Notebook Writer

Notebook Writer Skill

You are a specialist in creating well-structured Jupyter notebooks for scientific analyses and documentation.

When to Use This Skill

Use this skill when:

• Creating parameter sweeps or sensitivity analyses
• Documenting calculations with reproducible code
• Generating analysis reports that combine code, results, and interpretation
• Packaging agent work (Calculator, Researcher) into shareable notebooks

Notebook Format: Jupytext Markdown

We use Jupytext-compatible Markdown for notebooks to enable git-friendly version control.

Cell Markers

• Markdown cells: Regular Markdown text (no special marker)
• Code cells: Start with # %% on its own line

Example Structure

---
jupyter:
  kernelspec:
    display_name: Python 3
    language: python
    name: python3
---

# Analysis Title

Brief description of what this notebook does.

## Section 1: Data Loading

# %%
import pandas as pd
import numpy as np

# %%
data = pd.read_csv('data.csv')
data.head()

## Section 2: Analysis

Explanation of the analysis approach.

# %%
# Perform calculation
result = np.mean(data['value'])
print(f"Mean: {result:.2f}")

Python Utility API

Many projects provide src/utils/notebook_builder.py with helper functions for programmatic notebook creation.

Core Function: create_notebook_markdown

create_notebook_markdown(
    title: str,
    cells: List[Dict[str, str]],
    output_path: Path,
    kernelspec: Optional[Dict] = None
) -> Path

Parameters:

• title: Notebook title (becomes H1 header)
• cells: List of dicts with 'type' ('code' or 'markdown') and 'content'
• output_path: Where to save .md file
• kernelspec: Optional kernel specification (defaults to Python 3)

Example:

from pathlib import Path
from src.utils.notebook_builder import create_notebook_markdown

cells = [
    {'type': 'markdown', 'content': '## Introduction\n\nThis analysis...'},
    {'type': 'code', 'content': 'import numpy as np'},
    {'type': 'code', 'content': 'x = np.linspace(0, 10)\nprint(x)'}
]

create_notebook_markdown(
    title="My Analysis",
    cells=cells,
    output_path=Path('docs/analysis/my_analysis.md')
)

Template: Parameter Sweep

create_parameter_sweep_notebook(
    param_name: str,
    param_range: str,
    calculation_code: str,
    output_path: Path
) -> Path

Creates a notebook with:

• Imports (numpy, matplotlib, pandas)
• Parameter range definition
• Your calculation code
• Visualization boilerplate

Example:

from pathlib import Path
from src.utils.notebook_builder import create_parameter_sweep_notebook

create_parameter_sweep_notebook(
    param_name='temperature',
    param_range='np.linspace(20, 40, 20)',
    calculation_code='''
# Reaction rate calculation
results = []
for T in temperature_values:
    rate = arrhenius_equation(T, activation_energy)
    results.append(rate)
''',
    output_path=Path('analysis/temperature_sweep.md')
)

Template: Analysis Report

create_analysis_report_notebook(
    analysis_title: str,
    sections: List[Dict[str, str]],
    output_path: Path
) -> Path

Section dict keys:

• title: Section heading (required)
• description: Explanatory text (optional)
• code: Code to execute (optional)
• interpretation: Results interpretation (optional)

Example:

from src.utils.notebook_builder import create_analysis_report_notebook

sections = [
    {
        'title': 'Model Setup',
        'description': 'Define parameters',
        'code': 'diffusion_coeff = 2.1e-5  # cm²/s'
    },
    {
        'title': 'Calculation',
        'code': 'result = compute_model(diffusion_coeff)',
        'interpretation': 'Result shows X is dominated by Y'
    }
]

create_analysis_report_notebook(
    'Transport Analysis',
    sections,
    Path('analysis/transport.md')
)

Validation Function

validate_notebook(notebook_path: Path) -> bool

Validates .ipynb structure using nbformat. Returns True if valid, raises exception if invalid.

Example:

from pathlib import Path
from src.utils.notebook_builder import validate_notebook

validate_notebook(Path('analysis/notebook.ipynb'))
# Returns True or raises ValidationError

Workflow

1. Create notebook using utility or manual Markdown
2. Edit .md file directly (agents write Markdown well)
3. Convert to .ipynb: python3 -m jupytext --to ipynb notebook.md
4. Run in Jupyter: jupyter notebook notebook.ipynb
5. Sync changes back: python3 -m jupytext --sync notebook.ipynb (bidirectional)

Jupyter AI Integration

Modern Jupyter environments (JupyterLab 4.0+, JetBrains IDEs) provide AI-powered assistance to enhance productivity and reduce errors.

%%ai Magic Commands

The %%ai cell magic enables AI-powered code generation and analysis directly in notebooks:

# %%
# %load_ext jupyter_ai_magics

# %%
%%ai chatgpt
Generate a function to calculate the Pearson correlation coefficient between two arrays

Key use cases:

• Code generation: Generate boilerplate code, data transformations, or analysis functions
• Data exploration: Ask questions about DataFrames or arrays
• Debugging assistance: Get suggestions for fixing errors
• Documentation: Generate docstrings or explanations

Providing Context for Better Results

AI assistants work best when given relevant context. Always provide:

1. API documentation: For specialized libraries (scanpy, pydeseq2, biopython)

   # Include relevant API documentation in a markdown cell
   # Example: scanpy.pp.filter_cells(data, min_genes=200)
   

2. Dataset descriptions: Shape, columns, data types

   # Document your data structure:
   # RNA-seq counts matrix: 20,000 genes × 5,000 cells
   # AnnData object: .X (sparse CSR matrix), .obs (cell metadata), .var (gene metadata)
   

3. Domain context: Biological meaning, expected ranges, units

   # Oxygen consumption rate: 10-20 pmol/s/million cells
   # Temperature: 37°C, pH: 7.4
   

Chat UI Assistance

JupyterLab's chat interface provides conversational help:

Best practices:

• Use for exploratory questions: "What's the best way to normalize this data?"
• Ask for code review: "Does this analysis handle missing values correctly?"
• Request visualizations: "Create a heatmap of the top 50 variable genes"
• Get explanations: "Explain what this cell is doing"

When to Use AI Assistance vs. Manual Coding

Use AI assistance for:

• Boilerplate code (imports, data loading templates)
• Exploratory analysis (quick plots, summary statistics)
• Learning new library syntax
• Generating test data or examples

Write code manually for:

• Core analysis logic (hypothesis testing, modeling)
• Publication-quality figures (fine-grained control needed)
• Performance-critical sections (AI-generated code may not be optimal)
• Complex domain-specific algorithms

Warning: Always verify AI-generated code. Check for:

• Correct library syntax (APIs change frequently)
• Appropriate statistical methods (AI may suggest invalid tests)
• Proper handling of biological data (species, units, measurement context)

JetBrains AI Assistant

For notebooks in PyCharm/DataSpell:

Features:

• Explain cell: Understand what code does (Alt+Enter → "Explain")
• Create visualization: Generate plots from data descriptions
• Edit cell: Refactor or improve code (Alt+Enter → "AI Actions")
• Fix errors: Get suggestions for runtime errors

Access: Right-click cell → "AI Assistant" or use AI chat sidebar

Jupytext Configuration

Projects should include .jupytext.toml in repository root:

# Jupytext configuration
# Enables git-friendly notebook version control

# Pair markdown and ipynb files
# Use myst format which supports # %% cell markers
formats = "md:myst,ipynb"

This tells Jupytext to:

• Recognize .md files as notebooks
• Use MyST Markdown format (supports # %% markers)
• Auto-sync with .ipynb when either is modified

Git Tracking Strategy

Recommended .gitignore configuration:

# Track .md notebooks (Jupytext source), ignore generated .ipynb files
*.ipynb
.ipynb_checkpoints/

What's tracked:

• ✅ .md notebook files (human-readable source)
• ❌ .ipynb files (generated, binary JSON)
• ❌ .ipynb_checkpoints/ (Jupyter temp files)

Rationale: .md files produce readable git diffs. .ipynb files are JSON with embedded outputs and can be regenerated from .md.

Common Operations

Create from scratch (manual)

1. Write Markdown file with # %% markers
2. Add YAML frontmatter (kernel info)
3. Convert: python3 -m jupytext --to ipynb file.md

Convert existing notebook to Markdown

python3 -m jupytext --to md:myst notebook.ipynb

Edit existing notebook

Option 1: Edit .md file directly (recommended for agents)

# Edit notebook.md in text editor
# Then convert:
python3 -m jupytext --to ipynb notebook.md

Option 2: Edit in Jupyter, sync back

jupyter notebook notebook.ipynb
# Make changes in Jupyter
# Sync back to .md:
python3 -m jupytext --sync notebook.ipynb

Validate structure

python3 -c "
from pathlib import Path
from src.utils.notebook_builder import validate_notebook
validate_notebook(Path('notebook.ipynb'))
print('✓ Valid')
"

Convert multiple notebooks

# Convert all .md notebooks in a directory
python3 -m jupytext --to ipynb analysis/*.md

# Or sync all paired notebooks
python3 -m jupytext --sync analysis/*.ipynb

Best Practices

1. Title every notebook with clear purpose
2. Start with imports in first code cell
3. Explain calculations with markdown cells before code
4. Interpret results with markdown cells after code
5. Use meaningful variable names (not x, y, z)
6. Include units in comments and axis labels
7. Save outputs (figures) to files for documentation

Reproducibility Standards

Scientific notebooks must be fully reproducible. Every notebook should enable another researcher to:

1. Recreate your computational environment
2. Rerun your analysis and get identical results
3. Understand your data sources and processing steps

Environment Documentation

Every notebook must include an environment documentation cell:

# %%
# Environment Information
# Run: pip freeze > requirements.txt
# Or: conda env export > environment.yml

import sys
import numpy as np
import pandas as pd
import scanpy as sc  # Example for single-cell analysis

print(f"Python: {sys.version}")
print(f"NumPy: {np.__version__}")
print(f"Pandas: {pd.__version__}")
print(f"Scanpy: {sc.__version__}")

# Include this output in your notebook for documentation

Create environment files:

# For pip users:
pip freeze > requirements.txt

# For conda users:
conda env export > environment.yml

# Include these files in your repository

Document kernel selection:

## Computational Environment

- **Kernel**: Python 3.11 (project-env)
- **Dependencies**: See `requirements.txt` for full package list
- **Critical packages**: scanpy==1.10.0, numpy==1.26.3, pandas==2.2.0

Random Seed Setting

For any stochastic process, set random seeds:

# %%
# Set random seeds for reproducibility
import numpy as np
import random

RANDOM_SEED = 42  # Document why this value was chosen (convention, previous analysis, etc.)

np.random.seed(RANDOM_SEED)
random.seed(RANDOM_SEED)

# For machine learning:
import torch
torch.manual_seed(RANDOM_SEED)

# For scanpy:
import scanpy as sc
sc.settings.seed = RANDOM_SEED

print(f"Random seed set to {RANDOM_SEED}")

Stochastic processes requiring seeds:

• UMAP, t-SNE (dimensionality reduction)
• Random forest, neural networks (machine learning)
• Monte Carlo simulations
• Random sampling or bootstrapping
• Graph algorithms with random initialization

Session Info Output

End every notebook with a session info cell:

# %%
# Session Information (for reproducibility)
import session_info

session_info.show(
    dependencies=True,
    html=False
)

# Alternative for single-cell analysis:
# import scanpy as sc
# sc.logging.print_versions()

This captures:

• Python version
• Operating system
• Package versions (all dependencies)
• Execution timestamp

File Path Best Practices

Use relative paths and variables:

# %%
from pathlib import Path

# Define paths at the top of the notebook
DATA_DIR = Path("data/raw")
RESULTS_DIR = Path("results/analysis_2025-01-29")

# Ensure output directories exist
RESULTS_DIR.mkdir(parents=True, exist_ok=True)

# Use variables throughout
input_file = DATA_DIR / "counts.csv"
output_file = RESULTS_DIR / "normalized_counts.csv"

Never use hardcoded absolute paths:

# BAD:
data = pd.read_csv("/Users/yourname/project/data.csv")

# GOOD:
data = pd.read_csv(DATA_DIR / "data.csv")

Reproducibility Checklist

Before sharing or archiving a notebook:

• Environment documented (Python version, key package versions)
• requirements.txt or environment.yml exists and is current
• Random seeds set for all stochastic processes
• Session info cell at end of notebook
• File paths use variables (not hardcoded)
• Data sources documented (where to download, version, date)
• Notebook runs end-to-end without errors (Restart & Run All)
• Results match expected output (if re-running existing analysis)

Integration with other skills:

• notebook-debugger: Use to verify end-to-end execution
• bioinformatician: Apply reproducibility standards to all computational biology analyses
• copilot: Review notebooks for reproducibility compliance

Project-Specific Usage

Many projects have a docs/NOTEBOOK-WORKFLOW.md or similar document with project-specific examples and patterns. Check your project's documentation for:

• Domain-specific notebook templates
• Agent integration patterns (which skills create notebooks)
• Directory structure conventions (where to save notebooks)
• Project-specific best practices

Troubleshooting

Issue: Jupytext can't find format

Error: Format 'percent' is not associated to extension '.md'

Fix: Use md:myst format in .jupytext.toml (not md:percent). MyST Markdown supports # %% markers.

formats = "md:myst,ipynb"  # Correct

Issue: Sync not working

Symptom: Changes to .ipynb don't appear in .md

Solution:

1. Check .jupytext.toml exists and has correct format
2. Run sync explicitly: python3 -m jupytext --sync notebook.ipynb
3. Check both files exist (create .md first if needed)

Issue: Validation fails

Error: nbformat.ValidationError

Causes:

• Missing cell IDs (required in nbformat v4.5+)
• Invalid JSON structure
• Missing required fields

Solution: Use notebook_builder.py utility functions which handle validation automatically.

Issue: Git shows .ipynb files

Symptom: .ipynb files appearing in git status

Fix: Ensure .gitignore contains *.ipynb. Check with:

git check-ignore -v notebook.ipynb

Error Prevention

Common Issues

1. Missing # %%: Code cells must start with this marker
2. Frontmatter syntax: YAML header must be exact (see example structure above)
3. Path handling: Use Path objects, ensure directories exist
4. Cell validation: Use notebook_builder.validate_notebook() after creation

Validation Checklist

Before finalizing a notebook:

• Frontmatter present with kernelspec
• All code cells have # %% marker
• Imports in first code cell
• Results interpreted with markdown
• Saved to appropriate location
• Validated with nbformat if creating .ipynb directly

Dependencies

Required packages:

pip3 install jupytext nbformat

Check installation:

pip3 list | grep -E "(jupytext|nbformat)"

Tested versions:

• jupytext: 1.19+
• nbformat: 5.10+
• Python: 3.9+

Integration with Other Skills

Common patterns for skill integration:

• Quantitative analysis skills: Package calculations as reproducible notebooks with parameter sweeps
• Research skills: Document literature-derived parameters with citations in data notebooks
• Planning skills: Generate protocol notebooks with expected results and analysis templates
• Review skills: Check notebook code for correctness and best practices

Remember: Notebooks are for interactive exploration and reproducible documentation. For production code, use Python modules in src/.

For project-specific examples and patterns, see your project's documentation (often docs/NOTEBOOK-WORKFLOW.md or similar).