These land together because they are interleaved in extract.py/engine.py.
#2584 (PR #2588, thanks @phudayyy): the 0.9.38 dynamic-import dedupe keyed
only on target, so an in-function import() suppressed the file-level edge
affected follows. Dedupe now keys on the importing file, emitting one
file-level dynamic_import edge per file/target while keeping the call-site
edge.
#2586 / #2417 (PR #2586, thanks @EZZEASY): a Python member call on an
untyped receiver (x.get(...)) no longer binds by name to a same-named
module function. walk_calls now defers non-self/cls/super Python member
calls to the evidence-gated resolver; super().method() still resolves.
Known trade: same-file x = Thing(); x.method() loses its evidence-free
edge (precision over recall, per #2553).
#2589/#2591 resolver arm (in _resolve_objc_member_calls): the @protocol
exclusion and the self.field/_ivar receiver resolution (paired with the
objc.py extractor changes committed separately).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
These changes are interleaved across engine.py/extract.py by function, so
they land as one batch.
#2568 (thanks @imagineers-tyler): the 0.9.37 #2552 callback-body fix
unioned sibling closures' local names under the shared declaration, so a
local in one callback suppressed a real indirect_call in a sibling. Locals
are now scoped per body (keyed by body id, via walk_calls' extra_locals).
Restore-only, never fabricates; #2552 capture preserved.
#2565 (thanks @kskchaitanya1993): Kotlin property initializers — class,
top-level, companion, and `by lazy {}` — now seed call extraction, so
`val repo = createRepo()` produces a calls edge; literal initializers
produce none; FQ calls compose with the #2550 resolver.
#2561 (thanks @fakewaffle): Swift receiver typing now handles
`@Environment(Store.self)` (whitelisted; @Query/keypath/dotted skipped to
avoid a wrong edge) and in-corpus factory bindings via a marked concrete
return type; opaque/array/out-of-corpus returns stay unresolved.
#2577 (thanks @wilyan09007, PR #2579): the SQL extractor no longer emits a
reads_from edge to a CTE name. WITH names are scoped per query (a subquery
CTE no longer suppresses an outer real table of the same name), so a CTE
no longer mints a bare stub that binds to an unrelated same-named symbol.
#2575 (thanks @phudayyy, PR #2574): a dynamic `import('…')` inside a nested
function or at module scope now produces an edge, dynamic_import is
included in affected, and calls inside nested named functions are
collected; a dynamic import already captured as a deferred imports_from is
not double-counted.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#2543 (adopts PR #2546, thanks @michaelxer): a failed extraction is no
longer stamped in the incremental manifest as up-to-date, so graphify
update retries it instead of skipping it forever; a manifest already
poisoned by the old behavior is healed on the next run; genuinely
unchanged files are not re-processed. Extended to the watch save_manifest
paths too.
#2554 (adopts PR #2555, thanks @annieyii): the claude-cli backend now
inspects the stdout envelope for an is_error result (e.g. a rate limit
returned with exit code 0) and raises it on both the zero and non-zero
exit paths, instead of parsing it as an empty success and bisecting
against a live rate limit.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The Windows skill variant had a PowerShell Step 1 but its later steps came
from the shared core fragment as bash-only shell (cat-piped interpreter
invocations, rm -f, find -delete). The skillgen renderer now translates the
composed core to PowerShell for powershell-shell platforms (here-string
interpreter invocations, Remove-Item cleanup); POSIX skills are unchanged
and step / #2490 parity is enforced by a generator check. Not a regression
from 0.9.35 (skill files were unchanged between 0.9.34 and 0.9.35).
Thanks @tannermosher2015-debug.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#2508 (thanks @Tomaskobel): callflow loads the graph directed and recovers
direction from _src/_tgt markers (consistent with the path fix), so
caller/callee columns are correct; indirect calls are now counted.
#2507 (thanks @filipechagas): relational-intent verbs (calls/uses/extends/
...) are excluded from the per-term seed guarantee, so a decoy matching
only the verb no longer becomes a traversal root, while a verb that is a
real symbol name can still be seeded on merit.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#2486 (thanks @adminwat): normalize dict-shaped hyperedge members to ids
(or drop with a warning) so a malformed hyperedge can't abort a completed
merge with a TypeError.
#2484 (thanks @sortakool; approach from @oleksii-tumanov's #1691):
merge-graphs relabels hyperedge member ids and ids with the repo prefix,
unions both inputs' hyperedges instead of clobbering, and writes both
persistence slots.
#2485 (thanks @sortakool): build_from_json reads hyperedges from the
top-level and nested slots; a full validation wipeout is reported loudly.
#2490 (thanks @PapiScholz): the skill Step-5 flow passes curated
community_labels to to_json, so graph.json ships community_name.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#2411 (thanks @JensD-git): key the C# partial-class merge on assembly
(nearest ancestor .csproj/.fsproj/.vbproj) in addition to namespace and
name, so same-name partial classes in different assemblies stay distinct
while genuine partial halves within one project still merge. Fixes a
0.9.32 regression from #2332.
#2437/#2438 (thanks @aryanbonigala, builds on PR #2439): incremental
rebuilds no longer drop member-call and indirect_call edges from a
changed file into an unchanged target. Re-resolution now sees the
unchanged corpus (nodes, contains/method edges, and _callable markers,
which now persist to graph.json like _origin); edges to a genuinely
removed target are still evicted.
#2444/#2445 (thanks @Baziar, builds on PRs #2461/#2458): a
BrokenProcessPool triggers the sequential fallback instead of being
swallowed per future, a failed worker file is retried sequentially
rather than merged as empty, and a whole-pass AST failure on a fresh
build exits non-zero instead of writing a zero-node graph
(--allow-partial opts into a best-effort partial graph).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
mcp 2.0 removed the low-level decorator API the server was built on and
changed several models. _build_server now defines the four handlers as
plain coroutines and binds them at the end in a version-aware way: the
@server.list_tools()/... decorators on 1.x, the on_list_tools=/...
constructor callbacks (with explicit ListToolsResult/CallToolResult/
ListResourcesResult/ReadResourceResult wrapping) on 2.x. Model diffs
handled: Tool.inputSchema is input_schema on 2.x (constructor aliases
work on both, attribute access does not); Resource.uri is a plain str
on 2.x and rejects AnyUrl instances, so resource URIs are passed as
strings (1.x coerces them). The 2.x server also reports graphifyy's own
version in serverInfo. Extras relaxed from mcp>=1,<2 to mcp>=1,<3.
Verified: full stdio handshake (initialize / tools/list / tools/call /
resources/list / resources/read) and the tests in test_serve.py +
test_serve_http.py (145 passed) under BOTH mcp 1.29.0 and mcp 2.0.0.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
mcp 2.0.0 dropped mcp.types.AnyUrl and the Server decorator-registration
API graphify/serve.py relies on, so an unpinned resolve broke graphify-mcp
on every fresh graphifyy[mcp]/[all] install. Cap mcp>=1,<2 (resolves 1.29.0)
and starlette>=1.3.1,<2 in both extras; re-lock. Bump to 0.9.30. Porting to
the mcp 2.x API is a tracked follow-up.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Apache 2.0 adds an explicit patent grant, a patent-retaliation clause,
and explicit inbound-contribution terms. MIT's sublicense right permits
relicensing the combined work, so this needs no per-contributor consent;
prior contributions were made under MIT and remain available under those
terms. The original MIT text is retained in LICENSE-MIT and referenced
from NOTICE.
- LICENSE: verbatim Apache License 2.0
- LICENSE-MIT: preserved MIT text for prior contributions
- NOTICE: attribution + pointer to LICENSE-MIT
- pyproject: license = "Apache-2.0" (PEP 639 SPDX), license-files, setuptools>=77
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The .graphifyinclude loader and its two matcher helpers had no consumers:
commit df40e4d (#873, index dot dirs) removed the blanket dot-prefix
exclusion and with it the only call sites, leaving detect() parsing the
file on every run and then discarding the result. A .graphifyinclude was
silently a no-op.
Delete _load_graphifyinclude, _is_included, _could_contain_included_path
and the orphaned assignment; add .graphifyinclude to _SKIP_FILES so a
leftover file no longer lands in unclassified; and print a one-time
stderr note when one is present at the scan root, pointing to ! negation
patterns in .graphifyignore. Bump to 0.9.25.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Homepage/Repository/Issues were stale from the org move (safishamsi/graphify).
Aligning them to Graphify-Labs/graphify fixes the PyPI "Issues" link and is a
prerequisite for PyPI to mark the Repository link Verified once releases publish
via a GitHub trusted publisher.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Agents routinely ignore the advisory "run graphify query first" nudge and read
raw files anyway. `graphify install --project --strict` (or `graphify claude
install --strict`) now installs a hook that BLOCKS the first raw source read of a
session via permissionDecision:"deny" with a redirect to graphify query, then
downgrades to the soft nudge — it fires at most once per session (atomic
per-session marker) so it can never strand the agent, and a recent
query/explain/path refreshes a stamp that suppresses it. Claude Code only;
Bash-grep and Glob stay nudge-only; Gemini/Codex/OpenCode are unchanged.
GRAPHIFY_HOOK_STRICT=1/0 toggles at runtime without a reinstall; default installs
are byte-identical (soft nudge).
Also fixes#1840 for the default soft nudge: the guard no longer fires for reads
of out-of-project files, and softens to a non-mandatory nudge when the graph is
stale for the target file. Gating is ~3 stat calls (no corpus walk) and fails
open. Begins the 0.9.19 cycle.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Bumps to 0.9.17 (unreleased) and records the batch implemented via Fable
subagents in isolated worktrees, integrated onto v8: out-of-scope node
drop, manifest stamping, merge-driver registration, hooksPath configparser
fix, obsidian prune, multilingual query stopwords, .skill classification,
and the postgres package-name hint.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The #1757 batch-scoping followup built the per-chunk allowlist by reading
FileSlice.rel, which does not exist (a FileSlice carries its parent file
in .path). So every chunk containing a sliced oversized document leaked
the FileSlice object into the allowlist, save_semantic_cache raised
TypeError on Path(FileSlice), and the best-effort except swallowed it:
extraction finished but those chunks were never checkpointed, so a
re-run or a crash/rate-limit resume re-billed them.
Resolve each unit through the canonical unit_path() helper so a slice
maps to its parent file. Adds a regression test that slices a real
oversized .md and asserts the checkpoint writes without swallowing a
TypeError.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The HTML report's neighbor "focus" links dropped an unescaped
JSON.stringify(nid) into a double-quoted inline onclick. The stringified
value carries its own quotes, so the attribute was truncated on every
node (links never worked), and a node id/label containing a double-quote
broke out of the attribute and injected live event handlers. AST ids are
[a-z0-9_]-safe, but ids/labels from documents or titles scraped via
`graphify add <url>` are not, so a hostile source could plant an
executable handler into a locally-opened report.
Carry the id in an HTML-escaped data-nid attribute and dispatch via one
delegated listener bound to document (survives the innerHTML rebuild that
recreates #neighbors-list). Closes the injection and repairs the links.
Reported by @edgestack-ai.
Co-Authored-By: edgestack-ai <edgestack-ai@users.noreply.github.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A solution folder is a virtual grouping, not a file: VS writes its name
as both the display name and the "path" (name == path, no real file).
extract_sln resolved it to an absolute filesystem path anyway and keyed
the node id off that. The CLI id-relativization pass only remaps ids of
real files in the scan set, so a virtual folder never matched and its
absolute id (with the local username) survived into a committed
graph.json.
Detect solution folders (name == path) and key their id/source_file off
the folder name only; real project files still resolve as before. Adds a
regression test asserting the folder node id is relative.
The earlier fix (0.9.13) covered .csproj/.sln file nodes but missed the
virtual folders, so #1789 was closed prematurely; this completes it.
Reported and diagnosed by @fremat79.
Co-Authored-By: fremat79 <fremat79@users.noreply.github.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
_rewire_unique_stub_nodes gated merge targets through _is_type_like_definition,
which rejects any label ending in `)`. So a function referenced from another
module (passed by name, e.g. FastAPI's Depends(get_db)) left its reference edge
dangling on a sourceless name-only stub while the real def had zero incoming
edges — "who references this function" returned nothing. Class/type symbols were
fine; only functions/methods suffered.
Top-level function defs (label `name()`, not `.name()` methods or `Class.m()`
qualifiers) are now eligible rewire targets, but only when:
- the label key matches exactly one such function corpus-wide (existing
unique-candidate guard — two same-named functions stay unresolved), AND
- the candidate shares a language family with the stub's referrers, so a
Python `get_db` reference can't bind to a unique Go `get_db()` (#1718/#1749
interop guard), AND
- the stub is not used as a supertype (inherits/implements/extends) — you
don't inherit from a function.
Types are unchanged. Regression tests: cross-module function ref binds to def;
cross-language, ambiguous, and supertype cases all correctly left unresolved.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Two classes with the same simple name in different Maven modules
(FinancialEntryValidator in payment/ and core/) already survive as distinct
path-scoped nodes on v8 -- the "node silently disappears" report from 0.9.9 is
fixed. But a cross-module field/type `references` edge was still left dangling
on a sourceless phantom stub: _resolve_java_type_references (#1318) re-pointed
implements/inherits/extends/imports edges to the real definition using the
importing file's `import` statement, but its REPOINT_RELATIONS omitted
`references`, so bare-name resolution's shadow stub survived for field types.
A query about the referenced class could then miss it.
Add `references` to the Java resolver's REPOINT_RELATIONS. The C# sibling
already covers references; this brings Java to parity. The reference now
resolves to the imported package's class (falling back to same-package), and
the orphaned phantom is dropped. Regression test covers the ambiguous
two-module case: both reals present, no phantom, reference lands on the
imported class.
Reported with a precise root-cause and repro by @aviciot.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Decompose extract.py / __main__.py / export.py into focused modules (#1737,
verbatim, no behavior change). Plus fixes since 0.9.10: merge-graphs distinct
repo tags (#1729), uninstall cleans Claude .local files (#1731), and
extract --code-only for keyless code-only indexing of a mixed repo (#1734).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
setuptools uses an explicit package list, so the new graphify/exporters/ package
(base, html, graphdb — split out of export.py) was absent from the built wheel,
which would break `import graphify.exporters.*` for installed users. Add it
alongside graphify and graphify.extractors. No version change.
Verified: fresh-venv install of the rebuilt wheel imports every new module,
resolves all backward-compat re-exports, builds a multi-language graph, and runs
query/path/explain and install/uninstall.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Correctness batch since 0.9.9: TS/JS builtin-typed receiver no longer collapses
onto a same-named user symbol (#1726); no cross-language calls edges (#1718);
build_merge ambiguous-alias no longer merges unrelated files (#1713); base-class
stubs tagged with origin_file (#1707); Java enum constants as nodes (#1719);
rebuild recovers from a deleted hook cwd (#1703); per-chunk semantic-cache
checkpoint (#1715); SECURITY.md http-transport doc + GRAPHIFY_MAX_GRAPH_BYTES
tests (#1714, #1722). Nine merged PRs plus #1726.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Fixes since 0.9.8: explain punctuated-label matching (#1704); surface code files
with no AST extractor instead of dropping them silently (#1689); consistent
AST-extraction progress denominator (#1693); no dangling Obsidian wikilinks in
GRAPH_REPORT.md by default (#1712); MATLAB .m no longer force-parsed by the
Objective-C grammar (#1702); corrected the /graphify usage comment in the skill
files (#1681); surface unclassified files (Dockerfile/Makefile/...) instead of
vanishing (#1692).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
extract_pascal() already imports tree-sitter-pascal for AST-quality
extraction and falls back to a regex extractor when it is absent (#781),
but the grammar was not declared anywhere in the package metadata, so it
was never installed and the AST path never ran out of the box.
Declare a `pascal` extra (and add it to `all`) so users can opt into the
AST extractor with `uv tool install "graphifyy[pascal]"`. tree-sitter-pascal
publishes prebuilt wheels for every platform (win/macOS/Linux), so unlike
the `dm` extra it needs no C toolchain.
On a mid-size Delphi codebase the AST path yields notably more accurate
relationship edges than the regex fallback (calls and inherits both up
~25%). README extras table and uv.lock updated accordingly.
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>
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>
Ruby type-aware member-call resolution and workspace exports-map
resolution, the #1529 alias/workspace import-edge regression fix, tsconfig
paths fallbacks, semantic-cache pruning, three ObjC extractor fixes, Swift
static-call confidence, the secondary LLM timeout, GraphML null coercion,
host-generic install wording, and Dependabot dep bumps. See CHANGELOG.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
`safety` was declared in the dev group but never invoked — the CI
security-scan job only runs bandit and pip-audit, and pip-audit already
provides the same dependency-CVE scanning. Its only practical effect was
pulling in nltk, which carries an unpatched HIGH path-traversal advisory
(GHSA-p4gq-832x-fm9v) with no fix available.
Removing safety drops nltk (and safety-schemas/typer/tenacity/tomlkit)
from the lockfile entirely, closing the alert with no loss of coverage.
Updated the stale CI comment that referenced safety. Full suite green
(2537 passed); pip-audit and bandit unaffected.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Patch over 0.9.0: completes the node-ID work (fully closes#1504 via injective
salt #1522), stops origin_file leaking into graph.json (#1516), extends cross-file
stub disambiguation to the six dedicated extractors (#1515), Java type-param skip
(#1518) + record component refs (#1519), prunes a deleted import's edge on update
(#1521), and retries rate-limited (429) requests instead of dropping chunks (#1523).
All non-breaking.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
BREAKING: node IDs now include the full repo-relative path (#1504, #1509) — fixes
silent data loss when same-named files live in different directories, and aligns
the AST and LLM id rules. Existing graphs migrate automatically on next build;
`graphify extract --force` to recover previously-collided nodes; Neo4j persisted
stores need a re-import. Also ships the --timing flag (#1490).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
