Add calculation of minimum spanning trees

nickjcroucher commented 3 years ago

This is an inadequate implementation currrently. A design choice needs to be made about whether:

multiple trees should be returned if a network is not fully connected (I am not aware of a viewer of multiple MSTs since eBURST v3, so this would limit visualisation possibilities)
fully-connected networks could be constructed (but this is too slow for large datasets)
a threshold could be identified for making the network sparse but fully connected (this seems to require constructing an MST)
connections could be made between distinct components(either arbitrary or calculated between selected references - these could be the "founders", as identified by eBURST CCs, for which there is already code when selecting the dendropy seed_node)

johnlees commented 3 years ago

@nickjcroucher Could you merge the master branch in? Then I should be able to take a look on Monday

nickjcroucher commented 3 years ago

Will do - just for inspiration, here is the MSTree code from Grapetree, which may be helpful: https://github.com/achtman-lab/GrapeTree/blob/master/module/MSTrees.py

johnlees commented 3 years ago

Also I'm not sure why the tests aren't running on this PR, I can try and sort that out too

johnlees commented 3 years ago

Also I'm not sure why the tests aren't running on this PR, I can try and sort that out too

I've edited the config slightly on master, so hopefully merging master in should get the testing running on this branch

bacpop / PopPUNK