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Notes

This docker stack uses modified startup scripts from jupyter/docker-stacks.
ℹ️ Nevertheless, all Docker Options and Permission-specific configurations can be used for the images of this docker stack.

Tweaks

In comparison to jupyter/docker-stacks and/or rocker-org/rocker-versioned2, these images are tweaked as follows:

Jupyter startup scripts

Shell script /usr/local/bin/start.sh is modified to

  • allow bind mounting of a home directory.
  • reset CODE_WORKDIR for custom NB_USERs.

Jupyter startup hooks

The following startup hooks are put in place:

Custom scripts

/usr/local/bin/busy is executed during screen/tmux sessions to update the last-activity timestamps on JupyterHub.

ℹ️ This prevents the JupyterHub Idle Culler Service from shutting down idle or long-running Jupyter Notebook servers, allowing for unattended computations.

Environment variables

  • CRAN: The CRAN mirror URL.
  • R_BINARY_PACKAGES: R package type to use.
    • unset: Source packages. (default)
    • 1/yes: Binary packages.
  • DOWNLOAD_STATIC_LIBV8=1: R (V8): Installing V8 on Linux, the alternative way.
  • RETICULATE_MINICONDA_ENABLED=0: R (reticulate): Disable prompt to install miniconda.
  • CS_DISABLE_GETTING_STARTED_OVERRIDE=1: code-server: Hide the coder/coder promotion in Help: Getting Started

Versions

  • R_VERSION
  • PYTHON_VERSION
  • JUPYTERHUB_VERSION
  • JUPYTERLAB_VERSION
  • CODE_SERVER_VERSION
  • RSTUDIO_VERSION
  • NEOVIM_VERSION
  • GIT_VERSION
  • GIT_LFS_VERSION
  • PANDOC_VERSION
  • QUARTO_VERSION (verse+ images)

Miscellaneous

  • BASE_IMAGE: Its very base, a Docker Official Image.
  • PARENT_IMAGE: The image it was derived from.
  • BUILD_DATE: The date it was built (ISO 8601 format).
  • CTAN_REPO: The CTAN mirror URL. (verse+ images)

MRAN

Environment variable MRAN is deprecated:

After January 31, 2023, we [Microsoft] will no longer maintain the CRAN Time Machine snapshots.

Current situation regarding frozen images:

  • R version < 4.2.2: MRAN retired; CRAN snapshots broken.
  • 4.2.2 ≤ R version < 4.3.1: No CRAN snapshots available.
    • Use renv to create reproducible environments for your R projects.
  • R version ≥ 4.3.1: CRAN snapshots reinstated (P3M).

Shell

The default shell is Zsh, further enhanced with

Extensions (code-server)

Pre-installed extensions are treated as built-in and therefore cannot be updated at user level.

TeX packages (verse+ images)

In addition to the TeX packages used in rocker/verse, jupyter/scipy-notebook and required for nbconvert, the packages requested by the community are installed.

Settings

Default

  • R: $(R RHOME)/etc/Rprofile.site
    • IRkernel: Only enable image/svg+xml and application/pdf for plot display.
    • R Extension (code-server): Disable help panel and revert to old behaviour.
  • IPython:
    • Only enable figure formats svg and pdf for IPython.
  • JupyterLab:
  • code-server
    • Features > Chat > Disable AI Features: true
    • Text Editor > Tab Size: 2
    • Extensions > GitLab Workflow
      • GitLab Duo Pro > Duo Code Suggestions: false
      • GitLab Duo Pro > Duo Chat: false
      • GitLab Duo Pro > Duo Agent Platform: false
      • GitLab Duo Pro > Enabled Without Gitlab Project: false
    • Extensions > GitLens — Git supercharged
      • General > Show Welcome On Install: false
      • General > Show Whats New After Upgrade: false
      • Graph commands disabled where possible
    • Extensions > Python
      • Language Server: Jedi
    • Extensions > R
      • Bracketed Paste: true
      • Plot: Use Httpgd: true
      • Rterm: Linux: /usr/local/bin/arf
        ℹ️ If set to /usr/local/bin/radian, it will execute /usr/local/bin/arf for backwards compatibility.
      • Rterm: Option: ["--no-save", "--no-restore"]
      • Workspace Viewer: Show Object Size: true
    • Extensions > Resource Monitor Configuration
      • Show: Battery: false
      • Show: Cpufreq: false
    • Application > Telemetry: Telemetry Level: off
    • Features > Terminal > Integrated: Font Family: MesloLGS NF
    • Workbench > Appearance > Color Theme: Default Dark Modern
  • QGIS (qgisprocess images):
    • Append /usr/lib/python3/dist-packages to PYTHONPATH.
      ℹ️ 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
      • Update last-activity timestamps while in screen/tmux session
    • Powerlevel10k wizard options:
      • nerdfont-v3 + powerline
      • small icons
      • rainbow
      • unicode
      • 24h time
      • angled separators
      • sharp heads
      • flat tails
      • 2 lines
      • dotted
      • left frame
      • light-ornaments
      • sparse
      • many icons
      • concise
      • instant_prompt=off
  • Bash: /etc/profile.d/00-reset-path.sh and /etc/skel/.profile
    • Update PATH for login shells, e.g. when started as a server associated with JupyterHub.

Customise

  • R: Create file ~/.Rprofile
    • Valid plot mimetypes: image/png, image/jpeg, image/svg+xml, application/pdf.
      ℹ️ MIME type text/plain must always be specified.
  • IPython: Create file ~/.ipython/profile_default/ipython_config.py
    • Valid figure formats: png, retina, jpeg, svg, pdf.
  • JupyterLab: Settings > Advanced Settings Editor
  • code-server: Manage > Settings
  • Zsh
    • Oh My Zsh: Edit ~/.zshrc.
    • Powerlevel10k: Run p10k configure or edit ~/.p10k.zsh.
      • Update command: git -C ${ZSH_CUSTOM:-$HOME/.oh-my-zsh/custom}/themes/powerlevel10k pull

Python

The Python version is selected as follows:

This Python version is installed at /usr/local/bin.

Additional notes on CUDA

The CUDA version is selected as follows:

  • CUDA: The lastest version that has image flavour devel including cuDNN available.

Tweaks

  • Provide NVBLAS-enabled R_ and Rscript_.
    • Enabled at runtime and only if nvidia-smi and at least one GPU are present.

Environment variables

Versions

  • CUDA_VERSION

Miscellaneous

  • CUDA_IMAGE: The CUDA image it is derived from.

Settings

Default

  • code-server
    • Extensions > R > Rterm: Linux: /usr/local/bin/R

Basic Linear Algebra Subprograms (BLAS)

These images use OpenBLAS by default.

To have R and Rscript use NVBLAS instead,

  1. copy the NVBLAS-enabled executables to ~/.local/bin 
    for file in $(which {R,Rscript}); do
  cp "$file"_ "$HOME/.local/bin/$(basename "$file")";
done
  2. set Extensions > R > Rterm > Linux: /home/USER/.local/bin/R in code-server settings
    👉 Substitute USER with your user name.

and restart the R terminal.

ℹ️ The xgboost package benefits greatly from NVBLAS, if it is installed correctly.

Additional notes on subtag devtools

Node.js is installed with corepack enabled by default. Use it to manage Yarn and/or pnpm:

System Python

Package libsecret-1-dev depends on python3 from the system's package repository.

The system's Python version is installed at /usr/bin.

ℹ️ Because a more recent Python version is installed at /usr/local/bin, it takes precedence over the system's Python version.