feat: port template upgrades (citations, eval, chunking, nomic prefixes)
mcp 2.x already on origin/main (#10). Does not change BM25-first search_docs — n=6 is too small to flip the default. - Numbered [1] citations via docs_mcp/format.py - Eval P@1 + JSONL sidecar + eval.pvalue + eval.trace - Heading-recursive chunker, keep chunk-0 and MAX_CHARS=4000 - Nomic prefixes at embed time only; stored text unprefixed Closes #12
This commit is contained in:
+156
@@ -0,0 +1,156 @@
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"""Paired permutation test between two eval JSONL sidecars.
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Compares per-query scores from two `eval.run_eval` sidecar files so
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"P@1 went 0.88 → 0.91 on 25 queries" is not treated as a win.
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python -m eval.pvalue \\
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--a eval/results/baseline.jsonl \\
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--b eval/results/new.jsonl \\
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--metric rr
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Exit 0 even when the difference is not significant — this is a report,
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not a gate. No third-party deps; `random.Random(seed)` is enough.
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"""
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from __future__ import annotations
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import argparse
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import json
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import random
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from pathlib import Path
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def load_sidecar(path: Path) -> list[dict]:
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rows: list[dict] = []
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with open(path) as fh:
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for line in fh:
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line = line.strip()
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if line:
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rows.append(json.loads(line))
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return rows
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def paired_permutation(
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a: list[float],
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b: list[float],
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n_resamples: int = 10000,
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seed: int = 0,
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) -> dict:
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"""Two-sided paired permutation test on per-query scores.
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Null: each pair is exchangeable (randomly flipping the sign of
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A_i - B_i). p_value is the fraction of permutations whose
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|mean diff| is at least as large as the observed |mean(A-B)|.
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"""
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if len(a) != len(b):
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raise ValueError(f"paired lengths differ: {len(a)} vs {len(b)}")
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if not a:
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raise ValueError("no paired queries to compare")
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diffs = [x - y for x, y in zip(a, b)]
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n = len(diffs)
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observed = sum(diffs) / n
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abs_obs = abs(observed)
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rng = random.Random(seed)
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extreme = 0
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for _ in range(n_resamples):
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total = 0.0
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for d in diffs:
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total += d if rng.random() < 0.5 else -d
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if abs(total / n) >= abs_obs - 1e-15:
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extreme += 1
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p_value = extreme / n_resamples
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return {
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"A_mean": sum(a) / n,
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"B_mean": sum(b) / n,
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"Diff(A-B)": observed,
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"p_value": p_value,
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"significant": p_value < 0.05,
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"n": n,
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"n_resamples": n_resamples,
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}
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def _index(rows: list[dict], metric: str) -> dict[tuple[str, str], float]:
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"""Map (retriever, query) -> score."""
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out: dict[tuple[str, str], float] = {}
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for row in rows:
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retriever = str(row.get("retriever") or "")
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query = str(row.get("query") or "")
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if metric == "p_at_1":
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score = float(row.get("p_at_1") or 0)
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else:
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score = float(row.get("rr") or 0)
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out[(retriever, query)] = score
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return out
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def compare(
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rows_a: list[dict],
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rows_b: list[dict],
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metric: str = "rr",
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retriever: str | None = None,
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n_resamples: int = 10000,
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seed: int = 0,
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) -> list[dict]:
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"""Join on (retriever, query). One result dict per shared retriever."""
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ia, ib = _index(rows_a, metric), _index(rows_b, metric)
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retrievers = sorted({r for r, _ in ia} & {r for r, _ in ib})
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if retriever:
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retrievers = [r for r in retrievers if r == retriever]
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if not retrievers:
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raise ValueError(f"retriever {retriever!r} not in both sidecars")
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reports = []
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for name in retrievers:
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queries = sorted({q for r, q in ia if r == name} & {q for r, q in ib if r == name})
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if not queries:
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continue
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a_scores = [ia[(name, q)] for q in queries]
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b_scores = [ib[(name, q)] for q in queries]
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report = paired_permutation(a_scores, b_scores, n_resamples=n_resamples, seed=seed)
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report["retriever"] = name
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report["metric"] = metric
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reports.append(report)
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if not reports:
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raise ValueError("no overlapping (retriever, query) pairs")
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return reports
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def render(reports: list[dict]) -> str:
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lines = ["# Permutation test", ""]
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for r in reports:
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sig = "yes" if r["significant"] else "no"
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lines += [
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f"## `{r['retriever']}` ({r['metric']}, n={r['n']})",
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"",
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f"- A_mean: `{r['A_mean']:.4f}`",
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f"- B_mean: `{r['B_mean']:.4f}`",
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f"- Diff(A-B): `{r['Diff(A-B)']:.4f}`",
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f"- p_value: `{r['p_value']:.4f}` ({r['n_resamples']} resamples)",
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f"- significant (p < 0.05): **{sig}**",
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"",
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]
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return "\n".join(lines)
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def main() -> int:
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p = argparse.ArgumentParser(description="Paired permutation test on two eval JSONL sidecars.")
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p.add_argument("--a", type=Path, required=True, help="sidecar JSONL (system A)")
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p.add_argument("--b", type=Path, required=True, help="sidecar JSONL (system B)")
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p.add_argument("--metric", choices=("rr", "p_at_1"), default="rr")
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p.add_argument("--retriever", default=None, help="restrict to one retriever name")
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p.add_argument("--n-resamples", type=int, default=10000)
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p.add_argument("--seed", type=int, default=0)
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args = p.parse_args()
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reports = compare(
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load_sidecar(args.a),
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load_sidecar(args.b),
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metric=args.metric,
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retriever=args.retriever,
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n_resamples=args.n_resamples,
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seed=args.seed,
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)
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print(render(reports), end="")
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return 0
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if __name__ == "__main__":
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raise SystemExit(main())
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+3
-1
@@ -51,7 +51,9 @@ class DenseRetriever:
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self.pool = pool
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def retrieve(self, query: str, k: int = 10) -> list[tuple[str, str]]:
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res = self.col.query(query_texts=[query], n_results=self.pool)
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from rag.embeddings import EMBED_QUERY_PREFIX, embed_texts
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qvec = embed_texts([query], prefix=EMBED_QUERY_PREFIX)[0]
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res = self.col.query(query_embeddings=[qvec], n_results=self.pool)
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ids = (res.get("ids") or [[]])[0]
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return _collapse_to_pages(ids, k)
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+38
-8
@@ -34,6 +34,12 @@ def load_queries(path: Path) -> list[dict]:
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return [json.loads(line) for line in fh if line.strip()]
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def p_at_1(retrieved: list[tuple[str, str]], expected: list[tuple[str, str]]) -> float:
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if not retrieved or not expected:
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return 0.0
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return 1.0 if retrieved[0] in set(expected) else 0.0
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def reciprocal_rank(retrieved: list[tuple[str, str]], expected: list[tuple[str, str]]) -> float:
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expected_set = set(expected)
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for i, page in enumerate(retrieved, start=1):
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@@ -65,8 +71,12 @@ def main() -> int:
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p = argparse.ArgumentParser()
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p.add_argument("--queries", type=Path, default=Path("eval/queries.jsonl"))
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p.add_argument("--k", type=int, default=5)
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p.add_argument("--ks", default="1,5,10,20", help="comma-separated k-curve")
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p.add_argument("--output", type=Path, default=Path("eval/results/baseline.md"))
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p.add_argument("--compare", type=Path, default=None)
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args = p.parse_args()
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ks = sorted({int(x) for x in args.ks.split(",") if x.strip()}) or [args.k]
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max_k = max(ks + [args.k])
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if not args.queries.exists():
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print(f"queries file not found: {args.queries}")
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@@ -83,7 +93,7 @@ def main() -> int:
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from rag.bm25 import BM25Index
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from eval.retrievers import DenseRetriever, BM25Retriever, HybridRetriever
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product = os.environ.get("PRODUCT_NAME", "hvm")
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product = os.environ.get("PRODUCT_NAME", "morpheus")
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repo_root = Path(__file__).resolve().parent.parent
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client = chromadb.PersistentClient(path=str(repo_root / "chroma"),
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settings=Settings(anonymized_telemetry=False))
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@@ -109,34 +119,39 @@ def main() -> int:
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rows: dict[str, dict[str, float]] = {}
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per_query: list[dict] = []
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for r in retrievers:
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mrr_sum = recall_sum = ndcg_sum = 0.0
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mrr_sum = recall_sum = ndcg_sum = p1_sum = 0.0
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elapsed_sum = 0.0
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for q in queries:
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expected = [(e["bundle_id"], e["page_id"]) for e in q["expected"]]
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t0 = time.time()
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retrieved = r.retrieve(q["query"], k=max(args.k, 10))
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retrieved = r.retrieve(q["query"], k=max(max_k, 10))
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elapsed = time.time() - t0
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mrr = reciprocal_rank(retrieved, expected)
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p1 = p_at_1(retrieved, expected)
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recall = recall_at_k(retrieved, expected, args.k)
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ndcg = ndcg_at_k(retrieved, expected, args.k)
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mrr_sum += mrr
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p1_sum += p1
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recall_sum += recall
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ndcg_sum += ndcg
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elapsed_sum += elapsed
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per_query.append({
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"retriever": r.name, "query": q["query"],
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"mrr": mrr, "recall@k": recall, "ndcg@k": ndcg,
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"mrr": mrr, "p_at_1": int(p1), "recall@k": recall, "ndcg@k": ndcg,
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"top1": list(retrieved[0]) if retrieved else None,
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"ranked": [list(p) for p in retrieved],
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"elapsed_s": round(elapsed, 3),
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})
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n = len(queries)
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rows[r.name] = {
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"P@1": p1_sum / n,
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"MRR": mrr_sum / n,
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f"Recall@{args.k}": recall_sum / n,
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f"nDCG@{args.k}": ndcg_sum / n,
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"avg_latency_s": elapsed_sum / n,
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}
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print(f" {r.name}: MRR={rows[r.name]['MRR']:.3f} "
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print(f" {r.name}: P@1={rows[r.name]['P@1']:.3f} "
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f"MRR={rows[r.name]['MRR']:.3f} "
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f"Recall@{args.k}={rows[r.name][f'Recall@{args.k}']:.3f} "
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f"nDCG@{args.k}={rows[r.name][f'nDCG@{args.k}']:.3f} "
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f"avg={rows[r.name]['avg_latency_s']*1000:.0f}ms")
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@@ -144,10 +159,10 @@ def main() -> int:
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args.output.parent.mkdir(parents=True, exist_ok=True)
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md = [f"# Retrieval eval — k={args.k}", "",
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f"_{len(queries)} hand-curated queries, generated {time.strftime('%Y-%m-%d %H:%M:%S')}_", "",
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"| Retriever | MRR | Recall@{k} | nDCG@{k} | avg latency |".replace("{k}", str(args.k)),
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"| --- | ---: | ---: | ---: | ---: |"]
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"| Retriever | P@1 | MRR | Recall@{k} | nDCG@{k} | avg latency |".replace("{k}", str(args.k)),
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"| --- | ---: | ---: | ---: | ---: | ---: |"]
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for name, m in rows.items():
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md.append(f"| `{name}` | {m['MRR']:.3f} | {m[f'Recall@{args.k}']:.3f} "
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md.append(f"| `{name}` | {m['P@1']:.3f} | {m['MRR']:.3f} | {m[f'Recall@{args.k}']:.3f} "
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f"| {m[f'nDCG@{args.k}']:.3f} | {m['avg_latency_s']*1000:.0f}ms |")
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md += ["", "## Per-query results", "",
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"| Retriever | Query | MRR | top-1 |", "| --- | --- | ---: | --- |"]
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@@ -155,7 +170,22 @@ def main() -> int:
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top1 = f"`{r['top1'][0]}/{r['top1'][1][:24]}...`" if r["top1"] else "—"
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md.append(f"| `{r['retriever']}` | {r['query'][:60]} | {r['mrr']:.3f} | {top1} |")
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args.output.write_text("\n".join(md) + "\n")
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sidecar = args.output.with_suffix(".jsonl")
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with open(sidecar, "w") as fh:
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for r in per_query:
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fh.write(json.dumps({
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"query": r["query"],
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"retriever": r["retriever"],
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"ranked": r.get("ranked") or [],
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"rr": r["mrr"],
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"p_at_1": r["p_at_1"],
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}) + "\n")
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print(f"wrote {args.output}")
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print(f"wrote {sidecar}")
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if args.compare:
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from eval.pvalue import compare, load_sidecar, render
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print()
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print(render(compare(load_sidecar(sidecar), load_sidecar(args.compare))), end="")
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return 0
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@@ -0,0 +1,84 @@
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"""Stdlib tests for eval metrics + the permutation test.
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Must not open Chroma — the template has no corpus. Run with:
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python -m unittest eval.test_metrics
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"""
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from __future__ import annotations
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import math
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import unittest
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from eval.pvalue import compare, paired_permutation
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from eval.run_eval import ndcg_at_k, p_at_1, recall_at_k, reciprocal_rank
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A, B, C, X, Y = ("b", "a"), ("b", "b"), ("b", "c"), ("b", "x"), ("b", "y")
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class MetricTests(unittest.TestCase):
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def test_reciprocal_rank(self) -> None:
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# Q1: expected at rank 1
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self.assertEqual(reciprocal_rank([A, B, C], [A]), 1.0)
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# Q2: expected at rank 2
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self.assertEqual(reciprocal_rank([B, A], [A]), 0.5)
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# Q3: miss
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self.assertEqual(reciprocal_rank([X, Y], [A]), 0.0)
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def test_p_at_1(self) -> None:
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self.assertEqual(p_at_1([A, B], [A]), 1.0)
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self.assertEqual(p_at_1([B, A], [A]), 0.0)
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self.assertEqual(p_at_1([], [A]), 0.0)
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self.assertEqual(p_at_1([A], []), 0.0)
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def test_recall_at_k(self) -> None:
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self.assertEqual(recall_at_k([A, B, C], [A], 1), 1.0)
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self.assertEqual(recall_at_k([B, A], [A], 1), 0.0)
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self.assertEqual(recall_at_k([B, A], [A], 2), 1.0)
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self.assertEqual(recall_at_k([X, Y], [A], 5), 0.0)
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self.assertEqual(recall_at_k([A, B], [A, C], 1), 0.5)
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def test_ndcg_at_k(self) -> None:
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self.assertEqual(ndcg_at_k([A], [A], 1), 1.0)
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# expected at rank 2: dcg = 1/log2(3), idcg = 1
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self.assertAlmostEqual(
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ndcg_at_k([B, A], [A], 2),
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(1.0 / math.log2(3)) / 1.0,
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)
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self.assertEqual(ndcg_at_k([X, Y], [A], 5), 0.0)
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class PermutationTests(unittest.TestCase):
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def test_identical_lists_not_significant(self) -> None:
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scores = [0.5, 1.0, 0.0, 1.0, 0.5]
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report = paired_permutation(scores, list(scores), n_resamples=2000, seed=0)
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self.assertEqual(report["Diff(A-B)"], 0.0)
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self.assertEqual(report["p_value"], 1.0)
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self.assertFalse(report["significant"])
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def test_large_paired_difference_is_significant(self) -> None:
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a = [1.0] * 20
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b = [0.0] * 20
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report = paired_permutation(a, b, n_resamples=5000, seed=0)
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self.assertGreater(report["Diff(A-B)"], 0.9)
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self.assertLess(report["p_value"], 0.05)
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self.assertTrue(report["significant"])
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def test_compare_joins_on_retriever_and_query(self) -> None:
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rows_a = (
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[{"retriever": "dense", "query": f"q{i}", "rr": 1.0, "p_at_1": 1} for i in range(20)]
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+ [{"retriever": "bm25", "query": "q0", "rr": 0.0, "p_at_1": 0}]
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)
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rows_b = (
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[{"retriever": "dense", "query": f"q{i}", "rr": 0.0, "p_at_1": 0} for i in range(20)]
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+ [{"retriever": "bm25", "query": "q0", "rr": 0.0, "p_at_1": 0}]
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)
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reports = compare(rows_a, rows_b, metric="rr", n_resamples=2000, seed=0)
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by_name = {r["retriever"]: r for r in reports}
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self.assertIn("dense", by_name)
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self.assertTrue(by_name["dense"]["significant"])
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self.assertFalse(by_name["bm25"]["significant"])
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if __name__ == "__main__":
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unittest.main()
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+114
@@ -0,0 +1,114 @@
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"""Page-level miss dump using this clone's Dense/BM25 retrievers.
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python -m eval.trace --queries eval/queries.jsonl
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"""
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from __future__ import annotations
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import argparse
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import json
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from pathlib import Path
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from eval.run_eval import load_queries, p_at_1
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|
||||
|
||||
def classify_top1_source(top1, dense_pages, bm25_pages) -> str:
|
||||
if top1 is None:
|
||||
return "neither"
|
||||
in_d, in_b = top1 in dense_pages, top1 in bm25_pages
|
||||
if in_d and in_b:
|
||||
return "both"
|
||||
if in_d:
|
||||
return "dense_only"
|
||||
if in_b:
|
||||
return "bm25_only"
|
||||
return "neither"
|
||||
|
||||
|
||||
def first_ranks(pages: list[tuple[str, str]]) -> dict[str, int]:
|
||||
out: dict[str, int] = {}
|
||||
for i, (bid, pid) in enumerate(pages, start=1):
|
||||
key = f"{bid}/{pid}"
|
||||
if key not in out:
|
||||
out[key] = i
|
||||
return out
|
||||
|
||||
|
||||
def render_misses(rows: list[dict]) -> str:
|
||||
misses = [r for r in rows if not r.get("hit")]
|
||||
if not misses:
|
||||
return "# Eval misses\n\n_(none)_\n"
|
||||
lines = [f"# Eval misses ({len(misses)})", ""]
|
||||
for row in misses:
|
||||
lines += [
|
||||
f"## {row['query']}",
|
||||
"",
|
||||
f"- expected: `{row['expected']}`",
|
||||
f"- top-5: `{row['ranked_pages'][:5]}`",
|
||||
f"- top1_source: `{row['top1_source']}`",
|
||||
"",
|
||||
]
|
||||
return "\n".join(lines)
|
||||
|
||||
|
||||
def main() -> int:
|
||||
p = argparse.ArgumentParser()
|
||||
p.add_argument("--queries", type=Path, default=Path("eval/queries.jsonl"))
|
||||
p.add_argument("--trace-out", type=Path, default=Path("eval/results/trace.jsonl"))
|
||||
p.add_argument("--misses-out", type=Path, default=Path("eval/results/misses.md"))
|
||||
args = p.parse_args()
|
||||
if not args.queries.exists():
|
||||
print(f"queries file not found: {args.queries}")
|
||||
return 1
|
||||
try:
|
||||
import os
|
||||
import chromadb
|
||||
from chromadb.config import Settings
|
||||
from rag.embeddings import embedding_function
|
||||
from rag.bm25 import BM25Index
|
||||
from eval.retrievers import BM25Retriever, DenseRetriever
|
||||
product = os.environ.get("PRODUCT_NAME", "morpheus")
|
||||
root = Path(__file__).resolve().parent.parent
|
||||
col = chromadb.PersistentClient(
|
||||
path=str(root / "chroma"),
|
||||
settings=Settings(anonymized_telemetry=False),
|
||||
).get_collection(f"{product}_docs", embedding_function=embedding_function())
|
||||
bm = BM25Index(str(root / "bm25" / f"{product}_docs.db"))
|
||||
dense_r, bm25_r = DenseRetriever(col), BM25Retriever(bm)
|
||||
except Exception as e:
|
||||
args.trace_out.parent.mkdir(parents=True, exist_ok=True)
|
||||
args.trace_out.write_text("")
|
||||
args.misses_out.write_text("# Eval misses\n\nno index\n")
|
||||
print(f"no index ({e}); wrote empty trace")
|
||||
return 0
|
||||
|
||||
rows = []
|
||||
for q in load_queries(args.queries):
|
||||
expected = [(e["bundle_id"], e["page_id"]) for e in q["expected"]]
|
||||
dense_pages = dense_r.retrieve(q["query"], k=50)
|
||||
bm25_pages = bm25_r.retrieve(q["query"], k=50)
|
||||
ranked = bm25_pages or dense_pages # default retrieval is BM25-first
|
||||
top1 = ranked[0] if ranked else None
|
||||
p1 = p_at_1(ranked, expected)
|
||||
rows.append({
|
||||
"query": q["query"],
|
||||
"expected": [list(p) for p in expected],
|
||||
"hit": bool(p1),
|
||||
"p_at_1": int(p1),
|
||||
"dense_rank": first_ranks(dense_pages),
|
||||
"bm25_rank": first_ranks(bm25_pages),
|
||||
"top1": list(top1) if top1 else None,
|
||||
"top1_source": classify_top1_source(top1, set(dense_pages), set(bm25_pages)),
|
||||
"ranked_pages": [list(p) for p in ranked],
|
||||
})
|
||||
args.trace_out.parent.mkdir(parents=True, exist_ok=True)
|
||||
with open(args.trace_out, "w") as fh:
|
||||
for row in rows:
|
||||
fh.write(json.dumps(row) + "\n")
|
||||
args.misses_out.write_text(render_misses(rows))
|
||||
print(f"wrote {args.trace_out} ({len(rows)} queries)")
|
||||
print(f"wrote {args.misses_out}")
|
||||
return 0
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
raise SystemExit(main())
|
||||
Reference in New Issue
Block a user