without `-` character has...

It looks like this comes down to a technicality of NEXUS format, which the Newick output is sharing logic with. The relevant section is at the end > Word.—Except for...

I think the solution here will be to create specialized logic for the (less restrictive) escaping of newick words and replace the current calls to `escape_nexus_token`