Professional restructuring for v0.1 release

[GiggleLiu]

Summary

This PR transforms BPDecoderPlus from a winter school training project into a professional, production-ready Python package following modern open-source standards.

Closes #28

What's Changed

🆕 Added

• LICENSE file (MIT License) - Legal requirement for open source distribution
• CONTRIBUTING.md - Development guidelines, setup instructions, and contribution process
• CHANGELOG.md - Following Keep a Changelog format
• .pre-commit-config.yaml - Automated code quality checks (ruff, security, file validation)
• .editorconfig - Consistent coding styles across all editors
• Project metadata in pyproject.toml:
  • Project URLs (Homepage, Documentation, Repository, Issues, Changelog)
  • Maintainers field
• Development tooling:
  • Ruff configuration (linting & formatting, line-length: 100)
  • Updated dev dependencies: pytest, pytest-cov, ruff, pre-commit, mypy
  • New Makefile targets: format, lint, lint-fix, type-check, pre-commit, check, dev-setup

📦 Changed

• Dataset reorganization - Single-source flat structure:
  • All dataset files moved from subdirectories to datasets/ root
  • Visualization PNGs moved to datasets/visualizations/
  • Updated CLI default path: datasets/noisy_circuits → datasets
  • Updated documentation to reflect new structure
• Documentation updates:
  • README.md focused on Python implementation
  • Removed winter school training references
  • Removed Julia code examples (kept as reference links)
• Configuration improvements:
  • Fixed pyproject.toml structure (dependencies before project.urls)
  • Migrated deprecated tool.uv.dev-dependencies → dependency-groups.dev
• File organization:
  • Moved lecture notes from docs/ to note/ directory
  • Updated .gitignore with development tools and binary file patterns

❌ Removed

• Duplicate dataset files from subdirectories (circuits/, dems/, uais/, syndromes/, noisy_circuits/)
• Julia code examples from README (kept as reference implementations)
• Winter school training context from project description

Testing

✅ All 71 tests pass
✅ Package builds and imports correctly
✅ Dataset structure validated
✅ No regressions in functionality

Validation Checklist

• LICENSE file exists (MIT)
• pyproject.toml package path correct: packages = ["bpdecoderplus"]
• All tests pass with new dataset structure
• No duplicate dataset files (single-source structure)
• No binary PDF/Typst files in docs/ (moved to note/)
• All standard files present: CONTRIBUTING.md, CHANGELOG.md
• Package imports correctly (v0.1.0)

Next Steps

After merging:

1. Run make dev-setup to install pre-commit hooks
2. Use new Makefile targets for development workflow
3. Follow CONTRIBUTING.md for future contributions

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR restructures BPDecoderPlus from a winter school training project into a professional, production-ready Python package for v0.1 release. The changes include adding standard open-source project files, reorganizing the dataset structure into a flat hierarchy, and modernizing the development toolchain.

Changes:

• Added standard project files (LICENSE, CONTRIBUTING.md, CHANGELOG.md) and development tools (.pre-commit-config.yaml, .editorconfig)
• Reorganized datasets from nested subdirectories to a flat structure in datasets/ root with visualizations separated
• Updated CLI default output path from datasets/noisy_circuits to datasets with corresponding test updates

Reviewed changes

Copilot reviewed 17 out of 37 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/test_cli.py	Updated test to verify new CLI default path datasets
src/bpdecoderplus/cli.py	Changed CLI default output directory to datasets
pyproject.toml	Added project metadata, URLs, maintainers; migrated dev dependencies; configured ruff; contains package path issue
note/lecture_note.typ	Moved lecture notes to note/ directory (new comprehensive documentation)
datasets/*.stim, datasets/*.npz	Dataset files reorganized to flat structure in root
datasets/visualizations/*.png	Visualization files separated into subdirectory
datasets/syndromes/test.npz	Test syndrome data (retained in subdirectory)
LICENSE	Added MIT License for open source distribution

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[Copilot]

The package path configuration appears incorrect. The packages field should point to the source directory containing the package code. Since the package source is located at src/bpdecoderplus/, the correct configuration should be packages = ["src/bpdecoderplus"] rather than packages = ["bpdecoderplus"]. This may cause the package to fail to build or install correctly.

[GiggleLiu]

@copilot open a new pull request to apply changes based on this feedback

[Copilot]

@GiggleLiu I've opened a new pull request, #36, to work on those changes. Once the pull request is ready, I'll request review from you.