writeTopologyLevel1 changes the network when printID=true

[crsl4]

In writeTopologyLevel1, the option of printID=true means that only branch lengths that are identifiable will be printed. The function first changes all non-identifiable branch lengths to -1, and then write the parenthetical format. This is confusing because the function is in fact modifying an argument (the network) and it does not end in !. Also, it is difficult to debug when a function that is meant to simply write the parenthetical format changes the actual network object.
An easy fix could be to do a deepcopy of the network object at the beginning of writeTopologyLevel1, but it might be worth to re-thinking the role of writeTopologyLevel1 with the update of root and non-identifiable BLs at the end of snaq!.

[cecileane]

Instead of doing a deep copy of the full network, could the vector of branch lengths be saved, e.g. [e.length for e in net.edge], so that edge lengths can be restored afterwards?

[crsl4]

yes, this is a good idea!