fix(python): resolve submodule imports inside PEP 420 namespace packages

[flaukowski]

What

from . import brain, ledger inside a directory with no __init__.py — a PEP 420 namespace package, which python -m pkg.mod runs without complaint — produces no edges at all. _resolve_python_module_path returns None when there is no module file to probe, and the #1146 submodule-import branch in _collect_python_symbol_resolution_facts sits behind that None, so the whole statement is skipped. Every brain.think() / ledger.write() call in such a repo is therefore invisible to the #1883 module-call arm, and the most-called functions carry in-degree 0.

With an __init__.py present the same lines resolve correctly (checked the relative, absolute, aliased, parent-relative and subpackage spellings), so this is specific to namespace packages.

Fix

• _resolve_python_namespace_dir mirrors the module-path walk (relative base → scan root → sys.path-root ancestors, per Scan root silently changes the graph: src-layout project loses most 'imports' edges, same node count, no warning #2072) and returns only a directory that exists inside the scan root and has no __init__.py.
• _collect_python_symbol_resolution_facts uses it when the module path resolves to no file; the existing submodule probe then emits the same imports_from (submodule_import) edges a regular package gets, and the module arm resolves the calls.
• A name that is not a module file on disk still emits nothing, and a namespace package binds no symbols of its own (no _SymbolImportFact fallback), so nothing is fabricated.

Evidence

Same graphify version (0.9.56), with and without the change, on a 275-node Python repo laid out this way:

	calls edges	think() callers	remember()	ledger write()
unpatched	201	0	0	0
patched	307	15	10	20

Node count unchanged (275 → 275).

Tests

Three new tests in tests/test_extract.py, next to the #2082 tests: relative form (from . import a, b → two EXTRACTED calls edges plus the imports_from edges), absolute + parent-relative forms (from pkg import a; from .. import a from a nested namespace subpackage), and a negative (from . import data, missing where data/ holds no module file → no resolved edge, no raise). The two positive tests fail on v8 without the fix. pytest tests/test_extract.py -k python: 21 → 24 passed; the rest of the suite is unchanged.

No CHANGELOG entry, following the pattern of other fix PRs — happy to add one if you prefer contributors to.

🤖 Generated with Claude Code

https://claude.ai/code/session_01KTNEBgonu6ASph6w8R2Wcp

[graphify-labs]

Graphify reviewed this change.

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).

Formal verification. No changes could be formally verified in this run.

---

Graphify review — findings

No blocking issues surfaced.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 2067 functions depend on the 542 functions this change touches.

Health — this change adds coupling hotspots:

• new: extract() — 562 callers, 43 callees
• new: _rebuild_code() — 115 callers, 51 callees
• new: _extract_generic() — 18 callers, 26 callees
• new: extract_js() — 85 callers, 4 callees
• new: extract_xaml() — 19 callers, 17 callees
• new: _resolve_js_module_path() — 34 callers, 9 callees
• new: dispatch_command() — 2 callers, 124 callees
• new: extract_objc() — 27 callers, 9 callees
• …and 35 more — each is listed as a finding

Verification — 2067 functions in the blast radius were not formally verified this run (proofs are advisory here).

Gate & verification

graphify gate

PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.

Advisory (not blocking):

• verification_scope: 1165 function(s) in the blast radius were not formally verified this run

Test selection

Test selection

29 of 259 test file(s) selected (11%) via static blast radius.

• tests/test_astro_extraction.py — impact
• tests/test_build.py — impact
• tests/test_cjs_module_extension.py — impact
• tests/test_cpp_nested_and_cli.py — impact
• tests/test_dotnet.py — impact
• tests/test_extract.py — impact, changed-test
• tests/test_forwarding_review_findings.py — impact
• tests/test_import_extension_resolution.py — impact
• tests/test_indirect_dispatch.py — impact
• tests/test_indirect_dispatch_assign_return.py — impact
• tests/test_indirect_dispatch_getattr.py — impact
• tests/test_js_exported_scalar_bindings.py — impact
• tests/test_languages.py — impact
• tests/test_multilang.py — impact
• tests/test_package_json_subpath_imports.py — impact
• tests/test_pascal.py — impact
• tests/test_pascal_resolution.py — impact
• tests/test_phantom_external_import.py — impact
• tests/test_python_import_resolution.py — impact
• tests/test_python_underscore_resolution.py — impact
• tests/test_rationale.py — impact
• tests/test_ruby_resolution.py — impact
• tests/test_scala_self_type.py — impact
• tests/test_src_layout_import_resolution.py — impact
• tests/test_swift_computed_properties.py — impact
• tests/test_ts_new_expression_calls.py — impact
• tests/test_typescript_module_extensions.py — impact
• tests/test_unmapped_at_alias_resolution.py — impact
• tests/test_vue_extraction.py — impact

Selection is safe under the controlled-regression assumption; always-run tests + a periodic full run are the backstops. Advisory — it never changes the check verdict.

Formal verification

Could not verify: Could not verify \_collect\_python\_symbol\_resolution\_facts.

The verifier did not have enough to check \_collect\_python\_symbol\_resolution\_facts, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `root` is annotated `Path` — outside the synthesizable primitive/collection set

· 43 more finding(s) on lines outside this diff (see the check run).