feature: handle '+' in scientific notation floats (#223)

to parse newick

---------

Co-authored-by: Cecile Ane <[email protected]>

Author: cvigilv

docs/src/man/introduction.md

@@ -119,7 +119,7 @@ gene flow/hybridization or gene tree estimation error,
 and can be hard to interpret biologically.
 
 ```@raw html
-<img src="../assets/implicit.png" width="50%" alt="implicit split network" class="center"/>
+<img src="assets/implicit.png" width="50%" alt="implicit split network" class="center"/>
 ```
 
 In PhyloNetworks, we consider **explicit** phylogenetic networks exclusively.
@@ -130,14 +130,14 @@ In parenthetical format, internal nodes can have a name, like node `C` below,
 in a tree written as `(A,B)C` in newick format:
 
 ```@raw html
-<img src="../assets/intNode.png" width="45%" alt="internal tree node C" class="center"/>
+<img src="assets/intNode.png" width="45%" alt="internal tree node C" class="center"/>
 ```
 
 To represent networks in parenthetical format, the extended newick format splits
 each hybrid node into two nodes with the same name:
 
 ```@raw html
-<img src="../assets/netNewick.png" width="70%" alt="a hybrid node is split into 2 nodes with the same name, to represent a network as a tree" class="center"/>
+<img src="assets/netNewick.png" width="70%" alt="a hybrid node is split into 2 nodes with the same name, to represent a network as a tree" class="center"/>
 ```
 
 By convention, the hybrid tag is `# + H,LGT,R + number`, and the minor
@@ -174,4 +174,4 @@ the edge was a tree edge:
 setgamma!(net.edge[4], 0.7)
 # should return this:
 # ERROR: cannot change gamma in a tree edge
-```
+```

src/readwrite.jl

@@ -113,12 +113,12 @@ end
 
 # aux function to read floats like length or gamma values, to be read after a colon
 function readnewick_float(s::IO, c::Char)
-    if !(isdigit(c) || c in ['.','e','-','E'])
+    if !(isdigit(c) || c in ['.','e','-','E', '+'])
         a = read(s, String);
         error("Expected float digit after ':' but found $(c). remaining is $(a).");
     end
     num = ""
-    while isdigit(c) || c in ['.','e','-', 'E']
+    while isdigit(c) || c in ['.','e','-', 'E', '+']
         d = read(s, Char) # reads c and advances IO
         num = string(num,d);
         c = peekskip(s);

test/test_relaxed_reading.jl

@@ -35,6 +35,11 @@ global net
     @test_throws Exception readnewick("(E,((B)#H1") # doesn't end with ;
     @test_throws Exception readnewick(IOBuffer("E;")) # Expected beginning of tree with (
 end
+@testset "edge parameters" begin
+ net = readnewick("(A:2e-03,((B:1.2e1,#H1:1e+1):2.2E-02,(D:1.1E+2)#H1:4.4E+2::5.5E-10));")
+ @test [e.length for e in net.edge] == [0.002,12,10,0.022,110,440,-1]
+ @test [e.gamma for e in net.edge if e.hybrid] == [0.99999999945, 5.5e-10]
+end
 @testset "ismajor & gamma consistency, and miscellaneous" begin
     net = readnewick("((((B)#H1)#H2,((D,C,#H2:::0.8),(#H1,A))));");
     @test writenewick(net, round=true, digits=8) == "(#H2:::0.2,((D,C,((B)#H1)#H2:::0.8),(#H1,A)));"