From 1c4068edc8eb1d0b21d04f7cda4befeca21638c7 Mon Sep 17 00:00:00 2001
From: grallewellyn <grace.llewellyn@jpl.nasa.gov>
Date: Thu, 19 Feb 2026 09:06:56 -0800
Subject: [PATCH 1/2] separate r-base image and tested

---
 base_images/2i2c/pangeo/environment.yml       |  2 +-
 base_images/2i2c/r-base/docker/Dockerfile     | 71 +++++++++++++++++++
 base_images/2i2c/r-base/environment.yml       | 15 ++++
 base_images/2i2c/r-base/scripts/init-user.sh  | 33 +++++++++
 .../2i2c/{r => r-base}/scripts/install2.r     |  0
 .../scripts/install_cran_packages_r.sh        |  0
 .../scripts/print_package_versions.R          |  0
 .../scripts/r_package_versions.txt            |  0
 base_images/2i2c/r/docker/Dockerfile          | 47 +-----------
 base_images/2i2c/r/environment.yml            | 18 +----
 10 files changed, 124 insertions(+), 62 deletions(-)
 create mode 100644 base_images/2i2c/r-base/docker/Dockerfile
 create mode 100644 base_images/2i2c/r-base/environment.yml
 create mode 100644 base_images/2i2c/r-base/scripts/init-user.sh
 rename base_images/2i2c/{r => r-base}/scripts/install2.r (100%)
 rename base_images/2i2c/{r => r-base}/scripts/install_cran_packages_r.sh (100%)
 rename base_images/2i2c/{r => r-base}/scripts/print_package_versions.R (100%)
 rename base_images/2i2c/{r => r-base}/scripts/r_package_versions.txt (100%)

diff --git a/base_images/2i2c/pangeo/environment.yml b/base_images/2i2c/pangeo/environment.yml
index e8c57d6..10b13f7 100644
--- a/base_images/2i2c/pangeo/environment.yml
+++ b/base_images/2i2c/pangeo/environment.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - pip=25.2
+  - pip=26.0
   - pip:
     - rio-tiler==8.0.5
     - maap-py==4.2.0
diff --git a/base_images/2i2c/r-base/docker/Dockerfile b/base_images/2i2c/r-base/docker/Dockerfile
new file mode 100644
index 0000000..7fdcc44
--- /dev/null
+++ b/base_images/2i2c/r-base/docker/Dockerfile
@@ -0,0 +1,71 @@
+FROM ghcr.io/nmfs-opensci/container-images/py-rocket-geospatial-2:2026.01.25
+ENV LANG=en_US.UTF-8
+ENV TZ=US/Pacific
+ARG DEBIAN_FRONTEND=noninteractive
+
+USER root
+
+# Install system R and development libraries
+# R will be completely separate from conda
+RUN apt-get clean && apt-get update && \
+    apt-get install -y --no-install-recommends \
+    gdal-bin=3.8.4+dfsg-3ubuntu3 \
+    lbzip2=2.5-2.3 \
+    libfftw3-dev=3.3.10-1ubuntu3 \
+    libgdal-dev=3.8.4+dfsg-3ubuntu3 \
+    libgeos-dev=3.12.1-3build1 \
+    libgl1-mesa-dev=25.0.7-0ubuntu0.24.04.2 \
+    libglu1-mesa-dev=9.0.2-1.1build1 \
+    libhdf4-alt-dev=4.2.16-4build1 \
+    libhdf5-dev=1.10.10+repack-3.1ubuntu4 \
+    libjq-dev=1.7.1-3ubuntu0.24.04.1 \
+    libpq-dev=16.11-0ubuntu0.24.04.1 \
+    libproj-dev=9.4.0-1build2 \
+    libprotobuf-dev=3.21.12-8.2ubuntu0.2 \
+    libnetcdf-dev=1:4.9.2-5ubuntu4 \
+    libsqlite3-dev=3.45.1-1ubuntu2.5 \
+    libssl-dev=3.0.13-0ubuntu3.6 \
+    libudunits2-dev=2.2.28-7build1 \
+    netcdf-bin=1:4.9.2-5ubuntu4 \
+    postgis=3.4.2+dfsg-1ubuntu3 \
+    protobuf-compiler=3.21.12-8.2ubuntu0.2 \
+    sqlite3=3.45.1-1ubuntu2.5 \
+    tk-dev=8.6.14build1 \
+    unixodbc-dev=2.3.12-1ubuntu0.24.04.1 && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+USER ${NB_USER}
+
+# Install additional packages from environment.yml
+COPY ./environment.yml /tmp
+RUN conda env update -n ${CONDA_ENV} -f "/tmp/environment.yml" \
+    && find ${CONDA_DIR}/ -follow -type f -name '*.a' -delete \
+    && find ${CONDA_DIR}/ -follow -type f -name '*.js.map' -delete \
+    && ${CONDA_DIR}/bin/conda clean -afy
+
+RUN conda init
+
+USER root
+SHELL ["/bin/bash", "-c"]
+ADD . /
+RUN ["chmod", "+x", "/scripts/install_cran_packages_r.sh"]
+# Install R packages using SYSTEM R (not conda R)
+# Do NOT activate conda environment here
+# Clear conda's compiler paths to force use of system compiler
+RUN export PATH=/usr/local/bin:/usr/bin:/bin:$PATH && \
+    /scripts/install_cran_packages_r.sh
+
+RUN PYTHON_PATH=$(which python) && \
+    R_HOME=$(R RHOME) && \
+    echo "library(reticulate)" >> "$R_HOME/etc/Rprofile.site" && \
+    echo "use_python(\"$PYTHON_PATH\", required = TRUE)" >> "$R_HOME/etc/Rprofile.site" && \
+    echo "py_config()" >> "$R_HOME/etc/Rprofile.site"
+
+COPY scripts/init-user.sh /usr/local/bin/init-user.sh
+RUN chmod +x /usr/local/bin/init-user.sh
+
+USER ${NB_USER}
+
+# This script returns control to base image's /srv/start after 
+ENTRYPOINT ["/usr/local/bin/init-user.sh"]
\ No newline at end of file
diff --git a/base_images/2i2c/r-base/environment.yml b/base_images/2i2c/r-base/environment.yml
new file mode 100644
index 0000000..8a7485e
--- /dev/null
+++ b/base_images/2i2c/r-base/environment.yml
@@ -0,0 +1,15 @@
+name: notebook
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  # Python packages only - NO R packages in conda
+  - gdal=3.10.2
+  - nodejs=20.19.5
+  - rtree=1.4.1 
+  - unzip=6.0
+  - pip=26.0
+  - pip:
+    # - git+https://github.com/MAAP-Project/stac_ipyleaflet.git@0.3.6
+    - morecantile==6.1.0
+    - rio-tiler==7.2.2
\ No newline at end of file
diff --git a/base_images/2i2c/r-base/scripts/init-user.sh b/base_images/2i2c/r-base/scripts/init-user.sh
new file mode 100644
index 0000000..c02443f
--- /dev/null
+++ b/base_images/2i2c/r-base/scripts/init-user.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+R_SITE_ENV=$(R RHOME)/etc/Renviron.site
+
+# Variables we want to add to Renviron
+VARS=("AWS_ROLE_ARN" "AWS_WEB_IDENTITY_TOKEN_FILE" "AWS_DEFAULT_REGION" "MAAP_PGT")
+
+echo "--- Updating R Site Environment Variables ---"
+
+# Loop through the variables and append them if they exist in the current shell
+for var_name in "${VARS[@]}"; do
+    # Use indirect expansion to get the value of the variable name
+    var_value="${!var_name}"
+
+    if [ -n "$var_value" ]; then
+        echo "Adding $var_name to $R_SITE_ENV"
+        # Check if the line already exists to avoid duplicates
+        if ! grep -q "^$var_name=" "$R_SITE_ENV"; then
+            echo "$var_name=$var_value" >> "$R_SITE_ENV"
+        else
+            # Update existing line if it changed
+            sed -i "s|^$var_name=.*|$var_name=$var_value|" "$R_SITE_ENV"
+        fi
+    else
+        echo "Skipping $var_name: Not set in shell environment."
+    fi
+done
+
+# File ends with a newline 
+echo "" >> "$R_SITE_ENV"
+
+# Hand control to the base image's /srv/start which handles all initialization
+exec /srv/start "$@"
\ No newline at end of file
diff --git a/base_images/2i2c/r/scripts/install2.r b/base_images/2i2c/r-base/scripts/install2.r
similarity index 100%
rename from base_images/2i2c/r/scripts/install2.r
rename to base_images/2i2c/r-base/scripts/install2.r
diff --git a/base_images/2i2c/r/scripts/install_cran_packages_r.sh b/base_images/2i2c/r-base/scripts/install_cran_packages_r.sh
similarity index 100%
rename from base_images/2i2c/r/scripts/install_cran_packages_r.sh
rename to base_images/2i2c/r-base/scripts/install_cran_packages_r.sh
diff --git a/base_images/2i2c/r/scripts/print_package_versions.R b/base_images/2i2c/r-base/scripts/print_package_versions.R
similarity index 100%
rename from base_images/2i2c/r/scripts/print_package_versions.R
rename to base_images/2i2c/r-base/scripts/print_package_versions.R
diff --git a/base_images/2i2c/r/scripts/r_package_versions.txt b/base_images/2i2c/r-base/scripts/r_package_versions.txt
similarity index 100%
rename from base_images/2i2c/r/scripts/r_package_versions.txt
rename to base_images/2i2c/r-base/scripts/r_package_versions.txt
diff --git a/base_images/2i2c/r/docker/Dockerfile b/base_images/2i2c/r/docker/Dockerfile
index aa72b2b..ae1551a 100644
--- a/base_images/2i2c/r/docker/Dockerfile
+++ b/base_images/2i2c/r/docker/Dockerfile
@@ -1,40 +1,8 @@
-FROM ghcr.io/nmfs-opensci/container-images/py-rocket-geospatial-2:2026.01.25
+FROM mas.dit.maap-project.org/root/maap-workspaces/2i2c/r-base:develop
 ENV LANG=en_US.UTF-8
 ENV TZ=US/Pacific
 ARG DEBIAN_FRONTEND=noninteractive
 
-USER root
-
-# Install system R and development libraries
-# R will be completely separate from conda
-RUN apt-get clean && apt-get update && \
-    apt-get install -y --no-install-recommends \
-    gdal-bin=3.8.4+dfsg-3ubuntu3 \
-    lbzip2=2.5-2.3 \
-    libfftw3-dev=3.3.10-1ubuntu3 \
-    libgdal-dev=3.8.4+dfsg-3ubuntu3 \
-    libgeos-dev=3.12.1-3build1 \
-    libgl1-mesa-dev=25.0.7-0ubuntu0.24.04.2 \
-    libglu1-mesa-dev=9.0.2-1.1build1 \
-    libhdf4-alt-dev=4.2.16-4build1 \
-    libhdf5-dev=1.10.10+repack-3.1ubuntu4 \
-    libjq-dev=1.7.1-3ubuntu0.24.04.1 \
-    libpq-dev=16.11-0ubuntu0.24.04.1 \
-    libproj-dev=9.4.0-1build2 \
-    libprotobuf-dev=3.21.12-8.2ubuntu0.2 \
-    libnetcdf-dev=1:4.9.2-5ubuntu4 \
-    libsqlite3-dev=3.45.1-1ubuntu2.5 \
-    libssl-dev=3.0.13-0ubuntu3.6 \
-    libudunits2-dev=2.2.28-7build1 \
-    netcdf-bin=1:4.9.2-5ubuntu4 \
-    postgis=3.4.2+dfsg-1ubuntu3 \
-    protobuf-compiler=3.21.12-8.2ubuntu0.2 \
-    sqlite3=3.45.1-1ubuntu2.5 \
-    tk-dev=8.6.14build1 \
-    unixodbc-dev=2.3.12-1ubuntu0.24.04.1 && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
-
 USER ${NB_USER}
 
 # Install additional packages from environment.yml
@@ -44,15 +12,4 @@ RUN conda env update -n ${CONDA_ENV} -f "/tmp/environment.yml" \
     && find ${CONDA_DIR}/ -follow -type f -name '*.js.map' -delete \
     && ${CONDA_DIR}/bin/conda clean -afy
 
-RUN conda init
-
-USER root
-SHELL ["/bin/bash", "-c"]
-ADD . /
-RUN ["chmod", "+x", "/scripts/install_cran_packages_r.sh"]
-# Install R packages using SYSTEM R (not conda R)
-# Do NOT activate conda environment here
-# Clear conda's compiler paths to force use of system compiler
-RUN export PATH=/usr/local/bin:/usr/bin:/bin:$PATH && \
-    /scripts/install_cran_packages_r.sh
-USER ${NB_USER}
\ No newline at end of file
+RUN conda init
\ No newline at end of file
diff --git a/base_images/2i2c/r/environment.yml b/base_images/2i2c/r/environment.yml
index 5248c02..463c083 100644
--- a/base_images/2i2c/r/environment.yml
+++ b/base_images/2i2c/r/environment.yml
@@ -3,16 +3,8 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  # Python packages only - NO R packages in conda
-  - gdal=3.10.2
-  - nodejs=20.19.5
-  - rtree=1.4.1 
-  - unzip=6.0
-  - pip=25.2
+  - pip=26.0
   - pip:
-    # - git+https://github.com/MAAP-Project/stac_ipyleaflet.git@0.3.6
-    - morecantile==6.1.0
-    - rio-tiler==7.2.2
     - maap-py==4.2.0
     - maap-algorithms-jupyter-extension==0.5.1
     - maap-jupyter-server-extension==3.0.0
@@ -20,10 +12,4 @@ dependencies:
     # - maap-edsc-jupyter-extension==1.1.1
     - maap-help-jupyter-extension==2.0.2
     - maap-libs-jupyter-extension==1.2.5
-    - maap-user-workspace-management-jupyter-extension==1.0.0
-variables:
-  TITILER_STAC_ENDPOINT: 'https://openveda.cloud/api/stac'
-  TITILER_ENDPOINT: 'https://openveda.cloud/api/raster'
-  STAC_CATALOG_NAME: 'VEDA STAC'
-  STAC_CATALOG_URL: 'https://openveda.cloud/api/stac'
-  STAC_BROWSER_URL: 'https://openveda.cloud/'
\ No newline at end of file
+    - maap-user-workspace-management-jupyter-extension==1.0.0
\ No newline at end of file

From 9741aa38eb46b9c338bcfb90aad453c40905bb12 Mon Sep 17 00:00:00 2001
From: grallewellyn <grace.llewellyn@jpl.nasa.gov>
Date: Thu, 19 Feb 2026 12:57:10 -0800
Subject: [PATCH 2/2] removed r essentials and added awscliv2 post install
 command (and tested)

---
 base_images/2i2c/r-base/docker/Dockerfile                  | 2 ++
 base_images/2i2c/r-base/scripts/install_cran_packages_r.sh | 1 -
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/base_images/2i2c/r-base/docker/Dockerfile b/base_images/2i2c/r-base/docker/Dockerfile
index 7fdcc44..df4f18b 100644
--- a/base_images/2i2c/r-base/docker/Dockerfile
+++ b/base_images/2i2c/r-base/docker/Dockerfile
@@ -46,6 +46,8 @@ RUN conda env update -n ${CONDA_ENV} -f "/tmp/environment.yml" \
 
 RUN conda init
 
+RUN awscliv2 --install
+
 USER root
 SHELL ["/bin/bash", "-c"]
 ADD . /
diff --git a/base_images/2i2c/r-base/scripts/install_cran_packages_r.sh b/base_images/2i2c/r-base/scripts/install_cran_packages_r.sh
index e1e4159..160ef4b 100644
--- a/base_images/2i2c/r-base/scripts/install_cran_packages_r.sh
+++ b/base_images/2i2c/r-base/scripts/install_cran_packages_r.sh
@@ -14,7 +14,6 @@ Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r
 Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "tidyterra"
 Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "BIOMASS"
 Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "nlraa"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "essentials"
 Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "geojsonio"
 Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "future"
 Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://r-lidar.r-universe.dev" -n "$NCPUS" "lasR"