Release/v1.10.0

.github/labeler.yml

@@ -2,7 +2,6 @@
 # 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/**'
@@ -12,44 +11,36 @@
   - 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':
+'Web Frontend':
 - 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
-
+# TODO: scripts folder is due for a reorganization by theme;
+# update these tags when that is done
 'Scripts':
 - changed-files:
   - any-glob-to-any-file: 'scripts/**'
 
-# Add 'Tests' label to any changes in the tests directory
 'Tests':
 - all:
   - changed-files:

.github/workflows/check.yml

@@ -23,7 +23,6 @@ jobs:
 
     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
@@ -67,3 +66,11 @@ jobs:
 
     - name: check for out-of-date files
       uses: infotroph/tree-is-clean@v1
+
+    - name: check package versions
+      run: |
+        tag=$(\
+          curl -s https://api.github.com/repos/pecanproject/pecan/releases/latest \
+          | sed -n 's!.*"tag_name": "\(.*\)".*!\1!p')
+        git fetch --tags --depth=1
+        ./scripts/ensure_version_bump.sh "$tag"

.github/workflows/ci-weekly.yml

@@ -13,8 +13,8 @@ jobs:
       fail-fast: false
       matrix:
         R:
-          - "4.1"
           - "4.3"
+          - "4.5"
           - "devel"
     uses: ./.github/workflows/test.yml
     with:
@@ -26,8 +26,8 @@ jobs:
       fail-fast: false
       matrix:
         R:
-          - "4.1"
           - "4.3"
+          - "4.5"
           - "devel"
     uses: ./.github/workflows/check.yml
     with:
@@ -40,8 +40,8 @@ jobs:
       fail-fast: false
       matrix:
         R:
-          - "4.1"
           - "4.3"
+          - "4.5"
           - "devel"
     uses: ./.github/workflows/sipnet.yml
     with:

.github/workflows/docker.yml

@@ -20,18 +20,18 @@ on:
         type: choice
         default: "$DEFAULT_R_VERSION"
         options:
-          - 4.1
           - 4.2
           - 4.3
           - 4.4
+          - 4.5
           - devel
   schedule:
     # 1:30 AM UTC, different R version each day
     - cron: '30 1 * * 1' # Rdevel
-    - cron: '30 1 * * 2' # R4.4
+    - cron: '30 1 * * 2' # R4.2
     - cron: '30 1 * * 3' # R4.3
-    - cron: '30 1 * * 4' # R4.2
-    - cron: '30 1 * * 5' # R4.1
+    - cron: '30 1 * * 4' # R4.4
+    - cron: '30 1 * * 5' # R4.5
 
 jobs:
   # ----------------------------------------------------------------------
@@ -49,23 +49,33 @@ jobs:
         run: echo "R_VERSION=devel" >> "$GITHUB_OUTPUT"
       - id: tue
         if: github.event.schedule == '30 1 * * 2'
-        run: echo "R_VERSION=4.4" >> "$GITHUB_OUTPUT"
+        run: echo "R_VERSION=4.2" >> "$GITHUB_OUTPUT"
       - id: wed
         if: github.event.schedule == '30 1 * * 3'
         run: echo "R_VERSION=4.3" >> "$GITHUB_OUTPUT"
       - id: thu
         if: github.event.schedule == '30 1 * * 4'
-        run: echo "R_VERSION=4.2" >> "$GITHUB_OUTPUT"
+        run: echo "R_VERSION=4.4" >> "$GITHUB_OUTPUT"
       - id: fri
         if: github.event.schedule == '30 1 * * 5'
-        run: echo "R_VERSION=4.1" >> "$GITHUB_OUTPUT"
+        run: echo "R_VERSION=4.5" >> "$GITHUB_OUTPUT"
       - id: default
         if: github.event_name != 'schedule'
         run: echo "R_VERSION=${{ github.event.inputs.r_version || env.DEFAULT_R_VERSION }}" >> "$GITHUB_OUTPUT"
+      - id: platform
+        # upstream rocker/tidyverse image is only on ARM for R 4.5.* (so far)
+        shell: bash
+        run: |
+          if [[ "${{ join(steps.*.outputs.R_VERSION, '') }}" == "4.5" ]]; then
+            echo "PLATFORMS=linux/amd64,linux/arm64" >> "$GITHUB_OUTPUT"
+          else
+            echo "PLATFORMS=linux/amd64" >> "$GITHUB_OUTPUT"
+          fi
     outputs:
       # Note: "steps.*" seems to mean "all step ids", not "all steps"
       # If seeing weird results here, check that all steps above have an id set.
       R_VERSION: ${{ join(steps.*.outputs.R_VERSION, '') }}
+      PLATFORMS: ${{ join(steps.platform.outputs.PLATFORMS, '') }}
 
   # ----------------------------------------------------------------------
   # depends image has all the dependencies installed
@@ -80,7 +90,7 @@ jobs:
       build-context: docker/depends
       dockerfile: docker/depends/Dockerfile
       r-version: ${{ needs.rversion.outputs.R_VERSION }}
-      platforms: "linux/amd64"
+      platforms: ${{ needs.rversion.outputs.PLATFORMS }}
     secrets: inherit
 
   # ----------------------------------------------------------------------
@@ -95,7 +105,7 @@ jobs:
       dockerfile: docker/base/Dockerfile
       r-version: ${{ needs.rversion.outputs.R_VERSION }}
       parent-image: "depends"
-      platforms: "linux/amd64"
+      platforms: ${{ needs.rversion.outputs.PLATFORMS }}
     secrets: inherit
 
 # ----------------------------------------------------------------------
@@ -110,6 +120,7 @@ jobs:
       dockerfile: docker/models/Dockerfile
       r-version: ${{ needs.rversion.outputs.R_VERSION }}
       parent-image: "base"
+      platforms: ${{ needs.rversion.outputs.PLATFORMS }}
     secrets: inherit
 
 # ----------------------------------------------------------------------
@@ -131,37 +142,31 @@ jobs:
           - name: basgra
             CONTEXT: models/basgra
             DOCKERFILE: models/basgra/Dockerfile
-            PLATFORM: "linux/amd64"
             MODEL: basgra
             VERSION: BASGRA_N_v1
           - name: biocro
             CONTEXT: models/biocro
             DOCKERFILE: models/biocro/Dockerfile
-            PLATFORM: "linux/amd64"
             MODEL: biocro
             VERSION: "0.95"
           # - name: ed2_2.2.0
           #   CONTEXT: models/ed
           #   DOCKERFILE: models/ed/Dockerfile
-          #   PLATFORM: "linux/amd64"
           #   MODEL: ed2
           #   VERSION: "2.2.0"
           - name: ed2_git
             CONTEXT: models/ed
             DOCKERFILE: models/ed/Dockerfile
-            PLATFORM: "linux/amd64"
             MODEL: ed2
             VERSION: "git"
           - name: maespa
             CONTEXT: models/maespa
             DOCKERFILE: models/maespa/Dockerfile
-            PLATFORM: "linux/amd64"
             MODEL: maespa
             VERSION: "git"
           - name: sipnet
             CONTEXT: models/sipnet
             DOCKERFILE: models/sipnet/Dockerfile
-            PLATFORM: "linux/amd64"
             MODEL: sipnet
             VERSION: "git"
     uses: ./.github/workflows/docker-build-image.yml
@@ -172,7 +177,7 @@ jobs:
       r-version: ${{ needs.rversion.outputs.R_VERSION }}
       parent-image: "models"
       model-version: ${{ matrix.VERSION }}
-      platforms: ${{ matrix.PLATFORM }}
+      platforms: ${{ needs.rversion.outputs.PLATFORMS }}
     secrets: inherit
 
   # ----------------------------------------------------------------------
@@ -191,22 +196,20 @@ jobs:
           - name: docs
             CONTEXT: .
             DOCKERFILE: docker/docs/Dockerfile
-            PLATFORM: "linux/amd64"
           - name: executor
             CONTEXT: docker/executor
             DOCKERFILE: docker/executor/Dockerfile
-            PLATFORM: "linux/amd64"
           - name: api
             CONTEXT: apps/api
             DOCKERFILE: apps/api/Dockerfile
-            PLATFORM: "linux/amd64"
     uses: ./.github/workflows/docker-build-image.yml
     with:
       image-name: ${{ matrix.name }}
       build-context: ${{ matrix.CONTEXT }}
       dockerfile: ${{ matrix.DOCKERFILE }}
       r-version: ${{ needs.rversion.outputs.R_VERSION }}
-      platforms: ${{ matrix.PLATFORM }}
+      parent-image: "base"
+      platforms: ${{ needs.rversion.outputs.PLATFORMS }}
     secrets: inherit
 
   # ----------------------------------------------------------------------
@@ -229,7 +232,7 @@ jobs:
             DOCKERFILE: docker/web/Dockerfile
             PLATFORM: "linux/amd64,linux/arm64"
           - name: shiny-dbsync
-            CONTEXT: .
+            CONTEXT: shiny/dbsync
             DOCKERFILE: shiny/dbsync/Dockerfile
             PLATFORM: "linux/amd64"
           - name: data

.github/workflows/pkgdown.yml

@@ -16,15 +16,16 @@ jobs:
     runs-on: ubuntu-latest  
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      PECAN_GIT_BRANCH: ${{ github.event_name == 'pull_request' && github.base_ref || github.ref_name }}
 
     container: 
-      image: pecan/depends:develop
+      image: pecan/base:develop
 
     steps:
     # Checkout source code
     - uses: actions/checkout@v4
 
-    # Install pkgdown
+    # Install dependencies
     - name: Install dependencies
       run: Rscript -e 'install.packages("pkgdown")'
 

.github/workflows/render-quarto.yml

@@ -0,0 +1,51 @@
+name: Render Demo Notebooks
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  render-notebook:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Build PEcAn base Docker image
+        run: |
+          docker build -t pecan-base-ci:latest -f docker/base/Dockerfile .
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          version: '1.8.17'
+
+      - name: Check R code style with styler
+        run: |
+          docker run --rm -v ${{ github.workspace }}:/work pecan-base-ci:latest bash -c "Rscript -e '
+            if (!requireNamespace(\"styler\", quietly = TRUE)) install.packages(\"styler\");
+            files_to_check <- c(
+              \"/work/documentation/tutorials/Demo_1_Basic_Run/run_pecan.qmd\",
+              \"/work/documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd\"
+            );
+            unstyled <- styler::style_file(files_to_check);
+            if (is.data.frame(unstyled) && \"changed\" %in% names(unstyled) && any(unstyled\$changed == TRUE)) {
+              print(unstyled[unstyled\$changed, ]);
+              stop(\"One or more .qmd files are not styled. Please run styler::style_file() locally and commit the changes.\");
+            } else {
+              cat(\"All checked .qmd files are styled.\\n\");
+            }
+          '"
+
+      - name: Render Demo 1 notebook to HTML
+        run: |
+          docker run --rm -v ${{ github.workspace }}:/work pecan-base-ci:latest bash -c "
+            quarto render /work/documentation/tutorials/Demo_1_Basic_Run/run_pecan.qmd --to html
+          "
+      - name: Render Demo 2 notebook to HTML
+        run: |
+          docker run --rm -v ${{ github.workspace }}:/work pecan-base-ci:latest bash -c "
+            quarto render /work/documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd --to html
+          "

.github/workflows/sipnet.yml

@@ -54,15 +54,12 @@ jobs:
         curl -L -o sipnet-linux "https://github.com/PecanProject/sipnet/releases/download/v1.3.0/sipnet-linux-v1.3.0"
         chmod +x sipnet-linux
 
-    - name: Download climate file from GitHub
-      run: |
-        curl -L -o niwot.clim "https://raw.githubusercontent.com/PecanProject/sipnet/refs/heads/master/tests/smoke/niwot.clim"
-
-
     # compile PEcAn code
     - name: build
       run: make -j1
 
     # run SIPNET test
+    - name: copy met file into working directory
+      run: Rscript -e 'file.copy(system.file("niwot.clim", package = "PEcAn.SIPNET"), "niwot.clim")'
     - name: integration test
       run: ./tests/integration.sh ghaction

.gitignore

@@ -110,3 +110,11 @@ contrib/modellauncher/modellauncher
 
 # don't track project level .Rprofile
 .Rprofile
+
+
+# Ignore any folder named demo_outdir (Quarto notebook outputs)
+**/demo_outdir/
+dbfiles/
+**/temperate.coniferous/
+*.sensitivity.analysis.*.pdf
+*.variance.decomposition.*.pdf