Reproducibility Review (main)

[Robert-Roth]

Repository: Arcadia-Science/2025-raman-spectrometer-comparison
Branch: main
Commit: 55bf35c28f
Reviewed: 2026-06-29 17:57 UTC

Summary

This is a well-structured notebook publication with pinned dependencies, all data committed to the repo, and a clean Python package for spectrum loading. The main reproducibility issue is that the README's setup/contribution links are broken (they point to root paths instead of pages/), which obstructs the path to the actual setup instructions. Once those links are fixed, the analysis should be reproducible top-to-bottom.

Critical issues

• Broken links to setup instructions in README.md (lines 57, 61). The README directs reproducers to [SETUP.qmd](SETUP.qmd) and [CONTRIBUTING.qmd](CONTRIBUTING.qmd), but these files actually live at pages/SETUP.qmd and pages/CONTRIBUTING.qmd. On GitHub the links 404. Since the README has no other setup guidance (no conda env create, no pip install -e ., no quarto installation step), a reproducer who follows the documented entry point lands on a dead link. Either fix the relative paths to pages/SETUP.qmd / pages/CONTRIBUTING.qmd, or inline the setup steps into the README.

Warnings

None found.

Polish/nice to have

• Broken link in README "Working with the data" section (line 48). The README references [load_spectra.py](../src/analysis/load_spectra.py). From the README's location at the repo root this should be src/analysis/load_spectra.py (no ../). The current link 404s on GitHub.
• Operating system not documented in the main README. No mention of which OS the analysis was developed/tested on. Adding a note (Linux/macOS/Windows + version) would help reproducers know what to expect.

Suggestions

• Move (or duplicate) the essential setup steps (conda env create -n <name> -f env.yml, conda activate <name>, pip install -e ., quarto render index.ipynb --execute) directly into the top-level README.md so reproducers don't depend on the existence/resolution of separate documentation files.

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Automated reproducibility review • model: claude-opus-4-7 • tokens: 68176 in / 2928 out