Freeze Python v3.13.0

Author: benz0li

VERSION_MATRIX.md

@@ -43,7 +43,7 @@ Topmost entry = Tag `latest`
 
 | Python     | CTAN date  | Quarto      |
 |:-----------|:-----------|:------------|
-| 3.13.0[^1] |            | 1.6.39      |
+| 3.13.0[^1] | 2024‑12‑03 | 1.6.39      |
 | 3.12.8     |            | 1.6.39      |
 | 3.12.7     | 2024‑12‑03 | 1.6.39      |
 | 3.11.10    | 2024‑12‑03 | 1.6.39      |

base/.gitlab-ci.yml

@@ -1,7 +1,7 @@
 .env:
   variables:
-    PYTHON_VERSION: "3.12.8"
-    TAG_VERSION_MAJ_MIN: "true"
+    PYTHON_VERSION: "3.13.0"
+    TAG_VERSION_MAJ_MIN: "false"
     TAG_VERSION_MAJ: "false"
 
 .before-script-build: &before-script-build

base/3.13.0.Dockerfile

@@ -0,0 +1,334 @@
+ARG BASE_IMAGE=debian
+ARG BASE_IMAGE_TAG=12
+ARG BUILD_ON_IMAGE=glcr.b-data.ch/python/ver
+ARG PYTHON_VERSION=3.13.0
+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 CODE_BUILTIN_EXTENSIONS_DIR=/opt/code-server/lib/vscode/extensions
+ARG CODE_SERVER_VERSION=4.95.3
+ARG NEOVIM_VERSION=0.10.2
+ARG GIT_VERSION=2.47.1
+ARG GIT_LFS_VERSION=3.6.0
+ARG PANDOC_VERSION=3.4
+
+FROM ${BUILD_ON_IMAGE}${PYTHON_VERSION:+:}${PYTHON_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMAGE_FLAVOR} AS files
+
+ARG NB_UID
+ENV NB_GID=100
+
+RUN mkdir /files
+
+COPY assets /files
+COPY conf/ipython /files
+COPY conf/jupyter /files
+COPY conf/jupyterlab /files
+COPY conf/shell /files
+COPY conf${CUDA_IMAGE:+/cuda}/shell /files
+COPY conf/user /files
+COPY scripts /files
+
+  ## Copy content of skel directory to backup
+RUN cp -a /files/etc/skel/. /files/var/backups/skel \
+  && chown -R ${NB_UID}:${NB_GID} /files/var/backups/skel \
+  ## Copy custom fonts
+  && mkdir -p /files/usr/local/share/jupyter/lab/static/assets \
+  && cp -a /files/opt/code-server/src/browser/media/css \
+    /files/usr/local/share/jupyter/lab/static/assets \
+  && cp -a /files/opt/code-server/src/browser/media/fonts \
+    /files/usr/local/share/jupyter/lab/static/assets \
+  && if [ -n "${CUDA_VERSION}" ]; then \
+    ## Use entrypoint of CUDA image
+    mv /opt/nvidia/entrypoint.d /opt/nvidia/nvidia_entrypoint.sh \
+      /files/usr/local/bin; \
+    mv /files/usr/local/bin/start.sh \
+      /files/usr/local/bin/entrypoint.d/99-start.sh; \
+    mv /files/usr/local/bin/nvidia_entrypoint.sh \
+      /files/usr/local/bin/start.sh; \
+  fi \
+  ## Ensure file modes are correct when using CI
+  ## Otherwise set to 777 in the target image
+  && find /files -type d -exec chmod 755 {} \; \
+  && find /files -type f -exec chmod 644 {} \; \
+  && find /files/usr/local/bin -type f -exec chmod 755 {} \; \
+  && find /files/etc/profile.d -type f -exec chmod 755 {} \;
+
+FROM glcr.b-data.ch/neovim/nvsi:${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 ${BUILD_ON_IMAGE}${PYTHON_VERSION:+:}${PYTHON_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMAGE_FLAVOR}
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG BUILD_ON_IMAGE
+ARG CUDA_IMAGE_FLAVOR
+ARG NB_USER
+ARG NB_UID
+ARG JUPYTERHUB_VERSION
+ARG JUPYTERLAB_VERSION
+ARG CODE_BUILTIN_EXTENSIONS_DIR
+ARG CODE_SERVER_VERSION
+ARG NEOVIM_VERSION
+ARG GIT_VERSION
+ARG GIT_LFS_VERSION
+ARG PANDOC_VERSION
+ARG BUILD_START
+
+ARG CODE_WORKDIR
+
+ARG CUDA_IMAGE_LICENSE=${CUDA_VERSION:+"NVIDIA Deep Learning Container License"}
+ARG IMAGE_LICENSE=${CUDA_IMAGE_LICENSE:-"MIT"}
+ARG IMAGE_SOURCE=https://gitlab.b-data.ch/jupyterlab/python/docker-stack
+ARG IMAGE_VENDOR="b-data GmbH"
+ARG IMAGE_AUTHORS="Olivier Benz <olivier.benz@b-data.ch>"
+
+LABEL org.opencontainers.image.licenses="$IMAGE_LICENSE" \
+      org.opencontainers.image.source="$IMAGE_SOURCE" \
+      org.opencontainers.image.vendor="$IMAGE_VENDOR" \
+      org.opencontainers.image.authors="$IMAGE_AUTHORS"
+
+ENV PARENT_IMAGE=${BUILD_ON_IMAGE}${PYTHON_VERSION:+:}${PYTHON_VERSION}${CUDA_IMAGE_FLAVOR:+-}${CUDA_IMAGE_FLAVOR} \
+    NB_USER=${NB_USER} \
+    NB_UID=${NB_UID} \
+    JUPYTERHUB_VERSION=${JUPYTERHUB_VERSION} \
+    JUPYTERLAB_VERSION=${JUPYTERLAB_VERSION} \
+    CODE_SERVER_VERSION=${CODE_SERVER_VERSION} \
+    NEOVIM_VERSION=${NEOVIM_VERSION} \
+    GIT_VERSION=${GIT_VERSION} \
+    GIT_LFS_VERSION=${GIT_LFS_VERSION} \
+    PANDOC_VERSION=${PANDOC_VERSION} \
+    BUILD_DATE=${BUILD_START}
+
+ENV NB_GID=100
+
+## Install Neovim
+COPY --from=nvsi /usr/local /usr/local
+## Install Git
+COPY --from=gsi /usr/local /usr/local
+## Install Git LFS
+COPY --from=glfsi /usr/local /usr/local
+
+USER root
+
+RUN dpkgArch="$(dpkg --print-architecture)" \
+  ## Unminimise if the system has been minimised
+  && if [ $(command -v unminimize) ]; then \
+    yes | unminimize; \
+  fi \
+  && apt-get update \
+  && apt-get -y install --no-install-recommends \
+    bash-completion \
+    build-essential \
+    curl \
+    file \
+    fontconfig \
+    g++ \
+    gcc \
+    gfortran \
+    gnupg \
+    htop \
+    info \
+    jq \
+    libclang-dev \
+    man-db \
+    nano \
+    ncdu \
+    procps \
+    psmisc \
+    screen \
+    sudo \
+    swig \
+    tmux \
+    vim-tiny \
+    wget \
+    zsh \
+    ## Neovim: Additional runtime recommendations
+    ripgrep \
+    ## Git: Additional runtime dependencies
+    libcurl3-gnutls \
+    liberror-perl \
+    ## Git: Additional runtime recommendations
+    less \
+    ssh-client \
+  ## Python: Additional dev dependencies
+  && if [ -z "$PYTHON_VERSION" ]; then \
+    apt-get -y install --no-install-recommends \
+      python3-dev \
+      ## Install Python package installer
+      ## (dep: python3-distutils, python3-setuptools and python3-wheel)
+      python3-pip \
+      ## Install venv module for python3
+      python3-venv; \
+    ## 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; \
+  else \
+    ## Force update pip, setuptools and wheel
+    pip install --upgrade --force-reinstall pip; \
+  fi \
+  ## Install font MesloLGS NF
+  && mkdir -p /usr/share/fonts/truetype/meslo \
+  && curl -sL https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Regular.ttf -o "/usr/share/fonts/truetype/meslo/MesloLGS NF Regular.ttf" \
+  && curl -sL https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Bold.ttf -o "/usr/share/fonts/truetype/meslo/MesloLGS NF Bold.ttf" \
+  && curl -sL https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Italic.ttf -o "/usr/share/fonts/truetype/meslo/MesloLGS NF Italic.ttf" \
+  && curl -sL https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Bold%20Italic.ttf -o "/usr/share/fonts/truetype/meslo/MesloLGS NF Bold Italic.ttf" \
+  && fc-cache -fsv \
+  ## Git: Set default branch name to main
+  && git config --system init.defaultBranch main \
+  ## Git: Store passwords for one hour in memory
+  && git config --system credential.helper "cache --timeout=3600" \
+  ## Git: Merge the default branch from the default remote when "git pull" is run
+  && git config --system pull.rebase false \
+  ## Install pandoc
+  && curl -sLO https://github.com/jgm/pandoc/releases/download/${PANDOC_VERSION}/pandoc-${PANDOC_VERSION}-1-${dpkgArch}.deb \
+  && dpkg -i pandoc-${PANDOC_VERSION}-1-${dpkgArch}.deb \
+  && rm pandoc-${PANDOC_VERSION}-1-${dpkgArch}.deb \
+  ## Delete potential user with UID 1000
+  && if grep -q 1000 /etc/passwd; then \
+    userdel --remove $(id -un 1000); \
+  fi \
+  ## Do not set user limits for sudo/sudo-i
+  && sed -i 's/.*pam_limits.so/#&/g' /etc/pam.d/sudo \
+  && if [ -f "/etc/pam.d/sudo-i" ]; then \
+    sed -i 's/.*pam_limits.so/#&/g' /etc/pam.d/sudo-i; \
+  fi \
+  ## Add user
+  && useradd -l -m -s $(which zsh) -N -u ${NB_UID} ${NB_USER} \
+  ## Mark home directory as populated
+  && touch /home/${NB_USER}/.populated \
+  && chown ${NB_UID}:${NB_GID} /home/${NB_USER}/.populated \
+  && chmod go+w /home/${NB_USER}/.populated \
+  ## Create backup directory for home directory
+  && mkdir -p /var/backups/skel \
+  && chown ${NB_UID}:${NB_GID} /var/backups/skel \
+  ## Install Tini
+  && curl -sL https://github.com/krallin/tini/releases/download/v0.19.0/tini-${dpkgArch} -o /usr/local/bin/tini \
+  && chmod +x /usr/local/bin/tini \
+  ## Clean up
+  && rm -rf /tmp/* \
+  && rm -rf /var/lib/apt/lists/* \
+    ${HOME}/.cache
+
+ENV PATH=/opt/code-server/bin:$PATH \
+    CS_DISABLE_GETTING_STARTED_OVERRIDE=1
+
+## Install code-server
+RUN mkdir /opt/code-server \
+  && cd /opt/code-server \
+  && curl -sL https://github.com/coder/code-server/releases/download/v${CODE_SERVER_VERSION}/code-server-${CODE_SERVER_VERSION}-linux-$(dpkg --print-architecture).tar.gz | tar zxf - --no-same-owner --strip-components=1 \
+  ## Copy custom fonts
+  && mkdir -p /opt/code-server/src/browser/media/fonts \
+  && cp -a /usr/share/fonts/truetype/meslo/*.ttf /opt/code-server/src/browser/media/fonts \
+  ## Include custom fonts
+  && sed -i 's|</head>|	<link rel="preload" href="{{BASE}}/_static/src/browser/media/fonts/MesloLGS NF Regular.woff2" as="font" type="font/woff2" crossorigin="anonymous">\n	</head>|g' /opt/code-server/lib/vscode/out/vs/code/browser/workbench/workbench.html \
+  && sed -i 's|</head>|	<link rel="preload" href="{{BASE}}/_static/src/browser/media/fonts/MesloLGS NF Italic.woff2" as="font" type="font/woff2" crossorigin="anonymous">\n	</head>|g' /opt/code-server/lib/vscode/out/vs/code/browser/workbench/workbench.html \
+  && sed -i 's|</head>|	<link rel="preload" href="{{BASE}}/_static/src/browser/media/fonts/MesloLGS NF Bold.woff2" as="font" type="font/woff2" crossorigin="anonymous">\n	</head>|g' /opt/code-server/lib/vscode/out/vs/code/browser/workbench/workbench.html \
+  && sed -i 's|</head>|	<link rel="preload" href="{{BASE}}/_static/src/browser/media/fonts/MesloLGS NF Bold Italic.woff2" as="font" type="font/woff2" crossorigin="anonymous">\n	</head>|g' /opt/code-server/lib/vscode/out/vs/code/browser/workbench/workbench.html \
+  && sed -i 's|</head>|	<link rel="stylesheet" type="text/css" href="{{BASE}}/_static/src/browser/media/css/fonts.css">\n	</head>|g' /opt/code-server/lib/vscode/out/vs/code/browser/workbench/workbench.html \
+  ## Install code-server extensions
+  && cd /tmp \
+  && curl -sLO https://dl.b-data.ch/vsix/piotrpalarz.vscode-gitignore-generator-1.0.3.vsix \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension piotrpalarz.vscode-gitignore-generator-1.0.3.vsix \
+  && curl -sLO https://dl.b-data.ch/vsix/mutantdino.resourcemonitor-1.0.7.vsix \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension mutantdino.resourcemonitor-1.0.7.vsix \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension alefragnani.project-manager \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension GitHub.vscode-pull-request-github \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension GitLab.gitlab-workflow \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension ms-python.python \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension ms-toolsai.jupyter \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension christian-kohler.path-intellisense \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension eamodio.gitlens@11.7.0 \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension mhutchie.git-graph \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension redhat.vscode-yaml \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension grapecity.gc-excelviewer \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension editorconfig.editorconfig \
+  && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension DavidAnson.vscode-markdownlint \
+  ## Create folders temp and tmp for Jupyter extension
+  && cd /opt/code-server/lib/vscode/extensions/ms-toolsai.jupyter-* \
+  && mkdir -m 1777 temp \
+  && mkdir -m 1777 tmp \
+  ## Clean up
+  && rm -rf /tmp/* \
+    ${HOME}/.config \
+    ${HOME}/.local
+
+## Install JupyterLab
+RUN export PIP_BREAK_SYSTEM_PACKAGES=1 \
+  && pip install \
+    jupyter-server-proxy \
+    jupyterhub==${JUPYTERHUB_VERSION} \
+    jupyterlab==${JUPYTERLAB_VERSION} \
+    jupyterlab-git \
+    jupyterlab-lsp \
+    notebook \
+    nbclassic \
+    nbconvert \
+    python-lsp-server[all] \
+  ## Jupyter Server Proxy: Set maximum allowed HTTP body size to 10 GiB
+  && sed -i 's/AsyncHTTPClient(/AsyncHTTPClient(max_body_size=10737418240, /g' \
+    /usr/local/lib/python*/*-packages/jupyter_server_proxy/handlers.py \
+  ## Jupyter Server Proxy: Set maximum allowed websocket message size to 1 GiB
+  && sed -i 's/"_default_max_message_size",.*$/"_default_max_message_size", 1024 \* 1024 \* 1024/g' \
+    /usr/local/lib/python*/*-packages/jupyter_server_proxy/websocket.py \
+  && sed -i 's/_default_max_message_size =.*$/_default_max_message_size = 1024 \* 1024 \* 1024/g' \
+    /usr/local/lib/python*/*-packages/tornado/websocket.py \
+  ## Copy custom fonts
+  && mkdir -p /usr/local/share/jupyter/lab/static/assets/fonts \
+  && cp -a /usr/share/fonts/truetype/meslo/*.ttf /usr/local/share/jupyter/lab/static/assets/fonts \
+  ## Include custom fonts
+  && sed -i 's|</head>|<link rel="preload" href="{{page_config.fullStaticUrl}}/assets/fonts/MesloLGS NF Regular.woff2" as="font" type="font/woff2" crossorigin="anonymous"></head>|g' /usr/local/share/jupyter/lab/static/index.html \
+  && sed -i 's|</head>|<link rel="preload" href="{{page_config.fullStaticUrl}}/assets/fonts/MesloLGS NF Italic.woff2" as="font" type="font/woff2" crossorigin="anonymous"></head>|g' /usr/local/share/jupyter/lab/static/index.html \
+  && sed -i 's|</head>|<link rel="preload" href="{{page_config.fullStaticUrl}}/assets/fonts/MesloLGS NF Bold.woff2" as="font" type="font/woff2" crossorigin="anonymous"></head>|g' /usr/local/share/jupyter/lab/static/index.html \
+  && sed -i 's|</head>|<link rel="preload" href="{{page_config.fullStaticUrl}}/assets/fonts/MesloLGS NF Bold Italic.woff2" as="font" type="font/woff2" crossorigin="anonymous"></head>|g' /usr/local/share/jupyter/lab/static/index.html \
+  && sed -i 's|</head>|<link rel="stylesheet" type="text/css" href="{{page_config.fullStaticUrl}}/assets/css/fonts.css"></head>|g' /usr/local/share/jupyter/lab/static/index.html \
+  ## Clean up
+  && rm -rf /tmp/* \
+    ${HOME}/.cache
+
+## Switch back to ${NB_USER} to avoid accidental container runs as root
+USER ${NB_USER}
+
+ENV HOME=/home/${NB_USER} \
+    CODE_WORKDIR=${CODE_WORKDIR:-/home/${NB_USER}/projects} \
+    SHELL=/usr/bin/zsh \
+    TERM=xterm-256color
+
+WORKDIR ${HOME}
+
+## Install Oh My Zsh with Powerlevel10k theme
+RUN sh -c "$(curl -fsSL https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh)" "" --unattended \
+  && git clone --depth=1 https://github.com/romkatv/powerlevel10k.git ${HOME}/.oh-my-zsh/custom/themes/powerlevel10k \
+  && ${HOME}/.oh-my-zsh/custom/themes/powerlevel10k/gitstatus/install -f \
+  && sed -i 's/ZSH="\/home\/jovyan\/.oh-my-zsh"/ZSH="$HOME\/.oh-my-zsh"/g' ${HOME}/.zshrc \
+  && sed -i 's/ZSH_THEME="robbyrussell"/ZSH_THEME="powerlevel10k\/powerlevel10k"/g' ${HOME}/.zshrc \
+  && echo "\n# set PATH so it includes user's private bin if it exists\nif [ -d \"\$HOME/bin\" ] && [[ \"\$PATH\" != *\"\$HOME/bin\"* ]] ; then\n    PATH=\"\$HOME/bin:\$PATH\"\nfi" | tee -a ${HOME}/.bashrc ${HOME}/.zshrc \
+  && echo "\n# set PATH so it includes user's private bin if it exists\nif [ -d \"\$HOME/.local/bin\" ] && [[ \"\$PATH\" != *\"\$HOME/.local/bin\"* ]] ; then\n    PATH=\"\$HOME/.local/bin:\$PATH\"\nfi" | tee -a ${HOME}/.bashrc ${HOME}/.zshrc \
+  && echo "\n# Update last-activity timestamps while in screen/tmux session\nif [ ! -z \"\$TMUX\" -o ! -z \"\$STY\" ] ; then\n    busy &\nfi" >> ${HOME}/.bashrc \
+  && echo "\n# Update last-activity timestamps while in screen/tmux session\nif [ ! -z \"\$TMUX\" -o ! -z \"\$STY\" ] ; then\n    setopt nocheckjobs\n    busy &\nfi" >> ${HOME}/.zshrc \
+  && echo "\n# To customize prompt, run \`p10k configure\` or edit ~/.p10k.zsh." >> ${HOME}/.zshrc \
+  && echo "[[ ! -f ~/.p10k.zsh ]] || source ~/.p10k.zsh" >> ${HOME}/.zshrc \
+  ## Create user's private bin
+  && mkdir -p ${HOME}/.local/bin \
+  ## Record population timestamp
+  && date -uIseconds > ${HOME}/.populated \
+  ## Create backup of home directory
+  && cp -a ${HOME}/. /var/backups/skel
+
+## Copy files as late as possible to avoid cache busting
+COPY --from=files /files /
+COPY --from=files /files/var/backups/skel ${HOME}
+
+EXPOSE 8888
+
+## Configure container startup
+ENTRYPOINT ["tini", "-g", "--", "start.sh"]
+CMD ["start-notebook.sh"]