Pull from upstream and resolve conflicts

.github/labeler.yml

@@ -0,0 +1,57 @@
+#
+# Add project labels
+#
+
+# Add 'Documentation' label to any changes in the documentation
+
+'Documentation':
+  - book_source/**
+  - documentation/**
+  - CONTRIBUTING.md
+  - DEBUGING.md
+  - DEV-INTRO.md
+  - README.md
+
+# Add 'Dockerfile' label to any changes in the docker directory
+'Dockerfile':
+  - docker/**
+
+
+# Add 'Website' label to any changes in the web directory
+
+'Website':
+  - web/**
+
+# Add 'Base' label to any changes in the base directory
+
+'Base':
+  - base/**
+
+# Add 'Models' label to any changes in the models directory
+
+'Models':
+  - models/**
+
+# Add 'Modules' label to any changes in the modules directory
+
+'Modules':
+  - modules/**
+
+# Add 'GitHub Actions' label to any changes in the .github/workflows directory
+
+'GitHub Actions':
+  - .github/workflows/**
+
+# Add 'Scripts' label to any changes in the scripts directory
+
+'Scripts':
+  - scripts/**
+
+# Add 'Tests' label to any changes in the tests directory
+
+'Tests':
+  - tests/**
+  - '**/tests/**'
+  - '!**/tests/Rcheck_reference.log'
+
+

.github/settings.yml

@@ -0,0 +1,30 @@
+#Define the colour of labels over here
+
+labels:
+
+  - name: "Documentation"
+    color: a2dcf2
+
+  - name: "Dockerfile"
+    color: 0052CC
+
+  - name: "Website"
+    color: 84b6eb
+
+  - name: "Base"
+    color: 1ED626
+
+  - name: "Models"
+    color: C5DEF5
+
+  - name: "Modules"
+    color: FBCA04
+
+  - name: "GitHub Actions"
+    color: 84b6eb
+
+  - name: "Scripts"
+    color: 3B8924
+
+  - name: "Tests"
+    color: ff8c00

.github/workflows/book.yml

@@ -24,11 +24,13 @@ jobs:
 
     steps:
     # checkout source code
-    - uses: actions/checkout@v3
-    # install rmarkdown
-    - name: Install rmarkdown
+    - uses: actions/checkout@v4
+    # install bookdown
+    - name: Install bookdown
       run: |
-        Rscript -e 'install.packages(c("rmarkdown","bookdown"))'
+        Rscript \
+          -e 'repos <- c(getOption("repos"), sub(r"(\d{4}-\d{2}-\d{2})", "latest", getOption("repos")))' \
+          -e 'remotes::install_version("bookdown", ">= 0.31", dependencies = TRUE, upgrade = FALSE, repos = repos)'
     # copy files
     - name: copy extfiles
       run: |
@@ -53,7 +55,7 @@ jobs:
     # download documentation repo
     - name: Checkout documentation repo
       if: github.event_name == 'push'
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: ${{ github.repository_owner }}/pecan-documentation
         path: pecan-documentation

.github/workflows/ci-weekly.yml

@@ -41,7 +41,7 @@ jobs:
     # checkout source code
     - name: work around https://github.com/actions/checkout/issues/766
       run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         set-safe-directory: false
 
@@ -53,7 +53,8 @@ jobs:
     - name: check for out-of-date dependencies files
       uses: infotroph/tree-is-clean@v1
     - name: install newly-added dependencies
-      run: Rscript docker/depends/pecan.depends.R
+      working-directory: docker/depends
+      run: Rscript pecan.depends.R
 
     # initialize database
     - name: db setup
@@ -97,15 +98,15 @@ jobs:
     # checkout source code
     - name: work around https://github.com/actions/checkout/issues/766
       run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         set-safe-directory: false
 
     # install additional tools needed
     - name: install utils
       run: apt-get update && apt-get install -y postgresql-client qpdf
     - name: install new dependencies
-      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
+      run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R
 
     # run PEcAn checks
     - name: check
@@ -144,15 +145,15 @@ jobs:
     # checkout source code
     - name: work around https://github.com/actions/checkout/issues/766
       run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         set-safe-directory: false
 
     # install additional tools needed
     - name: install utils
       run: apt-get update && apt-get install -y postgresql-client qpdf
     - name: install new dependencies
-      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
+      run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R
 
     # initialize database
     - name: db setup
@@ -162,7 +163,7 @@ jobs:
 
     # install sipnet
     - name: Check out SIPNET
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: PecanProject/sipnet
         path: sipnet

.github/workflows/ci.yml

@@ -53,7 +53,7 @@ jobs:
     # checkout source code
     - name: work around https://github.com/actions/checkout/issues/766
       run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         set-safe-directory: false
 
@@ -65,7 +65,8 @@ jobs:
     - name: check for out-of-date dependencies files
       uses: infotroph/tree-is-clean@v1
     - name: install newly-added dependencies
-      run: Rscript docker/depends/pecan.depends.R
+      working-directory: docker/depends
+      run: Rscript pecan.depends.R
 
     # initialize database
     - name: db setup
@@ -111,7 +112,7 @@ jobs:
     # checkout source code
     - name: work around https://github.com/actions/checkout/issues/766
       run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         set-safe-directory: false
 
@@ -128,7 +129,7 @@ jobs:
     - name: install utils
       run: apt-get update && apt-get install -y postgresql-client qpdf
     - name: install new dependencies
-      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
+      run: Rscript scripts/generate_dependencies.R && cd docker/depends/ && Rscript pecan.depends.R
 
     # run PEcAn checks
     # The package names of base, modules, and models are passed as matrix variables to avoid repeatability of code
@@ -170,15 +171,15 @@ jobs:
     # checkout source code
     - name: work around https://github.com/actions/checkout/issues/766
       run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         set-safe-directory: false
 
     # install additional tools needed
     - name: install utils
       run: apt-get update && apt-get install -y postgresql-client qpdf
     - name: install new dependencies
-      run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R
+      run: Rscript scripts/generate_dependencies.R && cd docker/depends/ && Rscript pecan.depends.R
 
     # initialize database
     - name: db setup
@@ -188,7 +189,7 @@ jobs:
 
     # install sipnet
     - name: Check out SIPNET
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: PecanProject/sipnet
         path: sipnet

.github/workflows/depends.yml

@@ -5,6 +5,7 @@ on:
     branches:
       - develop
       - master
+  workflow_dispatch:
 
   # this runs on the develop branch
   schedule:
@@ -27,7 +28,6 @@ jobs:
       fail-fast: false
       matrix:
         R:
-          - "4.0"
           - "4.1"
           - "4.2"
           - "4.3"
@@ -36,12 +36,12 @@ jobs:
     steps:
       - name: Work around https://github.com/actions/checkout/issues/766
         run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           set-safe-directory: false
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
         with:
           driver: docker
           buildkitd-flags: --debug
@@ -50,7 +50,10 @@ jobs:
       # calculate some variables that are used later
       - name: github branch
         # build Rdevel only on Mondays, others every day (but not twice on Mondays)
-        if: (matrix.R != 'devel' && github.event.schedule == '0 0 * * *') || (matrix.R == 'devel' && github.event.schedule == '30 1 * * 1')
+        if: |
+          github.event_name == 'workflow_dispatch' ||
+          (matrix.R != 'devel' && github.event.schedule == '0 0 * * *') ||
+          (matrix.R == 'devel' && github.event.schedule == '30 1 * * 1')
         run: |
           BRANCH=${GITHUB_REF##*/}
           echo "GITHUB_BRANCH=${BRANCH}" >> $GITHUB_ENV

.github/workflows/docker.yml

@@ -41,11 +41,11 @@ jobs:
     steps:
       - name: Work around https://github.com/actions/checkout/issues/766
         run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           set-safe-directory: false
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
         with:
           driver: docker
           buildkitd-flags: --debug

.github/workflows/integration-test.yml

@@ -18,7 +18,7 @@ jobs:
 
     steps:
     - name: Checkout source code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Run tests
       run: |

.github/workflows/prlabeler.yml

@@ -0,0 +1,22 @@
+# This workflow is based on github action official label action v4.
+# This workflow action is triggered on pull request event(on both fork & inside repo)
+# Labels will be applied based on filepath modification in PR.
+# This workflow uses a regex based labeling config file(.github/labeler.yml) to take labeling decision.
+
+name: "PR Labeler"
+on:
+  - pull_request_target
+jobs:
+  label:
+    permissions:
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/labeler@v4
+        with:
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+          configuration-path: ".github/labeler.yml"
+          sync-labels: false
+          dot: true

.github/workflows/styler-actions.yml

@@ -14,7 +14,7 @@ jobs:
         run: echo '${{ steps.file_changes.outputs.files_modified }}'
       - name: work around https://github.com/actions/checkout/issues/766
         run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           set-safe-directory: false
       - uses: r-lib/actions/pr-fetch@master
@@ -51,7 +51,7 @@ jobs:
     steps:
       - name: work around https://github.com/actions/checkout/issues/766
         run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           set-safe-directory: false
       - uses: r-lib/actions/pr-fetch@v1
@@ -62,7 +62,8 @@ jobs:
       - name: install any new dependencies
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-        run: Rscript docker/depends/pecan.depends.R
+        working-directory: docker/depends
+        run: Rscript pecan.depends.R
       - id: file_changes
         uses: trilom/[email protected]
       - name : make
@@ -82,7 +83,7 @@ jobs:
         run: |
           git config --global user.email "[email protected]"
           git config --global user.name "PEcAn stylebot"
-          git add \*.Rd \*NAMESPACE Makefile.depends docker/depends/pecan.depends.R
+          git add \*.Rd \*NAMESPACE Makefile.depends docker/depends/pecan_package_dependencies.R docker/depends/pecan_deps_from_github.txt
           if [ "$(git diff --name-only --cached)" != "" ]; then  git commit -m 'automated documentation update' ; fi
       - uses: r-lib/actions/pr-push@master
         with:

Makefile

@@ -153,7 +153,8 @@ clean:
 	+ ./scripts/time.sh "roxygen2 ${1}" Rscript -e ${SETROPTIONS} \
 		-e "if (!requireNamespace('roxygen2', quietly = TRUE)" \
 		-e "    || packageVersion('roxygen2') != '7.2.3') {" \
-		-e "  devtools::install_github('r-lib/[email protected]')" \
+		-e "  cran <- c(getOption('repos'), 'cloud.r-project.org')" \
+		-e "  remotes::install_version('roxygen2', '7.2.3', repos = cran, upgrade = FALSE)" \
 		-e "}"
 	$(eval INSTALLED_ROXYGEN_VERSION := 7.2.3)
 	echo `date` > $@