test: add coverage for lab_results dir loading and toxicity flag branches

tests/test_batch_pack.py

@@ -213,6 +213,37 @@ def test_risk_thresholds_present(self):
         assert "risk_thresholds" in report
         assert "hydrophobic_fraction_high" in report["risk_thresholds"]
 
+    def test_high_charge_density_flagged(self):
+        cand = [_make_candidate("HIGH-CHG", "KKKKKKKKK")]
+        cand[0]["features"]["charge_density"] = 0.70
+        report = toxicity_hemolysis_risk_report(cand)
+        assert "high_charge_density" in report["candidates"][0]["risk_flags"]
+
+    def test_high_cysteine_fraction_flagged(self):
+        cand = [_make_candidate("HIGH-CYS", "CCCCCKKKK")]
+        cand[0]["features"]["cysteine_fraction"] = 0.55
+        report = toxicity_hemolysis_risk_report(cand)
+        assert "high_cysteine_fraction" in report["candidates"][0]["risk_flags"]
+
+    def test_long_repeat_run_flagged(self):
+        cand = [_make_candidate("REPEAT", "KKKKKKRRL")]
+        cand[0]["features"]["longest_repeat_run"] = 6
+        report = toxicity_hemolysis_risk_report(cand)
+        assert "long_repeat_run" in report["candidates"][0]["risk_flags"]
+
+    def test_length_exceeds_35aa_flagged(self):
+        long_seq = "KWKLFKKIGAVLKVLKWKLFKKIGAVLKVLKWKLFK"  # 36 AA (> 35 threshold)
+        cand = [_make_candidate("LONG", long_seq)]
+        report = toxicity_hemolysis_risk_report(cand)
+        assert "length_exceeds_35aa" in report["candidates"][0]["risk_flags"]
+
+    def test_n_with_risk_flags_counts_correctly(self):
+        clean = _make_candidate("CLEAN", "KWKLFKKIGAVLKVL")
+        risky = _make_candidate("RISKY", "LLLLLLLLLLL")
+        risky["features"]["hydrophobic_fraction"] = 0.90
+        report = toxicity_hemolysis_risk_report([clean, risky])
+        assert report["n_with_risk_flags"] == 1
+
 
 class TestSynthesisFeasibilityReport:
     def test_report_type_field(self):
@@ -382,3 +413,19 @@ def test_markdown_requires_human_review(self, ranked_jsonl, tmp_path):
         write_batch_pack_markdown(pack, md_path)
         content = md_path.read_text()
         assert "Human Review" in content or "human expert" in content.lower()
+
+    def test_markdown_truncates_clusters_beyond_20(self, tmp_path):
+        _CANONICAL = list("ACDEFGHIKLMNPQRSTVWY")
+        rows = []
+        for i, aa in enumerate(_CANONICAL):
+            rows.append(_make_candidate(f"CAND-{i:03d}", aa * 10, novelty=0.5 + i * 0.001))
+        rows.append(_make_candidate("CAND-020", "KWKLFKKIGAVLKVLKWKLFK", novelty=0.6))
+        jsonl_path = tmp_path / "big.jsonl"
+        with open(jsonl_path, "w") as f:
+            for r in rows:
+                f.write(json.dumps(r) + "\n")
+        pack = generate_batch_pack(jsonl_path)
+        md_path = tmp_path / "big.md"
+        write_batch_pack_markdown(pack, md_path)
+        content = md_path.read_text()
+        assert "more clusters" in content

tests/test_lab_results.py

@@ -5,16 +5,19 @@
   - Invalid lab results are rejected with useful errors
   - summarise_lab_results produces correct aggregates
   - candidate_result_map groups correctly
+  - load_lab_results_dir loads all valid files, skips invalid, returns sorted
 """
 from __future__ import annotations
 
 import json
+import warnings
 
 import pytest
 
 from openamp_foundry.data.lab_results import (
     candidate_result_map,
     load_lab_result,
+    load_lab_results_dir,
     summarise_lab_results,
 )
 
@@ -172,3 +175,71 @@ def test_unknown_candidate_not_in_map(self):
 
     def test_empty_results_gives_empty_map(self):
         assert candidate_result_map([]) == {}
+
+
+class TestLoadLabResultsDir:
+    def test_empty_directory_returns_empty_list(self, tmp_path):
+        results = load_lab_results_dir(tmp_path)
+        assert results == []
+
+    def test_loads_all_valid_files(self, results_dir):
+        results = load_lab_results_dir(results_dir)
+        assert len(results) == 3
+
+    def test_sorted_by_assay_date(self, tmp_path):
+        date_map = {0: "2026-07-03", 1: "2026-07-01", 2: "2026-07-02"}
+        for i in range(3):
+            result = _valid_result(
+                result_id=f"RES-{i:03d}",
+                candidate_id=f"CAND-{i:03d}",
+                assay_date=date_map[i],
+            )
+            (tmp_path / f"RES-{i:03d}.json").write_text(json.dumps(result))
+        results = load_lab_results_dir(tmp_path)
+        dates = [r["assay_date"] for r in results]
+        assert dates == sorted(dates)
+        assert dates[0] == "2026-07-01"
+
+    def test_sorted_by_result_id_within_same_date(self, tmp_path):
+        for i in [3, 1, 2]:
+            result = _valid_result(
+                result_id=f"RES-{i:03d}",
+                candidate_id=f"CAND-{i:03d}",
+                assay_date="2026-07-10",
+            )
+            (tmp_path / f"RES-{i:03d}.json").write_text(json.dumps(result))
+        results = load_lab_results_dir(tmp_path)
+        ids = [r["result_id"] for r in results]
+        assert ids == sorted(ids)
+
+    def test_skips_invalid_json_file_with_warning(self, tmp_path):
+        valid = _valid_result(result_id="GOOD-001", candidate_id="CAND-A", assay_date="2026-07-01")
+        (tmp_path / "good.json").write_text(json.dumps(valid))
+        (tmp_path / "bad.json").write_text("this is not valid json {{{")
+        with warnings.catch_warnings(record=True) as caught:
+            warnings.simplefilter("always")
+            results = load_lab_results_dir(tmp_path)
+        assert len(results) == 1
+        assert results[0]["result_id"] == "GOOD-001"
+        assert any("bad.json" in str(w.message) or "Skipped" in str(w.message) for w in caught)
+
+    def test_skips_schema_invalid_file_with_warning(self, tmp_path):
+        valid = _valid_result(result_id="GOOD-001", candidate_id="CAND-A", assay_date="2026-07-01")
+        invalid = _valid_result()
+        del invalid["candidate_id"]
+        (tmp_path / "good.json").write_text(json.dumps(valid))
+        (tmp_path / "invalid_schema.json").write_text(json.dumps(invalid))
+        with warnings.catch_warnings(record=True) as caught:
+            warnings.simplefilter("always")
+            results = load_lab_results_dir(tmp_path)
+        assert len(results) == 1
+        assert results[0]["result_id"] == "GOOD-001"
+        assert any("Skipped" in str(w.message) for w in caught)
+
+    def test_non_json_files_ignored(self, tmp_path):
+        valid = _valid_result(result_id="R001", candidate_id="C001", assay_date="2026-07-01")
+        (tmp_path / "result.json").write_text(json.dumps(valid))
+        (tmp_path / "notes.txt").write_text("not a json file")
+        (tmp_path / "data.csv").write_text("col1,col2\n1,2")
+        results = load_lab_results_dir(tmp_path)
+        assert len(results) == 1