adjusted documentation to point outwards when referencing functions t…

…hat are in PhyloNetworks
JuliaPhylo · Oct 29, 2024 · cab4f1e · cab4f1e
1 parent 8337f34
commit cab4f1e
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diff --git a/docs/make.jl b/docs/make.jl
@@ -1,7 +1,7 @@
-using SNaQ
+using SNaQ, PhyloNetworks
 using Documenter
 
-DocMeta.setdocmeta!(SNaQ, :DocTestSetup, :(using SNaQ); recursive=true)
+DocMeta.setdocmeta!(SNaQ, :DocTestSetup, :(using SNaQ, PhyloNetworks); recursive=true)
 
 makedocs(;
     modules=[SNaQ],

diff --git a/src/descriptive.jl b/src/descriptive.jl
@@ -71,7 +71,7 @@ except for edges in
 
 will break if `inCycle` attributes are not initialized (at -1) or giving a correct node number.
 
-see [`Node`](@ref) for the meaning of boolean attributes
+see [`PhyloNetworks.Node`](https://juliaphylo.github.io/PhyloNetworks.jl/stable/lib/internals/#PhyloNetworks.Node) for the meaning of boolean attributes
 `isBadTriangle` (which corresponds to a "good" triangle above),
 `isBadDiamondI` and `isBadDiamondII`.
 """

diff --git a/src/readData.jl b/src/readData.jl
@@ -277,7 +277,7 @@ end
 Read a text file with a list of trees/networks in parenthetical format
 (one tree per line) and transform them like [`readTopologyLevel1`](@ref)
 does: to be unrooted, with resolved polytomies, missing branch lengths
-set to 1.0, etc. See [`readMultiTopology`](@ref) to read multiple
+set to 1.0, etc. See [`PhyloNetworks.readMultiTopology`](https://juliaphylo.github.io/PhyloNetworks.jl/stable/lib/public/#PhyloNetworks.readMultiTopology) to read multiple
 trees or networks with no modification.
 
 Output: array of HybridNetwork objects.

diff --git a/src/types.jl b/src/types.jl
@@ -58,7 +58,7 @@ do not appear in `hasEdge` nor `index`. Need to study this.
 julia> net0 = readTopology("(s17:13.76,(((s3:10.98,(s4:8.99,s5:8.99)I1:1.99)I2:0.47,(((s6:2.31,s7:2.31)I3:4.02,(s8:4.97,#H24:0.0::0.279)I4:1.36)I5:3.64,((s9:8.29,((s10:2.37,s11:2.37)I6:3.02,(s12:2.67,s13:2.67)I7:2.72)I8:2.89)I9:0.21,((s14:2.83,(s15:1.06,s16:1.06)I10:1.78)I11:2.14)#H24:3.52::0.72)I12:1.47)I13:1.48)I14:1.26,(((s18:5.46,s19:5.46)I15:0.59,(s20:4.72,(s21:2.40,s22:2.40)I16:2.32)I17:1.32)I18:2.68,(s23:8.56,(s1:4.64,s2:4.64)I19:3.92)I20:0.16)I21:3.98)I22:1.05);");
 
 julia> net = readTopologyLevel1(writeTopology(net0)) ## need level1 attributes for functions below
-PhyloNetworks.HybridNetwork, Un-rooted Network
+HybridNetwork, Un-rooted Network
 46 edges
 46 nodes: 23 tips, 1 hybrid nodes, 22 internal tree nodes.
 tip labels: s17, s3, s4, s5, ...