Session 3 - Quarto & GitLab as a reproducibility toolkit

Repo setup, folder structure, and putting the protocol into Quarto

Wednesday 14 October 2026, 15:00–17:00

Student-led input

Two group inputs on the theory, each 15 min input + 15 min open discussion, based on resources below.

Group Input topic Resource
#5 Dynamic reporting and Quarto CRS Primer: Dynamic Reporting – 10.5281/zenodo.7565735
#6 Version control (using Gitlab, UZH) CRS Primer: Digital Collaboration – 10.5281/zenodo.7716290
#6 Folder structure and file naming conventions CRS Primer: File Naming Conventions – 10.5281/zenodo.10091966

Hands-on repository setup

Groups set up their own GitLab.UZH repository (forked from a template) and add their protocol draft to quarto – with peer and instructor support in the room. Each group:

  • Adds a README describing the reproduction effort, with a link to the original paper.
  • Decides on a folder structure (a suggested structure to adapt will be provided).
  • Starts filling folders with original code, material, and links to data [prefer linking to the original raw data over copying it into the reproduction repo].

Instructor

Homework briefing.

Homework (5 weeks, until 18 Nov) — the core of the course
  1. Finalise the protocol and lock it on GitLab (via a tagged commit).
  2. Peer review: share with your paired group, who has one week to give feedback via GitLab (e.g., as a GitLab issue).
  3. Implement the feedback: the instructor can be consulted before locking the protocol for good (second tagged commit).
  4. Start executing the reproduction: logging every deviation or ambiguity as you go.
  5. Draft reproduction report: For the write-up groups will start filling the “Standardized Reproduction Template” (StaRT, brxtd/files/wyxd3). Note that the protocol template was based on the same document; so much of the content can directly be copied from the protocol.