Merge 87ea575 into 26a8b5c

.github/workflows/CompatHelper.yaml

@@ -0,0 +1,37 @@
+name: CompatHelper
+
+on:
+  push:
+    branches:
+      - master
+  schedule:
+    - cron: '0 4 * * 0'  # Weekly at 4 AM GMT Sunday
+
+jobs:
+  CompatHelper:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version:
+          - '1'
+        arch:
+          - x86
+        os:
+          - ubuntu-latest
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: ${{ matrix.arch }}
+      - name: Pkg.add("CompatHelper")
+        run: |
+          julia -e '
+            using Pkg
+            Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          julia -e '
+            using CompatHelper
+            CompatHelper.main()'

.github/workflows/TagBot.yaml

@@ -0,0 +1,14 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/docs.yaml

@@ -0,0 +1,34 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - 'v*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Set up julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: x64
+      - name: Install dependencies
+        run: |
+          julia --project=docs/ -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()
+            Pkg.add("Documenter")'
+      - name: Build and deploy
+        run: |
+          julia --project=docs/ --color=yes docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/nightly.yaml

@@ -0,0 +1,21 @@
+name: JuliaNightly
+# Nightly Scheduled Julia Nightly Run
+on:
+  schedule:
+    - cron: '0 2 * * 0'  # Weekly at 2 AM UTC Sunday
+jobs:
+  test:
+    name: Julia Nightly - Ubuntu - x64
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Set up julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: nightly
+          arch: x64
+      - name: Build package
+        uses: julia-actions/julia-buildpkg@latest
+      - name: Run tests
+        uses: julia-actions/julia-runtest@latest

.github/workflows/testing.yaml

@@ -0,0 +1,68 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+      - claireh93/actions
+    tags:
+      - 'v*'
+  pull_request:
+
+jobs:
+  diversity-tests:
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
+    strategy:
+      matrix:
+        julia-version:
+          - '1.4'
+          - '1'
+          - '~1.6.0-rc1'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        R-version:
+          - 'release'
+        arch:
+          - x64
+        experimental:
+          - false
+        include:
+          - julia-version: 'nightly'
+            os: ubuntu-latest
+            R-version: 'release'
+            arch: x64
+            experimental: true
+      fail-fast: false
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+    - name: Set up julia
+      uses: julia-actions/setup-julia@v1
+      with:
+        version: ${{ matrix.julia-version }}
+        arch: ${{ matrix.arch }}
+    - name: Install R
+      if: matrix.os == 'macOS-latest'
+      uses: r-lib/actions/setup-r@master
+      with:
+        r-version: ${{ matrix.R-version }}
+    - name: Install ape
+      if: matrix.os == 'macOS-latest'
+      run: |
+        R -e 'install.packages("ape", repos="http://cran.r-project.org")'
+    - name: Build package
+      uses: julia-actions/julia-buildpkg@master
+    - name: Running
+      uses: julia-actions/julia-runtest@master
+    - 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

Project.toml

@@ -1,7 +1,7 @@
 name = "Diversity"
 uuid = "d3d5718d-52de-57ab-b67a-eca7fd6175a4"
-version = "0.5.1"
 author = ["Richard Reeve <Richard.Reeve@glasgow.ac.uk>"]
+version = "0.5.1"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
@@ -15,16 +15,16 @@ Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
-julia = "^1"
 AxisArrays = "^0.4"
-DataFrames = "^0.20"
+DataFrames = "^0.21"
 Distances = "^0.8"
 EcoBase = "^0.1"
 Missings = "^0,4"
 Phylo = "^0.4.1"
 RecipesBase = "0.6,0.7,0.8,1"
 Requires = "^1"
 StatsBase = "0.32,0.33"
+julia = "^1"
 
 [extras]
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"

docs/make.jl

@@ -3,7 +3,8 @@ using Diversity
 
 makedocs(modules = [Diversity,
                     Diversity.Ecology, Diversity.Jost, Diversity.Hill],
-         clean   = false)
+         clean   = false,
+         sitename = "Diversity.jl")
 
 deploydocs(deps = Deps.pip("pygments",
                            "mkdocs",