update accessors getchild etc. deprecated in PN v0.16

also CI update: r-lib install etc

.github/workflows/ci.yml

@@ -9,6 +9,12 @@ on:
       - master
     tags: '*'
 
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -26,7 +32,7 @@ jobs:
           - x64
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
       - name: set R lib path to be found by julia RCall
         if: matrix.os == 'ubuntu-latest'
         run: echo "LD_LIBRARY_PATH=$(R RHOME)/lib" >> $GITHUB_ENV
@@ -47,20 +53,20 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v2
         with:
           file: lcov.info
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
       - run: echo "LD_LIBRARY_PATH=$(R RHOME)/lib" >> $GITHUB_ENV
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1'
-      - name: install dependencie
+      - name: install dependencies
         run: |
           julia --project=docs -e '
             using Pkg

Project.toml

@@ -12,7 +12,7 @@ RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
 
 [compat]
 DataFrames = "0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 1.0"
-PhyloNetworks = "0.9, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 1" # extras to let PN build its documentation of new releases
+PhyloNetworks = "0.16, 0.17.0, 1.0.0" # extras to let PN build its documentation of new releases
 RCall = "0.11, 0.12, 0.13"
 julia = "0.7, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7"
 

src/PhyloPlots.jl

@@ -4,7 +4,6 @@ module PhyloPlots
 
 # standard libraries
 using DataFrames: _broadcast_unalias_helper, LatexTableFormat
-using PhyloNetworks: getMinorParent, getParent, getChildren, getMajorParentEdge, getChild, Edge, getMinorParentEdge
 using Markdown
 using Printf: @printf, @sprintf
 

src/phylonetworksPlots.jl

@@ -75,8 +75,9 @@ function edgenode_coordinates(net::HybridNetwork, useedgelength::Bool, useSimple
     while !isempty(cladewise_queue)
         cur_edge = pop!(cladewise_queue); # deliberate choice over shift! for cladewise order
         # increment spacing and add to node_y if leaf
-        if getChild(cur_edge).leaf
-            ni = findfirst(x->x===getChild(cur_edge), net.node)
+        cur_child = getchild(cur_edge)
+        if cur_child.leaf
+            ni = findfirst(x->x===cur_child, net.node)
             node_y[ni]  = nexty
             node_yB[ni] = nexty
             node_yE[ni] = nexty
@@ -92,8 +93,8 @@ function edgenode_coordinates(net::HybridNetwork, useedgelength::Bool, useSimple
 
         # push children edges if this is a major edge:
         if cur_edge.isMajor
-            for e in getChild(cur_edge).edge
-                if getParent(e) === getChild(cur_edge)# don't go backwards
+            for e in cur_child.edge
+                if getparent(e) === cur_child # don't go backwards
                     push!(cladewise_queue, e)
                 end
             end
@@ -109,11 +110,11 @@ function edgenode_coordinates(net::HybridNetwork, useedgelength::Bool, useSimple
         minor_yB  = ymax; minor_yE  = ymin;
         nomajorchild=useSimpleHybridLines # only use this var if using simple hybrid lines
         for e in nn.edge
-            if nn == PhyloNetworks.getParent(e) # if e = child of node
+            if nn == getparent(e) # if e = child of node
                 if useSimpleHybridLines
                     # old simple hybrid lines
                     if e.isMajor || nomajorchild
-                        cc = PhyloNetworks.getChild(e)
+                        cc = getchild(e)
                         yy = node_y[findfirst(x -> x===cc, net.node)]
                         yy!==nothing || error("oops, child $(cc.number) has not been visited before node $(nn.number).")
                     end
@@ -128,7 +129,7 @@ function edgenode_coordinates(net::HybridNetwork, useedgelength::Bool, useSimple
                 else
                     # new pretty hybrid lines
                     if e.isMajor
-                        cc = PhyloNetworks.getChild(e)
+                        cc = getchild(e)
                         child_y = node_y[findfirst(x -> x===cc, net.node)]
                         child_y!==nothing || error("oops, child $(cc.number) has not been visited before node $(nn.number).")
                     else
@@ -183,7 +184,7 @@ function edgenode_coordinates(net::HybridNetwork, useedgelength::Bool, useSimple
             for e in net.nodes_changed[i].edge # loop over children only
                 if net.nodes_changed[i] == (e.isChild1 ? e.node[2] : e.node[1])
                     node_age[ni] = max(node_age[ni], 1 +
-                     node_age[findfirst(x -> x=== PhyloNetworks.getChild(e), net.node)])
+                     node_age[findfirst(x -> x=== getchild(e), net.node)])
                 end
             end
         end
@@ -211,7 +212,7 @@ function edgenode_coordinates(net::HybridNetwork, useedgelength::Bool, useSimple
         end
         ei !== nothing || error("oops, could not find major parent edge of node number $ni.")
         edge_yB[ei] = node_y[ni]
-        pni = findfirst(x -> x===PhyloNetworks.getParent(net.edge[ei]), net.node) # parent node index
+        pni = findfirst(x -> x===getparent(net.edge[ei]), net.node) # parent node index
         edge_xB[ei] = node_x[pni]
         if elenCalculate
             elen[ei] = node_age[pni] - node_age[ni]
@@ -230,8 +231,8 @@ function edgenode_coordinates(net::HybridNetwork, useedgelength::Bool, useSimple
     for i=1:net.numEdges
         if !net.edge[i].isMajor # minor hybrid edges
             # indices of child and parent nodes
-            cni = findfirst(x -> x===PhyloNetworks.getChild( net.edge[i]), net.node)
-            pni = findfirst(x -> x===PhyloNetworks.getParent(net.edge[i]), net.node)
+            cni = findfirst(x -> x===getchild( net.edge[i]), net.node)
+            pni = findfirst(x -> x===getparent(net.edge[i]), net.node)
 
             edge_xB[i] = node_x[pni]
             edge_xE[i] = useSimpleHybridLines ? edge_xB[i] : (useedgelength ? edge_xB[i] + elen[i] : node_x[cni])