newick parsing: handle negative edge lengths, comments

[cecileane]

• negative edge lengths: fixes readTopology with negative edge lengths #176 by setting these lengths (and gamma values) to 0 and sending a log message of :error level
• allows for (and ignore) nexus-style comments within the extended newick, such as written by other software to add information about population size, posterior probability, mapping of a tip name to a population etc.

[codecov]

Codecov Report

Merging #177 (6a1fb88) into master (1f78b2a) will increase coverage by 0.05%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #177      +/-   ##
==========================================
+ Coverage   85.88%   85.93%   +0.05%     
==========================================
  Files          29       29              
  Lines       11827    11842      +15     
==========================================
+ Hits        10158    10177      +19     
+ Misses       1669     1665       -4     

Impacted Files	Coverage Δ
src/readwrite.jl	81.26% <100.00%> (+1.68%)	⬆️
src/phyLiNCoptimization.jl	94.16% <0.00%> (-0.82%)	⬇️

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[cecileane]

@crsl4 @bstkj @fogg-uw : all the tests pass so I'm ready to merge this PR. But network parsing is quite fundamental, so I'd be happy to give this some time, for you or others to review and perhaps test more cases if you have the leisure to do so (!)

The examples from #176 now give the following with this PR:

julia> net = readTopology("((A:1,B:1):-1,C:2);");
┌ Error: expecting non-negative value but read '-', left parenthesis 2. will set to 0.
└ @ PhyloNetworks ~/.julia/dev/PhyloNetworks/src/readwrite.jl:303

julia> net
HybridNetwork, Rooted Network
4 edges
5 nodes: 3 tips, 0 hybrid nodes, 2 internal tree nodes.
tip labels: A, B, C
((A:1.0,B:1.0):0.0,C:2.0);


julia> net = readTopology("((A:1,B:-1):1,C:2);");
┌ Error: expecting non-negative value but read '-', left parenthesis 2. will set to 0.
└ @ PhyloNetworks ~/.julia/dev/PhyloNetworks/src/readwrite.jl:303

julia> writeTopology(net)
"((A:1.0,B:0.0):1.0,C:2.0);"

and here is an example with nexus-style comments:

julia> net = readTopology("((A:1,B_[&Theta=0.1]:1)[&length=9.47][&prob=0.9]:0.4,C:2);");

julia> writeTopology(net)
"((A:1.0,B_:1.0):0.4,C:2.0);"