CUDA.md

@@ -88,7 +88,7 @@ cd base && docker build \
   --build-arg BASE_IMAGE=ubuntu \
   --build-arg BASE_IMAGE_TAG=22.04 \
   --build-arg BUILD_ON_IMAGE=glcr.b-data.ch/cuda/r/ver \
-  --build-arg R_VERSION=4.4.1 \
+  --build-arg R_VERSION=4.4.2 \
   --build-arg CUDA_IMAGE_FLAVOR=devel \
   -t jupyterlab/cuda/r/base \
   -f latest.Dockerfile .
@@ -224,7 +224,7 @@ docker run -it --rm \
 **What makes this project different:**
 
 1. Multi-arch: `linux/amd64`, `linux/arm64/v8`
-1. Derived from [`nvidia/cuda:12.6.2-devel-ubuntu22.04`](https://hub.docker.com/r/nvidia/cuda/tags?page=1&name=12.6.2-devel-ubuntu22.04)
+1. Derived from [`nvidia/cuda:12.8.0-devel-ubuntu22.04`](https://hub.docker.com/r/nvidia/cuda/tags?page=1&name=12.8.0-devel-ubuntu22.04)
     * including development libraries and headers
 1. TensortRT and TensorRT plugin libraries
     * including development libraries and headers

CUDA_VERSION_MATRIX.md

@@ -6,6 +6,7 @@ Topmost entry = Tag `latest`
 
 | R     | Python  | SAGA[^1] | CUDA   | cuBLAS    | cuDNN     | NCCL   | TensorRT[^2]            | Linux distro |
 |:------|:--------|:---------|:-------|:----------|:----------|:-------|:------------------------|:-------------|
+| 4.4.2 | 3.12.9  | 7.3.0    | 12.8.0 | 12.8.3.14 | 8.9.7.29  | 2.25.1 | 10.8.0.43/<br>10.3.0.26 | Ubuntu 22.04 |
 | 4.4.1 | 3.12.7  | 7.3.0    | 12.6.2 | 12.6.3.3  | 8.9.7.29  | 2.23.4 | 10.6.0.26/<br>10.3.0.26 | Ubuntu 22.04 |
 | 4.4.0 | 3.12.4  | 7.3.0    | 12.5.0 | 12.5.2.13 | 8.9.7.29  | 2.21.5 | 10.0.1.6                | Ubuntu 22.04 |
 | 4.3.3 | 3.11.9  | 7.3.0    | 11.8.0 | 11.11.3.6 | 8.9.6.50  | 2.15.5 | 8.5.3[^3]               | Ubuntu 22.04 |
@@ -23,6 +24,7 @@ Topmost entry = Tag `latest`
 
 | Python | CUDA | PyTorch[^4]    | TensorFlow[^5]        |
 |:-------|:-----|:---------------|:----------------------|
+| 3.12   | 12.8 | version ≥ 2.2  | version ≥ 2.16        |
 | 3.12   | 12.6 | version ≥ 2.2  | version ≥ 2.16        |
 | 3.12   | 12.5 | version ≥ 2.2  | version ≥ 2.16        |
 | 3.11   | 11.8 | version ≥ 2.0  | 2.15 ≥ version > 2.12 |
@@ -38,6 +40,7 @@ given.
 
 | CUDA   | Linux driver version | Windows driver version[^6] |
 |:-------|:---------------------|:---------------------------|
+| 12.8.0 | ≥ 570.26             | ≥ 570.65                   |
 | 12.6.2 | ≥ 560.35.03          | ≥ 560.94                   |
 | 12.5.0 | ≥ 555.42.02          | ≥ 555.85                   |
 | 11.8.0 | ≥ 520.61.05          | ≥ 520.06                   |
@@ -53,6 +56,7 @@ Only works with
 
 | CUDA   | Driver version 535[^7] | Driver version 470[^8] |
 |:-------|:----------------------:|:----------------------:|
+| 12.8.0 | 🟢                      | 🔵                      |
 | 12.6.2 | 🟢                      | 🔵                      |
 | 12.5.0 | 🟢                      | 🔵                      |
 | 11.8.0 | 🟡                      | 🟢                      |

NOTES.md

@@ -45,7 +45,7 @@ The following startup hooks are put in place:
   * set environment variables in `$(R RHOME)/etc/Renviron.site`.
   * put inital RStudio settings in place.
   * create user's working folder.
-* [/usr/local/bin/before-notebook.d/70-qgis.sh](qgisprocess/scripts/usr/local/bin/before-notebook.d/70-qgis.sh) to
+* [/usr/local/bin/before-notebook.d/70-qgis.sh](qgisprocess/scripts/usr/local/bin/before-notebook.d/70-qgis.sh) (qgisprocess images) to
   * put inital QGIS settings in place.
   * copy plugin 'Processing Saga NextGen Provider'.
 * [/usr/local/bin/before-notebook.d/71-tensorboard.sh](base/scripts/usr/local/bin/before-notebook.d/71-tensorboard.sh)
@@ -172,6 +172,13 @@ are installed.
   * Application > Telemetry: Telemetry Level: off
   * Features > Terminal > Integrated: Font Family: MesloLGS NF
   * Workbench > Appearance > Color Theme: Default Dark+
+* [QGIS](qgisprocess/conf/user/var/backups/skel/.local/share/QGIS/QGIS3/profiles/default/QGIS/QGIS3.ini) (qgisprocess images):
+  * Append `/usr/lib/python3/dist-packages` to `PYTHONPATH`.  
+    :information_source: One distro refused to find the Python bindings to QGIS
+    (at `/usr/lib/python3/dist-packages/qgis`)... Kept for backwards
+    compatibility.
+  * Set UI Theme to 'Night Mapping'.
+  * Set OTB application folder and OTB folder.
 * Zsh
   * Oh My Zsh: `~/.zshrc`
     * Set PATH so it includes user's private bin if it exists

README.md

@@ -154,7 +154,7 @@ To install docker, follow the instructions for your platform:
 
 ```bash
 cd base && docker build \
-  --build-arg R_VERSION=4.4.1 \
+  --build-arg R_VERSION=4.4.2 \
   -t jupyterlab/r/base \
   -f latest.Dockerfile .
 ```
@@ -352,6 +352,8 @@ b-data tailors the JupyterLab images to your needs, e.g.
   services on the intranet.
 * Setting up the necessary environment variables so that everything works
   behind a corporate proxy server.
+* If supported by the NVIDIA GPU(s): Correctly handle CUDA forward compatibility
+  for GPU accelerated images.
 
 Additionally, the
 [JupyterHub](https://github.com/b-data/docker-deployment-jupyter) setup can be

VERSION_MATRIX.md

@@ -8,6 +8,7 @@ Topmost entry = Tag `latest`
 
 | R     | Python  | Jupyter Hub | Jupyter Lab | code‑server (Code) | RStudio       | Neovim | Git    | Git LFS | Pandoc | CRAN date  | Linux distro |
 |:------|:--------|:------------|:------------|:-------------------|:--------------|:-------|:-------|:--------|:-------|:-----------|:-------------|
+| 4.4.2 | 3.12.9  | 5.2.1       | 4.3.5       | 4.97.2 (1.97.2)    | 2024.12.1+563 | 0.10.4 | 2.48.1 | 3.6.1   | 3.4    | 2025‑02‑28 | Debian 12    |
 | 4.4.1 | 3.12.7  | 5.2.1       | 4.2.5       | 4.93.1 (1.93.1)    | 2024.09.0+375 | 0.10.2 | 2.47.0 | 3.5.1   | 3.2    | 2024‑10‑31 | Debian 12    |
 | 4.4.0 | 3.12.4  | 5.0.0       | 4.2.2       | 4.90.0 (1.90.0)    | 2024.04.2+764 | n/a    | 2.45.2 | 3.5.1   | 3.1.11 | 2024‑06‑14 | Debian 12    |
 | 4.3.3 | 3.11.9  | 4.1.5       | 4.1.6       | 4.23.0 (1.88.0)    | n/a           | n/a    | 2.44.0 | 3.5.1   | 3.1.11 | 2024‑04‑24 | Debian 12    |
@@ -23,6 +24,7 @@ Topmost entry = Tag `latest`
 
 | R     | CTAN date  | Quarto      |
 |:------|:-----------|:------------|
+| 4.4.2 | 2025‑02‑28 | 1.6.42      |
 | 4.4.1 | 2024‑10‑31 | 1.5.57      |
 | 4.4.0 | 2024‑06‑14 | 1.4.555     |
 | 4.3.3 | 2024‑04‑24 | 1.4.553     |
@@ -38,6 +40,7 @@ Topmost entry = Tag `latest`
 
 | R     | QGIS   | SAGA  | OTB[^1] |
 |:------|:-------|:------|:--------|
+| 4.4.2 | 3.42.0 | 9.1.3 | 9.1.0   |
 | 4.4.1 | 3.40.0 | 9.1.3 | 9.1.0   |
 | 4.4.0 | 3.36.3 | 9.1.3 | 9.0.0   |
 | 4.3.3 | 3.36.2 | 9.1.3 | 9.0.0   |

base/.gitlab-ci.yml

 .env:
   variables:
-    R_VERSION: "4.4.1"
+    R_VERSION: "4.4.2"
+    RSTUDIO_VERSION: "2024.12.1+563"
     TAG_VERSION_MAJ_MIN: "false"
     TAG_VERSION_MAJ: "false"
 
@@ -67,6 +68,7 @@ build:latest-linux-amd64:
       --build-arg BASE_IMAGE_TAG
       --build-arg BUILD_ON_IMAGE
       --build-arg R_VERSION
+      --build-arg RSTUDIO_VERSION
       --build-arg CUDA_IMAGE_FLAVOR
       --build-arg CUDA_IMAGE_LICENSE
       --build-arg NCPUS=$((`nproc`/2+1))
@@ -114,6 +116,7 @@ build:latest-linux-arm64v8:
       --build-arg BASE_IMAGE_TAG
       --build-arg BUILD_ON_IMAGE
       --build-arg R_VERSION
+      --build-arg RSTUDIO_VERSION
       --build-arg CUDA_IMAGE_FLAVOR
       --build-arg CUDA_IMAGE_LICENSE
       --build-arg NCPUS=$((`nproc`/2+1))

base/conf/jupyter/etc/jupyter/jupyter_server_config.py

@@ -10,8 +10,8 @@ from pathlib import Path
 from jupyter_core.paths import jupyter_data_dir
 
 c = get_config()  # noqa: F821 # type: ignore
-c.ServerApp.ip = "0.0.0.0"
-c.ServerApp.port = 8888
+# Listen on all interfaces (IPv4 and IPv6)
+c.ServerApp.ip = ""
 #c.ServerApp.open_browser = False
 
 # https://github.com/jupyter/notebook/issues/3130

base/latest.Dockerfile

@@ -7,14 +7,14 @@ ARG CUDA_IMAGE_FLAVOR
 ARG NB_USER=jovyan
 ARG NB_UID=1000
 ARG JUPYTERHUB_VERSION=5.2.1
-ARG JUPYTERLAB_VERSION=4.2.5
+ARG JUPYTERLAB_VERSION=4.3.5
 ARG CODE_BUILTIN_EXTENSIONS_DIR=/opt/code-server/lib/vscode/extensions
-ARG CODE_SERVER_VERSION=4.93.1
-ARG RSTUDIO_VERSION=2024.09.0+375
-ARG NEOVIM_VERSION=0.10.2
-ARG GIT_VERSION=2.47.0
-ARG GIT_LFS_VERSION=3.5.1
-ARG PANDOC_VERSION=3.2
+ARG CODE_SERVER_VERSION=4.97.2
+ARG RSTUDIO_VERSION
+ARG NEOVIM_VERSION=0.10.4
+ARG GIT_VERSION=2.48.1
+ARG GIT_LFS_VERSION=3.6.1
+ARG PANDOC_VERSION=3.4
 
 FROM ${BUILD_ON_IMAGE}:${R_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMAGE_FLAVOR} AS files
 
@@ -78,7 +78,18 @@ FROM glcr.b-data.ch/neovim/nvsi:${NEOVIM_VERSION} AS nvsi
 FROM glcr.b-data.ch/git/gsi/${GIT_VERSION}/${BASE_IMAGE}:${BASE_IMAGE_TAG} AS gsi
 FROM glcr.b-data.ch/git-lfs/glfsi:${GIT_LFS_VERSION} AS glfsi
 
-FROM ${BUILD_ON_IMAGE}:${R_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMAGE_FLAVOR}
+FROM ${BUILD_ON_IMAGE}:${R_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMAGE_FLAVOR} AS base
+
+FROM ${BUILD_ON_IMAGE}:${R_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMAGE_FLAVOR} AS base-rstudio
+
+ARG RSTUDIO_VERSION
+
+ENV RSTUDIO_VERSION=${RSTUDIO_VERSION}
+
+## Connect to RStudio via unix socket
+ENV JUPYTER_RSESSION_PROXY_USE_SOCKET=1
+
+FROM base${RSTUDIO_VERSION:+-rstudio}
 
 ARG NCPUS=1
 
@@ -92,7 +103,6 @@ ARG JUPYTERHUB_VERSION
 ARG JUPYTERLAB_VERSION
 ARG CODE_BUILTIN_EXTENSIONS_DIR
 ARG CODE_SERVER_VERSION
-ARG RSTUDIO_VERSION
 ARG NEOVIM_VERSION
 ARG GIT_VERSION
 ARG GIT_LFS_VERSION
@@ -118,7 +128,6 @@ ENV PARENT_IMAGE=${BUILD_ON_IMAGE}:${R_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMA
     JUPYTERHUB_VERSION=${JUPYTERHUB_VERSION} \
     JUPYTERLAB_VERSION=${JUPYTERLAB_VERSION} \
     CODE_SERVER_VERSION=${CODE_SERVER_VERSION} \
-    RSTUDIO_VERSION=${RSTUDIO_VERSION} \
     NEOVIM_VERSION=${NEOVIM_VERSION} \
     GIT_VERSION=${GIT_VERSION} \
     GIT_LFS_VERSION=${GIT_LFS_VERSION} \
@@ -410,6 +419,14 @@ RUN apt-get update \
       >> $(which radian)_; \
     echo "$(which radian) \"\${@}\"" >> $(which radian)_; \
   fi \
+  ## Install httpgd
+  ## Archived on 2025-02-14 as requires archived package 'unigd'.
+  && install2.r --error --skipinstalled -n $NCPUS \
+    unigd \
+    AsioHeaders \
+  && curl -sLO https://cran.r-project.org/src/contrib/Archive/httpgd/httpgd_2.0.2.tar.gz \
+  && R CMD INSTALL httpgd_2.0.2.tar.gz \
+  && rm httpgd_2.0.2.tar.gz \
   ## Install the R kernel for Jupyter, languageserver and httpgd
   && install2.r --error --deps TRUE --skipinstalled -n $NCPUS \
     IRkernel \
@@ -491,7 +508,10 @@ RUN sh -c "$(curl -fsSL https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master
 COPY --from=files /files /
 COPY --from=files /files/var/backups/skel ${HOME}
 
-EXPOSE 8888
+ARG JUPYTER_PORT=8888
+ENV JUPYTER_PORT=${JUPYTER_PORT}
+
+EXPOSE $JUPYTER_PORT
 
 ## Configure container startup
 ENTRYPOINT ["tini", "-g", "--", "start.sh"]

base/scripts/usr/local/bin/before-notebook.d/12-r.sh

@@ -5,6 +5,9 @@
 set -e
 
 if [ "$(id -u)" == 0 ] ; then
+  if [ "${NB_USER}" = "root" ] && [ "${NB_UID}" = "$(id -u "${NB_USER}")" ] && [ "${NB_GID}" = "$(id -g "${NB_USER}")" ]; then
+    HOME="/home/root"
+  fi
   # Create user's R package library
   RLU=$(run_user_group Rscript -e "cat(Sys.getenv('R_LIBS_USER'))")
   run_user_group mkdir -p "$RLU"

base/scripts/usr/local/bin/start-singleuser.sh

@@ -4,10 +4,7 @@
 
 set -e
 
-# set default ip to 0.0.0.0
-if [[ "${NOTEBOOK_ARGS} $*" != *"--ip="* ]]; then
-    NOTEBOOK_ARGS="--ip=0.0.0.0 ${NOTEBOOK_ARGS}"
-fi
+# JupyterHub singleuser arguments are set using environment variables
 
 echo "Executing: jupyterhub-singleuser" "${NOTEBOOK_ARGS}" "$@"
 # shellcheck disable=SC1091,SC2086

base/scripts/usr/local/bin/start.sh

@@ -116,8 +116,8 @@ if [ "$(id -u)" == 0 ]; then
         userdel "${NB_USER}"
         useradd --no-log-init --home "/home/${NB_USER}${DOMAIN:+@$DOMAIN}" --shell "$(which zsh)" --uid "${NB_UID}" --gid "${NB_GID}" --groups 100 "${NB_USER}"
     else
-        # Otherwise, and if not the jovyan user, add it to the default group
-        if [[ "${NB_USER}" != "jovyan" ]]; then
+        # Otherwise, and if not jovyan or root, add it to the default group
+        if [[ "${NB_USER}" != "jovyan" && "${NB_USER}" != "root" ]]; then
             usermod -a -G 100 "${NB_USER}"
         fi
     fi

common/subtags/devtools/4.4.2.Dockerfile

+ARG BASE_IMAGE=debian
+ARG BASE_IMAGE_TAG=12
+ARG BUILD_ON_IMAGE
+ARG R_VERSION=4.4.2
+
+ARG NODE_VERSION=20.18.1
+ARG CODE_BUILTIN_EXTENSIONS_DIR=/opt/code-server/lib/vscode/extensions
+
+FROM glcr.b-data.ch/nodejs/nsi/${NODE_VERSION}/${BASE_IMAGE}:${BASE_IMAGE_TAG} AS nsi
+
+FROM ${BUILD_ON_IMAGE}:${R_VERSION}
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG BUILD_ON_IMAGE
+
+ARG NODE_VERSION
+ARG CODE_BUILTIN_EXTENSIONS_DIR
+ARG BUILD_START
+
+ENV PARENT_IMAGE=${BUILD_ON_IMAGE}:${R_VERSION} \
+    NODE_VERSION=${NODE_VERSION} \
+    BUILD_DATE=${BUILD_START}
+
+## Prevent Corepack showing the URL when it needs to download software
+ENV COREPACK_ENABLE_DOWNLOAD_PROMPT=0
+
+## Install Node.js
+COPY --from=nsi /usr/local /usr/local
+
+USER root
+
+ENV HOME=/root
+
+WORKDIR ${HOME}
+
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    bats \
+    libkrb5-dev \
+    libsecret-1-dev \
+    libx11-dev \
+    libxkbfile-dev \
+    libxt6 \
+    quilt \
+    rsync \
+  && if [ -n "$PYTHON_VERSION" ]; then \
+    ## make some useful symlinks that are expected to exist
+    ## ("/usr/bin/python" and friends)
+    for src in pydoc3 python3 python3-config; do \
+      dst="$(echo "$src" | tr -d 3)"; \
+      if [ -s "/usr/bin/$src" ] && [ ! -e "/usr/bin/$dst" ]; then \
+        ln -svT "$src" "/usr/bin/$dst"; \
+      fi \
+    done; \
+  fi \
+  ## Clean up Node.js installation
+  && bash -c 'rm -f /usr/local/bin/{docker-entrypoint.sh,yarn*}' \
+  && bash -c 'mv /usr/local/{CHANGELOG.md,LICENSE,README.md} \
+    /usr/local/share/doc/node' \
+  ## Enable corepack (Yarn, pnpm)
+  && corepack enable \
+  ## Install nFPM
+  && echo 'deb [trusted=yes] https://repo.goreleaser.com/apt/ /' \
+    | tee /etc/apt/sources.list.d/goreleaser.list \
+  && apt-get update \
+  && apt-get install -y --no-install-recommends nfpm \
+  ## Install code-server extensions
+  && code-server --extensions-dir "$CODE_BUILTIN_EXTENSIONS_DIR" \
+    --install-extension dbaeumer.vscode-eslint \
+  && code-server --extensions-dir "$CODE_BUILTIN_EXTENSIONS_DIR" \
+    --install-extension esbenp.prettier-vscode \
+  && code-server --extensions-dir "$CODE_BUILTIN_EXTENSIONS_DIR" \
+    --install-extension ms-python.black-formatter \
+  && code-server --extensions-dir "$CODE_BUILTIN_EXTENSIONS_DIR" \
+    --install-extension timonwong.shellcheck \
+  ## Enable shellcheck system-wide
+  && ln -sf "$CODE_BUILTIN_EXTENSIONS_DIR"/timonwong.shellcheck-*/binaries/*/*/shellcheck \
+    /usr/local/bin/shellcheck \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/* \
+    "$HOME/.config" \
+    "$HOME/.local"
+
+## Switch back to ${NB_USER} to avoid accidental container runs as root
+USER ${NB_USER}
+
+ENV HOME=/home/${NB_USER}
+
+WORKDIR ${HOME}

common/subtags/devtools/latest.Dockerfile

@@ -3,7 +3,7 @@ ARG BASE_IMAGE_TAG=12
 ARG BUILD_ON_IMAGE
 ARG R_VERSION
 
-ARG NODE_VERSION=20.18.0
+ARG NODE_VERSION=20.18.1
 ARG CODE_BUILTIN_EXTENSIONS_DIR=/opt/code-server/lib/vscode/extensions
 
 FROM glcr.b-data.ch/nodejs/nsi/${NODE_VERSION}/${BASE_IMAGE}:${BASE_IMAGE_TAG} AS nsi

geospatial/.gitlab-ci.yml

 .env:
   variables:
-    R_VERSION: "4.4.1"
+    R_VERSION: "4.4.2"
     TAG_VERSION_MAJ_MIN: "false"
     TAG_VERSION_MAJ: "false"
 

geospatial/4.4.2.Dockerfile

+ARG BUILD_ON_IMAGE=glcr.b-data.ch/jupyterlab/r/verse
+ARG R_VERSION=4.4.2
+
+FROM ${BUILD_ON_IMAGE}:${R_VERSION}
+
+ARG NCPUS=1
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG BUILD_ON_IMAGE
+ARG BUILD_START
+
+ENV PARENT_IMAGE=${BUILD_ON_IMAGE}:${R_VERSION} \
+    BUILD_DATE=${BUILD_START}
+
+USER root
+
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    libfftw3-dev \
+    libgdal-dev \
+    libgeos-dev \
+    libgsl0-dev \
+    #libgl1-mesa-dev \
+    #libglu1-mesa-dev \
+    libhdf4-alt-dev \
+    #libhdf5-dev \
+    libjq-dev \
+    #libpq-dev \
+    libproj-dev \
+    libprotobuf-dev \
+    libnetcdf-dev \
+    #libsqlite3-dev \
+    #libssl-dev \
+    libudunits2-dev \
+    nco \
+    netcdf-bin \
+    postgis \
+    protobuf-compiler \
+    sqlite3 \
+    tk-dev \
+    #unixodbc-dev
+  && install2.r --error --skipinstalled -n $NCPUS \
+    #RColorBrewer \
+    RNetCDF \
+    classInt \
+    deldir \
+    gstat \
+    hdf5r \
+    lidR \
+    mapdata \
+    mapview \
+    ncdf4 \
+    proj4 \
+    raster \
+    rlas \
+    sf \
+    sfarrow \
+    sp \
+    spacetime \
+    spatstat \
+    spatialreg \
+    spdep \
+    stars \
+    terra \
+    tidync \
+    tmap \
+    geoR \
+    geosphere \
+  ## from bioconductor
+  && R -e "BiocManager::install('rhdf5', update = FALSE, ask = FALSE)" \
+  ## Strip libraries of binary packages installed from P3M
+  && RLS=$(Rscript -e "cat(Sys.getenv('R_LIBS_SITE'))") \
+  && strip ${RLS}/*/libs/*.so \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/*
+
+## Switch back to ${NB_USER} to avoid accidental container runs as root
+USER ${NB_USER}

qgisprocess/.gitlab-ci.yml

 .env:
   variables:
-    R_VERSION: "4.4.1"
-    QGIS_VERSION: "3.40.0"
+    R_VERSION: "4.4.2"
+    QGIS_VERSION: "3.42.0"
     OTB_VERSION: "9.1.0"
     TAG_VERSION_MAJ_MIN: "false"
     TAG_VERSION_MAJ: "false"

qgisprocess/4.4.2.Dockerfile

+ARG BASE_IMAGE=debian
+ARG BASE_IMAGE_TAG=12
+ARG BUILD_ON_IMAGE=glcr.b-data.ch/jupyterlab/r/geospatial
+ARG R_VERSION=4.4.2
+ARG QGIS_VERSION=3.42.0
+
+ARG SAGA_VERSION
+ARG OTB_VERSION
+## OTB_VERSION=9.1.0
+
+ARG PROC_SAGA_NG_VERSION
+
+FROM ${BASE_IMAGE}:${BASE_IMAGE_TAG} AS files
+
+ARG OTB_VERSION
+
+ARG NB_UID=1000
+ENV NB_GID=100
+
+RUN mkdir /files
+
+COPY conf/user /files
+COPY scripts /files
+
+RUN if [ "$(uname -m)" = "x86_64" ]; then \
+    ## QGIS: Set OTB application folder and OTB folder
+    qgis3Ini="/files/var/backups/skel/.local/share/QGIS/QGIS3/profiles/default/QGIS/QGIS3.ini"; \
+    echo "\n[Processing]" >> ${qgis3Ini}; \
+    if [ -z "${OTB_VERSION}" ]; then \
+      echo "Configuration\OTB_APP_FOLDER=/usr/lib/otb/applications" >> \
+        ${qgis3Ini}; \
+      echo "Configuration\OTB_FOLDER=/usr\n" >> ${qgis3Ini}; \
+    else \
+      echo "Configuration\OTB_APP_FOLDER=/usr/local/lib/otb/applications" >> \
+        ${qgis3Ini}; \
+      echo "Configuration\OTB_FOLDER=/usr/local\n" >> ${qgis3Ini}; \
+    fi \
+  fi \
+  && chown -R ${NB_UID}:${NB_GID} /files/var/backups/skel \
+  ## Ensure file modes are correct when using CI
+  ## Otherwise set to 777 in the target image
+  && find /files -type d -exec chmod 755 {} \; \
+  && find /files -type f -exec chmod 644 {} \; \
+  && find /files/usr/local/bin -type f -exec chmod 755 {} \;
+
+FROM glcr.b-data.ch/qgis/qgissi/${QGIS_VERSION}/${BASE_IMAGE}:${BASE_IMAGE_TAG} AS qgissi
+FROM glcr.b-data.ch/saga-gis/saga-gissi${SAGA_VERSION:+/}${SAGA_VERSION:-:none}${SAGA_VERSION:+/$BASE_IMAGE}${SAGA_VERSION:+:$BASE_IMAGE_TAG} AS saga-gissi
+FROM glcr.b-data.ch/orfeotoolbox/otbsi${OTB_VERSION:+/}${OTB_VERSION:-:none}${OTB_VERSION:+/$BASE_IMAGE}${OTB_VERSION:+:$BASE_IMAGE_TAG} AS otbsi
+
+FROM ${BUILD_ON_IMAGE}:${R_VERSION}
+
+ARG NCPUS=1
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG BUILD_ON_IMAGE
+ARG QGIS_VERSION
+ARG SAGA_VERSION
+ARG OTB_VERSION
+ARG PROC_SAGA_NG_VERSION
+ARG BUILD_START
+
+ENV PARENT_IMAGE=${BUILD_ON_IMAGE}:${R_VERSION} \
+    QGIS_VERSION=${QGIS_VERSION} \
+    SAGA_VERSION=${SAGA_VERSION} \
+    OTB_VERSION=${OTB_VERSION} \
+    BUILD_DATE=${BUILD_START}
+
+USER root
+
+ENV HOME=/root \
+    ## GRASS GIS: Make sure the distro's python is used
+    GRASS_PYTHON=/usr/bin/python3
+
+WORKDIR ${HOME}
+
+## Install QGIS
+COPY --from=qgissi /usr /usr
+## Install SAGA GIS
+COPY --from=saga-gissi /usr /usr
+## Install Orfeo Toolbox
+COPY --from=otbsi /usr/local /usr/local
+ENV GDAL_DRIVER_PATH=${OTB_VERSION:+disable} \
+    OTB_APPLICATION_PATH=${OTB_VERSION:+/usr/local/lib/otb/applications} \
+    OTB_INSTALL_DIR=${OTB_VERSION:+/usr/local}
+ENV OTB_APPLICATION_PATH=${OTB_APPLICATION_PATH:-/usr/lib/otb/applications} \
+    OTB_INSTALL_DIR=${OTB_INSTALL_DIR:-/usr}
+
+RUN apt-get update \
+  && apt-get -y install --no-install-recommends \
+    ## Multimedia files trancoding
+    ffmpeg \
+    ## QGIS: Additional runtime dependencies
+    '^libexiv2-[0-9]+$' \
+    '^libgdal[0-9]+$' \
+    libgeos-c1v5 \
+    '^libgsl[0-9]+$' \
+    libjs-jquery \
+    libjs-leaflet \
+    '^libprotobuf-lite[0-9]+$' \
+    libqca-qt5-2-plugins \
+    '^libqscintilla2-qt5-[0-9]+$' \
+    libqt5core5a \
+    libqt5gui5 \
+    libqt5keychain1 \
+    libqt5multimediawidgets5 \
+    libqt5network5 \
+    libqt5quickwidgets5 \
+    libqt5serialport5 \
+    libqt5sql5 \
+    libqt5webkit5 \
+    libqt5widgets5 \
+    libqt5xml5 \
+    libqwt-qt5-6 \
+    '^libspatialindex[0-9]+$' \
+    '^libzip[0-9]+$' \
+    ocl-icd-libopencl1 \
+    qt3d-assimpsceneimport-plugin \
+    qt3d-defaultgeometryloader-plugin \
+    qt3d-gltfsceneio-plugin \
+    qt3d-scene2d-plugin \
+    qt5-image-formats-plugins \
+    ## QGIS: Python 3 Support
+    gdal-bin \
+    libfcgi0ldbl \
+    libsqlite3-mod-spatialite \
+    python3-gdal \
+    python3-jinja2 \
+    python3-lxml \
+    python3-matplotlib \
+    python3-owslib \
+    python3-plotly \
+    python3-psycopg2 \
+    python3-pygments \
+    python3-pyproj \
+    python3-pyqt5 \
+    python3-pyqt5.qsci \
+    python3-pyqt5.qtmultimedia \
+    python3-pyqt5.qtpositioning \
+    python3-pyqt5.qtserialport \
+    python3-pyqt5.qtsql \
+    python3-pyqt5.qtsvg \
+    python3-pyqt5.qtwebkit \
+    python3-sip \
+    python3-yaml \
+    qttools5-dev-tools \
+    ## QGIS: Additional runtime recommendations
+    grass \
+    ## QGIS: Additional runtime suggestions
+    gpsbabel \
+    ## SAGA GIS: Supplementary runtime dependencies [^1]
+    libdxflib3 \
+    libhpdf-2.3.0 \
+    libsvm3 \
+    libwxgtk3.*-dev \
+    $(test -z "${SAGA_VERSION}" && echo "saga") \
+  ## Orfeo Toolbox: Supplementary runtime dependencies
+  && if [ "$(uname -m)" = "x86_64" ]; then \
+    apt-get -y install --no-install-recommends \
+      '^libboost-filesystem[0-9].[0-9]+.[0-9]$' \
+      '^libboost-serialization[0-9].[0-9]+.[0-9]$' \
+      libglew2.* \
+      '^libinsighttoolkit4.[0-9]+$' \
+      libmuparser2v5 \
+      libmuparserx4.* \
+      '^libopencv-core[0-9][0-9.][0-9][a-z]?$' \
+      '^libopencv-ml[0-9][0-9.][0-9][a-z]?$' \
+      libtinyxml-dev \
+      $(test -z "${OTB_VERSION}" && echo "otb-* monteverdi"); \
+    if [ ! -z "${OTB_VERSION}" ]; then \
+      if [ "$(echo ${OTB_VERSION} | cut -c 1)" -lt "8" ]; then \
+        apt-get -y install --no-install-recommends \
+          '^libopenthreads[0-9]+$' \
+          libossim1; \
+      fi; \
+      ## Orfeo Toolbox: Clean up installation
+      bash -c 'rm -rf /usr/local/{otbenv.profile,recompile_bindings.sh,tools}'; \
+      if [ -f /usr/local/README ]; then \
+        mv /usr/local/README /usr/local/share/doc/otb; \
+      fi; \
+      if [ -f /usr/local/LICENSE ]; then \
+        mv /usr/local/LICENSE /usr/local/share/doc/otb; \
+      fi \
+    else \
+      mkdir -p /usr/lib/otb; \
+      ln -rs /usr/lib/$(uname -m)-linux-gnu/otb/applications \
+        /usr/lib/otb/applications; \
+    fi \
+  fi \
+  ## GRASS GIS: Configure dynamic linker run time bindings
+  && echo "$(grass --config path)/lib" | tee /etc/ld.so.conf.d/libgrass.conf \
+  && ldconfig \
+  ## SAGA GIS: Add en_GB.UTF-8 and update locale
+  && sed -i "s/# $LANG/$LANG/g" /etc/locale.gen \
+  && sed -i "s/# en_GB.UTF-8/en_GB.UTF-8/g" /etc/locale.gen \
+  && locale-gen \
+  ## [^1]: SAGA GIS: libvigraimpex11 is not available for jammy
+  && if $(! grep -q "jammy" /etc/os-release); then \
+    apt-get -y install --no-install-recommends '^libvigraimpex[0-9]+$'; \
+  fi \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/* \
+    ${HOME}/.cache \
+    ${HOME}/.grass*
+
+## Install QGIS related stuff
+RUN apt-get update \
+  ## Install QGIS-Plugin-Manager
+  && apt-get -y install --no-install-recommends python3-pip \
+  && export PIP_BREAK_SYSTEM_PACKAGES=1 \
+  && /usr/bin/pip install qgis-plugin-manager \
+  ## Install qgisprocess, the R interface to QGIS
+  && install2.r --error --skipinstalled -n $NCPUS qgisprocess \
+  ## Strip libraries of binary packages installed from P3M
+  && RLS=$(Rscript -e "cat(Sys.getenv('R_LIBS_SITE'))") \
+  && strip ${RLS}/*/libs/*.so \
+  ## Clean up
+  && if [ ! -z "$PYTHON_VERSION" ]; then \
+    apt-get -y purge python3-pip; \
+    apt-get -y autoremove; \
+  fi \
+  && rm -rf /var/lib/apt/lists/* \
+    ${HOME}/.cache \
+    ${HOME}/.config \
+    ${HOME}/.local
+
+## Switch back to ${NB_USER} to avoid accidental container runs as root
+USER ${NB_USER}
+
+ENV HOME=/home/${NB_USER} \
+    ## Qt: Support running on headless computer
+    QT_QPA_PLATFORM=offscreen
+
+WORKDIR ${HOME}
+
+## Copy files as late as possible to avoid cache busting
+COPY --from=files /files /
+COPY --from=files /files/var/backups/skel ${HOME}
+
+  ## QGIS: Install plugin 'Processing Saga NextGen Provider'
+RUN mkdir -p ${HOME}/.local/share/QGIS/QGIS3/profiles/default/python/plugins \
+  && cd ${HOME}/.local/share/QGIS/QGIS3/profiles/default/python/plugins \
+  && qgis-plugin-manager init \
+  && qgis-plugin-manager update \
+  && qgis-plugin-manager install 'Processing Saga NextGen Provider'=="${PROC_SAGA_NG_VERSION:-0.0.7}" \
+  ## QGIS: Enable plugins
+  && qgis_process plugins enable processing_saga_nextgen \
+  && qgis_process plugins enable grassprovider \
+  && if [ "$(uname -m)" = "x86_64" ]; then \
+    ## QGIS: Install and enable OTB plugin
+    qgis-plugin-manager install 'OrfeoToolbox Provider'; \
+    qgis_process plugins enable orfeoToolbox_provider; \
+  fi \
+  && rm -rf .cache_qgis_plugin_manager \
+  ## Clean up
+  && rm -rf \
+    ${HOME}/.cache/QGIS \
+    ${HOME}/.cache/qgis_process_ \
+    ${HOME}/.config \
+    ${HOME}/.grass* \
+  ## Create backup of QGIS settings
+  && cp -a ${HOME}/.local/share/QGIS /var/backups/skel/.local/share
+
+ENV PYTHONPATH=${PYTHONPATH:+$PYTHONPATH:}${OTB_VERSION:+/usr/local/lib/otb/python}

qgisprocess/latest.Dockerfile

@@ -209,15 +209,6 @@ RUN apt-get update \
   && apt-get -y install --no-install-recommends python3-pip \
   && export PIP_BREAK_SYSTEM_PACKAGES=1 \
   && /usr/bin/pip install qgis-plugin-manager \
-  ## QGIS: Make sure qgis_mapserver and qgis_process find the qgis module
-  && cp -a $(which qgis_mapserver) $(which qgis_mapserver)_ \
-  && echo '#!/bin/bash' > $(which qgis_mapserver) \
-  && echo "PYTHONPATH=/usr/lib/python3/dist-packages $(which qgis_mapserver)_ \"\${@}\"" >> \
-    $(which qgis_mapserver) \
-  && cp -a $(which qgis_process) $(which qgis_process)_ \
-  && echo '#!/bin/bash' > $(which qgis_process) \
-  && echo "PYTHONPATH=/usr/lib/python3/dist-packages $(which qgis_process)_ \"\${@}\"" >> \
-    $(which qgis_process) \
   ## Install qgisprocess, the R interface to QGIS
   && install2.r --error --skipinstalled -n $NCPUS qgisprocess \
   ## Strip libraries of binary packages installed from P3M

tidyverse/.gitlab-ci.yml

 .env:
   variables:
-    R_VERSION: "4.4.1"
+    R_VERSION: "4.4.2"
     TAG_VERSION_MAJ_MIN: "false"
     TAG_VERSION_MAJ: "false"