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john-data-chenjohn-data-chen/hermes-agent-backup/skills/data-science/jupyter-live-kernel/SKILL.md

jupyter-live-kernel

Skill2 starsChanged 4 months agoMITView on GitHub

Iterative Python via live Jupyter kernel (hamelnb).

  • Sends data out

We split this skill into the rules it gives an agent

10 rules. 7 are common, 0 are distinctive, and 3 are very specific to this project.

  • 7

    Common

    Most of the 6 edited versions we read keep these.

  • 0

    Distinctive

    This author's own choices. Worth a look.

  • 3

    Very specific

    Tied to their project's names, files or tools. Probably skip.

  • Common
  • Distinctive
  • Very specific
  1. Common:

    Rule of thumb: If you'd want a Jupyter notebook for the task, use this skill.

    line 28
  2. Very specific:

    uv must be installed (check: which uv)

    line 32
  3. Very specific:

    JupyterLab: must be installed: uv tool install jupyterlab

    line 33
  4. Common:

    If not cloned yet:

    line 43
  5. Common:

    Check if a server is already running:

    line 50
  6. Common:

    If no servers found, start one:

    line 55
  7. Common:

    If you just need a REPL (no existing notebook), create a minimal notebook file:

    line 66
  8. Common:

    Write a minimal .ipynb JSON file with one empty code cell, then start a kernel session via the Jupyter REST API:

    line 70
  9. Very specific:

    All commands return structured JSON.

    line 80
  10. Common:

    Only use when the user asks for a clean verification or you need to confirm the notebook runs top-to-bottom:

    line 129

“Common” is measured: kept by at least 6 in 10 of the 6 edited versions of this file we could read. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Keep what fits and drop the rest. Your version, ready for your agents.
Files
SKILL.md

Jupyter Live Kernel (hamelnb)

Gives you a stateful Python REPL via a live Jupyter kernel. Variables persist across executions. Use this instead of execute_code when you need to build up state incrementally, explore APIs, inspect DataFrames, or iterate on complex code.

When to Use This vs Other Tools

ToolUse When
This skillIterative exploration, state across steps, data science, ML, "let me try this and check"
execute_codeOne-shot scripts needing hermes tool access (web_search, file ops). Stateless.
terminalShell commands, builds, installs, git, process management

Rule of thumb: If you'd want a Jupyter notebook for the task, use this skill.

Prerequisites

  1. uv must be installed (check: which uv)
  2. JupyterLab must be installed: uv tool install jupyterlab
  3. A Jupyter server must be running (see Setup below)

Setup

The hamelnb script location:

SCRIPT="$HOME/.agent-skills/hamelnb/skills/jupyter-live-kernel/scripts/jupyter_live_kernel.py"

If not cloned yet:

git clone https://github.com/hamelsmu/hamelnb.git ~/.agent-skills/hamelnb

Starting JupyterLab

Check if a server is already running:

uv run "$SCRIPT" servers

If no servers found, start one:

jupyter-lab --no-browser --port=8888 --notebook-dir=$HOME/notebooks \
  --IdentityProvider.token='' --ServerApp.password='' > /tmp/jupyter.log 2>&1 &
sleep 3

Note: Token/password disabled for local agent access. The server runs headless.

Creating a Notebook for REPL Use

If you just need a REPL (no existing notebook), create a minimal notebook file:

mkdir -p ~/notebooks

Write a minimal .ipynb JSON file with one empty code cell, then start a kernel session via the Jupyter REST API:

curl -s -X POST http://127.0.0.1:8888/api/sessions \
  -H "Content-Type: application/json" \
  -d '{"path":"scratch.ipynb","type":"notebook","name":"scratch.ipynb","kernel":{"name":"python3"}}'

Core Workflow

All commands return structured JSON. Always use --compact to save tokens.

1. Discover servers and notebooks

uv run "$SCRIPT" servers --compact
uv run "$SCRIPT" notebooks --compact

2. Execute code (primary operation)

uv run "$SCRIPT" execute --path <notebook.ipynb> --code '<python code>' --compact

State persists across execute calls. Variables, imports, objects all survive.

Multi-line code works with $'...' quoting:

uv run "$SCRIPT" execute --path scratch.ipynb --code $'import os\nfiles = os.listdir(".")\nprint(f"Found {len(files)} files")' --compact

3. Inspect live variables

uv run "$SCRIPT" variables --path <notebook.ipynb> list --compact
uv run "$SCRIPT" variables --path <notebook.ipynb> preview --name <varname> --compact

4. Edit notebook cells

# View current cells
uv run "$SCRIPT" contents --path <notebook.ipynb> --compact

# Insert a new cell
uv run "$SCRIPT" edit --path <notebook.ipynb> insert \
  --at-index <N> --cell-type code --source '<code>' --compact

# Replace cell source (use cell-id from contents output)
uv run "$SCRIPT" edit --path <notebook.ipynb> replace-source \
  --cell-id <id> --source '<new code>' --compact

# Delete a cell
uv run "$SCRIPT" edit --path <notebook.ipynb> delete --cell-id <id> --compact

5. Verification (restart + run all)

Only use when the user asks for a clean verification or you need to confirm the notebook runs top-to-bottom:

uv run "$SCRIPT" restart-run-all --path <notebook.ipynb> --save-outputs --compact

Practical Tips from Experience

  1. First execution after server start may timeout — the kernel needs a moment to initialize. If you get a timeout, just retry.
  2. The kernel Python is JupyterLab's Python — packages must be installed in that environment. If you need additional packages, install them into the JupyterLab tool environment first.
  3. --compact flag saves significant tokens — always use it. JSON output can be very verbose without it.
  4. For pure REPL use, create a scratch.ipynb and don't bother with cell editing. Just use execute repeatedly.
  5. Argument order matters — subcommand flags like --path go BEFORE the sub-subcommand. E.g.: variables --path nb.ipynb list not variables list --path nb.ipynb.
  6. If a session doesn't exist yet, you need to start one via the REST API (see Setup section). The tool can't execute without a live kernel session.
  7. Errors are returned as JSON with traceback — read the ename and evalue fields to understand what went wrong.
  8. Occasional websocket timeouts — some operations may timeout on first try, especially after a kernel restart. Retry once before escalating.

Timeout Defaults

The script has a 30-second default timeout per execution. For long-running operations, pass --timeout 120. Use generous timeouts (60+) for initial setup or heavy computation.

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