From 3cd0135f63676d8e272652303f6f74bde0aead55 Mon Sep 17 00:00:00 2001
From: Seongho Bae <me@seonghobae.me>
Date: Thu, 17 Sep 2026 09:19:27 +0900
Subject: [PATCH] fix: mark virtual workspace Cargo.toml manifests as skipped,
 not zero-node
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A Cargo.toml with only [workspace] (no [package]) legitimately declares no
package node of its own. extract_package_manifest already returned an empty
result for it, but without a "skipped" marker, extract.py's #1666
empty-source detector could not tell that apart from an unexplained
extraction failure, so every run printed a persistent "produced zero nodes"
warning for a manifest that was never supposed to emit one.

_parse_cargo now reports workspace_only=True when [workspace] is present with
no [package], and extract_package_manifest returns skipped=True for that
case only — a manifest missing a name for any other reason still warns.

Fixes downstream report at ContextualWisdomLab/fast-mlsirm#1833.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BXYRNTJhYLB2bYveuaFe74
---
 graphify/manifest_ingest.py   | 10 ++++++++++
 tests/test_manifest_ingest.py | 15 +++++++++++++++
 2 files changed, 25 insertions(+)

diff --git a/graphify/manifest_ingest.py b/graphify/manifest_ingest.py
index 313465334f..5c470e7f27 100644
--- a/graphify/manifest_ingest.py
+++ b/graphify/manifest_ingest.py
@@ -92,6 +92,14 @@ def extract_package_manifest(path: Path) -> dict[str, Any]:
     except Exception as exc:  # noqa: BLE001 — a malformed manifest must not abort extraction
         return {"nodes": [], "edges": [], "error": f"manifest parse error: {exc}"}
     if not info or not info.get("name"):
+        # A virtual workspace root (Cargo `[workspace]`, no `[package]`) is a
+        # legitimate zero-node result, not a failure (#1833): mark it
+        # "skipped" so extract.py's #1666 empty-source detector doesn't print
+        # a persistent "produced zero nodes" warning for a manifest that was
+        # never supposed to emit a package node. A manifest missing a name
+        # for any other reason keeps warning, since that IS unexplained.
+        if info and info.get("workspace_only"):
+            return {"nodes": [], "edges": [], "skipped": True}
         return {"nodes": [], "edges": []}
 
     name = info["name"]
@@ -237,6 +245,8 @@ def _parse_cargo(text: str) -> dict | None:
     # package of its own — emit nothing rather than a fabricated node. ``name`` is
     # never workspace-inheritable in Cargo, but guard on the type anyway.
     if not isinstance(name, str) or not name:
+        if isinstance(data.get("workspace"), dict):
+            return {"name": None, "workspace_only": True, "deps": []}
         return None
     # ``version`` may be workspace-inherited (``version.workspace = true``), which
     # parses to a table; keep only a concrete string version.
diff --git a/tests/test_manifest_ingest.py b/tests/test_manifest_ingest.py
index 9f01675c4f..92ca9f1c29 100644
--- a/tests/test_manifest_ingest.py
+++ b/tests/test_manifest_ingest.py
@@ -144,6 +144,21 @@ def test_cargo_virtual_workspace_manifest_emits_no_package(tmp_path):
     assert _pkg_nodes(r) == []
 
 
+def test_cargo_virtual_workspace_manifest_is_marked_skipped(tmp_path):
+    # #1833: a virtual workspace root (no [package]) legitimately emits zero
+    # nodes by design. Without an explicit "skipped" marker, extract.py's
+    # #1666 empty-source detector treats this as an unexplained failure and
+    # prints a persistent "produced zero nodes" warning on every run. A
+    # manifest with no [workspace] table either (i.e. genuinely malformed,
+    # missing a name) must NOT be marked skipped — that would hide a real
+    # problem.
+    ws = _write(tmp_path / "ws" / "Cargo.toml", '[workspace]\nmembers = ["a"]\n')
+    assert extract_package_manifest(ws).get("skipped") is True
+
+    broken = _write(tmp_path / "broken" / "Cargo.toml", '[dependencies]\nserde = "1"\n')
+    assert extract_package_manifest(broken).get("skipped") is not True
+
+
 def test_cargo_target_conditional_deps_are_collected(tmp_path):
     # Platform-gated deps under [target.'cfg(...)'.dependencies] are common in
     # real crates and must not be dropped just because they are conditional.