Merge pull request #16 from jporobicg/master

updating yml and code
Atlantis-Ecosystem-Model · Oct 30, 2023 · 54024ab · 54024ab
2 parents 47d305a + a834ad8
commit 54024ab
Show file tree

Hide file tree

Showing 2 changed files with 19 additions and 40 deletions.
diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml
@@ -6,50 +6,29 @@ on:
       - main
       - master
 
-
 jobs:
-  pkgdown:
-    runs-on: macOS-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+  deploy:
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@master
-
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - name: Query dependencies
+      - name: Install R
         run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+          sudo apt-get update
+          sudo apt-get install r-base
+      - name: Checkout code
+        uses: actions/checkout@v2
 
-      - name: Cache R packages
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-
-      - name: Install binary dependencies
-        if: runner.os != 'Linux'
-        run: |
-          remotes::install_deps(dependencies = TRUE, type="binary")
-        shell: Rscript {0}
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
 
-      - name: Install pkgdown          
+      - name: Install dependencies
         run: |
-          install.packages("pkgdown", type = "binary")
-        shell: Rscript {0}
-
-      - name: Install package
-        run: R CMD INSTALL .
+          Rscript -e "install.packages('remotes')"
+          Rscript -e "remotes::install_deps(dependencies = TRUE)"
+          Rscript -e "install.packages('pkgdown')"
 
-      - name: Deploy package
+      - name: Build and deploy
         run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+          Rscript -e "pkgdown::build_site()"
+          bash deploy.sh
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/R/initGen.R b/R/initGen.R
@@ -172,7 +172,7 @@ generate.vars.init <- function(grp.file, cum.depths, df.atts, ice_model) {
                 att.index <- c(att.index, indx)
             }
             if (df.grp$needsLight[grp]) { ## single light adaptation group
-                Variable <- c(Variable, paste("Light_Adaptn_", df.grp$Code[grp],
+                Variable <- c(Variable, paste("Light_Adaptn_", df.grp$code[grp],
                                               sep = ""))
                 indx <- which(df.atts$name == "Light3D")
                 long_name <- c(long_name, paste("Light adaption of",