Refactor repo structure and move package management to uv

[masquare]

Refactor repo structure and move package management to uv

♻️ Current situation & Problem

This PR restructures the repository for better organization and modernizes the package management by migrating from requirements.txt to uv (a fast Python package installer and resolver). This addresses:

• Organization: Improved project structure with proper separation of concerns
• Package Management: Migration to uv for faster, more reliable dependency resolution
• Maintainability: Cleaner project layout that aligns with Python best practices
• Submodule Cleanup: Removal of unused submodule dependencies

Resolves the ongoing effort to improve project organization and developer experience.

⚙️ Release Notes

Features

• Package Management Migration: Migrated from requirements.txt to pyproject.toml with uv.lock for reproducible builds

  • Faster dependency resolution with uv
  • Better lock file management for reproducible environments
  • Centralized project metadata in pyproject.toml

• Repository Structure Improvements:

  • Moved root-level utility scripts to scripts/ directory for better organization
  • Converted .gitignore files to .gitkeep in empty directories (data/, notebooks/)
  • Removed unused .gitmodules and submodule references
  • Updated .python-version to specify Python 3.12

• Updated Documentation: README now reflects the new structure and package management approach

Migration Guide for Users

If you were previously using requirements.txt:

Before:

pip install -r requirements.txt

After:

uv sync

📚 Documentation

The project now uses pyproject.toml as the single source of truth for project metadata and dependencies. Key sections include:

• Project Metadata: Name, version, description, authors, keywords, and classifiers
• Dependencies: All runtime and optional development dependencies are clearly specified
• Python Requirements: Requires Python >= 3.12

For detailed project information, see README.md and the inline documentation in pyproject.toml.

The repository structure has been improved:

opentslm/
├── src/                 # Source code
├── test/                # Test suite
├── scripts/             # Utility scripts
├── demo/                # Demo notebooks and examples
├── evaluation/          # Evaluation tools and scripts
├── data/                # Data storage
└── notebooks/           # Jupyter notebooks

✅ Testing

This PR maintains full backward compatibility with existing tests. No new test files were added as this is primarily a structural and tooling refactoring:

• All existing tests remain in the test/ directory
• Import paths in model files were updated to reflect organizational changes
• Development environment can be tested using uv sync followed by test execution

Manual testing steps:

1. Clone/update the repository
2. Run uv sync to install all dependencies
3. Verify scripts in scripts/ directory are executable and functional
4. Run the existing test suite to ensure no regressions

Code of Conduct & Contributing Guidelines

By creating and submitting this pull request, you agree to follow our Code of Conduct and Contributing Guidelines:

• I agree to follow the Code of Conduct and Contributing Guidelines.

[PSchmiedmayer]

@masquare As noted on Slack; created #39 to address the REUSE questions. CC: @RealLast

[RealLast]

Accepted #39 @masquare @PSchmiedmayer

[PSchmiedmayer]

Thanks @RealLast and thanks for the work here @masquare 🚀

[ThomasKaar]

thanks a lot for the work here @masquare !! 🚀

added some minor questions. the one from common_evaluator_plot.py needs to be resolved, the others are fine either way for me
when those are resolved it is good to go