| name | domain-check |
| description | Use whenever you write or run scientific analysis code (physics, earth/geo, biology, chemistry, or social science) in this workspace — before executing it and again after generating results. Runs a deterministic domain-correctness gate that catches code which runs but is scientifically wrong (unit/dimension mismatch, Euclidean distance on lat/lon without a CRS, 0-based/1-based coordinate and strand errors, impossible SMILES valence, uncorrected multiple comparisons, averaging a categorical code). Surfaces structured findings; never claims the code is correct. |
Domain-correctness gate
Across every field the top complaint is code that executes cleanly but is
scientifically wrong. This gate intercepts that field's classic error classes
deterministically — by analysing the code you actually wrote, not by
recalling rules. It verifies specific error classes; it never proves correctness.
Run it as a normal step of any analysis — it is fast, offline, and stdlib-only.
When to run
- Before executing analysis code you generated (catch the bug before it
produces a plausible-but-wrong number).
- After generating results, as a final gate before you report figures or
numbers to the user.
- Whenever the user asks to check, validate, or audit an analysis for
correctness.
How to run
The gate ships beside this SKILL.md. Run it on the code files in play (or with
no arguments to scan the workspace):
python "$XDG_CONFIG_HOME/opencode/skills/domain-check/domain_check.py" <file.py|notebook.ipynb|analysis.R ...>
It prints exactly one ```review fenced JSON block on stdout.
What it catches (one rule set per discipline)
- physics · units — adding/subtracting/comparing quantities of different
dimensions (e.g.
t_seconds + d_meters); trig on a degree-valued angle.
- earth · crs — Euclidean/Pythagorean distance on latitude/longitude
(
sqrt((lat1-lat2)**2 + (lon1-lon2)**2)); a geopandas geometric op with no
CRS ever set.
- biology · coords / strand — off-by-one on BED intervals (0-based
half-open, so length is
end - start, never +1); a sequence sliced from a
stranded feature file (GFF/GTF/BED) with no reverse-complement for the -
strand.
- chem · valence — a SMILES string literal (assigned to a
smiles/smi
variable, or passed to MolFromSmiles/MolFromSmarts) that cannot be a real
molecule. If RDKit is installed it is used as the authoritative judge —
Chem.MolFromSmiles sanitizes the parse, so it catches far more than a
five-bond carbon (bad ring closures, impossible aromaticity, over-valent
N/O/S) and, being authoritative, clears molecules a heuristic would
wrongly flag. Without RDKit it falls back to a stdlib bond-counter (carbon
4, over-bonded halogen; bails on bracket atoms for precision).
- social · multiple-comparisons — a significance test (
ttest_ind,
pearsonr, f_oneway, chi2_contingency, …) run inside a loop or ≥3 times
with no multipletests/FDR/Bonferroni correction anywhere — the inflated
family-wise false-positive rate that silent p-hacking produces.
- social · categorical — a numeric reduction (
.mean()/.median()/.std()
…) taken directly on a nominal category code (gender, race, region,
condition, …), treating an unordered label as an interval quantity. A
groupby('gender') key is correct usage and is not flagged.
Rules favour precision: an unrecognized unit, arithmetic with no discipline
signal, a SMILES using bracket atoms (which carry their own valence/charge), a
single significance test, or a categorical used only as a groupby key is left
silent rather than flagged.
Reporting findings
Copy the ```review block the tool prints as the last thing in your
message — the app renders it as dismissible reviewer cards. Do not paraphrase
the findings into prose and drop the block; the structured block is the
contract. If the gate found nothing, say so plainly and keep the block (its
note states that no findings is not a guarantee of correctness).
Never tell the user the code is "correct" or "error-free" — the gate checks
known error classes only.
Adding a discipline
Add a check_<field>(ctx) function in domain_check.py and append it to
VALIDATORS. No other change is needed — the review contract and the app's
rendering are discipline-agnostic (each finding carries its own tag).
