Merge pull request #23 from EcoJulia/rr/metadata

Filling in metadata

.JuliaFormatter.toml

@@ -0,0 +1,10 @@
+style = "sciml"
+margin = 80
+remove_extra_newlines = true
+always_use_return = true
+trailing_comma = false
+join_lines_based_on_source = true
+yas_style_nesting = true
+always_for_in = true
+annotate_untyped_fields_with_any = true
+normalize_line_endings = "unix"

.github/dependabot.yaml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/CompatHelper.yml → .github/workflows/CompatHelper.yaml

@@ -19,7 +19,7 @@ jobs:
         os:
           - ubuntu-latest
     steps:
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.julia-version }}
           arch: ${{ matrix.arch }}
@@ -28,7 +28,7 @@ jobs:
           import Pkg
           name = "CompatHelper"
           uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
-          version = "2"
+          version = "3"
           Pkg.add(; name, uuid, version)
         shell: julia --color=yes {0}
       - name: "Run CompatHelper"
@@ -38,3 +38,4 @@ jobs:
         shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/TagBot.yaml

@@ -0,0 +1,31 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: "3"
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+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 }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/metadata.yaml

@@ -0,0 +1,38 @@
+name: Metadata and hygene
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - 'v*'
+  pull_request:
+  workflow_dispatch:
+
+permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+  actions: write
+  contents: read
+
+jobs:
+  metadata:
+    name: RSMD - ${{ github.event_name }}
+    timeout-minutes: 60
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up julia
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+          arch: x64
+      - name: Cache
+        uses: julia-actions/cache@v2
+      - name: Build package
+        uses: julia-actions/julia-buildpkg@v1
+      - name: Running
+        uses: julia-actions/julia-runtest@v1
+        env:
+          RSMD_CROSSWALK: TRUE

.github/workflows/nightly.yml → .github/workflows/nightly.yaml

@@ -1,27 +1,26 @@
 name: JuliaNightly
 # Nightly Scheduled Julia Nightly Run
+
 on:
-  push:
-    branches:
-      - main
-    tags:
-      - 'v*'
   schedule:
     - cron: '0 2 * * 0'  # Weekly at 2 AM UTC Sunday
+  workflow_dispatch:
 
 jobs:
   test:
     name: Julia Nightly - Ubuntu - x64
     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
+        uses: julia-actions/setup-julia@v2
         with:
           version: nightly
           arch: x64
       - name: Build package
-        uses: julia-actions/julia-buildpkg@latest
+        uses: julia-actions/julia-buildpkg@v1
+        with:
+          ignore-no-cache: true
       - name: Run tests
-        uses: julia-actions/julia-runtest@latest
+        uses: julia-actions/julia-runtest@v1

.github/workflows/testing.yaml

@@ -0,0 +1,69 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - 'v*'
+  pull_request:
+
+permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+  actions: write
+  contents: read
+
+jobs:
+  Diversity-tests:
+    name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    timeout-minutes: 60
+    runs-on: ${{ matrix.os }}
+    continue-on-error: false
+    strategy:
+      matrix:
+        julia-version:
+          - '1.6'
+          - '1.8'
+          - '1'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+          - arm64
+        exclude:
+          - os: macOS-latest
+            julia-version: '1.6'
+            arch: arm64
+          - os: macOS-latest
+            julia-version: '1.8'
+            arch: arm64
+          - os: macOS-latest
+            julia-version: '1'
+            arch: x64
+          - os: ubuntu-latest
+            arch: arm64
+          - os: windows-latest
+            arch: arm64
+      fail-fast: false
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+    - name: Set up julia
+      uses: julia-actions/setup-julia@v2
+      with:
+        version: ${{ matrix.julia-version }}
+        arch: ${{ matrix.arch }}
+    - name: Cache
+      uses: julia-actions/cache@v2
+    - 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@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true

.gitignore

@@ -3,3 +3,4 @@
 *.jl.mem
 .DS_Store
 Manifest.toml
+.vscode/settings.json

.zenodo.json

@@ -1,30 +1,41 @@
 {
-    "title": "EcoBase.jl - A package implementing an abstract interface to data types used in ecological analyses",
-    "description": "This package implements an abstract interface to data types used in ecological analyses in Julia",
+    "title": "EcoBase.jl",
     "upload_type": "software",
     "creators": [
         {
-            "affiliation": "GLOBE Institute, University of Copenhagen",
-            "name": "Borregaard, Michael Krabbe",
-            "orcid": "0000-0002-8146-8435"
+            "name": "Borregaard, Michael",
+            "orcid": "0000-0002-8146-8435",
+            "affiliation": "University of Copenhagen",
+            "ror": "035b05819"
         },
         {
-            "affiliation": "University of Glasgow",
             "name": "Reeve, Richard",
-            "orcid": "0000-0003-2589-8091"
+            "orcid": "0000-0003-2589-8091",
+            "affiliation": "University of Glasgow",
+            "ror": "00vtgdb53"
+        },
+        {
+            "name": "Bonham, Kevin",
+            "orcid": "0000-0003-3200-7533",
+            "affiliation": "Wellesley College",
+            "ror": "01srpnj69"
         }
     ],
     "access_right": "open",
-    "license": "mit-license",
+    "license": "MIT",
     "related_identifiers": [
         {
             "scheme": "url",
             "identifier": "https://github.com/EcoJulia/EcoBase.jl",
-            "relation": "isIdenticalTo"
+            "relation": "isOriginalFormOf"
         }
     ],
     "keywords": [
+        "EcoJulia",
+        "biology",
+        "ecology",
+        "geography",
         "julia",
-        "ecology"
+        "macroecology"
     ]
 }

LICENSE

@@ -1,21 +1,9 @@
 MIT License
 
-Copyright (c) 2018-2021: Michael K. Borregaard, Richard Reeve and EcoJulia
+Copyright (c) 2018-2024 Michael Borregaard, Richard Reeve and Kevin Bonham
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.