Fixes#777. Relativize manifest keys, .graphify_root, and cache source_file fields on persist; re-anchor on load. In-memory callers still see absolute paths. Symlink round-trip fixed in follow-up commit 8f09326.
Per adversarial review of the #1127 fix:
- Apply the filesystem-path allowlist to sys.executable before embedding it in
the generated hook script. Paths with metacharacters outside [a-zA-Z0-9/_.@:\-]
(spaces, dollar signs, backticks, semicolons) are replaced with an empty string
so the pinned probe is safely skipped rather than injecting shell commands that
execute on every git commit.
- Change _PINNED='...' to single-quote assignment so no shell expansion can occur
even if a character slipped through the allowlist (belt and suspenders).
- Quote $GRAPHIFY_PYTHON in both nohup exec lines so paths with spaces work
(common in Windows C:\Program Files\... installs).
- Update test to assert the sanitized value, not raw sys.executable, so the test
stays correct after any future sanitization changes.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The issue reporter correctly noted that the hooks never consulted
graphify-out/.graphify_python -- the runtime interpreter source the skill and
README already rely on. Added as a second probe (after the pinned sys.executable,
before the launcher shebang and python3/python fallbacks). This covers Windows/Git
Bash where the uv-tool launcher is a binary with no parseable shebang, and where
the pinned exe may go stale after a reinstall.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
graphify hook install generated scripts that resolved the Python interpreter
purely at git-trigger time via 'command -v graphify'. GUI git clients (VS Code,
GitKraken), CI runners, and non-login shells often run with a minimal PATH that
omits ~/.local/bin -- the uv-tool / pipx launcher location. command -v graphify
returned empty, the python3/python fallbacks could not import graphify (it lives
only in the isolated venv), and the hook silently exited 0 with no output.
Fix: embed sys.executable of the currently-running install process as a pinned
first probe. Since 'graphify hook install' itself runs under the correct isolated
interpreter, sys.executable is always the right path. It is validated at
hook-runtime via 'import graphify' before use, so a stale pinned path safely
falls through to the existing dynamic detection rather than breaking the hook.
Also make the final fallback loud: print a diagnostic to stderr before exiting 0
so the failure is visible rather than invisible.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
test_manifest_written_after_extract assumes a docs corpus fails with no LLM
backend, but _run inherited the developer's environment. With a real
ANTHROPIC_API_KEY exported and the anthropic package present (now pulled by
[all]), the claude backend was detected and the extract succeeded, breaking the
'no backend' assertion. Strip the backend-selecting env vars in _run so the
tests hold regardless of the developer's shell. CI has no keys set, so it was
green there already.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
uv tool install graphifyy runs graphify in an isolated venv, so when a backend
needs anthropic/openai/boto3 the old 'Run: pip install anthropic' advice never
reached it. Worse, claude was the only backend with no [extra] at all, so a user
with ANTHROPIC_API_KEY set could not satisfy it without --with anthropic.
Add an anthropic optional extra (and include it in [all]), and replace the
package-missing ImportError messages with a shared _backend_pkg_hint that points
at 'uv tool install graphifyy[<extra>] --force' first, then the pip/venv path.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The Bash search hook only nudges grep/rg/find, so an agent that answers a
codebase question by Read-ing many source files one by one (the most common way
the graph gets skipped) slips right past it (#1114). Add _READ_SETTINGS_HOOK
matching Read|Glob: it fires only when graphify-out/graph.json exists, only for
a source/doc file outside graphify-out/, injects the same query-first
additionalContext, and never blocks (every branch fails open). Install and
uninstall now register and dedup both hooks idempotently.
Implemented independently rather than merging the community PR #1120; same idea,
our own hook (Read/Glob only, no fragile multi-file cat/head/tail heuristic).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
graphify install --project --platform antigravity went through the skill-only
branch (grouped with copilot/pi/kimi), so it copied SKILL.md but never wrote
.agents/rules/graphify.md or .agents/workflows/graphify.md - antigravity's
always-on layer - even though the project uninstall path removes them. Extract
the frontmatter + rules + workflows writes into _antigravity_finalize and call
it from both the global antigravity install and the project-scoped path.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Locks the body<->refs coupling: gemini ships claude's lean skill.md body but
resolves references through a separate path, so a real install with the real
claude bundle must leave every references/ pointer in SKILL.md resolvable.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
F2: replace the header-trust ratio check with an authoritative bounded
streaming-decompression pass. The zip central-directory sizes are
attacker-controlled, so a member that under-declares its size could dodge the
declared-size checks; now every member is stream-decompressed with a hard byte
ceiling, so actual expansion past the cap is caught regardless of the headers.
The cheap declared-size pre-filter stays as a fast reject for honest bombs.
F3: _validate_ollama_base_url now resolves the host, so an alias that points at
a link-local/metadata IP is blocked too, not just literal IPs. The extract
command gains an early gate that turns the metadata block into a clean
'error: ...' exit(2) instead of a deep traceback; a warn toggle keeps the
single user-facing LAN warning in the in-flow call.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
F3: OLLAMA_BASE_URL pointing at a link-local or cloud-metadata address
(169.254.x, metadata.google.*, 0.0.0.0) now fails closed instead of only
warning, since no real Ollama host lives there and it is a classic SSRF
target. General LAN hosts still warn-and-allow.
F5: the Fortran C-preprocessor call now passes an absolute path. cpp has no
'--' end-of-options terminator, so an attacker-named corpus file like
'-I/etc/x.F90' could otherwise be parsed as a cpp option; an absolute path
always begins with '/' and cannot be.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
.docx/.xlsx are zip+XML containers parsed during a corpus scan with no size
guard, so a few-KB zip-bomb could decompress to gigabytes and OOM-kill the
process. Screen every office/PDF file before openpyxl/python-docx/pypdf touch
it: an on-disk size cap, a total-uncompressed cap, and a compression-ratio
check on the archive members. Files that exceed the caps are skipped (treated
as empty) rather than parsed.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
A custom provider's base_url is where the full corpus and the user's API key
are sent. A project-local ./.graphify/providers.json travels with a cloned or
shared repo, so loading it silently was a corpus/key exfiltration channel.
Require GRAPHIFY_ALLOW_LOCAL_PROVIDERS=1 to load the project-local file (the
user's own ~/.graphify/providers.json stays trusted), reject non-http(s)
schemes on load and on 'provider add', and warn on plaintext-http egress. We
deliberately do not apply the ingest SSRF guard here so legitimate on-prem
https LLM gateways still work.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
gemini has no _PLATFORM_CONFIG entry and installs claude's skill.md body
verbatim. Since #1121 that body is the lean progressive core that links to
references/, but _packaged_skill_refs_dir returned None for gemini, so the
install laid down a SKILL.md with 8 dead reference pointers. Resolve gemini
to the claude references bundle (the same body it already ships) and guard
it in test_claude_twins_ride_the_claude_bundle.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
claude_uninstall only stripped the CLAUDE.md section, so `graphify uninstall`
and `graphify claude uninstall` orphaned the whole installed skill tree
(SKILL.md + references/ + version stamp) - gemini_uninstall already removes its
skill, this makes claude consistent. The #1121 split made the orphan a 10-file
directory; this restores the removal that the alternative PR #1119 had. Scoped
name removal preserves sibling user files; project-scope uninstall passes
project=True so it never touches the user-scope skill.
Verified: claude/bare uninstall now remove the tree and keep a sibling
user_notes.md; full suite 1755 passed; real extract still builds a clean graph.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Same 3.11+-stdlib issue as gen.py: this test imported tomllib directly, failing
the 3.10 job. Fall back to tomli on <3.11.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
test_skillgen.py (added in #1121) reads pre-split skill bodies from the
immutable baseline commit via `git show`, and on Python 3.10 imports tomllib
via the tomli fallback. The test job used a shallow checkout (no baseline tree)
and the lock didn't carry tomli, so the 3.10 job failed two ways. Add
fetch-depth: 0 to the test job (mirroring skillgen-check) and lock tomli under
the python_version < 3.11 marker so --frozen sync installs it.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
gen.py imported tomllib unconditionally, but that is 3.11+ stdlib only and
graphify supports (and CI tests) 3.10 - so importing tools.skillgen.gen, and
thus collecting test_skillgen.py, crashed the 3.10 test job with
ModuleNotFoundError. Fall back to the tomli backport on <3.11 and add tomli to
the dev group under that marker. Verified the fallback loads and parses with
tomllib forced absent.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
R1: the 6 always-on blocks were read into module-level constants at import,
so a missing/corrupt always_on/*.md crashed `import graphify.__main__` and
bricked every CLI command, not just install. Make _always_on lazy + lru_cached,
raising a clear "reinstall" error only on the install path that needs the block;
a module __getattr__ keeps the legacy constant names importable for the tests.
Verified: deleting a block no longer crashes `graphify --version`.
skillgen baselines: the self-check guards pinned to the moving `origin/v8` ref,
which stops pointing at the pre-split state once the split lands on v8 (the
always-on-roundtrip guard then fails in CI and monolith-roundtrip goes vacuous).
Pin _v8_baseline_ref, ALWAYS_ON_BASELINE_REF, and the two monolith roundtrip_refs
to the immutable pre-split commit SHA, matching the stated "does not track HEAD"
intent; update the 4 tests that asserted the old ref string.
R2: add tests/test_wheel_packaging.py - build the wheel and assert every
references bundle and always-on block ships in it, so a package-data glob miss
can't pass the repo-tree guards yet hard-exit `graphify install` for real users.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
All-platform progressive-disclosure skill split + generator (addresses #1106).
Splits each platform's skill into a lean core (~615 lines, full default pipeline inline) + on-demand references/, generated from a single source via tools/skillgen with a CI/pre-commit drift gate. 13 hosts split, aider/devin stay monoliths. Also fixes the stale bare-path bugs across the previously hand-maintained variants and moves the always-on blocks into packaged markdown.
Verified: all 5 generator guards pass, byte-verbatim load-bearing slices, lean cores self-sufficient on the default path across all 13 split hosts, references gated to non-default branches, description preserves the graphify-out-query-first clause. Supersedes #1119 (Claude-first subset).
Known follow-up applied on top: harden _always_on() against a missing packaged file so a partial install can't brick the CLI.
Follow-up to the file-ordering fix. The from-scratch build writes each node's
community field straight from cluster()'s enumerate() after a STABLE size-sort,
so the hundreds of equal-sized small communities in a sparse graph were ordered
by the partitioner's (not seed-stable) enumeration order. Their integer IDs
permuted run-to-run, which reads as 77-88% "community churn" in a per-node cid
diff even though the actual grouping is reproducible.
Add a tuple(sorted(nodes)) tiebreak to make the sort a total order, so an
identical grouping always yields identical community IDs. Verified: with the
partition returned in shuffled order across 5 runs, the node->cid map is now
identical. (A separate ~0.06% community-count drift remains - likely
non-canonical edge weights upstream - tracked separately.)
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
tree-sitter-dm (BYOND DreamMaker) publishes only a Windows wheel, so on
Linux/macOS uv/pip compiled it from source and aborted the entire
`uv tool install graphifyy` when a C toolchain or python3-dev was missing.
It is the only core grammar lacking Linux/Mac wheels. Move it from core
dependencies to an optional `dm` extra (also in `all`); the default install
now needs no compiler. extract_dm already imports the grammar lazily with a
graceful fallback, and .dmi/.dmm/.dmf use no tree-sitter, so only .dm/.dme
AST parsing is gated behind the extra.
Also: guard the .dm grammar tests with pytest.importorskip so a plain
`uv sync` (no extras) doesn't hard-fail; bump to 0.8.28 with a changelog
upgrade note; switch the README extras table + type notes from pip to
`uv tool install` (uv is the recommended installer, and pip-into-a-uv-tool-env
is the exact ModuleNotFoundError the README already warns about). 0.8.28 also
ships Kilo Code (#512) and the Dart parser modernization (#1098).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Modernizes the Dart extractor: comment stripping, `part of` redirection, nested-generic-aware extends/with/implements parsing, generic type-argument mapping, and generic call detection.
Verified against current v8: merges cleanly, full suite 1530 passed, and inheritance edges connect to same-file class nodes with no ghost-node splits or dangling edges (consistent with the #1033/#1096 node-ID invariants).
Adds Kilo Code as a supported platform: native skill + /graphify command, install/uninstall, and a .kilo tool.execute.before plugin (mirroring the OpenCode integration).
JSONC config is handled non-destructively - existing .kilo/kilo.jsonc is read but never rewritten; automated plugin registration goes to kilo.json, preserving user comments (addresses the Qodo review flag).
Verified locally: full suite 1525 passed, install/uninstall smoke test works.
The auto-labeling branch wrote .graphify_labels.json, but the unconditional
write at the end of cluster-only already persists the final labels dict
(LLM or placeholder). Removed the duplicate; no behavior change.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
No behavior change. label_communities / generate_community_labels live next
to the backend dispatch (_call_llm, detect_backend) they use, so the lazy
import and separate file are no longer needed. Tests unchanged except the
import path; they still monkeypatch graphify.llm._call_llm.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Community labeling was an agent-only step (skill.md Step 5): inside Claude Code
or Gemini CLI the agent names communities itself. Run as a bare CLI
(python -m graphify extract . --backend X), no agent does Step 5, so labels
stayed Community 0/1/2 for every backend.
Add graphify/labeling.py: one batched _call_llm asking the backend for a
{cid: name} map from each community's top node labels (god nodes first),
with per-community placeholder fallback and graceful degradation (no backend,
API error, or malformed reply -> Community N, never crashes).
Wire it in:
- cluster-only auto-labels when no .graphify_labels.json exists (the reported
repro path); --no-label opts out, --backend=<name> overrides auto-detect
- new `graphify label <path>` subcommand force-regenerates names
- extract prints a hint pointing standalone users at cluster-only
Tests mock the backend (no network): happy path, partial/fenced/malformed
replies, no-backend and error fallback, god_nodes dict shape.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The #1033 remap relativized file node IDs but symbol IDs still embedded the
absolute parent-dir stem, so a root-level file's symbols became
<rootdir>_main_run while the file node was correctly main and the skill.md
spec (and semantic subagent) wants main_run -- splitting every top-level
file's symbols into AST/semantic ghost pairs.
Extend the remap chokepoint to also canonicalize the symbol stem prefix
(old _file_node_id(path) -> new _file_node_id(rel)), gated by source_file so
two files sharing a prefix cannot cross-contaminate. raw_calls.caller_nid is
rewritten too, since the cross-file call pass consumes it after the remap and
would otherwise dangle. No-op for nested files (immediate parent identical in
absolute and relative form).
The originally-filed root cause (facts-collector path form) was a stale-cache
red herring; the real bug is the symbol-level continuation of #1033.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Two gaps in TypeScript inheritance:
1. interface heritage is an extends_type_clause node, not class_heritage,
so the walker never saw it and interface extends produced no inherits
edge. Add an extends_type_clause branch reusing _ts_heritage_clause_entries
(handles multiple extends).
2. a same-file superclass has no import alias, so the use-fact resolver
(which only consulted the import table) dropped it; only imported bases
resolved. Add a same-file fallback against the file's own symbol_nodes,
scoped to inherits/implements so it does not duplicate same-file calls
that already resolve via the call-graph pass. Import resolution still
takes precedence.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
to_obsidian and to_canvas built note filenames from node labels with no
length cap, so a label >=255 bytes crashed write_text with OSError. Add a
shared _cap_filename helper that caps on UTF-8 bytes (not chars, so CJK
labels don't slip past) and appends an 8-char hash of the full label when
truncating, so two distinct labels sharing a long prefix stay distinct.
Both safe_name builders route node, community and canvas filenames through
it; wikilinks stay consistent because they read the same filename dict.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
AST file nodes were ID'd from the full relative path plus extension
(match_script_pipeline_step_py) while semantic subagents follow the
{parent_dir}_{stem} spec (script_pipeline_step), so every file split
into two disconnected ghost nodes.
Fix at the single remap chokepoint in extract(): file node IDs and all
edge endpoints already funnel through the #502 relative-path remap, so
changing that remap to emit _file_node_id (one parent dir, no extension)
converts the node and every referencing edge together - Python, TS, Lua,
C and bash import edges all stay connected. symbol_resolution pre-computes
the canonical form directly (bypassing the remap) so it is synced too.
Per-site conversion (as attempted in #1038/#1065) orphans edges because
it moves the node without the edge targets; the chokepoint approach
avoids that entirely.
Backward compat for existing graphs: graphify extract --force, as the
skill.md spec already documents.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
os.walk order is non-deterministic across runs (filesystem b-tree order
shifts with cache/mount state), causing first-writer-wins decisions in
cross-file resolution to produce different node IDs each run; sorting
all_files and per-FileType lists stabilises graph.json without changing
any parent-child or connectivity semantics (closes#1090)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
pytest derives tmp_path from the test name, so the path contained
"incremental" and the bare-word assertion always failed; check for
the actual incremental-mode phrases instead
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
reconfigure stdout/stderr to UTF-8 at startup; replace → and — in all
print statements with ASCII equivalents as belt-and-suspenders fallback
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* feat: detect circular import dependencies at file level
- Add find_import_cycles() to analyze.py
- Collapses symbol nodes to parent files, builds directed file graph
- Uses nx.simple_cycles() bounded by max_cycle_length (default 5)
- Deduplicates rotations, returns shortest cycles first
- Considers both imports_from and re_exports edges
Tested on a 976-file Next.js codebase: found 4 cycles including
a known utils↔barrel circular dependency and a 4-file API cycle.
* fix: resolve import-cycle merge blockers
- use source_file-only endpoint resolution (no label fallback)
- support Graph/DiGraph orientation via edge source_file
- return structured cycle records and include self-loops
- integrate Import Cycles section into GRAPH_REPORT.md
- expand cycle tests for real-schema IDs, undirected input,
missing source_file nodes, and non-import relations
Safi