Merge pull request #38 from boydorr/dev-remerge

Dev remerge

.codecov.yml

@@ -2,3 +2,8 @@
 # as relies on access to v large datasets.
 ignore:
   - "src/ClimatePref"
+coverage:
+  status:
+     project:
+       default:
+         threshold: 0.2%

.github/workflows/CompatHelper.yaml

@@ -0,0 +1,38 @@
+name: CompatHelper
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  schedule:
+    - cron: '0 4 * * *'  # Daily at 4 AM
+
+jobs:
+  CompatHelper:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version:
+          - '1.6'
+        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 +1,16 @@
+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 }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/docs.yaml

@@ -3,21 +3,34 @@ name: Documentation
 on:
   push:
     branches:
+      - main
       - dev
-    tags: '*'
-  pull_request:
+    tags:
+      - 'v*'
+  workflow_dispatch:
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Set up julia
+        uses: julia-actions/setup-julia@v1
         with:
-          version: '1.5'
+          version: '1.6'
+          arch: x64
       - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.instantiate(); Pkg.build()'
+        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:
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-        run: julia --project=docs/ docs/make.jl
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          GITHUB_EVENT_NAME: push

.github/workflows/nightly.yaml

@@ -0,0 +1,28 @@
+name: JuliaNightly
+# Nightly Scheduled Julia Nightly Run
+on:
+  push:
+    branches:
+      - main
+      - dev
+    tags:
+      - 'v*'
+  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

@@ -1,29 +1,51 @@
-name: EcoSISTEM testing
+name: CI
 
 on:
   push:
+    branches:
+      - main
+      - dev
+    tags:
+      - 'v*'
   pull_request:
 
 jobs:
   simulation-tests:
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
     strategy:
-      fail-fast: false
       matrix:
-        julia-version: ['1.4', '1.5']
-        os: [ubuntu-latest, macOS-latest, windows-latest]
+        julia-version:
+          - '1.6'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        R-version:
+          - 'release'
+        arch:
+          - x64
+        experimental:
+          - false
+      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: 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: Upload to Codecov
+    - 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

CONTRIBUTING.md

@@ -4,7 +4,6 @@ Thanks for contributing to EcoSISTEM.jl! Please read the below on how best to ma
 
 ## Pull Request Process
 
-
 1. Please branch from within boydorr/EcoSISTEM.jl
 
    - Please **don't** fork this repository to your own github.com/username or other organisation.
@@ -23,6 +22,6 @@ Thanks for contributing to EcoSISTEM.jl! Please read the below on how best to ma
 
 By contributing to this project (e.g. by submitting a pull request or providing advice on code), you agree - unless simultaneously and expressly stated otherwise - that your contribution may be included in the source code of the project and published under the following copyright licenses:
 
-[GNU GPL-3.0 (or any later version)](LICENSE.md) with a special exception to allow distribution under the [2-Clause BSD License](https://opensource.org/licenses/BSD-2-Clause) if the package as a whole is rereleased under that license.
+[GNU GPL-3.0 (or any later version)](LICENSE.md) with a special exception to allow distribution under the [2-Clause BSD License](https://opensource.org/licenses/BSD-2-Clause) if the package as a whole is rereleased under that license (such a decision can only be made by the lead developers of the package - currently Claire Harris and Richard Reeve).
 
 and that the contribution was created in whole or in part by you and you have the right to submit it under the open source license indicated above.