Migrate to uv for dependency management

[annakrystalli]

Migrate project from conda to uv

Summary

Currently the project uses conda for environment management and requirements.txt for Python dependencies. We want to migrate to uv for faster, simpler, and more reproducible Python environments.

Motivation

• Faster installs and dependency resolution with uv
• No need for conda to install nodejs (we can manage Node separately)
• Easier cross-platform support (uv works on Linux, macOS, Windows)
• Simpler developer onboarding:

  uv venv reprohack-uv
  source reprohack-uv/bin/activate
  uv pip install -r requirements/local.txt

Tasks

• Replace conda instructions with uv equivalents in docs
• Add .venv (reprohack-uv) to .gitignore
• Test uv setup on Linux, macOS, Windows runners
• Update developer docs:
• How to activate/deactivate env
• How to install Node dependencies
• How to run uv run pip-audit for security checks
• Update upgrade procedure:
  • Use uv pip install --upgrade -r requirements/local.txt
  • Run uv run pip-audit for vulnerability checks
  • Freeze updated deps with uv pip freeze > requirements/local.txt

Acceptance Criteria

• All developers can run setup without conda
• Documentation includes uv-based workflows
• pip-audit integrated into upgrade procedure
• CI and deploy.sh updated to use uv instead of conda

[rgaiacs]

Hi @annakrystalli, you should also check pixi.

[annakrystalli]

Thanks @rgaiacs ! Will take a look!