Merge pull request #51 from EcoJulia/rr/phylo

Fix type issues in Phylo extension
EcoJulia · Apr 15, 2024 · cf827ee · cf827ee · richardreeve · Apr 15, 2024
2 parents 8f8009c + 68db0a7
commit cf827ee
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Showing 39 changed files with 896 additions and 732 deletions.
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
@@ -18,7 +18,7 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
       - name: Set up julia
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: '1'
           arch: x64
@@ -29,10 +29,10 @@ jobs:
             Pkg.instantiate()
             Pkg.add("Phylo")
             Pkg.add("Documenter")
-        shell: julia --project=docs/ --color=yes {0}
+        shell: julia --project=docs --color=yes {0}
       - name: Build and deploy
         run: |
-          julia --project=docs/ --color=yes docs/make.jl
+          julia --project=docs --color=yes docs/make.jl
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

diff --git a/.github/workflows/nightly.yaml b/.github/workflows/nightly.yaml
@@ -1,13 +1,10 @@
 name: JuliaNightly
 # Nightly Scheduled Julia Nightly Run
+
 on:
-  push:
-    branches:
-      - dev
-    tags:
-      - 'v*'
   schedule:
     - cron: '0 2 * * 0'  # Weekly at 2 AM UTC Sunday
+  workflow_dispatch:
 
 jobs:
   test:
@@ -17,11 +14,13 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
       - name: Set up julia
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: nightly
           arch: x64
       - name: Build package
         uses: julia-actions/julia-buildpkg@v1
+        with:
+          ignore-no-cache: true
       - name: Run tests
         uses: julia-actions/julia-runtest@v1
diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml
@@ -8,8 +8,12 @@ on:
       - 'v*'
   pull_request:
 
+permissions:
+  actions: write
+  contents: read
+
 jobs:
-  diversity-tests:
+  Diversity-tests:
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.experimental }}
     strategy:
@@ -32,7 +36,7 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v4
     - name: Set up julia
-      uses: julia-actions/setup-julia@v1
+      uses: julia-actions/setup-julia@v2
       with:
         version: ${{ matrix.julia-version }}
         arch: ${{ matrix.arch }}
@@ -48,11 +52,16 @@ jobs:
         install.packages("vegan", repos="http://cran.r-project.org")
         install.packages("rdiversity", repos="http://cran.r-project.org")
       shell: R --vanilla --file={0}
+    - name: Cache
+      uses: julia-actions/cache@v1
     - name: Build package
       uses: julia-actions/julia-buildpkg@v1
     - name: Running
       uses: julia-actions/julia-runtest@v1
     - name: Process coverage
       uses: julia-actions/julia-processcoverage@v1
     - name: Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true
diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,12 @@
 # NEWS
 
+- v0.5.12
+  - Move Phylo structs into extension
+- v0.5.11
+  - Update Phylo compat
 - v0.5.10
   - Use extensions for Julia 1.9+
-  - Allow AxisArrays to name types
+  - Allow AxisArrays to name types through extension
   - Improve testing
 - v0.5.9
   - Introduce Gower

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Diversity"
 uuid = "d3d5718d-52de-57ab-b67a-eca7fd6175a4"
 author = ["Richard Reeve <Richard.Reeve@glasgow.ac.uk>", "Claire Harris", "Isaac Peetom Heida"]
-version = "0.5.11"
+version = "0.5.12"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"

diff --git a/docs/make.jl b/docs/make.jl
@@ -3,10 +3,12 @@ using Diversity
 using Phylo
 
 makedocs(modules = [Diversity,
-                    Diversity.Ecology, Diversity.Jost,
-                    Diversity.Hill,
-                    Diversity.ShortNames, Diversity.API],
+             Diversity.Ecology, Diversity.Jost,
+             Diversity.Hill,
+             Diversity.ShortNames, Diversity.API],
          sitename = "Diversity.jl")
 
 deploydocs(repo = "github.com/EcoJulia/Diversity.jl.git",
-           devbranch = "dev")
+           push_preview = true,
+           devbranch = "dev",
+           devurl = "dev")
diff --git a/ext/DiversityAxisArraysExt.jl b/ext/DiversityAxisArraysExt.jl
@@ -1,21 +1,20 @@
 module DiversityAxisArraysExt
 
 isdefined(Base, :get_extension) ? (using AxisArrays) : (using ..AxisArrays)
-using Diversity
-
-import Diversity: GeneralTypes
-function GeneralTypes(zmatrix::AM) where
-    {FP <: AbstractFloat, M <: AbstractMatrix{FP}, LR, LC, NAMES,
-     T <: Tuple{Axis{LR, NAMES}, Axis{LC, NAMES}},
-     AM <: AxisMatrix{FP, M, T}}
+import Diversity
 
+function Diversity.GeneralTypes(zmatrix::AM) where
+         {FP <: AbstractFloat, M <: AbstractMatrix{FP}, LR, LC, NAMES,
+          T <: Tuple{Axis{LR, NAMES}, Axis{LC, NAMES}},
+          AM <: AxisMatrix{FP, M, T}}
     size(zmatrix, 1) == size(zmatrix, 2) ||
-    throw(DimensionMismatch("Similarity matrix is not square"))
+        throw(DimensionMismatch("Similarity matrix is not square"))
 
     AxisArrays.axes(zmatrix, 1).val == AxisArrays.axes(zmatrix, 2).val ||
-    throw(DimensionMismatch("Similarity matrix does not have matching row and column labels"))
+        throw(DimensionMismatch("Similarity matrix does not have matching row and column labels"))
 
-    return GeneralTypes(zmatrix, collect(AxisArrays.axes(zmatrix, 1).val))
+    return Diversity.GeneralTypes(zmatrix,
+                                  collect(AxisArrays.axes(zmatrix, 1).val))
 end
 
 end
diff --git a/ext/DiversityPhyloExt.jl b/ext/DiversityPhyloExt.jl
@@ -1,83 +1,97 @@
 module DiversityPhyloExt
 
 isdefined(Base, :get_extension) ? (using Phylo) : (using ..Phylo)
-import Diversity: AbstractPhyloTypes
-import Diversity: PhyloBranches
-using Diversity
+import Diversity
 using Diversity.API
 using Statistics
+using Diversity: AbstractPhyloTypes
 
-import Diversity.API: _addedoutputcols
-function _addedoutputcols(::AbstractPhyloTypes{TS}) where
-    {LABEL, RT, NL, N, B, TS <: TreeSet{LABEL, RT, NL, N, B, <: AbstractTree}}
-    return Dict{Symbol, Type}(:treename => LABEL)
-end
+struct PhyloBranches{Tree <: AbstractTree} <: Diversity.PhyloBranches{Tree}
+    tree::Tree
+    nleaf::Int64
+    nancestral::Int64
+    leafnames::Vector{String}
+    ancestralnames::Vector{String}
+    ancestralmatrix::Matrix{Float64}
+    Zmatrix::Matrix{Float64}
 
-import Diversity.API: _getaddedoutput
-function _getaddedoutput(pt::AbstractPhyloTypes{TS}) where
-    {LABEL, RT, NL, N, B, TS <: TreeSet{LABEL, RT, NL, N, B, <: AbstractTree}}
-    return Dict{Symbol, LABEL}(:treename => first(gettreenames(pt.tree)))
-end
+    function PhyloBranches(tree::Tree) where {Tree <: AbstractTree}
+        leafnames = [getnodename(tree, node)
+                     for node in traversal(tree, preorder)
+                     if isleaf(tree, node)]
+        nleaf = length(leafnames)
+        nleaf > 0 || error("Too few species")
+        leafinfo = Dict{String, Float64}()
+        speciesinfo = Dict{String, Tuple{String, String, Float64}}()
+        ancestralnames = String[]
 
-function PhyloBranches(tree::Tree) where Tree <: AbstractTree
-    leafnames = [getnodename(tree, node)
-                 for node in traversal(tree, preorder) if isleaf(tree, node)]
-    nleaf = length(leafnames)
-    nleaf > 0 || error("Too few species")
-    leafinfo = Dict{String, Float64}()
-    speciesinfo = Dict{String, Tuple{String, String, Float64}}()
-    ancestralnames = String[]
-
-    for leaf in leafnames
-        branches = branchhistory(tree, leaf)
-        leafinfo["$leaf"] = heighttoroot(tree, leaf)
-        for branch in branches
-            branchname = getbranchname(tree, branch)
-            name = "$leaf : $branchname"
-            push!(ancestralnames, name)
-            speciesinfo[name] =
-                tuple("$leaf", "$branchname",
-                      getlength(tree, branch) / leafinfo["$leaf"])
+        for leaf in leafnames
+            branches = branchhistory(tree, leaf)
+            leafinfo["$leaf"] = heighttoroot(tree, leaf)
+            for branch in branches
+                branchname = getbranchname(tree, branch)
+                name = "$leaf : $branchname"
+                push!(ancestralnames, name)
+                speciesinfo[name] = tuple("$leaf", "$branchname",
+                                          getlength(tree, branch) /
+                                          leafinfo["$leaf"])
+            end
         end
-    end
 
-    nancestral = length(ancestralnames)
-    Lbar = Statistics.mean(collect(values(leafinfo)))
-    ancestralmatrix = Matrix{Float64}(undef, nancestral, nleaf)
-    fill!(ancestralmatrix, 0.0)    
-    for i in 1:nancestral
-        for j in 1:nleaf
-            if speciesinfo[ancestralnames[i]][1] == leafnames[j]
-                ancestralmatrix[i, j] =
-                    speciesinfo[ancestralnames[i]][3] * leafinfo[leafnames[j]]
+        nancestral = length(ancestralnames)
+        Lbar = Statistics.mean(collect(values(leafinfo)))
+        ancestralmatrix = Matrix{Float64}(undef, nancestral, nleaf)
+        fill!(ancestralmatrix, 0.0)
+        for i in 1:nancestral
+            for j in 1:nleaf
+                if speciesinfo[ancestralnames[i]][1] == leafnames[j]
+                    ancestralmatrix[i, j] = speciesinfo[ancestralnames[i]][3] *
+                                            leafinfo[leafnames[j]]
+                end
             end
         end
-    end
-
-    Zmatrix = Matrix{Float64}(undef, nancestral, nancestral)
-    fill!(Zmatrix, 0.0)
-    for i in 1:nancestral
-        for j in 1:nancestral
-            if haskey(speciesinfo,
-                      "$(speciesinfo[ancestralnames[j]][1]) : " *
-                      "$(speciesinfo[ancestralnames[i]][2])")
-                Zmatrix[i, j] = 1.0 /
-                    leafinfo[speciesinfo[ancestralnames[j]][1]]
+
+        Zmatrix = Matrix{Float64}(undef, nancestral, nancestral)
+        fill!(Zmatrix, 0.0)
+        for i in 1:nancestral
+            for j in 1:nancestral
+                if haskey(speciesinfo,
+                          "$(speciesinfo[ancestralnames[j]][1]) : " *
+                          "$(speciesinfo[ancestralnames[i]][2])")
+                    Zmatrix[i, j] = 1.0 /
+                                    leafinfo[speciesinfo[ancestralnames[j]][1]]
+                end
             end
         end
+
+        return new{Tree}(tree, nleaf, nancestral, leafnames,
+                         ancestralnames, ancestralmatrix, Zmatrix)
+    end
+
+    function PhyloBranches(treeset::TS) where {TS <: TreeSet}
+        ntrees(treeset) == 1 ||
+            error("Can currently only handle one tree in a PhyloSet")
+        pt = PhyloBranches(first(treeset))
+        return new{TS}(treeset, pt.nleaf, pt.nancestral,
+                       pt.leafnames, pt.ancestralnames,
+                       pt.ancestralmatrix, pt.Zmatrix)
     end
-
-    return PhyloBranches{Tree}(tree, nleaf, nancestral, leafnames,
-                               ancestralnames, ancestralmatrix, Zmatrix)
 end
 
-function PhyloBranches(treeset::TS) where TS <: TreeSet
-    ntrees(treeset) == 1 ||
-        error("Can currently only handle one tree in a PhyloSet")
-    pt = PhyloBranches(first(treeset))
-    return PhyloBranches{TS}(treeset, pt.nleaf, pt.nancestral,
-                             pt.leafnames, pt.ancestralnames,
-                             pt.ancestralmatrix, pt.Zmatrix)
+Diversity.PhyloBranches(args...) = PhyloBranches(args...)
+
+import Diversity.API: _addedoutputcols
+function _addedoutputcols(::AbstractPhyloTypes{TS}) where
+         {LABEL, RT, NL, N, B,
+          TS <: TreeSet{LABEL, RT, NL, N, B, <:AbstractTree}}
+    return Dict{Symbol, Type}(:treename => LABEL)
+end
+
+import Diversity.API: _getaddedoutput
+function _getaddedoutput(pt::AbstractPhyloTypes{TS}) where
+         {LABEL, RT, NL, N, B,
+          TS <: TreeSet{LABEL, RT, NL, N, B, <:AbstractTree}}
+    return Dict{Symbol, LABEL}(:treename => first(gettreenames(pt.tree)))
 end
 
 import Diversity.API: _gettypenames
@@ -92,7 +106,7 @@ end
 
 import Diversity.API: _calcabundance
 function _calcabundance(phy::PhyloBranches,
-                        raw::AbstractMatrix{<: AbstractFloat})
+                        raw::AbstractMatrix{<:AbstractFloat})
     processed = phy.ancestralmatrix * raw
     scale = sum(processed)
     processed ./= scale
@@ -106,7 +120,7 @@ end
 
 import Diversity.API: _calcordinariness
 function _calcordinariness(phy::PhyloBranches,
-                           processed::AbstractMatrix{<: AbstractFloat},
+                           processed::AbstractMatrix{<:AbstractFloat},
                            scale::Real)
     return (phy.Zmatrix * processed) .* scale
 end