[vitali87]

Summary

• Root cause (Python): an incremental sync parses only the changed files, so ImportProcessor.import_mapping holds maps only for those files. In from pkg import Client, the name pkg.Client turns into pkg._client.Client only through pkg/__init__.py's own map. That file is unchanged and was skipped, so its map was missing. client = Client() lost its type, and client.send() fell back to the name-only heuristic, which picked the re-exported free function pkg._api.send.
• Root cause (Rust, both comments): a receiver typed from a call (Get::new(k).into_frame(), let b = Builder::new(); b.build()) gets its type from method_return_types. Pass 2 fills that record only while it parses the file that defines the fn. When get.rs or the my-beta crate is unchanged, the record is empty. The chained form then got no edge, and the local form bound by name to db::Shared::into_frame, or to my-alpha's Builder::build, a crate app does not depend on.
• Fix:
  • Import maps: after registry rehydration, GraphUpdater._restore_reached_import_state starts from the maps of the re-parsed files. For each module an import names whose map is missing, it reads that module's imports back from disk (ImportProcessor.restore_unparsed_imports).
    • It walks the full import closure of the re-parsed files, and every restored module is walked in turn. That includes the module of a reached definition, because resolving the definition's own annotations (def make() -> Client) reads that module's map.
    • Each restored map is pointed at its own-language stem sibling ([Bug]: adding a same-stem file in another language (util.js next to util.py) renames the existing module's qualified names and hands them to the newcomer; glosses written on the old definitions silently re-attach to the new file #2586) before its targets are looked up, so from shim import Widget next to a shim.js reaches shim.py.
    • Modules no re-parsed file reaches are never opened, and a full build restores nothing.
    • parse_imports(..., defer_edges=False) keeps the restored modules from queuing IMPORTS edges again, since those edges are still in the graph.
    • On a synthetic 600-module project where every module imports three earlier ones, a consumer-only sync restored 152 maps and took 0.6s, against 19s for a full index.
  • Rust return types: _rehydrate_rust_return_types rebuilds the records of unchanged Rust fns from the return_type annotation each rehydrated graph row already carries. rs_utils.return_type_name_from_annotation re-parses the annotation inside a stub fn, so Self, Result<Self, E> and &T reduce exactly as they do at parse time. Trait methods get no record, because a clean index records none. A re-parsed file's own record always wins.

Demo

Animated runs

There are three before/after terminal runs against Memgraph 3.3. Each one makes a fresh index, applies the issue's edit, runs an incremental cgr start --update-graph and calls cgr graph callees:

1. py-reexport: this is the issue's Python repro. After only the test file is edited, test_send goes from pkg._client.Client.send (exact) to pkg._api.send (heuristic) on main. On this branch it stays pkg._client.Client.send (exact).
2. rs-reexport: this is the first comment. Only the two re-export lines are edited. On main, the unchanged client_b.rs has no into_frame edge for chained, and local resolves to db.Shared.into_frame (heuristic). On this branch all three forms resolve to Get.into_frame (exact).
3. rs-workspace: this is the second comment. After crates/app/src/main.rs is edited, b.build() resolves to crates.alpha...Builder.build (heuristic) on main. On this branch it stays crates.beta...Builder.build (exact).

I re-ran all three on 73c617b and got the same branch output.

Type of Change

• Bug fix
• New feature
• Performance improvement
• Refactoring (no functional changes)
• Documentation
• CI/CD or tooling
• Dependencies

Related Issues

Fixes #2559

Related:

• fix(rust): resolve bare 2018-edition pub use re-exports to the local module #2599 (bare 2018-edition pub use, the [Bug]: Rust: method calls on a type imported through a pub use re-export get no CALLS edge, or a heuristic edge to the wrong type's method #2542 setup that the Rust comment starts from) and fix(rust): bind Type::f() to the type a scoped or external use names #2791 ([Bug]: Rust Type::new() ignores the use that names Type: use regex_syntax::Parser and mod tests { use my_beta::Builder } bind exact to a same-named first-party type, even in a crate that isn't a dependency (ripgrep: 803 cross-crate edges into non-dependencies) #2622, the name trie ignoring crate dependencies) touch neighbouring code. Both merge cleanly with this branch.
• git merge-tree against every open PR that touches the same files (33 PRs) shows no conflict.
• fix(embeddings): key vectors by symbol and prune a project's stale ones on sync #2550 conflicted on the collections import line, so the closure walk now uses a plain list.

Test Plan

• New tests added: codebase_rag/tests/test_incremental_reexport_typing.py (22 tests). They build a fresh index, edit a file, run an incremental sync, and compare the result with a clean index of the same tree.
• Manual testing: the three runs above, with cgr start into Memgraph 3.3.
• Unit tests pass. I did not run the full unit suite locally, because several agents share the machine; CI runs it on push. Targeted scope I ran at 73c617b, all passing:
  • the new file: 22 passed
  • every test_graph_updater_incremental*, test_incremental_*, test_reingest*, test_cpp_incremental* and test_csharp_incremental* file, plus test_graph_updater_phase_order.py, test_graph_updater_pruning.py, test_same_stem_other_language.py, test_sibling_mixin_resolution.py, test_sibling_stem_registry_sweep.py and test_js_ts_module_system*.py: 482 passed, 1 skipped
  • every test_rust*, test_type_inference* and test_python_*infer* file, plus test_instance_attr_type_inference.py and test_graph_determinism.py: 644 passed, 3 skipped
  • test_import_*, test_reexport_chain_resolution.py, test_package_reexport_inheritance.py, and the other test files that exercise parse_imports or import_mapping (41 files): 937 passed
  • ruff check, ruff format and ty check are clean.

Red tests. 16 of them fail against main's production files:

• TestPythonPackageReexport:
  • test_receiver_typed_through_reexport_stays_exact and test_factory_return_typed_through_reexport_stays_exact: on main these give assert None == 'exact', because the call binds to pkg._api.send.
  • test_base_class_reached_through_reexport_keeps_inherits: main loses Child INHERITS pkg._client.Client.
  • test_incremental_graph_equals_a_clean_index
  • test_scoped_reingest_on_a_fresh_updater_stays_exact: the MCP per-file path.
• TestRustReexport:
  • test_every_receiver_form_stays_exact[src/client_b.rs|src/cmd/mod.rs]: on main, chained and local lose Get.into_frame.
  • test_incremental_graph_equals_a_clean_index[...]
  • test_return_types_of_unchanged_files_match_a_clean_index: Self, Result<Self, _> and free fns.
• TestRustWorkspace:
  • test_cross_crate_receiver_stays_in_the_dependency
  • test_incremental_graph_equals_a_clean_index
• TestReturnTypeFromAnnotation (2): the new helper.

The review follow-up adds 4 more. Each fails on 28a6e43 and passes on 73c617b:

• TestPythonFactoryModule::test_factory_receiver_stays_exact and test_incremental_graph_equals_a_clean_index. The consumer does from pkg.factory import make, and the unchanged factory.py does from pkg import Client. Before the fix the result was {'pkg.factory.make': 'exact', 'pkg._api.send': 'heuristic'}.
• TestStemSiblingReexport::test_receiver_through_suffixed_module_stays_exact and test_incremental_graph_equals_a_clean_index. Here shim.py sits beside shim.js, and api.py does from shim import Widget. Before the fix the result was {'decoy.render': 'heuristic'}.

Negative tests:

• test_unreached_unchanged_module_is_not_parsed: an unchanged module that no re-parsed file's imports lead to is never read.
• test_restored_modules_write_no_import_edges: restored modules queue no IMPORTS edges, and the re-parsed file still writes its own.
• test_full_build_restores_nothing: a forced full run parses no module a second time.
• test_trait_methods_get_no_return_type: a trait's own fn make() -> Self gains no return type on a sync, because a clean index has none.
• test_self_names_nothing_without_an_impl: Self in a free fn reduces to nothing.

Sonar follow-up (68d7d97)

• S3776 on _restore_reached_import_state (complexity 16): fixed. The import-closure walk moved into a new helper, _restore_import_closure, which returns how many modules it restored. The method keeps its docstring, the early return when every map is already held, and the log line. Behaviour and order of operations are unchanged. The method now scores 2 and the helper 14.
• S7504, an "unnecessary" list() (line ~2118): kept, now as an explicit snapshot. targets = list(...) carries a comment explaining why the copy is needed.
  • Why it is needed: restoring a Rust module can write into the very map being walked, when an inline mod shares its qualified name with a cfg twin's file. The write is retracted before the next step.
  • Why that is still unsafe without a copy: an add-then-delete that forces a resize can make a dict iterator silently skip an entry.
  • How this was checked: a scratch run on a Rust cfg-twin repo showed the iterated map growing from 2 to 42 entries during a restore.
• Results: 205 passed and 1 skipped across the incremental and phase-order suites. 282 passed across the reingest, per-language import and Rust module suites, and 9 passed in the watcher suite. ruff and ty are clean.

Checklist

• PR title follows Conventional Commits format
• All pre-commit checks pass (make pre-commit)
• No hardcoded strings in non-config/non-constants files
• No # type: ignore, cast(), Any, or object type hints
• New comments and docstrings explain why, not what (see Comment Policy)

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https://claude.ai/code/session_01QjpNsgSNyL5gsmAFqfuoD6

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Summary by CodeRabbit

• Bug Fixes
  • Improved incremental indexing so unchanged modules retain import information, helping keep references accurate without requiring a clean re-index.
  • Improved Rust return-type recovery during incremental updates, including annotations on functions and methods.
  • Improved handling of duplicate definition markers so their ordering remains consistent with a clean index.
• Tests
  • Added coverage comparing incremental indexing with clean indexing across Python and Rust imports, re-exports, and return types.

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📒 Files selected for processing (6)

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📝 Walkthrough

Walkthrough

Incremental graph updates restore import mappings for reachable unchanged modules and rebuild Rust return-type entries from rehydrated definitions. Added tests compare incremental graph results with clean indexes.

Changes

Incremental graph restoration

Layer / File(s)	Summary
Restore reachable import maps codebase_rag/parsers/import_processor.py, codebase_rag/graph_updater.py, codebase_rag/logs.py, codebase_rag/tests/test_incremental_reexport_typing.py	ImportProcessor can rebuild import state without deferring edges. GraphUpdater restores imports for reachable unchanged modules, remaps imports to language siblings, and skips modules without required Pass 2 inputs. Tests cover Python and Rust re-exports, workspace dependencies, and inline modules.
Rebuild Rust return types codebase_rag/constants/ast_rust.py, codebase_rag/parsers/rs/utils.py, codebase_rag/graph_updater.py, codebase_rag/utils/qn_markers.py, codebase_rag/tests/test_incremental_reexport_typing.py, codebase_rag/tests/test_qn_marker_grammar.py	Rust annotations are parsed from function stubs to restore return-type names for rehydrated definitions. Duplicate definitions are replayed in registration order, using file walk positions and marker positions. Tests cover annotation forms and duplicate definitions.

Priority: ➖ Normal

Estimated code review effort: 4 (Complex) | ~45 minutes

Change: Bug fix · Severity of issue fixed: Medium

Suggested reviewers: claude

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Merge Risk: ⚪ Minimal · up to 3c741

Incremental sync now keeps exact receiver typing through unchanged re-exports and Rust return types, matching a fresh index. No concrete merge-blocking risk was identified in the supplied changes.

Security Architecture Review

Security architecture risk: 🔵 Low · up to 81c3d

The change restores missing analysis information without establishing a new execution or privilege boundary. Remaining uncertainty concerns recovery after parsing failures and consistent selection of duplicate Rust method return types; no introduced security vulnerability was verified.

Retained concerns
No architecture-level concerns identified.

Security review details

Security Blast Radius

• inferred — A repository author can influence the import closure and annotations consumed by recovery. An incremental update can consequently inspect an entire reachable closure of indexed modules, rather than only changed files. The traced outcomes are source parsing and graph-resolution data, not execution of imported repository code or a demonstrated expansion into another project's authority.

Trust Boundaries and Controls

• observed — Incremental module seeding checks project ownership and surviving eligible paths. Restoration selects indexed holders and checks repository-relative paths, language capabilities, frontend coverage, and AST availability before parsing. The repository-relative check is lexical: the inspected code does not establish a symlink-safe filesystem sandbox. Disk reload uses the existing reader, also present at the PR base.

Resilience and Maintainability Implications

• inferred — Restoration inherits a non-atomic parsing policy: parse_imports creates the module map before parsing and catches parsing exceptions without returning failure. Restoration therefore cannot distinguish a completed map from a partial map left by such an exception. Durable incomplete-run markers contain propagated failures, but do not detect this caught-error case. No concrete trigger or introduced security impact was verified.

Hardening Proposals

• proposed — Consider explicit restoration-completion status and provisional map publication so a failed parse remains retryable instead of being represented as a held map. This would strengthen recovery semantics; it is not a verified vulnerability finding.

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Pre-merge checks | 3 | 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Out of Scope Changes check		[#2559] The linked issue covers the Python package re-export regression. The PR also adds Rust return-type rehydration, Rust-specific parser and graph logic, and the unrelated `qn_markers.marker_posit…	Remove the independent Rust and qn_markers changes from this PR, or link active coding requirements that require them.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check		The title clearly summarizes the main incremental-sync fixes for unchanged re-exports and Rust return types. It is concise and follows Conventional Commits format.
Description check		The description is complete and directly matches the implementation. It covers the root causes, fixes, demonstrations, related issue, tests, manual validation, checklist, and known limitation that the…
Linked Issues check		[#2559] The PR restores import maps for unchanged modules reached from re-parsed files and follows the reached import closure. This preserves the package __init__.py map needed for `from pkg import …

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Full details: Out of Scope Changes check

Explanation

[#2559] The linked issue covers the Python package re-export regression. The PR also adds Rust return-type rehydration, Rust-specific parser and graph logic, and the unrelated qn_markers.marker_position change with tests. The linked issue does not require these changes, and related pull requests do not establish scope.

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[greptile-apps]

Confidence Score: 5/5

[Medium impact] No outstanding numbered findings or new findings block merging.

Summary

This PR restores import maps reached by changed files and rebuilds return types for unchanged Rust functions. Restored maps are followed through re-exports before call resolution, Rust inline imports remain available to that walk, and Rust return types are replayed in file and definition order. The current code addresses all four supplied prior findings. No new issue was identified.

_{Reviews (9) · Last reviewed commit: "Merge remote-tracking branch 'origin/mai..." · Reviewed by Greptile}

[vitali87]

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[vitali87]

PR Title Convention failed on 68d7d97 with API rate limit exceeded for installation. The repository's Actions token was rate-limited (from 18:38Z), so the job stopped at an API call, not on anything in this PR.

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Actionable comments posted: 1

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Inline comments:
Review comments at @codebase_rag/graph_updater.py:
- Around line 3469-3473: Update _rust_return_type_record rehydration to group
restored rows by their natural method key and select the row with the same
last-definition precedence as parsing before populating the map. Call setdefault
only once per selected key so freshly parsed entries remain unchanged and
unordered duplicate rows cannot determine the restored return type.

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[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
94.7% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud