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fix #201, #205, Documenter v1, ready for v0.16.3 (#206)
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* fix #205: AbstractString in signatures
* fix #201: error instead of warning if 2-cycle
* up to v0.16.3
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@cecileane
cecileane authored Nov 19, 2023
1 parent 3f1e097 commit 9e93501
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Showing 11 changed files with 122 additions and 192 deletions.
2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "PhyloNetworks"
uuid = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
license = "MIT"
version = "0.16.2"
version = "0.16.3"

[deps]
BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
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3 changes: 1 addition & 2 deletions docs/Project.toml
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Expand Up @@ -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"
10 changes: 8 additions & 2 deletions docs/make.jl
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@@ -1,4 +1,4 @@
using Documenter, DocumenterMarkdown
using Documenter

using Pkg
Pkg.add(PackageSpec(name="PhyloPlots", rev="master"))
Expand All @@ -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" => [
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53 changes: 15 additions & 38 deletions src/auxiliary.jl
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Expand Up @@ -481,17 +481,6 @@ function getIndexHybrid(node::Node, net::Network)
return i
end

# function that given a hybrid node, it gives you the minor hybrid edge
# warning: assumes level-1 network: see getparentedgeminor for a general network
function getHybridEdge(node::Node)
node.hybrid || error("node $(node.number) is not hybrid node, cannot get hybrid edges")
a = nothing;
for e in node.edge
(e.hybrid && !e.isMajor) ? a = e : nothing; # assumes level-1: child of hybrid node must be a tree edge
end
isa(a,Nothing) ? error("hybrid node $(node.number) does not have minor hybrid edge, edges: $([e.number for e in node.edge])") : return a
end


# function that given two nodes, it gives you the edge that connects them
# returns error if they are not connected by an edge
Expand Down Expand Up @@ -684,36 +673,24 @@ end
# function to delete an internal node with only 2 edges
function deleteIntNode!(net::Network, n::Node)
size(n.edge,1) == 2 || error("node $(n.number) does not have only two edges")
# isEqual(n,net.node[net.root]) && println("deleting the root $(n.number) because it has only two edges attached")
index = n.edge[1].number < n.edge[2].number ? 1 : 2;
edge1 = n.edge[index];
edge2 = n.edge[index==1 ? 2 : 1];
if(!edge1.hybrid && !edge2.hybrid)
node1 = getOtherNode(edge1,n);
node2 = getOtherNode(edge2,n);
removeEdge!(node2,edge2);
removeNode!(n,edge1);
setEdge!(node2,edge1);
setNode!(edge1,node2);
deleteNode!(net,n);
deleteEdge!(net,edge2);
else
@warn "the two edges $([edge1.number,edge2.number]) attached to node $(n.number) must be tree edges to delete node"
if(edge1.hybrid)
hybedge = edge1
otheredge = edge2
elseif(edge2.hybrid)
hybedge = edge2
otheredge = edge1
edge1 = n.edge[index]; # edge1 will be kept
edge2 = n.edge[index==1 ? 2 : 1] # we will delete edge2 and n, except if edge2 is hybrid
if edge2.hybrid
(edge2, edge1) = (edge1, edge2)
if getchild(edge1) === n || edge2.hybrid
@error "node with incoming hybrid edge or incident to 2 hybrid edges: will not be removed"
return nothing
end
othernode = getOtherNode(otheredge,n)
removeNode!(n,hybedge)
removeEdge!(othernode,otheredge)
setEdge!(othernode,hybedge)
setNode!(hybedge,othernode)
deleteNode!(net,n)
deleteEdge!(net,otheredge)
end
node2 = getOtherNode(edge2,n)
removeEdge!(node2,edge2)
removeNode!(n,edge1)
setEdge!(node2,edge1)
setNode!(edge1,node2)
deleteNode!(net,n)
deleteEdge!(net,edge2)
return nothing
end


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51 changes: 15 additions & 36 deletions src/deleteHybrid.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@
function identifyInCycle(net::Network,node::Node)
node.hybrid || error("node $(node.number) is not hybrid, cannot identifyInCycle")
start = node;
hybedge = getHybridEdge(node);
last = getOtherNode(hybedge,node);
hybedge = getparentedgeminor(node)
lastnode = getOtherNode(hybedge,node)
dist = 0;
queue = PriorityQueue();
path = Node[];
Expand All @@ -33,32 +33,19 @@ function identifyInCycle(net::Network,node::Node)
return true, net.edges_changed, net.nodes_changed
else
curr = dequeue!(queue);
if(isEqual(curr,last))
if isEqual(curr,lastnode)
found = true;
push!(path,curr);
else
if(!net.visited[getIndex(curr,net)])
net.visited[getIndex(curr,net)] = true;
if(isEqual(curr,start))
for e in curr.edge
if(!e.hybrid || e.isMajor)
other = getOtherNode(e,curr);
other.prev = curr;
dist = dist+1;
enqueue!(queue,other,dist);
end
end
else
for e in curr.edge
if(!e.hybrid || e.isMajor)
other = getOtherNode(e,curr);
if(!other.leaf && !net.visited[getIndex(other,net)])
other.prev = curr;
dist = dist+1;
enqueue!(queue,other,dist);
end
end
end
elseif !net.visited[getIndex(curr,net)]
net.visited[getIndex(curr,net)] = true
atstart = isEqual(curr,start)
for e in curr.edge
e.isMajor || continue
other = getOtherNode(e,curr)
if atstart || (!other.leaf && !net.visited[getIndex(other,net)])
other.prev = curr
dist = dist+1
enqueue!(queue,other,dist)
end
end
end
Expand Down Expand Up @@ -149,17 +136,9 @@ function deleteHybridizationUpdate!(net::HybridNetwork, hybrid::Node, random::Bo
push!(edgesRoot, edges[2])
undoContainRoot!(edgesRoot);
end
@debug begin
msg = ""
if edges[1].gamma < 0.5
msg = "strange major hybrid edge $(edges[1].number) with gamma $(edges[1].gamma) less than 0.5"
end
if edges[1].gamma == 1.0
msg = "strange major hybrid edge $(edges[1].number) with gamma $(edges[1].gamma) equal to 1.0"
end
msg
end
limit = edges[1].gamma
@debug (limit < 0.5 ? "strange major hybrid edge $(edges[1].number) with γ $limit < 0.5" :
(limit == 1.0 ? "strange major hybrid edge $(edges[1].number) with γ = $limit" : ""))
if(random)
minor = rand() < limit ? false : true
else
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20 changes: 12 additions & 8 deletions src/manipulateNet.jl
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Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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
Expand Down
15 changes: 5 additions & 10 deletions src/readwrite.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -750,16 +750,11 @@ function cleanAfterRead!(net::HybridNetwork, leaveRoot::Bool)
nodes = copy(net.node)
for n in nodes
if isNodeNumIn(n,net.node) # very important to check
if size(n.edge,1) == 2
if !n.hybrid
if !leaveRoot || !isEqual(net.node[net.root],n) #if n is the root
deleteIntNode!(net,n);
end
else
hyb = count([e.hybrid for e in n.edge]);
if hyb == 1
deleteIntNode!(net,n);
end
if size(n.edge,1) == 2 # delete n if:
if (!n.hybrid && (!leaveRoot || !isEqual(net.node[net.root],n)) ||
(n.hybrid && sum(e.hybrid for e in n.edge) == 1))
deleteIntNode!(net,n)
continue # n was deleted: skip the rest
end
end
if !n.hybrid
Expand Down
16 changes: 8 additions & 8 deletions src/traitsLikDiscrete.jl
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Expand Up @@ -133,7 +133,7 @@ The `rvsymbol` should be as required by [`RateVariationAcrossSites`](@ref).
The network's gamma values are modified if they are missing. After that,
a deep copy of the network is passed to the inner constructor.
"""
function StatisticalSubstitutionModel(net::HybridNetwork, fastafile::String,
function StatisticalSubstitutionModel(net::HybridNetwork, fastafile::AbstractString,
modsymbol::Symbol, rvsymbol=:noRV::Symbol, ratecategories=4::Int;
maxhybrid=length(net.hybrid)::Int)
for e in net.edge # check for missing or inappropriate γ values
Expand Down Expand Up @@ -449,14 +449,14 @@ end

#species, dat version, no ratemodel
function fitdiscrete(net::HybridNetwork, model::SubstitutionModel,
species::Array{String}, dat::DataFrame; kwargs...)
species::Array{<:AbstractString}, dat::DataFrame; kwargs...)
ratemodel = RateVariationAcrossSites(ncat=1)
fitdiscrete(net, model, ratemodel, species, dat; kwargs...)
end

#species, dat version with ratemodel
function fitdiscrete(net::HybridNetwork, model::SubstitutionModel,
ratemodel::RateVariationAcrossSites, species::Array{String},
ratemodel::RateVariationAcrossSites, species::Array{<:AbstractString},
dat::DataFrame; kwargs...)
dat2 = traitlabels2indices(dat, model) # vec of vec, indices
o, net = check_matchtaxonnames!(copy(species), dat2, net)
Expand All @@ -465,7 +465,7 @@ end

#wrapper: species, dat version with model symbol
function fitdiscrete(net::HybridNetwork, modSymbol::Symbol,
species::Array{String}, dat::DataFrame, rvSymbol=:noRV::Symbol; kwargs...)
species::Array{<:AbstractString}, dat::DataFrame, rvSymbol=:noRV::Symbol; kwargs...)
rate = startingrate(net)
labels = learnlabels(modSymbol, dat)
if modSymbol == :JC69
Expand Down Expand Up @@ -498,7 +498,7 @@ end
#dnadata with dnapatternweights version with ratemodel
function fitdiscrete(net::HybridNetwork, model::SubstitutionModel,
ratemodel::RateVariationAcrossSites,dnadata::DataFrame,
dnapatternweights::Array{Float64}; kwargs...)
dnapatternweights::Array{<:AbstractFloat}; kwargs...)
dat2 = traitlabels2indices(dnadata[!,2:end], model)
o, net = check_matchtaxonnames!(dnadata[:,1], dat2, net)
kwargs = (:siteweights => dnapatternweights, kwargs...)
Expand All @@ -508,7 +508,7 @@ end

#wrapper for dna data
function fitdiscrete(net::HybridNetwork, modSymbol::Symbol, dnadata::DataFrame,
dnapatternweights::Array{Float64}, rvSymbol=:noRV::Symbol; kwargs...)
dnapatternweights::Array{<:AbstractFloat}, rvSymbol=:noRV::Symbol; kwargs...)
rate = startingrate(net)
if modSymbol == :JC69
model = JC69([1.0], true) # 1.0 instead of rate because relative version
Expand Down Expand Up @@ -580,7 +580,7 @@ function fit!(obj::SSM; optimizeQ=true::Bool, optimizeRVAS=true::Bool,
return obj
end
if optimizeQ
function loglikfun(x::Vector{Float64}, grad::Vector{Float64}) # modifies obj
function loglikfun(x::Vector{<:AbstractFloat}, grad::Vector{<:AbstractFloat}) # modifies obj
setrates!(obj.model, x)
res = discrete_corelikelihood!(obj)
verbose && println("loglik: $res, model rates: $x")
Expand Down Expand Up @@ -609,7 +609,7 @@ function fit!(obj::SSM; optimizeQ=true::Bool, optimizeRVAS=true::Bool,
verbose && println("got $(round(fmax, digits=5)) at $(round.(xmax, digits=5)) after $(optQ.numevals) iterations (return code $(ret))")
end
if optimizeRVAS
function loglikfunRVAS(alpha::Vector{Float64}, grad::Vector{Float64})
function loglikfunRVAS(alpha::Vector{<:AbstractFloat}, grad::Vector{<:AbstractFloat})
setparameters!(obj.ratemodel, alpha)
res = discrete_corelikelihood!(obj)
verbose && println("loglik: $res, rate variation model shape parameter alpha: $(alpha[1])")
Expand Down
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Registration pull request created: JuliaRegistries/General/95631

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.16.3 -m "<description of version>" 9e9350130ef9b41e77fa901b39067baee1706886
git push origin v0.16.3

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