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>
The graph_has_legacy_ids nudge flagged fresh v9 graphs that contain Go code,
because the Go extractor scopes a type node by package directory
(_make_id(pkg_dir, name) -> "sub_thing"), which coincides with the OLD one-parent
file-stem form of pkg/sub/thing.go even though it's a current, by-design
package-scoped id (methods on a type across files in a package share one node).
The detector now inspects only file-level nodes (source_location "L1"), whose id is
unambiguously the file stem and which the migration actually re-keys. This still
catches a genuine pre-#1504 graph (its file nodes carry the old stem) while leaving
package/dir-scoped symbol ids alone. Verified end-to-end: a fresh Go graph no longer
triggers the rebuild nudge; a real legacy graph still does.
The migration itself was already correct — file nodes and Python/AST symbols
migrate to full-path ids; Go's package-scoped type ids are intentional and
unaffected. This only fixes the over-eager warning.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Two pre-0.9.0 safety to-dos from the migration spike:
1. Auto-detect-and-warn: graph_has_legacy_ids() samples a loaded graph's node ids
and detects the pre-#1504 (parent-dir/filename) scheme. Read-only consumers that
don't re-extract — `graphify query` and the MCP serve loader — now print a
one-line nudge to rebuild with `extract --force` when they load an old graph.
Fires only on legacy graphs (verified: canonical graphs stay silent).
2. Re-key source_file contract: pinned with tests that a relative source_file is
migrated to the full-path id while an absolute/unrelativizable one is skipped
(its on-disk path must never leak into a persisted id). The is_absolute() guard
already enforced this; the tests make the contract explicit.
Full suite 2507 passed. Lands on v9.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Rigorous testing surfaced the nuance: the ID-format migration is automatic, but
same-named files that already collapsed into one node under the old rule are only
recovered as distinct nodes by a fresh extract --force (migrating an already-
collided graph/cache can't resurrect already-dropped nodes; edges referencing a
shared old id are ambiguous). Fresh extraction yields distinct nodes as expected.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
BREAKING node-ID format change. The stem that prefixes every node id was the
immediate parent dir + filename, so same-named files in different directories
collided into one last-writer-wins node and silently dropped graph content
(docs/v1/api/README.md and docs/v2/api/README.md both -> api_readme). The stem is
now the full repo-relative path (docs_v1_api_readme vs docs_v2_api_readme);
top-level files are unchanged (setup.py -> setup).
- extractors/base.py::_file_stem -> full path (as_posix; make_id collapses
separators). The two hand-copied stems (symbol_resolution, mcp_ingest) now
import the canonical one, so they can't drift again.
- llm.py system prompt + extraction-spec fragments aligned to the same rule,
fixing the #1509 AST<->LLM divergence (prompt used zero parent dirs -> ghosts).
Regenerated + blessed the per-host specs.
- build_from_json deterministically re-keys every non-AST node id from its
source_file via the new stem (and registers old-stem aliases), so a cached or
pre-migration semantic fragment carrying an old short id reconciles with the
AST node instead of spawning a ghost. The semantic cache is unversioned, so
this code-side re-key (not LLM prose) is what makes it survive the format change
with no re-bill. AST nodes are already canonical and skipped.
- Migration: existing graphs migrate automatically on the next build/update (the
re-key runs in build_from_json, including the whole graph fed back through
build_merge); `graphify extract --force` for a clean rebuild. Neo4j persisted
stores need a re-import; GraphML layouts go stale.
Full suite green (2505 passed); #1504 collision fixed and old-id fragments
re-keyed verified by smoke. Lands on v9 for review before a 0.9.0 release.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Adds an opt-in --timing flag that prints per-stage wall-clock timings to stderr so
slow stages are visible on large corpora. extract reports detect / AST extract /
semantic extract / build / cluster / analyze / export (and write on --no-cluster);
cluster-only reports load / cluster / analyze / label / report / export; both end
with a total. A small _StageTimer helper uses monotonic perf_counter.
Off by default and stderr-only, so default output and machine-read stdout/graph.json
are byte-identical (the extract arg loop already swallows unknown flags). Added a
regression test asserting the lines appear with --timing and are absent without it.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The --obsidian-dir flag was undocumented in the README. Add it to the command
list with a note that exporting into an existing vault never overwrites the user's
own notes or .obsidian config (the guard shipped in 0.8.51).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
to_obsidian wrote one note per node straight into the target directory and
unconditionally replaced .obsidian/graph.json. Pointing --obsidian-dir at a real
vault could therefore clobber a user note whose name matched a graph node
(Database.md) and destroy the user's graph-view settings — silently, no backup,
irreversible.
graphify now records the files it owns in .graphify_obsidian_manifest.json and
refuses to overwrite any pre-existing file it didn't create: such a file is skipped
and reported in a single aggregated warning. A re-run still updates graphify's own
notes (they're in the manifest), and .obsidian/graph.json is only written when it
doesn't already exist or graphify owns it. The default graphify-out/obsidian output
and the flat note layout are unchanged.
Added regression tests: existing-vault preserves user note + .obsidian settings,
empty dir still gets the full vault, and a re-run updates own notes but not a
user-added file. The CHANGELOG also records the @oleksii-tumanov Java fixes
(#1512/#1510) and the @nuthalapativarun Windows GBK fix (#1505) committed just prior.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
On Windows where claude.cmd emits GBK/cp936 bytes, the claude-cli subprocess
decoding raised UnicodeDecodeError and crashed extraction. Both claude-cli
subprocess.run sites (_call_claude_cli and the claude-cli branch of _call_llm) now
pass errors="replace", so incidental non-UTF8 console chatter decodes to
replacement chars instead of crashing — the structured JSON payload (ASCII/UTF-8
on stdout) is unaffected. capture_output=True means the single errors= covers both
stdout and stderr.
Ported from PR #1507 by @nuthalapativarun (dropped an unrelated .gitignore change).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A generic parent — `class Foo extends Bar<T>` or `implements List<T>` — is a
`generic_type` node in the tree, but the inheritance extractor only fired on a
bare `type_identifier`, so those inherits/implements edges were silently dropped.
The parent type is now unwrapped to its base (`Bar<T>` -> `Bar`) for the
inherits/implements edge, and the type arguments are emitted as `generic_arg`
references.
Ported from PR #1511 by @oleksii-tumanov. Known pre-existing limitation (not
introduced here, worth a separate follow-up): the extractor has no type-parameter
tracking, so a bare parameter like `T` in `extends Container<T>` still produces a
`generic_arg` reference to `T`; the inherits/implements edge itself always targets
the real base type, never `T`.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Java `enum` and `@interface` (annotation) declarations weren't in _JAVA_CONFIG's
class_types, so they were never emitted as type nodes — a field typed as an enum or
a class annotated with a project annotation referenced a node that didn't exist
(dangling). enum_declaration and annotation_type_declaration are now extracted as
first-class (sourced) type nodes, so those references resolve onto them.
Ported from PR #1513 by @oleksii-tumanov.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A path query like `explain "app/api/route.ts"` tokenized to terms that matched no
node, so explain/affected returned "No node matching". Source-file paths are now
part of the search index and matched exactly (serve._find_node gains a leading
source-exact tier; affected.resolve_seed gains a source-file match). When several
nodes share a source_file (e.g. a file-level node plus a function node), the lookup
prefers the file-level node — the L1 node whose label basename matches the queried
filename, falling back to the unique L1 or unique basename match, else None.
Ported from PR #1503 by @behavio1. Maintainer fixes on top: aligned trailing-
separator handling between resolve_seed and _find_node (affected previously
returned None for a trailing-slash path that explain resolved), corrected the
stale "three-tier" _find_node docstring, and added regression tests for the
trailing-slash parity and the ambiguous-no-file-node -> None case.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Documents two expected uv behaviors that read as bugs on macOS: (1) uv tool
install puts `graphify` in ~/.local/bin which a fresh zsh shell may not have on
PATH (run `uv tool update-shell`); (2) `uvx graphify` fails because the package is
`graphifyy` and `graphify` is only its console script — use
`uvx --from graphifyy graphify install`. README install note + Troubleshooting.
Ported from PR #1474 by @TPAteeq. Maintainer fix on port: moved the CHANGELOG
entry from the already-released 0.8.50 block (where the stale base placed it) into
the current Unreleased section.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The README showed `global add graph.json myrepo` (positional tag) writing to
`~/.graphify/global.json`. The real CLI takes the tag via `--as` (the positional
was silently ignored) and the file is `~/.graphify/global-graph.json`. Corrected
to `global add graph.json --as myrepo`.
Ported from PR #1489 by @MikeKatsoulakis.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Two files that both import and use the same type as a bare name (e.g.
`from pathlib import Path` used as a type hint in a.py and b.py) collapsed into one
node, even with no project definition to anchor them. The referencing file is now
recorded in an internal `origin_file` field and used as the disambiguation key when
_disambiguate_colliding_node_ids splits same-id nodes — while source_file stays
empty, so the corpus-level rewire still collapses these stubs onto a real project
definition when one exists (the #1402 path is untouched). origin_file is read only
inside disambiguation; the rewire and the Java/C# type resolvers key off
source_file as before.
Ported from PR #1479 by @jiangyq9 (squash-merged onto current v8; the branch's
stale base made the raw diff appear to revert later features — the 3-way merge
applies only the surgical origin_file change). Resolved a test-adjacency conflict
with #1500 by keeping both cross-file tests.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Adds _resolve_csharp_type_references (graphify/extractors/csharp.py), the C#
counterpart to _resolve_java_type_references. It re-points dangling
inherits/implements/references edges from no-source shadow stubs onto the real
definitions, disambiguating same-named types across namespaces using the
referencing file's `using` directives + enclosing namespace; ambiguous matches
are refused (unique-hit guardrail), not guessed. Runs after id-disambiguation and
the sourceless-stub rewire, on the ambiguous remainder, behind a log-and-skip
try/except. _CSHARP_CONFIG is broadened to extract enum/struct/record as type
definitions so references to them resolve too.
Ported from PR #1466 by @TheFedaikin. Known follow-up: types declared in
nested/multiple namespaces in one file aren't registered as targets yet (fails
safe — under-resolves to a stub, never mis-resolves). Advances #1318 for C#.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Go's ensure_named_node emitted a SOURCED stub for a cross-file type reference,
unlike the generic/ObjC/Java extractors which emit sourceless ones. A sourced stub
bakes the referencing file's path into the node id at disambiguation time, which
blocks the corpus-level rewire from collapsing it onto the real definition — so a
type defined in one Go file and referenced from two others produced three nodes
(the real def plus two phantom per-file duplicates). Go now emits a sourceless
stub like the other languages, so the rewire collapses them to a single node.
Ported from PR #1501 by @TPAteeq. Closes the #1402 gap for Go.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
`graphify label --missing-only` restricts LLM labeling to communities that are
unnamed or still hold a `Community N` placeholder, preserving existing
non-placeholder labels read from .graphify_labels.json and merging new labels over
them. Lets a large graph be relabeled incrementally without re-naming (and paying
for) communities that already have good names.
Ported from PR #1481 by @jiangyq9. This supersedes the earlier #1421 by
@matiasduartee, which proposed the same flag — credit to @matiasduartee for the
original; #1481 is written against the current label signature (post-#1390
max-concurrency/batch-size) and merges clean, where #1421 had drifted.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Metal Shading Language is C++14, so .metal files are classified as code and routed
through the existing C++ extractor, mirroring the CUDA .cu/.cuh reuse. Also adds
.cu/.cuh/.metal to build.py's _LANG_FAMILY map (they were all missing), so the
cross-language phantom-`calls`-edge filter treats them as C++. README language
table updated.
Ported from PR #1480 by @jiangyq9. This supersedes the earlier #1450 by
@GoodOlClint (same .metal -> C++ approach and fixture) — credit to @GoodOlClint
for the original; #1480 additionally closes the CUDA family-map gap and updates
the docs, and merges clean against current v8.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
to_wiki emitted Obsidian `[[Title]]` wikilinks. Outside Obsidian `[[Domain Data
Models]]` resolves to a literal "Domain Data Models.md", but the article file is
the slugged "Domain_Data_Models.md", so nearly every community/god-node link
opened an empty page; god-node articles also linked node-level neighbors that
never get an article file, so those were dead even inside Obsidian.
Links are now standard `[display](slug.md)` with the target URL-encoded (spaces,
&, parentheses, # survive in CommonMark and Obsidian alike); a link whose target
has no article is rendered as plain text instead of left dangling. A label->slug
resolver is built up front so a link points at the real on-disk filename incl. the
case-fold collision suffix.
Ported from PR #1465 by @TPAteeq. Maintainer edit: trimmed the CHANGELOG wording
that overstated the guarantee ("always matches ... collision suffix and all") —
two articles sharing a byte-identical label still keep the first slug (pre-existing
behavior, same as the old [[label]]), so the claim is scoped to the case-fold case.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Some OpenAI-compatible gateways default to SSE streaming when `stream` is omitted,
but graphify always reads the result as a single resp.choices[0]. The call would
then fail against those gateways. Pass `stream: False` explicitly.
Ported from PR #1482 by @jiangyq9 (covers the extraction dispatch path,
_call_openai_compat). Maintainer fix on top: applied the same `stream: False` to
the second OpenAI-compatible call site, _call_llm, which feeds the --dedup-llm
tiebreaker and had the identical bug.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Annotations on Java classes/interfaces/records (e.g. @Service, @Entity) produced
no edge, so type-level framework wiring was invisible even though method-level
annotations were already captured. The class/interface/record handler now emits
`references` edges with the existing `attribute` context, reusing the renamed
`_java_annotation_names` helper (was `_java_method_annotation_names`; logic
unchanged) at both the type and method call sites.
Ported from PR #1487 by @oleksii-tumanov. Resolved an additive test conflict with
#1485 by keeping both new test functions.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Java field declarations produced no `references` edge for their type, so a class's
data dependencies (its field types) were missing from the graph even though
parameter and return types were already captured. The field handler now collects
the declared type via the same `_java_collect_type_refs` helper used elsewhere,
preserving the `field` and `generic_arg` contexts and skipping primitives
(int/boolean/etc.), matching the existing C#/PHP/Kotlin field handlers.
Ported from PR #1485 by @oleksii-tumanov.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A detailed report (#1475) showed the ObjC extractor silently dropping ~60% of
code-level relationships. Five fixes:
1. Dispatch: ObjC `.h` headers were parsed by extract_c (1 node, 0 edges, losing
every @interface/@protocol/@property/method). _get_extractor now routes a `.h`
to extract_objc when it contains an ObjC-only directive
(@interface/@protocol/@implementation/@import) — these are illegal in C/C++, so
the sniff never hijacks a genuine C/C++ header (verified: a plain C/C++ `.h`
stays on its existing extractor).
2. Calls: the method-body pass produced zero `calls` edges because it matched
child types `selector`/`keyword_argument_list`, but tree-sitter-objc tags
selector parts with the field name `method` (type `identifier`). The selector
is now reconstructed from every `method`-field child, explicitly skipping the
`receiver` field — so self/super/ClassName receivers are never mistaken for a
selector, and compound sends ([self a:x b:y]) resolve too. (Avoids the report's
suggested `"identifier"` fix, which would have matched receivers as selectors.)
3. Generic property types: NSArray<Product *> * wraps the type in a
generic_specifier, so the old direct-type_identifier scan saw nothing. The
element (Product) and container (NSArray) are now both referenced.
4. Class methods: `+ (…)shared` was labeled -shared; the +/- sigil is now read
from the method node's first child.
5. @import: `@import Foundation;` (a module_import node) now emits an imports edge.
Dot-syntax property `accesses` (Bug 5) and @selector(...) target-action edges
(Bug 6b) need type/name resolution policy and are left as follow-ups. Added six
regression tests; the reporter's claim that compound messages lack a
message_expression wrapper (Bug 6a) was checked against the real AST and refuted —
they share Bug 2's root cause, fixed by the same field-name change.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Builds on the initial XAML support (#1460). Resolves a view to its ViewModel from
an explicit <Window.DataContext><vm:MainViewModel/>, a design-time
d:DataContext="{d:DesignInstance Type=...}", the View->ViewModel naming
convention, or Prism ViewModelLocator.AutoWireViewModel="True". Resolution is
always against an actually-extracted C# class node, so a name matching no class
(or an ambiguous 2+) emits no edge -- explicit DataContext is EXTRACTED,
convention/Prism are INFERRED. Also extracts binding paths ({Binding User.Name},
Path=Order.Total), commands (Command="{Binding SaveCommand}"), converters, and
CommunityToolkit [ObservableProperty]/[RelayCommand] generated members.
The #1460 event-handler hardening is preserved unchanged: events still resolve
only to methods with a .NET (object sender, ...EventArgs e) signature, and the
free-form-attribute denylist still prevents values like Content="Save" from
fabricating event edges (both regression tests still pass). ViewModel discovery is
bounded to the active extraction root.
Ported from PR #1473 by @MikeKatsoulakis (clean 3-way merge onto current v8).
Maintainer fix on top: the CommunityToolkit member reader now reads the
code-behind with errors="replace", so a non-UTF8 ViewModel .cs can't raise
UnicodeDecodeError and abort extract_xaml (matches every other reader in the
module). Added a regression test for that case.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
.vue files were dispatched to extract_js, which picks a tree-sitter grammar by
suffix. .vue is neither .ts nor .tsx, so the whole SFC -- <template> markup,
<script>, and <style> -- was fed to the JavaScript grammar, producing a top-level
ERROR node and recovering no imports, symbols, or type references.
A dedicated extract_vue masks everything outside <script> (replacing it with
spaces so symbol line numbers stay accurate) and parses just the script with the
grammar named by `lang` (ts default; tsx/js/jsx honored). .vue also joins the
cross-file symbol-resolution pass now that it parses cleanly.
Ported from PR #1468 by @papinto. Maintainer fix on top: the <script> open-tag
scan now skips over quoted attribute values, so a `>` inside one (Vue 3.3+ generic
components, e.g. generic="T extends Record<string, unknown>") no longer ends the
tag early and swallow the body. Added a regression test for that case.
(CHANGELOG also records #1470, committed just prior.)
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
graphify reflect renders LESSONS.md from the memory docs and the
.graphify_analysis.json / .graphify_labels.json sidecars, but reflect --if-stale
only stat'd the memory docs and graph.json. So after community analysis or labels
changed (without the graph changing), --if-stale wrongly reported lessons fresh and
skipped the regen, leaving LESSONS.md stale. The freshness check now also stats the
analysis and labels sidecars, using the same custom --analysis / --labels paths the
run itself uses (so the check and the run can't disagree about which files matter),
and treats a missing sidecar as not-an-input. This makes the documented "no-op when
LESSONS.md is newer than every input" contract actually true.
Ported from PR #1470 by @oleksii-tumanov.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The Read|Glob PreToolUse hook (the "run graphify first" nudge, shared by the
Claude Code and CodeBuddy installers via _READ_SETTINGS_HOOK) decided whether to
nudge by substring-scanning the joined file_path/pattern/path for known
extensions. That had two opposite failures: '.js' is a substring of '.json' so
package.json / tsconfig.json spuriously fired, and .astro/.vue/.svelte weren't in
the set so Astro/Vue/Svelte projects never nudged on their primary source type.
The hook now compares each value's real trailing extension (segment after the
last '/', then after the last '.') against the set, and adds .astro/.vue/.svelte.
package.json -> tail .json (silent); **/*.astro -> tail .astro (fires); an
extension on a directory component (my.ts/file) correctly stays silent. The
graphify-out/ suppression and fail-open behavior are unchanged.
Ported from PR #1464 by @marketechniks onto current v8. Added three regression
tests on top of the PR's (multi-dot a.test.tsx / foo.min.js, a Windows backslash
path, and the directory-extension trap) to pin the trickiest parts of the new
segment-split logic.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Hermes and the other AGENTS.md hosts (Codex, Aider, OpenClaw, Droid, Trae, ...)
run the graphify CLI directly and do not dispatch subagents. The Step 3 extraction
guidance only described the no-API-key path as "fall straight through to subagent
dispatch", so on `/graphify .` those agents had no path they could take, fixated on
the GEMINI/ANTHROPIC key language, and looped for minutes insisting on a missing key
before eventually proceeding (a pure-code corpus is AST-only and needs no key at all).
Step 3 now opens with a hoisted, host-agnostic statement -- graphify needs no API
key, never prompt for one, never block on one; code is AST-only; a code-only corpus
skips semantic extraction entirely -- and the no-key fallback now spells out a
terminal-only path (write the empty semantic file and continue, or extract content
inline) instead of assuming subagent dispatch.
Applied in the shared core fragment and in the aider/devin core variants, so all 16
skill bodies carry it; the aider/devin change is registered as a sanctioned
monolith-roundtrip diff. Regression test (test_extraction_states_no_api_key_required_
for_every_host) renders every host and pins the wording, ordering, and the
non-subagent fallback so this can't silently regress.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Makes .xaml a first-class code input. extract_xaml() uses stdlib XML (no new
parser dependency) behind the same DOCTYPE/ENTITY and size guards as the .csproj
extractor, and captures: the root element, named controls (x:Name/Name) and their
control types, {Binding ...} references, x:Class, and -- the useful part -- a
bridge from the view markup to its .xaml.cs code-behind by resolving event-handler
attributes to the matching methods on the partial class.
Ported from PR #1460 by @MikeKatsoulakis onto current v8.
Maintainer hardening on top of the original PR: event resolution is now gated so
it can't fabricate edges. The original matched any attribute value against
code-behind method names, so Content="Save" next to a business method Save(), or
Tag="<a-handler-name>", produced spurious "event" edges. Resolution now requires
(a) the attribute is not a known free-form/identity property (Content, Text, Tag,
Title, ToolTip, Header, ...), (b) the value is a bare identifier, and (c) the
matched method actually has the .NET event-handler signature
(object sender, <T>EventArgs e) -- read from the code-behind source since the C#
extractor does not record parameter lists on method nodes. Added regression tests
for both false-positive cases.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The kimi, gemini, and deepseek backends hardcoded their base_url, so users
behind an OpenAI-compatible proxy/gateway or running a self-hosted relay had no
way to redirect them (unlike ollama/openai, which already read *_BASE_URL). Each
backend now reads KIMI_BASE_URL / GEMINI_BASE_URL / DEEPSEEK_BASE_URL and falls
back to its official default when unset, so behavior is unchanged for anyone who
doesn't set the variable.
Ported from PR #1458 by @jc2shile onto current v8. The PR branch carried 624
unrelated files from a stale base; this lands just the clean 16-line llm.py
change. Added subprocess-based tests covering both the override and the default
for all three backends (BACKENDS reads the env at import time, so each case runs
in a fresh interpreter).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
to_canvas sized each community group box for a ceil(sqrt(n))-column grid but the
placement loop hardcoded 3 columns, so any community bigger than ~9 members
rendered as a cramped 3-wide strip in an over-wide, mostly-empty box (and the box
width/height didn't even agree — w used sqrt(n), h used /3). The column count is
now computed once per community (inner_cols) and reused for box width, box height,
and card placement, so the cards fill the box. Cosmetic, no data change.
Ported from PR #1459 by @TPAteeq onto current v8 (clean: only the grid math
changed, the #1457 dedup helper is untouched). Verified the geometry on a real
canvas: n=25 -> 5x5 grid with every card inside its box; n=10 -> 4 columns.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
to_obsidian / to_canvas / to_wiki keyed filename dedup on the exact-case name,
so two labels differing only by case (e.g. `References` vs `references`) counted
as non-colliding and the second write clobbered the first on case-insensitive
filesystems (macOS/APFS, Windows/NTFS) — silently, no suffix, no warning.
Dedup now folds case (keyed on the lowercased name) while emitting the
original-case filename, so any pair that would collide on disk gets a numeric
suffix. The obsidian/canvas dedup is one shared helper (`_dedup_node_filenames`)
so they can't drift; wiki's slug dedup gets the matching fix; the `_COMMUNITY_*`
overview notes (which had no dedup at all) are covered; and a generated `base_1`
is re-checked so it can't overwrite a node literally labelled `base_1`.
Ported from PR #1457 by @TPAteeq onto current v8. Verified with a rigorous
edge-case battery (case-only collision, base_1 literal re-check -> base_1_1,
community-label case fold, determinism) plus the PR's tests; full suite 2404
passed, ruff + skillgen clean.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
0.8.48 added graphify/extractors/ (the per-language split, #1212) but
[tool.setuptools] packages listed only "graphify", so the subpackage was
omitted from the wheel and `graphify extract` raised ModuleNotFoundError on a
fresh install. Editable/dev installs and the test suite import from the source
tree, so it passed CI and local smoke but broke the published package. Add
graphify.extractors to packages; verified the rebuilt wheel imports and extracts
in a clean venv. 0.8.48 is yanked.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
get_community shows the community name (#1448); starlette floored >=1.3.1 for
CVE-2026-48818 / CVE-2026-54283 (#1391, #1396); begin per-language extractor
split into graphify/extractors/ (#1212); parallel community labeling via
--max-concurrency / --batch-size (#1390); reflect dedups dead-ends/corrections;
and the work-memory loop no longer depends on the git hook (reflect --if-stale).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
get_community was the only graph tool still returning a bare numeric id, while
get_node and the query-traversal output already render the community_name
attribute to_json writes onto every node. Read the name from the community's
member nodes and put it in the header ("Community 12 — Auth & Sessions"),
sanitised like every other LLM-derived field.
Ported from PR #1448 by @rmart1308 onto current v8, with two additions: the name
is skipped when it is just the "Community N" placeholder (written for unnamed
communities) so the header never doubles to "Community 12 — Community 12", and
the formatting is extracted to a module-level _community_header() with focused
tests (named / placeholder / empty / sanitised). Full suite 2397 passed.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
starlette underpins the HTTP MCP transport (serve_http); graphify/serve.py
imports it directly (Starlette/Middleware/Route) but it was only present
transitively via mcp, with no version floor — so end users installing
graphifyy[mcp] could resolve a vulnerable starlette even after a lockfile bump.
Declare it in the mcp (and all) extras and floor at >=1.3.1, which carries the
fixes for both CVEs (1.3.1 >= the 1.1.0 fix for CVE-2026-48818 and is the fix
for CVE-2026-54283). Lock regenerated 1.0.0 -> 1.3.1.
Supersedes the lock-only bumps in #1391 and #1396 (both targeted 1.3.1 from a
stale base) with a pyproject floor that also protects end users. stdio MCP and
CLI are unaffected. serve/MCP/HTTP tests pass on 1.3.1; full suite 2393 passed.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The extractor-split port (b3ab221) moved `_make_id` (the only user of
`make_id`) into graphify/extractors/base.py, leaving the top-level
`from .ids import make_id` in extract.py unused. Remove it. Surfaced by
`ruff --select F` (F401); harmless at runtime and not in the enforced lint
set, but it is dead code from the move. extract.py F-issue count back to the
pre-port baseline; module imports and the zig/elixir/razor/blade tests pass.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Move the blade/elixir/razor/zig extractors and the shared primitives
(_make_id, _file_stem, _read_text, _LANGUAGE_BUILTIN_GLOBALS) out of the
13k-line extract.py into a graphify/extractors/ package: base.py holds the
shared pieces, one module per language, and __init__ seeds a
LANGUAGE_EXTRACTORS registry for future dispatch. Import direction is strictly
extract.py -> extractors/ (extractors never import extract), so there is no
cycle. extract.py re-exports every moved name, leaving all callers and the
dispatch table unchanged.
Ported from PR #1291 by @TheFedaikin onto current v8 as a thin, behavior-neutral
slice (the PR itself was branched 31 commits behind and entangled with unrelated
files). Verified the moved code is byte-identical to current v8 before porting;
full suite 2393 passed, the zig/elixir/razor/blade extractor tests pass, ruff and
skillgen --check clean. Also gitignores .DS_Store.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
label_communities ran batches one LLM call at a time, so a large graph needed
hundreds of sequential calls even on backends that allow heavy concurrency. It
now fans batches out across a thread pool, mirroring extract_corpus_parallel:
results are returned per batch and merged on the main thread (labels dict is
never mutated concurrently, no lock), and workers==1 keeps the original
sequential path verbatim. ollama and claude-cli are forced serial unless the
matching GRAPHIFY_*_PARALLEL env opt-in is set (same guard as extract).
generate_community_labels threads max_concurrency + batch_size through, and the
cluster-only/label CLI parses --max-concurrency and --batch-size (both `--flag N`
and `--flag=N` forms; the space form is parsed explicitly so the value is not
mistaken for the positional scan path by the arg-walk's catch-all).
Output is deterministic regardless of concurrency (keyed by community id). Tests:
parallel == sequential result, batch-size controls batch count, batches actually
run concurrently, ollama forced serial, and the CLI parses both new flags. Full
suite 2393 passed; ruff clean.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Saving the same Q&A more than once duplicated lines in the "known dead ends" and
"corrections" sections: both lists were appended per memory doc with no key, while
node scoring already dedups by node. They now collapse by question, keeping the
most recent entry (docs are processed oldest-first, so a re-corrected question
shows its latest correction). Output stays deterministic, ordered by (date,
question). Applied to both the flat lists and the per-community buckets.
Found by a user running it on a 104-file Go codebase. Added a regression test
covering the dedupe and the recency-wins correction. Full suite 2389 passed.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Both the agent (session start) and the post-commit hook can run reflect; the runs
are deterministic and idempotent, but back-to-back ones are wasted work. Add
`graphify reflect --if-stale`, which no-ops when LESSONS.md is already at least as
new as every input (the memory docs and the graph). The skill's session-start
guidance now uses `--if-stale`, so when the hook just refreshed the file the
agent's run costs almost nothing, while a skill-only install still refreshes
on demand.
New lessons_fresh() helper + 5 tests (mtime freshness in each direction, and the
CLI skip/run behavior). Regenerated per-host references + re-blessed expected/;
all five skillgen guards pass; full suite 2388 passed.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A skill-only install (no `graphify hook install`) recorded outcomes via
save-result but never ran reflect, so LESSONS.md was never generated or
refreshed and the lessons never surfaced. The query reference now instructs the
agent to run `graphify reflect` itself at the start of graph work (cheap,
deterministic, no-op with no saved outcomes) before reading LESSONS.md. The
post-commit hook stays as a between-session freshness optimization, not a
requirement. Regenerated per-host references/query.md + re-blessed expected/;
all five skillgen guards pass; full suite 2383 passed.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Work-memory (#1441): save-result --outcome + graphify reflect, with recency-decayed
scoring, corroboration threshold, label-matched node-existence gate, contested
handling, and zero-config adoption (skill reads LESSONS.md + records outcomes; git
hooks auto-reflect). Fixes: Python ClassName.method() qualified-call edges (#1446);
validate_extraction/build crash on non-hashable id (#1447); graphify update now
prunes a symbol removed from a surviving file without --force.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Make the self-improving loop "just work" once graphify is installed:
- Skill: the query reference now tells the agent to read
graphify-out/reflections/LESSONS.md at the start of graph work (start from
preferred sources, skip known dead ends, see prior corrections) and to record
--outcome useful|dead_end|corrected (+ --correction) on save-result.
- Hooks: the post-commit and post-checkout rebuild bodies now auto-run reflect
after _rebuild_code — best-effort, only when graphify-out/memory/ holds saved
outcomes, and never fails the hook — so LESSONS.md refreshes on every rebuild
without a manual `graphify reflect`.
Regenerated the per-host references/query.md and re-blessed expected/; all five
skillgen guards pass (check, audit-coverage, schema-singleton, monolith-roundtrip,
always-on-roundtrip). Verified end-to-end: install hook, save-result --outcome,
commit a code change -> hook rebuilds and writes LESSONS.md with the outcome.
Full suite 2383 passed; ruff clean.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
safishamsi