fix(parser): extract Python module-level calls (closes #291)

[Wolfvin]

Root cause

PythonParser._extract_references_impl gated call-edge emission behind elif node.type == 'call' and fn_id:. A call written as a bare top-level statement (e.g. setup_app()) is walked with fn_id is None (no enclosing def/class), so the branch was skipped entirely — no CALLS edge. Result: a function called only at module level got ref_count=0 / status=dead (false positive) and was invisible to trace --direction up. This is issue #219, already fixed for the TS/JS parsers, but never applied to the Python parser.

Pattern mirrored from #219

The TS/JS fix attributes module-top-level calls to a synthetic source id <file>:0:<module> with no corresponding graph_nodes row (graph_model.is_module_level_source_id() recognises it; _module_level_caller_entry renders it in trace-up). Applied the analogous change in python_parser.py:

• Compute module_node_id = f"{file_path}:0:<module>" once.
• Change elif node.type == 'call' and fn_id: -> elif node.type == 'call':, with source_id = fn_id if fn_id else module_node_id, and emit edges from=source_id.

Same synthetic-id format, no new format invented, no fake node created.

Fix location

scripts/parsers/python_parser.py — _extract_references_impl (call-edge branch + new module_node_id).

Verification

Repro def setup_app / helper / caller + module-level setup_app() / caller():

Before: setup_app rc=0/dead, caller rc=0/dead (both wrong); only edge caller->helper.
After (parser output):

{'from': 'foo.py:3', 'to_fn': 'helper'}
{'from': 'foo.py:0:<module>', 'to_fn': 'setup_app'}
{'from': 'foo.py:0:<module>', 'to_fn': 'caller'}

Full scan: setup_app rc=1, caller rc=1.

Anti-pollution (#223 constraint): SELECT COUNT(*) FROM graph_nodes WHERE name='<module>' = 0; backend.json has no <module> node.

No regression: helper (called from caller's body) still rc>=1; a genuinely-never-called py_never_called stays rc=0/dead (control).

Tests

Added 3 Python golden cases to tests/test_graph_accuracy_golden.py (mirrors the TS #219/#223 fixtures): rc>=1 + caller-from-file for module-level-called fns, trace-up surfaces the module_level=True caller, and a genuinely-dead control stays dead.

tests/test_graph_accuracy_golden.py  10 passed
pytest -k "python_parser or parser or graph_accuracy or issue291"  247 passed

Closes #291.

🤖 Generated with Claude Code

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Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

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