[pull] v8 from safishamsi:v8#100
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…1574, #1571) build_merge backs `graphify --update`. Two incremental-update data bugs: #1574 — it read only nodes+edges from the existing graph.json, never hyperedges, and build() only sees the new chunks' hyperedges. So every --update collapsed the graph's hyperedge set (the highest-signal semantic groupings) down to just the re-extracted files'. Now existing hyperedges are carried forward via attach_hyperedges (id-dedup): re-extracted files' prior hyperedges are replaced by their new version (by source_file), deleted files' are dropped via the prune set, and unchanged/global ones are preserved. This mirrors what watch.py already did. #1571 — when a caller omits `root`, absolute prune_sources (from detect_incremental) never relativized to the stored relative source_file keys, so deleted files' nodes survived as ghosts and accumulated across runs. Added _infer_merge_root: fall back to the committed graphify-out/.graphify_root marker, else the output dir's parent. This root now drives BOTH the prune set and the replace-per-source normalization, so both work without an explicit root. The CLI --update path and all shipped runbooks already pass root; this hardens the library for any other caller. 5 tests: hyperedge preservation (unchanged/global kept, re-extracted replaced, with and without root), deleted-file hyperedge prune, and root-less prune via both the grandparent and .graphify_root-marker fallbacks. Full suite 2742. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…slice 3) Reflective dispatch by string literal — getattr(obj, "handler") — resolves the attribute name to a callable def and emits it under indirect_call (context "getattr", INFERRED) at both function and module scope, so `graphify affected handler` now covers getattr call sites. The name is a STRING, not an identifier: it names an attribute and is never shadowed by a param/local, so it resolves without the identifier shadow guard — the inverse of the #1565/#1566 identifier paths. A dynamic name (a variable, f-string, concatenation, or any expression) is not statically resolvable and emits nothing; obj.getattr(...) (a method, not the builtin) and the 1-arg form are ignored. Refactors the shared resolve-and-emit core out of _emit_indirect_ref into _emit_indirect_by_name so the getattr path reuses it (callable-target-only, cross-file deferral, dedup) without duplicating the guard; the identifier wrapper is behavior-preserving. Full suite green.
…n LLM)
Community labels defaulted to "Community N" whenever no LLM backend was configured,
making the report + suggested questions unreadable ("why does log_action connect
Community 70 to Community 129?"). Add `label_communities_by_hub`: name each community
after its highest-degree member — the structural hub — so the report reads "log_action"
/ "auth" with zero LLM cost. Ties break by node id for run-to-run stability; a community
with no members in the graph keeps the "Community N" placeholder.
Wired as the default base at both label-building sites — the label/standalone path in
__main__ and the watch/detect rebuild in watch.py. A configured LLM naming pass still
runs and overrides these with richer names; its no-backend placeholder fallback is
guarded so it can't clobber the hub labels.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…to-called deduplicate_by_label is never wired into build(); the active dedup path is deduplicate_entities (imported and called in build). Its docstring claimed "Called in build() automatically," which was never true. Correct it to say the helper is dormant/unused and to warn that it merges by label alone with no file_type guard, so it must not be enabled for code nodes — same-label symbols from different files/packages (e.g. two Account types) would collapse, the cross-file conflation deduplicate_entities deliberately avoids for code (#1205). Docstring only; no behavior change. The function is unused and superseded, so it could reasonably be deleted instead — left in place here, flagged for your call. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Wrap unguarded json.loads() in build_merge(), load_graph(), and _read_json_file() so corrupted graph.json files produce an actionable RuntimeError instead of an unhelpful JSONDecodeError traceback. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…ata loss (#1504) When two LLM extraction chunks each process a file with the same name in different directories, they independently generate the same node IDs and deduplicate_entities() silently drops one node (first-writer-wins). The data loss had no indication in any log, counter, or output. Adds a stderr WARNING when a duplicate ID comes from a different source_file, telling the user which files collided and recommending the per-subfolder extract + merge-graphs workflow to avoid it.
`class Dog < Animal` exposes the base in the `superclass` field, but the inheritance handler in `_extract_generic` had branches for java/kotlin/c#/scala/cpp/php/swift/python and none for Ruby, so every Ruby `inherits` edge was silently dropped (contains/methods/calls unaffected). Add a Ruby branch that reads the `superclass` field, handling both a bare `constant` (`< Animal`) and a `scope_resolution` (`< Foo::Bar` -> Bar). Adds a subclass to the Ruby fixture and a regression test. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
tree-sitter-groovy exposes inheritance via the same `superclass` and `interfaces`/`type_list` fields as tree-sitter-java, but the inheritance- emitting block in `_extract_generic` was gated on `ts_module == "tree_sitter_java"`. Groovy was the only class-based JVM language in the file with no inheritance handler, so every Groovy `extends`/`implements` was silently dropped (contains/methods/imports/calls were unaffected). Widen the gate to include `tree_sitter_groovy`; the existing `_emit_java_parent_type` path handles the identical node shapes verbatim. Adds a base class + interface to the Groovy fixture and two regression tests (extends -> inherits, implements -> implements). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#1537 shipped with a manual test checklist only. Add automated tests that corrupt a graph.json and assert the actionable RuntimeError at all three load paths (build_merge, affected.load_graph, diagnostics._read_json_file) plus a happy-path guard. Also record the six merged small fixes in the changelog. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…low-up) Rigorous smoke testing surfaced an edge case the canonical-tmp unit tests couldn't reach: when the scan root is under a symlink (macOS /var -> /private/var, a symlinked home or git worktree), the absolute prune path and the resolved root differ by prefix, so _norm_source_file's lexical relative_to fails and the prune/replace match silently misses — deleted files' ghost nodes survive. Latent in the pre-existing #1007 path too, now that build_merge resolves the root. Fix: when lexical relative_to fails, retry with both sides fully resolved. Only the failure path resolves, so the common lexical match stays filesystem-free (no per-node stat on the hot replace-per-source loop). Adds a symlinked-root prune regression test (POSIX-only). Full suite 2768, and the full end-to-end smoke battery (indirect_call all contexts, JS, Ruby/Groovy inherits, hyperedge preservation, symlinked-root ghost prune, corrupt-json errors, dedup collision warning) is green. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
indirect_call dispatch arc (call args + cross-file, dispatch tables, assignment/return, getattr, JS/TS), two incremental-update data fixes (hyperedge preservation + ghost-node prune, incl. symlinked-root hardening), direction-aware skill-version warning, deterministic hub community labels, Ruby/Groovy inheritance edges, corrupt-graph.json error handling, cross-chunk collision warning, Windows hook worker limit. Built wheel validated in a clean venv: CLI reports 0.9.4, import resolves to the installed package, new-feature smoke battery green, and a real `graphify extract` produces indirect_call + inherits edges end-to-end. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…9.4 regression) Local install-testing of 0.9.4 surfaced that `graphify extract .` dropped every cross-file indirect_call edge — the headline feature, broken on the primary code path — while the extract() API worked. Root cause: the cross-file callable-target guard unioned per-file `callable_nids` (pre-remap ids), but extract() rewrites node ids afterward (id_remap / prefix sym_remap / _disambiguate_colliding_node_ids). When the scan root relativizes ids (cache_root == project root, which the CLI passes), the guard set went stale and `tgt not in callable_nids` rejected every remapped target. In-file indirect edges survived (emitted with consistently-remapped endpoints), which masked it — only cross-file dropped. Fix: mark callable defs with a `_callable` attribute on the node dict instead of exporting an id list. A marker rides through every id remap; callable_nids is rebuilt from the final (post-remap) nodes right before the pass that uses it, and the marker is stripped before output (like origin_file). Regression test extracts with cache_root == project root (the CLI shape) and asserts the cross-file edge survives and _callable never ships to graph.json. Full suite 2769. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Reported from a real run: after re-scoping a repo (5807->3710 nodes), the 228-community re-cluster kept run-1's 300 saved labels, so cids now covering a different community wore the wrong (LLM) names — silently. cluster-only reused .graphify_labels.json wholesale, and the overlap-based cid remap grabs a prior cid on any overlap, inheriting a stale name. Fix: write a per-community membership signature (sha256 of sorted member ids) beside the labels. On reuse, keep a saved label only when the community's signature is unchanged; a changed community is renamed by its deterministic hub (correct-by-construction) with a warning to run `graphify label` for fresh LLM names. For label files predating the signature, fall back to a community- count check (a differing count means a different clustering -> don't trust cid labels). Unchanged graphs reuse labels silently — no false warnings. Verified: stale legacy labels (42) on a 12-community graph -> warned + hub- renamed all + sig written; rerun on the unchanged graph -> silent reuse, labels stable. Unit tests for the signature (deterministic, order-independent, changes on membership change). Full suite 2771. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
`alias Foo.{Bar, Baz}` (and the same import/require/use brace form) emitted
NO imports edges. tree-sitter-elixir represents it as a `dot` node holding the
base alias plus a trailing `tuple` of member aliases, but the import handler
only matched a bare `alias` child, so every multi-alias import was silently
dropped.
Add `_get_alias_modules`, which expands the brace form to `Foo.Bar`,
`Foo.Baz`, … while leaving the single form (`alias Foo.Bar`) unchanged. Adds a
fixture line + regression test.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Function calls (`y = f(x)`) were silently dropped — only `subroutine_call` (`call sub(...)`) was handled in walk_calls. tree-sitter-fortran represents a function invocation as a `call_expression`, which had no branch, so every function-to-function call produced no edge. Handle `call_expression`. Because Fortran uses the same `name(...)` syntax for array indexing, the callee is resolved against procedures defined in the file (`target_nid in seen_ids`) before emitting — so array accesses like `arr(i)` cannot fabricate spurious `calls` edges. Adds a function + caller to the fixture and a regression test. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Enum variant payload types were silently dropped — `struct_item` and
`trait_item` had type-reference handlers but `enum_item` had none, so the
variant field types were never traversed.
Add an `enum_item` branch that walks
`enum_variant_list -> enum_variant -> ordered_field_declaration_list`
(tuple variants, `Click(Logger)`) and `field_declaration_list` (struct
variants, `Resize { size: Dim }`), emitting a `references` edge from the enum
to each field type. Reuses the same type collection as the struct path. Adds
an enum to the fixture and a regression test.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
… forms Only bare-identifier imports (`using Foo`) emitted edges. tree-sitter-julia wraps qualified paths in `scoped_identifier` (`using Base.Threads`), relative paths in `import_path` (`using ..Sibling`), and the package of a `selected_import` may itself be a `scoped_identifier` (`import Base.Threads: nthreads`). None of those were matched, so qualified and relative imports were silently dropped, and scoped selected-imports pointed at the selected symbol instead of the module. Resolve the module name from identifier / scoped_identifier / import_path in all three positions. Adds fixture lines + a regression test. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
extract_rust() only traversed field_declaration_list (named-struct bodies), so tuple structs -- whose positional fields nest under ordered_field_declaration_list -- had every field type reference silently dropped from the graph. This is the same node shape the enum handler already accounts for (tuple variants nest their types under ordered_field_declaration_list); the struct path was simply left behind. Add an additive branch that, for each type node in a tuple struct's ordered_field_declaration_list, collects type refs via _rust_collect_type_refs and emits references edges with the appropriate field / generic_arg context. The named-struct path is untouched. For `struct Wrapper(Logger, Config);` with Logger/Config defined in-file, no field edges were produced before; both are now emitted. Adds test_rust_tuple_struct_field_references and a tuple struct to the shared Rust fixture covering plain and generic positional field types.
The SystemVerilog class-body field regex in _augment_systemverilog_semantics matched only unqualified `<type> <name>;` declarations. Its `^\s*` prefix consumes leading whitespace but not leading class-property qualifiers, so a qualified field such as `rand Config m_cfg;` (three tokens) failed the two-token shape and its type reference was silently dropped from the graph. Consume optional leading qualifiers (rand/randc/local/protected/static/const/ automatic/var) before the type token. Zero qualifiers preserves the existing behavior; the type and name capture are unchanged. Adds test_systemverilog_qualified_field_references plus rand- and protected-qualified fields (and a Config class) to the shared .sv fixture.
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