| name | code-review |
| description | Review code, diffs, or PRs for correctness, plus research/cluster pitfalls — hardcoded scratch paths, resource mismatch, GPFS tiny-file storms, package installs inside arrays. TRIGGER when reviewing code or a diff/PR, or before committing. |
| related | ["programming-and-coding","coding-in-python","coding-in-r","using-git-and-github","running-python","running-r"] |
| updated | 2026-05-22T00:00:00.000Z |
Code Review
Find bugs that affect results, reproducibility, data safety, or cluster use. Skip style nits.
Findings must be
- New in this change, unless asked for a broad audit.
- Impactful: name the input/scenario.
- Actionable: give the fix.
Severity
- P0: blocks commit/run/merge. Wrong result, lost data, secret leak, cannot rerun, serious cluster misuse.
- P1: fix before commit/merge. Realistic failure.
- P2: fix later.
- P3: nit. Do not report unless asked.
Verdict:
- LGTM: no P0/P1.
- FAIL: P0/P1 found.
Always check
- Hardcoded personal paths:
/Users/..., C:\Users\..., /home/netid/..., /gpfs/scratch60/netid/....
- Raw data, secrets, env dirs, or large outputs staged.
- Missing seeds in simulation, bootstrap, train/test split, UMAP, random forest, stochastic optimizer.
- Silent data loss:
dropna(), na.omit(), failed joins, duplicate drops, broad filters without counts.
- Lockfile drift: deps changed but
uv.lock / renv.lock not updated.
- Raw data mutation: code writes into
data/raw/ or overwrites inputs.
- HPC resource mismatch: requested 1 CPU but uses all cores; requested GPU but code does not use it.
- GPFS tiny-file storms.
- Package installs inside arrays.
- Scraping/API code without rate limit, cache, retry/backoff.
Process
- Read changed files fully.
- Check
git status --short and staged files.
- Run existing checks if practical.
- Run a small realistic smoke test if practical.
- For Slurm changes: check resources, thread env vars, paths, logs, resumability.
Output
## Findings
### [P1] Missing seed makes bootstrap estimates non-reproducible
**File**: scripts/bootstrap.py:42
**Issue**: `np.random.default_rng()` is called without a fixed seed.
**Fix**: create `rng = np.random.default_rng(42)` at the entry point and pass it in.
## Verdict
FAIL
If clean:
## Findings
None.
## Verdict
LGTM
Checklist
Further reading
