`@Component`, `@Injectable`, `@Input`, `@Inject`, `@Entity`, … produced no
edge — the `decorator` node kind was never walked. This is framework-critical
(Angular, NestJS, Vue class components, TypeORM): the decorators are the
primary signal of what a class is and does.
Decorators occur only on classes, class members, and parameters, so one pass
over each class declaration covers them. `_ts_emit_decorator_edges` emits a
`references` edge (context="decorator") from the decorated entity to the
decorator symbol:
- class decorators -> the class. Handles both `@Deco class C` (decorator is
a child of the class) and `@Deco export class C` (decorator sits on the
wrapping export_statement), plus stacked decorators.
- method decorators -> the method node. They are siblings preceding the
`method_definition`; stacked decorators are skipped past to find it.
- field / accessor decorators -> the class (the field is not a graph node).
- parameter decorators (`@Inject(T)`) -> the enclosing method/constructor.
The symbol is the head identifier: `@Injectable`, the `function` of
`@Component({...})`, or the `property` of `@ns.Component()`. Targets go
through `ensure_named_node`, so a decorator defined outside the corpus
becomes a sourceless stub, consistent with type references — one per
referencing file, matching the cross-file stub disambiguation introduced
with full-path node IDs in 0.9.0.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
`namespace Foo {}` parses as `internal_module` and `module Bar {}` (and
ambient `declare module "pkg" {}`) as a named `module` node. Neither kind
was in `class_types`/`function_types` nor handled by an extra-walk, so the
container produced no node — its members were still reached by the default
recurse, but the namespace/module itself was invisible to the graph and its
members lost their namespace context.
Add `_ts_extra_walk`, dispatched for TypeScript after `_js_extra_walk`,
mirroring `_csharp_extra_walk`: it emits a container node + a file→container
`contains` edge and recurses the body, leaving members file-contained as
before. `internal_module` exposes `name`/`body` fields; `module` exposes
none, so name (identifier / nested_identifier / quote-stripped string) and
body (`statement_block`) are found positionally. The `is_named` guard skips
the anonymous `module` keyword token, which shares the `module` type string.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Generator functions were invisible to the graph. The declaration form
`function* g()` parses as `generator_function_declaration`, which was
absent from the JS/TS `function_types`, so it produced no node; the
expression form `const h = function*(){}` parses as `generator_function`,
which was absent from the JS function-value types, so it was never captured
when assigned to a module-level const. Generator *methods* (`*gen()` in a
class) were already covered — they parse as `method_definition`.
Add `generator_function_declaration` to the JS and TS `function_types` (so
it emits a node and its body is walked) and to `function_boundary_types`
(so its calls are scoped to it, parity with `function_declaration`); add
`generator_function` to `_JS_FUNCTION_VALUE_TYPES` (so the const-assigned
expression form is captured like `function_expression`).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
`import x = require("./m")` produced no edge at all: tree-sitter parses it
as an `import_statement` whose module string sits inside an
`import_require_clause`, not as a direct child of the statement, so the
direct-child string scan in `_import_js` never found it. The file-level
dependency was silently dropped while the equivalent ESM form
(`import * as x from "./m"`) was captured — an invisible hole in the
import graph of TS codebases that interop with CommonJS modules.
Restructure the scan to first locate the module string — a direct `string`
child for ESM imports/re-exports, or the `string` nested inside an
`import_require_clause` for the import-equals form — then emit the
`imports_from` edge from the single shared path. Relative paths, tsconfig
aliases, and bare modules all resolve through the same
`_resolve_js_import_target` as ESM, giving the import-equals form exact
parity with a namespace import: one file-level `imports_from` edge.
Plain JS is unaffected (the grammar has no `import_require_clause`), and
the pure namespace alias form (`import A = B.C`) is out of scope — it has
no module string and models an intra-code alias, not an import.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
`.mts` (ESM) and `.cts` (CommonJS) are the TypeScript counterparts of the
already-supported `.mjs`/`.cjs`, but graphify handled them in neither the
code-extension detection nor the TypeScript grammar path — so they were either
skipped entirely (classified as non-code) or, once detected, parsed with the plain
JavaScript grammar, which silently drops every `type`/`interface`/type-alias
declaration.
Detection — add `.mts`/`.cts` alongside their siblings in:
- detect.CODE_EXTENSIONS (the code / non-code gate)
- analyze._LANG_FAMILY (cross-language edge family → "js")
- extract._JS_RESOLVE_EXTS (import target resolution)
- extract._JS_CACHE_BYPASS_SUFFIXES
- build.py per-node language map (→ "js")
TypeScript grammar — route `.mts`/`.cts` to the plain TypeScript grammar (like
`.ts`; neither is JSX), so their TS-only syntax is captured:
- extract_js() (grammar selector: .mts/.cts → _TS_CONFIG)
- extract._DISPATCH (.mts/.cts → extract_js)
- the use_ts tree-sitter selector
- the typescript_member_calls resolver frozenset
Result: a `.mts`/`.cts` file now extracts identically to the equivalent `.ts`.
Verified on a real 47 KB `.mts` source — 36 nodes for `.mts`/`.cts`, matching `.ts`
exactly (was 22 with the JS grammar; the 14 dropped nodes were TS type/interface
declarations). No new dependency — same tree-sitter-typescript grammar as `.ts`.
Tests: tests/test_typescript_module_extensions.py — membership regression locks for
the extension sets, dispatch routing, and end-to-end parity asserting `.mts`/`.cts`
capture the TS `type`/`interface` nodes and match the `.ts` node set.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The claude-cli backend passed the extraction schema via --system-prompt with
only the raw file dump in the user turn, assuming a replacement system prompt
is the model's sole authority. Claude Code >= ~2.1 (verified on 2.1.197) does
not honour that: it still layers in the local coding-agent context
(CLAUDE.md/AGENTS.md in cwd, skills, MCP) and, given a user turn that is just a
file with no request, replies conversationally ("I see the file, but there's no
actual request attached"). That prose parses to zero nodes/edges, so
_response_is_hollow flags it as truncation and the adaptive-retry path bisects
the chunk indefinitely (94 -> 47 -> 23 -> ...), never converging and never
writing graph.json.
Move the full extraction schema plus an explicit imperative into the user turn
and drop --system-prompt, so the CLI emits the JSON object directly. The
<untrusted_source> prompt-injection guardrails are carried verbatim; model
override, --add-dir image handling, timeout, and token accounting are untouched.
Two 0.9.4 regressions (CLI cross-file indirect_call, stale community labels on
re-cluster), the case-folding god-node fix (#1581), ~15 language extractor
fixes (Ruby/Groovy/Elixir/Fortran/Rust/Julia/SystemVerilog/Scala/PowerShell/
ObjC/PHP/C#/C++/Swift), merge-graphs mixed-type handling (#1606), Swift
singleton-into-local resolution (#1604), Homebrew python@ shebang (#1586),
hooks foreground-stall perf (#1601), serve query stopwords (#1597) and
multi-project MCP serving (#1594), plus JSON-loading hardening, dedup collision
warning, and Windows hook worker limit.
Built wheel validated in a clean venv: CLI reports 0.9.5, import resolves to the
installed package, the case-folding and Swift-singleton fixes verified, 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>
Add an optional project_path to every MCP tool so one server process can
answer against many projects. Omitted -> the server's default graph (fully
backward-compatible); an absolute project_path -> that project's
<GRAPHIFY_OUT>/graph.json, routed per call.
Implementation (all in _build_server):
- _ctx_cache + _load_ctx(): per-graph context cache with mtime+size
hot-reload, unified across the default graph and every project graph.
Unlike _load_graph it raises instead of sys.exit on a bad file.
- _resolve_graph_path()/_select_graph(): map project_path to a graph.json
and rebind G/communities/active_graph_path per call. No hot-path lock:
select+handler run in one synchronous span of the call_tool coroutine.
- Tolerant startup: serve with no default graph (pure multi-project mode)
instead of exiting; a bad project_path is a tool error, not a crash.
- project_path injected as an optional (non-required) field on all tools.
Tests: 3 new HTTP-transport tests (optional-on-every-tool, routing,
bad-path-no-crash). Full serve suite green (91 passed).
`graphify query "<question>"` tokenised the whole question and seeded BFS on
every word, so natural-language scaffolding dominated retrieval. "how does the
frontier cache work" seeded on "how"/"the"/"work" — which prefix-match prose
labels like "Working Principles" at the 100x prefix tier — instead of on
"frontier"/"cache", landing in the wrong part of the graph.
Filter a set of English question/filler words from the query terms so content
words drive seeding, with a fallback to the unfiltered terms when a query is all
stopwords ("how does it work"). Applied to query terms only — node text is never
filtered, so a symbol literally named `work` stays findable via explain/path.
Updates the one test that pinned "what" as a kept term and adds coverage for the
new drop + all-stopword fallback. Full suite green (2745 passed, 28 skipped).
Three foreground costs ran on every commit before the detached rebuild
launcher even started:
1. Interpreter probes imported the full package. Each probe executed
'import graphify' wholesale — measured 13s per probe cold on a Windows 11
dev box with AV-scanned site-packages — and up to four probes could run
synchronously. Probes now use importlib.util.find_spec, which locates the
package without executing it (interpreter startup cost only). A broken
install under the selected interpreter still fails loudly in the rebuild
log, as before.
2. The shebang probe read a binary. Git for Windows' command -v can return
the launcher path WITHOUT its .exe suffix, so the '*.exe)' guard missed
and head -1 read a PE binary: the shell warned 'ignored null byte in
input' on every commit and the garbage always fell through to the slow
python3/python fallbacks. The Windows pip layout is now resolved directly
(Scripts/graphify -> sibling ../python.exe, or ./python.exe for venvs),
and the remaining POSIX shebang read strips NULs first.
3. GIT_DIR was re-derived. git exports GIT_DIR to hooks; the unconditional
rev-parse added ~1.3s more on machines where every git exec is scanned.
Now reused from the environment with rev-parse as the manual-run fallback.
Measured on the affected machine: hook foreground drops from 26s+ (cold) to
~1.4s, warnings gone. Behavior is unchanged on healthy POSIX setups — probe
order and fallback semantics are preserved.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
`let manager = NetworkManager.shared` followed by `manager.fetchData()` on a
later line produced zero call edges. Two gaps: (1) local let/var bindings inside
method bodies were never typed (only class-level properties and function params
populated the per-file type table), and (2) a static-member initializer
(`Type.shared`, a navigation_expression) wasn't recognized as typing the local
even in the class-property path — only constructor calls (`Type()`) were.
Add _swift_local_var_types (mirrors _cpp_local_var_types): walk each function
body and type a local from a constructor OR a `Type.staticProp` access whose head
is upper-cased. `x.method()` then resolves to the receiver type through the
existing single-definition god-node guard. The class-property path also learns
the Type.shared shape. Reported on a 23k-file iOS corpus where this idiom is the
median call pattern.
Verified: the repro resolves (loadIfNeeded -> fetchData/isLoading); constructor
locals still resolve; a lowercase-head init (`other.child`) does NOT falsely
type; and an ambiguous method name resolves to the receiver-typed class only.
Swift + full suite 2789 passed.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#1586: the skill's interpreter-detection allowlist rejected any shebath path
with a char outside [a-zA-Z0-9/_.-], so Homebrew's versioned python@3.13 path
was skipped and detection fell through to a bare python3 without graphify.
Allow @ in the skillgen source fragments (core/devin/aider/posix), regenerate
all skill artifacts, and register the change as a sanctioned monolith diff.
Injection chars (; $ ( etc.) are still rejected.
#1606: graphify merge-graphs crashed with an unhandled NetworkXError when
inputs disagreed on directed/multigraph. _to_simple only converted MultiGraph,
leaving a DiGraph to fail compose. Normalize every input to a plain undirected
Graph (the merged cross-repo view is undirected anyway).
Also confirmed on v8: `graphify kilo install` (#1605) works (reporter was on an
older version), and `pip3 install graphifyy` failing on macOS (#1585) is a
broken Homebrew Python 3.14 / pyexpat env, not a graphify issue — pip crashes
in its own vendored distlib before graphify is touched.
skillgen --check / --monolith-roundtrip / --schema-singleton all green; shell
smoke accepts python@3.13 and still rejects `; rm -rf /` and `$(evil)`. Full
suite 2789.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Swap the personal LinkedIn link for the Graphify Labs company page across the
main README and all translated READMEs; relabel the badge to Graphify Labs.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The Swift `enum_entry` handler in `_swift_extra_walk` iterated the entry's
children only for the `simple_identifier` case name (emitting a `case_of`
edge) and never descended into the sibling `enum_type_parameters` node, where
associated-value types live (`enum_type_parameters -> user_type ->
type_identifier`). As a result `case started(Session)` silently dropped the
`Event -> Session` type reference.
Descend into each `enum_type_parameters` child after emitting `case_of`, run
`_swift_collect_type_refs` over its named children, and emit a `references`
edge from the enum node to each collected type (context `type`, or
`generic_arg` for generic roles), guarding target != enum node. Mirrors the
existing Swift property/parameter/return-type emit style.
Fixture: add `case failed(Config)` to `NetworkError` in sample.swift.
Test: assert (`NetworkError`, `Config`) in references(context=type).
The C++ base_class_clause handler's `template_type` branch read the base
name (`sub.child_by_field_name("name")`) and emitted the `inherits` edge,
but never descended into the base's `template_argument_list`. As a result
`class Car : public Base<Dep>` emitted `Car -> Base` (inherits) yet dropped
the `Car -> Dep` generic_arg reference entirely.
The Java handler `_emit_java_parent_type` already emits these generic_arg
references for base-class type arguments; C++ was the asymmetric gap.
Fix: after emitting the `inherits` edge, grab the base's `arguments` field
(the `template_argument_list`) and run `_cpp_collect_type_refs` over each
named argument with the generic flag set, emitting a `references` edge
(context "generic_arg") per collected type, guarding target != class node.
`_cpp_collect_type_refs` already handles nested/qualified args, so
`Base<std::vector<Dep>>` is covered too.
Adds a templated base (`Connection<T>`) + derived class
(`PooledClient : public Connection<HttpClient>`) to tests/fixtures/sample.cpp
and a test mirroring the Java generic-parents test.
The C# class-body walker only handled field_declaration, so a
property's type produced no references(field) edge. In idiomatic C#,
auto-properties (`public Widget Main { get; set; }`) — not bare fields
— are the standard way to declare state, so this silently dropped most
of a class's type relationships.
Add a property_declaration branch alongside the field_declaration
handler, guarded the same way (ts_module == tree_sitter_c_sharp,
parent_class_nid set). A property exposes its type on the node directly
(no variable_declaration wrapper), so read it via
child_by_field_name("type") and collect refs with
_csharp_collect_type_refs, mirroring the Java/PHP/Kotlin siblings so
List<Widget> yields both the List field ref and the Widget generic_arg
ref. Only emit when target != parent_class_nid.
PHP 8 constructor property promotion (`__construct(private Repo $repo)`)
parses the promoted parameter as `property_promotion_parameter`, not
`simple_parameter`. The PHP parameter loop filtered on `simple_parameter`
only, so promoted params were skipped entirely: their type emitted no
`parameter_type` edge on the constructor, and — because a promoted param
is also a real class field — no `field` edge on the class either. A
non-promoted param in the same signature still emitted `parameter_type`,
so the type reference was silently dropped for exactly the promoted case.
The promoted param's type sits in the same direct named-child shape the
loop already reads for `simple_parameter`, so widening the filter to
accept `property_promotion_parameter` makes the existing type extraction
emit the `parameter_type` edge. Additionally, for a promoted param, emit
a `field`-context references edge on the class (mirroring the
`property_declaration` handler), guarded so it only fires when a parent
class is in scope and the target is not the class node itself. Normal
`simple_parameter` behaviour is unchanged.
Adds a promoted-property constructor to tests/fixtures/sample.php and
test_php_constructor_property_promotion_contexts asserting the promoted
type appears as both `field` and `parameter_type`, and that a
non-promoted param does not leak a field edge.
`@protocol Derived <Base>` dropped the protocol-adoption (inheritance)
edge. The protocol_declaration handler in extract_objc walked children
for method declarations but ignored the protocol_reference_list child
that holds the adopted protocols, so no implements edge was ever emitted
for protocol-on-protocol adoption.
The extractor already handled `@interface Foo <Proto>` adoption, but that
nests the protocol name under a parameterized_arguments node; protocol-on-
protocol adoption uses a different grammar node (protocol_reference_list)
whose adopted-name is a direct `identifier` child, so it was never
matched. Walk protocol_reference_list and emit an implements edge for each
adopted protocol, mirroring the @interface handling.
Adds a defined Base/Derived protocol pair to the ObjC fixture and a
regression test asserting the Derived->Base implements edge.
The `class_statement` handler read only the first `simple_name` child —
the class name — and never inspected the base type(s) after the `:`
token. As a result `class Dog : Animal` dropped the Dog->Animal
inheritance edge entirely; derived classes appeared as isolated nodes.
Walk the class_statement children, and once the `:` token is seen treat
each following `simple_name` as a base type. Matching the C# convention
(PowerShell has no syntactic base-vs-interface split), the first base is
emitted as `inherits` and the rest as `implements`, resolved via
ensure_named_node.
Adds a Shape/Circle inheritance pair to tests/fixtures/sample.ps1 and a
regression test asserting ("Circle","Shape") in the inherits edges.
The Scala field handler matched only `val_definition`, so a mutable field
(`var b: Repo`), which parses as `var_definition`, had its type reference
silently dropped from the graph. val and var nodes are structurally identical
(both expose a `type` field), so the existing type-collection logic works
unchanged. Widen the guard to accept var_definition.
Adds a var field to the Scala fixture and a regression test.
Cross-file name resolution folded case for every language, so `from pathlib
import Path` resolved to a shell script's `export PATH=...` node — one variable
becoming the corpus's #1 god-node (266 false incoming edges on a real repo),
polluting god-node rankings, affected blast-radius, and clustering. Reported
with a precise diagnosis by @sheik-hiiobd.
Case is semantic in Python/Rust/Go/Java/C#/Kotlin/Swift/Ruby/C/C++/JS/TS: `Path`
(class), `PATH` (env var), `path` (variable) are distinct. Fix gates folding by
language at the two resolution sites the repro exercised:
- global cross-file CALL resolver: index by exact case; a folded index is built
only for case-insensitive-language nodes (PHP/SQL/Nim) and consulted only when
the calling file is such a language.
- type-reference STUB rewire (_rewire_unique_stub_nodes): match stubs to real
defs by exact case, with a folded fallback restricted to case-insensitive-
language definitions — so a case-sensitive `PATH` can never absorb a `Path`.
For case-sensitive languages this only ever removes false edges. Concept/doc
dedup (dedup.py, guarded to non-code nodes) is intentionally left folding.
Regression tests: Python `Path` no longer hits shell `PATH`; a case-differing
cross-file ref doesn't resolve; exact-case resolution still works; PHP fold
preserved. Full suite 2777.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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.
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.
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>
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>
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>
`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>
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>
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>
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>
#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>
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>
`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>
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.
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>
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>
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.
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.
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>
A function bound to a name (cb = handler) or returned from a factory
(def make(): return handler) is a real reference, but indirect_call only
covered call arguments and dispatch tables, so `affected` still dropped these
callers.
Emit indirect_call (context "assignment"/"return", INFERRED) for the value-side
identifiers of a Python assignment RHS and a return, at function scope (owner =
enclosing function) and module scope (owner = file node). Reuses the shared
_emit_indirect_ref guard. Scans the VALUE side only -- the assignment target is
a new local binding, not a reference -- so the existing param/local shadow guard
still rejects the false edges #1565 fixed.
Negatives covered: param-shadow, local-shadow, non-callable emit nothing.
Full suite green; ruff clean.
safishamsi