Reproducibility toolkit

Appendix C · coming soon

soon This appendix is planned and not yet written.

What it will cover

• git for scientists: commits, branches, what to commit and what to ignore
• Environments: conda/mamba, uv, lock files, and recording versions
• Project layout: data/, notebooks/, src/, tests/, results/
• Seeds, logging and recording the exact inputs of every result
• Turning a notebook into a script and a script into a package
• Sharing: README, licence, citation, and a one-command rebuild

Planned learning outcomes

1. Keep a project under version control and explain every commit.
2. Reproduce a result from a clean clone with one command.
3. Package a small analysis so that a colleague can run and extend it.

Until then, the reproducibility checklist in episode 2.6 and the Setup episode cover the essentials.