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graphify-labs--graphify/graphify/cli.py
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rajarshidattapy eccc6cf0bf feat(extract): add --no-dedup so incremental merges can skip fuzzy dedup (#2881) 
Adds --no-dedup (default off, so dedup stays on) to skip the fuzzy near-duplicate merge
pass on build and incremental merge, for operators who would rather keep distinct symbols
that fuzzy-matched than pay the merge. Exact-id uniqueness is unaffected (it is a graph
structural invariant, not a dedup responsibility), and the flag arms the #479 shrink
guard so a surprising node drop is refused loudly. Mutually exclusive with --dedup-llm.
2026-08-20 16:10:49 +01:00

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"""graphify command dispatch — every non-install subcommand.
Extracted verbatim from __main__.main(); __main__ now calls dispatch_command(cmd)
after the install/platform dispatch. Kept out of __main__ to shrink the CLI entry
module. The path-redirect (`graphify <path>` -> extract) re-enters via a lazy
import of main to avoid a cli<->__main__ import cycle.
"""
from __future__ import annotations
import json
import os
import re
import sys
import time
from graphify.paths import GRAPHIFY_OUT as _GRAPHIFY_OUT
from pathlib import Path, PurePosixPath, PureWindowsPath
_SEARCH_NUDGE = json.dumps({
"hookSpecificOutput": {
"hookEventName": "PreToolUse",
"additionalContext": (
'MANDATORY: graphify-out/graph.json exists. You MUST run '
'`graphify query "<question>"` before grepping raw files. Only grep '
'after graphify has oriented you, or to modify/debug specific lines.'
),
}
}, ensure_ascii=False, separators=(",", ":")) + "\n"
_READ_NUDGE = json.dumps({
"hookSpecificOutput": {
"hookEventName": "PreToolUse",
"additionalContext": (
'MANDATORY: graphify-out/graph.json exists. You MUST run graphify '
'before reading source files. Use: `graphify query "<question>"` '
'(scoped subgraph), `graphify explain "<concept>"`, or '
'`graphify path "<A>" "<B>"`. Only read raw files after graphify has '
'oriented you, or to modify/debug specific lines. This rule applies to '
'subagents too — include it in every subagent prompt involving code '
'exploration.'
),
}
}, ensure_ascii=False, separators=(",", ":")) + "\n"
_READ_NUDGE_STALE = json.dumps({
"hookSpecificOutput": {
"hookEventName": "PreToolUse",
"additionalContext": (
'graphify-out/graph.json exists but may be STALE for this file (the file '
'changed after the last build). Prefer `graphify query "<question>"` for '
'orientation, and run `graphify update` to refresh the graph. Reading the '
'file directly is fine.'
),
}
}, ensure_ascii=False, separators=(",", ":")) + "\n"
# Strict-mode block (opt-in). Claude Code PreToolUse honors
# hookSpecificOutput.permissionDecision == "deny" and shows permissionDecisionReason
# to the model. Fires at most once per session (see _mark_session_denied) so it can
# never strand an agent: the very next read proceeds with the soft nudge.
_READ_DENY = json.dumps({
"hookSpecificOutput": {
"hookEventName": "PreToolUse",
"permissionDecision": "deny",
"permissionDecisionReason": (
'graphify strict mode: this project has a fresh knowledge graph that covers '
'this file. Run `graphify query "<your question>"` (or `graphify explain` / '
'`graphify path`) FIRST to orient yourself, then re-issue this Read — it '
'will be allowed. This block fires at most once per session; reading raw '
'files to modify or debug specific lines is fine after one query. Apply the '
'same rule in any subagent prompt that explores code.'
),
}
}, ensure_ascii=False, separators=(",", ":")) + "\n"
_HOOK_SOURCE_EXTS = (
'.py', '.js', '.cjs', '.ts', '.tsx', '.jsx', '.astro', '.vue', '.svelte', '.go',
'.rs', '.java', '.rb', '.c', '.h', '.cpp', '.hpp', '.cc', '.cs', '.kt',
'.swift', '.php', '.scala', '.lua', '.sh', '.md', '.rst', '.txt', '.mdx',
)
_GEMINI_NUDGE_TEXT = (
'graphify: knowledge graph at graphify-out/. For focused questions, run '
'`graphify query "<question>"` (scoped subgraph, usually much smaller than '
'GRAPH_REPORT.md) instead of grepping raw files. Read GRAPH_REPORT.md only '
'for broad architecture context.'
)
def _default_graph_path() -> str:
return str(Path(_GRAPHIFY_OUT) / "graph.json")
def _stamped_manifest_files(
files_by_type: dict[str, list[str]],
sem_result: dict,
root: Path,
partial_source_files: "set[str] | None" = None,
failed_ast_sources: "set[str] | list[str] | None" = None,
) -> dict[str, list[str]]:
"""Manifest-safe files dict: only stamp semantic files that actually
produced output (cache hit or fresh extraction). Files whose chunk failed
have no source_file entry in sem_result — leaving their semantic_hash
empty so detect_incremental re-queues them (#933).
A file in ``partial_source_files`` DID produce output this run, but only a
truncated fragment of it, so it is excluded from stamping too — otherwise
detect_incremental would see it "done" and never re-dispatch it, leaving the
incomplete node set live forever on the warm-incremental path. Same #933
mechanism: leave it unstamped and it is re-queued next run.
Both sides of the membership test are resolved against the scan ``root``
before comparing (#1897): node/edge/hyperedge ``source_file`` values are
root-relative on a fresh extraction while ``files_by_type`` entries are
absolute (from detect()), so a raw string comparison never matched and
every freshly-extracted semantic doc was dropped from the manifest.
Mirrors the #1890 path normalization in graphify.llm.
Hyperedges are counted as output (#1920): a chunk whose only result for a
document is a hyperedge (3+ nodes sharing a concept) is valid output that
the semantic cache persists per-``source_file`` — omitting it here left the
doc unstamped, so detect_incremental re-queued it on every run. The stamping
condition mirrors the cache-write keying (a hyperedge carries its own
``source_file``); do not derive it from member nodes.
``failed_ast_sources`` (#2543): code files whose AST extractor errored
(missing optional extra, etc.) or returned zero nodes. They must not be
stamped as up-to-date or a later install of the extra will never re-run.
"""
root = Path(root)
def _resolve(value: str) -> Path:
p = Path(value)
if not p.is_absolute():
p = root / p
try:
return p.resolve()
except (OSError, RuntimeError):
return p
sem_extracted: set[Path] = set()
for coll in ("nodes", "edges", "hyperedges"):
for item in sem_result.get(coll, []):
sf = item.get("source_file", "")
if sf:
sem_extracted.add(_resolve(sf))
partial_resolved = {_resolve(p) for p in (partial_source_files or set())}
failed_ast_resolved = {_resolve(p) for p in (failed_ast_sources or [])}
sem_types = {"document", "paper", "image"}
return {
ftype: [
f for f in flist
if _resolve(f) not in failed_ast_resolved
and (
ftype not in sem_types
or (_resolve(f) in sem_extracted and _resolve(f) not in partial_resolved)
)
]
for ftype, flist in files_by_type.items()
}
def _stale_graph_sources(
graph_path: Path,
scan_root: Path,
seen_files: set[str],
detection: dict | None = None,
) -> list[str]:
"""Source files graph.json still references but the current scan no longer
contains (#1909).
Incremental extract's prune set was historically derived from the manifest
alone (``manifest - corpus``), so a file that became EXCLUDED
(.graphifyignore/.gitignore/--exclude changed) without being listed in the
manifest kept its stale nodes in graph.json forever. Derive prune
candidates from the graph's own node ``source_file``s instead: anything
the graph references that the post-exclude detect corpus no longer
contains is stale, whether the file was deleted or newly excluded.
Only IN-ROOT paths are candidates: out-of-root/absolute entries
(--include sources, symlinked external corpora) are never walked by
detect, so their absence from the corpus is not staleness evidence.
Relative entries are re-anchored against both the scan root and the
graph's own output root; only anchors that land inside the scan root
count. Since #1941 extracts always store source_file relative to the SCAN
root, so the scan-root anchor is the live one; the out-root anchor stays
for graphs written by <=0.9.16, which stored them relative to the OUT root
(e.g. ``../project/x.py``, #555/#1899).
``seen_files`` must be the FULL detect output including unclassified
files, so nodes from walked-but-unsupported sources (e.g. introspected
Cargo.toml manifests) are not misread as stale.
Paths are compared NFC-normalized on both sides: macOS reports NFD
filenames while graph ``source_file`` entries are typically NFC, and a
raw-string membership test misread every accented live file as stale
(#2210; same class as the manifest-layer #2221/#2224).
Fail-closed liveness guard (#2210, mirrors watch.py's excluded-vs-deleted
distinction): a source missing from the scan corpus is only pruned when
the file is gone from disk, or when its exclusion is PROVABLE from the
same scan that produced ``seen_files`` — ``detection``'s ``ignored`` /
``pruned_noise_dirs`` / ``skipped_sensitive`` output, or detect's
sensitivity predicate. An alive file that merely failed the membership
test (path-spelling drift the normalization didn't cover, walk errors,
…) is KEPT and reported, never mass-evicted.
"""
from graphify.paths import nfc
try:
data = json.loads(graph_path.read_text(encoding="utf-8"))
except Exception:
return []
if not isinstance(data, dict):
return []
try:
root_res = scan_root.resolve()
except (OSError, RuntimeError):
root_res = scan_root
# <out>/graphify-out/graph.json — relative source_files may be anchored here.
out_base = graph_path.parent.parent
try:
out_base = out_base.resolve()
except (OSError, RuntimeError):
pass
def _within_root(p: Path) -> bool:
try:
p.relative_to(root_res)
return True
except ValueError:
pass
try:
p.resolve().relative_to(root_res)
return True
except (ValueError, OSError, RuntimeError):
return False
seen_nfc = {nfc(s) for s in seen_files}
seen_basenames = {nfc(os.path.basename(s)) for s in seen_files}
def _in_seen(p: Path) -> bool:
if nfc(str(p)) in seen_nfc:
return True
try:
return nfc(str(p.resolve())) in seen_nfc
except (OSError, RuntimeError):
return False
# Provable-exclusion evidence from the scan that produced seen_files:
# individually ignored files are exact entries; ignored/noise-pruned
# directories are recorded once with a trailing separator and cover
# their whole subtree. skipped_sensitive entries may carry a
# " [reason]" suffix.
excluded_exact: set[str] = set()
excluded_prefixes: list[str] = []
if detection:
for entry in list(detection.get("ignored", [])) + list(
detection.get("pruned_noise_dirs", [])
):
e = nfc(str(entry))
if e.endswith(os.sep) or e.endswith("/"):
excluded_prefixes.append(e)
else:
excluded_exact.add(e)
for entry in detection.get("skipped_sensitive", []):
excluded_exact.add(nfc(str(entry).split(" [", 1)[0]))
def _provably_excluded(c: Path) -> bool:
spellings = [nfc(str(c))]
try:
spellings.append(nfc(str(c.resolve())))
except (OSError, RuntimeError):
pass
for s in spellings:
if s in excluded_exact:
return True
if any(s.startswith(pref) for pref in excluded_prefixes):
return True
try:
from graphify.detect import _is_sensitive as _det_sensitive
if _det_sensitive(c):
return True
except Exception:
pass
return False
stale: list[str] = []
kept_alive: list[str] = []
checked: set[str] = set()
for n in data.get("nodes", []):
if not isinstance(n, dict):
continue
sf = n.get("source_file")
if not sf or not isinstance(sf, str) or sf in checked:
continue
checked.add(sf)
if "://" in sf:
continue # remote/virtual source (e.g. Google Workspace), not a scanned path
p = Path(sf)
if p.is_absolute():
candidates = [p]
else:
rel = sf.replace("\\", "/")
bases = [root_res]
if out_base != root_res:
bases.append(out_base)
candidates = [
Path(os.path.normpath(str(base / rel))) for base in bases
]
in_root = [c for c in candidates if _within_root(c)]
if not in_root:
continue # out-of-root under every anchor: never prune
if any(_in_seen(c) for c in in_root):
continue # still part of the scan corpus
# Fail-closed liveness guard (#2210): absence from the corpus is
# only deletion evidence when the file is actually gone from disk.
alive = []
for c in in_root:
try:
if c.exists():
alive.append(c)
except OSError:
pass
if alive:
if all(_provably_excluded(c) for c in alive):
stale.append(sf) # alive but excluded under current rules (#1909)
else:
kept_alive.append(sf)
continue
# No anchored candidate exists, but a legacy bare-basename spelling
# can't be anchored reliably — a live corpus file with the same name
# means deletion is unproven; keep.
rel_sf = sf.replace("\\", "/")
if "/" not in rel_sf and nfc(rel_sf) in seen_basenames:
kept_alive.append(sf)
continue
stale.append(sf)
if kept_alive:
print(
f"[graphify] fail-closed: kept node(s) from {len(kept_alive)} "
"source file(s) that left the scan corpus but still exist on disk "
"(ignore rules or filters changed?). Run a full re-extraction to "
"purge them if the exclusion is intentional.",
file=sys.stderr,
)
return stale
def _zero_node_stamped_code_sources(
graph_path: Path,
scan_root: Path,
unchanged_code: list[str],
) -> list[str]:
"""Manifest-stamped code files with a registered extractor but ZERO nodes
in the existing graph.json (#2543 heal).
The failed-source unstamping only covers failures that happen AFTER it
shipped; a manifest poisoned by an earlier run (extraction failed, hashes
stamped anyway) keeps reporting the file unchanged forever, and the only
documented recovery was deleting graphify-out/. A stamped file that the
graph has no nodes for, despite an extractor being wired up for it, is
exactly that state — re-queue it as changed. Bounded by the same no-wedge
property: if it fails again this run it is now left unstamped, and if it
succeeds its nodes enter graph.json so the next scan stops re-queuing it.
Membership mirrors the ``source_file`` spellings extracts store (#1897/
#1941: scan-root-relative, forward slash; absolute for out-of-root) and
compares NFC-normalized (#2210/#2221).
"""
if not unchanged_code:
return []
from graphify.paths import nfc
try:
data = json.loads(graph_path.read_text(encoding="utf-8"))
except Exception:
return []
if not isinstance(data, dict):
return []
try:
root_res = scan_root.resolve()
except (OSError, RuntimeError):
root_res = scan_root
# <out>/graphify-out/graph.json — legacy relative source_files may be
# anchored here instead of the scan root (<=0.9.16, #555/#1899).
out_base = graph_path.parent.parent
try:
out_base = out_base.resolve()
except (OSError, RuntimeError):
pass
present: set[str] = set()
for n in data.get("nodes", []):
if not isinstance(n, dict):
continue
sf = n.get("source_file")
if not sf or not isinstance(sf, str):
continue
present.add(nfc(sf))
p = Path(sf)
if p.is_absolute():
try:
present.add(nfc(str(p.resolve())))
except (OSError, RuntimeError):
pass
else:
rel = sf.replace("\\", "/")
for base in (root_res, out_base):
present.add(nfc(os.path.normpath(str(base / rel))))
from graphify.extract import _get_extractor
healed: list[str] = []
for f in unchanged_code:
p = Path(f)
if _get_extractor(p) is None:
continue # no extractor: absence from the graph is expected
spellings = {nfc(str(p))}
try:
spellings.add(nfc(str(p.resolve())))
except (OSError, RuntimeError):
pass
try:
spellings.add(nfc(p.resolve().relative_to(root_res).as_posix()))
except (ValueError, OSError, RuntimeError):
pass
if spellings & present:
continue # the graph has this file: stamp is honest
healed.append(f)
return healed
def _prune_graph_json_sources(graph_path: Path, stale_sources: list[str]) -> int:
"""Drop nodes/edges/hyperedges owned by ``stale_sources`` from graph.json
in place. Returns the number of nodes removed.
Used by the ``--no-cluster`` incremental early-exit: that path never runs
``build_merge`` (it would raw-dump only the new chunks), so an
exclusion-only change must prune the existing raw graph directly or the
newly-excluded file's nodes survive forever (#1909).
``stale_sources`` comes from :func:`_stale_graph_sources`, i.e. the
graph's own ``source_file`` spellings, so exact string matching is enough.
"""
try:
data = json.loads(graph_path.read_text(encoding="utf-8"))
except Exception:
return 0
if not isinstance(data, dict):
return 0
stale = set(stale_sources)
links_key = "links" if "links" in data else "edges"
nodes = [n for n in data.get("nodes", []) if isinstance(n, dict)]
kept_nodes = [n for n in nodes if n.get("source_file") not in stale]
removed_ids = {
n.get("id") for n in nodes if n.get("source_file") in stale
}
n_removed = len(nodes) - len(kept_nodes)
kept_edges = [
e for e in data.get(links_key, [])
if isinstance(e, dict)
and e.get("source_file") not in stale
and e.get("source") not in removed_ids
and e.get("target") not in removed_ids
]
kept_hyper = [
h for h in data.get("hyperedges", [])
if isinstance(h, dict) and h.get("source_file") not in stale
]
if n_removed == 0 and len(kept_edges) == len(data.get(links_key, [])) and (
len(kept_hyper) == len(data.get("hyperedges", []))
):
return 0
data["nodes"] = kept_nodes
data[links_key] = kept_edges
if "hyperedges" in data:
data["hyperedges"] = kept_hyper
from graphify.export import backup_if_protected as _backup
_backup(graph_path.parent)
from graphify.paths import write_json_atomic
write_json_atomic(graph_path, data, indent=2)
return n_removed
class _StageTimer:
"""Print per-stage wall-clock timings to stderr when --timing is set (#1490).
Monotonic (perf_counter), diagnostic-only: emits ``[graphify timing] <stage>:
N.Ns`` after each stage and a final total. Off by default, so normal output is
byte-identical and machine-read stdout is untouched.
"""
def __init__(self, enabled: bool) -> None:
import time as _time
self._now = _time.perf_counter
self.enabled = enabled
self.start = self._now()
self._last = self.start
def mark(self, stage: str) -> None:
now = self._now()
if self.enabled:
print(f"[graphify timing] {stage}: {now - self._last:.1f}s", file=sys.stderr)
self._last = now
def total(self) -> None:
if self.enabled:
print(f"[graphify timing] total: {self._now() - self.start:.1f}s", file=sys.stderr)
def _enforce_graph_size_cap_or_exit(gp: Path) -> None:
"""Reject oversized graph files before parsing (CLI exit-on-fail flavor).
Delegates to ``graphify.security.check_graph_file_size_cap`` and turns the
raised ``ValueError`` into a CLI-style ``error: ...`` message + exit 1.
Use this from ``__main__.py`` subcommands that already use the ``print +
sys.exit(1)`` idiom. Library/MCP/loader callers (``serve._load_graph``,
``build``, ``benchmark``, ``tree_html``, ``callflow_html``, ``prs``,
``global_graph``, ``watch``, ``export``) call the security helper directly
and let the ``ValueError`` propagate.
"""
from graphify.security import check_graph_file_size_cap
try:
check_graph_file_size_cap(gp)
except ValueError as exc:
print(f"error: {exc}", file=sys.stderr)
sys.exit(1)
def _hook_strict_enabled(flag: bool) -> bool:
"""Resolve strict mode: GRAPHIFY_HOOK_STRICT env overrides the baked-in flag
(truthy forces on without a reinstall, falsy is the kill switch); unset defers
to the flag the installed hook command carried."""
v = os.environ.get("GRAPHIFY_HOOK_STRICT", "").strip().lower()
if v in ("1", "true", "yes", "on"):
return True
if v in ("0", "false", "no", "off"):
return False
return flag
def _touch_query_stamp(graph_path: "Path") -> None:
"""Record that graphify oriented the agent recently, next to the queried graph.
The strict guard suppresses its block while this stamp is fresh. Fail-silent."""
try:
from graphify.paths import write_text_atomic
stamp = Path(graph_path).parent / "cache" / "last_query_stamp"
stamp.parent.mkdir(parents=True, exist_ok=True)
write_text_atomic(stamp, str(time.time()))
except Exception:
pass
def _query_stamp_fresh() -> bool:
"""True if a query/explain/path ran within GRAPHIFY_HOOK_STRICT_TTL (default
1800s) — recent orientation, so strict mode does not block this read."""
from graphify.paths import out_path
try:
ttl = float(os.environ.get("GRAPHIFY_HOOK_STRICT_TTL", "1800"))
return (time.time() - out_path("cache", "last_query_stamp").stat().st_mtime) < ttl
except Exception:
return False
def _mark_session_denied(session_id: str) -> bool:
"""Atomically claim a one-time strict block for this session. Returns True only
on the FIRST call for a given session id (O_EXCL create wins once); every later
call — or any error — returns False, so a session is blocked at most once and an
agent can never be stranded. Best-effort GC of markers older than 24h."""
from graphify.paths import out_path
sid = re.sub(r"[^A-Za-z0-9_-]", "_", str(session_id))[:64]
if not sid:
return False
try:
d = out_path("cache", "hook_sessions")
d.mkdir(parents=True, exist_ok=True)
fd = os.open(str(d / f"{sid}.denied"), os.O_CREAT | os.O_EXCL | os.O_WRONLY, 0o644)
os.close(fd)
try:
cutoff = time.time() - 86400
for entry in os.scandir(d):
try:
if entry.stat().st_mtime < cutoff:
os.unlink(entry.path)
except OSError:
pass
except OSError:
pass
return True
except FileExistsError:
return False
except Exception:
return False
def _run_hook_guard(kind: str, strict: bool = False) -> None:
"""Shell-agnostic PreToolUse guard (#522).
Reads the tool-call JSON from stdin and, when a fresh in-project knowledge graph
exists, nudges the agent to use graphify instead of grepping/reading raw files.
Replaces the old inline bash hooks that failed to parse on Windows.
Fails open everywhere: any error, or a non-matching tool call, prints nothing
and the caller exits 0, so a legitimate tool call is never blocked by a bug.
In strict mode (opt-in, Claude Code Read only) the FIRST raw read of indexed,
in-project, fresh code per session is DENIED with a redirect to `graphify query`
(permissionDecision), then downgrades to the soft nudge — it fires at most once
per session and can never strand the agent. Search (Bash) and Glob stay
nudge-only: a compound shell command has no single parseable target and blocking
file listing would strand navigation. #1840: reads of out-of-project files are
ignored, and a graph that is stale for the target file softens to a non-mandatory
nudge instead of blocking or demanding.
"""
from graphify.paths import out_path, GRAPHIFY_OUT_NAME
# Gemini's BeforeTool hook takes no stdin and must ALWAYS return a decision so
# the tool is never blocked; the graph nudge is appended only when a graph
# exists. Handled before the stdin read below (which the search/read guards need).
if kind == "gemini":
payload = {"decision": "allow"}
try:
if out_path("graph.json").is_file():
payload["additionalContext"] = _GEMINI_NUDGE_TEXT
except Exception:
pass
sys.stdout.write(json.dumps(payload, ensure_ascii=False, separators=(",", ":")))
return
try:
d = json.loads(sys.stdin.buffer.read().decode("utf-8", "replace"))
except Exception:
return
if not isinstance(d, dict):
return
t = d.get("tool_input", d)
if not isinstance(t, dict):
return
try:
if kind == "search":
cmd_str = str(t.get("command", "") or "")
# Two input shapes reach this guard (matcher "Bash|Grep", #1986):
# the Bash tool carries `command`, while Claude Code's dedicated
# Grep tool carries `pattern` (plus optional path/glob) and no
# command — a Grep call IS a content search by definition, so it
# nudges whenever a graph exists. For Bash, keep matching the same
# set the old `case` matched: *grep*, *ripgrep*, and rg/find/fd/
# ack/ag as a token (name followed by a space). Nudge-only, even in
# strict mode — see the docstring.
is_grep_tool = not cmd_str and bool(t.get("pattern"))
is_bash_search = any(tok in cmd_str for tok in (
"grep", "ripgrep", "rg ", "find ", "fd ", "ack ", "ag "))
if (is_grep_tool or is_bash_search) and out_path("graph.json").is_file():
sys.stdout.write(_SEARCH_NUDGE)
elif kind == "read":
vals = [str(t.get("file_path") or ""), str(t.get("pattern") or ""), str(t.get("path") or "")]
j = " ".join(vals).lower().replace("\\", "/")
tails = [
"." + seg.rsplit(".", 1)[-1]
for v in vals if v
for seg in [v.lower().replace("\\", "/").rsplit("/", 1)[-1]]
if "." in seg
]
under_out = "graphify-out/" in j or (GRAPHIFY_OUT_NAME.lower() + "/") in j
if under_out or not any(tl in _HOOK_SOURCE_EXTS for tl in tails):
return
# #1840 (a): skip files outside the graph's project. cwd (or
# CLAUDE_PROJECT_DIR, which Claude Code sets) is the project root, since
# the guard only triggers when graph.json exists relative to cwd. A path
# candidate that resolves outside that root is out-of-project.
root = Path(os.environ.get("CLAUDE_PROJECT_DIR") or os.getcwd())
try:
root = root.resolve()
except (OSError, RuntimeError):
pass
path_vals = [str(t.get("file_path") or ""), str(t.get("path") or "")]
explicit = [v for v in path_vals if v]
if explicit:
in_project = False
for v in explicit:
p = Path(v)
if _is_cwd_relative(v):
in_project = True # relative -> anchored at cwd == in project
break
try:
p.resolve().relative_to(root)
in_project = True
break
except (ValueError, OSError, RuntimeError):
continue
if not in_project:
return
# One stat for existence + mtime of the graph.
try:
gmtime = os.stat(str(out_path("graph.json"))).st_mtime
except OSError:
return
# #1840 (b): stale-for-target -> soften, never block. The target file
# changed after the last build, or watch flagged the tree.
stale = False
fp = str(t.get("file_path") or "")
if fp:
try:
stale = os.stat(fp).st_mtime > gmtime
except OSError:
stale = False
try:
if out_path("needs_update").exists():
stale = True
except Exception:
pass
if stale:
sys.stdout.write(_READ_NUDGE_STALE)
return
# Strict block: Read tool only, first time per session, not recently
# oriented, and the file is demonstrably indexed.
tool_name = d.get("tool_name")
if _hook_strict_enabled(strict) and tool_name in (None, "Read") \
and not _query_stamp_fresh() \
and _target_is_indexed(fp, root) \
and _mark_session_denied(str(d.get("session_id") or "")):
sys.stdout.write(_READ_DENY)
return
sys.stdout.write(_READ_NUDGE)
except Exception:
pass
def _is_cwd_relative(value: str) -> bool:
r"""Whether *value* is anchored at the current working directory.
The hook's out-of-project guard needs "is this path resolved against cwd?",
and ``Path.is_absolute()`` is the wrong question for it on Windows. A
driveless rooted path like ``/tmp/x.py`` — the form POSIX-shaped hosts, WSL
and Git Bash send — is NOT absolute there (no drive letter), but it is not
cwd-relative either: Windows anchors it at the current DRIVE root, so
``Path("/somewhere/else/x.py").resolve()`` is ``C:\somewhere\else\x.py``,
which is outside the project unless the project sits at ``C:\``. Reading it
as cwd-relative made the guard declare it in-project and emit the read nudge
(and, in strict mode, the once-per-session deny) for files the graph has
nothing to say about.
``C:x.py`` is the same trap from the other side: drive-relative, anchored at
that drive's current directory rather than cwd.
So the test is "no root and no drive", not "not absolute". These stay the
host's own rules — the path is about to be resolved against this filesystem,
so ``paths.is_absolute_any_platform`` (for stored, portable paths) is
deliberately not used. On POSIX ``root`` is set exactly when the path is
absolute and ``drive`` is always empty, so this is unchanged there.
"""
pure = PureWindowsPath(value) if os.name == "nt" else PurePosixPath(value)
return not pure.root and not pure.drive
def _target_is_indexed(file_path: str, root: "Path") -> bool:
"""Guard the strict deny: only block a read of a file the graph actually indexes.
Reads manifest.json (cheap, capped); on any doubt (missing/corrupt/oversized
manifest, unresolvable path) returns True so the once-per-session deny still
applies — that block is self-limiting, so erring toward it is safe."""
from graphify.paths import out_path
if not file_path:
return True
try:
mp = out_path("manifest.json")
st = mp.stat()
if st.st_size > 2_000_000:
return True
manifest = json.loads(mp.read_text(encoding="utf-8"))
if not isinstance(manifest, dict) or not manifest:
return True
p = Path(file_path)
rels = set()
try:
rels.add(p.resolve().relative_to(root).as_posix())
except (ValueError, OSError, RuntimeError):
pass
rels.add(p.name)
keys = {str(k).replace("\\", "/") for k in manifest}
abskey = str(p).replace("\\", "/")
return abskey in keys or any(r and (r in keys or any(k.endswith("/" + r) or k == r for k in keys)) for r in rels)
except Exception:
return True
def _clone_repo(
url: str, branch: str | None = None, out_dir: Path | None = None
) -> Path:
"""Clone a GitHub repo to a local cache dir and return the path.
Clones into ~/.graphify/repos/<owner>/<repo> by default so repeated
runs on the same URL reuse the existing clone (git pull instead of clone).
"""
import subprocess as _sp
import re as _re
# Normalise URL — strip trailing .git if present
url = url.rstrip("/")
if not url.endswith(".git"):
git_url = url + ".git"
else:
git_url = url
url = url[:-4]
# Extract owner/repo from URL
m = _re.search(r"github\.com[:/]([^/]+)/([^/]+?)(?:\.git)?$", url)
if not m:
print(f"error: not a recognised GitHub URL: {url}", file=sys.stderr)
sys.exit(1)
owner, repo = m.group(1), m.group(2)
if out_dir:
dest = out_dir
else:
dest = Path.home() / ".graphify" / "repos" / owner / repo
if branch and branch.startswith("-"):
print(f"error: invalid branch name: {branch!r}", file=sys.stderr)
sys.exit(1)
if dest.exists():
print(f"Repo already cloned at {dest} - pulling latest...", flush=True)
cmd = ["git", "-C", str(dest), "pull"]
if branch:
cmd += ["origin", "--", branch]
result = _sp.run(cmd, capture_output=True, text=True)
if result.returncode != 0:
print(f"warning: git pull failed:\n{result.stderr}", file=sys.stderr)
else:
dest.parent.mkdir(parents=True, exist_ok=True)
print(f"Cloning {url} -> {dest} ...", flush=True)
cmd = ["git", "clone", "--depth", "1"]
if branch:
cmd += ["--branch", branch]
cmd += ["--", git_url, str(dest)]
result = _sp.run(cmd, capture_output=True, text=True)
if result.returncode != 0:
print(f"error: git clone failed:\n{result.stderr}", file=sys.stderr)
sys.exit(1)
print(f"Ready at: {dest}", flush=True)
return dest
def _reenter_main() -> None:
from graphify.__main__ import main
main()
def dispatch_command(cmd: str) -> None:
if cmd == "provider":
from graphify.llm import _custom_providers_path, BACKENDS
import json as _json
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
global_path = _custom_providers_path(global_=True)
if subcmd == "list":
global_path.parent.mkdir(parents=True, exist_ok=True)
existing: dict = {}
if global_path.is_file():
try:
existing = _json.loads(global_path.read_text(encoding="utf-8"))
except Exception:
pass
if not existing:
print("No custom providers registered.")
else:
for name in existing:
print(f" {name} ({existing[name].get('base_url', '')})")
elif subcmd == "show":
name = sys.argv[3] if len(sys.argv) > 3 else ""
if not name:
print("Usage: graphify provider show <name>", file=sys.stderr)
sys.exit(1)
existing = {}
if global_path.is_file():
try:
existing = _json.loads(global_path.read_text(encoding="utf-8"))
except Exception:
pass
if name not in existing:
print(f"Provider '{name}' not found.", file=sys.stderr)
sys.exit(1)
print(_json.dumps({name: existing[name]}, indent=2))
elif subcmd == "add":
args = sys.argv[3:]
name = args[0] if args and not args[0].startswith("-") else ""
if not name:
print("Usage: graphify provider add <name> --base-url URL --default-model MODEL --env-key KEY", file=sys.stderr)
sys.exit(1)
if name in BACKENDS:
print(f"Error: '{name}' is a built-in provider and cannot be overridden.", file=sys.stderr)
sys.exit(1)
base_url = ""
default_model = ""
env_key = ""
pricing_input = 0.0
pricing_output = 0.0
i = 1
while i < len(args):
a = args[i]
if a == "--base-url" and i + 1 < len(args):
base_url = args[i + 1]; i += 2
elif a.startswith("--base-url="):
base_url = a.split("=", 1)[1]; i += 1
elif a == "--default-model" and i + 1 < len(args):
default_model = args[i + 1]; i += 2
elif a.startswith("--default-model="):
default_model = a.split("=", 1)[1]; i += 1
elif a == "--env-key" and i + 1 < len(args):
env_key = args[i + 1]; i += 2
elif a.startswith("--env-key="):
env_key = a.split("=", 1)[1]; i += 1
elif a == "--pricing-input" and i + 1 < len(args):
pricing_input = float(args[i + 1]); i += 2
elif a == "--pricing-output" and i + 1 < len(args):
pricing_output = float(args[i + 1]); i += 2
else:
i += 1
if not base_url or not default_model or not env_key:
print("Error: --base-url, --default-model, and --env-key are required.", file=sys.stderr)
sys.exit(1)
from graphify.llm import provider_base_url_ok
if not provider_base_url_ok(base_url, name):
print(f"Error: refusing to add provider with unsafe base_url {base_url!r}.", file=sys.stderr)
sys.exit(1)
global_path.parent.mkdir(parents=True, exist_ok=True)
existing = {}
if global_path.is_file():
try:
existing = _json.loads(global_path.read_text(encoding="utf-8"))
except Exception:
pass
existing[name] = {
"base_url": base_url,
"default_model": default_model,
"env_key": env_key,
"pricing": {"input": pricing_input, "output": pricing_output},
"temperature": 0,
}
global_path.write_text(_json.dumps(existing, indent=2) + "\n", encoding="utf-8")
print(f"Provider '{name}' added. Use with: graphify extract . --backend {name}")
elif subcmd == "remove":
name = sys.argv[3] if len(sys.argv) > 3 else ""
if not name:
print("Usage: graphify provider remove <name>", file=sys.stderr)
sys.exit(1)
existing = {}
if global_path.is_file():
try:
existing = _json.loads(global_path.read_text(encoding="utf-8"))
except Exception:
pass
if name not in existing:
print(f"Provider '{name}' not found.", file=sys.stderr)
sys.exit(1)
del existing[name]
global_path.write_text(_json.dumps(existing, indent=2) + "\n", encoding="utf-8")
print(f"Provider '{name}' removed.")
else:
print("Usage: graphify provider [add|list|show|remove]", file=sys.stderr)
if subcmd:
sys.exit(1)
elif cmd == "prs":
from graphify.prs import cmd_prs
cmd_prs(sys.argv[2:])
elif cmd == "hook":
from graphify.hooks import (
install as hook_install,
uninstall as hook_uninstall,
status as hook_status,
)
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
print(hook_install(Path(".")))
elif subcmd == "uninstall":
print(hook_uninstall(Path(".")))
elif subcmd == "status":
print(hook_status(Path(".")))
else:
print("Usage: graphify hook [install|uninstall|status]", file=sys.stderr)
sys.exit(1)
elif cmd == "query":
if len(sys.argv) < 3:
print("Usage: graphify query \"<question>\" [--dfs] [--context C] [--budget N] [--graph path]", file=sys.stderr)
sys.exit(1)
from graphify.serve import _query_graph_text
from graphify.security import sanitize_label
from networkx.readwrite import json_graph
from graphify import querylog
question = sys.argv[2]
use_dfs = "--dfs" in sys.argv
budget = 2000
graph_path = _default_graph_path()
context_filters: list[str] = []
args = sys.argv[3:]
i = 0
while i < len(args):
if args[i] == "--budget" and i + 1 < len(args):
try:
budget = int(args[i + 1])
except ValueError:
print(f"error: --budget must be an integer", file=sys.stderr)
sys.exit(1)
i += 2
elif args[i].startswith("--budget="):
try:
budget = int(args[i].split("=", 1)[1])
except ValueError:
print(f"error: --budget must be an integer", file=sys.stderr)
sys.exit(1)
i += 1
elif args[i] == "--context" and i + 1 < len(args):
context_filters.append(args[i + 1])
i += 2
elif args[i].startswith("--context="):
context_filters.append(args[i].split("=", 1)[1])
i += 1
elif args[i] == "--graph" and i + 1 < len(args):
graph_path = args[i + 1]
i += 2
else:
i += 1
gp = Path(graph_path).resolve()
if not gp.exists():
print(f"error: graph file not found: {gp}", file=sys.stderr)
sys.exit(1)
if not gp.suffix == ".json":
print(f"error: graph file must be a .json file", file=sys.stderr)
sys.exit(1)
_enforce_graph_size_cap_or_exit(gp)
try:
import json as _json
import networkx as _nx
_raw = _json.loads(gp.read_text(encoding="utf-8"))
if "links" not in _raw and "edges" in _raw:
_raw = dict(_raw, links=_raw["edges"])
# `query` deliberately keeps the graph undirected (unlike `path` /
# `explain`, which force directed=True): BFS/DFS here must explore
# both callers and callees of the seed node to build useful
# context, and forcing a DiGraph would make G.neighbors() return
# successors only, silently dropping every caller-side result for
# a seed with no outgoing edges. Direction is instead preserved
# per-edge below (mirrors graphify/build.py's _src/_tgt pattern)
# so the *rendering* stays correct without narrowing traversal.
# Keep in-file markers when present (#2309): unconditionally
# overwriting them with source/target would clobber the true
# direction of a link persisted in flipped endpoint order.
_raw = dict(
_raw,
links=[
{
**link,
"_src": link.get("_src", link.get("source")),
"_tgt": link.get("_tgt", link.get("target")),
}
for link in _raw.get("links", [])
],
)
try:
G = json_graph.node_link_graph(_raw, edges="links")
except TypeError:
G = json_graph.node_link_graph(_raw)
try:
from graphify.build import graph_has_legacy_ids as _legacy
if _legacy(_raw.get("nodes", [])):
print(
"[graphify] note: this graph uses the pre-#1504 node-ID scheme; "
"rebuild with `graphify extract --force` to get path-qualified IDs "
"(fixes same-name-file collisions).",
file=sys.stderr,
)
except Exception:
pass
except Exception as exc:
print(f"error: could not load graph: {exc}", file=sys.stderr)
sys.exit(1)
import time as _time
_t0 = _time.perf_counter()
_mode = "dfs" if use_dfs else "bfs"
_result = _query_graph_text(
G,
question,
mode=_mode,
depth=2,
token_budget=budget,
context_filters=context_filters,
graph_path=str(gp),
)
querylog.log_query(
kind="query",
question=question,
corpus=str(gp),
result=_result,
mode=_mode,
depth=2,
token_budget=budget,
duration_ms=(_time.perf_counter() - _t0) * 1000,
)
_touch_query_stamp(gp)
print(_result)
elif cmd == "affected":
if len(sys.argv) < 3:
print("Usage: graphify affected \"<node-or-label>\" [--relation R] [--depth N] [--graph path]", file=sys.stderr)
sys.exit(1)
from graphify.affected import DEFAULT_AFFECTED_RELATIONS, format_affected, load_graph
query = sys.argv[2]
graph_path = _default_graph_path()
depth = 2
relations: list[str] = []
args = sys.argv[3:]
i = 0
while i < len(args):
if args[i] == "--graph" and i + 1 < len(args):
graph_path = args[i + 1]
i += 2
elif args[i].startswith("--graph="):
graph_path = args[i].split("=", 1)[1]
i += 1
elif args[i] == "--depth" and i + 1 < len(args):
try:
depth = int(args[i + 1])
except ValueError:
print("error: --depth must be an integer", file=sys.stderr)
sys.exit(1)
i += 2
elif args[i].startswith("--depth="):
try:
depth = int(args[i].split("=", 1)[1])
except ValueError:
print("error: --depth must be an integer", file=sys.stderr)
sys.exit(1)
i += 1
elif args[i] == "--relation" and i + 1 < len(args):
relations.append(args[i + 1])
i += 2
elif args[i].startswith("--relation="):
relations.append(args[i].split("=", 1)[1])
i += 1
else:
i += 1
gp = Path(graph_path).resolve()
if not gp.exists():
print(f"error: graph file not found: {gp}", file=sys.stderr)
sys.exit(1)
if not gp.suffix == ".json":
print("error: graph file must be a .json file", file=sys.stderr)
sys.exit(1)
try:
graph = load_graph(gp)
except Exception as exc:
print(f"error: could not load graph: {exc}", file=sys.stderr)
sys.exit(1)
# Derive the analysed repo root from the graph's own location so an
# absolute-path seed resolves without requiring cwd to be that root
# (#2706). The graph is written to <root>/<GRAPHIFY_OUT_NAME>/graph.json,
# so the root is the output dir's parent; a graph pointed at directly by
# --graph falls back to its own directory.
from graphify.paths import GRAPHIFY_OUT_NAME
graph_root = gp.parent.parent if gp.parent.name == GRAPHIFY_OUT_NAME else gp.parent
print(
format_affected(
graph,
query,
relations=relations or DEFAULT_AFFECTED_RELATIONS,
depth=depth,
root=graph_root,
)
)
elif cmd in ("god-nodes", "god_nodes"):
# god_nodes has long been an analyzer (analyze.py), an MCP tool, and a
# README-advertised capability, but never a CLI subcommand — `graphify
# god_nodes` fell through to "unknown command" (#2004). Wire it as a
# read-only graph query, mirroring `affected`.
from graphify.affected import load_graph
from graphify.analyze import god_nodes as _god_nodes
from graphify.security import sanitize_label as _sanitize_label
graph_path = _default_graph_path()
top_n = 10
as_json = "--json" in sys.argv
args = sys.argv[2:]
i = 0
while i < len(args):
if args[i] == "--graph" and i + 1 < len(args):
graph_path = args[i + 1]
i += 2
elif args[i].startswith("--graph="):
graph_path = args[i].split("=", 1)[1]
i += 1
elif args[i] == "--top" and i + 1 < len(args):
try:
top_n = int(args[i + 1])
except ValueError:
print("error: --top must be an integer", file=sys.stderr)
sys.exit(1)
i += 2
elif args[i].startswith("--top="):
try:
top_n = int(args[i].split("=", 1)[1])
except ValueError:
print("error: --top must be an integer", file=sys.stderr)
sys.exit(1)
i += 1
else:
i += 1
gp = Path(graph_path).resolve()
if not gp.exists():
print(f"error: graph file not found: {gp}", file=sys.stderr)
sys.exit(1)
if not gp.suffix == ".json":
print("error: graph file must be a .json file", file=sys.stderr)
sys.exit(1)
try:
G = load_graph(gp)
except Exception as exc:
print(f"error: could not load graph: {exc}", file=sys.stderr)
sys.exit(1)
gods = _god_nodes(G, top_n=top_n)
if as_json:
print(json.dumps(gods, indent=2))
else:
print("God nodes (most connected):")
for rank, n in enumerate(gods, 1):
print(f" {rank}. {_sanitize_label(str(n['label']))} - {n['degree']} edges")
elif cmd == "save-result":
# graphify save-result --question Q --answer A [--type T] [--nodes N1 N2 ...]
# [--outcome useful|dead_end|corrected] [--correction TEXT]
import argparse as _ap
p = _ap.ArgumentParser(prog="graphify save-result")
p.add_argument("--question", required=True)
p.add_argument("--answer", default=None)
p.add_argument("--answer-file", dest="answer_file", default=None)
p.add_argument("--type", dest="query_type", default="query")
p.add_argument("--nodes", nargs="*", default=[])
p.add_argument("--outcome", choices=("useful", "dead_end", "corrected"), default=None)
p.add_argument("--correction", default=None)
p.add_argument("--memory-dir", default=str(Path(_GRAPHIFY_OUT) / "memory"))
opts = p.parse_args(sys.argv[2:])
if opts.answer_file:
opts.answer = Path(opts.answer_file).read_text(encoding="utf-8").strip()
elif not opts.answer:
p.error("--answer or --answer-file is required")
from graphify.ingest import save_query_result as _sqr
out = _sqr(
question=opts.question,
answer=opts.answer,
memory_dir=Path(opts.memory_dir),
query_type=opts.query_type,
source_nodes=opts.nodes or None,
outcome=opts.outcome,
correction=opts.correction,
)
print(f"Saved to {out}")
elif cmd == "reflect":
import argparse as _ap
p = _ap.ArgumentParser(prog="graphify reflect")
p.add_argument("--memory-dir", default=str(Path(_GRAPHIFY_OUT) / "memory"))
p.add_argument(
"--out",
default=str(Path(_GRAPHIFY_OUT) / "reflections" / "LESSONS.md"),
)
p.add_argument("--graph", default=None)
p.add_argument("--analysis", default=None)
p.add_argument("--labels", default=None)
p.add_argument("--half-life-days", type=float, default=30.0,
help="signal weight halves every N days (default 30)")
p.add_argument("--min-corroboration", type=int, default=2,
help="distinct useful results to promote a node to preferred (default 2)")
p.add_argument("--if-stale", action="store_true",
help="skip when LESSONS.md is already newer than every input "
"(e.g. the git hook just refreshed it)")
opts = p.parse_args(sys.argv[2:])
from graphify.reflect import reflect as _reflect, lessons_fresh as _lessons_fresh
graph_arg = opts.graph
if graph_arg is None:
default_graph = Path(_GRAPHIFY_OUT) / "graph.json"
if default_graph.exists():
graph_arg = str(default_graph)
_gp = Path(graph_arg) if graph_arg else None
_analysis_path = None
_labels_path = None
if _gp is not None:
_analysis_path = Path(opts.analysis) if opts.analysis else (
_gp.parent / ".graphify_analysis.json")
_labels_path = Path(opts.labels) if opts.labels else (
_gp.parent / ".graphify_labels.json")
if opts.if_stale and _lessons_fresh(
Path(opts.out), Path(opts.memory_dir), _gp, _analysis_path, _labels_path
):
print(f"Lessons already up to date -> {opts.out} (skipped; omit --if-stale to force)")
else:
out_path, agg = _reflect(
memory_dir=Path(opts.memory_dir),
out_path=Path(opts.out),
graph_path=_gp,
analysis_path=_analysis_path,
labels_path=_labels_path,
half_life_days=opts.half_life_days,
min_corroboration=opts.min_corroboration,
)
c = agg["counts"]
print(
f"Reflected {agg['total']} memories "
f"({c['useful']} useful, {c['dead_end']} dead ends, "
f"{c['corrected']} corrected) -> {out_path}"
)
elif cmd == "path":
if len(sys.argv) < 4:
print(
'Usage: graphify path "<source>" "<target>" [--graph path] '
"[--directed|--undirected]",
file=sys.stderr,
)
sys.exit(1)
from graphify.serve import _pick_scored_endpoint, _score_nodes
from networkx.readwrite import json_graph
import networkx as _nx
source_label = sys.argv[2]
target_label = sys.argv[3]
graph_path = _default_graph_path()
args = sys.argv[4:]
direction_flag = None
for i, a in enumerate(args):
if a == "--graph" and i + 1 < len(args):
graph_path = args[i + 1]
elif a == "--directed":
if direction_flag == "undirected":
print(
"error: --directed and --undirected are mutually exclusive",
file=sys.stderr,
)
sys.exit(1)
direction_flag = "directed"
elif a == "--undirected":
if direction_flag == "directed":
print(
"error: --directed and --undirected are mutually exclusive",
file=sys.stderr,
)
sys.exit(1)
direction_flag = "undirected"
# Directed by default (#2487): direction truth exists in every
# graph.json (arc order on post-#563 files, _src/_tgt markers on legacy
# canonicalized files), so respect it unless the caller opts out.
undirected = direction_flag == "undirected"
gp = Path(graph_path).resolve()
if not gp.exists():
print(f"error: graph file not found: {gp}", file=sys.stderr)
sys.exit(1)
_enforce_graph_size_cap_or_exit(gp)
_raw = json.loads(gp.read_text(encoding="utf-8"))
if "links" not in _raw and "edges" in _raw:
_raw = dict(_raw, links=_raw["edges"])
# Force directed so the renderer can recover stored caller→callee
# direction, and multigraph so exact-pair parallel links (e.g. a
# `references` and a `calls` edge between the same two nodes) survive load
# instead of being silently collapsed last-writer-wins — otherwise the
# printed relation could be one the traversed pair doesn't actually
# carry (#2074). Local to this read; serve's shared graph is untouched.
_raw = {**_raw, "directed": True, "multigraph": True}
try:
G = json_graph.node_link_graph(_raw, edges="links")
except TypeError:
G = json_graph.node_link_graph(_raw)
src_scored = _score_nodes(G, [t.lower() for t in source_label.split()])
tgt_scored = _score_nodes(G, [t.lower() for t in target_label.split()])
if not src_scored:
print(f"No node matching '{source_label}' found.", file=sys.stderr)
sys.exit(1)
if not tgt_scored:
print(f"No node matching '{target_label}' found.", file=sys.stderr)
sys.exit(1)
src_nid = _pick_scored_endpoint(G, src_scored, source_label)
tgt_nid = _pick_scored_endpoint(G, tgt_scored, target_label)
# Ambiguity guard: when both queries resolve to the same node, the
# shortest path is trivially zero hops, which is almost never what the
# caller wanted (see bug #828).
if src_nid == tgt_nid:
print(
f"'{source_label}' and '{target_label}' both resolved to the same "
f"node '{src_nid}'. Use a more specific label or the exact node ID.",
file=sys.stderr,
)
sys.exit(1)
for _name, _scored, _nid in (
("source", src_scored, src_nid),
("target", tgt_scored, tgt_nid),
):
# A close runner-up only made the resolution ambiguous when the raw
# score head is what got picked; a full-token override was chosen on
# token coverage, not score, so the head's margin is irrelevant.
if len(_scored) >= 2 and _nid == _scored[0][1]:
_top, _runner = _scored[0][0], _scored[1][0]
if _top > 0 and (_top - _runner) / _top < 0.10:
print(
f"warning: {_name} match was ambiguous "
f"(top score {_top:g}, runner-up {_runner:g})",
file=sys.stderr,
)
# Deterministic shortest path (#2074): hash-seeded neighbor views
# returned an arbitrary route among equal-length paths that varied per
# process. Build a sorted, materialized graph so neighbor order — and
# thus the chosen path — is canonical for a given graph.json.
try:
if undirected:
_und = _nx.Graph()
_und.add_nodes_from(sorted(G.nodes))
_und.add_edges_from(sorted((min(u, v), max(u, v)) for u, v in G.edges()))
path_nodes = _nx.shortest_path(_und, src_nid, tgt_nid)
else:
# Directed by default (#2487). True direction is NOT raw arc
# order: legacy canonicalized files persist a flipped arc with
# _src/_tgt markers (#2309), so build the digraph from _src/_tgt
# (falling back to the loaded arc) rather than to_directed().
_dg = _nx.DiGraph()
_dg.add_nodes_from(sorted(G.nodes))
_dg.add_edges_from(sorted(
(d.get("_src", u), d.get("_tgt", v)) for u, v, d in G.edges(data=True)
))
path_nodes = _nx.shortest_path(_dg, src_nid, tgt_nid)
except (_nx.NetworkXNoPath, _nx.NodeNotFound):
if undirected:
print(f"No path found between '{source_label}' and '{target_label}'.")
else:
print(
f"No directed path found between '{source_label}' and "
f"'{target_label}'. Re-run with --undirected to search "
"ignoring edge direction."
)
sys.exit(0)
hops = len(path_nodes) - 1
segments = []
from graphify.build import edge_datas
for i in range(len(path_nodes) - 1):
u, v = path_nodes[i], path_nodes[i + 1]
# Report the ACTUAL stored relation(s) of the traversed pair and
# direction — never a fabricated `calls` (#2074). A pair may carry
# several parallel relations; show all, and fall back to an honest
# "related" when the stored edge has no relation.
# Direction truth lives in the per-link _src/_tgt markers (#2309):
# undirected NetworkX storage canonicalizes endpoint order, so the
# persisted source/target arc can be flipped relative to the real
# caller→callee direction. Recover it from _src when present, else
# fall back to the loaded arc tail (markerless canonical files keep
# today's behavior).
fwd, bwd = [], []
for a, b in ((u, v), (v, u)):
if G.has_edge(a, b):
for d in edge_datas(G, a, b):
(fwd if d.get("_src", a) == u else bwd).append(d)
datas = fwd or bwd
forward = bool(fwd)
rels = sorted({d.get("relation") for d in datas if d.get("relation")})
rel = "/".join(rels) if rels else "related"
confs = sorted({d.get("confidence") for d in datas if d.get("confidence")})
conf_str = f" [{'/'.join(confs)}]" if confs else ""
if i == 0:
segments.append(G.nodes[u].get("label", u))
if forward:
segments.append(f"--{rel}{conf_str}--> {G.nodes[v].get('label', v)}")
else:
segments.append(f"<--{rel}{conf_str}-- {G.nodes[v].get('label', v)}")
print(f"Shortest path ({hops} hops):\n " + " ".join(segments))
from graphify import querylog
querylog.log_query(
kind="path",
question=f"{sys.argv[2]} -> {sys.argv[3]}",
corpus=str(gp),
nodes_returned=hops,
)
_touch_query_stamp(gp)
elif cmd == "explain":
if len(sys.argv) < 3:
print('Usage: graphify explain "<node>" [--graph path]', file=sys.stderr)
sys.exit(1)
from graphify.serve import _find_node, find_node_ambiguity
from networkx.readwrite import json_graph
label = sys.argv[2]
graph_path = _default_graph_path()
args = sys.argv[3:]
for i, a in enumerate(args):
if a == "--graph" and i + 1 < len(args):
graph_path = args[i + 1]
gp = Path(graph_path).resolve()
if not gp.exists():
print(f"error: graph file not found: {gp}", file=sys.stderr)
sys.exit(1)
_enforce_graph_size_cap_or_exit(gp)
_raw = json.loads(gp.read_text(encoding="utf-8"))
if "links" not in _raw and "edges" in _raw:
_raw = dict(_raw, links=_raw["edges"])
# Force directed so the renderer can recover stored caller→callee direction.
_raw = {**_raw, "directed": True}
try:
G = json_graph.node_link_graph(_raw, edges="links")
except TypeError:
G = json_graph.node_link_graph(_raw)
matches = _find_node(G, label)
if not matches:
print(f"No node matching '{label}' found.")
sys.exit(0)
rivals = find_node_ambiguity(G, label)
if rivals:
print(f"Ambiguous: '{label}' matches {len(rivals)} nodes in different files.")
for rival in rivals:
print(f" {G.nodes[rival].get('source_file') or rival}")
print(f" id: {rival}")
print("Retry with the repo-relative path or the full node id.")
sys.exit(1)
nid = matches[0]
d = G.nodes[nid]
print(f"Node: {d.get('label', nid)}")
print(f" ID: {nid}")
print(
f" Source: {d.get('source_file', '')} {d.get('source_location', '')}".rstrip()
)
print(f" Type: {d.get('file_type', '')}")
print(f" Community: {d.get('community_name') or d.get('community', '')}")
# Work-memory overlay: a derived experiential hint from `graphify reflect`,
# merged in display-only from the .graphify_learning.json sidecar next to
# graph.json. No line when the node has no overlay entry.
try:
from graphify.reflect import load_learning_overlay as _llo
from graphify.security import sanitize_label as _sl
_overlay = _llo(gp)
_entry = _overlay.get(str(nid))
if _entry:
_status = _sl(str(_entry.get("status", "")))
if _status == "contested":
_line = (f" Lesson: contested (useful {_entry.get('uses', 0)} / "
f"dead-end {_entry.get('neg', 0)})")
elif _status == "preferred":
_line = (f" Lesson: preferred source (start here) — "
f"{_entry.get('uses', 0)} useful, score={_entry.get('score', 0)}")
else:
_line = (f" Lesson: {_status or 'tentative'} — "
f"{_entry.get('uses', 0)} useful, score={_entry.get('score', 0)}")
if _entry.get("stale"):
_line += " [code changed since — re-verify]"
print(_line)
except Exception:
pass
print(f" Degree: {G.degree(nid)}")
from graphify.build import edge_data
connections: list[tuple[str, str, dict]] = [] # (direction, neighbor_id, edge_data)
# Classify by the edge's TRUE direction, not the loaded arc order:
# a link persisted in flipped endpoint order carries its truth in the
# per-edge _src marker (#2309). Markerless edges fall back to the arc
# tail (today's behavior).
for nb in G.successors(nid):
_ed = edge_data(G, nid, nb)
connections.append(
("out" if _ed.get("_src", nid) == nid else "in", nb, _ed)
)
for nb in G.predecessors(nid):
_ed = edge_data(G, nb, nid)
connections.append(
("in" if _ed.get("_src", nb) == nb else "out", nb, _ed)
)
if connections:
print(f"\nConnections ({len(connections)}):")
connections.sort(key=lambda c: G.degree(c[1]), reverse=True)
for direction, nb, edata in connections[:20]:
rel = edata.get("relation", "")
conf = edata.get("confidence", "")
arrow = "-->" if direction == "out" else "<--"
# Append the edge's location — the actual call/import/reference
# SITE (in the caller's file for an incoming call), not a def
# line (#BUG1). Labeled by [rel] so the meaning is unambiguous.
loc = edata.get("source_location") or ""
sfile = edata.get("source_file") or ""
at = f" {sfile}:{loc}" if loc else ""
print(f" {arrow} {G.nodes[nb].get('label', nb)} [{rel}] [{conf}]{at}")
if len(connections) > 20:
remainder = connections[20:]
print(f" ... and {len(remainder)} more")
# #2009: a bare count silently hides the answer on high-degree
# nodes ("who calls this, what's the impact?"). Group the cut
# connections by direction + file so their shape is visible
# without falling back to a repo-wide grep.
by_file: dict[tuple[str, str], int] = {}
for direction, _nb, edata in remainder:
sfile = edata.get("source_file") or "(unknown file)"
key = (direction, sfile)
by_file[key] = by_file.get(key, 0) + 1
# Count desc, then (direction, file) so equal-count groups have a
# byte-stable order (not the degree-derived insertion order).
grouped = sorted(by_file.items(), key=lambda kv: (-kv[1], kv[0]))
print(" Grouped by file:")
for (direction, sfile), count in grouped[:20]:
arrow = "-->" if direction == "out" else "<--"
noun = "connection" if count == 1 else "connections"
print(f" {arrow} {sfile}: {count} {noun}")
if len(grouped) > 20:
print(f" ... and {len(grouped) - 20} more files")
from graphify import querylog
querylog.log_query(
kind="explain",
question=sys.argv[2],
corpus=str(gp),
nodes_returned=len(connections),
)
_touch_query_stamp(gp)
elif cmd == "diagnose":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd != "multigraph":
print(
"Usage: graphify diagnose multigraph "
"[--graph path] [--json] [--max-examples N] "
"[--directed] [--undirected] [--extract-path path]",
file=sys.stderr,
)
sys.exit(1)
graph_path = Path(_default_graph_path())
max_examples = 5
directed: bool | None = None
direction_flag: str | None = None
json_output = False
extract_path: Path | None = None
i = 3
while i < len(sys.argv):
arg = sys.argv[i]
if arg == "--graph":
i += 1
if i >= len(sys.argv):
print("error: --graph requires a path", file=sys.stderr)
sys.exit(1)
graph_path = Path(sys.argv[i])
elif arg == "--json":
json_output = True
elif arg == "--max-examples":
i += 1
if i >= len(sys.argv):
print("error: --max-examples requires an integer", file=sys.stderr)
sys.exit(1)
try:
max_examples = int(sys.argv[i])
except ValueError:
print("error: --max-examples requires an integer", file=sys.stderr)
sys.exit(1)
if max_examples < 0:
print("error: --max-examples must be >= 0", file=sys.stderr)
sys.exit(1)
elif arg == "--directed":
if direction_flag == "undirected":
print(
"error: --directed and --undirected are mutually exclusive",
file=sys.stderr,
)
sys.exit(1)
direction_flag = "directed"
directed = True
elif arg == "--undirected":
if direction_flag == "directed":
print(
"error: --directed and --undirected are mutually exclusive",
file=sys.stderr,
)
sys.exit(1)
direction_flag = "undirected"
directed = False
elif arg == "--extract-path":
i += 1
if i >= len(sys.argv):
print("error: --extract-path requires a path", file=sys.stderr)
sys.exit(1)
extract_path = Path(sys.argv[i])
else:
print(f"error: unknown diagnose option {arg}", file=sys.stderr)
sys.exit(1)
i += 1
from graphify.diagnostics import (
diagnose_file,
format_diagnostic_json,
format_diagnostic_report,
)
try:
summary = diagnose_file(
graph_path,
directed=directed,
root=Path(".").resolve(),
max_examples=max_examples,
extract_path=extract_path,
)
except Exception as exc:
print(f"error: {exc}", file=sys.stderr)
sys.exit(1)
if json_output:
print(json.dumps(format_diagnostic_json(summary), indent=2))
else:
print(format_diagnostic_report(summary))
elif cmd == "add":
if len(sys.argv) < 3:
print(
"Usage: graphify add <url> [--author Name] [--contributor Name] [--dir ./raw]",
file=sys.stderr,
)
sys.exit(1)
from graphify.ingest import ingest as _ingest
url = sys.argv[2]
author: str | None = None
contributor: str | None = None
target_dir = Path("raw")
args = sys.argv[3:]
i = 0
while i < len(args):
if args[i] == "--author" and i + 1 < len(args):
author = args[i + 1]
i += 2
elif args[i] == "--contributor" and i + 1 < len(args):
contributor = args[i + 1]
i += 2
elif args[i] == "--dir" and i + 1 < len(args):
target_dir = Path(args[i + 1])
i += 2
else:
i += 1
try:
saved = _ingest(url, target_dir, author=author, contributor=contributor)
print(f"Saved to {saved}")
print("Run /graphify --update in your AI assistant to update the graph.")
except Exception as exc:
print(f"error: {exc}", file=sys.stderr)
sys.exit(1)
elif cmd == "watch":
watch_path = Path(sys.argv[2]) if len(sys.argv) > 2 else Path(".")
if not watch_path.exists():
print(f"error: path not found: {watch_path}", file=sys.stderr)
sys.exit(1)
from graphify.watch import watch as _watch
try:
_watch(watch_path)
except ImportError as exc:
print(f"error: {exc}", file=sys.stderr)
sys.exit(1)
elif cmd in ("cluster-only", "label"):
# `label` is `cluster-only` that always (re)generates community names with
# the configured backend, even when a .graphify_labels.json already exists.
force_relabel = cmd == "label"
# Mirror the tree/export arg-parsing pattern: walk argv so flags and
# the optional positional path can appear in any order (#724).
no_viz = "--no-viz" in sys.argv
no_label = "--no-label" in sys.argv
missing_only = "--missing-only" in sys.argv
co_timing = "--timing" in sys.argv
_backend_arg = next((a for a in sys.argv if a.startswith("--backend=")), None)
label_backend = _backend_arg.split("=", 1)[1] if _backend_arg else None
_model_arg = next((a for a in sys.argv if a.startswith("--model=")), None)
label_model = _model_arg.split("=", 1)[1] if _model_arg else None
_min_cs_arg = next((a for a in sys.argv if a.startswith("--min-community-size=")), None)
min_community_size = int(_min_cs_arg.split("=")[1]) if _min_cs_arg else 3
args = sys.argv[2:]
watch_path: Path | None = None
graph_override: Path | None = None
co_resolution: float = 1.0
co_exclude_hubs: float | None = None
label_max_concurrency: int = 4
label_batch_size: int = 100
# #2534: defaults make presence undetectable for these, so track whether
# the user actually passed them — the label-reuse branch below warns when
# labeling flags are silently ignored. (--backend/--model default to None,
# so `is not None` already means "explicitly passed" for those.)
label_max_concurrency_explicit = False
label_batch_size_explicit = False
i_arg = 0
while i_arg < len(args):
a = args[i_arg]
if a == "--graph" and i_arg + 1 < len(args):
graph_override = Path(args[i_arg + 1]); i_arg += 2
elif a == "--backend" and i_arg + 1 < len(args):
label_backend = args[i_arg + 1]; i_arg += 2
elif a.startswith("--backend="):
label_backend = a.split("=", 1)[1]; i_arg += 1
elif a == "--model" and i_arg + 1 < len(args):
label_model = args[i_arg + 1]; i_arg += 2
elif a.startswith("--model="):
label_model = a.split("=", 1)[1]; i_arg += 1
elif a == "--resolution" and i_arg + 1 < len(args):
co_resolution = float(args[i_arg + 1]); i_arg += 2
elif a.startswith("--resolution="):
co_resolution = float(a.split("=", 1)[1]); i_arg += 1
elif a == "--exclude-hubs" and i_arg + 1 < len(args):
co_exclude_hubs = float(args[i_arg + 1]); i_arg += 2
elif a.startswith("--exclude-hubs="):
co_exclude_hubs = float(a.split("=", 1)[1]); i_arg += 1
elif a == "--max-concurrency" and i_arg + 1 < len(args):
label_max_concurrency = int(args[i_arg + 1]); label_max_concurrency_explicit = True; i_arg += 2
elif a.startswith("--max-concurrency="):
label_max_concurrency = int(a.split("=", 1)[1]); label_max_concurrency_explicit = True; i_arg += 1
elif a == "--batch-size" and i_arg + 1 < len(args):
label_batch_size = int(args[i_arg + 1]); label_batch_size_explicit = True; i_arg += 2
elif a.startswith("--batch-size="):
label_batch_size = int(a.split("=", 1)[1]); label_batch_size_explicit = True; i_arg += 1
elif a in ("--no-viz", "--missing-only") or a.startswith("--min-community-size="):
i_arg += 1
elif a.startswith("--"):
i_arg += 1
elif watch_path is None:
watch_path = Path(a); i_arg += 1
else:
i_arg += 1
if watch_path is None:
watch_path = Path(".")
graph_json = graph_override if graph_override is not None else watch_path / _GRAPHIFY_OUT / "graph.json"
if not graph_json.exists():
print(
f"error: no graph found at {graph_json} — run /graphify first",
file=sys.stderr,
)
sys.exit(1)
from networkx.readwrite import json_graph as _jg
from graphify.build import build_from_json
from graphify.cluster import cluster, score_all, remap_communities_to_previous
from graphify.analyze import (
god_nodes,
surprising_connections,
suggest_questions,
)
from graphify.report import generate
from graphify.export import to_json, to_html
stages = _StageTimer(co_timing)
print("Loading existing graph...")
# Solution 3 (#1019): don't hard-exit on an oversized graph.json here.
# Core outputs (graph.json + GRAPH_REPORT.md) still get written. The
# visualization policy below uses its own node-count limit.
from graphify.security import check_graph_file_size_cap as _check_cap
try:
_check_cap(graph_json)
except ValueError:
try:
_over_cap_bytes = graph_json.stat().st_size
except OSError:
_over_cap_bytes = -1
print(
f"warning: graph.json exceeds cap ({_over_cap_bytes} bytes); "
"continuing with best-effort visualization",
file=sys.stderr,
)
_raw = json.loads(graph_json.read_text(encoding="utf-8"))
_directed = bool(_raw.get("directed", False))
G = build_from_json(_raw, directed=_directed)
print(f"Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges")
stages.mark("load")
print("Re-clustering...")
communities = cluster(G, resolution=co_resolution, exclude_hubs_percentile=co_exclude_hubs)
# Mirror the watch/update path (#822): map new cids to prior ones by
# node-overlap so the existing .graphify_labels.json keeps attaching
# to the same conceptual community after re-clustering. Without this,
# labels follow raw cid index and become misaligned whenever the
# graph has changed between labeling and cluster-only (#1027).
previous_node_community = {
n["id"]: n["community"]
for n in _raw.get("nodes", [])
if n.get("community") is not None and n.get("id") is not None
}
if previous_node_community:
communities = remap_communities_to_previous(communities, previous_node_community)
stages.mark("cluster")
cohesion = score_all(G, communities)
gods = god_nodes(G)
surprises = surprising_connections(G, communities)
stages.mark("analyze")
# Where outputs (GRAPH_REPORT.md, re-clustered graph.json, labels,
# analysis, html) land. When `--graph` points at a graph INSIDE a
# graphify-out/ dir (another project/tenant's output), write beside it,
# not into a stray graphify-out/ in the CWD (#1747). But when `--graph`
# points at an arbitrary path — e.g. a `backup/graph.json` archived
# before re-clustering (#934) — fall back to the CWD's graphify-out/,
# which is the restore-into-place workflow that test pins. The default
# (no --graph) case already has graph_json under watch_path/graphify-out.
_out_name = Path(_GRAPHIFY_OUT).name
if graph_override is not None and graph_json.parent.name == _out_name:
out = graph_json.parent
else:
out = watch_path / _GRAPHIFY_OUT
out.mkdir(parents=True, exist_ok=True)
labels_path = out / ".graphify_labels.json"
existing_labels: dict[int, str] = {}
if labels_path.exists():
try:
existing_labels = {
int(k): v
for k, v in json.loads(labels_path.read_text(encoding="utf-8")).items()
if isinstance(v, str)
}
except Exception:
existing_labels = {}
# Accumulate token usage from the labeling LLM calls so cluster-only mode
# reports real cost instead of a hardcoded zero (#1694). Stays {0, 0} on
# the reuse / no-label paths, which make no LLM calls.
label_token_usage = {"input": 0, "output": 0}
# #2073: a --no-label run produces only "Community N" placeholders.
# Persisting them (plus a matching .sig) made the reuse branch treat them
# as fresh forever, permanently blocking real labeling on later runs.
placeholder_only = False
if labels_path.exists() and not force_relabel:
# #2534: this branch never calls the LLM, so labeling flags would be
# silently ignored. Reuse is still the correct (exit 0) outcome — but
# say so, instead of letting `--backend openai` look like it relabeled.
_ignored_label_flags = [flag for flag, given in (
("--backend", label_backend is not None),
("--model", label_model is not None),
("--batch-size", label_batch_size_explicit),
("--max-concurrency", label_max_concurrency_explicit),
) if given]
if _ignored_label_flags:
print(
f"[graphify] warning: {'/'.join(_ignored_label_flags)} ignored: "
f"reusing saved labels at {labels_path}. "
f"Run `graphify label` to relabel, or delete the labels file.",
file=sys.stderr,
)
# Reuse saved labels, but don't blindly trust them: the graph may have
# been re-scoped/re-clustered since labeling, in which case a cid now
# covers a DIFFERENT community and its old (LLM) name is wrong (#label-stale).
# Validate each community against the membership signature saved beside the
# labels; any community that changed (or has no saved label) is renamed by
# its current hub — deterministic and correct-by-construction — and the user
# is told to `graphify label` for fresh LLM names. Unchanged communities keep
# their saved label. When no signature sidecar exists (labels predate this),
# fall back to hub-filling only the communities missing a label.
from graphify.cluster import community_member_sigs, label_communities_by_hub
sig_path = labels_path.parent / (labels_path.name + ".sig")
saved_sigs: dict[int, str] = {}
if sig_path.exists():
try:
saved_sigs = {
int(k): v for k, v in
json.loads(sig_path.read_text(encoding="utf-8")).items()
if isinstance(v, str)
}
except Exception:
saved_sigs = {}
cur_sigs = community_member_sigs(communities)
count_mismatch = len(existing_labels) != len(communities)
labels = {}
hub_labels: dict[int, str] | None = None
changed = 0
for cid in communities:
# A persisted "Community {cid}" is a placeholder, not an earned
# label — treat it as absent so the hub labeler replaces it and an
# already-polluted sidecar (e.g. from a prior --no-label run) heals
# instead of suppressing real labels forever (#2073).
have_label = (
cid in existing_labels
and existing_labels[cid] != f"Community {cid}"
)
if saved_sigs:
# Precise: the membership signature tells us if this exact
# community changed since it was labeled.
fresh = have_label and saved_sigs.get(cid) == cur_sigs.get(cid)
else:
# No signature sidecar (labels predate it). A differing community
# COUNT means the labels describe a different clustering, so a cid's
# old label can't be trusted; equal count is the best "same" signal.
fresh = have_label and not count_mismatch
if fresh:
labels[cid] = existing_labels[cid]
else:
if hub_labels is None:
hub_labels = label_communities_by_hub(G, communities)
labels[cid] = hub_labels[cid]
if have_label:
changed += 1
if changed:
print(
f"[graphify] community set changed since labeling "
f"({len(existing_labels)} saved labels, {len(communities)} communities now; "
f"renamed {changed} community(ies) by their hub). "
f"Run `graphify label` to refresh names with the LLM.",
file=sys.stderr,
)
elif no_label and not force_relabel:
labels = {cid: f"Community {cid}" for cid in communities}
placeholder_only = True
else:
# No labels file yet (or `graphify label` forced a refresh). When run
# standalone there is no orchestrating agent to do skill.md Step 5, so
# auto-name communities rather than leave "Community N" (#1097).
from graphify.cluster import label_communities_by_hub
from graphify.llm import generate_community_labels
print("Labeling communities...")
# Deterministic, LLM-free base labels: name each community after its
# highest-degree hub, so the report is readable even with no backend
# (previously bare "Community N"). A configured LLM backend overrides these
# with richer names below; its no-backend placeholder fallback does NOT.
hub_labels = label_communities_by_hub(G, communities)
label_communities_input = communities
labels = dict(hub_labels)
if missing_only:
labels = {
cid: existing_labels.get(cid, hub_labels[cid])
for cid in communities
}
label_communities_input = {
cid: members
for cid, members in communities.items()
if cid not in existing_labels or existing_labels.get(cid) == f"Community {cid}"
}
generated_labels, _ = generate_community_labels(
G, label_communities_input, backend=label_backend, model=label_model, gods=gods,
max_concurrency=label_max_concurrency, batch_size=label_batch_size,
usage_out=label_token_usage,
)
# Only let the LLM OVERRIDE where it produced a real name — its no-backend
# fallback returns "Community {cid}" placeholders, which must not clobber
# the deterministic hub labels. Also reject a model echoing the prompt
# key back ("5" for community 5) — that is an id, not a name (#2534).
labels.update({
cid: v for cid, v in generated_labels.items()
if v and v != f"Community {cid}" and v != str(cid)
})
stages.mark("label")
questions = suggest_questions(G, communities, labels)
# cluster-only re-clusters an EXISTING graph: the code content is exactly
# what extract saw, so keep the extract-time commit stamp instead of
# re-deriving it from the shell's cwd — running from another repo used to
# re-stamp graph.json with THAT repo's HEAD (#2534). When the loaded
# graph predates the stamp, fall back to the analysed repo's HEAD via
# the cwd-aware helper (#2316).
_commit = _raw.get("built_at_commit")
if not _commit:
from graphify.watch import _git_head as _gh
_commit = _gh(cwd=watch_path)
# Snapshot BEFORE any artifact is replaced: GRAPH_REPORT.md was written
# first, so the dated folder held the NEW report, not the previous (#2402).
from graphify.export import backup_if_protected as _backup
from graphify.exporters.html import _HTML_STALE_MARKER
_backup(out)
html_stale_marker = out / _HTML_STALE_MARKER
def _clear_html_stale_marker() -> None:
try:
html_stale_marker.unlink(missing_ok=True)
except OSError as exc:
print(
"warning: graph.html stale marker could not be cleared; "
f"regeneration may be retried: {exc}",
file=sys.stderr,
)
stale_marker_preexisted = html_stale_marker.exists()
# Mark before graph.json advances. Report/sidecar generation or process
# interruption must not leave an older HTML looking current.
html_stale_marker.touch()
# The #479 guard can refuse this write, so it goes before the sidecars —
# a report and labels describing a clustering graph.json does not contain
# are worse than no run at all (#2436).
if not to_json(G, communities, str(out / "graph.json"),
community_labels=labels, built_at_commit=_commit):
if not stale_marker_preexisted:
_clear_html_stale_marker()
print(
"graph.json NOT written: refusing to overwrite (see warning above). "
"GRAPH_REPORT.md, .graphify_labels.json and .graphify_analysis.json "
"left untouched.",
file=sys.stderr,
)
sys.exit(1)
tokens = label_token_usage
from graphify.report import load_learning_for_report as _llfr
report = generate(G, communities, cohesion, labels, gods, surprises,
{"warning": "cluster-only mode — file stats not available"},
tokens, str(watch_path), suggested_questions=questions,
min_community_size=min_community_size, built_at_commit=_commit,
learning=_llfr(out / "graph.json"))
(out / "GRAPH_REPORT.md").write_text(report, encoding="utf-8")
stages.mark("report")
analysis = {
"communities": {str(k): v for k, v in communities.items()},
"cohesion": {str(k): v for k, v in cohesion.items()},
"gods": gods,
"surprises": surprises,
"questions": questions,
}
(out / ".graphify_analysis.json").write_text(
json.dumps(analysis, indent=2, ensure_ascii=False),
encoding="utf-8",
)
# Don't persist placeholder-only labels (or their .sig): leaving the
# sidecar absent lets a later run generate real labels instead of reading
# back "Community N" as authoritative (#2073).
if not placeholder_only:
from graphify.paths import write_json_atomic as _wja
_wja(labels_path, {str(k): v for k, v in labels.items()}, ensure_ascii=False)
# Membership signatures beside the labels so a later cluster-only can
# detect which communities changed and avoid reusing a stale label
# (see reuse above).
from graphify.cluster import community_member_sigs as _cms
(labels_path.parent / (labels_path.name + ".sig")).write_text(
json.dumps({str(k): v for k, v in _cms(communities).items()}), encoding="utf-8")
# Mirror watch.py pattern: gate to_html so core outputs (graph.json +
# GRAPH_REPORT.md) always land. Honor --no-viz explicitly; otherwise
# fall back to ValueError handling so an oversized graph doesn't crash
# the CLI mid-write and leave a stale graph.html on disk.
html_target = out / "graph.html"
if no_viz:
if html_target.exists():
html_target.unlink()
_clear_html_stale_marker()
stages.mark("export"); stages.total()
print(f"Done - {len(communities)} communities. GRAPH_REPORT.md and graph.json updated (--no-viz; graph.html removed).")
else:
html_written = False
skip_reason: str | None = None
try:
from graphify.exporters.html import _viz_node_limit
viz_limit = _viz_node_limit()
if viz_limit <= 0:
html_target.unlink(missing_ok=True)
_clear_html_stale_marker()
skip_reason = "GRAPHIFY_VIZ_NODE_LIMIT=0 disables HTML visualization"
else:
# Passing the positive visualization limit explicitly selects
# the community meta-graph when the full graph is too large.
html_written = to_html(
G,
communities,
str(html_target),
community_labels=labels or None,
node_limit=viz_limit,
)
if html_written:
_clear_html_stale_marker()
else:
skip_reason = "no useful community aggregation could be generated"
if html_target.exists():
skip_reason += "; existing graph.html left unchanged"
except ValueError as viz_err:
skip_reason = str(viz_err)
if html_target.exists():
skip_reason += "; existing graph.html left unchanged"
if skip_reason:
print(f"Skipped graph.html: {skip_reason}")
stages.mark("export"); stages.total()
if html_written:
print(f"Done - {len(communities)} communities. GRAPH_REPORT.md, graph.json and graph.html updated.")
else:
print(f"Done - {len(communities)} communities. GRAPH_REPORT.md and graph.json updated.")
elif cmd == "update":
force = os.environ.get("GRAPHIFY_FORCE", "").lower() in ("1", "true", "yes")
no_cluster = False
args = sys.argv[2:]
watch_arg: str | None = None
for a in args:
if a == "--force":
force = True
continue
if a == "--no-cluster":
no_cluster = True
continue
if a.startswith("-"):
print(f"error: unknown update option: {a}", file=sys.stderr)
sys.exit(2)
if watch_arg is not None:
print("error: update accepts at most one path argument", file=sys.stderr)
sys.exit(2)
watch_arg = a
if watch_arg is not None:
watch_path = Path(watch_arg)
else:
# Try to recover the scan root saved by the last full build
saved = Path(_GRAPHIFY_OUT) / ".graphify_root"
if saved.exists():
watch_path = Path(saved.read_text(encoding="utf-8").strip())
else:
watch_path = Path(".")
if not watch_path.exists():
print(f"error: path not found: {watch_path}", file=sys.stderr)
sys.exit(1)
from graphify.watch import _rebuild_code
print(f"Re-extracting code files in {watch_path} (no LLM needed)...")
# Interactive CLI: block on the per-repo lock rather than skip, so the
# user sees their explicit `graphify update` complete instead of
# exiting silently when a hook-driven rebuild happens to be running.
ok = _rebuild_code(watch_path, force=force, no_cluster=no_cluster, block_on_lock=True)
if ok:
print("Code graph updated. For doc/paper/image changes run /graphify --update in your AI assistant.")
if not (
os.environ.get("GEMINI_API_KEY")
or os.environ.get("GOOGLE_API_KEY")
or os.environ.get("MOONSHOT_API_KEY")
or os.environ.get("DEEPSEEK_API_KEY")
or os.environ.get("GRAPHIFY_NO_TIPS")
):
print("Tip: set GEMINI_API_KEY or GOOGLE_API_KEY to use Gemini for semantic extraction.")
else:
print(
"Nothing to update or rebuild failed — check output above.",
file=sys.stderr,
)
sys.exit(1)
elif cmd == "hook-check":
# Codex Desktop rejects hookSpecificOutput.additionalContext on PreToolUse.
# Keep this as a cross-platform no-op so installed hooks never break Bash
# tool calls. Graph guidance reaches the agent via AGENTS.md / skill instead.
sys.exit(0)
elif cmd == "hook-guard":
# Shell-agnostic Claude/Codebuddy PreToolUse guard (#522). Replaces the old
# inline-bash hooks that failed on Windows. Prints an additionalContext nudge
# toward graphify when a fresh in-project graph exists; always exits 0. In
# strict mode (opt-in, `hook-guard read --strict`) it blocks the first raw
# read per session via the JSON permissionDecision payload — never via exit
# code — and downgrades to the nudge thereafter.
_run_hook_guard(
sys.argv[2] if len(sys.argv) > 2 else "",
strict="--strict" in sys.argv[3:],
)
sys.exit(0)
elif cmd == "check-update":
if len(sys.argv) < 3:
print("Usage: graphify check-update <path>", file=sys.stderr)
sys.exit(1)
from graphify.watch import check_update
check_update(Path(sys.argv[2]).resolve())
sys.exit(0)
elif cmd == "tree":
# Emit a D3 v7 collapsible-tree HTML view of graph.json:
# expand-all / collapse-all / reset-view buttons, multi-line
# wrapText labels with separately-coloured name + count,
# depth-based palette, click-to-toggle subtree, hover inspector
# showing top-K outbound edges per symbol.
from typing import Optional as _Opt
from graphify.tree_html import write_tree_html, DEFAULT_MAX_CHILDREN
graph_path = Path(_GRAPHIFY_OUT) / "graph.json"
output_path: "_Opt[Path]" = None
root: "_Opt[str]" = None
max_children = DEFAULT_MAX_CHILDREN
top_k_edges = 0
project_label: "_Opt[str]" = None
args = sys.argv[2:]
i_arg = 0
while i_arg < len(args):
a = args[i_arg]
if a == "--graph" and i_arg + 1 < len(args):
graph_path = Path(args[i_arg + 1]); i_arg += 2
elif a == "--output" and i_arg + 1 < len(args):
output_path = Path(args[i_arg + 1]); i_arg += 2
elif a == "--root" and i_arg + 1 < len(args):
root = args[i_arg + 1]; i_arg += 2
elif a == "--max-children" and i_arg + 1 < len(args):
max_children = int(args[i_arg + 1]); i_arg += 2
elif a == "--top-k-edges" and i_arg + 1 < len(args):
top_k_edges = int(args[i_arg + 1]); i_arg += 2
elif a == "--label" and i_arg + 1 < len(args):
project_label = args[i_arg + 1]; i_arg += 2
elif a in ("-h", "--help"):
print("Usage: graphify tree [--graph PATH] [--output HTML]")
print(" --graph PATH path to graph.json (default graphify-out/graph.json)")
print(" --output HTML output path (default graphify-out/GRAPH_TREE.html)")
print(" --root PATH filesystem root (default: longest common dir of all source_files)")
print(" --max-children N cap visible children per node (default 200)")
print(" --top-k-edges N pre-compute top-K outbound edges per symbol (default 12)")
print(" --label NAME project label shown in the page header")
return
else:
i_arg += 1
if not graph_path.is_file():
print(f"error: graph.json not found at {graph_path}", file=sys.stderr)
sys.exit(1)
_enforce_graph_size_cap_or_exit(graph_path)
if output_path is None:
output_path = graph_path.parent / "GRAPH_TREE.html"
try:
out = write_tree_html(
graph_path=graph_path, output_path=output_path,
root=root, max_children=max_children,
top_k_edges=top_k_edges, project_label=project_label,
)
except ValueError as exc:
# e.g. an explicit --root that matches no source_file — the tree
# would silently flatten, so fail loudly instead (#2534).
print(f"error: {exc}", file=sys.stderr)
sys.exit(1)
size_kb = out.stat().st_size / 1024
print(f"wrote {out} ({size_kb:.1f} KB)")
print(f"open with: xdg-open {out} (or file://{out.resolve()})")
sys.exit(0)
elif cmd == "merge-driver":
# git merge driver for graph.json — takes (base, current, other) and writes
# the union of current+other nodes/edges back to current. Exits 1 on
# corrupt input so git surfaces the conflict instead of silently
# accepting a poisoned merge (see F-005).
# Usage: graphify merge-driver %O %A %B (set in .git/config merge driver)
if len(sys.argv) < 5:
print("Usage: graphify merge-driver <base> <current> <other>", file=sys.stderr)
sys.exit(1)
_base_path, _current_path, _other_path = sys.argv[2], sys.argv[3], sys.argv[4]
# Hard caps so a malicious or corrupted graph.json cannot exhaust memory
# at parse time. 50 MB / 100k nodes are well above any realistic graph
# (typical graphs are <5 MB / <50k nodes); anything larger should fail
# the merge so a human can investigate.
_MERGE_MAX_BYTES = 50 * 1024 * 1024
_MERGE_MAX_NODES = 100_000
import networkx as _nx
from networkx.readwrite import json_graph as _jg
def _load_graph(p: str):
path_obj = Path(p)
try:
size = path_obj.stat().st_size
except OSError as exc:
raise RuntimeError(f"cannot stat {p}: {exc}") from exc
if size > _MERGE_MAX_BYTES:
raise RuntimeError(
f"graph.json {p} is {size} bytes, exceeds {_MERGE_MAX_BYTES}-byte cap"
)
data = json.loads(path_obj.read_text(encoding="utf-8"))
# A committed raw (--no-cluster) graph stores edges under "edges";
# parse via the shared links/edges-normalizing loader (#2212).
from graphify.paths import load_node_link_graph as _lnlg
return _lnlg(data), data
try:
G_cur, _ = _load_graph(_current_path)
G_oth, _ = _load_graph(_other_path)
except Exception as exc:
print(f"[graphify merge-driver] error loading graphs: {exc}", file=sys.stderr)
sys.exit(1) # surface the conflict so git doesn't accept a corrupt merge
merged = _nx.compose(G_cur, G_oth)
if merged.number_of_nodes() > _MERGE_MAX_NODES:
print(
f"[graphify merge-driver] merged graph has {merged.number_of_nodes()} nodes, "
f"exceeds {_MERGE_MAX_NODES}-node cap; aborting merge.",
file=sys.stderr,
)
sys.exit(1)
try:
out_data = _jg.node_link_data(merged, edges="links")
except TypeError:
out_data = _jg.node_link_data(merged)
from graphify.paths import write_json_atomic
write_json_atomic(_current_path, out_data, indent=2)
sys.exit(0)
elif cmd == "merge-graphs":
# graphify merge-graphs graph1.json graph2.json ... --out merged.json
args = sys.argv[2:]
graph_paths: list[Path] = []
out_path = Path(_GRAPHIFY_OUT) / "merged-graph.json"
i = 0
while i < len(args):
if args[i] == "--out" and i + 1 < len(args):
out_path = Path(args[i + 1])
i += 2
else:
graph_paths.append(Path(args[i]))
i += 1
if len(graph_paths) < 2:
print(
"Usage: graphify merge-graphs <graph1.json> <graph2.json> [...] [--out merged.json]",
file=sys.stderr,
)
sys.exit(1)
import networkx as _nx
from networkx.readwrite import json_graph as _jg
from graphify.build import prefix_graph_for_global as _prefix, distinct_repo_tags as _repo_tags
graphs = []
for gp in graph_paths:
if not gp.exists():
print(f"error: not found: {gp}", file=sys.stderr)
sys.exit(1)
_enforce_graph_size_cap_or_exit(gp)
data = json.loads(gp.read_text(encoding="utf-8"))
# Normalize edges/links key before loading — graphify writes "links"
# via node_link_data but older runs may have used "edges" (#738).
if "links" not in data and "edges" in data:
data = dict(data, links=data["edges"])
# Preserve stored edge direction across undirected node_link_graph (#2261).
# Mirrors cli.py's query pattern and export.py's _src/_tgt restoration.
# Keep in-file markers when present (#2309): unconditionally
# overwriting them with source/target would clobber the true
# direction of a link persisted in flipped endpoint order.
data = dict(
data,
links=[
{
**link,
"_src": link.get("_src", link.get("source")),
"_tgt": link.get("_tgt", link.get("target")),
}
for link in data.get("links", [])
],
)
try:
G = _jg.node_link_graph(data, edges="links")
except TypeError:
G = _jg.node_link_graph(data)
# node_link_graph restores only the nested `graph.hyperedges` slot;
# a graph.json whose hyperedges live only at the top level (the
# other half of to_json's dual-slot shape, #2485) would silently
# lose them here. Fall back to the top-level key (#2484).
if "hyperedges" not in G.graph and isinstance(data.get("hyperedges"), list):
G.graph["hyperedges"] = data["hyperedges"]
graphs.append(G)
# nx.compose requires all graphs to be the same type. When input graphs
# come from different sources (e.g. an AST-only run vs a full LLM run) one
# may be a MultiGraph and another a Graph. Normalise everything to Graph
# (the graphify default) by converting MultiGraphs with nx.Graph().
def _to_simple(g: "_nx.Graph") -> "_nx.Graph":
# nx.compose requires every graph to be the same type. Inputs may
# disagree on BOTH axes — directed vs undirected, and multi vs simple
# — because per-repo graph.json files are written by different extract
# paths at different times. Normalise everything to a plain undirected
# Graph (the merged cross-repo view is undirected anyway), which covers
# DiGraph / MultiGraph / MultiDiGraph. Without this a directed input
# crashed compose with "All graphs must be directed or undirected" (#1606).
if type(g) is not _nx.Graph:
return _nx.Graph(g)
return g
# Unique repo tag per graph. The bare `graphify-out/..` dir name is not
# unique across inputs (src/graphify-out and frontend/src/graphify-out both
# → "src"), which collides same-stem node ids and silently merges unrelated
# entities (#1729). distinct_repo_tags guarantees a distinct prefix per graph.
repo_tags = _repo_tags(graph_paths)
naive_tags = [gp.parent.parent.name for gp in graph_paths]
if len(set(naive_tags)) != len(naive_tags):
print(f" note: repo dir names collide; using distinct tags: {', '.join(repo_tags)}")
merged = _nx.Graph()
# nx.compose merges graph attrs with dict.update, so each iteration
# CLOBBERED the previously accumulated hyperedge list — only the last
# input's hyperedges survived (#2484, after @oleksii-tumanov's
# diagnosis in PR #1691). Collect every input's prefixed hyperedges
# and re-attach the union after composing.
collected_hyperedges: list = []
for G, repo_tag in zip(graphs, repo_tags):
prefixed = _to_simple(_prefix(G, repo_tag))
hes = prefixed.graph.get("hyperedges")
if isinstance(hes, list):
collected_hyperedges.extend(h for h in hes if isinstance(h, dict))
merged = _nx.compose(merged, prefixed)
# Drop whatever compose left behind (the last input's list, possibly
# with internal duplicates) so attach_hyperedges dedups the full
# collection by id from a clean slate.
merged.graph.pop("hyperedges", None)
if collected_hyperedges:
from graphify.export import attach_hyperedges as _attach
_attach(merged, collected_hyperedges)
try:
out_data = _jg.node_link_data(merged, edges="links")
except TypeError:
out_data = _jg.node_link_data(merged)
# Restore original edge direction from _src/_tgt markers (same pattern as export.py #563/#2261)
for link in out_data.get("links", []):
tsrc = link.pop("_src", None)
ttgt = link.pop("_tgt", None)
if tsrc is not None and ttgt is not None:
link["source"] = tsrc
link["target"] = ttgt
# Persist BOTH hyperedge slots (#2484): node_link_data only nests graph
# attrs under `graph`, so without this line the union would survive
# solely in the slot historic readers ignored (#2485). Mirror to_json's
# dual-slot shape so every writer agrees.
out_data["hyperedges"] = merged.graph.get("hyperedges", [])
out_path.parent.mkdir(parents=True, exist_ok=True)
from graphify.paths import write_json_atomic as _wja
_wja(out_path, out_data, indent=2)
print(f"Merged {len(graphs)} graphs -> {merged.number_of_nodes()} nodes, {merged.number_of_edges()} edges")
print(f"Written to: {out_path}")
elif cmd == "clone":
if len(sys.argv) < 3:
print(
"Usage: graphify clone <github-url> [--branch <branch>] [--out <dir>]",
file=sys.stderr,
)
sys.exit(1)
url = sys.argv[2]
branch: str | None = None
out_dir: Path | None = None
args = sys.argv[3:]
i = 0
while i < len(args):
if args[i] == "--branch" and i + 1 < len(args):
branch = args[i + 1]
i += 2
elif args[i] == "--out" and i + 1 < len(args):
out_dir = Path(args[i + 1])
i += 2
else:
i += 1
local_path = _clone_repo(url, branch=branch, out_dir=out_dir)
print(local_path)
elif cmd == "export":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd not in ("html", "callflow-html", "obsidian", "wiki", "svg", "graphml", "neo4j", "falkordb"):
print("Usage: graphify export <format>", file=sys.stderr)
print(" html [--graph PATH] [--labels PATH] [--node-limit N] [--no-viz]", file=sys.stderr)
print(" callflow-html [GRAPH|DIR] [--graph PATH] [--labels PATH] [--report PATH] [--sections PATH] [--output HTML]", file=sys.stderr)
print(" [--lang auto|zh-CN|en] [--max-sections N] [--diagram-scale N]", file=sys.stderr)
print(" obsidian [--graph PATH] [--labels PATH] [--dir PATH]", file=sys.stderr)
print(" wiki [--graph PATH] [--labels PATH]", file=sys.stderr)
print(" svg [--graph PATH] [--labels PATH]", file=sys.stderr)
print(" graphml [--graph PATH]", file=sys.stderr)
print(" neo4j [--graph PATH] [--push URI] [--user U] [--password P]", file=sys.stderr)
print(" (or set NEO4J_PASSWORD instead of --password to keep it off argv)", file=sys.stderr)
print(" falkordb [--graph PATH] [--push URI] [--user U] [--password P]", file=sys.stderr)
print(" (or set FALKORDB_PASSWORD instead of --password to keep it off argv)", file=sys.stderr)
sys.exit(1)
# Parse shared args
args = sys.argv[3:]
graph_path = Path(_GRAPHIFY_OUT) / "graph.json"
graph_path_explicit = False
labels_path = Path(_GRAPHIFY_OUT) / ".graphify_labels.json"
labels_path_explicit = False
report_path = Path(_GRAPHIFY_OUT) / "GRAPH_REPORT.md"
report_path_explicit = False
sections_path: Path | None = None
callflow_output: Path | None = None
callflow_lang = "auto"
callflow_max_sections = 15
callflow_diagram_scale = 1.0
callflow_max_diagram_nodes = 18
callflow_max_diagram_edges = 24
analysis_path = Path(_GRAPHIFY_OUT) / ".graphify_analysis.json"
node_limit = 5000
no_viz = False
obsidian_dir = Path(_GRAPHIFY_OUT) / "obsidian"
# Shared push-connection settings for the graph-database sinks (neo4j,
# falkordb), parsed from the generic --push/--user/--password flags below.
push_uri: str | None = None
push_user = "neo4j" # Neo4j default user; FalkorDB auth is optional and ignores it
# F-031: prefer an env var so the password never appears on argv (visible
# in `ps` output / shell history). The explicit --password flag still
# overrides it. Each sink reads its own var: FALKORDB_PASSWORD for falkordb,
# NEO4J_PASSWORD otherwise.
push_password: str | None = (
os.environ.get("FALKORDB_PASSWORD") if subcmd == "falkordb"
else os.environ.get("NEO4J_PASSWORD")
) or None
i = 0
while i < len(args):
a = args[i]
if a == "--graph" and i + 1 < len(args):
graph_path = Path(args[i + 1])
graph_path_explicit = True
i += 2
elif a == "--labels" and i + 1 < len(args):
labels_path = Path(args[i + 1])
labels_path_explicit = True
i += 2
elif a == "--report" and i + 1 < len(args):
report_path = Path(args[i + 1])
report_path_explicit = True
i += 2
elif a == "--sections" and i + 1 < len(args):
sections_path = Path(args[i + 1]); i += 2
elif a == "--output" and i + 1 < len(args):
callflow_output = Path(args[i + 1]).expanduser()
if not callflow_output.is_absolute():
callflow_output = Path.cwd() / callflow_output
i += 2
elif a == "--lang" and i + 1 < len(args):
callflow_lang = args[i + 1]; i += 2
elif a == "--max-sections" and i + 1 < len(args):
callflow_max_sections = int(args[i + 1]); i += 2
elif a == "--diagram-scale" and i + 1 < len(args):
callflow_diagram_scale = float(args[i + 1]); i += 2
elif a == "--max-diagram-nodes" and i + 1 < len(args):
callflow_max_diagram_nodes = int(args[i + 1]); i += 2
elif a == "--max-diagram-edges" and i + 1 < len(args):
callflow_max_diagram_edges = int(args[i + 1]); i += 2
elif a in ("-h", "--help") and subcmd == "callflow-html":
print("Usage: graphify export callflow-html [GRAPH|DIR] [--graph PATH] [--labels PATH]")
print(" --report PATH path to GRAPH_REPORT.md")
print(" --sections PATH JSON section definitions")
print(" --output HTML output path (default graphify-out/<project>-callflow.html)")
print(" --lang LANG auto, zh-CN, en, etc. (default auto)")
print(" --max-sections N maximum auto-derived sections (default 15)")
print(" --diagram-scale N Mermaid diagram scale (default 1.0)")
print(" --max-diagram-nodes N representative nodes per section (default 18)")
print(" --max-diagram-edges N representative edges per section (default 24)")
sys.exit(0)
elif a == "--node-limit" and i + 1 < len(args):
node_limit = int(args[i + 1]); i += 2
elif a == "--no-viz":
no_viz = True; i += 1
elif a == "--dir" and i + 1 < len(args):
obsidian_dir = Path(args[i + 1]); i += 2
elif a == "--push" and i + 1 < len(args):
push_uri = args[i + 1]; i += 2
elif a == "--user" and i + 1 < len(args):
push_user = args[i + 1]; i += 2
elif a == "--password" and i + 1 < len(args):
push_password = args[i + 1]; i += 2
elif subcmd == "callflow-html" and not a.startswith("-") and not graph_path_explicit:
candidate = Path(a)
if candidate.name == "graph.json" or candidate.suffix.lower() == ".json":
graph_path = candidate
elif (candidate / "graph.json").exists():
graph_path = candidate / "graph.json"
else:
graph_path = candidate / _GRAPHIFY_OUT / "graph.json"
graph_path_explicit = True
i += 1
else:
i += 1
graph_path = graph_path.expanduser()
if graph_path_explicit:
graph_out_dir = graph_path.parent
if not labels_path_explicit:
labels_path = graph_out_dir / ".graphify_labels.json"
if not report_path_explicit:
report_path = graph_out_dir / "GRAPH_REPORT.md"
labels_path = labels_path.expanduser()
report_path = report_path.expanduser()
if not graph_path.exists():
print(f"error: graph not found: {graph_path}. Run /graphify <path> first.", file=sys.stderr)
sys.exit(1)
if subcmd == "callflow-html":
from graphify.callflow_html import write_callflow_html as _write_callflow_html
out = _write_callflow_html(
graph=graph_path,
report=report_path,
labels=labels_path,
sections=sections_path,
output=callflow_output,
lang=callflow_lang,
max_sections=callflow_max_sections,
diagram_scale=callflow_diagram_scale,
max_diagram_nodes=callflow_max_diagram_nodes,
max_diagram_edges=callflow_max_diagram_edges,
verbose=True,
)
print(f"callflow HTML written - open in any browser: {out}")
sys.exit(0)
from networkx.readwrite import json_graph as _jg
from graphify.build import build_from_json as _bfj
from graphify.security import check_graph_file_size_cap as _check_cap
# Solution 3 (#1019): for the HTML view, an oversized graph.json should
# not be a hard error. Detect the over-cap condition here and fall back
# to the community-aggregation view (node_limit=5000) below instead of
# exiting 1. All other subcommands keep the hard cap.
_over_cap = False
try:
_check_cap(graph_path)
except ValueError as _cap_err:
if subcmd == "html":
_over_cap = True
try:
_over_cap_bytes = graph_path.stat().st_size
except OSError:
_over_cap_bytes = -1
print(
f"warning: graph.json exceeds cap ({_over_cap_bytes} bytes); "
f"falling back to community-aggregation view (node_limit=5000)",
file=sys.stderr,
)
else:
print(f"error: {_cap_err}", file=sys.stderr)
sys.exit(1)
_raw = json.loads(graph_path.read_text(encoding="utf-8"))
if "links" not in _raw and "edges" in _raw:
_raw = dict(_raw, links=_raw["edges"])
try:
G = _jg.node_link_graph(_raw, edges="links")
except TypeError:
G = _jg.node_link_graph(_raw)
# Load optional analysis/labels
communities: dict[int, list[str]] = {}
if analysis_path.exists():
_an = json.loads(analysis_path.read_text(encoding="utf-8"))
communities = {int(k): v for k, v in _an.get("communities", {}).items()}
cohesion: dict[int, float] = {int(k): v for k, v in _an.get("cohesion", {}).items()}
gods_data = _an.get("gods", [])
else:
cohesion = {}
gods_data = []
# Fallback: graph.json carries the per-node community as a node attribute
# (`to_json` writes it on every node). The analysis sidecar is the
# canonical source — but the post-commit / watch rebuild path doesn't
# regenerate it, and `extract` may have its temp files cleaned up. When
# that happens, `graphify export html` previously bailed with
# "Single community - aggregated view not useful." even though the
# per-node attribute had the right data all along. Reconstruct from
# the graph itself so downstream subcommands (html, obsidian, wiki,
# svg, graphml, neo4j) don't silently produce a degraded artifact.
if not communities:
reconstructed: dict[int, list[str]] = {}
for node_id, data in G.nodes(data=True):
cid_raw = data.get("community")
if cid_raw is None:
continue
try:
cid = int(cid_raw)
except (TypeError, ValueError):
continue
reconstructed.setdefault(cid, []).append(str(node_id))
if reconstructed:
communities = reconstructed
labels: dict[int, str] = {}
if labels_path.exists():
labels = {int(k): v for k, v in json.loads(labels_path.read_text(encoding="utf-8")).items()}
out_dir = graph_path.parent
if subcmd == "html":
from graphify.export import to_html as _to_html
if no_viz:
html_target = out_dir / "graph.html"
if html_target.exists():
html_target.unlink()
print("--no-viz: skipped graph.html")
else:
# Over-cap fallback (#1019): force the community-aggregation
# path so the oversized graph still renders a usable artifact.
_effective_node_limit = 5000 if _over_cap else node_limit
_to_html(G, communities, str(out_dir / "graph.html"),
community_labels=labels or None, node_limit=_effective_node_limit)
if G.number_of_nodes() <= _effective_node_limit:
print(f"graph.html written - open in any browser, no server needed")
if _over_cap:
sys.exit(0)
elif subcmd == "obsidian":
from graphify.export import to_obsidian as _to_obsidian, to_canvas as _to_canvas
n = _to_obsidian(G, communities, str(obsidian_dir),
community_labels=labels or None, cohesion=cohesion or None)
print(f"Obsidian vault: {n} notes in {obsidian_dir}/")
_to_canvas(G, communities, str(obsidian_dir / "graph.canvas"),
community_labels=labels or None)
print(f"Canvas: {obsidian_dir}/graph.canvas")
print(f"Open {obsidian_dir}/ as a vault in Obsidian.")
elif subcmd == "wiki":
from graphify.wiki import to_wiki as _to_wiki
from graphify.analyze import god_nodes as _god_nodes
if not communities:
print(
"error: .graphify_analysis.json is missing or empty — refusing to export wiki to prevent data loss.\n"
"Run `graphify extract .` (or `graphify cluster-only .`) to regenerate community data first.",
file=sys.stderr,
)
sys.exit(1)
if not gods_data:
gods_data = _god_nodes(G)
n = _to_wiki(G, communities, str(out_dir / "wiki"),
community_labels=labels or None, cohesion=cohesion or None,
god_nodes_data=gods_data)
print(f"Wiki: {n} articles written to {out_dir}/wiki/")
print(f" {out_dir}/wiki/index.md -> agent entry point")
elif subcmd == "svg":
from graphify.export import to_svg as _to_svg
_to_svg(G, communities, str(out_dir / "graph.svg"),
community_labels=labels or None)
print(f"graph.svg written - embeds in Obsidian, Notion, GitHub READMEs")
elif subcmd == "graphml":
from graphify.export import to_graphml as _to_graphml
_to_graphml(G, communities, str(out_dir / "graph.graphml"))
print(f"graph.graphml written - open in Gephi, yEd, or any GraphML tool")
elif subcmd == "neo4j":
if push_uri:
from graphify.export import push_to_neo4j as _push
if push_password is None:
print("error: --password required for --push", file=sys.stderr)
sys.exit(1)
result = _push(G, uri=push_uri, user=push_user,
password=push_password, communities=communities)
print(f"Pushed to Neo4j: {result['nodes']} nodes, {result['edges']} edges")
else:
from graphify.export import to_cypher as _to_cypher
_to_cypher(G, str(out_dir / "cypher.txt"))
print(f"cypher.txt written - import with: cypher-shell < {out_dir}/cypher.txt")
elif subcmd == "falkordb":
if push_uri:
from graphify.export import push_to_falkordb as _push
result = _push(G, uri=push_uri, user=push_user,
password=push_password, communities=communities)
print(f"Pushed to FalkorDB: {result['nodes']} nodes, {result['edges']} edges")
else:
from graphify.export import to_cypher as _to_cypher
_to_cypher(G, str(out_dir / "cypher.txt"))
print(f"cypher.txt written ({out_dir}/cypher.txt) - statements are OpenCypher. "
f"FalkorDB's GRAPH.QUERY runs one statement at a time (no bulk script "
f"import), so load a graph with: graphify export falkordb --push "
f"falkordb://localhost:6379")
elif cmd == "benchmark":
from graphify.benchmark import run_benchmark, print_benchmark
graph_path = sys.argv[2] if len(sys.argv) > 2 else _default_graph_path()
_enforce_graph_size_cap_or_exit(Path(graph_path))
# Try to load corpus_words from detect output
corpus_words = None
detect_path = Path(".graphify_detect.json")
if detect_path.exists():
try:
detect_data = json.loads(detect_path.read_text(encoding="utf-8"))
corpus_words = detect_data.get("total_words")
except Exception:
pass
result = run_benchmark(graph_path, corpus_words=corpus_words)
print_benchmark(result)
elif cmd == "global":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
from graphify.global_graph import (
global_add as _global_add,
global_remove as _global_remove,
global_list as _global_list,
global_path as _global_path,
)
if subcmd == "add":
# graphify global add <graph.json> [--as <tag>]
args = sys.argv[3:]
source = None
tag = None
i = 0
while i < len(args):
if args[i] == "--as" and i + 1 < len(args):
tag = args[i + 1]; i += 2
elif not source:
source = Path(args[i]); i += 1
else:
i += 1
if not source:
print("Usage: graphify global add <graph.json> [--as <repo-tag>]", file=sys.stderr)
sys.exit(1)
tag = tag or source.parent.parent.name
try:
result = _global_add(source, tag)
if result["skipped"]:
print(f"'{tag}' unchanged since last add - global graph not modified.")
else:
print(f"Added '{tag}' to global graph: +{result['nodes_added']} nodes, "
f"-{result['nodes_removed']} pruned. Global: {_global_path()}")
except Exception as exc:
print(f"error: {exc}", file=sys.stderr); sys.exit(1)
elif subcmd == "remove":
tag = sys.argv[3] if len(sys.argv) > 3 else ""
if not tag:
print("Usage: graphify global remove <repo-tag>", file=sys.stderr); sys.exit(1)
try:
removed = _global_remove(tag)
print(f"Removed '{tag}' from global graph ({removed} nodes pruned).")
except KeyError as exc:
print(f"error: {exc}", file=sys.stderr); sys.exit(1)
elif subcmd == "list":
repos = _global_list()
if not repos:
print("Global graph is empty. Use 'graphify global add' to add a project.")
else:
print(f"Global graph: {_global_path()}")
for tag, info in repos.items():
print(f" {tag}: {info.get('node_count', '?')} nodes, added {info.get('added_at', '?')[:10]}")
elif subcmd == "path":
print(_global_path())
else:
print("Usage: graphify global [add|remove|list|path]", file=sys.stderr); sys.exit(1)
elif cmd == "extract":
# Headless full-pipeline extraction for CI / scripts (#698).
# Runs detect -> AST extraction on code -> semantic LLM extraction on
# docs/papers/images -> merge -> build -> cluster -> write outputs.
# Unlike the skill.md path (which runs through Claude Code subagents),
# this calls extract_corpus_parallel directly using whichever backend
# has an API key set.
if len(sys.argv) < 3:
print(
"Usage: graphify extract <path> [--backend gemini|kimi|claude|openai|deepseek|ollama] "
"[--model M] [--mode deep] [--out DIR|--output DIR] [--google-workspace] [--no-cluster] "
"[--no-gitignore] [--code-only] [--no-dedup] "
"[--max-workers N] [--token-budget N] [--max-concurrency N] "
"[--api-timeout S] [--postgres DSN] [--cargo] [--allow-partial] [--timing]",
file=sys.stderr,
)
sys.exit(1)
has_path = True
if sys.argv[2].startswith("-"):
has_path = False
target = Path(".").resolve()
else:
target = Path(sys.argv[2]).resolve()
if not target.exists():
print(f"error: path not found: {target}", file=sys.stderr)
sys.exit(1)
backend: str | None = None
model: str | None = None
extract_mode: str | None = None
out_dir: Path | None = None
cli_postgres_dsn: str | None = None
cli_cargo: bool = False
cli_allow_partial: bool = False
no_cluster = False
dedup_llm = False
# --no-dedup: skip entity deduplication entirely. On an incremental
# merge the fuzzy pass runs over the COMBINED node set (existing graph +
# new chunk), so a small diff merged into a large graph can collapse
# pre-existing nodes from files the diff never touched. Turning dedup
# off also arms build_merge's #479 shrink guard, which is disabled while
# dedup is on because fuzzy merging shrinks the graph legitimately (#2881).
no_dedup = False
google_workspace = False
global_merge = False
code_only = False
no_gitignore = False
global_repo_tag: str | None = None
# Performance/tuning knobs (issue #792). None means "use library default".
cli_max_workers: int | None = None
cli_token_budget: int | None = None
cli_max_concurrency: int | None = None
cli_api_timeout: float | None = None
# Clustering tuning knobs
cli_resolution: float = 1.0
cli_exclude_hubs: float | None = None
cli_excludes: list[str] = []
cli_timing: bool = False
# --force parity with `graphify update`: the flag or GRAPHIFY_FORCE=1
# disables the incremental gate and skips semantic-cache reads (#1894).
force = os.environ.get("GRAPHIFY_FORCE", "").lower() in ("1", "true", "yes")
def _parse_int(name: str, raw: str) -> int:
try:
v = int(raw)
except ValueError:
print(f"error: {name} must be a positive integer (got {raw!r})", file=sys.stderr)
sys.exit(2)
if v <= 0:
print(f"error: {name} must be > 0 (got {v})", file=sys.stderr)
sys.exit(2)
return v
def _parse_float(name: str, raw: str) -> float:
try:
v = float(raw)
except ValueError:
print(f"error: {name} must be a positive number (got {raw!r})", file=sys.stderr)
sys.exit(2)
if v <= 0:
print(f"error: {name} must be > 0 (got {v})", file=sys.stderr)
sys.exit(2)
return v
args = sys.argv[3:] if has_path else sys.argv[2:]
i = 0
while i < len(args):
a = args[i]
if a == "--backend" and i + 1 < len(args):
backend = args[i + 1]; i += 2
elif a.startswith("--backend="):
backend = a.split("=", 1)[1]; i += 1
elif a == "--model" and i + 1 < len(args):
model = args[i + 1]; i += 2
elif a.startswith("--model="):
model = a.split("=", 1)[1]; i += 1
elif a == "--mode" and i + 1 < len(args):
extract_mode = args[i + 1]; i += 2
elif a.startswith("--mode="):
extract_mode = a.split("=", 1)[1]; i += 1
elif a in ("--out", "--output") and i + 1 < len(args):
# --output is an alias of --out (#2004): it was silently dropped
# before, and `graphify tree` already documents --output, so the
# mistake is natural. (--output= does not startswith --out=.)
out_dir = Path(args[i + 1]); i += 2
elif a.startswith(("--out=", "--output=")):
out_dir = Path(a.split("=", 1)[1]); i += 1
elif a == "--no-cluster":
no_cluster = True; i += 1
elif a == "--dedup-llm":
dedup_llm = True; i += 1
elif a == "--no-dedup":
no_dedup = True; i += 1
elif a == "--code-only":
code_only = True; i += 1
elif a == "--google-workspace":
google_workspace = True; i += 1
elif a == "--no-gitignore":
no_gitignore = True; i += 1
elif a == "--global":
global_merge = True; i += 1
elif a == "--as" and i + 1 < len(args):
global_repo_tag = args[i + 1]; i += 2
elif a == "--max-workers" and i + 1 < len(args):
cli_max_workers = _parse_int("--max-workers", args[i + 1]); i += 2
elif a.startswith("--max-workers="):
cli_max_workers = _parse_int("--max-workers", a.split("=", 1)[1]); i += 1
elif a == "--token-budget" and i + 1 < len(args):
cli_token_budget = _parse_int("--token-budget", args[i + 1]); i += 2
elif a.startswith("--token-budget="):
cli_token_budget = _parse_int("--token-budget", a.split("=", 1)[1]); i += 1
elif a == "--max-concurrency" and i + 1 < len(args):
cli_max_concurrency = _parse_int("--max-concurrency", args[i + 1]); i += 2
elif a.startswith("--max-concurrency="):
cli_max_concurrency = _parse_int("--max-concurrency", a.split("=", 1)[1]); i += 1
elif a == "--api-timeout" and i + 1 < len(args):
cli_api_timeout = _parse_float("--api-timeout", args[i + 1]); i += 2
elif a.startswith("--api-timeout="):
cli_api_timeout = _parse_float("--api-timeout", a.split("=", 1)[1]); i += 1
elif a == "--resolution" and i + 1 < len(args):
cli_resolution = _parse_float("--resolution", args[i + 1]); i += 2
elif a.startswith("--resolution="):
cli_resolution = _parse_float("--resolution", a.split("=", 1)[1]); i += 1
elif a == "--exclude-hubs" and i + 1 < len(args):
cli_exclude_hubs = float(args[i + 1]); i += 2
elif a.startswith("--exclude-hubs="):
cli_exclude_hubs = float(a.split("=", 1)[1]); i += 1
elif a == "--exclude" and i + 1 < len(args):
cli_excludes.append(args[i + 1]); i += 2
elif a.startswith("--exclude="):
cli_excludes.append(a.split("=", 1)[1]); i += 1
elif a == "--postgres" and i + 1 < len(args):
cli_postgres_dsn = args[i + 1]; i += 2
elif a.startswith("--postgres="):
cli_postgres_dsn = a.split("=", 1)[1]; i += 1
elif a == "--cargo":
cli_cargo = True
i += 1
elif a == "--force":
force = True; i += 1
elif a == "--allow-partial":
cli_allow_partial = True; i += 1
elif a == "--timing":
cli_timing = True; i += 1
else:
i += 1
if not has_path and cli_postgres_dsn is None:
print("error: must specify a path to scan or a --postgres DSN", file=sys.stderr)
sys.exit(1)
if no_dedup and dedup_llm:
# --dedup-llm is pass 3 of the dedup pipeline, so with dedup off it
# would be a silent no-op that still demands an API key.
print(
"error: --no-dedup and --dedup-llm are mutually exclusive "
"(--dedup-llm is a tiebreaker inside the dedup pass)",
file=sys.stderr,
)
sys.exit(2)
_VALID_MODES = {"deep"}
if extract_mode is not None and extract_mode not in _VALID_MODES:
print(
f"error: unknown --mode '{extract_mode}'. "
f"Available: {', '.join(sorted(_VALID_MODES))}",
file=sys.stderr,
)
sys.exit(2)
deep_mode = extract_mode == "deep"
if deep_mode:
print("[graphify extract] deep mode enabled: richer semantic extraction")
# CLI flag wins over env var. Setting GRAPHIFY_API_TIMEOUT here so
# _call_openai_compat picks it up without needing a new kwarg path.
if cli_api_timeout is not None:
os.environ["GRAPHIFY_API_TIMEOUT"] = str(cli_api_timeout)
if cli_max_workers is not None:
os.environ["GRAPHIFY_MAX_WORKERS"] = str(cli_max_workers)
# Resolve output dir. The user-facing contract is "<out>/graphify-out/"
# so a fresh checkout writes graphify-out/ at the project root, matching
# the skill.md pipeline.
out_root = (out_dir.resolve() if out_dir else target)
graphify_out = out_root / _GRAPHIFY_OUT
graphify_out.mkdir(parents=True, exist_ok=True)
# Persist corpus-shaping options so later update/watch/hook rebuilds
# use the same file set as the initial extraction (#1886).
from graphify.watch import (
_write_build_config as _write_build_cfg,
_read_build_excludes as _read_build_ex,
_read_build_gitignore as _read_build_gi,
)
# #1971 persistence: an explicit --no-gitignore persists False; a later
# flag-less `graphify extract` must NOT clobber it back to True, which
# would make the git-ignored code silently disappear again (the exact
# complaint #1971 is about). Honor the persisted value for THIS run when
# the flag is absent (read before the write below), and write False only
# when the flag is set — None leaves the setting as-is, mirroring how
# #1886 persists --exclude.
_effective_gitignore = False if no_gitignore else _read_build_gi(graphify_out)
# An explicit list replaces the persisted one; omission reuses it.
_effective_excludes = cli_excludes or _read_build_ex(graphify_out)
_write_build_cfg(
graphify_out,
excludes=cli_excludes or None,
gitignore=False if no_gitignore else None,
)
stages = _StageTimer(cli_timing)
from graphify.detect import (
detect as _detect,
detect_incremental as _detect_incremental,
save_manifest as _save_manifest,
)
manifest_path = graphify_out / "manifest.json"
existing_graph_path = graphify_out / "graph.json"
# #1925: a missing manifest.json must not degrade to a full scan that
# discards the existing graph's semantic layer. An existing graph.json
# is a sufficient incremental baseline: detect_incremental treats an
# absent manifest as "everything is new" (re-extract all, nothing
# deleted), and build_merge + _stale_graph_sources reconcile replaced
# and genuinely-deleted sources against the current corpus, so doc/
# paper/image nodes survive a --code-only rebuild instead of being
# dropped with the rest of the committed graph.
incremental_mode = existing_graph_path.exists() if has_path else False
# --force: full scan, not the manifest-gated incremental diff — a warm
# unchanged tree would otherwise dispatch zero files (#1894).
incremental_mode = incremental_mode and not force
if force:
print("[graphify extract] --force: full re-scan, semantic cache reads skipped")
elif incremental_mode and not manifest_path.exists():
print(
"[graphify extract] manifest.json missing; using existing "
"graph.json as the incremental baseline (all files re-checked; "
"nodes for files outside this run's scope are preserved)"
)
if not has_path:
detection = {}
code_files = []
doc_files = []
paper_files = []
image_files = []
deleted_files = []
excluded_files = []
graph_stale_sources = []
unchanged_total = 0
files_by_type = {}
elif incremental_mode:
print(f"[graphify extract] incremental scan of {target}")
detection = _detect_incremental(
target,
manifest_path=str(manifest_path),
google_workspace=google_workspace or None,
extra_excludes=_effective_excludes or None,
gitignore=_effective_gitignore,
)
files_by_type = detection.get("files", {})
new_by_type = detection.get("new_files", {})
code_files = [Path(p) for p in new_by_type.get("code", [])]
doc_files = [Path(p) for p in new_by_type.get("document", [])]
paper_files = [Path(p) for p in new_by_type.get("paper", [])]
image_files = [Path(p) for p in new_by_type.get("image", [])]
deleted_files = list(detection.get("deleted_files", []))
excluded_files = list(detection.get("excluded_files", []))
unchanged_total = sum(len(v) for v in detection.get("unchanged_files", {}).values())
# #1909: derive the prune set from the existing graph itself, not
# just the manifest. A file that became excluded without ever
# being manifest-listed (every pre-#1897 graph is in this state)
# still has stale nodes carried forward by build_merge unless the
# graph's own sources are reconciled against the current corpus.
_seen_files = {f for _fl in files_by_type.values() for f in _fl}
_seen_files.update(detection.get("unclassified", []))
graph_stale_sources = _stale_graph_sources(
existing_graph_path, target, _seen_files, detection=detection
)
# #2543 heal: manifests poisoned BEFORE failed-source unstamping
# existed carry live hashes for code files whose extraction failed
# (missing extra, crash) — stamped up-to-date yet absent from
# graph.json, so the incremental gate skips them forever. Treat
# such a file as changed and re-queue it; if it fails again this
# run it is now left unstamped, so this cannot wedge.
_healed_sources = _zero_node_stamped_code_sources(
existing_graph_path,
target,
detection.get("unchanged_files", {}).get("code", []),
)
if _healed_sources:
print(
f"[graphify extract] re-queuing {len(_healed_sources)} "
f"manifest-stamped code file(s) with no nodes in graph.json "
f"(prior failed extraction, #2543)"
)
code_files.extend(Path(p) for p in _healed_sources)
else:
print(f"[graphify extract] scanning {target}")
detection = _detect(
target,
google_workspace=google_workspace or None,
extra_excludes=_effective_excludes or None,
cache_root=out_root,
gitignore=_effective_gitignore,
)
files_by_type = detection.get("files", {})
code_files = [Path(p) for p in files_by_type.get("code", [])]
doc_files = [Path(p) for p in files_by_type.get("document", [])]
paper_files = [Path(p) for p in files_by_type.get("paper", [])]
image_files = [Path(p) for p in files_by_type.get("image", [])]
deleted_files = []
excluded_files = []
graph_stale_sources = []
unchanged_total = 0
semantic_files = doc_files + paper_files + image_files
# --code-only: index code (pure local AST, no key) and skip the semantic
# (doc/paper/image) pass entirely, so a mixed repo doesn't hard-fail when no
# LLM backend is configured (#1734). Report what was skipped rather than
# silently dropping it.
if code_only and semantic_files:
print(
f"[graphify extract] --code-only: skipping {len(semantic_files)} "
f"non-code file(s) ({len(doc_files)} docs, {len(paper_files)} papers, "
f"{len(image_files)} images) — no LLM extraction"
)
semantic_files = []
doc_files = []
paper_files = []
image_files = []
if deep_mode and incremental_mode and not code_only:
# Deep mode reads/writes its own cache namespace
# (cache/semantic-deep/), so the manifest's changed-file gate is
# not a valid proxy for deep coverage: over a warm unchanged tree
# it dispatches zero files and `--mode deep` silently no-ops
# (#1894). Widen the semantic pass to the FULL live
# doc/paper/image set (``files_by_type`` from detect_incremental,
# which already excludes excluded files) and let the
# mode-namespaced cache decide hits/misses — the first deep run
# re-dispatches everything (deep namespace cold), later deep runs
# hit the deep cache.
_deep_all = [
Path(p)
for _ftype in ("document", "paper", "image")
for p in files_by_type.get(_ftype, [])
]
if len(_deep_all) != len(semantic_files):
print(
f"[graphify extract] deep mode: widening semantic pass from "
f"{len(semantic_files)} changed to {len(_deep_all)} live "
f"doc/paper/image file(s); the deep semantic cache decides "
f"what is re-extracted"
)
semantic_files = _deep_all
if incremental_mode:
# Excluded-but-alive files are reported separately from deletions
# (#1908): they still exist on disk, the scan just stopped
# covering them (ignore rules / --exclude changed).
_excl_note = f"; {len(excluded_files)} excluded" if excluded_files else ""
print(
f"[graphify extract] {len(code_files)} code, {len(doc_files)} docs, "
f"{len(paper_files)} papers, {len(image_files)} images changed; "
f"{unchanged_total} unchanged; {len(deleted_files)} deleted"
f"{_excl_note}"
)
else:
print(
f"[graphify extract] found {len(code_files)} code, "
f"{len(doc_files)} docs, {len(paper_files)} papers, "
f"{len(image_files)} images"
)
# Surface files that were seen but not classified (extensionless non-shebang
# project files like Dockerfile/Makefile, or unsupported extensions), so they
# are no longer invisible in graphify's own output (#1692).
_unclassified = detection.get("unclassified", []) if isinstance(detection, dict) else []
if _unclassified:
_names = ", ".join(sorted({Path(p).name for p in _unclassified})[:6])
_more = f" (+{len(_unclassified) - 6} more)" if len(_unclassified) > 6 else ""
print(
f"[graphify extract] {len(_unclassified)} file(s) not classified "
f"(no supported extension or shebang), skipped: {_names}{_more}"
)
# Name the files dropped by the sensitive-file filter so a wrongly-flagged
# source/doc is visible, not just a count (#2106). Operational skips
# (symlink/office/Workspace) carry a " [reason]" suffix; exclude those here
# so this line reports only the security-heuristic drops.
_sensitive = detection.get("skipped_sensitive", []) if isinstance(detection, dict) else []
_sec = [s for s in _sensitive if " [" not in s]
if _sec:
_snames = ", ".join(sorted({Path(p).name for p in _sec})[:6])
_smore = f" (+{len(_sec) - 6} more)" if len(_sec) > 6 else ""
print(
f"[graphify extract] {len(_sec)} file(s) skipped as potentially sensitive "
f"(rename or move if wrongly flagged): {_snames}{_smore}"
)
stages.mark("detect")
# Resolve the LLM backend only now that we know whether the corpus
# needs one. A code-only corpus is pure local AST and must not require
# an API key; the key is enforced below only when there's LLM work.
from graphify.llm import (
BACKENDS as _BACKENDS,
detect_backend as _detect_backend,
estimate_cost as _estimate_cost,
extract_corpus_parallel as _extract_corpus_parallel,
_format_backend_env_keys,
_get_backend_api_key,
)
needs_llm = bool(semantic_files) or dedup_llm
if backend is None and needs_llm:
backend = _detect_backend()
if backend is not None and backend not in _BACKENDS:
print(
f"error: unknown backend '{backend}'. "
f"Available: {', '.join(sorted(_BACKENDS))}",
file=sys.stderr,
)
sys.exit(1)
if needs_llm:
if backend is None:
reasons = []
if semantic_files:
reasons.append(
f"{len(semantic_files)} doc/paper/image file(s) need semantic extraction"
)
if dedup_llm:
reasons.append("--dedup-llm was passed")
hint = ""
if semantic_files:
hint = (" Or pass --code-only to index just the code "
"(local AST, no key) and skip the non-code files.")
print(
"error: no LLM API key found (" + "; ".join(reasons) + "). "
"Set GEMINI_API_KEY or GOOGLE_API_KEY (gemini), MOONSHOT_API_KEY "
"(kimi), ANTHROPIC_API_KEY (claude), OPENAI_API_KEY (openai), "
"DEEPSEEK_API_KEY (deepseek), or pass --backend. A code-only "
"corpus needs no key." + hint,
file=sys.stderr,
)
sys.exit(1)
if backend == "ollama":
from graphify.llm import _validate_ollama_base_url
_oll_url = os.environ.get("OLLAMA_BASE_URL", _BACKENDS["ollama"].get("base_url", ""))
try:
_validate_ollama_base_url(_oll_url, warn=False)
except ValueError as exc:
print(f"error: {exc}", file=sys.stderr)
sys.exit(2)
if not _get_backend_api_key(backend):
allow_no_key = False
if backend == "ollama":
from urllib.parse import urlparse
ollama_url = os.environ.get(
"OLLAMA_BASE_URL",
_BACKENDS["ollama"].get("base_url", ""),
)
try:
host = (urlparse(ollama_url).hostname or "").lower()
except Exception:
host = ""
allow_no_key = (
host in ("localhost", "127.0.0.1", "::1")
or host.startswith("127.")
)
elif backend == "bedrock":
allow_no_key = bool(
os.environ.get("AWS_PROFILE")
or os.environ.get("AWS_REGION")
or os.environ.get("AWS_DEFAULT_REGION")
or os.environ.get("AWS_ACCESS_KEY_ID")
)
elif backend == "claude-cli":
import shutil as _shutil
allow_no_key = _shutil.which("claude") is not None
if not allow_no_key:
print(
"error: backend 'claude-cli' requires the `claude` CLI on $PATH "
"(install Claude Code and run `claude` once to authenticate).",
file=sys.stderr,
)
sys.exit(1)
if not allow_no_key:
print(
f"error: backend '{backend}' requires {_format_backend_env_keys(backend)} to be set.",
file=sys.stderr,
)
sys.exit(1)
# Track whether this run's extraction was incomplete (a whole extractor
# pass crashed, or some semantic chunks failed). A partial result must not
# be force-written over a good complete graph — the final write falls back
# to the #479 shrink guard unless --allow-partial is set.
_extraction_incomplete = False
# A walk that couldn't fully enumerate the corpus (permission-denied
# subtree, I/O error) yields a legitimately smaller graph that must not
# be force-written over a complete one — same failure class as a crashed
# pass. detect()/detect_incremental() already record these; consume them.
if detection.get("walk_errors"):
_extraction_incomplete = True
# AST extraction on code files. Empty code list (docs-only corpus) is
# the issue #698 case — skip cleanly instead of crashing inside extract().
ast_result: dict = {"nodes": [], "edges": [], "input_tokens": 0, "output_tokens": 0}
if code_files:
from graphify.extract import extract as _ast_extract
# Anchor the cache at the output root, not the scanned project:
# with --out, a <target>/graphify-out/cache/ would leak a
# graphify-out/ dir into a project that asked for external output.
# `root` stays the scanned project so source_file/ids relativize
# against it; conflating the two basenamed every node (#1941).
ast_kwargs: dict = {"cache_root": out_root, "root": target}
if cli_max_workers is not None:
ast_kwargs["max_workers"] = cli_max_workers
# #2437/#2438 (the `graphify update` twin of watch's #2406 fix): an
# incremental re-scan extracts only the changed code files, so the
# cross-file resolvers cannot see a callee living in an unchanged
# file and every changed->unchanged call edge silently vanished on
# merge. Hand extract() read-only resolution context from the
# persisted graph: its AST-tier nodes (with their `_callable`/
# `_callable_class` markers, #2438) plus the contains/method edges
# the member-call resolvers walk (#2437), scoped to the UNCHANGED
# live corpus — never a re-extracted, deleted, or excluded file, so
# stale symbols cannot resurrect. Fails open (changed-batch-only
# resolution, the pre-fix behavior) on an unreadable graph.
if incremental_mode and existing_graph_path.exists():
_ctx_nodes: list[dict] = []
_ctx_edges: list[dict] = []
try:
from graphify.build import _is_ast_tier as _ctx_is_ast_tier
from graphify.security import (
check_graph_file_size_cap as _ctx_size_cap,
)
_ctx_size_cap(existing_graph_path)
_ctx_graph = json.loads(
existing_graph_path.read_text(encoding="utf-8")
)
_ctx_root = Path(os.path.abspath(target))
def _ctx_identity(source_file) -> str | None:
# graph.json source_file values are relative to the
# scanned root (`root=target` above); detect's
# unchanged_files keep their scan-time form. Compare
# both as absolute posix paths.
if not source_file:
return None
_p = Path(str(source_file))
if not _p.is_absolute():
_p = _ctx_root / _p
return Path(os.path.abspath(_p)).as_posix()
_ctx_live = {
_ctx_identity(f)
for _flist in detection.get("unchanged_files", {}).values()
for f in _flist
}
_ctx_live.discard(None)
for _node in _ctx_graph.get("nodes", []):
if not _node.get("id") or not _ctx_is_ast_tier(_node):
continue
_sf = _node.get("source_file")
if not _sf or _ctx_identity(_sf) not in _ctx_live:
continue
_ctx_node = {
"id": _node["id"],
"label": _node.get("label"),
"source_file": _sf,
"file_type": _node.get("file_type"),
"type": _node.get("type"),
}
for _marker in ("_callable", "_callable_class"):
if _node.get(_marker):
_ctx_node[_marker] = _node[_marker]
_ctx_nodes.append(_ctx_node)
for _edge in _ctx_graph.get(
"links", _ctx_graph.get("edges", [])
):
if _edge.get("relation") not in ("contains", "method"):
continue
if not _ctx_is_ast_tier(_edge):
continue
_sf = _edge.get("source_file")
if not _sf or _ctx_identity(_sf) not in _ctx_live:
continue
_ctx_edges.append({
"source": _edge.get("source"),
"target": _edge.get("target"),
"relation": _edge.get("relation"),
"source_file": _sf,
})
except Exception:
_ctx_nodes, _ctx_edges = [], []
if _ctx_nodes:
ast_kwargs["resolution_context_nodes"] = _ctx_nodes
if _ctx_edges:
ast_kwargs["resolution_context_edges"] = _ctx_edges
print(f"[graphify extract] AST extraction on {len(code_files)} code files...")
try:
ast_result = _ast_extract(code_files, **ast_kwargs)
except Exception as exc:
print(f"[graphify extract] AST extraction failed: {exc}", file=sys.stderr)
# #2445: losing the whole AST pass is fatal by default. The
# empty stand-in only reaches the shrink guard when an existing
# graph is larger — on a fresh build it used to be written as a
# 0-node graph with exit 0, indistinguishable from success.
# --allow-partial opts back into the best-effort continuation.
if not cli_allow_partial:
sys.exit(1)
ast_result = {"nodes": [], "edges": [], "input_tokens": 0, "output_tokens": 0}
_extraction_incomplete = True # the whole AST pass was lost
stages.mark("AST extract")
# Semantic extraction on docs/papers/images. Check cache first.
from graphify.cache import (
check_semantic_cache as _check_semantic_cache,
prune_semantic_cache as _prune_semantic_cache,
save_semantic_cache as _save_semantic_cache,
)
sem_result: dict = {
"nodes": [], "edges": [], "hyperedges": [],
"input_tokens": 0, "output_tokens": 0,
}
# Semantic files whose extraction truncated this run. They are left
# unstamped in the manifest so detect_incremental re-queues them next run
# (mirrors the #933 failed-chunk handling); captured below before the
# _partial markers are stripped from the corpus.
_partial_semantic_files: set[str] = set()
sem_cache_hits = 0
sem_cache_misses = 0
# Deep mode uses its own namespace (cache/semantic-deep/) so deep and
# standard results for the same content never shadow each other (#1894).
sem_cache_mode = "deep" if deep_mode else None
# Entries are attributed to the extraction prompt that produced them, so
# a release that changes the prompt re-extracts rather than replaying the
# older vintage alongside the new one (#1939). Read and write must pass
# the same prompt, or the write lands where the next read won't look.
from graphify.llm import _extraction_system as _sem_prompt_for
sem_prompt = _sem_prompt_for(deep=deep_mode)
if semantic_files:
sem_paths_str = [str(p) for p in semantic_files]
if force:
# --force: skip the cache READ so every semantic file is
# re-dispatched; the save below still runs so the fresh
# results replace the stale entries.
cached_nodes, cached_edges, cached_hyperedges = [], [], []
uncached_paths = list(sem_paths_str)
else:
cached_nodes, cached_edges, cached_hyperedges, uncached_paths = (
_check_semantic_cache(sem_paths_str, root=target, cache_root=out_root,
mode=sem_cache_mode, prompt=sem_prompt)
)
sem_cache_hits = len(semantic_files) - len(uncached_paths)
sem_cache_misses = len(uncached_paths)
sem_result["nodes"].extend(cached_nodes)
sem_result["edges"].extend(cached_edges)
sem_result["hyperedges"].extend(cached_hyperedges)
if sem_cache_hits:
print(f"[graphify extract] semantic cache: {sem_cache_hits} hit / {sem_cache_misses} miss")
if uncached_paths:
print(f"[graphify extract] semantic extraction on {len(uncached_paths)} files via {backend}...")
corpus_kwargs: dict = {
"backend": backend,
"model": model,
"root": target,
"cache_root": out_root,
}
if deep_mode:
corpus_kwargs["deep_mode"] = True
if cli_token_budget is not None:
corpus_kwargs["token_budget"] = cli_token_budget
if cli_max_concurrency is not None:
corpus_kwargs["max_concurrency"] = cli_max_concurrency
# Minimal progress callback so the CLI is no longer silent
# during long local-inference runs (issue #792 addendum).
# Also track per-chunk success so we can fail loudly when
# every chunk errors (e.g. missing backend SDK package).
_chunk_stats = {"total": 0, "succeeded": 0}
def _progress(idx: int, total: int, _result: dict) -> None:
_chunk_stats["total"] = total
_chunk_stats["succeeded"] += 1
print(
f"[graphify extract] chunk {idx + 1}/{total} done",
flush=True,
)
corpus_kwargs["on_chunk_done"] = _progress
try:
fresh = _extract_corpus_parallel(
[Path(p) for p in uncached_paths],
**corpus_kwargs,
)
except ImportError as exc:
print(f"error: {exc}", file=sys.stderr)
sys.exit(1)
except Exception as exc:
print(
f"[graphify extract] semantic extraction failed: {exc}",
file=sys.stderr,
)
fresh = {"nodes": [], "edges": [], "hyperedges": [], "input_tokens": 0, "output_tokens": 0}
_extraction_incomplete = True # the semantic pass crashed
# on_chunk_done only fires after a chunk succeeds. If fresh
# semantic extraction was requested and no chunks completed,
# fail instead of writing an AST-only graph with exit 0.
if uncached_paths and _chunk_stats["succeeded"] == 0:
print(
f"[graphify extract] error: all semantic chunks failed "
f"for backend '{backend}' ({len(uncached_paths)} uncached files) - "
f"see per-chunk errors above. If you see 'requires the X package', "
f"run `pip install X` and retry.",
file=sys.stderr,
)
sys.exit(1)
# Some (but not all) chunks failed — the graph is missing nodes
# from the failed chunks, so it must not clobber a larger complete
# graph without an explicit --allow-partial override.
if _chunk_stats["total"] and _chunk_stats["succeeded"] < _chunk_stats["total"]:
_extraction_incomplete = True
# Which files truncated this run (item markers + the empty-parse
# _partial_files set). Computed BEFORE the save so it can be passed
# as partial_source_files: without it, a file whose only truncated
# chunk parsed empty (so it has no item markers here) would be
# written as a complete cache entry, re-promoting it (#1950).
from graphify.llm import (
_partial_source_files as _partial_sf,
_strip_partial_markers as _strip_partial,
)
_partial_semantic_files = set(_partial_sf(fresh))
try:
_save_semantic_cache(
fresh.get("nodes", []),
fresh.get("edges", []),
fresh.get("hyperedges", []),
root=target,
cache_root=out_root,
allowed_source_files=uncached_paths,
mode=sem_cache_mode,
prompt=sem_prompt,
partial_source_files=_partial_semantic_files or None,
)
except Exception as exc:
print(f"[graphify extract] warning: could not write semantic cache: {exc}", file=sys.stderr)
# Strip the markers before the corpus feeds the graph so the
# internal flag never leaks into graph.json.
_strip_partial(fresh)
sem_result["nodes"].extend(fresh.get("nodes", []))
sem_result["edges"].extend(fresh.get("edges", []))
sem_result["hyperedges"].extend(fresh.get("hyperedges", []))
sem_result["input_tokens"] += fresh.get("input_tokens", 0)
sem_result["output_tokens"] += fresh.get("output_tokens", 0)
# Prune orphaned semantic cache entries. The semantic cache is
# content-hash-keyed and unversioned, so it is never swept by the AST
# version-cleanup: every content change or file deletion leaves a
# permanent orphan that accumulates unbounded (#1527). Sweep it against
# the FULL live document set (``files_by_type`` — present in both the
# incremental and full branches), NOT the incremental ``semantic_files``
# changed-subset, which would delete every unchanged doc's valid entry.
# Best-effort: a prune failure must never break extraction.
# Hash keys are anchored to the corpus (``target``) — the same anchor
# the cache read/write above use — while the stat-index artifact
# follows the cache location (``out_root``). Anchoring these hashes to
# ``out_root`` instead would mismatch every key under ``--out`` and
# sweep the entire fresh cache as orphaned (#1990/#1991).
try:
from graphify.cache import file_hash as _file_hash
_live_hashes: set[str] = set()
for _kind in ("document", "paper", "image"):
for _fp in files_by_type.get(_kind, []):
_abs = Path(_fp)
if not _abs.is_absolute():
_abs = Path(target) / _abs
if not _abs.is_file():
continue # deleted/missing — leave out so its entry is pruned
try:
_live_hashes.add(_file_hash(_abs, target, cache_root=out_root))
except OSError:
pass
# A pathless database extraction has no filesystem corpus to sweep.
if has_path:
_prune_semantic_cache(out_root, _live_hashes)
except Exception as exc:
print(f"[graphify extract] warning: could not prune semantic cache: {exc}", file=sys.stderr)
stages.mark("semantic extract")
pg_result: dict = {"nodes": [], "edges": []}
if cli_postgres_dsn is not None:
from graphify.pg_introspect import introspect_postgres
print(f"[graphify extract] introspecting PostgreSQL schema...")
try:
pg_result = introspect_postgres(cli_postgres_dsn)
except (ConnectionError, ImportError) as exc:
print(f"error: {exc}", file=sys.stderr)
sys.exit(1)
print(f"[graphify extract] PostgreSQL: {len(pg_result['nodes'])} nodes, "
f"{len(pg_result['edges'])} edges")
cargo_result: dict = {"nodes": [], "edges": []}
if cli_cargo:
from graphify.cargo_introspect import introspect_cargo
print("[graphify extract] introspecting Cargo workspace...")
try:
cargo_result = introspect_cargo(target)
except (ConnectionError, ImportError, OSError) as exc:
print(f"error: {exc}", file=sys.stderr)
sys.exit(1)
print(f"[graphify extract] Cargo: {len(cargo_result['nodes'])} nodes, "
f"{len(cargo_result['edges'])} edges")
# Merge AST + semantic + pg_result + cargo_result. Order matters for deduplication: passing AST
# first means semantic node attributes win on collision (richer labels
# for symbols also referenced in docs). Hyperedges only come from the
# semantic side.
merged: dict = {
"nodes": list(ast_result.get("nodes", [])) + list(sem_result.get("nodes", [])) + list(pg_result.get("nodes", [])) + list(cargo_result.get("nodes", [])),
"edges": list(ast_result.get("edges", [])) + list(sem_result.get("edges", [])) + list(pg_result.get("edges", [])) + list(cargo_result.get("edges", [])),
"hyperedges": list(sem_result.get("hyperedges", [])),
"input_tokens": ast_result.get("input_tokens", 0) + sem_result.get("input_tokens", 0),
"output_tokens": ast_result.get("output_tokens", 0) + sem_result.get("output_tokens", 0),
}
graph_json_path = graphify_out / "graph.json"
analysis_path = graphify_out / ".graphify_analysis.json"
# Build a manifest-safe files dict: only stamp semantic_hash for files
# that actually produced output (cache hit or fresh extraction). Files
# whose chunk failed have no source_file entry in sem_result — leaving
# their semantic_hash empty so detect_incremental re-queues them (#933).
# Path normalization against the scan root happens inside the helper
# (#1897) so fresh root-relative source_files match detect()'s
# absolute file lists.
# #2543: also drop AST sources that failed (missing optional extra /
# zero-node anomaly) so they are not frozen as up-to-date.
_failed_ast_sources = list(ast_result.get("failed_sources") or [])
_manifest_files = _stamped_manifest_files(
files_by_type,
sem_result,
target,
partial_source_files=_partial_semantic_files,
failed_ast_sources=_failed_ast_sources,
)
# Files dispatched this run but dropped by _stamped_manifest_files
# above (failed chunk, LLM omission, or any future exclusion) still
# carry a stale semantic_hash from a prior successful run in the
# on-disk manifest; save_manifest's seed loop would otherwise copy it
# verbatim and mask the omission (#1948). Derived from semantic_files
# — what was actually SENT to the backend this run (narrowed by the
# incremental gate and --code-only, widened by deep mode) — NOT from
# files_by_type: the full live corpus includes untouched files that
# were never dispatched, and clearing those would blank the whole
# manifest on every partial incremental run, forcing a full-corpus
# re-extraction on the next one.
_stamped_semantic = {
f for _flist in _manifest_files.values() for f in _flist
}
_cleared_semantic = {str(p) for p in semantic_files} - _stamped_semantic
# #2543: AST failures need both hashes blanked (clear_ast), not just
# semantic_hash — otherwise a prior bad stamp keeps the file "unchanged".
_cleared_ast = set(_failed_ast_sources)
# Full-scan manifest saves prune rows for in-root files that left the
# scan corpus but still exist on disk (#1908). The corpus must be the
# RAW detect output (files_by_type), NOT the #933-stamp-filtered
# _manifest_files above — pruning to the filtered set would erase
# failed-chunk/omitted-doc rows and every doc row on --code-only runs.
_scan_corpus = (
{f for _fl in files_by_type.values() for f in _fl}
if has_path else None
)
def _invalidate_file_manifest_for_db_graph() -> None:
if has_path:
return
try:
manifest_path.unlink(missing_ok=True)
except OSError as exc:
print(f"error: could not invalidate file manifest: {exc}", file=sys.stderr)
sys.exit(1)
if no_cluster:
# --no-cluster: dump the raw merged extraction as graph.json.
# No NetworkX, no community detection, no analysis sidecar.
# Dedupe nodes (by id) and parallel edges so the raw output matches the
# clustered path (whose DiGraph collapses both) and stays deterministic
# across modes (#1317; node dedup also collapses shared Swift module
# anchors emitted per importing file, #1327).
from graphify.build import dedupe_edges as _dedupe_edges, dedupe_nodes as _dedupe_nodes
from graphify.export import (
backup_if_protected as _backup,
existing_graph_node_count as _existing_graph_node_count,
)
if (
incremental_mode
and not code_files
and not semantic_files
and not deleted_files
and not pg_result.get("nodes")
and not pg_result.get("edges")
and not cargo_result.get("nodes")
and not cargo_result.get("edges")
):
# An exclusion-only change reaches this gate (excluded files
# are deliberately NOT in deleted_files, #1908) but must still
# scrub the newly-excluded sources from the raw graph (#1909).
# This path never runs build_merge, so prune in place.
if graph_stale_sources:
_n_pruned = _prune_graph_json_sources(
existing_graph_path, graph_stale_sources
)
if _n_pruned:
print(
f"[graphify extract] pruned {_n_pruned} node(s) from "
f"{len(graph_stale_sources)} source file(s) no longer "
"in the scan (deleted or excluded)."
)
print(
"[graphify extract] no incremental changes detected "
"(--no-cluster); outputs left untouched."
)
try:
_save_manifest(_manifest_files, manifest_path=str(manifest_path), kind="both", root=target, scan_corpus=_scan_corpus, clear_semantic=_cleared_semantic, clear_ast=_cleared_ast or None)
except Exception as exc:
print(f"[graphify extract] warning: could not write manifest: {exc}", file=sys.stderr)
stages.total()
sys.exit(0)
if incremental_mode:
# #2169: this raw path used to write ONLY this run's extraction
# over graph.json — on an incremental run that is just the
# changed files, silently dropping every node/edge owned by an
# unchanged file. Merge the existing graph forward first, with
# the same replace/prune semantics as the clustered path's
# build_merge: re-extracted sources replaced, deleted +
# excluded + graph-stale sources pruned, everything else
# carried. Survivors are prepended, so the dedupe below keeps
# this run's fresh attributes for re-extracted nodes.
from graphify.build import merge_raw_extraction as _merge_raw_extraction
_raw_prune_sources: list[str] = list(deleted_files)
for _src in list(excluded_files) + graph_stale_sources:
if _src not in _raw_prune_sources:
_raw_prune_sources.append(_src)
try:
merged = _merge_raw_extraction(
merged,
graph_path=existing_graph_path,
prune_sources=_raw_prune_sources or None,
root=target,
)
except RuntimeError as exc:
# Existing graph present but unparseable: refuse to
# raw-dump this run's partial extraction over it.
print(f"error: {exc}", file=sys.stderr)
sys.exit(1)
merged["nodes"] = _dedupe_nodes(merged["nodes"])
merged["edges"] = _dedupe_edges(merged["edges"])
# Disambiguate colliding-basename file-node labels (#2032). This raw
# --no-cluster path bypasses build_from_json (where the clustered path
# gets this), so apply it directly on the merged node list.
from graphify.build import disambiguate_file_labels_in_nodes as _disamb_labels
_disamb_labels(merged["nodes"])
# Backfill source_file from endpoint nodes — this raw path bypasses
# build_from_json's backfill, and semantic edges sometimes omit it (#1279).
_node_sf = {n.get("id"): n.get("source_file") for n in merged["nodes"]}
for _e in merged["edges"]:
if not _e.get("source_file"):
_e["source_file"] = (
_node_sf.get(_e.get("source")) or _node_sf.get(_e.get("target")) or ""
)
# RT-parity for the raw path: an incomplete build must not force a
# partial graph over a larger complete one here either. The clustered
# path gets this from to_json's #479 guard; this path never calls
# to_json, so replicate the shrink check against the existing file and
# exit before the write/manifest unless --allow-partial is set.
if _extraction_incomplete and not cli_allow_partial:
from graphify.export import MALFORMED_GRAPH as _MALFORMED_GRAPH
_existing_n = _existing_graph_node_count(graph_json_path)
_malformed = _existing_n is _MALFORMED_GRAPH
_shrinks = isinstance(_existing_n, int) and len(merged["nodes"]) < _existing_n
if _malformed or _shrinks:
_detail = (
f"the existing {graph_json_path} is present but unparseable "
"(corrupt or a mid-write), so a shrink cannot be ruled out"
if _malformed
else f"smaller than the existing {graph_json_path} "
f"({len(merged['nodes'])} < {_existing_n} nodes)"
)
print(
"[graphify extract] error: extraction was incomplete (an AST/"
f"semantic pass failed) and the resulting --no-cluster graph is {_detail}. "
"Refusing to overwrite a complete graph with a partial one. Re-run after "
"fixing the failures, or pass --allow-partial to overwrite anyway.",
file=sys.stderr,
)
sys.exit(1)
_backup(graphify_out)
_invalidate_file_manifest_for_db_graph()
from graphify.paths import write_json_atomic as _write_json_atomic
_write_json_atomic(graph_json_path, merged, indent=2)
try:
# Record the scan root so a later build_merge / update runbook can
# relativize deleted-file paths correctly even for a custom --out
# (its grandparent-of-graph.json fallback points at the wrong dir
# otherwise, and deleted files never prune — #2012/#1571).
(graphify_out / ".graphify_root").write_text(
str(Path(target).resolve()), encoding="utf-8"
)
except OSError:
pass
stages.mark("write")
cost = _estimate_cost(
backend, merged["input_tokens"], merged["output_tokens"]
)
print(
f"[graphify extract] wrote {graph_json_path} — "
f"{len(merged['nodes'])} nodes, {len(merged['edges'])} edges "
f"(no clustering)"
)
if merged["input_tokens"] or merged["output_tokens"]:
print(
f"[graphify extract] tokens: "
f"{merged['input_tokens']:,} in / "
f"{merged['output_tokens']:,} out, "
f"est. cost: ${cost:.4f}"
)
try:
if has_path:
_save_manifest(_manifest_files, manifest_path=str(manifest_path), kind="both", root=target, scan_corpus=_scan_corpus, clear_semantic=_cleared_semantic, clear_ast=_cleared_ast or None)
except Exception as exc:
print(f"[graphify extract] warning: could not write manifest: {exc}", file=sys.stderr)
if global_merge:
from graphify.global_graph import global_add as _global_add
_tag = global_repo_tag or target.name
try:
result = _global_add(graphify_out / "graph.json", _tag)
if result["skipped"]:
print(f"[graphify global] '{_tag}' unchanged since last add - skipped.")
else:
print(f"[graphify global] '{_tag}' merged into global graph "
f"(+{result['nodes_added']} nodes, -{result['nodes_removed']} pruned).")
except Exception as exc:
print(f"[graphify global] warning: failed to merge into global graph: {exc}", file=sys.stderr)
stages.total()
sys.exit(0)
# Build graph + cluster + score + write.
from graphify.build import (
build as _build,
build_from_json as _build_from_json,
build_merge as _build_merge,
)
from graphify.cluster import cluster as _cluster, score_all as _score_all
from graphify.export import to_json as _to_json
from graphify.analyze import god_nodes as _god_nodes, surprising_connections as _surprising
dedup_backend = backend if dedup_llm else None
if incremental_mode:
# Prune everything the current scan no longer covers: genuinely
# deleted manifest rows, excluded-but-alive manifest rows (#1908),
# and the graph's own stale sources — which catches files that
# became excluded without ever being manifest-listed (#1909).
_prune_sources: list[str] = list(deleted_files)
for _src in list(excluded_files) + graph_stale_sources:
if _src not in _prune_sources:
_prune_sources.append(_src)
try:
G = _build_merge(
[merged],
graph_path=existing_graph_path,
prune_sources=_prune_sources or None,
dedup=not no_dedup,
dedup_llm_backend=dedup_backend,
root=target,
)
except ValueError as exc:
# --no-dedup arms build_merge's #479 shrink guard, which refuses
# to drop nodes belonging to files this run neither re-extracted
# nor pruned. Report the refusal instead of a traceback (#2881):
# graph.json on disk is untouched, so the old graph is intact.
print(f"[graphify extract] {exc}", file=sys.stderr)
sys.exit(1)
else:
G = _build([merged], dedup=not no_dedup, dedup_llm_backend=dedup_backend, root=target)
stages.mark("build")
if G.number_of_nodes() == 0:
print(
"[graphify extract] graph is empty — extraction produced no nodes. "
"Possible causes: all files skipped, binary-only corpus, or LLM "
"returned no edges.",
file=sys.stderr,
)
sys.exit(1)
communities = _cluster(G, resolution=cli_resolution, exclude_hubs_percentile=cli_exclude_hubs)
stages.mark("cluster")
cohesion = _score_all(G, communities)
try:
gods = _god_nodes(G)
except Exception:
gods = []
try:
surprises = _surprising(G, communities)
except Exception:
surprises = []
stages.mark("analyze")
from graphify.export import backup_if_protected as _backup
_backup(graphify_out)
_invalidate_file_manifest_for_db_graph()
# force=True bypasses the #479 shrink guard entirely. A full build
# legitimately shrinks (fuzzy dedup collapse, deleted code) so it keeps
# force=True — EXCEPT when this run's extraction was incomplete (an
# extractor pass crashed or some semantic chunks failed). Then a partial
# graph could silently overwrite a good complete one, so fall back to the
# shrink guard (force=False) unless the user opts in with --allow-partial.
#
# Both write paths are guarded: the clustered path here via to_json's
# #479 check, and the `--no-cluster` raw-dump path above via the same
# shrink check against the existing file (existing_graph_node_count).
#
# Trade-off: this reuses to_json's coarse node-count guard, not the
# source-aware _check_shrink that watch/update use. On an incremental run
# a legitimate deletion that coincides with an unrelated transient chunk
# failure can therefore be refused here — recoverable by re-running or
# passing --allow-partial (the good graph is preserved and the manifest
# is not stamped, so the retry re-extracts).
_force_write = cli_allow_partial or not _extraction_incomplete
# Stamp provenance from the ANALYSED repo, not the shell's cwd: without
# this, to_json's fallback asks `git rev-parse HEAD` in whatever repo the
# command was invoked from, so `graphify extract <target>` run from
# another repo's root stamped the invoker's commit into the target's
# graph.json — and cluster then propagates that stamp into
# GRAPH_REPORT.md (#2534 keeps the extract-time stamp by design). Same
# cwd-anchoring mistake #2316 fixed for watch/update, surviving in the
# extract path.
from graphify.watch import _git_head as _gh_target
_wrote = _to_json(G, communities, str(graph_json_path), force=_force_write,
built_at_commit=_gh_target(cwd=Path(target).resolve()))
if not _wrote:
# The shrink guard refused: this partial build is smaller than the
# existing graph. Exit before writing the manifest/marker below, which
# would otherwise stamp these files as done and make the next
# incremental run skip re-extracting them (poisoning the manifest
# against the graph we declined to write). Exit non-zero so a retry
# re-attempts.
print(
"[graphify extract] error: extraction was incomplete (an AST/semantic "
f"pass failed) and the resulting graph is smaller than the existing "
f"{graph_json_path}. Refusing to overwrite a complete graph with a "
"partial one. Re-run after fixing the failures, or pass --allow-partial "
"to overwrite anyway.",
file=sys.stderr,
)
sys.exit(1)
try:
# See the --no-cluster path above: persist the scan root so build_merge
# can relativize deleted-file paths under a custom --out (#2012/#1571).
(graphify_out / ".graphify_root").write_text(
str(Path(target).resolve()), encoding="utf-8"
)
except OSError:
pass
stages.mark("export")
if merged.get("output_tokens", 0) > 0:
(graphify_out / ".graphify_semantic_marker").write_text(
json.dumps({"output_tokens": merged["output_tokens"]}), encoding="utf-8"
)
if global_merge:
from graphify.global_graph import global_add as _global_add
_tag = global_repo_tag or target.name
try:
result = _global_add(graphify_out / "graph.json", _tag)
if result["skipped"]:
print(f"[graphify global] '{_tag}' unchanged since last add - skipped.")
else:
print(f"[graphify global] '{_tag}' merged into global graph "
f"(+{result['nodes_added']} nodes, -{result['nodes_removed']} pruned).")
except Exception as exc:
print(f"[graphify global] warning: failed to merge into global graph: {exc}", file=sys.stderr)
analysis = {
"communities": {str(k): v for k, v in communities.items()},
"cohesion": {str(k): v for k, v in cohesion.items()},
"gods": gods,
"surprises": surprises,
"tokens": {
"input": merged["input_tokens"],
"output": merged["output_tokens"],
},
}
from graphify.paths import write_json_atomic as _wja
_wja(analysis_path, analysis, indent=2)
try:
if has_path:
_save_manifest(_manifest_files, manifest_path=str(manifest_path), kind="both", root=target, scan_corpus=_scan_corpus, clear_semantic=_cleared_semantic, clear_ast=_cleared_ast or None)
except Exception as exc:
print(f"[graphify extract] warning: could not write manifest: {exc}", file=sys.stderr)
cost = _estimate_cost(backend, merged["input_tokens"], merged["output_tokens"])
print(
f"[graphify extract] wrote {graph_json_path}: "
f"{G.number_of_nodes()} nodes, {G.number_of_edges()} edges, "
f"{len(communities)} communities"
)
print(f"[graphify extract] wrote {analysis_path}")
if incremental_mode:
_excl_note = f", {len(excluded_files)} excluded" if excluded_files else ""
print(
f"[graphify extract] incremental summary: "
f"{sem_cache_hits + unchanged_total} files cached/unchanged, "
f"{len(code_files) + sem_cache_misses} re-extracted, "
f"{len(deleted_files)} deleted{_excl_note}"
)
elif sem_cache_hits:
print(f"[graphify extract] semantic cache: {sem_cache_hits} cached, {sem_cache_misses} re-extracted")
if merged["input_tokens"] or merged["output_tokens"]:
print(
f"[graphify extract] tokens: "
f"{merged['input_tokens']:,} in / "
f"{merged['output_tokens']:,} out, "
f"est. cost (~{backend}): ${cost:.4f}"
)
# extract intentionally stops at graph.json + analysis; the report and
# community labels are produced by `cluster-only` (or an agent's Step 5).
# Point standalone users at it so communities get named (#1097).
print(
"[graphify extract] next: run "
f"`graphify cluster-only {graphify_out.parent}` "
"to generate GRAPH_REPORT.md and name communities"
)
stages.total()
elif cmd == "cache-check":
# graphify cache-check <files_from> [--root <dir>] [--mode <m> | --deep]
# [--prompt-file <path>]
# Reads file paths (one per line) from <files_from>, checks semantic cache.
# --mode deep (or --deep) checks the cache/semantic-deep/ namespace
# written by `extract --mode deep` instead of cache/semantic/ (#1894).
# --prompt-file names the extraction prompt the caller will use (an agent's
# references/extraction-spec.md), restricting hits to entries produced by
# that same prompt (#1939). Omitting it reads the unattributed layout, which
# cannot see entries a fingerprinted run wrote.
# Writes:
# graphify-out/.graphify_cached.json — already-cached nodes/edges/hyperedges
# graphify-out/.graphify_uncached.txt — paths that need extraction
# Stdout: "Cache: N hit, M miss"
from graphify.cache import check_semantic_cache
if len(sys.argv) < 3:
print("Usage: graphify cache-check <files_from> [--root <dir>] "
"[--mode <m> | --deep] [--prompt-file <path>]", file=sys.stderr)
sys.exit(1)
files_from = Path(sys.argv[2])
root = Path(".")
cache_mode: str | None = None
prompt_file: str | None = None
i = 3
while i < len(sys.argv):
if sys.argv[i] == "--root" and i + 1 < len(sys.argv):
root = Path(sys.argv[i + 1])
i += 2
elif sys.argv[i] == "--mode" and i + 1 < len(sys.argv):
cache_mode = sys.argv[i + 1]
i += 2
elif sys.argv[i].startswith("--mode="):
cache_mode = sys.argv[i].split("=", 1)[1]
i += 1
elif sys.argv[i] == "--deep":
cache_mode = "deep"
i += 1
elif sys.argv[i] == "--prompt-file" and i + 1 < len(sys.argv):
prompt_file = sys.argv[i + 1]
i += 2
elif sys.argv[i].startswith("--prompt-file="):
prompt_file = sys.argv[i].split("=", 1)[1]
i += 1
else:
i += 1
files = [f for f in files_from.read_text(encoding="utf-8").splitlines() if f.strip()]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(
files, root, mode=cache_mode, prompt_file=prompt_file
)
out = root / _GRAPHIFY_OUT
out.mkdir(parents=True, exist_ok=True)
if cached_nodes or cached_edges or cached_hyperedges:
(out / ".graphify_cached.json").write_text(
json.dumps({"nodes": cached_nodes, "edges": cached_edges, "hyperedges": cached_hyperedges},
ensure_ascii=False),
encoding="utf-8",
)
(out / ".graphify_uncached.txt").write_text("\n".join(uncached), encoding="utf-8")
print(f"Cache: {len(files) - len(uncached)} hit, {len(uncached)} miss")
elif cmd == "merge-chunks":
# graphify merge-chunks <chunk_glob_or_files...> --out <path>
# Concatenates .graphify_chunk_*.json files written by semantic subagents.
# Deduplicates nodes by id (first writer wins). Sums token counts.
import glob as _glob
if len(sys.argv) < 3:
print("Usage: graphify merge-chunks <chunk_files...> --out <path>", file=sys.stderr)
sys.exit(1)
out_path: Path | None = None
chunk_args: list[str] = []
i = 2
while i < len(sys.argv):
if sys.argv[i] == "--out" and i + 1 < len(sys.argv):
out_path = Path(sys.argv[i + 1])
i += 2
else:
chunk_args.append(sys.argv[i])
i += 1
if not out_path:
print("error: --out <path> required", file=sys.stderr)
sys.exit(1)
chunk_files: list[str] = []
for arg in chunk_args:
expanded = _glob.glob(arg)
chunk_files.extend(sorted(expanded) if expanded else [arg])
merged: dict = {"nodes": [], "edges": [], "hyperedges": [], "input_tokens": 0, "output_tokens": 0}
seen_ids: set[str] = set()
valid_chunks = 0
# These chunk files are untrusted subagent output. load_validated_...
# stats the file size BEFORE reading it (so a multi-GB chunk can't blow up
# memory), parses the JSON, and validates the security caps + the node/
# edge id charset that blocks path traversal (#825) — the same enforcement
# the skill merge path applies. A bad chunk is skipped with a warning
# while valid siblings still merge; if every chunk is invalid, fail
# closed instead of reporting success and replacing --out with an empty
# semantic layer. Deliberately NOT wired into
# build_from_json/load_graph_json, which must keep loading valid
# pre-existing graphs. file_type is left to build's coercion (#840).
from graphify.semantic_cleanup import load_validated_semantic_fragment
for cf in chunk_files:
chunk, _chunk_errs = load_validated_semantic_fragment(Path(cf))
if _chunk_errs:
print(
f"[graphify merge-chunks] warning: skipping invalid chunk {cf}: "
f"{'; '.join(_chunk_errs[:3])}",
file=sys.stderr,
)
continue
valid_chunks += 1
for n in chunk.get("nodes", []):
if n.get("id") not in seen_ids:
seen_ids.add(n["id"])
merged["nodes"].append(n)
merged["edges"].extend(chunk.get("edges", []))
merged["hyperedges"].extend(chunk.get("hyperedges", []))
# Coerce token counts: a chunk is untrusted, so a non-numeric
# input_tokens/output_tokens must not abort the whole merge with a
# TypeError after other chunks already merged.
for _tok in ("input_tokens", "output_tokens"):
_v = chunk.get(_tok, 0)
merged[_tok] += _v if isinstance(_v, (int, float)) else 0
if not valid_chunks:
print(
f"[graphify merge-chunks] error: no valid chunks to merge; "
f"refusing to write {out_path}",
file=sys.stderr,
)
sys.exit(1)
out_path.parent.mkdir(parents=True, exist_ok=True)
from graphify.paths import write_json_atomic as _wja
_wja(out_path, merged, ensure_ascii=False)
chunk_summary = (
f"{valid_chunks} chunks"
if valid_chunks == len(chunk_files)
else f"{valid_chunks} of {len(chunk_files)} chunks"
)
print(
f"Merged {chunk_summary}: {len(merged['nodes'])} nodes, {len(merged['edges'])} edges, "
f"{merged['input_tokens']:,} in / {merged['output_tokens']:,} out tokens"
)
elif cmd == "merge-semantic":
# graphify merge-semantic --cached <path> --new <path> --out <path>
# Merges cached semantic results with freshly-extracted chunk results.
# Deduplicates nodes by id (cached entries take priority over new ones).
if len(sys.argv) < 3:
print("Usage: graphify merge-semantic --cached <path> --new <path> --out <path>", file=sys.stderr)
sys.exit(1)
cached_path: Path | None = None
new_path: Path | None = None
out_path2: Path | None = None
i = 2
while i < len(sys.argv):
if sys.argv[i] == "--cached" and i + 1 < len(sys.argv):
cached_path = Path(sys.argv[i + 1]); i += 2
elif sys.argv[i] == "--new" and i + 1 < len(sys.argv):
new_path = Path(sys.argv[i + 1]); i += 2
elif sys.argv[i] == "--out" and i + 1 < len(sys.argv):
out_path2 = Path(sys.argv[i + 1]); i += 2
else:
i += 1
if not out_path2:
print("error: --out <path> required", file=sys.stderr)
sys.exit(1)
empty: dict = {"nodes": [], "edges": [], "hyperedges": []}
cached_data = json.loads(cached_path.read_text(encoding="utf-8")) if cached_path and cached_path.exists() else empty
new_data = json.loads(new_path.read_text(encoding="utf-8")) if new_path and new_path.exists() else empty
seen_ids2: set[str] = set()
all_nodes: list[dict] = []
for n in cached_data.get("nodes", []) + new_data.get("nodes", []):
if n.get("id") not in seen_ids2:
seen_ids2.add(n["id"])
all_nodes.append(n)
merged2 = {
"nodes": all_nodes,
"edges": cached_data.get("edges", []) + new_data.get("edges", []),
"hyperedges": cached_data.get("hyperedges", []) + new_data.get("hyperedges", []),
}
out_path2.parent.mkdir(parents=True, exist_ok=True)
from graphify.paths import write_json_atomic as _wja
_wja(out_path2, merged2, ensure_ascii=False)
print(f"Merged: {len(merged2['nodes'])} nodes, {len(merged2['edges'])} edges")
elif Path(cmd).exists() or cmd in (".", "..") or cmd.startswith(("./", "../", "/", "~")):
# User ran `graphify <path>` directly — treat as `graphify extract <path>`.
# Common when following the PowerShell note in README (`graphify .`) or
# copy-pasting skill invocations without the leading slash.
sys.argv.insert(2, sys.argv[1])
sys.argv[1] = "extract"
_reenter_main()
else:
print(f"error: unknown command '{cmd}'", file=sys.stderr)
print("Run 'graphify --help' for usage.", file=sys.stderr)
sys.exit(1)
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