Professional restructuring for v0.1 release

.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

.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

.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]']

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