Merge pull request #3311 from PecanProject/release/v1.8.0

release v1.8.0

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,6 +14,7 @@
 - [ ] Immediately
 - [ ] Within one week
 - [ ] When possible
+
 ## Types of changes
 <!--- What types of changes does your code introduce? Put an `x` in all the boxes that apply: -->
 - [ ] Bug fix (non-breaking change which fixes an issue) <!-- please add issue number -->
@@ -24,6 +25,7 @@
 <!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
 <!--- 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 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
+#
+
+# 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

@@ -5,11 +5,11 @@ on:
     branches:
       - master
       - develop
-
     tags:
       - '*'
-
   pull_request:
+  merge_group:
+  workflow_dispatch:
 
 jobs:
   bookdown:
@@ -18,48 +18,53 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     container: 
-      image: pecan/depends:R4.0.3
+      image: pecan/depends:R4.1
 
     steps:
     # checkout source code
-    - uses: actions/checkout@v2
-    # 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: |
         mkdir -p book_source/extfiles
         cp -f documentation/tutorials/01_Demo_Basic_Run/extfiles/* book_source/extfiles
     # compile PEcAn code
-    - name: build
-      run: make -j1
+    - name: build needed modules
+      run: |
+        R CMD INSTALL base/logger
+        R CMD INSTALL base/remote
+        R CMD INSTALL base/utils
     # render book
     - name: Render Book
       run: |
         cd book_source
         Rscript -e 'options(bookdown.render.file_scope=FALSE); bookdown::render_book("index.Rmd", "bookdown::gitbook")'
     # save artifact
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
         name: pecan-documentation
         path: book_source/_book/
     # download documentation repo
     - name: Checkout documentation repo
-      if: github.event_name != 'pull_request'
-      uses: actions/checkout@v2
+      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,.*/,,' )
         cd pecan-documentation
         mkdir -p $VERSION
         rsync -a --delete ../book_source/_book/ ${VERSION}/

.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

.github/workflows/ci-weekly.yml

@@ -0,0 +1,43 @@
+name: Weekly Checks
+
+on:
+  #  every Monday at 4:30 AM
+  # (hopefully after the 1:30 AM `depends` build has completed)
+  schedule:
+    - cron: '30 4 * * 1'
+  workflow_dispatch:
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        R:
+          - "devel"
+    uses: ./.github/workflows/test.yml
+    with:
+      R-version: ${{ matrix.R }}
+    secrets: inherit
+
+  check:
+    strategy:
+      fail-fast: false
+      matrix:
+        R:
+          - "devel"
+    uses: ./.github/workflows/check.yml
+    with:
+      R-version: ${{ matrix.R }}
+      make-grouping: "check"
+    secrets: inherit
+
+  sipnet:
+    strategy:
+      fail-fast: false
+      matrix:
+        R:
+          - "devel"
+    uses: ./.github/workflows/sipnet.yml
+    with:
+      R-version: ${{ matrix.R }}
+    secrets: inherit