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.
_check_skill_version advised "Run 'graphify install' to update" on ANY
version mismatch. But `install` writes the package's OWN bundled skill and
re-stamps .graphify_version, so when the skill on disk is NEWER than the
running package, following that advice silently DOWNGRADES the skill to
silence the warning. The docstring even said "warn if the skill is from an
OLDER version" but the code never checked direction.
Compare versions numerically (new _version_tuple, so 0.10 > 0.9 and a
malformed stamp degrades instead of raising). When the skill is newer than
the package, recommend upgrading the package (uv tool upgrade / pip install
-U) instead of install; the older-skill case is unchanged. Hit in practice
by a stale `uv tool` CLI and by contributors whose dev checkout stamped a
newer skill. Reported by @TPAteeq.
4 tests (numeric ordering, both mismatch directions, silent-when-equal).
Full suite 2730 passed.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Brings the indirect_call model to JavaScript and TypeScript, the next-
biggest callback-passing ecosystem. Now captured:
- callbacks passed by name as call arguments: `arr.map(fn)`, `setTimeout(fn)`,
`el.addEventListener("x", fn)` — function-scoped, attributed to the caller.
- module-level callback registration (idiomatic in JS, unlike Python):
Express routes `app.get("/", handler)`, event wiring `emitter.on("e", h)`,
timers — attributed to the file.
- object/array dispatch tables: `const ROUTES = { create: handler }`,
`const HOOKS = [onStart, onStop]`, object shorthand `{ handler }`.
Arrow-const functions (`const cb = () => {}`) are registered as callable
targets (threaded callable_def_nids + local_bound_names through
_js_extra_walk). Guards mirror Python: shadowing by param/local/module
reassignment is rejected (JS module shadow set excludes function-valued
declarators so arrow-consts stay resolvable), object KEYS and non-callable
values are excluded, inline arrows/function expressions are direct defs not
references, single-definition god-node guard cross-file.
Two cross-file fixes the JS import model exposed:
- a name that resolves to an import-surfaced FOREIGN symbol (JS named
imports map the real node into the importing file's label map) is now
deferred to the cross-file resolver instead of being mistaken for a local
non-callable; the global callable_nids guard still rejects imported data.
- indirect_call dedup is now call-aware: a benign `imports` edge from a file
to the symbol it imports no longer suppresses the indirect_call to it
(only a real calls/indirect_call edge does).
Shared the resolve-and-emit helper across Python and JS/TS. 9 new tests
(func-arg, module object/array, Express-style registration, inline-arrow
negative, param-shadow, key/data exclusion, shorthand, cross-file import,
TS typed params). Full suite 2726 passed.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Slice 1 of #1566. A function referenced as a VALUE in a dict/list/set/
tuple literal — the registry/route-table idiom (`ROUTES = {"create":
create_user}`, `HOOKS = [on_start, on_stop]`) — is an indirect dependency
that blast-radius must see, but the call-argument capture (#1565) didn't
cover it. Emit an indirect_call edge for each callable value:
- module-level tables attribute to the file node; function-scoped tables
attribute to the enclosing function. Same-file and cross-file (an
imported handler in a table routes through the cross-file resolver).
- dict KEYS are excluded (only values are references); non-callable values
(a number, a string) never resolve; a name shadowed by a param/local or
rebound at module scope is the local value, not the function.
Refactors the resolve-and-emit logic shared by the argument and table
paths into one guarded helper (_emit_python_indirect_ref) and threads the
edge `context` ("argument" | "collection") through the cross-file pass.
Adds _python_module_bound_names for the module-scope shadow set.
7 new tests (module dict/list, function-scoped, dict-keys-excluded,
non-callable-value, module-reassign shadow, cross-file table). Full suite
2717 passed. Python only; assignment/return refs + other languages remain
on #1566.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#1565 captured a function passed by name as a call argument
(executor.submit(fn), Thread(target=fn), map(fn, xs)) only when the
callback was defined in the SAME file — it resolved through the in-file
label map. But the dominant real-world shape is cross-module: the callback
is imported (`from .handlers import on_event; pool.submit(on_event)`), so
the same-file map can't see it and the edge was dropped — exactly the
caller a blast-radius query must not miss.
When the argument identifier isn't defined in-file (and isn't shadowed by
a param/local — that guard already ran), emit an `indirect` raw_call and
let the existing cross-file resolution pass handle it, branching to a
distinct indirect_call/INFERRED edge instead of calls. It rides the same
single-definition god-node guard and import-evidence disambiguation as
direct calls (parity: when a direct call resolves, so does the indirect
one; when the name is ambiguous, both bail). Two added safeguards: the
target must be a real callable def (per-file callable_nids unioned across
the corpus) so an imported data constant can never become a dispatch
target, and an existing direct `calls` edge for the pair pre-empts it.
Smoke-verified: imported single-def callback resolves; ambiguous name
bails (same as direct); imported data constant rejected; direct+indirect
to the same target keeps only the direct edge; cross-file keyword
target=cb resolves. Full suite 2710 passed.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
`graphify affected` (blast radius) was blind to a function passed BY NAME as
a call argument — `executor.submit(fn)`, `Thread(target=fn)`, `map(fn, xs)`,
callbacks — so those callers were silently dropped from the affected set (an
under-counting blast radius reads complete while missing exactly where
regressions hide). Capture them as a distinct `indirect_call` relation
(INFERRED, context "argument"), kept separate from `calls` so strict
call-graph queries stay precise, and add it to DEFAULT_AFFECTED_RELATIONS.
Hardened over the original PR against the name-collision false edge (the
Doxygen #3748 trap): emit only when the argument identifier resolves to a
callable definition AND is not shadowed by a parameter or local binding in
the enclosing function. So `def via(pool, handler): pool.submit(handler)`
(handler is the param, not the module function) and `process(config)` where
`config` is local data emit no edge, while a genuine module function passed
by name still resolves. Dedup-safe against existing direct `calls` edges.
Python only; dict-literal / getattr-by-string / decorator dispatch deferred.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Cross-file member-call resolution for C++/ObjC (#1547/#1556) and
namespace-aware C# type resolution (#1562), the work-memory overlay
(#1441), test-mock call-graph fix (#1553), hyperedge member-key aliases
(#1561), plus the TS/JS/ObjC resolution fixes (#1316/#1544/#1552/#1475).
See CHANGELOG.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Extends the C# type-reference resolver (#1466) to be namespace-aware,
advancing the #1318 shadow-node umbrella for C#:
- The namespace is folded into the C# node id (_make_id(stem, namespace,
name)), so two same-named types in different namespaces in one file no
longer collapse — replacing #1466's detect-and-skip workaround for
multi-namespace files.
- Lexical per-block using-scope: a `using` applies only where it is in
scope (file-level, or the enclosing namespace block via a scope chain),
so sibling namespace blocks no longer share each other's usings.
- Qualified references (`Namespace.Type`) resolve via in-scope aliases
(`using Q = X.Y`) then exact known namespaces; generics are stripped.
Preserves (and tightens) the refuse-rather-than-guess discipline: a bare
reference resolves only when exactly one in-scope namespace provides the
type; an ambiguous reference (e.g. `using A; using B;` both defining
`Widget`) resolves to nothing rather than fanning out. Verified: `using A`
-> A.Widget only; ambiguous -> no edge; qualified `B.Widget` -> B.Widget
regardless of usings; sibling-block using-scope isolated; no dangling
edges or fan-out.
Reconciled onto current v8 (the PR predated the C++/ObjC member-call
resolvers); full suite green, the C++/ObjC resolution coexists.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Connects paired classes across files: Main.cpp's `Foo f; f.bar()` now resolves
to Foo::bar, and ObjC `Foo *f = [[Foo alloc] init]; [f doThing]` to Foo's
doThing — the "connect with other classes" goal of #1547/#1556.
Design grounded in prior-art research (ctags qualified-name matching, Doxygen's
name-keyed false-edge failure modes, PAIGE's receiver-type approach, Clang USR):
resolve by RECEIVER TYPE, never bare name, and skip when the type can't be
inferred rather than guess (a false call edge / god-node is worse than a missing
one). Mirrors the existing Swift/Python/Ruby/TS member-call resolvers.
- C++ extractor now captures the member-call receiver (field_expression /
qualified_identifier / pointer access) and builds a per-file type table from
local declarations (`Foo f;`, `Foo* f;`, `Foo *f = ...;`); emits raw_calls.
- ObjC extractor emits raw_calls for message sends with the receiver + selector
and a type table from `Foo *f = ...;` locals (existing in-file selector /
alloc-init / dot-syntax / @selector matching preserved).
- New _resolve_cpp_member_calls / _resolve_objc_member_calls, registered for
their suffixes. Receiver tiers: `Foo::bar()` / capitalized ObjC receiver and
this/self/super (enclosing class) -> EXTRACTED; local-var-typed -> INFERRED.
Single-definition god-node guard (skip unless exactly one type def matches);
the just-shipped decl/def class merge makes a paired class one def so the
guard resolves it. Verified: a.run() -> A::run only (not a same-named B::run);
an uninferable receiver with run() in two classes emits zero edges (no
fan-out); ObjC [f doThing] -> Foo only.
- build.py: the cross-language INFERRED-call prune treated .h/.cpp/.m as
different families and dropped header/impl interop calls; unified the C family
(.c .h .cc .cpp .hpp .cxx .hh .hxx .cu .cuh .metal .m .mm) so a .cpp/.m call to
a .h-declared method survives.
Still open (tracked on #1547/#1556): the file-level `#include` edge can stay
uncanonicalized when the project root isn't symlink-resolved (the extract()
id-remap `continue`s on a /var-vs-/private/var mismatch) — the class connection
above is robust to it; include-reachability candidate narrowing and ObjC
dynamic-dispatch/id-typed receivers also deferred (expected low ObjC recall, per
the research).
Reported by @c0dezer019 (#1547) and @JabberYQ (#1556).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A class declared in a header (Foo.h/@interface) and defined in its impl
(Foo.cpp/Foo.m/@implementation) fragmented into two nodes: _file_stem
drops the extension so Foo.h and Foo.cpp share a node id, which
_disambiguate_colliding_node_ids then split apart by path — and the two
"defs" tripped every resolver's single-definition god-node guard,
cascading into missing .h<->.m/.cpp linkage and cross-file/cross-language
edges.
- Routing: a `.h` using `#import` now routes to extract_objc (#1556 bridging
headers — extract_c drops `#import` as a preproc_call), and a `.h` with
C++-only signals (class/namespace/template/::/access-specifiers) routes
to extract_cpp (#1547 — the C grammar has no class_specifier, so a C++
header previously yielded a junk node and lost every method). ObjC sniff
keeps priority; a plain C header still routes to extract_c.
- Merge: a new _merge_decl_def_classes post-pass collapses the header/impl
id-collision onto the header (declaration) variant, modeled on
_merge_swift_extensions, gated so it fires ONLY for a clean sibling
header/impl pair (same dir, same base stem, exactly one header) — two
same-named classes in different directories have different stems and
never collide, so they are never merged (god-node guard verified). C++
method definitions retain their `Foo::` qualifier so a `Foo::bar` def
keys onto the header declaration (one method node, not two); free
functions keep their bare-name ids.
Result: one canonical class node per .h/.m or .h/.cpp pair with methods
unified, which unblocks the existing member-call resolvers (verified
Swift->ObjC calls and Swift `extension` folding now resolve). Strict
improvement over v8 (which produced junk/fragmented nodes here, verified).
Still open as follow-ups: cross-file C++ #include edge resolution and a
C++/ObjC cross-file member-call resolver (a pre-existing gap, not a
regression).
Reported by @JabberYQ (#1556) and @c0dezer019 (#1547).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
safishamsi