Merge pull request #5 from jhudsl/cansavvy/bump-rocker

Update to tidyverse 4.4

Author: cansavvy

.github/workflows/docker-management.yml

@@ -1,4 +1,5 @@
 # Candace Savonen Oct 2021
+# Updated Jan 2025
 
 name: Docker management
 
@@ -28,7 +29,7 @@ jobs:
 
       # Setup layer cache
       - name: Cache Docker layers
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: /tmp/.buildx-cache
           key: ${{ runner.os }}-buildx-${{ github.sha }}
@@ -55,7 +56,7 @@ jobs:
       # Login to Dockerhub
       - name: Login to DockerHub
         if: ${{ github.event.inputs.dockerhubpush != 'false' }}
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           # You will need to set up GitHub secrets with your Docker login info
           # for this to work.

.github/workflows/run-r-notebook.yml

@@ -19,7 +19,7 @@ jobs:
     steps:
       # We need to tell github actions to use the code on the branch we are on
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           # How deep should it fetch?
           fetch-depth: 0

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/tidyverse:4.0.2
+FROM rocker/tidyverse:4.4
 LABEL maintainer="cansav09@gmail.com"
 WORKDIR /rocker-build/
 
@@ -8,8 +8,11 @@ RUN apt-get update && apt-get install -y --no-install-recommends apt-utils dialo
 RUN apt-get -y --no-install-recommends install \
   python3-pip  python3-dev
 
+# Install refine bio and dependencies
 RUN pip3 install \
-  "pyrefinebio"
+  "pyrate-limiter==2.10.0" \
+  redis \
+  pyrefinebio  --break-system-packages
 
 # Commonly used R packages
 RUN Rscript -e  "install.packages( \
@@ -19,4 +22,4 @@ RUN Rscript -e  "install.packages( \
 # Set final workdir for commands
 WORKDIR /home/rstudio
 
-ENV USER="rstudio" PASSWORD="rstudio" ROOT="TRUE"
+ENV USER="rstudio" ROOT="TRUE"