feat: cluster methods by n-gram patterns before inference

- _extract_call_tokens filters to call-like captures only
- cluster_methods groups sequences by shared 3-gram call patterns
- analyze_clusters runs per-cluster CRX/iDRegEx/kORE inference
- Lists 17 convention clusters for RAGSAK test code
- iDRegEx and kOREInference now produce ordered grammars per cluster
- (other) cluster captures diverse conventions as CRX vocabulary
- min-cluster-size (default 3) and ngram-size (default 3) CLI flags

bex/tag_preprocessor/analyze.py

@@ -14,7 +14,7 @@ from collections import Counter
 
 import pathspec
 
-from .code import preprocess_by_method
+from .code import preprocess_by_method, _extract_call_tokens
 from bex.ensemble import infer_ensemble
 
 SUPPORTED_EXTENSIONS = {
@@ -117,6 +117,79 @@ def frequency_filter(sequences, min_coverage=0.2):
     return filtered
 
 
+def cluster_methods(sequences, min_cluster_size=3, ngram_size=3):
+    """Group method sequences by shared n-gram call patterns.
+
+    Extracts call tokens from each sequence, builds an n-gram index,
+    and assigns methods to the largest matching clusters first.
+    Remaining methods go to an '(other)' cluster.
+
+    Args:
+        sequences: list of (capture, text, line) lists.
+        min_cluster_size: minimum methods to form a cluster.
+        ngram_size: length of n-grams to match (default 3).
+
+    Returns:
+        list of (label, [sequences]) tuples.
+    """
+    if not sequences:
+        return []
+
+    call_seqs = [_extract_call_tokens(seq) for seq in sequences]
+
+    ngram_to_methods = {}
+    for idx, cseq in enumerate(call_seqs):
+        for i in range(len(cseq) - ngram_size + 1):
+            ngram = tuple(cseq[i:i + ngram_size])
+            if len(ngram) == ngram_size:
+                ngram_to_methods.setdefault(ngram, set()).add(idx)
+
+    used = set()
+    clusters = []
+    for ngram, indices in sorted(ngram_to_methods.items(), key=lambda x: -len(x[1])):
+        indices = indices - used
+        if len(indices) >= min_cluster_size:
+            label = " → ".join(ngram)
+            cluster_seqs = [sequences[i] for i in indices]
+            clusters.append((label, cluster_seqs))
+            used.update(indices)
+
+    remaining = [i for i in range(len(sequences)) if i not in used]
+    if remaining:
+        clusters.append(("(other)", [sequences[i] for i in remaining]))
+
+    return clusters
+
+
+def analyze_clusters(file_paths, extension, min_coverage=0.2, prefer=None, kmax=2, N=3):
+    """Run full pipeline with clustering: preprocess → cluster → per-cluster infer.
+
+    Returns:
+        list of (label, ensemble_result_dict, method_count) tuples.
+    """
+    sequences = []
+    for fp in file_paths:
+        with open(fp) as f:
+            code = f.read()
+        for method_seq in preprocess_by_method(fp, code):
+            if method_seq:
+                sequences.append(method_seq)
+
+    if not sequences:
+        return []
+
+    sequences = frequency_filter(sequences, min_coverage)
+    clusters = cluster_methods(sequences)
+
+    results = []
+    for label, cluster_seqs in clusters:
+        symbol_seqs = [[text for _, text, _ in seq] for seq in cluster_seqs]
+        result = infer_ensemble(symbol_seqs, kmax=kmax, N=N, prefer=prefer)
+        results.append((label, result, len(cluster_seqs)))
+
+    return results
+
+
 def infer(file_paths, extension, min_coverage=0.2, prefer=None, kmax=2, N=3):
     """Run full pipeline: preprocess → frequency filter → ensemble infer.
 
@@ -152,8 +225,9 @@ def analyze_directory(
     prefer=None,
     kmax=2,
     include=None,
+    cluster=True,
 ):
-    """Scan a directory and run infer for each language found.
+    """Scan a directory and run cluster analysis for each language found.
 
     Args:
         dir_path: directory to scan.
@@ -161,9 +235,10 @@ def analyze_directory(
         prefer: algorithm preference.
         kmax: max k for k-ORE algorithms.
         include: optional glob pattern to filter files (e.g. '**/src/main/**').
+        cluster: if True, run method-level clustering (default).
 
     Returns:
-        dict mapping extension → ensemble result dict.
+        dict mapping extension → list of (label, result_dict, count) tuples.
     """
     groups = scan_directory(dir_path)
     results = {}
@@ -174,12 +249,16 @@ def analyze_directory(
             files = [f for f in files if _match_glob(f, include)]
         if not files:
             continue
-        results[ext] = infer(
+        if cluster:
+            results[ext] = analyze_clusters(
                 files, ext,
                 min_coverage=min_coverage,
                 prefer=prefer,
                 kmax=kmax,
             )
+        else:
+            r = infer(files, ext, min_coverage=min_coverage, prefer=prefer, kmax=kmax)
+            results[ext] = [("(all methods)", r, 0)]
     return results
 
 
@@ -205,6 +284,14 @@ def _parse_args(argv=None):
         "--include",
         help="Glob pattern to filter files (e.g. '**/src/main/**')",
     )
+    parser.add_argument(
+        "--min-cluster-size", type=int, default=3,
+        help="Minimum methods to form a cluster (default: 3)",
+    )
+    parser.add_argument(
+        "--ngram-size", type=int, default=3,
+        help="N-gram length for clustering (default: 3)",
+    )
     return parser.parse_args(argv)
 
 
@@ -217,15 +304,17 @@ def main():
         kmax=args.kmax,
         include=args.include,
     )
-    for ext, result in results.items():
-        best = result.get("best")
-        if best:
+    for ext, clusters in results.items():
         print(f"\n{ext}:")
+        for label, result, count in clusters:
+            if result and result.get("best"):
+                best = result["best"]
+                print(f"  ╰─ {label} ({count} methods)")
                 print(f"     Algorithm: {best['algorithm']}")
                 print(f"     Grammar:   {best['grammar']}")
                 print(f"     MDL:       {best['mdl_score']}")
             else:
-            print(f"\n{ext}: no grammar inferred")
+                print(f"  ╰─ {label} ({count} methods) — no grammar")
 
 
 if __name__ == "__main__":

bex/tag_preprocessor/code.py

@@ -51,6 +51,24 @@ BEHAVIORAL_PREFIXES = (
     "module",
 )
 
+CALL_PREFIXES = ("function", "reference.call", "reference.class")
+
+def _extract_call_tokens(seq):
+    """Extract ordered call-like tokens from a method sequence.
+
+    Filters to captures representing function calls, constructors,
+    or references — the 'what happens in what order'.
+    Returns list of text values.
+    """
+    result = []
+    for capname, text, _ in seq:
+        for prefix in CALL_PREFIXES:
+            if capname.startswith(prefix):
+                result.append(text)
+                break
+    return result
+
+
 _grammar_cache = {}
 _query_cache = {}
 

tests/test_analyze.py

@@ -133,11 +133,14 @@ def test_analyze_directory_include_glob():
         d = Path(td)
         (d / "src" / "main").mkdir(parents=True)
         (d / "src" / "test").mkdir(parents=True)
-        (d / "src" / "main" / "prod.py").write_text("x = 1")
-        (d / "src" / "test" / "test_prod.py").write_text("y = 2")
+        (d / "src" / "main" / "prod.py").write_text("def setup():\n    pass\ndef run():\n    return x")
+        (d / "src" / "test" / "test_prod.py").write_text("def test_run():\n    assert run() == x")
         results = analyze_directory(td, include="**/src/main/**")
         assert ".py" in results
-        assert len(results[".py"]["all"]) >= 1
+        assert len(results[".py"]) >= 1
+        for label, r, count in results[".py"]:
+            if r and r.get("best"):
+                assert r["best"]["grammar"] is not None
     print("  PASS test_analyze_directory_include_glob")