Release/v1.9.0

.github/PULL_REQUEST_TEMPLATE.md

@@ -26,6 +26,9 @@
 <!--- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
 - [ ] My change requires a change to the documentation.
 - [ ] My name is in the list of CITATION.cff
+- [ ] I agree that PEcAn Project may distribute my contribution under any or all of
+	- the same license as the existing code,
+	- and/or the BSD 3-clause license.
 - [ ] I have updated the CHANGELOG.md.
 - [ ] I have updated the documentation accordingly.
 - [ ] I have read the **CONTRIBUTING** document.

.github/labeler.yml

@@ -1,57 +1,57 @@
 #
-# Add project labels
-#
-
-# Add 'Documentation' label to any changes in the documentation
+# Add project labels to PRs
+# Invocation is done by .github/workflows/prlabeler.yml
 
+# changes in the documentation
 'Documentation':
-  - book_source/**
-  - documentation/**
-  - CONTRIBUTING.md
-  - DEBUGING.md
-  - DEV-INTRO.md
-  - README.md
+- changed-files:
+  - any-glob-to-any-file: 'book_source/**'
+  - any-glob-to-any-file: 'documentation/**'
+  - any-glob-to-any-file: 'CONTRIBUTING.md'
+  - any-glob-to-any-file: 'DEBUGING.md'
+  - any-glob-to-any-file: 'DEV-INTRO.md'
+  - any-glob-to-any-file: 'README.md'
 
 # Add 'Dockerfile' label to any changes in the docker directory
 'Dockerfile':
-  - docker/**
+- changed-files:
+  - any-glob-to-any-file: 'docker/**'
 
 
 # Add 'Website' label to any changes in the web directory
-
 'Website':
-  - web/**
+- changed-files:
+  - any-glob-to-any-file: 'web/**'
 
 # Add 'Base' label to any changes in the base directory
-
 'Base':
-  - base/**
+- changed-files:
+  - any-glob-to-any-file: 'base/**'
 
 # Add 'Models' label to any changes in the models directory
-
 'Models':
-  - models/**
+- changed-files:
+  - any-glob-to-any-file: 'models/**'
 
 # Add 'Modules' label to any changes in the modules directory
-
 'Modules':
-  - modules/**
+- changed-files:
+  - any-glob-to-any-file: 'modules/**'
 
 # Add 'GitHub Actions' label to any changes in the .github/workflows directory
-
 'GitHub Actions':
-  - .github/workflows/**
+- changed-files:
+  - any-glob-to-any-file: '.github/workflows/**'
 
 # Add 'Scripts' label to any changes in the scripts directory
 
 'Scripts':
-  - scripts/**
+- changed-files:
+  - any-glob-to-any-file: 'scripts/**'
 
 # Add 'Tests' label to any changes in the tests directory
-
 'Tests':
-  - tests/**
-  - '**/tests/**'
-  - '!**/tests/Rcheck_reference.log'
-
-
+- all:
+  - changed-files:
+    - any-glob-to-any-file: ['tests/**', '**/tests/**']
+    - any-glob-to-any-file: '!**/tests/Rcheck_reference.log'

.github/workflows/book.yml

@@ -3,7 +3,7 @@ name: renderbook
 on:
   push:
     branches:
-      - master
+      - main
       - develop
     tags:
       - '*'
@@ -18,7 +18,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     container: 
-      image: pecan/depends:R4.1
+      image: pecan/depends:develop
 
     steps:
     # checkout source code
@@ -46,13 +46,22 @@ jobs:
         cd book_source
         Rscript -e 'options(bookdown.render.file_scope=FALSE); bookdown::render_book("index.Rmd", "bookdown::gitbook")'
     # save artifact
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: pecan-documentation
         path: book_source/_book/
+    # check if documentation repo exists
+    - name: Check if documentation repo exists
+      id: doc_exists
+      run: |
+        if git ls-remote https://github.com/${{ github.repository_owner }}/pecan-documentation.git > /dev/null 2>&1; then
+          echo "exists=true" >> $GITHUB_OUTPUT
+        else
+          echo "exists=false" >> $GITHUB_OUTPUT
+        fi
     # download documentation repo
     - name: Checkout documentation repo
-      if: github.event_name == 'push'
+      if: ${{ github.event_name == 'push' && steps.doc_exists.outputs.exists == 'true' }}
       uses: actions/checkout@v4
       with:
         repository: ${{ github.repository_owner }}/pecan-documentation
@@ -65,9 +74,12 @@ jobs:
         git config --global user.email "[email protected]"
         git config --global user.name "GitHub Documentation Robot"
         export VERSION=$(echo $GITHUB_REF | sed 's,.*/,,' )
+        if [ "$VERSION" = "main" ]; then
+          export VERSION=latest
+        fi
         cd pecan-documentation
         mkdir -p $VERSION
         rsync -a --delete ../book_source/_book/ ${VERSION}/
         git add --all *
         git commit -m "Build book from pecan revision ${GITHUB_SHA}" || true
-        git push -q origin master
+        git push -q origin main

.github/workflows/check.yml

@@ -32,7 +32,7 @@ jobs:
       _R_CHECK_SYSTEM_CLOCK_: 0
 
     container: 
-      image: pecan/depends:R${{ inputs.R-version }}
+      image: pecan/depends:develop-R${{ inputs.R-version }}
 
     steps:
     # checkout source code

.github/workflows/ci-weekly.yml

@@ -13,6 +13,8 @@ jobs:
       fail-fast: false
       matrix:
         R:
+          - "4.1"
+          - "4.3"
           - "devel"
     uses: ./.github/workflows/test.yml
     with:
@@ -24,6 +26,8 @@ jobs:
       fail-fast: false
       matrix:
         R:
+          - "4.1"
+          - "4.3"
           - "devel"
     uses: ./.github/workflows/check.yml
     with:
@@ -36,6 +40,8 @@ jobs:
       fail-fast: false
       matrix:
         R:
+          - "4.1"
+          - "4.3"
           - "devel"
     uses: ./.github/workflows/sipnet.yml
     with:

.github/workflows/ci.yml

@@ -3,11 +3,10 @@ name: CI
 on:
   push:
     branches:
-      - master
+      - main
       - develop
-
     tags:
-      - '*'
+      - "v*.*.*"
   pull_request:
   merge_group:
   issue_comment:
@@ -29,8 +28,8 @@ jobs:
       fail-fast: false
       matrix:
         R:
+          - "4.4"
           - "4.2"
-          - "4.1"
     uses: ./.github/workflows/test.yml
     with:
       R-version: ${{ matrix.R }}
@@ -43,8 +42,8 @@ jobs:
       matrix:
         package: [check_base, check_modules, check_models]
         R:
+          - "4.4"
           - "4.2"
-          - "4.1"
     uses: ./.github/workflows/check.yml
     with:
       R-version: ${{ matrix.R }}
@@ -57,8 +56,8 @@ jobs:
       fail-fast: false
       matrix:
         R:
+          - "4.4"
           - "4.2"
-          - "4.1"
     uses: ./.github/workflows/sipnet.yml
     with:
       R-version: ${{ matrix.R }}