# Notebook Guidance

> This skill guides the use of Jupyter notebooks for data analysis, exploration, and visualization, particularly with BigQuery. It outlines best practices for notebook execution and validation (supporting both cell-by-cell execution and full notebook generation depending on tool availability), library installation, and structuring notebooks for clarity. It also covers specific rules for data cleaning, plotting, and integrating with BigQuery SQL and machine learning workflows. Relevant when any of the following conditions are true: 1. The user request involves a data analysis, data exploration, data visualization, or data insights task that requires multiple steps, queries, or visualizations to answer. 2. The user explicitly requests a notebook (.ipynb). 3. You are creating, editing, or executing cells in a Jupyter notebook. 4. You need to query BigQuery from within a notebook. DO NOT use the Python BigQuery client library; instead, you MUST use the `%%bqsql` magics explained in this skill.

- Skill: `gemini-cli-extensions-data-agent-kit-starter-pack/notebook-guidance` (Agent Skill)
- Install (CLI): `npx skillmds@latest add gemini-cli-extensions-data-agent-kit-starter-pack/notebook-guidance`
- Raw SKILL.md: https://api.skillmd.com/api/skills/gemini-cli-extensions-data-agent-kit-starter-pack/notebook-guidance/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Data & Analytics
- License: Apache-2.0
- Author: gemini-cli-extensions (https://skillmd.com/u/gemini-cli-extensions-data-agent-kit-starter-pack)
- Updated: 2026-09-10
- Page: https://skillmd.com/skills/gemini-cli-extensions-data-agent-kit-starter-pack/notebook-guidance

---


# Notebook Guidance

## When to Use a Notebook

Before choosing to use a notebook, evaluate the task complexity using these
heuristics.

Use a notebook if you meet at least one of these criteria:

*   📈 **Data Insights & Storytelling**: Use a notebook for any request to "give
    insights", "find trends", "explore data", or "analyze data". These tasks
    benefit from using visualizations to present the data.
*   📊 **Visualizations are requested**: The user explicitly asks for charts or
    plots.
*   🔄 **Stateful / Iterative Exploration**: You need to run a query, inspect
    results, and decide the next query based on those results while keeping
    state in memory.

Do NOT use a notebook ONLY if:

*   📝 **Simple Fact/Status**: The request only requires a single number (e.g.,
    "how many rows") or a status check (e.g., "when was this table updated").
*   🏃‍♂️ **Schema Preview**: The request is only about the schema or field
    types.

**Golden Rule of Data Storytelling:** If any analytical insight, trend, or
comparison is involved, favor a notebook and a visualization. A notebook is the
"standard" environment for our developer workflow; do not avoid it because of
"overhead".

## Notebook Best Practices

> [!IMPORTANT]
>
> **Agent execution rules**: Your behavior MUST depend on whether the
> `notebook_execute_cell` tool is available in your current context: * **If
> notebook `execute_cell` tool is available**: You MUST follow the incremental
> GENERATE CELL -> EXECUTE CELL -> VALIDATE flow. * **If notebook `execute_cell`
> tool is NOT available**: You MUST generate the complete notebook and request
> user execution.

1.  **CONDITIONAL EXECUTION FLOW**:
    *   **If notebook `execute_cell` tool is available**: Follow the **STEP BY
        STEP GENERATE CELL -> EXECUTE CELL -> VALIDATE OUTPUT** flow. Generate
        ONE cell, execute it, then verify the output. If the output is data
        (e.g. a dataframe), you MUST inspect it to confirm the logic is correct
        before generating the next step. Batch generation of an entire notebook
        is strictly prohibited because error propagation in notebooks is
        expensive to fix.
    *   **If notebook `execute_cell` tool is NOT available**:
        *   Create the whole notebook at once.
        *   Tell the user to run the notebook.
        *   Tell the user to let you know once the notebook run is completed so
            you can check the outputs to verify it's correct and fix any errors.
2.  **IDENTIFY DATA EARLY**: Use `@skill:discovering-gcp-data-assets` or
    BigQuery list tools to find the correct `project.dataset.table` before
    writing ANY code. If the table ID is missing, ask the user.
3.  **CLEAN FINAL STATE**: The final notebook MUST NOT have failed cells. If a
    cell fails, you MUST fix it. If you tried several versions, delete the
    failed attempts before you present the notebook to the user.
4.  **LOGICAL CHUNK FIDELITY**: Keep cells small. One logical transformation or
    visualization per cell. Group related cells into logical units (e.g., a
    BigQuery `%%bqsql` magic cell followed immediately by a Python visualization
    cell for those results). Use descriptive **markdown cells** to separate and
    document different logical sections.
5.  **GENERATE VISUALIZATIONS**: Always accompany data insights with
    visualizations; charts are often more effective than raw numbers for
    communicating trends and comparisons.

## Kernel & Environment Management

Notebooks run in specific **Kernels** (execution backends). You MUST ensure the
kernel’s Python environment contains the necessary libraries (`bigframes`,
`ipykernel`, etc.).

### Kernel Types

1.  **Local Python**: Standard Python 3 kernel running on the notebook host
    (Managed instance, local machine).
2.  **Cloud Spark Remote (Dataproc Serverless)**: Transient Spark environment
    managed by GCP. Use for large-scale data processing.
3.  **Cloud Spark Remote (Dataproc Cluster)**: Persistent Spark clusters for
    shared or custom configurations.
4.  **Colab (Managed)**: Ephemeral Google-managed runtimes.

### No Active Kernel / Setup Check

1.  **Infer or Ask about Kernel Preferences**:
    -   **Infer from Context**:
        -   If the task mentions "Spark", "PySpark", or "distributed compute",
            or if the active workspace is already a Spark cluster, lean towards
            **Remote Spark**.
        -   If the task is focused on "BigQuery", "BigFrames", or standard API
            calls, lean towards **Local Python**.
    -   **Ask when Ambiguous**: If multiple options fit, ask if they prefer a
        **Local Python** or a **Cloud/Remote Kernel** (e.g., Colab, Spark).
2.  **For Local Setup**: Use `@skill:managing-python-dependencies` to verify if
    a virtual environment exists. If not, create one. Ensure `ipykernel` is
    installed in that environment. Install any other relevant libraries.
3.  **For Remote Setup**: Advise the user to use the UI to select the
    appropriate remote kernel.

> [!IMPORTANT]
>
> **HARD STOP on kernel failure**: If a cell execution returns "no active
> kernel" or any kernel-not-found error, you MUST **stop immediately**. Do NOT
> scaffold, generate, or insert any further cells. Inform the user which kernel
> is needed (e.g., PySpark / Dataproc Serverless) and wait for explicit
> confirmation that a kernel is active before proceeding with notebook
> execution.

### Proper Library Installation

#### 1. Local Kernels

Before installing any python libraries, you MUST use
`@skill:managing-python-dependencies` to detect how python dependencies are
managed in the project.

#### 2. Remote Kernels (Spark/Colab)

Since these are often ephemeral or managed by GCP:

*   **Check first (REQUIRED)**: Before writing any `%pip install` cell, run
    `%pip list` or `import <package>` to confirm the package is not already
    present. Managed runtimes (Dataproc Serverless, Colab) pre-install many
    common packages. Only install what is confirmed missing.
*   Use `%pip install <package>` in the first cell if a package is confirmed
    missing and it's the only way to modify the runtime.

When in doubt about the kernel type or preferred installation method, ask the
user for clarification.

## Data Analysis & Visualization Rules

Guidelines for performing exploratory data analysis, data cleaning, and
visualization in notebooks.

### Notebook Layout

The notebook should read like a story. While you have flexibility (e.g.,
multiple visualizations for one data cell, or data cells building on each
other), aim for this general flow:

1.  **Title & Objective** (Markdown Cell)
    *   What is this notebook for? (e.g., `# Retention Analysis`)
2.  **Section Header** (Markdown Cell)
    *   What are we looking at now? (e.g., `## Exploring User Retention`)
3.  **Data Acquisition/Transformation** (Python cell, may contain `%%bqsql`
    magics)
    *   Query BigQuery or transform data.
4.  **Verification (Optional but Recommended)** (Python Cell)
    *   `df.head()` or assert sanity checks.
5.  **Visualization (The Goal)** (Python Cell)
    *   Plot the insight (e.g., `df.plot()`).

*Repeat steps 2-5 for each new sub-topic or insight. You can have multiple Data
cells before a Visualization, or multiple Visualizations from one Data cell. The
key is to keep them grouped logically and separated by Markdown headers.*

1.  **Final Summary** (Markdown Cell)

    *   At the end of the notebook, add a markdown cell containing a summary
        paragraph that summarizes the findings to the user. The summary MUST
        follow these guidelines:
    *   MUST NOT add Python code to the summary.
    *   The summary MUST NOT start with a code block.
    *   The summary MUST be strictly grounded in the numerical data verified in
        the notebook.
    *   The summary MUST ONLY contain the following three sections:
        *   ### Q&A If the data analysis task contains questions (implied or
            explicit), you MUST answer them based on the solving process. Skip
            this section if there are no questions to answer.
        *   ### Data Analysis Key Findings Summarize the key analysis findings
            in bullet points, it's a plus to quote the numbers in the previous
            steps. Only report high-value findings, skip the obvious ones.
        *   ### Insights or Next Steps Provide 1-2 concise insights or next
            steps in bullet points.

2.  **Next Steps**: After the notebook has been successfully executed and
    verified, and the summary is complete, notify the user and propose next step
    suggestions.

### Plotting Rules

1.  You MUST use different colors for different features to ensure plots are
    readable for humans.
2.  When creating a plot, you MUST adjust the figure size based on the number of
    features. The labels and legends MUST NOT overlap.
3.  You SHOULD arrange the layout wisely. Using subplots CAN help in placing
    different plots effectively.
4.  You MUST use inline figures to present figures and plots along with code and
    text in the notebook.
5.  For clustering, use PCA to reduce to 2D before scatter plotting.
6.  Use **Line Charts** ONLY for continuous data (e.g. time series) where
    interpolation between points is meaningful.

### Data Cleaning Rules

1.  You MUST be careful about missing values and duplicated values.
2.  You MUST NOT drop columns unless absolutely necessary. Dropping columns is
    irreversible.
3.  You SHOULD focus on columns directly related to accomplishing the task; not
    every column NEEDS to be cleaned.

## Specialized Notebook Guidance

Refer to the following resources for guidance on specific notebook topics:

### 1. BigQuery in Notebooks

Use BigFrames magics `%%bqsql` for BigQuery SQL queries. These cells support
native BigQuery SQL execution and data export to BigFrames dataframes.

> [!IMPORTANT]
>
> *   Unless specified by the user, **always use SQL for querying BigQuery.**
> *   DO NOT use the standard BigQuery Python client library
>     (`google.cloud.bigquery`) or `pandas.read_gbq`.
> *   **Mandatory dataframe export**: Always provide a dataframe name e.g.
>     `%%bqsql <df_name>`. This makes it easy to use results in follow up Python
>     cells.
> *   Verify that `bigframes` version number `2.38.0` and above is installed in
>     the notebook runtime environment. If it is missing, ask the user if they
>     would like you to upgrade for them.

**Example %%bqsql magic usage:**

```python
# Initialize BigFrames and load %%bqsql magics
import bigframes
import bigframes.pandas as bpd
%load_ext bigframes
```

> [!CAUTION]
>
> Always use `%load_ext bigframes` exactly as shown. Do not load submodules —
> for example, `%load_ext bigframes.magics` or `%load_ext bigframes.bigquery`
> are not valid and must not be used.

> [!IMPORTANT]
>
> The `bigframes` library must be installed. Determine if bigframes needs to be
> installed by following @skill:managing-python-dependencies.

```python
%%bqsql df_sample
SELECT * FROM `project.dataset.table` LIMIT 10
```

#### Anti-patterns (NEVER DO THESE)

> [!CAUTION]
>
> 1.  **NO Python SDK for Queries**: Do not switch to
>     `client.query(sql).to_dataframe()` if SQL fails. Fix the SQL syntax
>     instead.
> 2.  **NO Mixing Logic**: Do not put Python code in the same cell as `%%bqsql`
>     magics.

#### Working with SQL Results in Python

Magic cells with `%%bqsql <df_name>` produce a **BigQuery DataFrame**. In
subsequent cells, you can use `<df_name>` directly.

> [!IMPORTANT]
>
> You MUST use BigFrames for data exploration, manipulation, splitting etc. You
> MUST use BQML SQL or bigframes.ml for machine learning tasks. You MUST NOT use
> pandas or Scikit-learn.

##### BigQuery DataFrame Tips

*   **Avoid `.to_pandas()`**: You MUST NOT use `.to_pandas()` to download the
    entire dataset into memory. There are some exceptions:
    *   An error message explicitly requests you to use `to_pandas()`
    *   You are going to visualize the data, **and** the visualization library
        does not accept BigFrames Dataframe/Series instances. In this case,
        reduce the amount of data you are going to download before calling
        `.to_pandas()`
*   **Avoid `read_gbq()` for SQL**: Do not write SQL queries and execute them
    with `read_gbq()`. Use BigFrames Dataframe/Series methods instead.
*   **Use BigFrames ML package for Machine Learning Tasks**: Do not use
    Scikit-learn or other ML libraries with BigFrames dataframes. Import your
    tools/classes from `bigframes.ml`.
*   **Stay in the Cloud**: Perform data cleaning, transformation, and analysis
    via BigFrames methods to leverage BigQuery's scale.
*   **Accessors over UDFs/Lambdas**:
    *   Prefer built-in accessors (e.g., `df.col.str.*`, `df.col.dt.*`) over
        remote UDFs.
    *   **Do not use lambdas** with `Series.map()` or `DataFrame.apply()`.
*   **Schema Verification**: Do not assume schema of intermediate outputs. Check
    `.dtypes` after loading, and use `display()` with `.head()` or `.peek()`.
*   **Visualization**: BigFrames Dataframe mostly works directly with
    Matplotlib, Seaborn, and other plotting libraries. If your attempt didn't
    work, try using the "plot" accessor. If that didn't work either, you MUST
    sample or aggregate your data to make it small enough before calling
    "to_pandas()".
*   **Model Persistence**: To persist a model. use `model.to_gbq()`. To load a
    persisted model, use `bpd.read_gbq_model()`.

### 2. Machine Learning in Notebooks

Integration with machine learning workflows and best practices. - **Guide**: Use
`@skill:ml-best-practices`. - **MUST READ WHEN**: The task involves machine
learning, training a model, clustering, classification, regression, or
time-series forecasting.

If any "MUST READ WHEN" condition is met, you MUST read the corresponding guide
before proceeding.