fix(report): make the report's headline numbers agree with themselves (#3148)

The GRAPH_REPORT headline figures disagreed: shown-community count included empty communities
the render loop skips, and the knowledge-gaps thin count used a hardcoded 3 beside a label
printing min_community_size. Drive every figure from one _real_count predicate so the counts
reconcile with what is actually rendered.

graphify/report.py

@@ -139,13 +139,25 @@ def generate(
         ]
 
     from .analyze import _is_file_node as _ifn
+
+    def _real_count(nodes) -> int:
+        return sum(1 for n in nodes if not _ifn(G, n))
+
     non_empty = {cid: nodes for cid, nodes in communities.items()
                  if any(not _ifn(G, n) for n in nodes)}
+    # One predicate for every figure the report prints about itself (#3148):
+    # "thin" is 0 < real < min_community_size, and "shown" is what the render
+    # loop below actually renders (real >= min_community_size) - previously
+    # shown was total-thin, which also counted communities with ZERO real
+    # nodes that the loop skips, overstating the count (#2129's residual).
     thin_count_summary = sum(
         1 for nodes in communities.values()
-        if 0 < sum(1 for n in nodes if not _ifn(G, n)) < min_community_size
+        if 0 < _real_count(nodes) < min_community_size
+    )
+    shown_count = sum(
+        1 for nodes in communities.values()
+        if _real_count(nodes) >= min_community_size
     )
-    shown_count = len(communities) - thin_count_summary
 
     lines += [
         "",
@@ -284,9 +296,13 @@ def generate(
         and not _is_concept_node(G, n)
         and G.nodes[n].get("file_type") != "rationale"
     ]
+    # Same threshold the Summary and Communities headers used (#3148): this
+    # was a hardcoded 3, so with --min-community-size anything else the count
+    # here disagreed with the label text beside it, which already printed
+    # min_community_size.
     thin_communities = {
         cid: nodes for cid, nodes in communities.items()
-        if 0 < sum(1 for n in nodes if not _is_file_node(G, n)) < 3
+        if 0 < sum(1 for n in nodes if not _is_file_node(G, n)) < min_community_size
     }
     gap_count = len(isolated) + len(thin_communities)
 
@@ -295,8 +311,13 @@ def generate(
         if isolated:
             isolated_labels = [G.nodes[n].get("label", n) for n in isolated[:5]]
             suffix = f" (+{len(isolated)-5} more)" if len(isolated) > 5 else ""
+            raw_isolated = sum(1 for n in G.nodes() if G.degree(n) <= 1)
             lines.append(f"- **{len(isolated)} isolated node(s):** {', '.join(f'`{l}`' for l in isolated_labels)}{suffix}")
-            lines.append("  These have ≤1 connection - possible missing edges or undocumented components.")
+            lines.append(
+                "  These have ≤1 connection - possible missing edges or undocumented components. "
+                f"(Counts symbols only; {raw_isolated} node(s) total have ≤1 connection when "
+                "file, concept and rationale nodes are included.)"
+            )
         if thin_communities:
             lines.append(f"- **{len(thin_communities)} thin communities (<{min_community_size} nodes) omitted from report** — run `graphify query` to explore isolated nodes.")
         if amb_pct > 20:

tests/test_report_gap_thresholds.py

@@ -0,0 +1,84 @@
+"""GRAPH_REPORT's headline numbers must agree with themselves (#3148).
+
+The Summary and Communities headers counted thin communities against the
+caller's --min-community-size, while the Knowledge Gaps section counted
+against a hardcoded 3 - beside label text that already printed
+min_community_size. And the "isolated node(s)" figure excludes file,
+concept and rationale nodes without saying so, so a plain degree<=1 recount
+from graph.json never matched it. Also the #2129 residual: "shown" was
+total-minus-thin, which counted zero-real-node communities the render loop
+skips.
+"""
+from __future__ import annotations
+
+import re
+
+import networkx as nx
+
+from graphify.report import generate
+
+
+def _graph_and_communities():
+    G = nx.Graph()
+    # community 0: 6 real symbol nodes (rendered at every threshold used here)
+    big = [f"big{i}" for i in range(6)]
+    # community 1: 4 real nodes - thin at min=5, NOT thin at the hardcoded 3
+    mid = [f"mid{i}" for i in range(4)]
+    for n in big + mid:
+        G.add_node(n, label=n, file_type="code", source_file=f"src/{n}.py",
+                   source_location="L1")
+    for group in (big, mid):
+        for a, b in zip(group, group[1:]):
+            G.add_edge(a, b, relation="calls", confidence="EXTRACTED")
+    # community 2: only a file node - the render loop skips it entirely
+    G.add_node("onlyfile", label="onlyfile.py", file_type="code", source_file="onlyfile.py")
+    # a lonely concept node: degree 0, excluded from the symbol-isolated list
+    G.add_node("lonely_concept", label="Lonely", file_type="concept", source_file="d.md")
+    communities = {0: big, 1: mid, 2: ["onlyfile"]}
+    return G, communities
+
+
+def _report(min_size):
+    G, communities = _graph_and_communities()
+    return generate(
+        G, communities, {}, {}, [], [],
+        {"total_files": 3, "total_words": 100}, {},
+        root="proj", min_community_size=min_size,
+    )
+
+
+def test_summary_and_gaps_count_thin_with_the_same_threshold():
+    text = _report(5)
+    assert "(1 shown, 1 thin omitted)" in text
+    m = re.search(r"\*\*(\d+) thin communit\w+ \(<(\d+) nodes\) omitted", text)
+    assert m, text
+    assert m.group(1) == "1" and m.group(2) == "5", m.group(0)
+
+
+def test_at_the_default_threshold_nothing_is_thin():
+    text = _report(3)
+    assert "0 thin omitted" in text
+    if "## Knowledge Gaps" in text:
+        gaps = text.split("## Knowledge Gaps")[-1].split("## ")[0]
+        assert "thin communit" not in gaps
+
+
+def test_shown_counts_only_what_the_render_loop_renders():
+    """The zero-real-node community is neither shown nor thin (#2129 residual):
+    shown must be 1 (the big community), not total-minus-thin = 2."""
+    text = _report(5)
+    header = re.search(r"## Communities \((\d+) total, (\d+) thin omitted\)", text)
+    assert header and header.group(2) == "1"
+    assert "(1 shown, 1 thin omitted)" in text
+    rendered = len(re.findall(r"### Community ", text))
+    assert rendered <= 1 or rendered == int(re.search(r"\((\d+) shown", text).group(1))
+
+
+def test_isolated_count_is_auditable_against_the_raw_graph():
+    text = _report(3)
+    assert "isolated node(s):" in text
+    assert "Counts symbols only" in text
+    m = re.search(r"(\d+) node\(s\) total have ≤1 connection", text)
+    assert m
+    G, _ = _graph_and_communities()
+    assert int(m.group(1)) == sum(1 for n in G.nodes() if G.degree(n) <= 1)