base: Update JupyterLab to v4.0.9

VERSION_MATRIX.md

@@ -4,7 +4,7 @@ Topmost entry = Tag `latest`
 
 | Python     | Jupyter Hub | Jupyter Lab | code‑server (Code) | Git    | Git LFS | Pandoc | CTAN date[^2] | Quarto[^2]  | Linux distro |
 |:-----------|:------------|:------------|:-------------------|:-------|:--------|:-------|:--------------|:------------|:-------------|
-| 3.11.6     | 4.0.2       | 3.6.6       | 4.19.0 (1.84.2)    | 2.43.0 | 3.4.0   | 3.1.1  |               | 1.3.450     | Debian 12    |
+| 3.11.6     | 4.0.2       | 4.0.9       | 4.19.0 (1.84.2)    | 2.43.0 | 3.4.0   | 3.1.1  |               | 1.3.450     | Debian 12    |
 | 3.11.5     | 4.0.2       | 3.6.6       | 4.17.1 (1.82.2)    | 2.42.0 | 3.4.0   | 3.1.1  | 2023‑10‑02    | 1.3.450     | Debian 12    |
 | 3.11.4     | 4.0.2       | 3.6.5       | 4.16.1 (1.80.2)    | 2.42.0 | 3.4.0   | 3.1.1  | 2023‑08‑24    | 1.3.450     | Debian 12    |
 | 3.10.13    | 4.0.2       | 3.6.5       | 4.16.1 (1.80.2)    | 2.42.0 | 3.4.0   | 3.1.1  | 2023‑08‑24    | 1.3.450     | Debian 12    |

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

@@ -1,14 +1,15 @@
 # Copyright (c) Jupyter Development Team.
 # Distributed under the terms of the Modified BSD License.
-
+# mypy: ignore-errors
 import os
 import shutil
 import stat
 import subprocess
+from pathlib import Path
 
 from jupyter_core.paths import jupyter_data_dir
 
-c = get_config()
+c = get_config()  # noqa: F821
 c.ServerApp.ip = "0.0.0.0"
 c.ServerApp.port = 8888
 #c.ServerApp.open_browser = False
@@ -61,15 +62,14 @@ def _codeserver_command(port):
 [req_distinguished_name]
 """
 if "GEN_CERT" in os.environ:
-    dir_name = jupyter_data_dir()
-    pem_file = os.path.join(dir_name, "notebook.pem")
-    os.makedirs(dir_name, exist_ok=True)
+    dir_name = Path(jupyter_data_dir())
+    dir_name.mkdir(parents=True, exist_ok=True)
+    pem_file = dir_name / "notebook.pem"
 
     # Generate an openssl.cnf file to set the distinguished name
-    cnf_file = os.path.join(os.getenv("CONDA_DIR", "/usr/lib"), "ssl", "openssl.cnf")
-    if not os.path.isfile(cnf_file):
-        with open(cnf_file, "w") as fh:
-            fh.write(OPENSSL_CONFIG)
+    cnf_file = Path("/usr/lib/ssl/openssl.cnf")
+    if not cnf_file.exists():
+        cnf_file.write_text(OPENSSL_CONFIG)
 
     # Generate a certificate if one doesn't exist on disk
     subprocess.check_call(
@@ -87,10 +87,9 @@ def _codeserver_command(port):
         ]
     )
     # Restrict access to the file
-    os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
-    c.ServerApp.certfile = pem_file
+    pem_file.chmod(stat.S_IRUSR | stat.S_IWUSR)
+    c.ServerApp.certfile = str(pem_file)
 
-# Change default umask for all subprocesses of the notebook server if set in
-# the environment
+# Change default umask for all subprocesses of the notebook server if set in the environment
 if "NB_UMASK" in os.environ:
     os.umask(int(os.environ["NB_UMASK"], 8))

base/latest.Dockerfile

@@ -7,7 +7,7 @@ ARG CUDA_IMAGE_FLAVOR
 ARG NB_USER=jovyan
 ARG NB_UID=1000
 ARG JUPYTERHUB_VERSION=4.0.2
-ARG JUPYTERLAB_VERSION=3.6.6
+ARG JUPYTERLAB_VERSION=4.0.9
 ARG CODE_BUILTIN_EXTENSIONS_DIR=/opt/code-server/lib/vscode/extensions
 ARG CODE_SERVER_VERSION=4.19.0
 ARG GIT_VERSION=2.43.0
@@ -235,6 +235,7 @@ RUN export PIP_BREAK_SYSTEM_PACKAGES=1 \
     jupyterlab-git \
     jupyterlab-lsp \
     notebook \
+    nbclassic \
     nbconvert \
     python-lsp-server[all] \
   ## Include custom fonts

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

@@ -12,43 +12,49 @@ if [ "$(id -u)" == 0 ] ; then
   # Update timezone if needed
   if [ "$TZ" != "Etc/UTC" ]; then
     echo "Setting TZ to $TZ"
-    ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
-      && echo $TZ > /etc/timezone
+    ln -snf "/usr/share/zoneinfo/$TZ" /etc/localtime \
+      && echo "$TZ" > /etc/timezone
   fi
 
   # Add/Update locale if needed
-  if [ ! -z "$LANGS" ]; then
+  if [ -n "$LANGS" ]; then
     for i in $LANGS; do
       sed -i "s/# $i/$i/g" /etc/locale.gen
     done
   fi
   if [ "$LANG" != "en_US.UTF-8" ]; then
     sed -i "s/# $LANG/$LANG/g" /etc/locale.gen
   fi
-  if [[ "$LANG" != "en_US.UTF-8" || ! -z "$LANGS" ]]; then
+  if [[ "$LANG" != "en_US.UTF-8" || -n "$LANGS" ]]; then
     locale-gen
   fi
   if [ "$LANG" != "en_US.UTF-8" ]; then
     echo "Setting LANG to $LANG"
-    update-locale --reset LANG=$LANG
+    update-locale --reset LANG="$LANG"
   fi
 
+  CS_USD="/home/$NB_USER/.local/share/code-server/User"
   # Update code-server settings
-  su $NB_USER -c "mkdir -p /home/$NB_USER/.local/share/code-server/User"
-  if [[ ! -f "/home/$NB_USER/.local/share/code-server/User/settings.json" ]]; then
-    su $NB_USER -c "cp ${CP_OPTS:--a} /var/backups/skel/.local/share/code-server/User/settings.json \
-      /home/$NB_USER/.local/share/code-server/User/settings.json"
-    chown :$NB_GID "/home/$NB_USER/.local/share/code-server/User/settings.json"
+  su "$NB_USER" -c "mkdir -p $CS_USD"
+  if [[ ! -f "$CS_USD/settings.json" ]]; then
+    su "$NB_USER" -c "cp ${CP_OPTS:--a} /var/backups/skel/.local/share/code-server/User/settings.json \
+      $CS_USD/settings.json"
+    chown :"$NB_GID" "$CS_USD/settings.json"
+  fi
+  # Update code-server settings
+  su "$NB_USER" -c "mv $CS_USD/settings.json $CS_USD/settings.json.bak"
+  su "$NB_USER" -c "sed -i ':a;N;\$!ba;s/,\n\}/\n}/g' $CS_USD/settings.json.bak"
+  if [[ $(jq . "$CS_USD/settings.json.bak" 2> /dev/null) ]]; then
+    su "$NB_USER" -c "jq -s '.[0] * .[1]' \
+      /var/backups/skel/.local/share/code-server/User/settings.json \
+      $CS_USD/settings.json.bak > \
+      $CS_USD/settings.json"
+  else
+    su "$NB_USER" -c "mv $CS_USD/settings.json.bak $CS_USD/settings.json"
   fi
 
-  su $NB_USER -c "mv /home/$NB_USER/.local/share/code-server/User/settings.json \
-    /home/$NB_USER/.local/share/code-server/User/settings.json.bak"
-  su $NB_USER -c "sed -i ':a;N;\$!ba;s/,\n\}/\n}/g' \
-    /home/$NB_USER/.local/share/code-server/User/settings.json.bak"
-  su $NB_USER -c "jq -s '.[0] * .[1]' \
-    /var/backups/skel/.local/share/code-server/User/settings.json \
-    /home/$NB_USER/.local/share/code-server/User/settings.json.bak > \
-    /home/$NB_USER/.local/share/code-server/User/settings.json"
+  # Remove old .zcompdump files
+  rm -f "/home/$NB_USER/.zcompdump"*
 else
   # Warn if the user wants to change the timezone but hasn't started the
   # container as root.
@@ -58,7 +64,7 @@ else
 
   # Warn if the user wants to change the locale but hasn't started the
   # container as root.
-  if [[ ! -z "$LANGS" ]]; then
+  if [[ -n "$LANGS" ]]; then
     echo "WARNING: Container must be started as root to add locale(s)!"
   fi
   if [[ "$LANG" != "en_US.UTF-8" ]]; then
@@ -67,22 +73,25 @@ else
     LANG=en_US.UTF-8
   fi
 
+  CS_USD="$HOME/.local/share/code-server/User"
   # Update code-server settings
-  mkdir -p /home/$NB_USER/.local/share/code-server/User
-  if [[ ! -f "/home/$NB_USER/.local/share/code-server/User/settings.json" ]]; then
+  mkdir -p "$CS_USD"
+  if [[ ! -f "$CS_USD/settings.json" ]]; then
     cp -a /var/backups/skel/.local/share/code-server/User/settings.json \
-      /home/$NB_USER/.local/share/code-server/User/settings.json
+      "$CS_USD/settings.json"
+  fi
+  # Update code-server settings
+  mv "$CS_USD/settings.json" "$CS_USD/settings.json.bak"
+  sed -i ':a;N;$!ba;s/,\n\}/\n}/g' "$CS_USD/settings.json.bak"
+  if [[ $(jq . "$CS_USD/settings.json.bak" 2> /dev/null) ]]; then
+    jq -s '.[0] * .[1]' \
+      /var/backups/skel/.local/share/code-server/User/settings.json \
+      "$CS_USD/settings.json.bak" > \
+      "$CS_USD/settings.json"
+  else
+    mv "$CS_USD/settings.json.bak" "$CS_USD/settings.json"
   fi
 
-  mv /home/$NB_USER/.local/share/code-server/User/settings.json \
-    /home/$NB_USER/.local/share/code-server/User/settings.json.bak
-  sed -i ':a;N;$!ba;s/,\n\}/\n}/g' \
-    /home/$NB_USER/.local/share/code-server/User/settings.json.bak
-  jq -s '.[0] * .[1]' \
-    /var/backups/skel/.local/share/code-server/User/settings.json \
-    /home/$NB_USER/.local/share/code-server/User/settings.json.bak > \
-    /home/$NB_USER/.local/share/code-server/User/settings.json
+  # Remove old .zcompdump files
+  rm -f "$HOME/.zcompdump"*
 fi
-
-# Remove old .zcompdump files
-rm -f /home/$NB_USER/.zcompdump*

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

@@ -6,13 +6,13 @@ set -e
 
 DIVISOR=1024
 
-if [[ "${SWAP_ENABLE}" == "1" || "${SWAP_ENABLE}" == "yes" ]]; then
-  FACTOR=$(echo 1 ${SWAP_FACTOR:-1} | awk '{ printf "%.1f", $1 + $2 }')
+if [[ "$SWAP_ENABLE" == "1" || "$SWAP_ENABLE" == "yes" ]]; then
+  FACTOR=$(echo 1 "${SWAP_FACTOR:-1}" | awk '{ printf "%.1f", $1 + $2 }')
 else
   FACTOR=1
 fi
 
-if [ ! -z "${MEM_LIMIT}" ]; then
-  ulimit -Sv $(echo $MEM_LIMIT $DIVISOR $FACTOR |
-    awk '{ printf "%.0f", $1 / $2 * $3 }')
+if [ -n "$MEM_LIMIT" ]; then
+  ulimit -Sv "$(echo "$MEM_LIMIT" "$DIVISOR $FACTOR" |
+    awk '{ printf "%.0f", $1 / $2 * $3 }')"
 fi

base/scripts/usr/local/bin/busy

@@ -2,10 +2,10 @@
 # Copyright (c) 2022 b-data GmbH.
 # Distributed under the terms of the MIT License.
 
-while [ ! -z $JUPYTERHUB_API_TOKEN ]; do
+while [ -n "$JUPYTERHUB_API_TOKEN" ]; do
   t=$(date -Iseconds)
   curl -s \
-    $JUPYTERHUB_ACTIVITY_URL -H \
+    "$JUPYTERHUB_ACTIVITY_URL" -H \
     "Authorization: token $JUPYTERHUB_API_TOKEN" -d \
     "{\"servers\":{\"$JUPYTERHUB_SERVER_NAME\":{\"last_activity\":\"$t\"}},\"last_activity\":\"$t\"}" \
     > /dev/null 2>&1

base/scripts/usr/local/bin/run-hooks.sh

@@ -24,11 +24,19 @@ for f in "${1}/"*; do
             echo "Sourcing shell script: ${f}"
             # shellcheck disable=SC1090
             source "${f}"
+            # shellcheck disable=SC2181
+            if [ $? -ne 0 ] ; then
+                echo "${f} has failed, continuing execution"
+            fi
             ;;
         *)
             if [ -x "${f}" ] ; then
                 echo "Running executable: ${f}"
                 "${f}"
+                # shellcheck disable=SC2181
+                if [ $? -ne 0 ] ; then
+                    echo "${f} has failed, continuing execution"
+                fi
             else
                 echo "Ignoring non-executable: ${f}"
             fi

scipy/latest.Dockerfile

@@ -121,7 +121,7 @@ RUN dpkgArch="$(dpkg --print-architecture)" \
   ## Install facets
   && cd /tmp \
   && git clone https://github.com/PAIR-code/facets.git \
-  && jupyter nbextension install facets/facets-dist/ --sys-prefix \
+  && jupyter nbclassic-extension install facets/facets-dist/ --sys-prefix \
   && cd / \
   ## Install code-server extensions
   && code-server --extensions-dir ${CODE_BUILTIN_EXTENSIONS_DIR} --install-extension quarto.quarto \