read newick format

[mufernando]

It would be cool to be able to import a Newick tree (with or without node ages) to form a base Deme object that can then be annotated with other details (split times, population sizes, etc).

Similar to msprimes feature: https://msprime.readthedocs.io/en/latest/tutorial.html#parsing-species-trees

I can definitely lend a hand if needed.

great work so far btw!!

[grahamgower]

Thanks @mufernando, that seems very doable!

[jeromekelleher]

Good idea. One downside though is that we start adding dependencies. We're using the newick package in msprime which is pretty lightweight, but it doesn't support extended newick, which would ultimately be needed to do this properly.

Still, it seems worth it, and we can mostly just copy the code from msprime I think.

[grahamgower]

For any GPL code we want to copy from msprime, we'll have to explicitly contact the original authors to check they're happy to have their code modified and more permissively licensed for inclusion in demes.

$ git blame species_trees.py -c | cut -f2 | sed 's/(//' | sort -u
Ben Jeffery
Jerome Kelleher
Michael Matschiner

[jeromekelleher]

I'm confident that we can get this approval.