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fix(jupyter): fix minor problems

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This commit is contained in:
Masaki Yatsu
2025-09-20 21:35:35 +09:00
parent 3f7986802f
commit 6c6a56a6ca
5 changed files with 169 additions and 4 deletions
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1
.gitignore vendored
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@@ -139,3 +139,4 @@ dist
/custom.just
/custom
/private/
.mcp.json

8
jupyterhub/images/datastack-cuda-notebook/Dockerfile
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@@ -91,6 +91,7 @@ RUN mamba install --yes \
'grpcio-status' \
'grpcio' \
'hvac' \
'jupyter-collaboration' \
'keras' \
'langchain' \
'langchain-ai21' \
@@ -126,6 +127,7 @@ RUN mamba install --yes \
'polars' \
'psycopg2' \
'pyarrow' \
'pyiceberg' \
'qdrant-client' \
'rapidfuzz' \
'simple-salesforce' \
@@ -159,6 +161,12 @@ RUN --mount=type=cache,target=/home/${NB_USER}/.cache/pip pip install -i "${pip_
RUN --mount=type=cache,target=/home/${NB_USER}/.cache/pip pip install -i "${pip_repository_url}" \
'dlt[clickhouse,databricks,deltalake,dremio,duckdb,filesystem,parquet,postgres,pyiceberg,qdrant,redshift,s3,snowflake,sql-database,sqlalchemy,workspace]'
# https://jupyter-mcp-server.datalayer.tech/setup/jupyter/local_mcp/
# RUN --mount=type=cache,target=/home/${NB_USER}/.cache/pip \
# pip install -i "${pip_repository_url}" 'jupyterlab==4.4.1' 'jupyter-collaboration==4.0.2' \
# && pip uninstall -y pycrdt datalayer_pycrdt \
# && pip install -i "${pip_repository_url}" 'datalayer_pycrdt==0.12.17'
# Install PyTorch with pip (https://pytorch.org/get-started/locally/)
# langchain-openai must be updated to avoid pydantic v2 error
# https://github.com/run-llama/llama_index/issues/16540https://github.com/run-llama/llama_index/issues/16540

7
jupyterhub/images/datastack-notebook/Dockerfile
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@@ -91,6 +91,7 @@ RUN mamba install --yes \
'grpcio-status' \
'grpcio' \
'hvac' \
'jupyter-collaboration' \
'keras' \
'langchain' \
'langchain-ai21' \
@@ -159,6 +160,12 @@ RUN --mount=type=cache,target=/home/${NB_USER}/.cache/pip pip install -i "${pip_
RUN --mount=type=cache,target=/home/${NB_USER}/.cache/pip pip install -i "${pip_repository_url}" \
'dlt[clickhouse,databricks,deltalake,dremio,duckdb,filesystem,parquet,postgres,pyiceberg,qdrant,redshift,s3,snowflake,sql-database,sqlalchemy,workspace]'
# https://jupyter-mcp-server.datalayer.tech/setup/jupyter/local_mcp/
# RUN --mount=type=cache,target=/home/${NB_USER}/.cache/pip \
# pip install -i "${pip_repository_url}" 'jupyterlab==4.4.1' 'jupyter-collaboration==4.0.2' \
# && pip uninstall -y pycrdt datalayer_pycrdt \
# && pip install -i "${pip_repository_url}" 'datalayer_pycrdt==0.12.17'
# Install PyTorch with pip (https://pytorch.org/get-started/locally/)
# langchain-openai must be updated to avoid pydantic v2 error
# https://github.com/run-llama/llama_index/issues/16540https://github.com/run-llama/llama_index/issues/16540

9
jupyterhub/jupyterhub-values.gomplate.yaml
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@@ -132,6 +132,10 @@ hub:
podSecurityContext:
fsGroup: {{ .Env.JUPYTER_FSGID }}
proxy:
service:
type: ClusterIP
singleuser:
storage:
{{ if env.Getenv "PVC_NAME" -}}
@@ -153,6 +157,7 @@ singleuser:
VAULT_ADDR: "{{ .Env.VAULT_ADDR }}"
NOTEBOOK_VAULT_TOKEN_TTL: "{{ .Env.NOTEBOOK_VAULT_TOKEN_TTL }}"
NOTEBOOK_VAULT_TOKEN_MAX_TTL: "{{ .Env.NOTEBOOK_VAULT_TOKEN_MAX_TTL }}"
# JUPYTERHUB_SINGLEUSER_EXTENSION: "0"
storage:
{{ if env.Getenv "PVC_NAME" -}}
@@ -361,8 +366,8 @@ cull:
adminUsers: true # Also cull admin users' server pods
users: false # Don't delete user accounts, only stop server pods
imagePullSecrets:
- name: regcred
# imagePullSecrets:
# - name: regcred
ingress:
enabled: true

148
jupyterhub/justfile
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@@ -9,7 +9,7 @@ export JUPYTERHUB_NFS_PV_ENABLED := env("JUPYTERHUB_NFS_PV_ENABLED", "")
export JUPYTERHUB_STORAGE_CLASS := env("JUPYTERHUB_STORAGE_CLASS", "")
export JUPYTERHUB_VAULT_INTEGRATION_ENABLED := env("JUPYTERHUB_VAULT_INTEGRATION_ENABLED", "")
export JUPYTERHUB_AIRFLOW_DAGS_PERSISTENCE_ENABLED := env("JUPYTERHUB_AIRFLOW_DAGS_PERSISTENCE_ENABLED", "")
export JUPYTER_PYTHON_KERNEL_TAG := env("JUPYTER_PYTHON_KERNEL_TAG", "python-3.12-42")
export JUPYTER_PYTHON_KERNEL_TAG := env("JUPYTER_PYTHON_KERNEL_TAG", "python-3.12-49")
export KERNEL_IMAGE_BUUN_STACK_REPOSITORY := env("KERNEL_IMAGE_BUUN_STACK_REPOSITORY", "buun-stack-notebook")
export KERNEL_IMAGE_BUUN_STACK_CUDA_REPOSITORY := env("KERNEL_IMAGE_BUUN_STACK_CUDA_REPOSITORY", "buun-stack-cuda-notebook")
export JUPYTER_PROFILE_MINIMAL_ENABLED := env("JUPYTER_PROFILE_MINIMAL_ENABLED", "false")
@@ -357,6 +357,150 @@ create-jupyterhub-vault-token root_token='':
echo " - TTL: ${JUPYTERHUB_VAULT_TOKEN_TTL} (will expire without renewal)"
echo " - Max TTL: Unlimited (can be renewed forever)"
echo " - Vault Agent will renew at TTL/2 intervals (minimum 30s)"
echo " - No more 30-day limitation!"
echo ""
echo "Token stored at: secret/jupyterhub/vault-token"
# Get JupyterHub API token for a user
get-api-token username:
#!/bin/bash
set -euo pipefail
USERNAME="{{ username }}"
if [ -z "${USERNAME}" ]; then
echo "Error: Username is required" >&2
echo "Usage: just jupyterhub::get-api-token <username>" >&2
exit 1
fi
# Get the pod name for the user
POD_NAME=$(kubectl get pods -n ${JUPYTERHUB_NAMESPACE} \
-l "app=jupyterhub,component=singleuser-server,hub.jupyter.org/username=${USERNAME}" \
-o jsonpath='{.items[0].metadata.name}' 2>/dev/null || true)
if [ -z "${POD_NAME}" ]; then
echo "Error: No running pod found for user '${USERNAME}'" >&2
echo "Make sure the user has an active Jupyter session" >&2
exit 1
fi
# Check if pod is ready
POD_STATUS=$(kubectl get pod -n ${JUPYTERHUB_NAMESPACE} ${POD_NAME} \
-o jsonpath='{.status.phase}' 2>/dev/null || true)
if [ "${POD_STATUS}" != "Running" ]; then
echo "Error: Pod ${POD_NAME} is not running (status: ${POD_STATUS})" >&2
exit 1
fi
# Get the API token from the pod's environment
API_TOKEN=$(kubectl exec -n ${JUPYTERHUB_NAMESPACE} ${POD_NAME} -- \
sh -c 'echo $JUPYTERHUB_API_TOKEN' 2>/dev/null || true)
if [ -z "${API_TOKEN}" ]; then
echo "Error: Could not retrieve API token from pod ${POD_NAME}" >&2
echo "The pod might not have JUPYTERHUB_API_TOKEN environment variable set" >&2
exit 1
fi
echo "${API_TOKEN}"
# Setup MCP server configuration for Claude Code (has auth problems)
setup-mcp-server username='' notebook='':
#!/bin/bash
set -euo pipefail
USERNAME="{{ username }}"
if [ -z "${USERNAME}" ]; then
USERNAME=$(gum input --prompt="JupyterHub username: " --width=100 --placeholder="e.g., buun")
fi
if [ -z "${USERNAME}" ]; then
echo "Error: Username is required" >&2
exit 1
fi
# Get the API token for the user
echo "Getting API token for user '${USERNAME}'..."
API_TOKEN=$(just jupyterhub::get-api-token ${USERNAME} 2>/dev/null || true)
if [ -z "${API_TOKEN}" ]; then
echo "Error: Could not get API token for user '${USERNAME}'" >&2
echo "Make sure the user has an active Jupyter session" >&2
exit 1
fi
# Get notebook path
NOTEBOOK="{{ notebook }}"
if [ -z "${NOTEBOOK}" ]; then
echo ""
echo "Available notebooks for user '${USERNAME}':"
kubectl exec -n ${JUPYTERHUB_NAMESPACE} jupyter-${USERNAME} -- \
curl -s -H "Authorization: token ${API_TOKEN}" \
"http://localhost:8888/user/${USERNAME}/api/contents" 2>/dev/null | \
jq -r '.content[]? | select(.type=="notebook") | .path' | head -20 || true
echo ""
NOTEBOOK=$(gum input --prompt="Notebook path (required): " --width=100 --placeholder="e.g., Untitled.ipynb or path/to/notebook.ipynb")
if [ -z "${NOTEBOOK}" ]; then
echo "Error: Notebook path is required for MCP server to function" >&2
exit 1
fi
fi
# Create .mcp.json configuration
MCP_CONFIG_FILE="../.mcp.json"
echo "Creating MCP server configuration..."
cat > "${MCP_CONFIG_FILE}" <<EOF
{
"mcpServers": {
"jupyter-${USERNAME}": {
"command": "docker",
"args": [
"run",
"-i",
"--rm",
"-e",
"DOCUMENT_URL",
"-e",
"DOCUMENT_TOKEN",
"-e",
"RUNTIME_URL",
"-e",
"RUNTIME_TOKEN",
"-e",
"DOCUMENT_ID",
"datalayer/jupyter-mcp-server:latest"
],
"env": {
"DOCUMENT_URL": "https://${JUPYTERHUB_HOST}/user/${USERNAME}",
"DOCUMENT_TOKEN": "${API_TOKEN}",
"DOCUMENT_ID": "${NOTEBOOK}",
"RUNTIME_URL": "https://${JUPYTERHUB_HOST}/user/${USERNAME}",
"RUNTIME_TOKEN": "${API_TOKEN}"
}
}
}
}
EOF
echo "✅ MCP server configuration created at: ${MCP_CONFIG_FILE}"
echo ""
echo "Configuration details:"
echo " Server name: jupyter-${USERNAME}"
echo " Jupyter URL: https://${JUPYTERHUB_HOST}/user/${USERNAME}"
echo " Token: ${API_TOKEN:0:8}..."
echo ""
echo "To use this configuration:"
echo "1. Open Claude Code in this directory (${PWD})"
echo "2. The MCP server will be automatically loaded from .mcp.json"
echo "3. You can access Jupyter notebooks through the MCP server"
echo ""
if [ -n "${NOTEBOOK}" ]; then
echo " Notebook: ${NOTEBOOK}"
else
echo ""
echo "Note: No specific notebook configured."
echo "To reconfigure with a specific notebook:"
echo " just jupyterhub::setup-mcp-server ${USERNAME} <notebook-path>"
fi