Merge branch 'main' of https://github.com/nmfs-opensci/container-images

.github/workflows/docker-image-coastwatch_patch.yml

@@ -0,0 +1,30 @@
+name: Docker Image CI coastwatch patch
+on:
+  workflow_dispatch: null
+  push:
+    branches: coastwatch-patch
+    paths: 
+      - 'images/coastwatch/**'
+      - '.github/workflows/docker-image-coastwatch_patch.yml'
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+      - uses: actions/checkout@v3
+      - name: Login to GitHub Container Registry
+        if: github.repository == 'nmfs-opensci/container-images'
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{github.actor}}
+          password: ${{secrets.GITHUB_TOKEN}}
+      - name: Build the Docker image
+        if: github.repository == 'nmfs-opensci/container-images'
+        run: |
+          docker build images/coastwatch -f images/coastwatch/Dockerfile  --tag ghcr.io/nmfs-opensci/container-images/coastwatch-patch:latest
+      - name: Publish
+        if: github.repository == 'nmfs-opensci/container-images'
+        run: |
+          docker push ghcr.io/nmfs-opensci/container-images/coastwatch-patch:latest
+

images/coastwatch/Dockerfile

@@ -1,46 +1,18 @@
-# devcontainer-focused Rocker
-FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
-# switch user to jovyan; later not working
-#RUN usermod -l rstudio jovyan
-
-# some Git preferences
-RUN git config --system pull.rebase false && \
-    git config --system credential.helper 'cache --timeout=36000'
-
-# Set up conda
-ENV NB_USER=rstudio
-ENV CONDA_ENV=/opt/miniforge3
-ENV PATH=${CONDA_ENV}/bin:${PATH}
-RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
-    bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} && \
-    chown ${NB_USER}:staff -R ${CONDA_ENV} && \
-    rm -f Miniforge3*.sh *.deb
-
+FROM openscapes/rocker:a7596b5
+# Make sure R uses the conda path
+USER root
 RUN echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
 
-# Initialize conda by default for all users:
-RUN conda init --system
-
-# Standard user setup here
-RUN usermod -d /home/jovyan rstudio
-USER ${NB_USER} 
-WORKDIR /home/jovyan
-RUN usermod -s /bin/bash ${NB_USER} 
+USER ${NB_USER}
+WORKDIR ${HOME}
 
-# install into the default environment
+# install into the coastwatch packages if missing environment
 COPY install.R install.R
 RUN Rscript install.R && rm install.R
 
 # set-up the base coastwatch environment
-# make sure we install in the base environment
+# make sure we install in the notebook environment which is default in the
+# Openscapes image
 COPY coastwatch-environment.yml coastwatch-environment.yml
-RUN conda env update --name base -f coastwatch-environment.yml && conda clean --all
+RUN mamba env update --name notebook -f coastwatch-environment.yml && mamba clean --all
 RUN rm coastwatch-environment.yml
-
-# add the packages needed for jupyterhubs
-# need the --name part so that this is put in the coastwatch env
-COPY jhub-environment.yml jhub-environment.yml
-RUN conda env update --name base -f jhub-environment.yml && conda clean --all
-RUN rm jhub-environment.yml
-
-

images/coastwatch/install.R

@@ -1,10 +1,13 @@
 #! /usr/local/bin/Rscript
 # install R dependencies
 
-list.of.packages <- c("ncdf4", "httr","plyr","lubridate", "parsedate", "rerddap","plotdap",
-                      "rerddapXtracto", "graphics", "maps", "mapdata","RColorBrewer",
-                      "ggplot2","scales","dplyr","utils","Rcurl","raster","colorRamps",
-                      "parsedate","sp","sf","reshape2","jsonlite","rgdal",
-                      "gridGraphics","grid","PBSmapping","date","viridis",
-                      "openair","cmocean", "terra")
-install.packages(list.of.packages)
+# to match rocker/geospatial:4.2 uses in openscapes/rocker:a7596b5
+repo <- "https://p3m.dev/cran/__linux__/jammy/2023-04-20"
+list.of.packages <- c("ncdf4", "httr", "plyr", "lubridate", "parsedate", "rerddap",
+                      "maps", "mapdata", "RColorBrewer",
+                      "ggplot2","scales", "dplyr", "RCurl", "raster", "colorRamps",
+                      "parsedate", "sp", "sf", "reshape2", "jsonlite",
+                      "gridGraphics", "PBSmapping", "date", "viridis",
+                      "openair","cmocean", "terra",
+                      "plotdap", "rerddapXtracto", "rgdal")
+install.packages(list.of.packages, repos=repo)