CHARSTATELABELS block?

[rbturnbull]

I think some phylogenetics programs need the CHARSTATELABELS block filled out. (I thought BEAUTi needed it for example). Is it possible to include it. I've got an example here: https://github.com/rbturnbull/phylopaul/blob/main/1Corinthians/1Corinthians.nexus
I was lazy with that example and I just called the readings/states State0 or State1. It might be good to slugify the readings and have them in the states. I also include the site/character label in as a comment in square brackets. There should be a command line option to not have the CHARSTATELABELS block if the user doesn't want it. What do you think?

[jjmccollum]

This sounds good. The NEXUS paper actually recommends using CHARSTATELABELS in place of CHARLABELS (which we currently use) and STATELABELS (which we don't), so I can work on that. I'll have to add some attributes to the Collation class for storing and mapping these properly. And yeah, we can include a --labels command-line option (or, more appropriately, a --no-labels option if labels are included by default).

[rbturnbull]

awesome. It might be good to use a library like one of these to slugify the readings:

• https://pypi.org/project/python-slugify/
• https://pypi.org/project/unicode-slugify/

[jjmccollum]

Will we need to change the unicode characters to ASCII if we're placing them in a NEXUS file?

[jjmccollum]

Okay, I've added support for this in the latest push to the cicd branch. I went with python-slugify for serializing the state labels. I'll plan to merge everything back into main once we have the other system tests incorporated into the CI pipeline.