Merge pull request #86 from EcoJulia/rr/fixes

- Update package to Julia extensions dependencies - Update workflows - Improve testing - Fix doc errors - Fix missing exports
EcoJulia · Nov 25, 2023 · 505323a · 505323a · richardreeve · Nov 25, 2023
2 parents d559533 + c964e54
commit 505323a
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diff --git a/.github/workflows/doc-cleanup.yaml b/.github/workflows/doc-cleanup.yaml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
       - name: Delete preview and history + push changes

diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Set up julia
         uses: julia-actions/setup-julia@v1
         with:

diff --git a/.github/workflows/nightly.yaml b/.github/workflows/nightly.yaml
@@ -15,13 +15,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Set up julia
         uses: julia-actions/setup-julia@v1
         with:
           version: nightly
           arch: x64
       - name: Build package
-        uses: julia-actions/julia-buildpkg@latest
+        uses: julia-actions/julia-buildpkg@v1
       - name: Run tests
-        uses: julia-actions/julia-runtest@latest
+        uses: julia-actions/julia-runtest@v1
diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml
@@ -30,7 +30,7 @@ jobs:
       fail-fast: false
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Set up julia
       uses: julia-actions/setup-julia@v1
       with:
@@ -47,15 +47,10 @@ jobs:
         install.packages("ape", repos="http://cran.r-project.org")
       shell: R --vanilla --file={0}
     - name: Build package
-      uses: julia-actions/julia-buildpkg@master
+      uses: julia-actions/julia-buildpkg@v1
     - name: Running
-      uses: julia-actions/julia-runtest@master
+      uses: julia-actions/julia-runtest@v1
     - name: Process coverage
       uses: julia-actions/julia-processcoverage@v1
-    - name: Coveralls
-      uses: coverallsapp/github-action@master
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        path-to-lcov: ./lcov.info
     - name: Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,4 @@
 *.jl.mem
 /Manifest.toml
 test/Manifest.toml
+docs/Manifest.toml
diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,7 @@
 # NEWS
 
+- v0.4.24
+  - Fix workflows
 - v0.4.23
   - Fix type warnings
 - v0.4.22

diff --git a/Project.toml b/Project.toml
@@ -1,15 +1,16 @@
 name = "Phylo"
 uuid = "aea672f4-3940-5932-aa44-993d1c3ff149"
 author = ["Richard Reeve <Richard.Reeve@glasgow.ac.uk>"]
-version = "0.4.23"
+version = "0.4.24"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-IterableTables = "1c8ee90f-4401-5389-894e-7a04a3dc0f4d"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+IterableTables = "1c8ee90f-4401-5389-894e-7a04a3dc0f4d"
 Missings = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -20,17 +21,40 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Tokenize = "0796e94c-ce3b-5d07-9a54-7f471281c624"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
+[weakdeps]
+RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
+Requires = "ae029012-a4dd-5104-9daa-d747884805df"
+
+[extensions]
+PhyloRCallExt = "RCall"
+
 [compat]
 AxisArrays = "0.4"
-DataFrames = "^1"
+DataFrames = "1"
 DataStructures = "0.17, 0.18"
+Distances = "0.10"
 Distributions = "0.24, 0.25"
-IterableTables = "^1"
-Graphs = "^1"
-Missings = "^1"
-RecipesBase = "^1"
-Requires = "^1"
+Graphs = "1"
+IterableTables = "1"
+Missings = "1"
+Plots = "1"
+Printf = "1"
+RCall = "0.13"
+Random = "1"
+RecipesBase = "1"
+Requires = "1"
 SimpleTraits = "0.9"
+Statistics = "1"
+Test = "1"
 Tokenize = "0.5"
-Unitful = "^1"
-julia = "^1"
+Unitful = "1"
+julia = "1"
+
+[extras]
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["DataFrames", "Plots", "RCall", "Test"]
diff --git a/docs/make.jl b/docs/make.jl
@@ -3,25 +3,22 @@ using Phylo
 
 makedocs(modules = [Phylo, Phylo.API],
          sitename = "Phylo.jl", 
-         pages = [
-             "Home" => "index.md",
-             "Tutorial / Quick start" => "tutorial.md",
-             "Manual" => Any[
-                 "Phylogeny data types" => "man/treetypes.md",
-                 "Creating phylogenies" => "man/input.md",
-                 "Manipulating and building phylogenies" => "man/manipulating.md",
-                 "Traversal and iterators" => "man/traversal.md",
-                 "Getting phylogeny attributes" => "man/attributes.md",
-                 "Modelling traits" => "man/modelling.md",
-                 "Plotting" => "man/plotting.md"
-             ],
-             "List of functions" => "functionlist.md",
-             "API" => "api.md"
-         ])
+         pages = ["Home" => "index.md",
+                  "Tutorial / Quick start" => "tutorial.md",
+                  "Manual" => Any[
+                    "Phylogeny data types" => "man/treetypes.md",
+                    "Creating phylogenies" => "man/input.md",
+                    "Manipulating and building phylogenies" => "man/manipulating.md",
+                    "Traversal and iterators" => "man/traversal.md",
+                    "Getting phylogeny attributes" => "man/attributes.md",
+                    "Modelling traits" => "man/modelling.md",
+                    "Plotting" => "man/plotting.md"
+                  ],
+                  "List of functions" => "functionlist.md",
+                  "API" => "api.md"];
+         format = Documenter.HTML(size_threshold_ignore = ["man/plotting.md",
+                                                           "man/input.md"]))
 
 deploydocs(repo = "github.com/EcoJulia/Phylo.jl.git",
            devbranch = "dev",
-           deps = Deps.pip("pygments",
-                           "mkdocs",
-                           "mkdocs-material",
-                           "python-markdown-math"))
+           push_preview = true)
diff --git a/docs/src/api.md b/docs/src/api.md
@@ -9,13 +9,13 @@ Providing additional code to extend the functionality of the system is simple:
 
 ```julia
 using Phylo
-importall Phylo.API
 
-type SimplestTree <: AbstractTree{Int, Int}
+struct SimplestTree <: AbstractTree{Int, Int}
     nodes::OrderedDict{Int, BinaryNode{Int}}
     branches::Dict{Int, Branch{Int}}
 end
 
+import Phylo.API: _addnode!
 function _addnode!(tree::SimplestTree, num)
     _setnode!(tree, num, BinaryNode{Int}())
     return num
@@ -31,7 +31,6 @@ implementations.
 
 ```@autodocs
 Modules = [Phylo.API]
-Private = false
 ```
 
 ```@index

diff --git a/docs/src/functionlist.md b/docs/src/functionlist.md
@@ -1,3 +1,4 @@
+# Function list
 
 ```@index
 ```
diff --git a/docs/src/man/attributes.md b/docs/src/man/attributes.md
@@ -1,40 +1,72 @@
 # Getting tree attributes
 
-### Methods on TreeSets
+## Methods on TreeSets
+
 ```@docs
 ntrees
+gettree
 gettrees
 nroots
 getroots
 gettreenames
 ```
 
-### Methods on Trees
+## Methods on Trees
+
 ```@docs
 mrca
 nodeheights
 getleafnames
 getleaves
 nleaves
 nnodes
+ninternal
 nbranches
 distance
 distances
 heighttoroot
 heightstoroot
+getroot
+treenametype
+gettreename
+roottype
+nodetype
+nodedatatype
+nodenametype
+branchtype
+branchdatatype
+branchnametype
+getnodenames
+getnodename
+hasnode
+getnode
+getnodes
+getinternalnodes
+getbranchnames
+getbranchname
+hasbranch
+getbranch
+getbranches
+gettreeinfo
+validate!
+branchdims
+treetype
 ```
 
-### Methods on Nodes
+## Methods on Nodes
+
 ```@docs
 isleaf
 isroot
 isinternal
 isunattached
+degree
 indegree
 outdegree
 hasinbound
 getinbound
 getoutbounds
+getconnections
 hasoutboundspace
 hasinboundspace
 getleafinfo
@@ -49,46 +81,21 @@ getparent
 getancestors
 getchildren
 getdescendants
+getsiblings
 ```
 
-### Methods on Branches
+## Methods on Branches
+
 ```@docs
 src
 dst
+conn
+conns
+haslength
 getlength
 hasrootheight
 getrootheight
 setrootheight!
 getbranchdata
 setbranchdata!
 ```
-
-
-
-```@docs
-getroot
-treenametype
-gettreename
-roottype
-nodetype
-nodedatatype
-nodenametype
-branchtype
-branchdatatype
-branchnametype
-
-getnodenames
-getnodename
-hasnode
-getnode
-getnodes
-getbranchnames
-getbranchname
-hasbranch
-getbranch
-getbranches
-validate!
-branchdims
-```
-
-