PGx phenotypes: pgx phenotype|annotate (PGX-024..028, CLI-034)

CPIC lookups by allele function counts or activity values (duplications N x activity, *5/*0 = 0, total-score
fallback), Indeterminate when feasible solutions disagree or an allele is not in the guideline; per-sample
simurg.pgx/1 JSON and diplotype_annotations.tsv with PGX-026 metadata lines.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

tests/unit/test_pgx_phenotype.py

@@ -0,0 +1,36 @@
+"""Diplotype → phenotype (spec PGX-024, PGX-025)."""
+
+from __future__ import annotations
+
+import json
+
+from simurg.pgx.phenotype import build_table, gene_phenotype, phenotype
+
+ACT_ROWS = [(json.dumps({"1.0": 2}), "2.0", "Normal Metabolizer"), (json.dumps({"0.0": 1, "1.0": 1}), "1.0",
+            "Intermediate Metabolizer"), (json.dumps({"0.0": 2}), "0.0", "Poor Metabolizer"),
+            (json.dumps({"1.0": 1, "2.0": 1}), "3.0", "Ultrarapid Metabolizer")]  # fmt: skip
+ACT_ALLELES = [("*1", "Normal function", "1.0"), ("*4", "No function", "0.0"), ("*10", "Decreased function", "0.25")]
+FUNC_ROWS = [(json.dumps({"Normal function": 2}), "n/a", "Normal Metabolizer"),
+             (json.dumps({"Normal function": 1, "No function": 1}), "n/a", "Intermediate Metabolizer")]  # fmt: skip
+FUNC_ALLELES = [("*1", "Normal function", None), ("*2", "No function", None)]
+
+
+def test_activity_genes() -> None:
+    t = build_table("CYP2D6", ACT_ROWS, ACT_ALLELES)
+    assert phenotype(t, ("*1", "*4")).phenotype == "Intermediate Metabolizer"
+    r = phenotype(t, ("*1x2", "*1"))  # duplication: 2 × activity
+    assert r.phenotype == "Ultrarapid Metabolizer" and r.activity_score == 3.0
+    assert phenotype(t, ("*1", "*5")).phenotype == "Intermediate Metabolizer"  # *5 = whole-gene deletion
+    r = phenotype(t, ("*1", "*10"))  # key absent → largest tabulated total ≤ 1.25
+    assert r.phenotype == "Intermediate Metabolizer" and r.activity_score == 1.25
+    r = phenotype(t, ("*1", "*99"))  # PGX-024: unknown allele never crashes
+    assert r.phenotype == "Indeterminate" and "phenotype_not_in_guideline" in r.flags
+
+
+def test_function_genes_and_disagreement() -> None:  # PGX-025
+    t = build_table("CYP2C19", FUNC_ROWS, FUNC_ALLELES)
+    assert phenotype(t, ("*2", "*1")).phenotype == "Intermediate Metabolizer"
+    res, per = gene_phenotype(t, [("*1", "*1"), ("*1", "*2")])
+    assert res.phenotype == "Indeterminate" and per == ["Normal Metabolizer", "Intermediate Metabolizer"]
+    res, per = gene_phenotype(t, [("*1", "*2"), ("*2", "*1")])
+    assert res.phenotype == "Intermediate Metabolizer" and per == []