v5.1.0 release

Makefile

@@ -8,7 +8,7 @@ export BASE_2i2c_IMAGE_NAME = "${PROJECT_PREFIX}2i2c_${2i2c_IMAGE_NAME}"
 
 # 2i2c commands
 build-2i2c-image:		
-	@cd base_images/2i2c/${IMAGE_NAME}; \
+	@cd base_images/2i2c/${2i2c_IMAGE_NAME}; \
 	pwd; \
 	docker buildx build --platform linux/amd64 --progress=plain $(RUN_OPTIONS) -t ${BASE_2i2c_IMAGE_NAME} -f docker/Dockerfile .
 

base_images/2i2c/isce3/docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM pangeo/base-notebook:2025.08.14
+FROM pangeo/base-notebook:2026.01.30
 ENV LANG=en_US.UTF-8
 ENV TZ=US/Pacific
 ARG DEBIAN_FRONTEND=noninteractive

base_images/2i2c/isce3/environment.yml

@@ -3,53 +3,56 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - anywidget=0.9.18
-  - awscli=1.42.49
+  - anywidget=0.9.21
+  - awscli=1.44.32
   - backoff=2.2.1
-  - boto3=1.40.49
-  - cython=3.1.6
-  - earthengine-api=1.6.14
-  - fsspec=2025.9.0
-  - gdal=3.11.4
-  - geopandas=1.1.1
+  - boto3=1.42.42
+  - code-server=3.3.1
+  - cython=3.2.4
+  - earthaccess=0.16.0
+  - earthengine-api=1.7.13
+  - fsspec=2026.2.0
+  - gdal=3.11.5
+  - geopandas=1.1.2
   - groff=1.23.0
   - h5py=3.15.1
   - hdf5=1.14.6
-  - httpx=0.28.1
-  - hvplot=0.12.1
-  - isce3=0.25.3
-  - jupyterlab=4.4.10
-  - lonboard=0.12.1
+  - hvplot=0.12.2
+  - isce3=0.25.7
+  - jupyter-vscode-proxy=0.7
+  - lonboard=0.13.0
   - mapclassify=2.10.0
-  - matplotlib=3.9.1
+  - matplotlib=3.10.8
   - mpl-scatter-density=0.8
-  - nodejs=24.9.0
-  - numba=0.62.1
-  - numpy=2.3.4
+  - nodejs=25.2.1
+  - numba=0.63.1
+  - numpy=2.3.5
+  - openssh=10.2p1
   - pandas=2.3.3
+  - pre_commit=4.5.1
   - pycurl=7.45.7
   - pyproj=3.7.2
-  #- pyogrio causes dependency conflicts with isce3
-  - pyopenssl=25.1.0
-  #- rasterio causes dependency conflicts with isce3
-  #- rasterstats causes dependency conflicts with isce3
-  - requests=2.32.5
-  #- rio-cogeo causes dependency conflicts with isce3
+  - pyopenssl=25.3.0
+  #- rasterstats
+  #- rio-cogeo
+  - pyviz_comms=3.0.4
   - rtree=1.4.1
-  - s3fs=2025.9.0
-  - scikit-learn=1.7.2
-  - scipy=1.16.3
+  - s3fs=2026.2.0
+  - scikit-learn=1.8.0
+  - scipy=1.17.0
   - seaborn=0.13.2
   - shapely=2.1.2
-  - sliderule=4.5.3
-  - statsmodels=0.14.5
-  - tqdm=4.67.1
-  - unidecode=1.3.8
+  - sliderule=5.0.7
+  - statsmodels=0.14.6
+  - tqdm=4.67.3
+  - unidecode=1.4.0
   - unzip=6.0
-  - xarray=2025.10.1
-  - pip=25.2
+  - xarray=2026.1.0
+  - pip=26.0
   - pip:
     - jupyter-resource-usage==1.2.0
+    - jupyter-sshd-proxy==0.3.0
+    - jupyterlab-bxplorer==0.2.30
     # - git+https://github.com/MAAP-Project/stac_ipyleaflet.git@0.3.6
     - morecantile==6.1.0
     - rio-tiler==7.2.2
@@ -60,10 +63,4 @@ 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/'
+    - maap-user-workspace-management-jupyter-extension==1.0.0

base_images/2i2c/pangeo/docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM pangeo/pangeo-notebook:2025.08.14
+FROM public.ecr.aws/nasa-veda/pangeo-notebook-veda-image:2025.12.30-v1
 ENV LANG=en_US.UTF-8
 ENV TZ=US/Pacific
 ARG DEBIAN_FRONTEND=noninteractive

base_images/2i2c/pangeo/environment.yml

@@ -3,24 +3,14 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - duckdb=1.3.2
-  - nodejs=24.9.0
-  - 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
+    - rio-tiler==8.0.5
     - maap-py==4.2.0
     - maap-algorithms-jupyter-extension==0.5.1
     - maap-jupyter-server-extension==3.0.0
     - maap-dps-jupyter-extension==0.7.7
     # - 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/'
+    - maap-user-workspace-management-jupyter-extension==1.0.0

base_images/2i2c/pytorch/docker/Dockerfile

@@ -0,0 +1,13 @@
+FROM quay.io/pangeo/pytorch-notebook:2025.12.30
+ENV LANG=en_US.UTF-8
+ENV TZ=US/Pacific
+ARG DEBIAN_FRONTEND=noninteractive
+
+# 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

base_images/2i2c/pytorch/environment.yml

@@ -0,0 +1,24 @@
+name: notebook
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  # Dependencies for VS Code IDE
+  - code-server>=3.2
+  - jupyter-vscode-proxy=0.7
+  - pre_commit=3.4.0
+  # Upgrade from py torch notebook image
+  - earthaccess>=0.16.0
+  # Pin down to avoid https://github.com/holoviz/pyviz_comms/issues/143
+  - pyviz_comms==3.0.4
+  - pip=25.2
+  - pip:
+    - jupyter-sshd-proxy==0.3.0
+    - jupyterlab-bxplorer==0.2.30
+    - maap-py==4.2.0
+    - maap-algorithms-jupyter-extension==0.5.1
+    - maap-jupyter-server-extension==3.0.0
+    - maap-dps-jupyter-extension==0.7.7
+    - maap-help-jupyter-extension==2.0.2
+    - maap-libs-jupyter-extension==1.2.5
+    - maap-user-workspace-management-jupyter-extension==1.0.0

base_images/2i2c/r-base/docker/Dockerfile

@@ -0,0 +1,74 @@
+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) && \
+    CONDA_LIB="${CONDA_DIR}/envs/${CONDA_ENV}/lib" && \
+    echo "# Preload conda OpenSSL libraries to prevent GDAL from loading system OpenSSL" >> "$R_HOME/etc/Rprofile.site" && \
+    echo "Sys.setenv(LD_PRELOAD = '$CONDA_LIB/libcrypto.so.3:$CONDA_LIB/libssl.so.3')" >> "$R_HOME/etc/Rprofile.site" && \
+    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"]

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

base_images/2i2c/r-base/scripts/init-user.sh

@@ -0,0 +1,38 @@
+#!/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"
+
+# Needed to run awsv2 and aws 
+awscliv2 --install
+CONDA_BIN=$(dirname $(which python))
+ln -sf $(which awsv2) "$CONDA_BIN/aws"
+
+# Hand control to the base image's /srv/start which handles all initialization
+exec /srv/start "$@"

base_images/2i2c/r/scripts/install_cran_packages_r.sh → base_images/2i2c/r-base/scripts/install_cran_packages_r.sh

@@ -10,10 +10,10 @@ R_LIB=${R_LIB:-/usr/local/lib/R/site-library}
 
 # Install recommended R packages first to avoid warnings
 Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "codetools"
+Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "tmap"
 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"

base_images/2i2c/r/docker/Dockerfile

@@ -1,40 +1,8 @@
-FROM ghcr.io/nmfs-opensci/container-images/py-rocket-geospatial:2025.04.26
+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=3.4.1+dfsg-1build4 \
-    lbzip2=2.5-2.3 \
-    libfftw3-dev=3.3.8-2ubuntu8 \
-    libgdal-dev=3.4.1+dfsg-1build4 \
-    libgeos-dev=3.10.2-1 \
-    libgl1-mesa-dev=23.2.1-1ubuntu3.1~22.04.3 \
-    libglu1-mesa-dev=9.0.2-1 \
-    libhdf4-alt-dev=4.2.15-4 \
-    libhdf5-dev=1.10.7+repack-4ubuntu2 \
-    libjq-dev=1.6-2.1ubuntu3.1 \
-    libpq-dev=14.19-0ubuntu0.22.04.1 \
-    libproj-dev=8.2.1-1 \
-    libprotobuf-dev=3.12.4-1ubuntu7.22.04.4 \
-    libnetcdf-dev=1:4.8.1-1 \
-    libsqlite3-dev=3.37.2-2ubuntu0.5 \
-    libssl-dev=3.0.2-0ubuntu1.20 \
-    libudunits2-dev=2.2.28-3 \
-    netcdf-bin=1:4.8.1-1 \
-    postgis=3.2.0+dfsg-1ubuntu1 \
-    protobuf-compiler=3.12.4-1ubuntu7.22.04.4 \
-    sqlite3=3.37.2-2ubuntu0.5 \
-    tk-dev=8.6.11+1build2 \
-    unixodbc-dev=2.3.9-5ubuntu0.1 && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
-
 USER ${NB_USER}
 
 # Install additional packages from environment.yml
@@ -45,14 +13,3 @@ RUN conda env update -n ${CONDA_ENV} -f "/tmp/environment.yml" \
     && ${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}