Merge branch 'develop' into LPJGUESS_SDA

.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

@@ -0,0 +1,57 @@
+#
+# Add project labels to PRs
+# Invocation is done by .github/workflows/prlabeler.yml
+
+# changes in the documentation
+'Documentation':
+- 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':
+- changed-files:
+  - any-glob-to-any-file: 'docker/**'
+
+
+# Add 'Website' label to any changes in the web directory
+'Website':
+- changed-files:
+  - any-glob-to-any-file: 'web/**'
+
+# Add 'Base' label to any changes in the base directory
+'Base':
+- changed-files:
+  - any-glob-to-any-file: 'base/**'
+
+# Add 'Models' label to any changes in the models directory
+'Models':
+- changed-files:
+  - any-glob-to-any-file: 'models/**'
+
+# Add 'Modules' label to any changes in the modules directory
+'Modules':
+- changed-files:
+  - any-glob-to-any-file: 'modules/**'
+
+# Add 'GitHub Actions' label to any changes in the .github/workflows directory
+'GitHub Actions':
+- changed-files:
+  - any-glob-to-any-file: '.github/workflows/**'
+
+# Add 'Scripts' label to any changes in the scripts directory
+
+'Scripts':
+- changed-files:
+  - any-glob-to-any-file: 'scripts/**'
+
+# Add 'Tests' label to any changes in the tests directory
+'Tests':
+- all:
+  - changed-files:
+    - any-glob-to-any-file: ['tests/**', '**/tests/**']
+    - any-glob-to-any-file: '!**/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

@@ -3,15 +3,13 @@ name: renderbook
 on:
   push:
     branches:
-      - master
+      - main
       - develop
-
     tags:
       - '*'
-
   pull_request:
-
   merge_group:
+  workflow_dispatch:
 
 jobs:
   bookdown:
@@ -24,11 +22,13 @@ 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: |
@@ -52,22 +52,25 @@ jobs:
         path: book_source/_book/
     # download documentation repo
     - name: Checkout documentation repo
-      if: github.event_name != 'pull_request'
-      uses: actions/checkout@v3
+      if: github.event_name == 'push'
+      uses: actions/checkout@v4
       with:
         repository: ${{ github.repository_owner }}/pecan-documentation
         path: pecan-documentation
         token: ${{ secrets.GH_PAT }}
     # upload new documentation
     - name: publish to github
-      if: github.event_name != 'pull_request'
+      if: github.event_name == 'push'
       run: |
         git config --global user.email "[email protected]"
         git config --global user.name "GitHub Documentation Robot"
-        export VERSION=${GITHUB_REF##*/}
+        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

@@ -0,0 +1,69 @@
+name: check
+
+on:
+  workflow_call:
+    inputs:
+      R-version:
+        required: true
+        type: string
+      make-grouping:
+        required: true
+        type: string
+
+env:
+  R_LIBS_USER: /usr/local/lib/R/site-library
+  LC_ALL: en_US.UTF-8
+  NCPUS: 2
+  PGHOST: postgres
+  CI: true
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      _R_CHECK_LENGTH_1_CONDITION_: true
+      _R_CHECK_LENGTH_1_LOGIC2_: true
+      # Avoid compilation check warnings that come from the system Makevars
+      # See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html
+      _R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time
+      # Keep R checks from trying to consult the very flaky worldclockapi.com
+      _R_CHECK_SYSTEM_CLOCK_: 0
+
+    container: 
+      image: pecan/depends:R${{ inputs.R-version }}
+
+    steps:
+    # checkout source code
+    - name: work around https://github.com/actions/checkout/issues/766
+      run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
+    - uses: actions/checkout@v4
+      with:
+        set-safe-directory: false
+
+    # Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't.
+    - name: check for filenames that would confuse Make
+      run: |
+        SPACENAMES=`find . -name '* *'`
+        if [ -n "$SPACENAMES" ]; then
+          echo "::error file=${SPACENAMES}::Spaces in filename(s): ${SPACENAMES}. Please rename these files by converting spaces to underscores."
+          exit 1
+        fi
+
+    # 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 && 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
+    - name: check
+      run: make -j1 ${{ inputs.make-grouping }}
+      env:
+        REBUILD_DOCS: "FALSE"
+        RUN_TESTS: "FALSE"
+
+    - name: check for out-of-date files
+      uses: infotroph/tree-is-clean@v1