Merge branch 'master' of github.com:waldronbios2/cunybios2

.github/workflows/build.yaml

@@ -8,10 +8,13 @@ env:
   IMAGE_NAME: ${{ github.repository }}
 jobs:
   job1:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     container: rocker/verse:4.2.0
     steps:
-      - uses: actions/checkout@v2
+      - name: Checkout repository and submodules
+        uses: actions/checkout@v3
+        with:
+          submodules: true
 
       # System dependencies
       - name: Install apt dependencies
@@ -42,18 +45,6 @@ jobs:
           key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-r-1-
 
-      - name: Create safe.directory
-        run: |
-          git config --global --add safe.directory /__w/cunybios2/cunybios2
-          git config --global --add safe.directory /home/rstudio
-
-      - name: Checkout submodules
-        uses: srt32/[email protected]
-
-      - name: What's in submodules
-        run: |
-          git submodule update --remote --merge
-
       # This lets us augment with additional dependencies
       - name: Install system dependencies
         if: runner.os == 'Linux'
@@ -96,11 +87,19 @@ jobs:
           email: [email protected]
 
       - name: Deploy ð
-        uses: JamesIves/[email protected]
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages # The branch the action should deploy to.
+          folder: docs # The folder the action should deploy.
+          workspace: $GITHUB_WORKSPACE
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v2
         with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          BRANCH: gh-pages # The branch the action should deploy to.
-          FOLDER: docs # The folder the action should deploy.
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_PAT }}
 
       # Build and push Docker image with Buildx (don't push on PR)
       # https://github.com/docker/build-push-action
@@ -110,7 +109,7 @@ jobs:
         with:
           context: .
           push: true
-          tags: user/app:latest
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest
 
       # Sign the resulting Docker image digest except on PRs.
       # This will only write to the public Rekor transparency log when the Docker

Dockerfile

@@ -5,14 +5,9 @@ COPY --chown=rstudio:rstudio . /home/rstudio/
 
 RUN apt-get update --fix-missing && apt-get install -yq libssl-dev libpng-dev libnetcdf-dev libxml2-dev libxt6 libharfbuzz-dev libfribidi-dev libv8-dev 
 
-## get submodules
-
-RUN git submodule init
-RUN git submodule update
-
 ## install R package and dependencies
 
 RUN Rscript -e "install.packages('devtools', ask=FALSE, Ncpus=max(1, parallel::detectCores(), na.rm=TRUE))"
-RUN Rscript -e "devtools::install('.', dependencies=TRUE, build_vignettes=FALSE, Ncpus=max(1, parallel::detectCores(), na.rm=TRUE))"
+RUN Rscript -e "devtools::install('.', dependencies=TRUE, build_vignettes=FALSE)"
 
 RUN chown -R rstudio:rstudio /home/rstudio