Merge branch 'develop' into ncvar_put-debug

.github/workflows/book.yml

@@ -22,7 +22,7 @@ jobs:
 
     steps:
     # checkout source code
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     # install rmarkdown
     - name: Install rmarkdown
       run: |
@@ -44,14 +44,14 @@ jobs:
         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
+      uses: actions/checkout@v3
       with:
         repository: ${{ github.repository_owner }}/pecan-documentation
         path: pecan-documentation

.github/workflows/depends.yml

@@ -38,6 +38,13 @@ jobs:
         with:
           set-safe-directory: false
 
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+        with:
+          driver: docker
+          buildkitd-flags: --debug
+          install: true
+
       # calculate some variables that are used later
       - name: github branch
         # build Rdevel only on Mondays, others every day (but not twice on Mondays)
@@ -59,7 +66,7 @@ jobs:
       # this will publish to the actor (person) github packages
       - name: Publish to GitHub
         if: env.TAG != ''
-        uses: elgohr/Publish-Docker-Github-Action@2.22
+        uses: elgohr/Publish-Docker-Github-Action@v4
         env:
           R_VERSION: ${{ matrix.R  }}
         with:
@@ -74,7 +81,7 @@ jobs:
       # this will publish to the clowder dockerhub repo
       - name: Publish to Docker Hub
         if: env.TAG != ''
-        uses: elgohr/Publish-Docker-Github-Action@2.18
+        uses: elgohr/Publish-Docker-Github-Action@v4
         env:
           R_VERSION: ${{ matrix.R  }}
         with:

.github/workflows/docker.yml

@@ -29,6 +29,7 @@ on:
 env:
   MASTER_REPO: PecanProject/pecan
   DOCKERHUB_ORG: pecan
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
   docker:
@@ -41,6 +42,12 @@ jobs:
       - uses: actions/checkout@v3
         with:
           set-safe-directory: false
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+        with:
+          driver: docker
+          buildkitd-flags: --debug
+          install: true
 
       # calculate some variables that are used later
       - name: get version tag
@@ -72,7 +79,7 @@ jobs:
         env:
           PECAN_GIT_CHECKSUM: ${{ github.sha }}
           PECAN_GIT_BRANCH: ${GITHUB_BRANCH}
-          VERSION: ${PECAN_VERSION}
+          VERSION: ${{ env.PECAN_VERSION }}
 
       # push all images to github
       - name: Publish to GitHub

.github/workflows/stale.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/stale@v4
+    - uses: actions/stale@v6
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         stale-issue-message: 'This issue is stale because it has been open 365 days with no activity.'

apps/api/Dockerfile

@@ -15,7 +15,9 @@ EXPOSE 8000
 # --------------------------------------------------------------------------
 
 # COMMAND TO RUN
-RUN   apt-get update \
+RUN  --mount=type=secret,id=github_token \
+  export GITHUB_PAT=`cat /run/secrets/github_token` \
+  &&  apt-get update \
   &&  apt-get install libsodium-dev -y \
   &&  rm -rf /var/lib/apt/lists/* \
   &&  Rscript -e "devtools::install_version('promises', '1.1.0')" \

docker.sh

@@ -121,6 +121,7 @@ echo "# ----------------------------------------------------------------------"
 if [ "${DEPEND}" == "build" ]; then
     ${DEBUG} docker build \
         --pull \
+        --secret id=github_token,env=GITHUB_PAT \
         --build-arg R_VERSION=${R_VERSION} ${GITHUB_WORKFLOW_ARG} \
         --tag pecan/depends:${IMAGE_VERSION} \
         docker/depends
@@ -146,6 +147,7 @@ echo ""
 # require all of PEcAn to build
 for x in base web docs; do
     ${DEBUG} docker build \
+        --secret id=github_token,env=GITHUB_PAT \
         --tag pecan/$x:${IMAGE_VERSION} \
         --build-arg FROM_IMAGE="${FROM_IMAGE:-depends}" \
         --build-arg IMAGE_VERSION="${IMAGE_VERSION}" ${GITHUB_WORKFLOW_ARG} \
@@ -230,6 +232,7 @@ done
 # build apps
 for x in api; do
     ${DEBUG} docker build \
+        --secret id=github_token,env=GITHUB_PAT \
         --tag pecan/$x:${IMAGE_VERSION} \
         --build-arg IMAGE_VERSION="${IMAGE_VERSION}" ${GITHUB_WORKFLOW_ARG} \
         --build-arg PECAN_VERSION="${VERSION}" \

docker/base/Dockerfile

@@ -26,7 +26,9 @@ COPY models   /pecan/models/
 # install all PEcAn packages
 # `make clean` is to remove artifacts copied in from host system
 #   (e.g. basgra.so)
-RUN cd /pecan \
+RUN --mount=type=secret,id=github_token \
+    export GITHUB_PAT=`cat /run/secrets/github_token` \
+    && cd /pecan \
     && make clean \
     && make \
     && rm -rf /tmp/downloaded_packages

docker/depends/Dockerfile

@@ -40,7 +40,9 @@ RUN apt-get update \
 # INSTALL DEPENDENCIES
 # ----------------------------------------------------------------------
 COPY pecan.depends.R /
-RUN  Rscript -e "install.packages(c('devtools'))" \
+RUN  --mount=type=secret,id=github_token \
+  export GITHUB_PAT=`cat /run/secrets/github_token` \
+  && Rscript -e "install.packages(c('devtools'))" \
   && Rscript -e "devtools::install_version('roxygen2', '7.1.2', repos = 'cran.r-project.org')" \
   && R_LIBS_USER='/usr/local/lib/R/site-library' Rscript /pecan.depends.R \
   && rm -rf /tmp/*