- Add .sh, .bash, .json to CODE_EXTENSIONS in detect.py so files reach extractor
- Fix test_detect_incremental manifest path collision with new .json extension
- Update test_watch to reflect .json/.sh are now watched extensions
- B-1: only emit source imports for paths that exist on disk
- J-1: replace stat()+read() with bounded read to eliminate TOCTOU
- J-3: move pair_count cap inside loop so it is honoured exactly
- J-4: namespace $ref/extends refs with "ref_" prefix to prevent ID collision
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
In a linked worktree .git is a file not a directory, so root/.git/hooks
fails with NotADirectoryError. Fall back to git rev-parse --path-format=absolute
--git-path hooks which resolves the correct hooks dir from any worktree.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- skill-windows.md: add graphify-out/ prefix to 5 paths in Step B3 that
were being read/written without prefix (lines 244,245,373,387,388,407,413)
causing semantic cache to always appear empty on Windows (#862)
- detect.py: gate converted office/Google Workspace sidecar paths through
_is_ignored() before appending to files list so .graphifyignore rules
apply to graphify-out/converted/ sidecars (#861)
- detect.py: split manifest entries from {mtime,hash} to
{mtime,ast_hash,semantic_hash}; save_manifest() accepts kind="ast"|
"semantic"|"both"; detect_incremental() accepts kind= and checks the
right hash field so graphify update (kind=ast) no longer prevents
graphify extract from re-running semantic extraction (#857)
- watch.py: all three save_manifest() calls use kind="ast" (AST-only rebuild)
- __main__.py: both extract save_manifest() calls use kind="both"
- backwards compatible: legacy {mtime,hash} entries treated as ast_hash only
775 tests passing
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Several host agents (Claude Code in particular) misread the current
phrasing and prompt the user for `ANTHROPIC_API_KEY` when no Gemini
key is set, instead of falling through to subagent dispatch. The
Gemini tip stays as-is; this just adds an explicit one-line callout
that no other provider keys are consulted, with `ANTHROPIC_API_KEY`
called out by name since that is the specific misread we hit in the
wild.
No behavior change — pure documentation.
The rebuild lock file accumulated concatenated PIDs across post-commit
rebuilds without a separator, and was never removed when the rebuild
finished. Two practical consequences for users:
1. Downstream tooling that polls for `.rebuild.lock` to disappear before
doing post-rebuild work (publish scripts copying graph.html to a web
root, etc.) blocked forever / until its own timeout.
2. The accumulated digit string could not be parsed by humans or tooling
to find the owning PID.
The `_rebuild_lock` context manager now:
- Opens the lock file with `a+` so a non-acquiring caller does not
truncate the existing holder's PID.
- After flock acquisition, truncates and writes a single `<pid>\n` line
so external readers can `kill -0 $(cat .rebuild.lock)` to check
liveness.
- Unlinks the lock file in the finally block (only when *we* held the
lock), restoring the "signal-by-absence" convention users rely on.
Four regression tests added under `tests/test_watch.py` covering the
PID-with-newline payload, post-release unlink, no-accumulation across
sequential acquisitions, and the non-blocking-caller-does-not-clobber
invariant.
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Astro files have a `---...---` TypeScript frontmatter block at the top
containing nearly all imports, followed by an HTML-with-expressions
template body, and optionally `<script>` blocks for client-side JS.
Feeding the whole file to the JS tree-sitter parser produces a top-level
ERROR node because the template isn't valid JS, so `import_statement`
nodes are never reached.
Mirrors `extract_svelte` (#713) — same regex-rescue strategy:
- Dynamic `import('...')` pass over the full source.
- Static `import X from '...'` pass over the frontmatter block plus any
`<script>` blocks.
Both static and dynamic imports honor tsconfig.json path aliases and
resolve relative paths through `_resolve_js_module_path` so node ids
match the targets that `_extract_generic` produces for sibling files.
Wired in:
- `detect.py:27` — `.astro` added to `CODE_EXTENSIONS`.
- `extract.py:5492` — `".astro": extract_astro` in the dispatch table.
Tests in `tests/test_astro_extraction.py` cover: extension registration,
frontmatter static imports, dynamic import in frontmatter, client-side
`<script>` block imports, frontmatter-less pages (must not crash), and
tsconfig.json path-alias resolution.
- skill.md + skill-windows.md: add encoding="utf-8" to all read_text()/write_text()
calls and ensure_ascii=False to json.dumps — bare calls defaulted to system
codepage on Chinese-locale Windows, mojibaking non-ASCII content (#832)
- skill.md + skill-windows.md: prefer uv tool install --upgrade graphifyy over
pip in the Step 1 install fallback — pip installs to the wrong env when
graphify was installed via uv tool (#831)
- serve.py + __main__.py: replace flat substring scoring in _score_nodes with
three-tier precedence (exact 1000 / prefix 100 / substring 1); _find_node
returns results ordered exact→prefix→substring; both path CLI and MCP now
emit a clear error when src and tgt resolve to the same node (#828)
- cache.py: normalize path key via .as_posix().lower() in file_hash so Windows
junction/case variants hash identically; mirror abs-path normalization from
save_semantic_cache into check_semantic_cache so relative source_file paths
resolve the same way on both sides (#826)
- __main__.py: add /graphify skill trigger line to _AGENTS_MD_SECTION — affects
all 7 AGENTS.md platforms (OpenCode, Codex, Aider, Trae, Hermes, Claw, Droid)
so typing /graphify actually invokes the skill tool (#827)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add a pre-cluster topology comparison fast path in update rebuilds so unchanged graphs short-circuit before clustering and report generation, preventing residual run-to-run community-count drift.
Co-authored-by: Cursor <cursoragent@cursor.com>
Use safe JSON serialization fallbacks for deterministic sort keys in clustering and graph canonicalization, and skip invalid community IDs with a stderr warning instead of raising during update rebuilds.
Co-authored-by: Cursor <cursoragent@cursor.com>
Make `graphify update` idempotent by skipping output rewrites when graph/report content is unchanged, add `update --no-cluster`, and preserve community IDs across runs via overlap-based remapping with deterministic partition inputs.
Co-authored-by: Cursor <cursoragent@cursor.com>
- Universal -h/--help/-? guard after cmd dispatch: any help flag anywhere in
argv stops execution and prints "Run 'graphify --help'" instead of triggering
the subcommand — cursor/kiro/gemini install --help no longer silently installs;
benchmark --help no longer crashes with FileNotFoundError (#821)
- --version / -v / version subcommand: print graphify {__version__} and exit (#818)
- GRAPHIFY_OLLAMA_NUM_CTX=<invalid> now falls through to auto-derived num_ctx
instead of hardcoding 131072 (the cap that causes OOM on constrained VRAM);
pinned num_ctx < estimated input now triggers an explicit truncation warning
with a suggested --token-budget correction (#820)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- extract/_make_id + build/_normalize_id: use NFKC normalization and casefold
so composed/decomposed Unicode forms produce the same ID; collapse consecutive
underscores; both functions are now byte-for-byte equivalent (#811)
- dedup: use explicit key-presence check instead of `or` for source/from
fallback; pop stale from/to keys so they don't leak into graph.json attrs (#803)
- skill --update: use build_merge() to avoid NetworkX round-trip direction flip;
fix dict merge ordering so explicit source/target win; pull hyperedges from
G.graph (merged) not new_extraction only (#801)
- skill subagents: inject absolute CHUNK_PATH so Write tool doesn't lose chunk
files to undefined cwd (#808)
- __main__: skip skill version check during hook-check (runs on every editor
tool use, must be silent); move warning to stderr
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
#796: add edge_data()/edge_datas() helpers in build.py that tolerate
MultiGraph/MultiDiGraph; replace all G.edges[u,v] 2-tuple call sites in
__main__.py, serve.py, wiki.py, export.py, analyze.py, benchmark.py;
fix same pattern in 10 skill file inline heredocs
#795: all 12 skill files now short-circuit on /graphify --help or -h
and print the Usage block without running any pipeline steps
#792 (hollow response): add _response_is_hollow() predicate in llm.py;
when Ollama (or any backend) returns empty/null/whitespace content or a
parsed result with no nodes/edges, rewrite finish_reason="length" so
_extract_with_adaptive_retry bisects the chunk instead of silently
dropping it; applied to _call_openai_compat, _call_claude, _call_bedrock
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
#791: per-repo fcntl flock in _rebuild_code prevents concurrent hook rebuilds
from exhausting memory; changed_paths wired through so only modified files are
re-extracted; stale nodes evicted on deletion; SIGALRM watchdog with
GRAPHIFY_REBUILD_TIMEOUT; Darwin-aware RLIMIT_DATA memory cap
#792: remove hard 8-worker cap (GRAPHIFY_MAX_WORKERS env var); add
--max-workers, --token-budget, --max-concurrency, --api-timeout CLI flags
to graphify extract; fix ollama API key gate for loopback URLs; explicit
timeout on OpenAI client (GRAPHIFY_API_TIMEOUT, default 600s); per-chunk
progress prints during extraction
#453 + #785: rename .agent -> .agents throughout antigravity install/uninstall;
add trigger:always_on YAML frontmatter to _ANTIGRAVITY_RULES so Antigravity
recognises the rules file
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Safi