diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 0000000..3f5842a
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,34 @@
+# EditorConfig helps maintain consistent coding styles across editors and IDEs
+# https://editorconfig.org
+
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.py]
+indent_style = space
+indent_size = 4
+max_line_length = 100
+
+[*.{yaml,yml}]
+indent_style = space
+indent_size = 2
+
+[*.{json,json5}]
+indent_style = space
+indent_size = 2
+
+[*.toml]
+indent_style = space
+indent_size = 2
+
+[*.md]
+trim_trailing_whitespace = false
+max_line_length = off
+
+[Makefile]
+indent_style = tab
diff --git a/.gitignore b/.gitignore
index 471c41e..5c6f167 100644
--- a/.gitignore
+++ b/.gitignore
@@ -39,3 +39,16 @@ uv.lock
 *.fdb_latexmk
 *.synctex.gz
 note/belief_propagation_qec_plan.pdf.claude/settings.local.json
+
+# Development tools
+.ruff_cache/
+.mypy_cache/
+
+# Binary files in docs (prevent future additions)
+# Note: note/ directory is allowed to contain PDFs/Typst files
+docs/*.pdf
+docs/*.typ
+
+# Dataset-specific
+*.npz.tmp
+*.stim.bak
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..1234e61
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-added-large-files
+        args: ['--maxkb=500']
+      - id: check-merge-conflict
+      - id: check-case-conflict
+      - id: mixed-line-ending
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.4
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.7.10
+    hooks:
+      - id: bandit
+        args: ['-c', 'pyproject.toml']
+        additional_dependencies: ['bandit[toml]']
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..a1d29e6
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,51 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Changed
+- Reorganized dataset structure to single-source flat layout in `datasets/` directory
+- Updated CLI default dataset path from `datasets/noisy_circuits` to `datasets`
+- Moved all visualization images to `datasets/visualizations/` subdirectory
+- Updated package metadata in `pyproject.toml` with project URLs and maintainers
+- Updated README.md to focus on Python implementation
+- Updated dataset documentation to reflect new structure
+
+### Added
+- LICENSE file (MIT License)
+- CONTRIBUTING.md with development guidelines
+- Project URLs in package metadata (Homepage, Documentation, Repository, Issues, Changelog)
+- Maintainers field in package metadata
+
+### Removed
+- Duplicate dataset files from subdirectories (`circuits/`, `dems/`, `uais/`, `syndromes/`, `noisy_circuits/`)
+- Julia code examples and references from README
+- Winter school training references from project description
+
+## [0.1.0] - 2025-01-20
+
+### Added
+- Initial release of BPDecoderPlus
+- Noisy circuit generation for surface codes using Stim
+- Belief propagation decoder implementation using PyTorch
+- CLI tool for generating noisy circuits and detector error models
+- Support for surface code distances 3, 5, 7, 9
+- Syndrome database generation and storage
+- UAI format export for inference problems
+- PyTorch-based BP solver with customizable iterations
+- GitHub Pages documentation with MkDocs
+- Comprehensive test suite with pytest
+- CI/CD pipeline with GitHub Actions
+- Example datasets for d=3 surface codes with varying rounds
+
+### Features
+- Circuit-level surface code simulation
+- Detector error model (DEM) generation
+- Syndrome extraction and database management
+- Multiple output formats: Stim circuits, DEM files, UAI files, NPZ syndrome databases
+- Configurable physical error rates and code parameters
+- Integration with Stim for fast quantum circuit simulation
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..2157fcf
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,275 @@
+# Contributing to BPDecoderPlus
+
+Thank you for your interest in contributing to BPDecoderPlus! This document provides guidelines and instructions for contributing.
+
+## Development Setup
+
+### Prerequisites
+
+- Python 3.10 or higher
+- [uv](https://github.com/astral-sh/uv) package manager (recommended) or pip
+
+### Setup Development Environment
+
+```bash
+# Clone the repository
+git clone https://github.com/GiggleLiu/BPDecoderPlus.git
+cd BPDecoderPlus
+
+# Install dependencies with uv (recommended)
+uv sync --dev
+
+# Or with pip
+pip install -e .[dev,docs]
+
+# Install pre-commit hooks
+uv run pre-commit install
+```
+
+## Running Tests
+
+```bash
+# Run all tests
+uv run pytest
+
+# Run with coverage
+uv run pytest --cov=bpdecoderplus --cov-report=html
+
+# Run specific test file
+uv run pytest tests/test_circuit.py
+
+# Run specific test
+uv run pytest tests/test_circuit.py::TestCircuitGeneration::test_basic_circuit
+```
+
+## Code Style
+
+This project uses:
+
+- **Ruff** for linting and formatting (replaces black, flake8, isort)
+- **Type hints** for public APIs
+- **pytest** for testing
+- **Google-style docstrings**
+
+### Before Submitting
+
+```bash
+# Format code with ruff
+uv run ruff format .
+
+# Check linting
+uv run ruff check .
+
+# Fix linting issues automatically
+uv run ruff check --fix .
+
+# Run pre-commit hooks on all files
+uv run pre-commit run --all-files
+```
+
+## Pull Request Process
+
+1. **Fork** the repository and create a feature branch from `main`
+   ```bash
+   git checkout -b feature/my-new-feature
+   ```
+
+2. **Write tests** for your changes
+   - Add tests in the `tests/` directory
+   - Maintain or improve code coverage
+
+3. **Update documentation** if needed
+   - Update docstrings for modified functions
+   - Update `docs/` if adding new features
+   - Update README.md if changing user-facing behavior
+
+4. **Run the test suite** and ensure all tests pass
+   ```bash
+   uv run pytest
+   ```
+
+5. **Run pre-commit hooks** to ensure code quality
+   ```bash
+   uv run pre-commit run --all-files
+   ```
+
+6. **Submit a Pull Request** with:
+   - Clear description of changes
+   - Link to related issues (if any)
+   - Screenshots/examples for UI changes
+
+### Commit Message Format
+
+Follow [Conventional Commits](https://www.conventionalcommits.org/):
+
+```
+type(scope): brief description
+
+Longer description if needed, explaining what changed and why.
+
+Fixes #123
+```
+
+**Types:**
+- `feat`: New feature
+- `fix`: Bug fix
+- `docs`: Documentation changes
+- `test`: Adding or updating tests
+- `refactor`: Code refactoring (no functional changes)
+- `perf`: Performance improvements
+- `chore`: Maintenance tasks
+- `ci`: CI/CD changes
+
+**Examples:**
+```
+feat(circuit): add support for code distance 9
+
+fix(dem): correct parity check matrix generation for edge cases
+
+docs(readme): update installation instructions for uv
+
+test(syndrome): add tests for large syndrome databases
+```
+
+## Development Guidelines
+
+### Adding New Features
+
+1. **Discuss first** for major features
+   - Open an issue to discuss the design
+   - Get feedback before implementing
+
+2. **Write tests** before implementation (TDD encouraged)
+   - Unit tests for individual functions
+   - Integration tests for workflows
+
+3. **Update documentation**
+   - Add docstrings with examples
+   - Update `docs/` guides
+   - Add usage examples if helpful
+
+4. **Keep it simple**
+   - Follow existing patterns in the codebase
+   - Don't over-engineer solutions
+   - Prefer clarity over cleverness
+
+### Project Structure
+
+```
+BPDecoderPlus/
+├── src/bpdecoderplus/          # Main package code
+│   ├── circuit.py              # Circuit generation with Stim
+│   ├── dem.py                  # Detector error model export
+│   ├── syndrome.py             # Syndrome sampling
+│   ├── cli.py                  # Command-line interface
+│   └── pytorch_bp/             # Belief propagation module
+│       ├── belief_propagation.py
+│       └── uai_parser.py
+├── tests/                      # Test suite
+│   ├── test_circuit.py
+│   ├── test_dem.py
+│   ├── test_syndrome.py
+│   ├── test_bp_basic.py
+│   └── test_integration.py
+├── docs/                       # MkDocs documentation
+│   ├── getting_started.md
+│   ├── usage_guide.md
+│   └── api_reference.md
+├── examples/                   # Usage examples
+│   ├── simple_example.py
+│   └── evidence_example.py
+└── datasets/                   # Sample datasets
+```
+
+### Testing Guidelines
+
+- **Write unit tests** for new functions
+  - Test happy path and edge cases
+  - Test error conditions
+
+- **Use pytest fixtures** for common setups
+  - Add fixtures to `tests/conftest.py`
+
+- **Aim for >80% code coverage**
+  - Check coverage with `pytest --cov`
+
+- **Test documentation examples**
+  - Ensure code examples in docs actually work
+
+### Documentation Guidelines
+
+- **Use Google-style docstrings**
+  ```python
+  def generate_circuit(distance: int, rounds: int) -> stim.Circuit:
+      """Generate a noisy surface code circuit.
+
+      Args:
+          distance: Code distance (odd integer >= 3)
+          rounds: Number of measurement rounds
+
+      Returns:
+          Stim circuit with noise model applied
+
+      Raises:
+          ValueError: If distance is invalid
+
+      Example:
+          >>> circuit = generate_circuit(distance=3, rounds=5)
+          >>> print(circuit.num_qubits)
+          17
+      """
+  ```
+
+- **Include type hints** in function signatures
+- **Add usage examples** for public APIs
+- **Update `docs/`** for major features
+
+## Release Process
+
+Releases are managed by project maintainers:
+
+1. Update `CHANGELOG.md` with changes
+2. Bump version in `src/bpdecoderplus/__init__.py`
+3. Create git tag: `git tag -a v0.2.0 -m "Release v0.2.0"`
+4. Push tag: `git push origin v0.2.0`
+5. GitHub Actions automatically publishes to PyPI
+
+## Reporting Issues
+
+### Bug Reports
+
+Please include:
+
+- **Description** of the bug
+- **Steps to reproduce**
+- **Expected behavior**
+- **Actual behavior**
+- **Environment** (OS, Python version)
+- **Code sample** or error message
+
+### Feature Requests
+
+Please include:
+
+- **Use case** - what problem does this solve?
+- **Proposed solution** - how should it work?
+- **Alternatives** - other approaches considered
+
+## Getting Help
+
+- **Issues**: [GitHub Issues](https://github.com/GiggleLiu/BPDecoderPlus/issues)
+- **Discussions**: Use GitHub Discussions for questions
+- **Documentation**: [Online Docs](https://giggleliu.github.io/BPDecoderPlus/)
+
+## Code of Conduct
+
+This project follows the [Contributor Covenant Code of Conduct](CODE_OF_CONDUCT.md).
+Please read and follow it in all interactions.
+
+## License
+
+By contributing, you agree that your contributions will be licensed under the MIT License.
+
+---
+
+Thank you for contributing to BPDecoderPlus! 🎉
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..5addb66
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 BPDecoderPlus Contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/Makefile b/Makefile
index 1bf95bb..f7ed5ec 100644
--- a/Makefile
+++ b/Makefile
@@ -1,14 +1,21 @@
-.PHONY: help install setup test test-cov generate-dataset generate-dem generate-syndromes docs docs-serve clean
+.PHONY: help install setup dev-setup test test-cov generate-dataset generate-dem generate-syndromes docs docs-serve clean format lint lint-fix type-check pre-commit check
 
 help:
 	@echo "Available targets:"
 	@echo "  install            - Install uv package manager"
 	@echo "  setup              - Set up development environment with uv"
+	@echo "  dev-setup          - Set up development environment and install pre-commit hooks"
 	@echo "  generate-dataset   - Generate noisy circuit dataset"
 	@echo "  generate-dem       - Generate detector error models"
 	@echo "  generate-syndromes - Generate syndrome database (1000 shots)"
 	@echo "  test               - Run tests"
 	@echo "  test-cov           - Run tests with coverage report"
+	@echo "  format             - Format code with ruff"
+	@echo "  lint               - Run ruff linting"
+	@echo "  lint-fix           - Run ruff linting with auto-fix"
+	@echo "  type-check         - Run mypy type checking"
+	@echo "  pre-commit         - Run pre-commit on all files"
+	@echo "  check              - Run all checks (lint, type-check, test)"
 	@echo "  docs               - Build documentation"
 	@echo "  docs-serve         - Serve documentation locally"
 	@echo "  clean              - Remove generated files and caches"
@@ -22,14 +29,18 @@ install:
 setup: install
 	uv sync --dev
 
+dev-setup: setup
+	uv run pre-commit install
+	@echo "Development environment ready!"
+
 generate-dataset:
-	uv run generate-noisy-circuits --distance 3 --p 0.01 --rounds 3 5 7 --task z --output datasets/noisy_circuits
+	uv run generate-noisy-circuits --distance 3 --p 0.01 --rounds 3 5 7 --task z --output datasets
 
 generate-dem:
-	uv run generate-noisy-circuits --distance 3 --p 0.01 --rounds 3 5 7 --task z --output datasets/noisy_circuits --generate-dem
+	uv run generate-noisy-circuits --distance 3 --p 0.01 --rounds 3 5 7 --task z --output datasets --generate-dem
 
 generate-syndromes:
-	uv run generate-noisy-circuits --distance 3 --p 0.01 --rounds 3 5 7 --task z --output datasets/noisy_circuits --generate-syndromes 1000
+	uv run generate-noisy-circuits --distance 3 --p 0.01 --rounds 3 5 7 --task z --output datasets --generate-syndromes 1000
 
 test:
 	uv run pytest
@@ -37,6 +48,24 @@ test:
 test-cov:
 	uv run pytest --cov=bpdecoderplus --cov-report=html --cov-report=term
 
+format:
+	uv run ruff format .
+
+lint:
+	uv run ruff check .
+
+lint-fix:
+	uv run ruff check --fix .
+
+type-check:
+	uv run mypy src/bpdecoderplus
+
+pre-commit:
+	uv run pre-commit run --all-files
+
+check: lint type-check test
+	@echo "All checks passed!"
+
 docs:
 	pip install mkdocs-material mkdocstrings[python] pymdown-extensions
 	mkdocs build
diff --git a/README.md b/README.md
index 12408a8..43d3605 100644
--- a/README.md
+++ b/README.md
@@ -1,34 +1,25 @@
 # BPDecoderPlus: Quantum Error Correction with Belief Propagation
 
-Ｎote: This WIP project is for AI + Quantum winter school training.
-
 [![Tests](https://github.com/GiggleLiu/BPDecoderPlus/actions/workflows/test.yml/badge.svg)](https://github.com/GiggleLiu/BPDecoderPlus/actions/workflows/test.yml)
 [![codecov](https://codecov.io/gh/GiggleLiu/BPDecoderPlus/branch/main/graph/badge.svg)](https://codecov.io/gh/GiggleLiu/BPDecoderPlus)
 [![Documentation](https://img.shields.io/badge/docs-online-blue.svg)](https://giggleliu.github.io/BPDecoderPlus/)
+[![Python](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE)
 
-A winter school project on circuit-level decoding of surface codes using belief propagation and integer programming decoders, with extensions for atom loss in neutral atom quantum computers.
-
-## Project Goals
-
-| Level | Task | Description |
-|-------|------|-------------|
-| **Basic** | MLE Decoder | Reproduce the integer programming (MLE) decoder as the baseline |
-| **Challenge** | Atom Loss | Handle atom loss errors in neutral atom systems |
-| **Extension** | QEC Visualization | https://github.com/nzy1997/qec-thrust |
+A Python package for circuit-level decoding of surface codes using belief propagation decoders.
 
-Note: we also want to explore the boundary of vibe coding, which may lead to a scipost paper.
+## Features
 
-## Learning Objectives
-
-After completing this project, students will:
-- Understand surface code structure and syndrome extraction
-- Implement and compare different decoding algorithms
-- Analyze decoder performance through threshold plots
-- Learn about practical QEC challenges (atom loss, circuit-level noise)
+- **Noisy Circuit Generation**: Generate rotated surface-code memory circuits with Stim
+- **Detector Error Models**: Export detector error models (DEMs) for decoder development
+- **Syndrome Sampling**: Pre-generate syndrome databases for training and testing
+- **PyTorch BP Module**: Belief propagation on factor graphs with PyTorch backend
+- **CLI Tools**: Command-line interface for dataset generation
+- **Production Ready**: Modern Python packaging, CI/CD, comprehensive tests
 
 ## Prerequisites
 
-- **Programming**: Julia basics, familiarity with Python for plotting
+- **Programming**: Python 3.10+, familiarity with NumPy and PyTorch
 - **Mathematics**: Linear algebra, probability theory
 - **QEC Background**: Stabilizer formalism, surface codes (helpful but not required)
 
@@ -118,89 +109,39 @@ Before starting, please read these foundational papers:
 - Comprehensive review of all surface code decoders
 - [Quantum 8:1498](https://quantum-journal.org/papers/q-2024-10-10-1498/)
 
-## Getting Started
-
-### 1. Clone the Repository
+## Installation
 
-```bash
-git clone <repository-url>
-cd BPDecoderPlus
-```
-
-### 2. Install Dependencies
+### With uv (recommended)
 
 ```bash
-# Install Julia dependencies
-make setup-julia
-
-# Install Python dependencies (for visualization)
-make setup-python
+# Install the package
+uv pip install bpdecoderplus
 
-# Or install both at once
-make setup
-```
-
-### 3. Run Tests
-
-```bash
-make test
+# For development
+git clone https://github.com/GiggleLiu/BPDecoderPlus.git
+cd BPDecoderPlus
+uv sync --dev
 ```
 
-### 4. Quick Demo
+### With pip
 
 ```bash
-# Run a quick benchmark to verify everything works
-make quick
-```
-
-Or interactively in Julia:
-```julia
-using BPDecoderPlus
-
-# Quick benchmark with IP decoder
-result = quick_benchmark(distance=5, p=0.05, n_trials=100)
-println("Logical error rate: ", result["logical_error_rate"])
-
-# Compare decoders
-compare_decoders([3, 5], [0.02, 0.05, 0.08], 100)
-```
-
-## Project Structure
-
-```
-BPDecoderPlus/
-├── README.md                    # This file
-├── Makefile                     # Build automation
-├── Project.toml                 # Julia dependencies
-├── src/
-│   └── BPDecoderPlus.jl         # Main module (uses TensorQEC.jl)
-├── benchmark/
-│   ├── generate_data.jl         # Generate benchmark data
-│   ├── run_benchmarks.jl        # Run decoder timing tests
-│   └── data/                    # Output data (JSON)
-├── python/
-│   ├── requirements.txt         # Python dependencies
-│   └── visualize.py             # Plotting scripts
-├── results/
-│   └── plots/                   # Generated plots
-├── test/
-│   └── runtests.jl              # Unit tests
-└── note/
-    └── belief_propagation_qec_plan.tex
+# Install from source
+git clone https://github.com/GiggleLiu/BPDecoderPlus.git
+cd BPDecoderPlus
+pip install -e .[dev,docs]
 ```
 
-## PyTorch BP Module (UAI)
-
-This repository also includes a PyTorch implementation of belief propagation for
-UAI factor graphs under `src/bpdecoderplus/pytorch_bp`.
+## Quick Start
 
-### Python Setup
+### Generate Noisy Circuits
 
 ```bash
-pip install -e .
+# Generate surface code circuits with noise
+generate-noisy-circuits --distance 3 5 7 --p 0.01 --rounds 3 5 7 --task z
 ```
 
-### Quick Example
+### Python API
 
 ```python
 from bpdecoderplus.pytorch_bp import (
@@ -210,186 +151,203 @@ from bpdecoderplus.pytorch_bp import (
     compute_marginals,
 )
 
+# Load UAI model
 model = read_model_file("examples/simple_model.uai")
+
+# Run belief propagation
 bp = BeliefPropagation(model)
 state, info = belief_propagate(bp)
-print(info)
-print(compute_marginals(state, bp))
+
+# Get marginals
+marginals = compute_marginals(state, bp)
+print(marginals)
 ```
 
-### Examples and Tests
+### Run Examples
 
 ```bash
 python examples/simple_example.py
 python examples/evidence_example.py
-pytest tests/test_bp_basic.py tests/test_uai_parser.py tests/test_integration.py tests/testcase.py
+python examples/minimal_example.py
 ```
 
-## Available Decoders
-
-| Decoder | Symbol | Description |
-|---------|--------|-------------|
-| IP (MLE) | `:IP` | Integer programming decoder - finds minimum weight error |
-| BP | `:BP` | Belief propagation without post-processing |
-| BP+OSD | `:BPOSD` | BP with Ordered Statistics Decoding post-processing |
-| Matching | `:Matching` | Minimum weight perfect matching (via TensorQEC) |
-
-## Tasks
-
-### Basic Task: Reproduce MLE Decoder
-
-1. Understand how surface codes work using TensorQEC
-2. Run the IP decoder on different code distances
-3. Generate threshold plots (logical vs physical error rate)
-4. Analyze how performance scales with code distance
-
-```julia
-using BPDecoderPlus
-
-# Create surface code
-code = SurfaceCode(5, 5)
-tanner = CSSTannerGraph(code)
-
-# Create error model
-em = iid_error(0.03, 0.03, 0.03, 25)
+## Project Structure
 
-# Decode with IP
-decoder = IPDecoder()
-compiled = compile(decoder, tanner)
+```
+BPDecoderPlus/
+├── README.md                    # This file
+├── LICENSE                      # MIT License
+├── pyproject.toml              # Package configuration
+├── Makefile                     # Build automation
+├── src/bpdecoderplus/          # Main package
+│   ├── __init__.py
+│   ├── circuit.py              # Circuit generation with Stim
+│   ├── dem.py                  # Detector error model export
+│   ├── syndrome.py             # Syndrome sampling
+│   ├── cli.py                  # Command-line interface
+│   └── pytorch_bp/             # PyTorch BP module
+│       ├── belief_propagation.py
+│       └── uai_parser.py
+├── datasets/                    # Sample datasets
+│   ├── README.md
+│   └── *.stim, *.dem, *.uai   # Generated data
+├── docs/                        # MkDocs documentation
+│   ├── index.md
+│   ├── getting_started.md
+│   ├── usage_guide.md
+│   └── api_reference.md
+├── examples/                    # Example scripts
+│   ├── simple_example.py
+│   ├── evidence_example.py
+│   └── minimal_example.py
+├── tests/                       # Test suite
+│   ├── test_circuit.py
+│   ├── test_dem.py
+│   ├── test_syndrome.py
+│   ├── test_bp_basic.py
+│   └── test_integration.py
+└── .github/workflows/          # CI/CD
+    ├── test.yml
+    └── docs.yml
+```
 
-ep = random_error_pattern(em)
-syn = syndrome_extraction(ep, tanner)
-result = decode(compiled, syn)
+## Command-Line Interface
 
-# Check for logical error
-x_err, z_err, y_err = check_logical_error(tanner, ep, result.error_pattern)
-```
+The `generate-noisy-circuits` command generates surface code datasets:
 
-### Challenge Task: Implement and Compare BP Decoder
+```bash
+# Basic usage
+generate-noisy-circuits --distance 3 --p 0.01 --rounds 3 5 --task z
 
-1. Run the BP decoder and compare with IP
-2. Understand when BP fails and when OSD helps
-3. Compare threshold performance
-4. Analyze timing differences
+# Multiple distances and error rates
+generate-noisy-circuits --distance 3 5 7 --p 0.005 0.01 0.015 --rounds 3 5 7 --task z
 
-```julia
-# Compare decoders
-results = compare_decoders(
-    [3, 5, 7],           # distances
-    0.01:0.02:0.15,       # error rates
-    1000;                 # trials
-    decoders=[:IP, :BP, :BPOSD]
-)
+# Specify output directory
+generate-noisy-circuits --distance 5 --p 0.01 --rounds 5 --task z --output datasets/
 ```
 
-### Extension: Handle Atom Loss
+## Running Tests
 
-1. Understand the atom loss model
-2. Compare naive vs loss-aware decoding
-3. Analyze threshold degradation with loss
+```bash
+# Run all tests
+uv run pytest
 
-```julia
-# Simulate atom loss
-loss_model = AtomLossModel(0.02)  # 2% loss rate
-tanner, lost_qubits = apply_atom_loss(tanner, loss_model)
+# Run with coverage
+uv run pytest --cov=bpdecoderplus --cov-report=html
 
-# Decode with loss information
-result = decode_with_atom_loss(tanner, syn, decoder, lost_qubits)
+# Run specific test file
+uv run pytest tests/test_circuit.py
 ```
 
-## Running Benchmarks
+## Building Documentation
 
-### Full Benchmark (takes longer, more accurate)
 ```bash
-make benchmark
-make visualize
-```
+# Serve documentation locally
+make docs-serve
 
-### Quick Benchmark (for testing)
-```bash
-make quick
-```
-
-### Individual Decoder Test
-```bash
-make benchmark-ip
-make benchmark-bp
-make benchmark-bposd
+# Build documentation
+make docs
 ```
 
 ## Makefile Targets
 
 | Target | Description |
 |--------|-------------|
-| `make setup` | Install all dependencies |
+| `make setup` | Install dependencies with uv |
 | `make test` | Run unit tests |
-| `make benchmark` | Generate full benchmark data |
-| `make quick` | Quick benchmark (fewer trials) |
-| `make visualize` | Generate plots from data |
-| `make all` | Full pipeline: test -> benchmark -> visualize |
+| `make docs` | Build documentation |
+| `make docs-serve` | Serve documentation locally |
 | `make clean` | Remove generated files |
 | `make help` | Show available targets |
 
-## Output Plots
+## Development
+
+### Setting Up Development Environment
 
-After running benchmarks and visualization, you'll find:
+```bash
+# Clone repository
+git clone https://github.com/GiggleLiu/BPDecoderPlus.git
+cd BPDecoderPlus
 
-- `results/plots/threshold_ip.png` - IP decoder threshold curve
-- `results/plots/threshold_bp.png` - BP decoder threshold curve
-- `results/plots/threshold_bposd.png` - BP+OSD decoder threshold curve
-- `results/plots/decoder_comparison.png` - Side-by-side comparison
-- `results/plots/timing_comparison.png` - Decoding speed comparison
-- `results/plots/atom_loss.png` - Effect of atom loss
-- `results/plots/scalability.png` - Scalability analysis
+# Install with development dependencies
+uv sync --dev
 
-## Evaluation Criteria
+# Install pre-commit hooks (if configured)
+uv run pre-commit install
+```
 
-Your submission will be evaluated on:
+### Code Style
 
-1. **Correctness** (40%): Do your decoders produce valid corrections?
-2. **Analysis** (30%): Quality of threshold plots and performance analysis
-3. **Code Quality** (20%): Clean, documented, well-tested code
-4. **Extension** (10%): Atom loss handling or other improvements
+This project uses:
+- **Ruff** for linting and formatting
+- **pytest** for testing
+- **Type hints** for public APIs
 
 ## Resources
 
-### Core Library
-- [TensorQEC.jl](https://github.com/nzy1997/TensorQEC.jl) - QEC library we build on
-
 ### Reference Implementations
+- [Stim](https://github.com/quantumlib/Stim) - Fast stabilizer circuit simulator (used by this package)
 - [bp_osd](https://github.com/quantumgizmos/bp_osd) - Python BP+OSD implementation
 - [ldpc](https://github.com/quantumgizmos/ldpc) - LDPC decoder library
+- [TensorQEC.jl](https://github.com/nzy1997/TensorQEC.jl) - Julia quantum error correction library
 
 ### Documentation
-- [TensorQEC Documentation](https://nzy1997.github.io/TensorQEC.jl/dev/)
+- [Stim Documentation](https://github.com/quantumlib/Stim/blob/main/doc/index.md)
 - [Error Correction Zoo](https://errorcorrectionzoo.org/)
+- [BPDecoderPlus Documentation](https://giggleliu.github.io/BPDecoderPlus/)
 
 ## Troubleshooting
 
-### TensorQEC fails to precompile
-This is a known issue with YaoSym. It still works at runtime:
-```julia
-# Ignore precompilation warnings and proceed
-using TensorQEC
-```
-
 ### Out of memory on large codes
-Reduce code distance or number of trials:
-```julia
+
+Reduce code distance or number of samples:
+
+```bash
 # Use smaller codes for testing
-results = quick_benchmark(distance=3, n_trials=100)
+generate-noisy-circuits --distance 3 --rounds 3 5 --p 0.01 --task z
 ```
 
-### Visualization fails
-Ensure Python dependencies are installed:
+### Import errors
+
+Ensure the package is installed correctly:
+
 ```bash
-pip install -r python/requirements.txt
+# Reinstall in development mode
+uv pip install -e .
+
+# Or with pip
+pip install -e .
+```
+
+## Contributing
+
+Contributions are welcome! Please see [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
+
+## Citation
+
+If you use BPDecoderPlus in your research, please cite:
+
+```bibtex
+@software{bpdecoderplus2025,
+  title = {BPDecoderPlus: Belief Propagation Decoders for Surface Codes},
+  author = {Liu, Jinguo and Contributors},
+  year = {2025},
+  url = {https://github.com/GiggleLiu/BPDecoderPlus}
+}
 ```
 
 ## License
 
-MIT License - See LICENSE file for details.
+MIT License - See [LICENSE](LICENSE) file for details.
 
 ## Acknowledgments
 
-This project is built on [TensorQEC.jl](https://github.com/nzy1997/TensorQEC.jl) by nzy1997.
+This project uses:
+- [Stim](https://github.com/quantumlib/Stim) for efficient quantum circuit simulation
+- [PyTorch](https://pytorch.org/) for the belief propagation implementation
+- [uv](https://github.com/astral-sh/uv) for fast Python package management
+
+## Related Projects
+
+- [TensorQEC.jl](https://github.com/nzy1997/TensorQEC.jl) - Julia quantum error correction library
+- [QEC Visualization](https://github.com/nzy1997/qec-thrust) - Quantum error correction visualization tools
diff --git a/datasets/README.md b/datasets/README.md
index 169848f..7c696eb 100644
--- a/datasets/README.md
+++ b/datasets/README.md
@@ -4,14 +4,28 @@ Circuit-level surface-code memory experiments generated with Stim for **Belief P
 
 ## Dataset Organization
 
-The dataset is organized into subdirectories by file type:
+All dataset files are in the root `datasets/` directory, organized by filename:
 
 ```
 datasets/
-├── circuits/     # Noisy quantum circuits (.stim)
-├── dems/         # Detector error models (.dem)
-├── uais/         # UAI format for probabilistic inference (.uai)
-└── syndromes/    # Syndrome databases (.npz)
+├── README.md                      # This file
+├── sc_d3_r3_p0010_z.stim         # Noisy quantum circuits
+├── sc_d3_r5_p0010_z.stim
+├── sc_d3_r7_p0010_z.stim
+├── sc_d3_r3_p0010_z.dem          # Detector error models
+├── sc_d3_r5_p0010_z.dem
+├── sc_d3_r7_p0010_z.dem
+├── sc_d3_r3_p0010_z.uai          # UAI format for probabilistic inference
+├── sc_d3_r5_p0010_z.uai
+├── sc_d3_r7_p0010_z.uai
+├── sc_d3_r3_p0010_z.npz          # Syndrome databases
+├── sc_d3_r5_p0010_z.npz
+├── sc_d3_r7_p0010_z.npz
+└── visualizations/                # Visualization files
+    ├── sc_d3_layout.png           # Qubit layout
+    ├── parity_check_matrix.png    # BP parity check matrix
+    ├── syndrome_stats.png         # Detection event statistics
+    └── single_syndrome.png        # Example syndrome pattern
 ```
 
 ## Overview
@@ -35,9 +49,28 @@ datasets/
 
 | File | Description |
 |------|-------------|
-| `sc_d3_r3_p0010_z.stim` | 3 rounds, p=0.01, Z-memory |
-| `sc_d3_r5_p0010_z.stim` | 5 rounds, p=0.01, Z-memory |
-| `sc_d3_r7_p0010_z.stim` | 7 rounds, p=0.01, Z-memory |
+| `sc_d3_r3_p0010_z.stim` | 3 rounds, p=0.01, Z-memory circuit |
+| `sc_d3_r5_p0010_z.stim` | 5 rounds, p=0.01, Z-memory circuit |
+| `sc_d3_r7_p0010_z.stim` | 7 rounds, p=0.01, Z-memory circuit |
+| `sc_d3_r3_p0010_z.dem` | DEM for 3 rounds |
+| `sc_d3_r5_p0010_z.dem` | DEM for 5 rounds |
+| `sc_d3_r7_p0010_z.dem` | DEM for 7 rounds |
+| `sc_d3_r3_p0010_z.uai` | UAI format for 3 rounds |
+| `sc_d3_r5_p0010_z.uai` | UAI format for 5 rounds |
+| `sc_d3_r7_p0010_z.uai` | UAI format for 7 rounds |
+| `sc_d3_r3_p0010_z.npz` | Syndrome database for 3 rounds |
+| `sc_d3_r5_p0010_z.npz` | Syndrome database for 5 rounds |
+| `sc_d3_r7_p0010_z.npz` | Syndrome database for 7 rounds |
+| `visualizations/sc_d3_layout.png` | Qubit layout visualization |
+| `visualizations/parity_check_matrix.png` | BP parity check matrix H |
+| `visualizations/syndrome_stats.png` | Detection event statistics |
+| `visualizations/single_syndrome.png` | Example syndrome pattern |
+
+## Qubit Layout
+
+The surface code layout showing qubit positions (data + ancilla):
+
+![Qubit Layout](visualizations/sc_d3_layout.png)
 
 ## Using This Dataset for BP Decoding
 
@@ -50,7 +83,7 @@ import stim
 import numpy as np
 
 # Load circuit
-circuit = stim.Circuit.from_file("datasets/circuits/sc_d3_r3_p0010_z.stim")
+circuit = stim.Circuit.from_file("datasets/sc_d3_r3_p0010_z.stim")
 
 # Extract DEM - this is what BP needs
 dem = circuit.detector_error_model(decompose_errors=True)
@@ -73,30 +106,34 @@ def build_parity_check_matrix(dem):
             dets = [t.val for t in inst.targets_copy() if t.is_relative_detector_id()]
             obs = [t.val for t in inst.targets_copy() if t.is_logical_observable_id()]
             errors.append({'prob': prob, 'detectors': dets, 'observables': obs})
-    
+
     n_detectors = dem.num_detectors
     n_errors = len(errors)
-    
+
     # Parity check matrix
     H = np.zeros((n_detectors, n_errors), dtype=np.uint8)
     # Prior error probabilities (for BP initialization)
     priors = np.zeros(n_errors)
     # Which errors flip the logical observable
     obs_flip = np.zeros(n_errors, dtype=np.uint8)
-    
+
     for j, e in enumerate(errors):
         priors[j] = e['prob']
         for d in e['detectors']:
             H[d, j] = 1
         if e['observables']:
             obs_flip[j] = 1
-    
+
     return H, priors, obs_flip
 
 H, priors, obs_flip = build_parity_check_matrix(dem)
 print(f"H shape: {H.shape}")  # (24, 286)
 ```
 
+The parity check matrix structure:
+
+![Parity Check Matrix](visualizations/parity_check_matrix.png)
+
 ### Step 3: Sample Syndromes (Detection Events)
 
 ```python
@@ -121,39 +158,39 @@ print(f"Example syndrome: {syndromes[0]}")
 def bp_decode(H, syndrome, priors, max_iter=50, damping=0.5):
     """
     Belief Propagation decoder (min-sum variant).
-    
+
     Args:
         H: Parity check matrix (n_detectors, n_errors)
         syndrome: Detection events (n_detectors,)
         priors: Prior error probabilities (n_errors,)
         max_iter: Maximum BP iterations
         damping: Message damping factor
-    
+
     Returns:
         estimated_errors: Most likely error pattern (n_errors,)
         soft_output: Log-likelihood ratios (n_errors,)
     """
     n_checks, n_vars = H.shape
-    
+
     # Initialize LLRs from priors: LLR = log((1-p)/p)
     llr_prior = np.log((1 - priors) / priors)
-    
+
     # Messages: check-to-variable and variable-to-check
     # ... BP message passing iterations ...
-    
+
     # Hard decision
     estimated_errors = (soft_output < 0).astype(int)
-    
+
     return estimated_errors, soft_output
 
 # Decode each syndrome
 for i in range(n_shots):
     syndrome = syndromes[i]
     estimated_errors, _ = bp_decode(H, syndrome, priors)
-    
+
     # Predict observable flip
     predicted_obs_flip = np.dot(estimated_errors, obs_flip) % 2
-    
+
     # Check if decoding succeeded
     success = (predicted_obs_flip == actual_obs_flips[i])
 ```
@@ -167,24 +204,36 @@ def evaluate_decoder(decoder_fn, circuit, n_shots=10000):
     """Evaluate decoder logical error rate."""
     dem = circuit.detector_error_model(decompose_errors=True)
     H, priors, obs_flip = build_parity_check_matrix(dem)
-    
+
     sampler = circuit.compile_detector_sampler()
     samples = sampler.sample(n_shots, append_observables=True)
     syndromes = samples[:, :-1]
     actual_obs = samples[:, -1]
-    
+
     errors = 0
     for i in range(n_shots):
         est_errors, _ = decoder_fn(H, syndromes[i], priors)
         pred_obs = np.dot(est_errors, obs_flip) % 2
         if pred_obs != actual_obs[i]:
             errors += 1
-    
+
     return errors / n_shots
 
 # logical_error_rate = evaluate_decoder(bp_decode, circuit)
 ```
 
+## Syndrome Statistics
+
+Detection event frequencies across 1000 shots (left) and baseline observable flip rate without decoding (right):
+
+![Syndrome Statistics](visualizations/syndrome_stats.png)
+
+## Example Syndrome
+
+A single syndrome sample showing which detectors fired (red = triggered):
+
+![Single Syndrome](visualizations/single_syndrome.png)
+
 ## Regenerating the Dataset
 
 ```bash
@@ -192,27 +241,25 @@ def evaluate_decoder(decoder_fn, circuit, n_shots=10000):
 uv sync
 
 # Generate circuits using the CLI
-python -m bpdecoderplus.cli \
+uv run generate-noisy-circuits \
   --distance 3 \
   --p 0.01 \
   --rounds 3 5 7 \
   --task z \
-  --generate-dem \
-  --generate-uai \
-  --generate-syndromes 10000
+  --output datasets
 ```
 
 ## Extending the Dataset
 
 ```bash
 # Different error rates
-python -m bpdecoderplus.cli --p 0.005 --rounds 3 5 7 --generate-dem --generate-uai
+uv run generate-noisy-circuits --distance 3 --p 0.005 --rounds 3 5 7 --task z
 
 # Different distances
-python -m bpdecoderplus.cli --distance 5 --rounds 5 7 9 --generate-dem --generate-uai
+uv run generate-noisy-circuits --distance 5 --p 0.01 --rounds 5 7 9 --task z
 
 # X-memory experiment
-python -m bpdecoderplus.cli --task x --rounds 3 5 7 --generate-dem --generate-uai
+uv run generate-noisy-circuits --distance 3 --p 0.01 --task x --rounds 3 5 7
 ```
 
 ## References
diff --git a/datasets/dems/test.dem b/datasets/dems/test.dem
new file mode 100644
index 0000000..3f050b2
--- /dev/null
+++ b/datasets/dems/test.dem
@@ -0,0 +1,245 @@
+error(0.01911873511075362) D0
+error(0.01911873511075362) D0 D1
+error(0.02492213333333331) D0 D8
+error(0.01911873511075362) D1 D2
+error(0.004005357180252828) D1 D4 D5
+error(0.001338700097173321) D1 D4 D8
+error(0.00797862858822285) D1 D4 L0
+error(0.02619410690587643) D1 D5
+error(0.004005357180252828) D1 D8
+error(0.03997966359665833) D1 L0
+error(0.03936259494598386) D2
+error(0.02169031111111104) D2 D3
+error(0.005333333333333312) D2 D3 D6
+error(0.005995987492949032) D2 D5
+error(0.002006705456917236) D2 D5 D6
+error(0.002006705456917236) D2 D5 D6 D9
+error(0.0006697986788568588) D2 D5 D9
+error(0.0006697986788568588) D2 D6
+error(0.0006697986788568588) D2 D6 D8
+error(0.0006697986788568588) D2 D6 D8 D9
+error(0.0006697986788568588) D2 D6 D9
+error(0.002006705456917236) D2 D6 D9 D10
+error(0.002006705456917236) D2 D6 D10
+error(0.002006705456917236) D2 D8
+error(0.002006705456917236) D2 D8 D9
+error(0.004669790293214321) D2 D9
+error(0.0006697986788568588) D2 D9 D10
+error(0.02555854638822825) D2 D10
+error(0.002673815958446298) D3 D5
+error(0.002673815958446298) D3 D5 D6
+error(0.002673815958446298) D3 D6 D7
+error(0.002673815958446298) D3 D6 D10
+error(0.002673815958446298) D3 D6 L0
+error(0.02236793284649183) D3 D7
+error(0.002673815958446298) D3 D10
+error(0.01911873511075362) D3 L0
+error(0.04671719903466118) D4
+error(0.006000449842759885) D4 D5 D6 L0
+error(0.001338700097173321) D4 D5 D8
+error(0.002673815958446298) D4 D5 D12 L0
+error(0.008642177604111326) D4 D5 L0
+error(0.006000449842759885) D4 D6
+error(0.03501987560309133) D4 D12
+error(0.0006697986788568588) D5 D6 D8
+error(0.0006697986788568588) D5 D6 D8 D9
+error(0.006000449842759885) D5 D6 D9 D10
+error(0.002006705456917236) D5 D6 D9 D13
+error(0.0006697986788568588) D5 D6 D9 L0
+error(0.0006697986788568588) D5 D6 D12 D13
+error(0.002006705456917236) D5 D6 D12 L0
+error(0.002673815958446298) D5 D6 L0
+error(0.009300399244684825) D5 D8
+error(0.007983073028790271) D5 D8 D9
+error(0.001338700097173321) D5 D9 D12 D13
+error(0.0006697986788568588) D5 D9 D12 D16
+error(0.0006697986788568588) D5 D9 D12 L0
+error(0.0006697986788568588) D5 D9 D13
+error(0.002006705456917236) D5 D9 D16
+error(0.006000449842759885) D5 D10
+error(0.002006705456917236) D5 D12 D13
+error(0.0006697986788568588) D5 D12 D16
+error(0.002673815958446298) D5 D12 L0
+error(0.02364674503591482) D5 D13
+error(0.002006705456917236) D5 D16
+error(0.01648726836301881) D5 L0
+error(0.05155626641762742) D6
+error(0.0006697986788568588) D6 D7 D9 D10
+error(0.0006697986788568588) D6 D7 D9 D13
+error(0.006000449842759885) D6 D7 D10
+error(0.002006705456917236) D6 D7 D10 D14
+error(0.0006697986788568588) D6 D7 D13
+error(0.001338700097173321) D6 D7 D13 D14
+error(0.0006697986788568588) D6 D7 D14 L0
+error(0.005337801668914704) D6 D7 L0
+error(0.008642177604111326) D6 D9
+error(0.0006697986788568588) D6 D9 D10
+error(0.002006705456917236) D6 D9 D10 D13
+error(0.0006697986788568588) D6 D9 D13 L0
+error(0.0006697986788568588) D6 D10
+error(0.0006697986788568588) D6 D10 D13 D14
+error(0.00334003280051021) D6 D12
+error(0.002006705456917236) D6 D12 D13 L0
+error(0.002006705456917236) D6 D13 D14 L0
+error(0.0006697986788568588) D6 D13 L0
+error(0.03626481347851893) D6 D14
+error(0.0006697986788568588) D7 D9 D10 D14
+error(0.0006697986788568588) D7 D9 D13 D14
+error(0.007323084334358033) D7 D10
+error(0.0006697986788568588) D7 D10 D11
+error(0.0006697986788568588) D7 D10 D11 D14
+error(0.002006705456917236) D7 D10 D14
+error(0.0006697986788568588) D7 D11 D14 D18
+error(0.0006697986788568588) D7 D11 D18
+error(0.001338700097173321) D7 D13
+error(0.0006697986788568588) D7 D13 D14
+error(0.002673815958446298) D7 D14 D15
+error(0.002006705456917236) D7 D14 D18
+error(0.002006705456917236) D7 D14 L0
+error(0.02236793284649183) D7 D15
+error(0.002006705456917236) D7 D18
+error(0.006662210334862288) D7 L0
+error(0.008642177604111326) D8
+error(0.006000449842759885) D8 D9
+error(0.002673815958446298) D8 D9 D16
+error(0.02236793284649183) D8 D16
+error(0.05215700045821763) D9
+error(0.002673815958446298) D9 D10
+error(0.006000449842759885) D9 D10 D11
+error(0.001338700097173321) D9 D10 D13 D14
+error(0.0006697986788568588) D9 D10 D13 D17
+error(0.0006697986788568588) D9 D10 D14 D16
+error(0.0006697986788568588) D9 D10 D16
+error(0.001338700097173321) D9 D10 D16 D17
+error(0.002006705456917236) D9 D10 D17
+error(0.006000449842759885) D9 D11
+error(0.001338700097173321) D9 D12
+error(0.0006697986788568588) D9 D12 D13 D16
+error(0.0006697986788568588) D9 D12 D13 L0
+error(0.0006697986788568588) D9 D13 D14 D16
+error(0.002006705456917236) D9 D13 D16
+error(0.002006705456917236) D9 D13 D16 D17
+error(0.001338700097173321) D9 D14
+error(0.002006705456917236) D9 D16
+error(0.0006697986788568588) D9 D16 D17
+error(0.03626481347851893) D9 D17
+error(0.01778182544467273) D10
+error(0.008642177604111326) D10 D11
+error(0.0006697986788568588) D10 D11 D14
+error(0.001338700097173321) D10 D11 D14 D18
+error(0.002006705456917236) D10 D11 D17
+error(0.0006697986788568588) D10 D11 D17 D18
+error(0.002006705456917236) D10 D11 D18
+error(0.004005357180252828) D10 D13
+error(0.002006705456917236) D10 D13 D14 D17
+error(0.0006697986788568588) D10 D14 D16 D17
+error(0.0006697986788568588) D10 D14 D17
+error(0.002006705456917236) D10 D14 D17 D18
+error(0.0006697986788568588) D10 D14 D18
+error(0.001338700097173321) D10 D16
+error(0.0006697986788568588) D10 D16 D17
+error(0.0006697986788568588) D10 D17
+error(0.02364674503591482) D10 D18
+error(0.04244381618308433) D11
+error(0.001338700097173321) D11 D14
+error(0.0006697986788568588) D11 D14 D18
+error(0.00334003280051021) D11 D17
+error(0.002006705456917236) D11 D17 D18
+error(0.002673815958446298) D11 D18
+error(0.002673815958446298) D11 D18 D19
+error(0.03501987560309133) D11 D19
+error(0.04244381618308433) D12
+error(0.006000449842759885) D12 D13 D14 L0
+error(0.0006697986788568588) D12 D13 D16
+error(0.008642177604111326) D12 D13 L0
+error(0.006000449842759885) D12 D14
+error(0.0006697986788568588) D13 D14 D16 D17
+error(0.006000449842759885) D13 D14 D17 D18
+error(0.002006705456917236) D13 D14 D17 D21
+error(0.0006697986788568588) D13 D14 D17 L0
+error(0.0006697986788568588) D13 D14 D21
+error(0.002673815958446298) D13 D14 L0
+error(0.007323084334358033) D13 D16
+error(0.006000449842759885) D13 D16 D17
+error(0.002673815958446298) D13 D17 D20
+error(0.002006705456917236) D13 D17 D21
+error(0.0006697986788568588) D13 D17 L0
+error(0.006000449842759885) D13 D18
+error(0.002673815958446298) D13 D20
+error(0.02555854638822825) D13 D21
+error(0.01778182544467273) D13 L0
+error(0.05215700045821762) D14
+error(0.0006697986788568588) D14 D15 D17 D18
+error(0.0006697986788568588) D14 D15 D17 D21
+error(0.007983073028790271) D14 D15 D18
+error(0.002006705456917236) D14 D15 D21
+error(0.006000449842759885) D14 D15 L0
+error(0.008642177604111326) D14 D17
+error(0.0006697986788568588) D14 D17 D18
+error(0.002006705456917236) D14 D17 D18 D21
+error(0.0006697986788568588) D14 D17 D21 L0
+error(0.0006697986788568588) D14 D18 D21
+error(0.004669790293214321) D14 D21 L0
+error(0.0006697986788568588) D15 D17 D18
+error(0.0006697986788568588) D15 D17 D21
+error(0.009300399244684827) D15 D18
+error(0.001338700097173321) D15 D18 D19
+error(0.001338700097173321) D15 D19 D22
+error(0.002006705456917236) D15 D21
+error(0.004005357180252828) D15 D22
+error(0.02492213333333331) D15 D23
+error(0.008642177604111326) D15 L0
+error(0.006662210334862289) D16
+error(0.005337801668914705) D16 D17
+error(0.002673815958446298) D16 D17 D20
+error(0.02236793284649183) D16 D20
+error(0.05155626641762741) D17
+error(0.002673815958446298) D17 D18
+error(0.006000449842759885) D17 D18 D19
+error(0.002673815958446298) D17 D18 D20
+error(0.002006705456917236) D17 D18 D21
+error(0.006000449842759885) D17 D19
+error(0.002673815958446298) D17 D20
+error(0.005333333333333312) D17 D20 D21
+error(0.0006697986788568588) D17 D21 L0
+error(0.01648726836301881) D18
+error(0.008642177604111326) D18 D19
+error(0.004005357180252828) D18 D19 D22
+error(0.002673815958446298) D18 D20
+error(0.005995987492949032) D18 D21
+error(0.02619410690587643) D18 D22
+error(0.04671719903466118) D19
+error(0.00797862858822285) D19 D22
+error(0.01262033963927737) D20
+error(0.01522666666666665) D20 D21
+error(0.01262033963927737) D21 D22
+error(0.02682881602833452) D21 L0
+error(0.02746267489612923) D22
+error(0.01262033963927737) D22 D23
+error(0.01262033963927737) D23 L0
+detector(0, 4, 0) D0
+detector(2, 2, 0) D1
+detector(4, 4, 0) D2
+detector(6, 2, 0) D3
+shift_detectors(0, 0, 1) 0
+detector(2, 0, 0) D4
+detector(2, 2, 0) D5
+detector(4, 2, 0) D6
+detector(6, 2, 0) D7
+detector(0, 4, 0) D8
+detector(2, 4, 0) D9
+detector(4, 4, 0) D10
+detector(4, 6, 0) D11
+shift_detectors(0, 0, 1) 0
+detector(2, 0, 0) D12
+detector(2, 2, 0) D13
+detector(4, 2, 0) D14
+detector(6, 2, 0) D15
+detector(0, 4, 0) D16
+detector(2, 4, 0) D17
+detector(4, 4, 0) D18
+detector(4, 6, 0) D19
+detector(0, 4, 1) D20
+detector(2, 2, 1) D21
+detector(4, 4, 1) D22
+detector(6, 2, 1) D23
\ No newline at end of file
diff --git a/datasets/noisy_circuits/README.md b/datasets/noisy_circuits/README.md
deleted file mode 100644
index 9bd1385..0000000
--- a/datasets/noisy_circuits/README.md
+++ /dev/null
@@ -1,234 +0,0 @@
-# Noisy Circuit Dataset (Surface Code, d=3)
-
-Circuit-level surface-code memory experiments generated with Stim for **Belief Propagation (BP) decoding** demonstrations.
-
-## Overview
-
-| Parameter | Value |
-|-----------|-------|
-| Code | Rotated surface code |
-| Distance | d = 3 |
-| Noise model | i.i.d. depolarizing |
-| Error rate | p = 0.01 |
-| Task | Z-memory experiment |
-| Rounds | 3, 5, 7 |
-
-### Noise Application Points
-- Clifford gates (`after_clifford_depolarization`)
-- Data qubits between rounds (`before_round_data_depolarization`)
-- Resets (`after_reset_flip_probability`)
-- Measurements (`before_measure_flip_probability`)
-
-## Files
-
-| File | Description |
-|------|-------------|
-| `sc_d3_r3_p0010_z.stim` | 3 rounds, p=0.01, Z-memory |
-| `sc_d3_r5_p0010_z.stim` | 5 rounds, p=0.01, Z-memory |
-| `sc_d3_r7_p0010_z.stim` | 7 rounds, p=0.01, Z-memory |
-| `sc_d3_layout.png` | Qubit layout visualization |
-| `parity_check_matrix.png` | BP parity check matrix H |
-| `syndrome_stats.png` | Detection event statistics |
-| `single_syndrome.png` | Example syndrome pattern |
-
-## Qubit Layout
-
-The surface code layout showing qubit positions (data + ancilla):
-
-![Qubit Layout](sc_d3_layout.png)
-
-## Using This Dataset for BP Decoding
-
-### Step 1: Load Circuit and Extract Detector Error Model (DEM)
-
-The Detector Error Model is the key input for BP decoding. It describes which errors trigger which detectors.
-
-```python
-import stim
-import numpy as np
-
-# Load circuit
-circuit = stim.Circuit.from_file("datasets/noisy_circuits/sc_d3_r3_p0010_z.stim")
-
-# Extract DEM - this is what BP needs
-dem = circuit.detector_error_model(decompose_errors=True)
-print(f"Detectors: {dem.num_detectors}")      # 24
-print(f"Error mechanisms: {dem.num_errors}")  # 286
-print(f"Observables: {dem.num_observables}")  # 1
-```
-
-### Step 2: Build Parity Check Matrix H
-
-BP operates on the parity check matrix where `H[i,j] = 1` means error `j` triggers detector `i`.
-
-```python
-def build_parity_check_matrix(dem):
-    """Convert DEM to parity check matrix H and prior probabilities."""
-    errors = []
-    for inst in dem.flattened():
-        if inst.type == 'error':
-            prob = inst.args_copy()[0]
-            dets = [t.val for t in inst.targets_copy() if t.is_relative_detector_id()]
-            obs = [t.val for t in inst.targets_copy() if t.is_logical_observable_id()]
-            errors.append({'prob': prob, 'detectors': dets, 'observables': obs})
-    
-    n_detectors = dem.num_detectors
-    n_errors = len(errors)
-    
-    # Parity check matrix
-    H = np.zeros((n_detectors, n_errors), dtype=np.uint8)
-    # Prior error probabilities (for BP initialization)
-    priors = np.zeros(n_errors)
-    # Which errors flip the logical observable
-    obs_flip = np.zeros(n_errors, dtype=np.uint8)
-    
-    for j, e in enumerate(errors):
-        priors[j] = e['prob']
-        for d in e['detectors']:
-            H[d, j] = 1
-        if e['observables']:
-            obs_flip[j] = 1
-    
-    return H, priors, obs_flip
-
-H, priors, obs_flip = build_parity_check_matrix(dem)
-print(f"H shape: {H.shape}")  # (24, 286)
-```
-
-The parity check matrix structure:
-
-![Parity Check Matrix](parity_check_matrix.png)
-
-### Step 3: Sample Syndromes (Detection Events)
-
-```python
-# Compile sampler
-sampler = circuit.compile_detector_sampler()
-
-# Sample detection events + observable flip
-n_shots = 1000
-samples = sampler.sample(n_shots, append_observables=True)
-
-# Split into syndrome and observable
-syndromes = samples[:, :-1]           # shape: (n_shots, n_detectors)
-actual_obs_flips = samples[:, -1]     # shape: (n_shots,)
-
-print(f"Syndrome shape: {syndromes.shape}")
-print(f"Example syndrome: {syndromes[0]}")
-```
-
-### Step 4: BP Decoding (Pseudocode)
-
-```python
-def bp_decode(H, syndrome, priors, max_iter=50, damping=0.5):
-    """
-    Belief Propagation decoder (min-sum variant).
-    
-    Args:
-        H: Parity check matrix (n_detectors, n_errors)
-        syndrome: Detection events (n_detectors,)
-        priors: Prior error probabilities (n_errors,)
-        max_iter: Maximum BP iterations
-        damping: Message damping factor
-    
-    Returns:
-        estimated_errors: Most likely error pattern (n_errors,)
-        soft_output: Log-likelihood ratios (n_errors,)
-    """
-    n_checks, n_vars = H.shape
-    
-    # Initialize LLRs from priors: LLR = log((1-p)/p)
-    llr_prior = np.log((1 - priors) / priors)
-    
-    # Messages: check-to-variable and variable-to-check
-    # ... BP message passing iterations ...
-    
-    # Hard decision
-    estimated_errors = (soft_output < 0).astype(int)
-    
-    return estimated_errors, soft_output
-
-# Decode each syndrome
-for i in range(n_shots):
-    syndrome = syndromes[i]
-    estimated_errors, _ = bp_decode(H, syndrome, priors)
-    
-    # Predict observable flip
-    predicted_obs_flip = np.dot(estimated_errors, obs_flip) % 2
-    
-    # Check if decoding succeeded
-    success = (predicted_obs_flip == actual_obs_flips[i])
-```
-
-### Step 5: Evaluate Decoder Performance
-
-After decoding, compare predicted vs actual observable flips to measure logical error rate.
-
-```python
-def evaluate_decoder(decoder_fn, circuit, n_shots=10000):
-    """Evaluate decoder logical error rate."""
-    dem = circuit.detector_error_model(decompose_errors=True)
-    H, priors, obs_flip = build_parity_check_matrix(dem)
-    
-    sampler = circuit.compile_detector_sampler()
-    samples = sampler.sample(n_shots, append_observables=True)
-    syndromes = samples[:, :-1]
-    actual_obs = samples[:, -1]
-    
-    errors = 0
-    for i in range(n_shots):
-        est_errors, _ = decoder_fn(H, syndromes[i], priors)
-        pred_obs = np.dot(est_errors, obs_flip) % 2
-        if pred_obs != actual_obs[i]:
-            errors += 1
-    
-    return errors / n_shots
-
-# logical_error_rate = evaluate_decoder(bp_decode, circuit)
-```
-
-## Syndrome Statistics
-
-Detection event frequencies across 1000 shots (left) and baseline observable flip rate without decoding (right):
-
-![Syndrome Statistics](syndrome_stats.png)
-
-## Example Syndrome
-
-A single syndrome sample showing which detectors fired (red = triggered):
-
-![Single Syndrome](single_syndrome.png)
-
-## Regenerating the Dataset
-
-```bash
-# Install the package with uv
-uv sync
-
-# Generate circuits using the CLI
-uv run generate-noisy-circuits \
-  --distance 3 \
-  --p 0.01 \
-  --rounds 3 5 7 \
-  --task z \
-  --output datasets/noisy_circuits
-```
-
-## Extending the Dataset
-
-```bash
-# Different error rates
-uv run generate-noisy-circuits --p 0.005 --rounds 3 5 7
-
-# Different distances
-uv run generate-noisy-circuits --distance 5 --rounds 5 7 9
-
-# X-memory experiment
-uv run generate-noisy-circuits --task x --rounds 3 5 7
-```
-
-## References
-
-- [Stim Documentation](https://github.com/quantumlib/Stim)
-- [BP+OSD Decoder Paper](https://arxiv.org/abs/2005.07016)
-- [Surface Code Decoding Review](https://quantum-journal.org/papers/q-2024-10-10-1498/)
diff --git a/datasets/noisy_circuits/sc_d3_r3_p0010_z.stim b/datasets/noisy_circuits/sc_d3_r3_p0010_z.stim
deleted file mode 100644
index 187876d..0000000
--- a/datasets/noisy_circuits/sc_d3_r3_p0010_z.stim
+++ /dev/null
@@ -1,89 +0,0 @@
-QUBIT_COORDS(1, 1) 1
-QUBIT_COORDS(2, 0) 2
-QUBIT_COORDS(3, 1) 3
-QUBIT_COORDS(5, 1) 5
-QUBIT_COORDS(1, 3) 8
-QUBIT_COORDS(2, 2) 9
-QUBIT_COORDS(3, 3) 10
-QUBIT_COORDS(4, 2) 11
-QUBIT_COORDS(5, 3) 12
-QUBIT_COORDS(6, 2) 13
-QUBIT_COORDS(0, 4) 14
-QUBIT_COORDS(1, 5) 15
-QUBIT_COORDS(2, 4) 16
-QUBIT_COORDS(3, 5) 17
-QUBIT_COORDS(4, 4) 18
-QUBIT_COORDS(5, 5) 19
-QUBIT_COORDS(4, 6) 25
-R 1 3 5 8 10 12 15 17 19
-X_ERROR(0.01) 1 3 5 8 10 12 15 17 19
-R 2 9 11 13 14 16 18 25
-X_ERROR(0.01) 2 9 11 13 14 16 18 25
-TICK
-DEPOLARIZE1(0.01) 1 3 5 8 10 12 15 17 19
-H 2 11 16 25
-DEPOLARIZE1(0.01) 2 11 16 25
-TICK
-CX 2 3 16 17 11 12 15 14 10 9 19 18
-DEPOLARIZE2(0.01) 2 3 16 17 11 12 15 14 10 9 19 18
-TICK
-CX 2 1 16 15 11 10 8 14 3 9 12 18
-DEPOLARIZE2(0.01) 2 1 16 15 11 10 8 14 3 9 12 18
-TICK
-CX 16 10 11 5 25 19 8 9 17 18 12 13
-DEPOLARIZE2(0.01) 16 10 11 5 25 19 8 9 17 18 12 13
-TICK
-CX 16 8 11 3 25 17 1 9 10 18 5 13
-DEPOLARIZE2(0.01) 16 8 11 3 25 17 1 9 10 18 5 13
-TICK
-H 2 11 16 25
-DEPOLARIZE1(0.01) 2 11 16 25
-TICK
-X_ERROR(0.01) 2 9 11 13 14 16 18 25
-MR 2 9 11 13 14 16 18 25
-X_ERROR(0.01) 2 9 11 13 14 16 18 25
-DETECTOR(0, 4, 0) rec[-4]
-DETECTOR(2, 2, 0) rec[-7]
-DETECTOR(4, 4, 0) rec[-2]
-DETECTOR(6, 2, 0) rec[-5]
-REPEAT 2 {
-    TICK
-    DEPOLARIZE1(0.01) 1 3 5 8 10 12 15 17 19
-    H 2 11 16 25
-    DEPOLARIZE1(0.01) 2 11 16 25
-    TICK
-    CX 2 3 16 17 11 12 15 14 10 9 19 18
-    DEPOLARIZE2(0.01) 2 3 16 17 11 12 15 14 10 9 19 18
-    TICK
-    CX 2 1 16 15 11 10 8 14 3 9 12 18
-    DEPOLARIZE2(0.01) 2 1 16 15 11 10 8 14 3 9 12 18
-    TICK
-    CX 16 10 11 5 25 19 8 9 17 18 12 13
-    DEPOLARIZE2(0.01) 16 10 11 5 25 19 8 9 17 18 12 13
-    TICK
-    CX 16 8 11 3 25 17 1 9 10 18 5 13
-    DEPOLARIZE2(0.01) 16 8 11 3 25 17 1 9 10 18 5 13
-    TICK
-    H 2 11 16 25
-    DEPOLARIZE1(0.01) 2 11 16 25
-    TICK
-    X_ERROR(0.01) 2 9 11 13 14 16 18 25
-    MR 2 9 11 13 14 16 18 25
-    X_ERROR(0.01) 2 9 11 13 14 16 18 25
-    SHIFT_COORDS(0, 0, 1)
-    DETECTOR(2, 0, 0) rec[-8] rec[-16]
-    DETECTOR(2, 2, 0) rec[-7] rec[-15]
-    DETECTOR(4, 2, 0) rec[-6] rec[-14]
-    DETECTOR(6, 2, 0) rec[-5] rec[-13]
-    DETECTOR(0, 4, 0) rec[-4] rec[-12]
-    DETECTOR(2, 4, 0) rec[-3] rec[-11]
-    DETECTOR(4, 4, 0) rec[-2] rec[-10]
-    DETECTOR(4, 6, 0) rec[-1] rec[-9]
-}
-X_ERROR(0.01) 1 3 5 8 10 12 15 17 19
-M 1 3 5 8 10 12 15 17 19
-DETECTOR(0, 4, 1) rec[-3] rec[-6] rec[-13]
-DETECTOR(2, 2, 1) rec[-5] rec[-6] rec[-8] rec[-9] rec[-16]
-DETECTOR(4, 4, 1) rec[-1] rec[-2] rec[-4] rec[-5] rec[-11]
-DETECTOR(6, 2, 1) rec[-4] rec[-7] rec[-14]
-OBSERVABLE_INCLUDE(0) rec[-7] rec[-8] rec[-9]
\ No newline at end of file
diff --git a/datasets/noisy_circuits/sc_d3_r5_p0010_z.stim b/datasets/noisy_circuits/sc_d3_r5_p0010_z.stim
deleted file mode 100644
index 79afc47..0000000
--- a/datasets/noisy_circuits/sc_d3_r5_p0010_z.stim
+++ /dev/null
@@ -1,89 +0,0 @@
-QUBIT_COORDS(1, 1) 1
-QUBIT_COORDS(2, 0) 2
-QUBIT_COORDS(3, 1) 3
-QUBIT_COORDS(5, 1) 5
-QUBIT_COORDS(1, 3) 8
-QUBIT_COORDS(2, 2) 9
-QUBIT_COORDS(3, 3) 10
-QUBIT_COORDS(4, 2) 11
-QUBIT_COORDS(5, 3) 12
-QUBIT_COORDS(6, 2) 13
-QUBIT_COORDS(0, 4) 14
-QUBIT_COORDS(1, 5) 15
-QUBIT_COORDS(2, 4) 16
-QUBIT_COORDS(3, 5) 17
-QUBIT_COORDS(4, 4) 18
-QUBIT_COORDS(5, 5) 19
-QUBIT_COORDS(4, 6) 25
-R 1 3 5 8 10 12 15 17 19
-X_ERROR(0.01) 1 3 5 8 10 12 15 17 19
-R 2 9 11 13 14 16 18 25
-X_ERROR(0.01) 2 9 11 13 14 16 18 25
-TICK
-DEPOLARIZE1(0.01) 1 3 5 8 10 12 15 17 19
-H 2 11 16 25
-DEPOLARIZE1(0.01) 2 11 16 25
-TICK
-CX 2 3 16 17 11 12 15 14 10 9 19 18
-DEPOLARIZE2(0.01) 2 3 16 17 11 12 15 14 10 9 19 18
-TICK
-CX 2 1 16 15 11 10 8 14 3 9 12 18
-DEPOLARIZE2(0.01) 2 1 16 15 11 10 8 14 3 9 12 18
-TICK
-CX 16 10 11 5 25 19 8 9 17 18 12 13
-DEPOLARIZE2(0.01) 16 10 11 5 25 19 8 9 17 18 12 13
-TICK
-CX 16 8 11 3 25 17 1 9 10 18 5 13
-DEPOLARIZE2(0.01) 16 8 11 3 25 17 1 9 10 18 5 13
-TICK
-H 2 11 16 25
-DEPOLARIZE1(0.01) 2 11 16 25
-TICK
-X_ERROR(0.01) 2 9 11 13 14 16 18 25
-MR 2 9 11 13 14 16 18 25
-X_ERROR(0.01) 2 9 11 13 14 16 18 25
-DETECTOR(0, 4, 0) rec[-4]
-DETECTOR(2, 2, 0) rec[-7]
-DETECTOR(4, 4, 0) rec[-2]
-DETECTOR(6, 2, 0) rec[-5]
-REPEAT 4 {
-    TICK
-    DEPOLARIZE1(0.01) 1 3 5 8 10 12 15 17 19
-    H 2 11 16 25
-    DEPOLARIZE1(0.01) 2 11 16 25
-    TICK
-    CX 2 3 16 17 11 12 15 14 10 9 19 18
-    DEPOLARIZE2(0.01) 2 3 16 17 11 12 15 14 10 9 19 18
-    TICK
-    CX 2 1 16 15 11 10 8 14 3 9 12 18
-    DEPOLARIZE2(0.01) 2 1 16 15 11 10 8 14 3 9 12 18
-    TICK
-    CX 16 10 11 5 25 19 8 9 17 18 12 13
-    DEPOLARIZE2(0.01) 16 10 11 5 25 19 8 9 17 18 12 13
-    TICK
-    CX 16 8 11 3 25 17 1 9 10 18 5 13
-    DEPOLARIZE2(0.01) 16 8 11 3 25 17 1 9 10 18 5 13
-    TICK
-    H 2 11 16 25
-    DEPOLARIZE1(0.01) 2 11 16 25
-    TICK
-    X_ERROR(0.01) 2 9 11 13 14 16 18 25
-    MR 2 9 11 13 14 16 18 25
-    X_ERROR(0.01) 2 9 11 13 14 16 18 25
-    SHIFT_COORDS(0, 0, 1)
-    DETECTOR(2, 0, 0) rec[-8] rec[-16]
-    DETECTOR(2, 2, 0) rec[-7] rec[-15]
-    DETECTOR(4, 2, 0) rec[-6] rec[-14]
-    DETECTOR(6, 2, 0) rec[-5] rec[-13]
-    DETECTOR(0, 4, 0) rec[-4] rec[-12]
-    DETECTOR(2, 4, 0) rec[-3] rec[-11]
-    DETECTOR(4, 4, 0) rec[-2] rec[-10]
-    DETECTOR(4, 6, 0) rec[-1] rec[-9]
-}
-X_ERROR(0.01) 1 3 5 8 10 12 15 17 19
-M 1 3 5 8 10 12 15 17 19
-DETECTOR(0, 4, 1) rec[-3] rec[-6] rec[-13]
-DETECTOR(2, 2, 1) rec[-5] rec[-6] rec[-8] rec[-9] rec[-16]
-DETECTOR(4, 4, 1) rec[-1] rec[-2] rec[-4] rec[-5] rec[-11]
-DETECTOR(6, 2, 1) rec[-4] rec[-7] rec[-14]
-OBSERVABLE_INCLUDE(0) rec[-7] rec[-8] rec[-9]
\ No newline at end of file
diff --git a/datasets/noisy_circuits/sc_d3_r7_p0010_z.stim b/datasets/noisy_circuits/sc_d3_r7_p0010_z.stim
deleted file mode 100644
index c79fed7..0000000
--- a/datasets/noisy_circuits/sc_d3_r7_p0010_z.stim
+++ /dev/null
@@ -1,89 +0,0 @@
-QUBIT_COORDS(1, 1) 1
-QUBIT_COORDS(2, 0) 2
-QUBIT_COORDS(3, 1) 3
-QUBIT_COORDS(5, 1) 5
-QUBIT_COORDS(1, 3) 8
-QUBIT_COORDS(2, 2) 9
-QUBIT_COORDS(3, 3) 10
-QUBIT_COORDS(4, 2) 11
-QUBIT_COORDS(5, 3) 12
-QUBIT_COORDS(6, 2) 13
-QUBIT_COORDS(0, 4) 14
-QUBIT_COORDS(1, 5) 15
-QUBIT_COORDS(2, 4) 16
-QUBIT_COORDS(3, 5) 17
-QUBIT_COORDS(4, 4) 18
-QUBIT_COORDS(5, 5) 19
-QUBIT_COORDS(4, 6) 25
-R 1 3 5 8 10 12 15 17 19
-X_ERROR(0.01) 1 3 5 8 10 12 15 17 19
-R 2 9 11 13 14 16 18 25
-X_ERROR(0.01) 2 9 11 13 14 16 18 25
-TICK
-DEPOLARIZE1(0.01) 1 3 5 8 10 12 15 17 19
-H 2 11 16 25
-DEPOLARIZE1(0.01) 2 11 16 25
-TICK
-CX 2 3 16 17 11 12 15 14 10 9 19 18
-DEPOLARIZE2(0.01) 2 3 16 17 11 12 15 14 10 9 19 18
-TICK
-CX 2 1 16 15 11 10 8 14 3 9 12 18
-DEPOLARIZE2(0.01) 2 1 16 15 11 10 8 14 3 9 12 18
-TICK
-CX 16 10 11 5 25 19 8 9 17 18 12 13
-DEPOLARIZE2(0.01) 16 10 11 5 25 19 8 9 17 18 12 13
-TICK
-CX 16 8 11 3 25 17 1 9 10 18 5 13
-DEPOLARIZE2(0.01) 16 8 11 3 25 17 1 9 10 18 5 13
-TICK
-H 2 11 16 25
-DEPOLARIZE1(0.01) 2 11 16 25
-TICK
-X_ERROR(0.01) 2 9 11 13 14 16 18 25
-MR 2 9 11 13 14 16 18 25
-X_ERROR(0.01) 2 9 11 13 14 16 18 25
-DETECTOR(0, 4, 0) rec[-4]
-DETECTOR(2, 2, 0) rec[-7]
-DETECTOR(4, 4, 0) rec[-2]
-DETECTOR(6, 2, 0) rec[-5]
-REPEAT 6 {
-    TICK
-    DEPOLARIZE1(0.01) 1 3 5 8 10 12 15 17 19
-    H 2 11 16 25
-    DEPOLARIZE1(0.01) 2 11 16 25
-    TICK
-    CX 2 3 16 17 11 12 15 14 10 9 19 18
-    DEPOLARIZE2(0.01) 2 3 16 17 11 12 15 14 10 9 19 18
-    TICK
-    CX 2 1 16 15 11 10 8 14 3 9 12 18
-    DEPOLARIZE2(0.01) 2 1 16 15 11 10 8 14 3 9 12 18
-    TICK
-    CX 16 10 11 5 25 19 8 9 17 18 12 13
-    DEPOLARIZE2(0.01) 16 10 11 5 25 19 8 9 17 18 12 13
-    TICK
-    CX 16 8 11 3 25 17 1 9 10 18 5 13
-    DEPOLARIZE2(0.01) 16 8 11 3 25 17 1 9 10 18 5 13
-    TICK
-    H 2 11 16 25
-    DEPOLARIZE1(0.01) 2 11 16 25
-    TICK
-    X_ERROR(0.01) 2 9 11 13 14 16 18 25
-    MR 2 9 11 13 14 16 18 25
-    X_ERROR(0.01) 2 9 11 13 14 16 18 25
-    SHIFT_COORDS(0, 0, 1)
-    DETECTOR(2, 0, 0) rec[-8] rec[-16]
-    DETECTOR(2, 2, 0) rec[-7] rec[-15]
-    DETECTOR(4, 2, 0) rec[-6] rec[-14]
-    DETECTOR(6, 2, 0) rec[-5] rec[-13]
-    DETECTOR(0, 4, 0) rec[-4] rec[-12]
-    DETECTOR(2, 4, 0) rec[-3] rec[-11]
-    DETECTOR(4, 4, 0) rec[-2] rec[-10]
-    DETECTOR(4, 6, 0) rec[-1] rec[-9]
-}
-X_ERROR(0.01) 1 3 5 8 10 12 15 17 19
-M 1 3 5 8 10 12 15 17 19
-DETECTOR(0, 4, 1) rec[-3] rec[-6] rec[-13]
-DETECTOR(2, 2, 1) rec[-5] rec[-6] rec[-8] rec[-9] rec[-16]
-DETECTOR(4, 4, 1) rec[-1] rec[-2] rec[-4] rec[-5] rec[-11]
-DETECTOR(6, 2, 1) rec[-4] rec[-7] rec[-14]
-OBSERVABLE_INCLUDE(0) rec[-7] rec[-8] rec[-9]
\ No newline at end of file
diff --git a/datasets/dems/sc_d3_r3_p0010_z.dem b/datasets/sc_d3_r3_p0010_z.dem
similarity index 100%
rename from datasets/dems/sc_d3_r3_p0010_z.dem
rename to datasets/sc_d3_r3_p0010_z.dem
diff --git a/datasets/syndromes/sc_d3_r3_p0010_z.npz b/datasets/sc_d3_r3_p0010_z.npz
similarity index 100%
rename from datasets/syndromes/sc_d3_r3_p0010_z.npz
rename to datasets/sc_d3_r3_p0010_z.npz
diff --git a/datasets/circuits/sc_d3_r3_p0010_z.stim b/datasets/sc_d3_r3_p0010_z.stim
similarity index 100%
rename from datasets/circuits/sc_d3_r3_p0010_z.stim
rename to datasets/sc_d3_r3_p0010_z.stim
diff --git a/datasets/uais/sc_d3_r3_p0010_z.uai b/datasets/sc_d3_r3_p0010_z.uai
similarity index 100%
rename from datasets/uais/sc_d3_r3_p0010_z.uai
rename to datasets/sc_d3_r3_p0010_z.uai
diff --git a/datasets/dems/sc_d3_r5_p0010_z.dem b/datasets/sc_d3_r5_p0010_z.dem
similarity index 100%
rename from datasets/dems/sc_d3_r5_p0010_z.dem
rename to datasets/sc_d3_r5_p0010_z.dem
diff --git a/datasets/syndromes/sc_d3_r5_p0010_z.npz b/datasets/sc_d3_r5_p0010_z.npz
similarity index 100%
rename from datasets/syndromes/sc_d3_r5_p0010_z.npz
rename to datasets/sc_d3_r5_p0010_z.npz
diff --git a/datasets/circuits/sc_d3_r5_p0010_z.stim b/datasets/sc_d3_r5_p0010_z.stim
similarity index 100%
rename from datasets/circuits/sc_d3_r5_p0010_z.stim
rename to datasets/sc_d3_r5_p0010_z.stim
diff --git a/datasets/uais/sc_d3_r5_p0010_z.uai b/datasets/sc_d3_r5_p0010_z.uai
similarity index 100%
rename from datasets/uais/sc_d3_r5_p0010_z.uai
rename to datasets/sc_d3_r5_p0010_z.uai
diff --git a/datasets/dems/sc_d3_r7_p0010_z.dem b/datasets/sc_d3_r7_p0010_z.dem
similarity index 100%
rename from datasets/dems/sc_d3_r7_p0010_z.dem
rename to datasets/sc_d3_r7_p0010_z.dem
diff --git a/datasets/syndromes/sc_d3_r7_p0010_z.npz b/datasets/sc_d3_r7_p0010_z.npz
similarity index 100%
rename from datasets/syndromes/sc_d3_r7_p0010_z.npz
rename to datasets/sc_d3_r7_p0010_z.npz
diff --git a/datasets/circuits/sc_d3_r7_p0010_z.stim b/datasets/sc_d3_r7_p0010_z.stim
similarity index 100%
rename from datasets/circuits/sc_d3_r7_p0010_z.stim
rename to datasets/sc_d3_r7_p0010_z.stim
diff --git a/datasets/uais/sc_d3_r7_p0010_z.uai b/datasets/sc_d3_r7_p0010_z.uai
similarity index 100%
rename from datasets/uais/sc_d3_r7_p0010_z.uai
rename to datasets/sc_d3_r7_p0010_z.uai
diff --git a/datasets/syndromes/test.npz b/datasets/syndromes/test.npz
new file mode 100644
index 0000000..549f93c
Binary files /dev/null and b/datasets/syndromes/test.npz differ
diff --git a/datasets/uais/test.uai b/datasets/uais/test.uai
new file mode 100644
index 0000000..d0bede6
--- /dev/null
+++ b/datasets/uais/test.uai
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diff --git a/datasets/noisy_circuits/parity_check_matrix.png b/datasets/visualizations/parity_check_matrix.png
similarity index 100%
rename from datasets/noisy_circuits/parity_check_matrix.png
rename to datasets/visualizations/parity_check_matrix.png
diff --git a/datasets/noisy_circuits/sc_d3_layout.png b/datasets/visualizations/sc_d3_layout.png
similarity index 100%
rename from datasets/noisy_circuits/sc_d3_layout.png
rename to datasets/visualizations/sc_d3_layout.png
diff --git a/datasets/noisy_circuits/single_syndrome.png b/datasets/visualizations/single_syndrome.png
similarity index 100%
rename from datasets/noisy_circuits/single_syndrome.png
rename to datasets/visualizations/single_syndrome.png
diff --git a/datasets/noisy_circuits/syndrome_stats.png b/datasets/visualizations/syndrome_stats.png
similarity index 100%
rename from datasets/noisy_circuits/syndrome_stats.png
rename to datasets/visualizations/syndrome_stats.png
diff --git a/docs/lecture_note.pdf b/note/lecture_note.pdf
similarity index 100%
rename from docs/lecture_note.pdf
rename to note/lecture_note.pdf
diff --git a/docs/lecture_note.typ b/note/lecture_note.typ
similarity index 100%
rename from docs/lecture_note.typ
rename to note/lecture_note.typ
diff --git a/pyproject.toml b/pyproject.toml
index b8bb1d7..8491a2b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,8 +6,12 @@ readme = "README.md"
 requires-python = ">=3.10"
 license = { text = "MIT" }
 authors = [
+    { name = "Jinguo Liu", email = "cacate0129@gmail.com" },
     { name = "BPDecoderPlus Contributors" }
 ]
+maintainers = [
+    { name = "Jinguo Liu", email = "cacate0129@gmail.com" }
+]
 keywords = ["quantum", "error-correction", "surface-code", "belief-propagation", "stim"]
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -19,17 +23,26 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Physics",
 ]
-
 dependencies = [
     "stim>=1.12.0",
     "numpy>=1.24.0",
     "torch>=2.0.0",
 ]
 
+[project.urls]
+Homepage = "https://github.com/GiggleLiu/BPDecoderPlus"
+Documentation = "https://giggleliu.github.io/BPDecoderPlus/"
+Repository = "https://github.com/GiggleLiu/BPDecoderPlus"
+Issues = "https://github.com/GiggleLiu/BPDecoderPlus/issues"
+Changelog = "https://github.com/GiggleLiu/BPDecoderPlus/blob/main/CHANGELOG.md"
+
 [project.optional-dependencies]
 dev = [
     "pytest>=7.0.0",
     "pytest-cov>=4.0.0",
+    "ruff>=0.8.0",
+    "pre-commit>=3.0.0",
+    "mypy>=1.0.0",
 ]
 docs = [
     "mkdocs-material>=9.0.0",
@@ -52,8 +65,28 @@ packages = ["src/bpdecoderplus"]
 testpaths = ["tests"]
 pythonpath = ["src"]
 
-[tool.uv]
-dev-dependencies = [
+[dependency-groups]
+dev = [
     "pytest>=7.0.0",
     "pytest-cov>=4.0.0",
+    "ruff>=0.8.0",
+    "pre-commit>=3.0.0",
+    "mypy>=1.0.0",
 ]
+
+[tool.ruff]
+target-version = "py310"
+line-length = 100
+indent-width = 4
+
+[tool.ruff.lint]
+select = ["E", "W", "F", "I", "N", "UP", "B", "C4", "SIM", "RUF"]
+ignore = ["E501"]  # Line too long (handled by formatter)
+fixable = ["ALL"]
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+
+[tool.ruff.lint.isort]
+known-first-party = ["bpdecoderplus"]
diff --git a/src/bpdecoderplus/cli.py b/src/bpdecoderplus/cli.py
index c99ca94..fc92b1c 100644
--- a/src/bpdecoderplus/cli.py
+++ b/src/bpdecoderplus/cli.py
@@ -29,7 +29,7 @@ def create_parser() -> argparse.ArgumentParser:
         "-o",
         "--output",
         type=pathlib.Path,
-        default=pathlib.Path("datasets/noisy_circuits"),
+        default=pathlib.Path("datasets"),
         help="Output directory for .stim circuits",
     )
     parser.add_argument(
diff --git a/tests/test_cli.py b/tests/test_cli.py
index fa13a45..0817a10 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -18,7 +18,7 @@ def test_parser_defaults(self):
         parser = create_parser()
         args = parser.parse_args([])
 
-        assert args.output == pathlib.Path("datasets/noisy_circuits")
+        assert args.output == pathlib.Path("datasets")
         assert args.distance == 3
         assert args.rounds == [3, 5, 7]
         assert args.p == 0.01