doc: upgraded to Documenter v1

docs/Project.toml

@@ -3,13 +3,12 @@ BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
 PhyloNetworks = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
 PhyloPlots = "c0d5b6db-e3fc-52bc-a87d-1d050989ed3b"
 RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 
 [compat]
-Documenter = "~0.27"
+Documenter = "~1"
 PhyloPlots = "1"

docs/make.jl

@@ -1,4 +1,4 @@
-using Documenter, DocumenterMarkdown
+using Documenter
 
 using Pkg
 Pkg.add(PackageSpec(name="PhyloPlots", rev="master"))
@@ -11,7 +11,13 @@ makedocs(
     sitename = "PhyloNetworks.jl",
     authors = "Claudia Solís-Lemus, Cécile Ané, Paul Bastide and contributors.",
     modules = [PhyloNetworks], # to list methods from PhyloNetworks only, not from Base etc.
-    format = Documenter.HTML(prettyurls = get(ENV, "CI", nothing) == "true"), # easier local build
+    format = Documenter.HTML(
+        prettyurls = get(ENV, "CI", nothing) == "true", # easier local build
+        size_threshold = 600 * 2^10, size_threshold_warn = 500 * 2^10), # 600 KiB
+    # exception, so warning-only for :missing_docs. List all others:
+    warnonly = Documenter.except(:autodocs_block, :cross_references, :docs_block,
+        :doctest, :eval_block, :example_block, :footnote, :linkcheck_remotes,
+        :linkcheck, :meta_block, :parse_error, :setup_block),
     pages = [
         "Home" => "index.md",
         "Manual" => [

src/manipulateNet.jl

@@ -95,18 +95,16 @@ end
 
 """
     hybridatnode!(net::HybridNetwork, nodeNumber::Integer)
-    hybridatnode(net, nodeNumber)
 
-Change the status of edges in network `net`,
+Change the direction and status of edges in network `net`,
 to move the hybrid node in a cycle to the node with number `nodeNumber`.
 This node must be in one (and only one) cycle, otherwise an error will be thrown.
+Check and update the nodes' field `inCycle`.
 
-The second method does not modify `net`, checks that it's of level 1, and
-returns the new network after hybrid modification.
+Output: `net` after hybrid modification.
 
-`net` is assumed to be of level 1, that is, each blob has a
+Assumption: `net` must be of level 1, that is, each blob has a
 single cycle with a single reticulation.
-Check and update the nodes' field `inCycle`.
 
 # example
 
@@ -150,7 +148,7 @@ Move the reticulation from `hybrid` to `newNode`,
 which must in the same cycle. `net` is assumed to be of level 1,
 but **no checks** are made and fields are supposed up-to-date.
 
-Called by `hybridatnode!(net, node number)`, which is itself
+Called by `hybridatnode!(net, nodenumber)`, which is itself
 called by [`undirectedOtherNetworks`](@ref).
 """
 function hybridatnode!(net::HybridNetwork, hybrid::Node, newNode::Node)
@@ -182,7 +180,13 @@ end
 # does not call hybridatnode! but repeats its code: oops! violates DRY principle
 # nodeNumber should correspond to the number assigned by readTopologyLevel1,
 # and the node numbers in `net` are irrelevant.
-@doc (@doc hybridatnode!) hybridatnode
+"""
+    hybridatnode(net::HybridNetwork, nodeNumber::Integer)
+
+Move the hybrid node in a cycle to make node number `nodeNumber` a hybrid node
+Compared to [`hybridatnode!`], this method checks that `net` is of level 1
+(required) and does not modify it.
+"""
 function hybridatnode(net0::HybridNetwork, nodeNumber::Integer)
     net = readTopologyLevel1(writeTopologyLevel1(net0)) # we need inCycle attributes
     ind = 0