Merge pull request #207 from nmfs-opensci/test

Fix problem with CRAN set to "latest"

.github/workflows/test-build.yml

@@ -5,12 +5,23 @@ on:
     branches: test
     paths:
       - '.github/workflows/test-build.yaml'
+      - 'Desktop/**'
+      - 'apt.txt'
+      - 'user-dirs.dirs'
+      - 'vscode-extensions.txt'
+      - 'environment.yml'
+      - 'start'
+      - 'postBuild'
+      - 'Dockerfile'
+      - 'custom_jupyter_server_config.json'
+      - 'scripts/**'
       - '!book/**'  # Ignore all changes in the /book directory
       - '!docs/**'  # Ignore all changes in the /docs directory
+      - '!base-image/**'
       - '!README.md'
       - '!conda-lock.yml'
       - '!LICENSE'
-
+      
 jobs:
   build:
     runs-on: ubuntu-latest

Dockerfile

@@ -1,10 +1,11 @@
 FROM ghcr.io/nmfs-opensci/py-rocket-base/base-image:latest
+
 LABEL org.opencontainers.image.maintainers="[email protected]"
 LABEL org.opencontainers.image.author="[email protected]"
 LABEL org.opencontainers.image.source=https://github.com/nmfs-opensci/py-rocket-base
-LABEL org.opencontainers.image.description="Geospatial Python (3.12), R (4.4) and Desktop"
+LABEL org.opencontainers.image.description="Python (3.12), R (4.4.1), Desktop and Publishing tools"
 LABEL org.opencontainers.image.licenses=Apache2.0
-LABEL org.opencontainers.image.version=2024.11.19
+LABEL org.opencontainers.image.version=2024.11.22
 
 USER root
 
@@ -13,6 +14,9 @@ USER root
 ENV REPO_DIR="/srv/repo" \
     DISPLAY=":1.0" \
     R_VERSION="4.4.1"
+# The latest rocker will set CRAN to 'latest' but we need a date stamped version for reproducibility
+# So pull the latest and use one earlier
+ARG R_VERSION_PULL="4.4.2"
 
 # Add NB_USER to staff group (required for rocker script)
 # Ensure the staff group exists first
@@ -34,7 +38,10 @@ RUN mkdir -p /pyrocket_scripts && \
 RUN /pyrocket_scripts/install-conda-packages.sh ${REPO_DIR}/environment.yml
 
 # Install R, RStudio via Rocker scripts. Requires the prefix for a rocker Dockerfile
-RUN /pyrocket_scripts/install-rocker.sh "verse_${R_VERSION}"
+RUN R_VERSION_PULL=$R_VERSION_PULL /pyrocket_scripts/install-rocker.sh "verse_${R_VERSION}"
+
+# Install Zotero; must be run before apt since zotero apt install requires this is run first
+RUN wget -qO- https://raw.githubusercontent.com/retorquere/zotero-deb/master/install.sh | bash 
 
 # Install extra apt packages
 # Install linux packages after R installation since the R install scripts get rid of packages
@@ -43,9 +50,6 @@ RUN /pyrocket_scripts/install-apt-packages.sh ${REPO_DIR}/apt.txt
 # Install some basic VS Code extensions
 RUN /pyrocket_scripts/install-vscode-extensions.sh ${REPO_DIR}/vscode-extensions.txt
 
-# Install Zotero
-RUN wget -qO- https://raw.githubusercontent.com/retorquere/zotero-deb/master/install.sh | bash 
-
 # Re-enable man pages disabled in Ubuntu 18 minimal image
 # https://wiki.ubuntu.com/Minimal
 RUN yes | unminimize

scripts/install-rocker.sh

@@ -17,7 +17,7 @@ fi
 
 # Check if a filename argument is provided
 if [ -z "$1" ]; then
-    echo "Error: install-rocker.sh requires a rocker Dockerfile prefix. Will looke like verse.4.1.1. Exiting." >&2
+    echo "Error: install-rocker.sh requires a rocker Dockerfile prefix. Will look like verse.4.1.1. Exiting." >&2
     echo "Usage: RUN /pyrocket_scripts/install-conda-packages.sh <filename>" >&2
     exit 1
 fi
@@ -34,15 +34,17 @@ R_DOCKERFILE="$1"
 export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 
 # Copy in the rocker files. Work in ${REPO_DIR} to make sure I don't clobber anything
+# R_VERSION_PULL may be different than R_VERSION. Specifically pulling latest but using R_VERSION prior to latest
+# So that CRAN repo is pinned to a date.
 cd ${REPO_DIR}
 ROCKER_DOCKERFILE_NAME="${R_DOCKERFILE}.Dockerfile"
 # For degugging use: wget https://github.com/eeholmes/rocker-versioned2/archive/refs/tags/R4.4.1.tar.gz
-wget https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${R_VERSION}.tar.gz
-tar zxvf R${R_VERSION}.tar.gz && \
-mv rocker-versioned2-R${R_VERSION}/scripts /rocker_scripts && \
-mv rocker-versioned2-R${R_VERSION}/dockerfiles/${ROCKER_DOCKERFILE_NAME} /rocker_scripts/original.Dockerfile && \
-rm R${R_VERSION}.tar.gz && \
-rm -rf rocker-versioned2-R${R_VERSION}
+wget https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${R_VERSION_PULL}.tar.gz
+tar zxvf R${R_VERSION_PULL}.tar.gz && \
+mv rocker-versioned2-R${R_VERSION_PULL}/scripts /rocker_scripts && \
+mv rocker-versioned2-R${R_VERSION_PULL}/dockerfiles/${ROCKER_DOCKERFILE_NAME} /rocker_scripts/original.Dockerfile && \
+rm R${R_VERSION_PULL}.tar.gz && \
+rm -rf rocker-versioned2-R${R_VERSION_PULL}
 
 cd /
 # Read the Dockerfile and process each line