beyhan/graphify
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
5cc7ec8a23bc959daf546ec5fdbec7a3fc17ec16
graphify/graphify/__main__.py
T
SafiandClaude Opus 4.8 5cc7ec8a23 close the Read-tool graph bypass with a Read/Glob PreToolUse hook 
The Bash search hook only nudges grep/rg/find, so an agent that answers a
codebase question by Read-ing many source files one by one (the most common way
the graph gets skipped) slips right past it (#1114). Add _READ_SETTINGS_HOOK
matching Read|Glob: it fires only when graphify-out/graph.json exists, only for
a source/doc file outside graphify-out/, injects the same query-first
additionalContext, and never blocks (every branch fails open). Install and
uninstall now register and dedup both hooks idempotently.

Implemented independently rather than merging the community PR #1120; same idea,
our own hook (Read/Glob only, no fragile multi-file cat/head/tail heuristic).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
2026-06-03 00:00:33 +01:00

4360 lines
190 KiB
Python
Raw Blame History

"""graphify CLI - `graphify install` sets up the Claude Code skill."""
from __future__ import annotations
import functools
import json
import os
import platform
import re
import shutil
import sys
from pathlib import Path
try:
from importlib.metadata import version as _pkg_version
__version__ = _pkg_version("graphifyy")
except Exception:
__version__ = "unknown"
# Output directory — override with GRAPHIFY_OUT env var for worktrees or shared-output setups.
# Accepts a relative name ("graphify-out-feature") or an absolute path ("/shared/graphify-out").
_GRAPHIFY_OUT = os.environ.get("GRAPHIFY_OUT", "graphify-out")
@functools.lru_cache(maxsize=None)
def _always_on(basename: str) -> str:
"""Read a packaged always-on instruction block from graphify/always_on/.
The six always-on blocks (CLAUDE.md / AGENTS.md / GEMINI.md / VS Code
Copilot instructions / Antigravity rules / Kiro steering) live as committed
markdown next to this module, generated by tools/skillgen from a single
human-edited fragment and guarded against drift by ``skillgen --check``. The
installer injects them verbatim via ``_replace_or_append_section``, so the
bytes here must match the former triple-quoted constant exactly — the
always-on-roundtrip validator proves that.
"""
path = Path(__file__).parent / "always_on" / f"{basename}.md"
try:
return path.read_text(encoding="utf-8")
except OSError as exc:
# Defer to use-time so a missing/corrupt packaged block can't crash module
# import (which would brick every CLI command, not just install). Reached
# only by an install/integration path that actually needs this block.
raise RuntimeError(
f"graphify install is incomplete: missing always-on block '{basename}' "
f"at {path}. Reinstall graphifyy (e.g. `uv tool install --reinstall graphifyy`)."
) from exc
_ALWAYS_ON_ALIASES = {
"_CLAUDE_MD_SECTION": "claude-md",
"_AGENTS_MD_SECTION": "agents-md",
"_GEMINI_MD_SECTION": "gemini-md",
"_VSCODE_INSTRUCTIONS_SECTION": "vscode-instructions",
"_ANTIGRAVITY_RULES": "antigravity-rules",
"_KIRO_STEERING": "kiro-steering",
}
def __getattr__(name: str) -> str:
# PEP 562: lazily resolve the legacy always-on section constants for external
# importers (e.g. the install-string tests). In-module code calls _always_on()
# directly; nothing is read at import time, so a missing block can no longer
# brick the CLI on `import graphify.__main__` (#1121 follow-up).
base = _ALWAYS_ON_ALIASES.get(name)
if base is not None:
return _always_on(base)
raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
def _default_graph_path() -> str:
return str(Path(_GRAPHIFY_OUT) / "graph.json")
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 _check_skill_version(skill_dst: Path) -> None:
"""Warn if the installed skill is from an older graphify version."""
version_file = skill_dst.parent / ".graphify_version"
if not version_file.exists():
return
if not skill_dst.exists():
print(" warning: skill dir exists but SKILL.md is missing. Run 'graphify install' to repair.")
return
# A progressive SKILL.md links to its references/ sidecar. If the body points
# at references/ but the dir is gone (manual delete, partial upgrade), the
# on-demand fragments won't load — flag it for repair.
try:
body = skill_dst.read_text(encoding="utf-8")
except OSError:
body = ""
if "references/" in body and not (skill_dst.parent / "references").exists():
print(" warning: skill references/ sidecar is missing. Run 'graphify install' to repair.", file=sys.stderr)
installed = version_file.read_text(encoding="utf-8").strip()
if installed != __version__:
print(f" warning: skill is from graphify {installed}, package is {__version__}. Run 'graphify install' to update.", file=sys.stderr)
def _refresh_all_version_stamps() -> None:
"""After a successful install, update .graphify_version in all other known skill dirs.
Prevents stale-version warnings from platforms that were installed previously
but not explicitly re-installed during this upgrade.
"""
for name in _PLATFORM_CONFIG:
skill_dst = _platform_skill_destination(name)
vf = skill_dst.parent / ".graphify_version"
if skill_dst.exists():
vf.write_text(__version__, encoding="utf-8")
def _platform_skill_destination(platform_name: str, *, project: bool = False, project_dir: Path | None = None) -> Path:
"""Return the skill destination for a platform and scope."""
if platform_name == "gemini":
if project:
return (project_dir or Path(".")) / ".gemini" / "skills" / "graphify" / "SKILL.md"
if platform.system() == "Windows":
return Path.home() / ".agents" / "skills" / "graphify" / "SKILL.md"
return Path.home() / ".gemini" / "skills" / "graphify" / "SKILL.md"
if platform_name == "opencode":
if project:
return (project_dir or Path(".")) / ".opencode" / "skills" / "graphify" / "SKILL.md"
return Path.home() / ".config" / "opencode" / "skills" / "graphify" / "SKILL.md"
if platform_name == "devin":
if project:
return (project_dir or Path(".")) / ".devin" / "skills" / "graphify" / "SKILL.md"
return Path.home() / ".config" / "devin" / "skills" / "graphify" / "SKILL.md"
if platform_name == "amp":
if project:
return (project_dir or Path(".")) / ".agents" / "skills" / "graphify" / "SKILL.md"
return Path.home() / ".config" / "agents" / "skills" / "graphify" / "SKILL.md"
if platform_name in ("antigravity", "antigravity-windows"):
if project:
return (project_dir or Path(".")) / ".agents" / "skills" / "graphify" / "SKILL.md"
# Global Antigravity skill dir (all workspaces): ~/.gemini/config/skills/
return Path.home() / ".gemini" / "config" / "skills" / "graphify" / "SKILL.md"
cfg = _PLATFORM_CONFIG[platform_name]
if project:
return (project_dir or Path(".")) / cfg["skill_dst"]
if platform_name in ("claude", "windows") and os.environ.get("CLAUDE_CONFIG_DIR"):
return Path(os.environ["CLAUDE_CONFIG_DIR"]) / "skills" / "graphify" / "SKILL.md"
return Path.home() / cfg["skill_dst"]
def _packaged_skill_refs_dir(platform_name: str) -> Path | None:
"""Return the packaged references source dir for a progressive platform, else None.
A platform opts into progressive disclosure by setting ``skill_refs`` in its
``_PLATFORM_CONFIG`` entry. The value names a bundle under
``graphify/skills/<bundle>/references/``. Reuse keys (e.g. trae-cn) point at
their twin's bundle.
``gemini`` has no ``_PLATFORM_CONFIG`` entry: it installs claude's
``skill.md`` body verbatim (see ``_copy_skill_file``). Since that body is the
lean progressive core that links to ``references/``, gemini needs claude's
references/ sidecar too, or its SKILL.md ships with dead pointers. So gemini
resolves to the claude bundle rather than opting out.
Bundles ship one platform-group at a time. A host whose bundle directory
``graphify/skills/<bundle>/`` is not in this build has not gone progressive
yet, so this returns None and the host installs today's monolithic SKILL.md
with no references/ sidecar. Only when the bundle directory IS present does
this return the references path; if that directory then lacks its
``references/`` subdir, ``_copy_skill_file`` hard-fails (a malformed bundle,
the empty-sidecar regression the wheel-content test also guards).
"""
if platform_name == "gemini":
bundle = "claude"
else:
bundle = _PLATFORM_CONFIG[platform_name].get("skill_refs")
if not bundle:
return None
bundle_dir = Path(__file__).parent / "skills" / bundle
if not bundle_dir.is_dir():
return None
return bundle_dir / "references"
def _install_skill_references(skill_dst: Path, refs_src: Path) -> None:
"""Atomically install a packaged references/ sidecar next to SKILL.md.
Stages the packaged dir into ``references.tmp`` (copytree), drops any stale
``references/`` already on disk, then ``os.replace``-renames the staged dir
into place. The rename is atomic on the same filesystem, so an interrupted
install never leaves a half-written references/ visible to the agent.
"""
refs_dst = skill_dst.parent / "references"
refs_staged = skill_dst.parent / "references.tmp"
if refs_staged.exists():
shutil.rmtree(refs_staged)
try:
shutil.copytree(refs_src, refs_staged)
if refs_dst.exists():
shutil.rmtree(refs_dst)
os.replace(refs_staged, refs_dst)
except Exception:
if refs_staged.exists():
shutil.rmtree(refs_staged, ignore_errors=True)
raise
def _copy_skill_file(platform_name: str, *, project: bool = False, project_dir: Path | None = None) -> Path:
"""Copy a packaged skill file and write its version stamp.
For progressive platforms (those with ``skill_refs`` set), the packaged
``references/`` sidecar is installed alongside SKILL.md and the single
``.graphify_version`` stamp covers both. For monolith platforms (no
``skill_refs``), any orphan ``references/`` left by a prior progressive
install is removed so the on-disk layout matches the package.
"""
skill_file = "skill.md" if platform_name == "gemini" else _PLATFORM_CONFIG[platform_name]["skill_file"]
skill_src = Path(__file__).parent / skill_file
if not skill_src.exists():
print(f"error: {skill_file} not found in package - reinstall graphify", file=sys.stderr)
sys.exit(1)
refs_src = _packaged_skill_refs_dir(platform_name)
if refs_src is not None and not refs_src.exists():
# Progressive platform declared a references bundle that is missing from
# the package. Fail loud rather than silently shipping an empty sidecar.
print(
f"error: references for '{platform_name}' not found in package "
f"({refs_src}) - reinstall graphify",
file=sys.stderr,
)
sys.exit(1)
skill_dst = _platform_skill_destination(platform_name, project=project, project_dir=project_dir)
skill_dst.parent.mkdir(parents=True, exist_ok=True)
# Install the references/ sidecar (or clear an orphan one) BEFORE writing
# SKILL.md, so SKILL.md is the last artifact laid down. An install that is
# interrupted partway then leaves no SKILL.md rather than a SKILL.md that
# points at an absent references/ dir.
if refs_src is not None:
_install_skill_references(skill_dst, refs_src)
print(f" references -> {skill_dst.parent / 'references'}")
else:
# Monolith (or progressive-with-no-refs): clear any orphan references/.
orphan_refs = skill_dst.parent / "references"
if orphan_refs.exists():
shutil.rmtree(orphan_refs)
# SKILL.md last (crash-safety), via an atomic temp + rename.
tmp_dst = skill_dst.with_suffix(skill_dst.suffix + ".tmp")
try:
shutil.copy(skill_src, tmp_dst)
os.replace(tmp_dst, skill_dst)
except Exception:
try:
tmp_dst.unlink(missing_ok=True)
except OSError:
pass
raise
(skill_dst.parent / ".graphify_version").write_text(__version__, encoding="utf-8")
print(f" skill installed -> {skill_dst}")
return skill_dst
def _remove_skill_file(platform_name: str, *, project: bool = False, project_dir: Path | None = None) -> bool:
"""Remove a platform skill file and its version stamp without touching other scopes."""
skill_dst = _platform_skill_destination(platform_name, project=project, project_dir=project_dir)
removed = False
if skill_dst.exists():
skill_dst.unlink()
print(f" skill removed -> {skill_dst}")
removed = True
version_file = skill_dst.parent / ".graphify_version"
if version_file.exists():
version_file.unlink()
removed = True
refs_dir = skill_dst.parent / "references"
if refs_dir.exists():
shutil.rmtree(refs_dir)
removed = True
for d in (skill_dst.parent, skill_dst.parent.parent, skill_dst.parent.parent.parent):
try:
d.rmdir()
except OSError:
break
return removed
def _project_scope_root(path: Path, project_dir: Path) -> Path:
"""Return the top-level project artifact for a project-scoped skill path."""
try:
rel = path.relative_to(project_dir)
except ValueError:
return path
return project_dir / rel.parts[0] if rel.parts else path
def _remove_claude_skill_registration(project_dir: Path) -> None:
"""Remove the project-scoped Claude skill registration file/section."""
claude_md = project_dir / ".claude" / "CLAUDE.md"
if not claude_md.exists():
return
content = claude_md.read_text(encoding="utf-8")
if "# graphify" not in content:
return
cleaned = re.sub(r"\n*# graphify\n.*?(?=\n# |\Z)", "", content, flags=re.DOTALL).rstrip()
if cleaned:
claude_md.write_text(cleaned + "\n", encoding="utf-8")
print(f" CLAUDE.md -> graphify skill registration removed from {claude_md}")
else:
claude_md.unlink()
print(f" CLAUDE.md -> deleted {claude_md}")
def _print_project_git_add_hint(paths: list[Path]) -> None:
unique: list[str] = []
for path in paths:
text = path.as_posix().rstrip("/")
if path.exists() and path.is_dir():
text += "/"
if text not in unique:
unique.append(text)
if not unique:
return
print()
print("Project-scoped install. Add to version control:")
print(f" git add {' '.join(unique)}")
_SETTINGS_HOOK = {
# Claude Code v2.1.117+ removed dedicated Grep/Glob tools; searches now go through Bash.
# We match on Bash and inspect the command string to avoid firing on every shell call.
"matcher": "Bash",
"hooks": [
{
"type": "command",
"command": (
"CMD=$(python3 -c \""
"import json,sys; d=json.load(sys.stdin); "
"print(d.get('tool_input',d).get('command',''))\" 2>/dev/null || true); "
"case \"$CMD\" in "
r"*grep*|*rg\ *|*ripgrep*|*find\ *|*fd\ *|*ack\ *|*ag\ *) "
" [ -f graphify-out/graph.json ] && "
r""" echo '{"hookSpecificOutput":{"hookEventName":"PreToolUse","additionalContext":"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."}}' """
" || true ;; "
"esac"
),
}
],
}
_READ_SETTINGS_HOOK = {
# The Bash hook above never sees a file read through the native Read tool or a
# Glob, which is the most common way an agent skips the graph: answering a
# codebase question by Read-ing many source files one by one (issue #1114).
# Match Read|Glob, inspect the target path, and nudge (never block) only for a
# source/doc file outside graphify-out/ when a graph exists. The parser is
# python3 (already a graphify dependency), the shell is POSIX, and every branch
# fails open, so a legitimate read always goes through. Reading the graph's own
# report under graphify-out/ is suppressed so it never starts a feedback loop.
"matcher": "Read|Glob",
"hooks": [
{
"type": "command",
"command": (
"HIT=$(python3 -c \""
"import json,sys;"
"d=json.load(sys.stdin);"
"t=d.get('tool_input',d);"
"s=(str(t.get('file_path') or '')+' '+str(t.get('pattern') or '')+' '+str(t.get('path') or '')).lower().replace(chr(92),'/');"
"exts=('.py','.js','.ts','.tsx','.jsx','.go','.rs','.java','.rb','.c','.h','.cpp','.hpp','.cc','.cs','.kt','.swift','.php','.scala','.lua','.sh','.md','.rst','.txt','.mdx');"
"sys.stdout.write('1' if 'graphify-out/' not in s and any(e in s for e in exts) else '')\" 2>/dev/null || true); "
"if [ \"$HIT\" = 1 ] && [ -f graphify-out/graph.json ]; then "
r"""echo '{"hookSpecificOutput":{"hookEventName":"PreToolUse","additionalContext":"graphify: knowledge graph at graphify-out/. For codebase questions, run `graphify query \"<question>\"` (scoped subgraph, usually much smaller than reading files one by one), `graphify explain \"<concept>\"`, or `graphify path \"<A>\" \"<B>\"`, instead of reading source files to answer. Read raw files to modify or debug specific code, or when the graph lacks the detail."}}'; """
"fi || true"
),
}
],
}
def _skill_registration(skill_path: str = "~/.claude/skills/graphify/SKILL.md") -> str:
return (
"\n# graphify\n"
f"- **graphify** (`{skill_path}`) "
"- any input to knowledge graph. Trigger: `/graphify`\n"
"When the user types `/graphify`, invoke the Skill tool "
"with `skill: \"graphify\"` before doing anything else.\n"
)
_PLATFORM_CONFIG: dict[str, dict] = {
"claude": {
"skill_file": "skill.md",
"skill_dst": Path(".claude") / "skills" / "graphify" / "SKILL.md",
"claude_md": True,
"skill_refs": "claude",
},
"codex": {
"skill_file": "skill-codex.md",
"skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "codex",
},
"opencode": {
"skill_file": "skill-opencode.md",
"skill_dst": Path(".config") / "opencode" / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "opencode",
},
"kilo": {
"skill_file": "skill-kilo.md",
"skill_dst": Path(".config") / "kilo" / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "kilo",
},
"aider": {
# Monolith: aider ships the full SKILL.md inline, no references/ sidecar.
"skill_file": "skill-aider.md",
"skill_dst": Path(".aider") / "graphify" / "SKILL.md",
"claude_md": False,
},
"copilot": {
"skill_file": "skill-copilot.md",
"skill_dst": Path(".copilot") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "copilot",
},
"claw": {
"skill_file": "skill-claw.md",
"skill_dst": Path(".openclaw") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "claw",
},
"droid": {
"skill_file": "skill-droid.md",
"skill_dst": Path(".factory") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "droid",
},
"trae": {
"skill_file": "skill-trae.md",
"skill_dst": Path(".trae") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "trae",
},
"trae-cn": {
# Reuses trae's split bundle (same skill body + references).
"skill_file": "skill-trae.md",
"skill_dst": Path(".trae-cn") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "trae",
},
"hermes": {
# Reuses claw's split bundle.
"skill_file": "skill-claw.md",
"skill_dst": Path(".hermes") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "claw",
},
"kiro": {
"skill_file": "skill-kiro.md",
"skill_dst": Path(".kiro") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "kiro",
},
"pi": {
"skill_file": "skill-pi.md",
"skill_dst": Path(".pi") / "agent" / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "pi",
},
"antigravity": {
# Rides claude's split bundle (shares skill.md).
"skill_file": "skill.md",
"skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "claude",
},
"antigravity-windows": {
# Rides windows' split bundle.
"skill_file": "skill-windows.md",
"skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "windows",
},
"windows": {
"skill_file": "skill-windows.md",
"skill_dst": Path(".claude") / "skills" / "graphify" / "SKILL.md",
"claude_md": True,
"skill_refs": "windows",
},
"kimi": {
# Reuses claude's split bundle (shares skill.md).
"skill_file": "skill.md",
"skill_dst": Path(".kimi") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "claude",
},
"amp": {
# Amp searches .agents/skills (project) and ~/.config/agents/skills (user),
# not .amp/skills. The user-scope path is set in _platform_skill_destination.
"skill_file": "skill-amp.md",
"skill_dst": Path(".agents") / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
"skill_refs": "amp",
},
"devin": {
# Monolith: devin ships the full SKILL.md inline, no references/ sidecar.
"skill_file": "skill-devin.md",
# User scope: ~/.config/devin/skills/graphify/SKILL.md
# Project scope: .devin/skills/graphify/SKILL.md (overridden in _platform_skill_destination)
"skill_dst": Path(".config") / "devin" / "skills" / "graphify" / "SKILL.md",
"claude_md": False,
},
}
def _replace_or_append_section(content: str, marker: str, new_section: str) -> str:
"""Idempotently update or append a graphify-owned section in shared files.
If ``marker`` is not in ``content``, append ``new_section`` to the end
(with a blank-line separator if there's existing content).
If ``marker`` IS in ``content``, replace the existing section in place.
The section runs from the first line containing ``marker`` to the line
before the next H2 heading (``## `` at line start), or to EOF if no later
H2 exists. This lets older installs receive the updated copy without
users having to uninstall and reinstall — important for the issue #580
fix where existing report-first text would otherwise silently linger.
"""
if marker not in content:
if content.strip():
return content.rstrip() + "\n\n" + new_section.lstrip()
return new_section.lstrip()
lines = content.split("\n")
start = next((i for i, line in enumerate(lines) if marker in line), None)
if start is None:
return content.rstrip() + "\n\n" + new_section.lstrip()
end = len(lines)
for j in range(start + 1, len(lines)):
if lines[j].startswith("## "):
end = j
break
head = "\n".join(lines[:start]).rstrip()
tail = "\n".join(lines[end:]).lstrip()
section = new_section.strip()
parts: list[str] = []
if head:
parts.append(head)
parts.append(section)
if tail:
parts.append(tail)
out = "\n\n".join(parts)
if not out.endswith("\n"):
out += "\n"
return out
def install(platform: str = "claude", *, project: bool = False, project_dir: Path | None = None) -> None:
if platform == "gemini":
gemini_install(project_dir=project_dir, project=project)
return
if platform == "cursor":
_cursor_install(Path("."))
return
# On Windows, antigravity needs the PowerShell skill, not the bash one
if platform == "antigravity" and sys.platform == "win32":
platform = "antigravity-windows"
if platform not in _PLATFORM_CONFIG:
print(
f"error: unknown platform '{platform}'. Choose from: {', '.join(_PLATFORM_CONFIG)}, gemini, cursor",
file=sys.stderr,
)
sys.exit(1)
cfg = _PLATFORM_CONFIG[platform]
project_dir = project_dir or Path(".")
skill_dst = _copy_skill_file(platform, project=project, project_dir=project_dir)
if platform == "kilo":
# Kilo Code also supports a native /graphify command file.
command_src = Path(__file__).parent / "command-kilo.md"
if not command_src.exists():
print(
f"error: command-kilo.md not found in package - reinstall graphify",
file=sys.stderr,
)
sys.exit(1)
command_dst = Path.home() / ".config" / "kilo" / "command" / "graphify.md"
command_dst.parent.mkdir(parents=True, exist_ok=True)
shutil.copy(command_src, command_dst)
print(f" command installed -> {command_dst}")
if cfg["claude_md"]:
# Register in the matching Claude Code scope.
claude_md = (project_dir / ".claude" / "CLAUDE.md") if project else Path.home() / ".claude" / "CLAUDE.md"
registration = _skill_registration(".claude/skills/graphify/SKILL.md" if project else "~/.claude/skills/graphify/SKILL.md")
if claude_md.exists():
content = claude_md.read_text(encoding="utf-8")
if "graphify" in content:
print(f" CLAUDE.md -> already registered (no change)")
else:
claude_md.write_text(content.rstrip() + registration, encoding="utf-8")
print(f" CLAUDE.md -> skill registered in {claude_md}")
else:
claude_md.parent.mkdir(parents=True, exist_ok=True)
claude_md.write_text(registration.lstrip(), encoding="utf-8")
print(f" CLAUDE.md -> created at {claude_md}")
if platform == "opencode":
_install_opencode_plugin(project_dir if project else Path("."))
# Refresh version stamps in all other previously-installed skill dirs so
# stale-version warnings don't fire for platforms not explicitly re-installed.
if project:
_print_project_git_add_hint([_project_scope_root(skill_dst, project_dir)])
else:
_refresh_all_version_stamps()
print()
print("Done. Open your AI coding assistant and type:")
print()
print(" /graphify .")
print()
def _print_install_usage() -> None:
platforms = ", ".join([*_PLATFORM_CONFIG, "gemini", "cursor"])
print("Usage: graphify install [--project] [--platform P|P]")
print(f"Platforms: {platforms}")
# The always-on instruction blocks are packaged markdown under graphify/always_on/,
# generated by tools/skillgen and guarded by `skillgen --check`. Reading them at
# load keeps the install-string / issue-#580 contract byte-for-byte while letting
# a human edit one fragment instead of a triple-quoted literal here.
_CLAUDE_MD_MARKER = "## graphify"
# AGENTS.md section for Codex, OpenCode, and OpenClaw.
# All three platforms read AGENTS.md in the project root for persistent instructions.
_AGENTS_MD_MARKER = "## graphify"
_GEMINI_MD_MARKER = "## graphify"
_GEMINI_HOOK = {
"matcher": "read_file|list_directory",
"hooks": [
{
"type": "command",
"command": (
'python -c "'
"import sys,pathlib,json;"
"e=pathlib.Path('graphify-out/graph.json').exists();"
"d={'decision':'allow'};"
"e and d.update({'additionalContext':'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.'});"
"sys.stdout.write(json.dumps(d))"
'"'
),
}
],
}
def gemini_install(project_dir: Path | None = None, *, project: bool = False) -> None:
"""Copy skill file, write GEMINI.md section, and install BeforeTool hook."""
project_dir = project_dir or Path(".")
skill_dst = _copy_skill_file("gemini", project=project, project_dir=project_dir)
target = project_dir / "GEMINI.md"
if target.exists():
content = target.read_text(encoding="utf-8")
new_content = _replace_or_append_section(
content, _GEMINI_MD_MARKER, _always_on("gemini-md")
)
else:
new_content = _always_on("gemini-md")
if target.exists() and new_content == target.read_text(encoding="utf-8"):
print(f"graphify already configured in {target.resolve()} (no change)")
else:
target.write_text(new_content, encoding="utf-8")
print(f"graphify section written to {target.resolve()}")
# Always re-install the Gemini hook so an older payload (e.g. pre-issue-#580
# wording) is replaced on upgrade.
_install_gemini_hook(project_dir)
if project:
_print_project_git_add_hint([_project_scope_root(skill_dst, project_dir), project_dir / "GEMINI.md", project_dir / ".gemini"])
print()
print("Gemini CLI will now check the knowledge graph before answering")
print("codebase questions and rebuild it after code changes.")
def _install_gemini_hook(project_dir: Path) -> None:
settings_path = project_dir / ".gemini" / "settings.json"
settings_path.parent.mkdir(parents=True, exist_ok=True)
try:
settings = (
json.loads(settings_path.read_text(encoding="utf-8"))
if settings_path.exists()
else {}
)
except json.JSONDecodeError:
settings = {}
before_tool = settings.setdefault("hooks", {}).setdefault("BeforeTool", [])
settings["hooks"]["BeforeTool"] = [
h for h in before_tool if "graphify" not in str(h)
]
settings["hooks"]["BeforeTool"].append(_GEMINI_HOOK)
settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
print(" .gemini/settings.json -> BeforeTool hook registered")
def _uninstall_gemini_hook(project_dir: Path) -> None:
settings_path = project_dir / ".gemini" / "settings.json"
if not settings_path.exists():
return
try:
settings = json.loads(settings_path.read_text(encoding="utf-8"))
except json.JSONDecodeError:
return
before_tool = settings.get("hooks", {}).get("BeforeTool", [])
filtered = [h for h in before_tool if "graphify" not in str(h)]
if len(filtered) == len(before_tool):
return
settings["hooks"]["BeforeTool"] = filtered
settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
print(" .gemini/settings.json -> BeforeTool hook removed")
def gemini_uninstall(project_dir: Path | None = None, *, project: bool = False) -> None:
"""Remove the graphify section from GEMINI.md, uninstall hook, and remove skill file."""
project_dir = project_dir or Path(".")
_remove_skill_file("gemini", project=project, project_dir=project_dir)
target = project_dir / "GEMINI.md"
if not target.exists():
print("No GEMINI.md found in current directory - nothing to do")
return
content = target.read_text(encoding="utf-8")
if _GEMINI_MD_MARKER not in content:
print("graphify section not found in GEMINI.md - nothing to do")
return
cleaned = re.sub(
r"\n*## graphify\n.*?(?=\n## |\Z)", "", content, flags=re.DOTALL
).rstrip()
if cleaned:
target.write_text(cleaned + "\n", encoding="utf-8")
print(f"graphify section removed from {target.resolve()}")
else:
target.unlink()
print(f"GEMINI.md was empty after removal - deleted {target.resolve()}")
_uninstall_gemini_hook(project_dir)
_VSCODE_INSTRUCTIONS_MARKER = "## graphify"
def vscode_install(project_dir: Path | None = None) -> None:
"""Install graphify skill for VS Code Copilot Chat + write .github/copilot-instructions.md."""
skill_src = Path(__file__).parent / "skill-vscode.md"
refs_bundle = "vscode"
if not skill_src.exists():
skill_src = Path(__file__).parent / "skill-copilot.md"
refs_bundle = "copilot"
skill_dst = Path.home() / ".copilot" / "skills" / "graphify" / "SKILL.md"
skill_dst.parent.mkdir(parents=True, exist_ok=True)
tmp_dst = skill_dst.with_suffix(skill_dst.suffix + ".tmp")
try:
shutil.copy(skill_src, tmp_dst)
os.replace(tmp_dst, skill_dst)
except Exception:
try:
tmp_dst.unlink(missing_ok=True)
except OSError:
pass
raise
# Progressive-capable: install the packaged references/ sidecar when present.
refs_src = Path(__file__).parent / "skills" / refs_bundle / "references"
if refs_src.exists():
_install_skill_references(skill_dst, refs_src)
print(f" references -> {skill_dst.parent / 'references'}")
else:
orphan_refs = skill_dst.parent / "references"
if orphan_refs.exists():
shutil.rmtree(orphan_refs)
(skill_dst.parent / ".graphify_version").write_text(__version__, encoding="utf-8")
print(f" skill installed -> {skill_dst}")
instructions = (project_dir or Path(".")) / ".github" / "copilot-instructions.md"
instructions.parent.mkdir(parents=True, exist_ok=True)
if instructions.exists():
content = instructions.read_text(encoding="utf-8")
new_content = _replace_or_append_section(
content, _VSCODE_INSTRUCTIONS_MARKER, _always_on("vscode-instructions")
)
if new_content == content:
print(f" {instructions} -> already configured (no change)")
else:
instructions.write_text(new_content, encoding="utf-8")
print(f" {instructions} -> graphify section {'updated' if _VSCODE_INSTRUCTIONS_MARKER in content else 'added'}")
else:
instructions.write_text(_always_on("vscode-instructions"), encoding="utf-8")
print(f" {instructions} -> created")
print()
print(
"VS Code Copilot Chat configured. Type /graphify in the chat panel to build the graph."
)
print("Note: for GitHub Copilot CLI (terminal), use: graphify copilot install")
def vscode_uninstall(project_dir: Path | None = None) -> None:
"""Remove graphify VS Code Copilot Chat skill and .github/copilot-instructions.md section."""
skill_dst = Path.home() / ".copilot" / "skills" / "graphify" / "SKILL.md"
if skill_dst.exists():
skill_dst.unlink()
print(f" skill removed -> {skill_dst}")
version_file = skill_dst.parent / ".graphify_version"
if version_file.exists():
version_file.unlink()
refs_dir = skill_dst.parent / "references"
if refs_dir.exists():
shutil.rmtree(refs_dir)
for d in (
skill_dst.parent,
skill_dst.parent.parent,
skill_dst.parent.parent.parent,
):
try:
d.rmdir()
except OSError:
break
instructions = (project_dir or Path(".")) / ".github" / "copilot-instructions.md"
if not instructions.exists():
return
content = instructions.read_text(encoding="utf-8")
if _VSCODE_INSTRUCTIONS_MARKER not in content:
return
cleaned = re.sub(
r"\n*## graphify\n.*?(?=\n## |\Z)", "", content, flags=re.DOTALL
).rstrip()
if cleaned:
instructions.write_text(cleaned + "\n", encoding="utf-8")
print(f" graphify section removed from {instructions}")
else:
instructions.unlink()
print(f" {instructions} -> deleted (was empty after removal)")
_ANTIGRAVITY_RULES_PATH = Path(".agents") / "rules" / "graphify.md"
_ANTIGRAVITY_WORKFLOW_PATH = Path(".agents") / "workflows" / "graphify.md"
_ANTIGRAVITY_WORKFLOW = """\
---
name: graphify
description: Turn any folder of files into a navigable knowledge graph
---
# Workflow: graphify
Follow the graphify skill installed at ~/.gemini/config/skills/graphify/SKILL.md to run the full pipeline.
If no path argument is given, use `.` (current directory).
"""
_KIRO_STEERING_MARKER = "graphify: A knowledge graph of this project"
def _kiro_install(project_dir: Path) -> None:
"""Write graphify skill + steering file for Kiro IDE/CLI."""
project_dir = project_dir or Path(".")
# Skill file → .kiro/skills/graphify/SKILL.md
skill_src = Path(__file__).parent / "skill-kiro.md"
skill_dst = project_dir / ".kiro" / "skills" / "graphify" / "SKILL.md"
skill_dst.parent.mkdir(parents=True, exist_ok=True)
skill_dst.write_text(skill_src.read_text(encoding="utf-8"), encoding="utf-8")
print(f" {skill_dst.relative_to(project_dir)} -> /graphify skill")
# Steering file → .kiro/steering/graphify.md (always-on)
steering_dir = project_dir / ".kiro" / "steering"
steering_dir.mkdir(parents=True, exist_ok=True)
steering_dst = steering_dir / "graphify.md"
if steering_dst.exists() and steering_dst.read_text(encoding="utf-8") == _always_on("kiro-steering"):
print(f" .kiro/steering/graphify.md -> already configured (no change)")
else:
# File is wholly graphify-owned. Overwrite on upgrade so older
# report-first wording does not silently linger (issue #580).
action = "updated" if steering_dst.exists() else "written"
steering_dst.write_text(_always_on("kiro-steering"), encoding="utf-8")
print(f" .kiro/steering/graphify.md -> always-on steering {action}")
print()
print("Kiro will now read the knowledge graph before every conversation.")
print("Use /graphify to build or update the graph.")
def _kiro_uninstall(project_dir: Path) -> None:
"""Remove graphify skill + steering file for Kiro."""
project_dir = project_dir or Path(".")
removed = []
skill_dst = project_dir / ".kiro" / "skills" / "graphify" / "SKILL.md"
if skill_dst.exists():
skill_dst.unlink()
removed.append(str(skill_dst.relative_to(project_dir)))
# Remove parent dir if empty
try:
skill_dst.parent.rmdir()
except OSError:
pass
steering_dst = project_dir / ".kiro" / "steering" / "graphify.md"
if steering_dst.exists():
steering_dst.unlink()
removed.append(str(steering_dst.relative_to(project_dir)))
print("Removed: " + (", ".join(removed) if removed else "nothing to remove"))
def _antigravity_finalize(skill_dst: Path, project_dir: Path) -> None:
"""Write Antigravity's always-on layer next to an installed skill.
Injects the native tool-discovery YAML frontmatter into *skill_dst*, then
writes ``.agents/rules/graphify.md`` and ``.agents/workflows/graphify.md``
under *project_dir*. Shared by the global ``antigravity install`` and the
project-scoped ``install --project --platform antigravity`` paths, so both lay
down the rules/workflows that the uninstall path already expects to remove.
"""
# Inject YAML frontmatter for native Antigravity tool discovery.
if skill_dst.exists():
content = skill_dst.read_text(encoding="utf-8")
if not content.startswith("---\n"):
frontmatter = "---\nname: graphify-manager\ndescription: Rebuild the code graph or perform manual CLI queries when MCP server is offline.\n---\n\n"
skill_dst.write_text(frontmatter + content, encoding="utf-8")
# .agents/rules/graphify.md
rules_path = project_dir / _ANTIGRAVITY_RULES_PATH
rules_path.parent.mkdir(parents=True, exist_ok=True)
if rules_path.exists():
existing = rules_path.read_text(encoding="utf-8")
if _always_on("antigravity-rules").strip() != existing.strip():
rules_path.write_text(_always_on("antigravity-rules"), encoding="utf-8")
print(f"graphify rule updated at {rules_path.resolve()}")
else:
print(f"graphify rule already configured at {rules_path.resolve()} (no change)")
else:
rules_path.write_text(_always_on("antigravity-rules"), encoding="utf-8")
print(f"graphify rule written to {rules_path.resolve()}")
# .agents/workflows/graphify.md
wf_path = project_dir / _ANTIGRAVITY_WORKFLOW_PATH
wf_path.parent.mkdir(parents=True, exist_ok=True)
if wf_path.exists():
existing = wf_path.read_text(encoding="utf-8")
if _ANTIGRAVITY_WORKFLOW.strip() != existing.strip():
wf_path.write_text(_ANTIGRAVITY_WORKFLOW, encoding="utf-8")
print(f"graphify workflow updated at {wf_path.resolve()}")
else:
print(f"graphify workflow already configured at {wf_path.resolve()} (no change)")
else:
wf_path.write_text(_ANTIGRAVITY_WORKFLOW, encoding="utf-8")
print(f"graphify workflow written to {wf_path.resolve()}")
def _antigravity_install(project_dir: Path) -> None:
"""Install graphify for Google Antigravity (global skill + .agents/rules + .agents/workflows)."""
# Copy the skill to ~/.gemini/config/skills/graphify/SKILL.md (global), then
# lay down the always-on rules/workflows under the project dir.
install(platform="antigravity")
_antigravity_finalize(_platform_skill_destination("antigravity"), project_dir)
print()
print("Antigravity will now check the knowledge graph before answering")
print("codebase questions. Run /graphify first to build the graph.")
print()
print(
"To enable full MCP architecture navigation, add this to ~/.gemini/antigravity/mcp_config.json:"
)
print(' "graphify": {')
print(' "command": "uv",')
print(
' "args": ["run", "--with", "graphifyy", "--with", "mcp", "-m", "graphify.serve", "${workspace.path}/graphify-out/graph.json"]'
)
print(" }")
def _antigravity_uninstall(project_dir: Path, *, project: bool = False) -> None:
"""Remove graphify Antigravity rules, workflow, and skill files."""
# Remove rules file
rules_path = project_dir / _ANTIGRAVITY_RULES_PATH
if rules_path.exists():
rules_path.unlink()
print(f"graphify rule removed from {rules_path.resolve()}")
else:
print("No graphify Antigravity rule found - nothing to do")
# Remove workflow file
wf_path = project_dir / _ANTIGRAVITY_WORKFLOW_PATH
if wf_path.exists():
wf_path.unlink()
print(f"graphify workflow removed from {wf_path.resolve()}")
# Remove skill file
skill_dst = _platform_skill_destination("antigravity", project=project, project_dir=project_dir)
if skill_dst.exists():
skill_dst.unlink()
print(f"graphify skill removed from {skill_dst}")
version_file = skill_dst.parent / ".graphify_version"
if version_file.exists():
version_file.unlink()
refs_dir = skill_dst.parent / "references"
if refs_dir.exists():
shutil.rmtree(refs_dir)
for d in (
skill_dst.parent,
skill_dst.parent.parent,
skill_dst.parent.parent.parent,
):
try:
d.rmdir()
except OSError:
break
_CURSOR_RULE_PATH = Path(".cursor") / "rules" / "graphify.mdc"
_CURSOR_RULE = """\
---
description: graphify knowledge graph context
alwaysApply: true
---
This project has a graphify knowledge graph at graphify-out/.
- For codebase or architecture questions, when `graphify-out/graph.json` exists, first run `graphify query "<question>"` (or `graphify path "<A>" "<B>"` / `graphify explain "<concept>"`). These return a scoped subgraph, usually much smaller than `GRAPH_REPORT.md` or raw grep output.
- If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
- Read graphify-out/GRAPH_REPORT.md only for broad architecture review or when query/path/explain do not surface enough context
- After modifying code files in this session, run `graphify update .` to keep the graph current (AST-only, no API cost)
"""
def _cursor_install(project_dir: Path) -> None:
"""Write .cursor/rules/graphify.mdc with alwaysApply: true."""
rule_path = (project_dir or Path(".")) / _CURSOR_RULE_PATH
rule_path.parent.mkdir(parents=True, exist_ok=True)
if rule_path.exists() and rule_path.read_text(encoding="utf-8") == _CURSOR_RULE:
print(f"graphify rule at {rule_path} already configured (no change)")
return
# File is wholly graphify-owned. Overwrite on upgrade so older
# report-first wording does not silently linger (issue #580).
action = "updated" if rule_path.exists() else "written"
rule_path.write_text(_CURSOR_RULE, encoding="utf-8")
print(f"graphify rule {action} at {rule_path.resolve()}")
print()
print("Cursor will now always include the knowledge graph context.")
print("Run /graphify . first to build the graph if you haven't already.")
def _cursor_uninstall(project_dir: Path) -> None:
"""Remove .cursor/rules/graphify.mdc."""
rule_path = (project_dir or Path(".")) / _CURSOR_RULE_PATH
if not rule_path.exists():
print("No graphify Cursor rule found - nothing to do")
return
rule_path.unlink()
print(f"graphify Cursor rule removed from {rule_path.resolve()}")
# Devin CLI — .windsurf/rules/graphify.md (always-on context)
# Devin reads .windsurf/rules/*.md files the same way Windsurf IDE does.
_DEVIN_RULES_PATH = Path(".windsurf") / "rules" / "graphify.md"
_DEVIN_RULES = """\
## graphify
This project has a graphify knowledge graph at graphify-out/.
Rules:
- For codebase or architecture questions, when `graphify-out/graph.json` exists, first run `graphify query "<question>"` (or `graphify path "<A>" "<B>"` / `graphify explain "<concept>"`). These return a scoped subgraph, usually much smaller than `GRAPH_REPORT.md` or raw grep output.
- If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
- Read graphify-out/GRAPH_REPORT.md only for broad architecture review or when query/path/explain do not surface enough context
- After modifying code files in this session, run `graphify update .` to keep the graph current (AST-only, no API cost)
"""
def _devin_rules_install(project_dir: Path) -> None:
"""Write .windsurf/rules/graphify.md for always-on Devin context."""
rules_path = (project_dir or Path(".")) / _DEVIN_RULES_PATH
rules_path.parent.mkdir(parents=True, exist_ok=True)
if rules_path.exists() and rules_path.read_text(encoding="utf-8") == _DEVIN_RULES:
print(f" {rules_path} -> already configured (no change)")
return
action = "updated" if rules_path.exists() else "written"
rules_path.write_text(_DEVIN_RULES, encoding="utf-8")
print(f" rules {action} -> {rules_path}")
def _devin_rules_uninstall(project_dir: Path) -> None:
"""Remove .windsurf/rules/graphify.md."""
rules_path = (project_dir or Path(".")) / _DEVIN_RULES_PATH
if not rules_path.exists():
return
rules_path.unlink()
print(f" rules removed -> {rules_path}")
_KILO_PLUGIN_JS = """\
// graphify Kilo plugin
// Injects a knowledge graph reminder before bash tool calls when the graph exists.
import { existsSync } from "fs";
import { join } from "path";
export const GraphifyPlugin = async ({ directory }) => {
let reminded = false;
return {
"tool.execute.before": async (input, output) => {
if (reminded) return;
if (!existsSync(join(directory, "graphify-out", "graph.json"))) return;
if (input.tool === "bash") {
output.args.command =
'echo "[graphify] Knowledge graph available. Read graphify-out/GRAPH_REPORT.md for god nodes and architecture context before searching files." && ' +
output.args.command;
reminded = true;
}
},
};
};
"""
_KILO_PLUGIN_PATH = Path(".kilo") / "plugins" / "graphify.js"
_KILO_CONFIG_JSON_PATH = Path(".kilo") / "kilo.json"
_KILO_CONFIG_JSONC_PATH = Path(".kilo") / "kilo.jsonc"
def _strip_json_comments(raw: str) -> str:
"""Remove JSONC-style comments while leaving string content intact."""
result: list[str] = []
in_string = False
escaped = False
line_comment = False
block_comment = False
i = 0
while i < len(raw):
ch = raw[i]
nxt = raw[i + 1] if i + 1 < len(raw) else ""
if line_comment:
if ch == "\n":
line_comment = False
result.append(ch)
i += 1
continue
if block_comment:
if ch == "*" and nxt == "/":
block_comment = False
i += 2
else:
i += 1
continue
if in_string:
result.append(ch)
if escaped:
escaped = False
elif ch == "\\":
escaped = True
elif ch == '"':
in_string = False
i += 1
continue
if ch == "/" and nxt == "/":
line_comment = True
i += 2
continue
if ch == "/" and nxt == "*":
block_comment = True
i += 2
continue
result.append(ch)
if ch == '"':
in_string = True
i += 1
return re.sub(r",(\s*[}\]])", r"\1", "".join(result))
def _load_json_like(config_file: Path) -> dict:
if not config_file.exists():
return {}
try:
raw = config_file.read_text(encoding="utf-8")
if config_file.suffix == ".jsonc":
raw = _strip_json_comments(raw)
loaded = json.loads(raw)
except (OSError, json.JSONDecodeError):
return {}
return loaded if isinstance(loaded, dict) else {}
def _kilo_config_path(project_dir: Path) -> Path:
kilo_dir = (project_dir or Path(".")) / ".kilo"
json_path = kilo_dir / _KILO_CONFIG_JSON_PATH.name
if json_path.exists():
return json_path
jsonc_path = kilo_dir / _KILO_CONFIG_JSONC_PATH.name
if jsonc_path.exists():
return jsonc_path
return json_path
def _kilo_config_write_path(project_dir: Path) -> Path:
"""Write automated Kilo edits to kilo.json so existing JSONC stays untouched."""
kilo_dir = (project_dir or Path(".")) / ".kilo"
return kilo_dir / _KILO_CONFIG_JSON_PATH.name
def _install_kilo_plugin(project_dir: Path) -> None:
"""Write graphify.js plugin and register it without rewriting user JSONC."""
plugin_file = project_dir / _KILO_PLUGIN_PATH
plugin_file.parent.mkdir(parents=True, exist_ok=True)
plugin_file.write_text(_KILO_PLUGIN_JS, encoding="utf-8")
print(f" {_KILO_PLUGIN_PATH} -> tool.execute.before hook written")
config_file = _kilo_config_path(project_dir)
write_config_file = _kilo_config_write_path(project_dir)
write_config_file.parent.mkdir(parents=True, exist_ok=True)
config = _load_json_like(config_file)
plugins = config.get("plugin")
if not isinstance(plugins, list):
plugins = []
config["plugin"] = plugins
entry = plugin_file.resolve().as_uri()
if entry not in plugins:
plugins.append(entry)
write_config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
print(f" {write_config_file.relative_to(project_dir)} -> plugin registered")
else:
print(
f" {config_file.relative_to(project_dir)} -> plugin already registered (no change)"
)
def _uninstall_kilo_plugin(project_dir: Path) -> None:
"""Remove graphify.js plugin and deregister it without rewriting user JSONC."""
plugin_file = project_dir / _KILO_PLUGIN_PATH
if plugin_file.exists():
plugin_file.unlink()
print(f" {_KILO_PLUGIN_PATH} -> removed")
config_file = _kilo_config_path(project_dir)
if not config_file.exists():
return
write_config_file = _kilo_config_write_path(project_dir)
config = _load_json_like(config_file)
plugins = config.get("plugin", [])
if not isinstance(plugins, list):
plugins = []
entry = plugin_file.resolve().as_uri()
if entry in plugins:
config["plugin"] = [plugin for plugin in plugins if plugin != entry]
if not config["plugin"]:
config.pop("plugin")
write_config_file.parent.mkdir(parents=True, exist_ok=True)
write_config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
print(
f" {write_config_file.relative_to(project_dir)} -> plugin deregistered"
)
# OpenCode tool.execute.before plugin — fires before every tool call.
# Injects a graph reminder into bash command output when graph.json exists.
_OPENCODE_PLUGIN_JS = """\
// graphify OpenCode plugin
// Injects a knowledge graph reminder before bash tool calls when the graph exists.
import { existsSync } from "fs";
import { join } from "path";
export const GraphifyPlugin = async ({ directory }) => {
let reminded = false;
return {
"tool.execute.before": async (input, output) => {
if (reminded) return;
if (!existsSync(join(directory, "graphify-out", "graph.json"))) return;
if (input.tool === "bash") {
output.args.command =
'echo "[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." && ' +
output.args.command;
reminded = true;
}
},
};
};
"""
_OPENCODE_PLUGIN_PATH = Path(".opencode") / "plugins" / "graphify.js"
_OPENCODE_CONFIG_PATH = Path(".opencode") / "opencode.json"
def _install_opencode_plugin(project_dir: Path) -> None:
"""Write graphify.js plugin and register it in opencode.json."""
plugin_file = project_dir / _OPENCODE_PLUGIN_PATH
plugin_file.parent.mkdir(parents=True, exist_ok=True)
plugin_file.write_text(_OPENCODE_PLUGIN_JS, encoding="utf-8")
print(f" {_OPENCODE_PLUGIN_PATH} -> tool.execute.before hook written")
config_file = project_dir / _OPENCODE_CONFIG_PATH
if config_file.exists():
try:
config = json.loads(config_file.read_text(encoding="utf-8"))
except json.JSONDecodeError:
config = {}
else:
config = {}
plugins = config.setdefault("plugin", [])
entry = _OPENCODE_PLUGIN_PATH.as_posix()
if entry not in plugins:
plugins.append(entry)
config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
print(f" {_OPENCODE_CONFIG_PATH} -> plugin registered")
else:
print(f" {_OPENCODE_CONFIG_PATH} -> plugin already registered (no change)")
def _uninstall_opencode_plugin(project_dir: Path) -> None:
"""Remove graphify.js plugin and deregister from opencode.json."""
plugin_file = project_dir / _OPENCODE_PLUGIN_PATH
if plugin_file.exists():
plugin_file.unlink()
print(f" {_OPENCODE_PLUGIN_PATH} -> removed")
config_file = project_dir / _OPENCODE_CONFIG_PATH
if not config_file.exists():
return
try:
config = json.loads(config_file.read_text(encoding="utf-8"))
except json.JSONDecodeError:
return
plugins = config.get("plugin", [])
entry = _OPENCODE_PLUGIN_PATH.as_posix()
if entry in plugins:
plugins.remove(entry)
if not plugins:
config.pop("plugin")
config_file.write_text(json.dumps(config, indent=2), encoding="utf-8")
print(f" {_OPENCODE_CONFIG_PATH} -> plugin deregistered")
_CODEX_HOOK = {
"hooks": {
"PreToolUse": [
{
"matcher": "Bash",
"hooks": [
{
"type": "command",
# Use the graphify CLI itself so the hook is shell-agnostic:
# no [ -f ] bash syntax, no python3 vs python Conda issue,
# no JSON escaping inside PowerShell strings. Works on
# Windows (PowerShell/cmd.exe), macOS, and Linux.
"command": "graphify hook-check",
}
],
}
]
}
}
def _resolve_graphify_exe() -> str:
"""Return the absolute path to the graphify executable.
Falls back to bare 'graphify' if resolution fails. Using an absolute path
ensures the hook works in environments where the venv Scripts/ directory is
not on PATH (e.g. VS Code Codex extension on Windows).
"""
import shutil
found = shutil.which("graphify")
if found:
return found
# Derive from sys.executable: same Scripts/ (Windows) or bin/ (Unix) dir
scripts_dir = Path(sys.executable).parent
for name in ("graphify.exe", "graphify"):
candidate = scripts_dir / name
if candidate.exists():
return str(candidate)
return "graphify"
def _install_codex_hook(project_dir: Path) -> None:
"""Add graphify PreToolUse hook to .codex/hooks.json."""
hooks_path = project_dir / ".codex" / "hooks.json"
hooks_path.parent.mkdir(parents=True, exist_ok=True)
if hooks_path.exists():
try:
existing = json.loads(hooks_path.read_text(encoding="utf-8"))
except json.JSONDecodeError:
existing = {}
else:
existing = {}
graphify_exe = _resolve_graphify_exe()
hook_entry = {
"hooks": {
"PreToolUse": [
{
"matcher": "Bash",
"hooks": [{"type": "command", "command": f"{graphify_exe} hook-check"}],
}
]
}
}
pre_tool = existing.setdefault("hooks", {}).setdefault("PreToolUse", [])
existing["hooks"]["PreToolUse"] = [h for h in pre_tool if "graphify" not in str(h)]
existing["hooks"]["PreToolUse"].extend(hook_entry["hooks"]["PreToolUse"])
hooks_path.write_text(json.dumps(existing, indent=2), encoding="utf-8")
print(f" .codex/hooks.json -> PreToolUse hook registered ({graphify_exe} hook-check)")
def _uninstall_codex_hook(project_dir: Path) -> None:
"""Remove graphify PreToolUse hook from .codex/hooks.json."""
hooks_path = project_dir / ".codex" / "hooks.json"
if not hooks_path.exists():
return
try:
existing = json.loads(hooks_path.read_text(encoding="utf-8"))
except json.JSONDecodeError:
return
pre_tool = existing.get("hooks", {}).get("PreToolUse", [])
filtered = [h for h in pre_tool if "graphify" not in str(h)]
existing["hooks"]["PreToolUse"] = filtered
hooks_path.write_text(json.dumps(existing, indent=2), encoding="utf-8")
print(f" .codex/hooks.json -> PreToolUse hook removed")
def _agents_install(project_dir: Path, platform: str) -> None:
"""Write the graphify section to the local AGENTS.md for always-on platforms."""
target = (project_dir or Path(".")) / "AGENTS.md"
if target.exists():
content = target.read_text(encoding="utf-8")
new_content = _replace_or_append_section(
content, _AGENTS_MD_MARKER, _always_on("agents-md")
)
else:
new_content = _always_on("agents-md")
if target.exists() and new_content == target.read_text(encoding="utf-8"):
print(f"graphify already configured in {target.resolve()} (no change)")
else:
target.write_text(new_content, encoding="utf-8")
print(f"graphify section written to {target.resolve()}")
if platform == "codex":
_install_codex_hook(project_dir or Path("."))
elif platform == "opencode":
_install_opencode_plugin(project_dir or Path("."))
elif platform == "kilo":
_install_kilo_plugin(project_dir or Path("."))
print()
print(
f"{platform.capitalize()} will now check the knowledge graph before answering"
)
print("codebase questions and rebuild it after code changes.")
if platform not in ("codex", "opencode", "kilo"):
print()
print("Note: unlike Claude Code, there is no PreToolUse hook equivalent for")
print(
f"{platform.capitalize()} — the AGENTS.md rules are the always-on mechanism."
)
def _amp_legacy_cleanup() -> None:
"""Best-effort removal of the pre-fix ~/.amp/skills/graphify install dir.
Older graphify versions wrote the Amp skill to ~/.amp/skills, which Amp does
not search. Clean it up on install so a stale, never-loaded copy does not
linger. Failures are ignored (the new path is what matters).
"""
legacy = Path.home() / ".amp" / "skills" / "graphify"
if legacy.exists():
shutil.rmtree(legacy, ignore_errors=True)
if not legacy.exists():
print(f" legacy removed -> {legacy}")
def _amp_install(project_dir: Path | None = None) -> None:
"""User-scope Amp install: skill into ~/.config/agents/skills + AGENTS.md."""
_amp_legacy_cleanup()
_copy_skill_file("amp")
_agents_install(project_dir or Path("."), "amp")
def _amp_uninstall(project_dir: Path | None = None) -> None:
"""User-scope Amp uninstall: remove the skill and the AGENTS.md section."""
removed = _remove_skill_file("amp")
if removed:
print("skill removed")
_agents_uninstall(project_dir or Path("."), platform="amp")
def _project_install(platform_name: str, project_dir: Path | None = None) -> None:
"""Install platform skill/config files in the current project."""
project_dir = project_dir or Path(".")
if platform_name in ("claude", "windows"):
install(platform=platform_name, project=True, project_dir=project_dir)
claude_install(project_dir)
_print_project_git_add_hint([project_dir / ".claude", project_dir / "CLAUDE.md"])
elif platform_name == "gemini":
gemini_install(project_dir, project=True)
elif platform_name == "cursor":
_cursor_install(project_dir)
_print_project_git_add_hint([project_dir / ".cursor"])
elif platform_name == "kiro":
_kiro_install(project_dir)
_print_project_git_add_hint([project_dir / ".kiro"])
elif platform_name in ("aider", "amp", "codex", "opencode", "claw", "droid", "trae", "trae-cn", "hermes"):
skill_dst = _copy_skill_file(platform_name, project=True, project_dir=project_dir)
_agents_install(project_dir, platform_name)
hint_paths = [_project_scope_root(skill_dst, project_dir), project_dir / "AGENTS.md"]
if platform_name == "opencode":
hint_paths.append(project_dir / ".opencode")
elif platform_name == "codex":
hint_paths.append(project_dir / ".codex")
_print_project_git_add_hint(hint_paths)
elif platform_name == "devin":
skill_dst = _copy_skill_file("devin", project=True, project_dir=project_dir)
_devin_rules_install(project_dir)
_print_project_git_add_hint([_project_scope_root(skill_dst, project_dir), project_dir / ".windsurf"])
elif platform_name == "antigravity":
# Project-scoped: skill in .agents/skills/ PLUS the .agents/rules +
# .agents/workflows always-on layer (previously this path wrote only the
# skill, leaving the rules/workflows the uninstall path removes unset).
skill_dst = _copy_skill_file("antigravity", project=True, project_dir=project_dir)
_antigravity_finalize(skill_dst, project_dir)
_print_project_git_add_hint([_project_scope_root(skill_dst, project_dir), project_dir / ".agents"])
elif platform_name in ("copilot", "pi", "kimi"):
skill_dst = _copy_skill_file(platform_name, project=True, project_dir=project_dir)
_print_project_git_add_hint([_project_scope_root(skill_dst, project_dir)])
else:
install(platform=platform_name, project=True, project_dir=project_dir)
def _project_uninstall(platform_name: str, project_dir: Path | None = None) -> None:
"""Remove project-scoped platform skill/config files only."""
project_dir = project_dir or Path(".")
if platform_name in ("claude", "windows"):
_remove_skill_file(platform_name, project=True, project_dir=project_dir)
_remove_claude_skill_registration(project_dir)
claude_uninstall(project_dir, project=True)
elif platform_name == "gemini":
gemini_uninstall(project_dir, project=True)
elif platform_name == "cursor":
_cursor_uninstall(project_dir)
elif platform_name == "kiro":
_kiro_uninstall(project_dir)
elif platform_name in ("aider", "amp", "codex", "opencode", "claw", "droid", "trae", "trae-cn", "hermes"):
_remove_skill_file(platform_name, project=True, project_dir=project_dir)
_agents_uninstall(project_dir, platform=platform_name)
if platform_name == "codex":
_uninstall_codex_hook(project_dir)
elif platform_name == "antigravity":
_antigravity_uninstall(project_dir, project=True)
elif platform_name == "devin":
removed = _remove_skill_file("devin", project=True, project_dir=project_dir)
_devin_rules_uninstall(project_dir)
if not removed:
print("nothing to remove")
elif platform_name in ("copilot", "pi", "kimi"):
removed = _remove_skill_file(platform_name, project=True, project_dir=project_dir)
if not removed:
print("nothing to remove")
else:
_remove_skill_file(platform_name, project=True, project_dir=project_dir)
def _project_uninstall_all(project_dir: Path | None = None) -> None:
"""Remove project-scoped install files without touching user-scope installs."""
project_dir = project_dir or Path(".")
print("Uninstalling project-scoped graphify files...\n")
for platform_name in _PLATFORM_CONFIG:
_project_uninstall(platform_name, project_dir)
for platform_name in ("gemini", "cursor"):
_project_uninstall(platform_name, project_dir)
print("\nDone.")
def _agents_uninstall(project_dir: Path, platform: str = "") -> None:
"""Remove the graphify section from the local AGENTS.md."""
target = (project_dir or Path(".")) / "AGENTS.md"
if not target.exists():
print("No AGENTS.md found in current directory - nothing to do")
if platform == "opencode":
_uninstall_opencode_plugin(project_dir or Path("."))
elif platform == "kilo":
_uninstall_kilo_plugin(project_dir or Path("."))
return
content = target.read_text(encoding="utf-8")
if _AGENTS_MD_MARKER not in content:
print("graphify section not found in AGENTS.md - nothing to do")
if platform == "opencode":
_uninstall_opencode_plugin(project_dir or Path("."))
elif platform == "kilo":
_uninstall_kilo_plugin(project_dir or Path("."))
return
cleaned = re.sub(
r"\n*## graphify\n.*?(?=\n## |\Z)",
"",
content,
flags=re.DOTALL,
).rstrip()
if cleaned:
target.write_text(cleaned + "\n", encoding="utf-8")
print(f"graphify section removed from {target.resolve()}")
else:
target.unlink()
print(f"AGENTS.md was empty after removal - deleted {target.resolve()}")
if platform == "opencode":
_uninstall_opencode_plugin(project_dir or Path("."))
elif platform == "kilo":
_uninstall_kilo_plugin(project_dir or Path("."))
def _kilo_uninstall_global() -> list[str]:
removed = []
command_dst = Path.home() / ".config" / "kilo" / "command" / "graphify.md"
if command_dst.exists():
command_dst.unlink()
removed.append(f"command removed: {command_dst}")
try:
command_dst.parent.rmdir()
except OSError:
pass
skill_dst = Path.home() / _PLATFORM_CONFIG["kilo"]["skill_dst"]
if skill_dst.exists():
skill_dst.unlink()
removed.append(f"skill removed: {skill_dst}")
version_file = skill_dst.parent / ".graphify_version"
if version_file.exists():
version_file.unlink()
for d in (
skill_dst.parent,
skill_dst.parent.parent,
skill_dst.parent.parent.parent,
):
try:
d.rmdir()
except OSError:
break
return removed
def _kilo_install(project_dir: Path) -> None:
"""Install native Kilo skill + command globally and always-on project wiring locally."""
install(platform="kilo")
_agents_install(project_dir or Path("."), "kilo")
def _kilo_uninstall(project_dir: Path) -> None:
"""Remove Kilo always-on project wiring and global skill/command files."""
_agents_uninstall(project_dir or Path("."), platform="kilo")
removed = _kilo_uninstall_global()
print("; ".join(removed) if removed else "nothing to remove")
def claude_install(project_dir: Path | None = None) -> None:
"""Write the graphify section to the local CLAUDE.md."""
target = (project_dir or Path(".")) / "CLAUDE.md"
if target.exists():
content = target.read_text(encoding="utf-8")
new_content = _replace_or_append_section(
content, _CLAUDE_MD_MARKER, _always_on("claude-md")
)
else:
new_content = _always_on("claude-md")
if target.exists() and new_content == target.read_text(encoding="utf-8"):
print(f"graphify already configured in {target.resolve()} (no change)")
else:
target.write_text(new_content, encoding="utf-8")
print(f"graphify section written to {target.resolve()}")
# Always re-install the Claude Code PreToolUse hook so an old hook
# payload (e.g. pre-issue-#580 wording) is replaced on upgrade.
_install_claude_hook(project_dir or Path("."))
print()
print("Claude Code will now check the knowledge graph before answering")
print("codebase questions and rebuild it after code changes.")
def _install_claude_hook(project_dir: Path) -> None:
"""Add graphify PreToolUse hook to .claude/settings.json."""
settings_path = project_dir / ".claude" / "settings.json"
settings_path.parent.mkdir(parents=True, exist_ok=True)
if settings_path.exists():
try:
settings = json.loads(settings_path.read_text(encoding="utf-8"))
except json.JSONDecodeError:
settings = {}
else:
settings = {}
hooks = settings.setdefault("hooks", {})
pre_tool = hooks.setdefault("PreToolUse", [])
hooks["PreToolUse"] = [h for h in pre_tool if not (h.get("matcher") in ("Glob|Grep", "Bash", "Read|Glob") and "graphify" in str(h))]
hooks["PreToolUse"].append(_SETTINGS_HOOK)
hooks["PreToolUse"].append(_READ_SETTINGS_HOOK)
settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
print(f" .claude/settings.json -> PreToolUse hooks registered (Bash search + Read/Glob)")
def _uninstall_claude_hook(project_dir: Path) -> None:
"""Remove graphify PreToolUse hook from .claude/settings.json."""
settings_path = project_dir / ".claude" / "settings.json"
if not settings_path.exists():
return
try:
settings = json.loads(settings_path.read_text(encoding="utf-8"))
except json.JSONDecodeError:
return
pre_tool = settings.get("hooks", {}).get("PreToolUse", [])
filtered = [h for h in pre_tool if not (h.get("matcher") in ("Glob|Grep", "Bash", "Read|Glob") and "graphify" in str(h))]
if len(filtered) == len(pre_tool):
return
settings["hooks"]["PreToolUse"] = filtered
settings_path.write_text(json.dumps(settings, indent=2), encoding="utf-8")
print(f" .claude/settings.json -> PreToolUse hook removed")
def uninstall_all(project_dir: Path | None = None, purge: bool = False) -> None:
"""Remove graphify from every platform detected in the current project."""
pd = project_dir or Path(".")
print("Uninstalling graphify from all detected platforms...\n")
# Skill-file / config-section uninstallers
claude_uninstall(pd)
gemini_uninstall(pd)
vscode_uninstall(pd)
_cursor_uninstall(pd)
_kiro_uninstall(pd)
_antigravity_uninstall(pd)
# AGENTS.md covers: codex, aider, opencode, claw, droid, trae, trae-cn, hermes, copilot
_agents_uninstall(pd)
# Amp also drops a user-scope skill at ~/.config/agents/skills, which the
# AGENTS.md cleanup above does not touch.
_remove_skill_file("amp")
_uninstall_opencode_plugin(pd)
_uninstall_codex_hook(pd)
# Git hook
try:
from graphify.hooks import uninstall as hook_uninstall
result = hook_uninstall(pd)
if result:
print(result)
except Exception:
pass
if purge:
import shutil as _shutil
out = pd / "graphify-out"
if out.exists():
_shutil.rmtree(out)
print(f"\n graphify-out/ -> deleted (--purge)")
else:
print("\n graphify-out/ -> not found (nothing to purge)")
print("\nDone. Run 'pip uninstall graphifyy' to remove the package itself.")
def claude_uninstall(project_dir: Path | None = None, *, project: bool = False) -> None:
"""Remove the graphify skill tree (SKILL.md + references/) and the CLAUDE.md section.
Mirrors gemini_uninstall: the bare `graphify uninstall` and `graphify claude
uninstall` must remove the installed skill, not just strip CLAUDE.md, or the
progressive-disclosure tree (SKILL.md + references/) is orphaned (#1121).
"""
project_dir = project_dir or Path(".")
_remove_skill_file("claude", project=project, project_dir=project_dir)
target = project_dir / "CLAUDE.md"
if not target.exists():
print("No CLAUDE.md found in current directory - nothing to do")
return
content = target.read_text(encoding="utf-8")
if _CLAUDE_MD_MARKER not in content:
print("graphify section not found in CLAUDE.md - nothing to do")
return
# Remove the ## graphify section: from the marker to the next ## heading or EOF
cleaned = re.sub(
r"\n*## graphify\n.*?(?=\n## |\Z)",
"",
content,
flags=re.DOTALL,
).rstrip()
if cleaned:
target.write_text(cleaned + "\n", encoding="utf-8")
print(f"graphify section removed from {target.resolve()}")
else:
target.unlink()
print(f"CLAUDE.md was empty after removal - deleted {target.resolve()}")
_uninstall_claude_hook(project_dir or Path("."))
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 main() -> None:
for _stream in (sys.stdout, sys.stderr):
if _stream is not None and hasattr(_stream, "reconfigure"):
try:
_stream.reconfigure(encoding="utf-8", errors="replace")
except Exception:
pass
# Check all known skill install locations for a stale version stamp.
# Skip during install/uninstall (hook writes trigger a fresh check anyway).
# Skip during hook-check — it runs on every editor tool use and must be silent.
# Deduplicate paths so platforms sharing the same install dir don't warn twice.
_silent_cmds = {"install", "uninstall", "hook-check"}
if not any(arg in _silent_cmds for arg in sys.argv):
# Resolve each platform's real user-scope destination so per-platform
# overrides (gemini, opencode, devin, antigravity, amp) check the dir
# they actually install into, not the bare cfg['skill_dst'].
for skill_dst in {_platform_skill_destination(name) for name in _PLATFORM_CONFIG}:
_check_skill_version(skill_dst)
if len(sys.argv) >= 2 and sys.argv[1] in ("-v", "--version", "version"):
print(f"graphify {__version__}")
return
if len(sys.argv) < 2 or sys.argv[1] in ("-h", "--help", "-?"):
print("Usage: graphify <command>")
print()
print("Commands:")
print(" install [--platform P] copy skill to platform config dir (claude|windows|codex|opencode|aider|amp|claw|droid|trae|trae-cn|gemini|cursor|antigravity|hermes|kiro|pi|devin)")
print(" uninstall remove graphify from all detected platforms in one shot")
print(" --purge also delete graphify-out/ directory")
print(" path \"A\" \"B\" shortest path between two nodes in graph.json")
print(" --graph <path> path to graph.json (default graphify-out/graph.json)")
print(" explain \"X\" plain-language explanation of a node and its neighbors")
print(" --graph <path> path to graph.json (default graphify-out/graph.json)")
print(" diagnose multigraph report same-endpoint edge collapse risk in graph.json")
print(" --graph <path> path to graph/extraction JSON")
print(" (default graphify-out/graph.json)")
print(" --json emit machine-readable JSON")
print(" --max-examples N max same-endpoint examples to print (default 5)")
print(" --directed force directed post-build simulation")
print(" --undirected force undirected post-build simulation")
print(" (default follows JSON directed flag;")
print(" raw extraction with no flag defaults directed)")
print(" --extract-path PATH extractor source for suppression scan")
print(" clone <github-url> clone a GitHub repo locally and print its path for /graphify")
print(" merge-driver <base> <current> <other> git merge driver: union-merge two graph.json files (set up via hook install)")
print(" merge-graphs <g1> <g2> merge two or more graph.json files into one cross-repo graph")
print(" --out <path> output path (default: graphify-out/merged-graph.json)")
print(" --branch <branch> checkout a specific branch (default: repo default)")
print(" --out <dir> clone to a custom directory (default: ~/.graphify/repos/<owner>/<repo>)")
print(" add <url> fetch a URL and save it to ./raw, then update the graph")
print(" --author \"Name\" tag the author of the content")
print(" --contributor \"Name\" tag who added it to the corpus")
print(" --dir <path> target directory (default: ./raw)")
print(" watch <path> watch a folder and rebuild the graph on code changes")
print(" update <path> re-extract code files and update the graph (no LLM needed)")
print(" --force overwrite graph.json even if the rebuild has fewer nodes")
print(" (also: GRAPHIFY_FORCE=1 env var; use after refactors that delete code)")
print(" --no-cluster skip clustering, write raw extraction only")
print(" cluster-only <path> rerun clustering on an existing graph.json and regenerate report")
print(" --no-viz skip graph.html generation (useful for >5000 node graphs / CI)")
print(" --graph <path> path to graph.json (default <path>/graphify-out/graph.json)")
print(" --no-label keep 'Community N' placeholders (skip LLM community naming)")
print(" --backend=<name> backend to use for community naming (default: auto-detect)")
print(" label <path> (re)name communities with the configured LLM backend, regenerate report")
print(" --backend=<name> backend to use (default: auto-detect from API keys)")
print(" query \"<question>\" BFS traversal of graph.json for a question")
print(" --dfs use depth-first instead of breadth-first")
print(" --context C explicit edge-context filter (repeatable)")
print(" --budget N cap output at N tokens (default 2000)")
print(" --graph <path> path to graph.json (default graphify-out/graph.json)")
print(" affected \"X\" reverse traversal to find nodes impacted by X")
print(" --relation R edge relation to traverse in reverse (repeatable)")
print(" --depth N reverse traversal depth (default 2)")
print(" --graph <path> path to graph.json (default graphify-out/graph.json)")
print(" save-result save a Q&A result to graphify-out/memory/ for graph feedback loop")
print(" --question Q the question asked")
print(" --answer A the answer to save")
print(
" --type T query type: query|path_query|explain (default: query)"
)
print(" --nodes N1 N2 ... source node labels cited in the answer")
print(" --memory-dir DIR memory directory (default: graphify-out/memory)")
print(" check-update <path> check needs_update flag and notify if semantic re-extraction is pending (cron-safe)")
print(" tree emit a D3 v7 collapsible-tree HTML for graph.json")
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 for the hierarchy")
print(" --max-children N cap children per node (default 200)")
print(" --top-k-edges N per-symbol outbound edges in inspector (default 12)")
print(" --label NAME project label in header")
print(" extract <path> headless full extraction (AST + semantic LLM) for CI/scripts")
print(" --backend B gemini|kimi|claude|openai|deepseek|ollama (default: whichever API key is set)")
print(" --model M override backend default model")
print(" --mode deep aggressive INFERRED-edge semantic extraction")
print(" --max-workers N AST extraction subprocess count (default: cpu_count)")
print(" --token-budget N per-chunk token cap for semantic extraction (default: 60000)")
print(" --max-concurrency N parallel semantic chunks in flight (default: 4; set 1 for local LLMs)")
print(" --api-timeout S per-request timeout in seconds for the LLM client (default: 600)")
print(" --out DIR output dir (default: <path>); writes <DIR>/graphify-out/")
print(" --google-workspace export .gdoc/.gsheet/.gslides shortcuts via gws before extraction")
print(" --no-cluster skip clustering, write raw extraction only")
print(" --global also merge the resulting graph into the global graph")
print(" --as <tag> repo tag for --global (default: target directory name)")
print(" global add <graph.json> add/update a project graph in the global graph (~/.graphify/global-graph.json)")
print(" --as <tag> repo tag (default: parent directory name)")
print(" global remove <tag> remove a repo's nodes from the global graph")
print(" global list list repos in the global graph")
print(" global path print path to the global graph file")
print(" benchmark [graph.json] measure token reduction vs naive full-corpus approach")
print(" export callflow-html emit Mermaid-based architecture/call-flow HTML")
print(" hook install install post-commit/post-checkout git hooks (all platforms)")
print(" hook uninstall remove git hooks")
print(" hook status check if git hooks are installed")
print(
" gemini install write GEMINI.md section + BeforeTool hook (Gemini CLI)"
)
print(" gemini uninstall remove GEMINI.md section + BeforeTool hook")
print(" cursor install write .cursor/rules/graphify.mdc (Cursor)")
print(" cursor uninstall remove .cursor/rules/graphify.mdc")
print(
" claude install write graphify section to CLAUDE.md + PreToolUse hook (Claude Code)"
)
print(
" claude uninstall remove graphify section from CLAUDE.md + PreToolUse hook"
)
print(" codex install write graphify section to AGENTS.md (Codex)")
print(" codex uninstall remove graphify section from AGENTS.md")
print(
" opencode install write graphify section to AGENTS.md + tool.execute.before plugin (OpenCode)"
)
print(
" opencode uninstall remove graphify section from AGENTS.md + plugin"
)
print(
" kilo install install native Kilo skill + command + AGENTS.md + .kilo plugin"
)
print(
" kilo uninstall remove native Kilo skill + command + AGENTS.md + .kilo plugin"
)
print(" aider install write graphify section to AGENTS.md (Aider)")
print(" aider uninstall remove graphify section from AGENTS.md")
print(
" copilot install copy graphify skill to ~/.copilot/skills (GitHub Copilot CLI)"
)
print(" copilot uninstall remove graphify skill from ~/.copilot/skills")
print(
" vscode install configure VS Code Copilot Chat (skill + .github/copilot-instructions.md)"
)
print(" vscode uninstall remove VS Code Copilot Chat configuration")
print(
" claw install write graphify section to AGENTS.md (OpenClaw)"
)
print(" claw uninstall remove graphify section from AGENTS.md")
print(
" droid install write graphify section to AGENTS.md (Factory Droid)"
)
print(" droid uninstall remove graphify section from AGENTS.md")
print(" trae install write graphify section to AGENTS.md (Trae)")
print(" trae uninstall remove graphify section from AGENTS.md")
print(" trae-cn install write graphify section to AGENTS.md (Trae CN)")
print(" trae-cn uninstall remove graphify section from AGENTS.md")
print(
" antigravity install write .agents/rules + .agents/workflows + skill (Google Antigravity)"
)
print(
" antigravity uninstall remove .agents/rules, .agents/workflows, and skill"
)
print(
" hermes install write skill to ~/.hermes/skills/graphify/ (Hermes)"
)
print(" hermes uninstall remove skill from ~/.hermes/skills/graphify/")
print(
" kiro install write skill to .kiro/skills/graphify/ + steering file (Kiro IDE/CLI)"
)
print(" kiro uninstall remove skill + steering file")
print(" pi install write skill to ~/.pi/agent/skills/graphify/ (Pi coding agent)")
print(" pi uninstall remove skill from ~/.pi/agent/skills/graphify/")
print(" devin install write skill to ~/.config/devin/skills/graphify/ (Devin CLI)")
print(" devin uninstall remove skill from ~/.config/devin/skills/graphify/")
print()
return
cmd = sys.argv[1]
# Universal help guard: -h/--help/-? anywhere after the command shows help
# and stops — prevents flags from silently triggering destructive subcommands
# (e.g. "cursor install --help" was silently installing into Cursor, #821).
# Exempt: free-text commands (user string may contain these tokens), and
# "install"/"uninstall" which have their own per-subcommand help handlers.
_FREE_TEXT_CMDS = {"query", "explain", "path", "save-result", "install", "uninstall"}
if cmd not in _FREE_TEXT_CMDS and any(a in {"-h", "--help", "-?"} for a in sys.argv[2:]):
print(f"Run 'graphify --help' for full usage.")
return
if cmd == "install":
# Default to windows platform on Windows, claude elsewhere
default_platform = "windows" if platform.system() == "Windows" else "claude"
selected_platform: str | None = None
project_scope = False
args = sys.argv[2:]
i = 0
while i < len(args):
arg = args[i]
if arg in ("-h", "--help"):
_print_install_usage()
return
if arg == "--project":
project_scope = True
i += 1
elif arg.startswith("--platform="):
candidate = arg.split("=", 1)[1]
if selected_platform and selected_platform != candidate:
print("error: specify install platform only once", file=sys.stderr)
sys.exit(1)
selected_platform = candidate
i += 1
elif arg == "--platform":
if i + 1 >= len(args):
print("error: --platform requires a value", file=sys.stderr)
sys.exit(1)
candidate = args[i + 1]
if selected_platform and selected_platform != candidate:
print("error: specify install platform only once", file=sys.stderr)
sys.exit(1)
selected_platform = candidate
i += 2
elif arg.startswith("-"):
print(f"error: unknown install option '{arg}'", file=sys.stderr)
sys.exit(1)
else:
if selected_platform and selected_platform != arg:
print("error: specify install platform only once", file=sys.stderr)
sys.exit(1)
selected_platform = arg
i += 1
chosen_platform = selected_platform or default_platform
if project_scope:
_project_install(chosen_platform, Path("."))
else:
install(platform=chosen_platform)
elif cmd == "uninstall":
args = sys.argv[2:]
purge = "--purge" in args
project_scope = "--project" in args
selected_platform = None
i = 0
while i < len(args):
arg = args[i]
if arg in ("--purge", "--project"):
i += 1
elif arg.startswith("--platform="):
selected_platform = arg.split("=", 1)[1]
i += 1
elif arg == "--platform":
if i + 1 >= len(args):
print("error: --platform requires a value", file=sys.stderr)
sys.exit(1)
selected_platform = args[i + 1]
i += 2
elif arg.startswith("-"):
print(f"error: unknown uninstall option '{arg}'", file=sys.stderr)
sys.exit(1)
else:
selected_platform = arg
i += 1
if project_scope:
if selected_platform:
_project_uninstall(selected_platform, Path("."))
else:
_project_uninstall_all(Path("."))
else:
uninstall_all(purge=purge)
elif cmd == "claude":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
if "--project" in sys.argv[3:]:
_project_install("claude", Path("."))
else:
claude_install()
elif subcmd == "uninstall":
if "--project" in sys.argv[3:]:
_project_uninstall("claude", Path("."))
else:
claude_uninstall()
else:
print("Usage: graphify claude [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif cmd == "gemini":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
gemini_install(project=("--project" in sys.argv[3:]))
elif subcmd == "uninstall":
gemini_uninstall(project=("--project" in sys.argv[3:]))
else:
print("Usage: graphify gemini [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif cmd == "cursor":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
_cursor_install(Path("."))
elif subcmd == "uninstall":
_cursor_uninstall(Path("."))
else:
print("Usage: graphify cursor [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif cmd == "vscode":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
vscode_install()
elif subcmd == "uninstall":
vscode_uninstall()
else:
print("Usage: graphify vscode [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif cmd == "copilot":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
if "--project" in sys.argv[3:]:
_project_install("copilot", Path("."))
else:
install(platform="copilot")
elif subcmd == "uninstall":
if "--project" in sys.argv[3:]:
_project_uninstall("copilot", Path("."))
else:
removed = _remove_skill_file("copilot")
print("skill removed" if removed else "nothing to remove")
else:
print("Usage: graphify copilot [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif cmd == "kilo":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
_kilo_install(Path("."))
elif subcmd == "uninstall":
_kilo_uninstall(Path("."))
else:
print("Usage: graphify kilo [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif cmd == "kiro":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
_kiro_install(Path("."))
elif subcmd == "uninstall":
_kiro_uninstall(Path("."))
else:
print("Usage: graphify kiro [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif cmd == "devin":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
if "--project" in sys.argv[3:]:
_project_install("devin", Path("."))
else:
install(platform="devin")
elif subcmd == "uninstall":
if "--project" in sys.argv[3:]:
_project_uninstall("devin", Path("."))
else:
removed = _remove_skill_file("devin")
print("skill removed" if removed else "nothing to remove")
else:
print("Usage: graphify devin [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif cmd == "pi":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
if "--project" in sys.argv[3:]:
_project_install("pi", Path("."))
else:
install("pi")
elif subcmd == "uninstall":
if "--project" in sys.argv[3:]:
_project_uninstall("pi", Path("."))
else:
_remove_skill_file("pi")
else:
print("Usage: graphify pi [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif cmd == "amp":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
if "--project" in sys.argv[3:]:
_project_install("amp", Path("."))
else:
_amp_install(Path("."))
elif subcmd == "uninstall":
if "--project" in sys.argv[3:]:
_project_uninstall("amp", Path("."))
else:
_amp_uninstall(Path("."))
else:
print("Usage: graphify amp [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif cmd in ("aider", "codex", "opencode", "claw", "droid", "trae", "trae-cn", "hermes"):
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
if "--project" in sys.argv[3:]:
_project_install(cmd, Path("."))
else:
_agents_install(Path("."), cmd)
elif subcmd == "uninstall":
if "--project" in sys.argv[3:]:
_project_uninstall(cmd, Path("."))
else:
_agents_uninstall(Path("."), platform=cmd)
if cmd == "codex":
_uninstall_codex_hook(Path("."))
else:
print(f"Usage: graphify {cmd} [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif cmd == "antigravity":
subcmd = sys.argv[2] if len(sys.argv) > 2 else ""
if subcmd == "install":
if "--project" in sys.argv[3:]:
_project_install("antigravity", Path("."))
else:
_antigravity_install(Path("."))
elif subcmd == "uninstall":
if "--project" in sys.argv[3:]:
_project_uninstall("antigravity", Path("."))
else:
_antigravity_uninstall(Path("."))
else:
print("Usage: graphify antigravity [install|uninstall]", file=sys.stderr)
sys.exit(1)
elif 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
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"])
try:
G = json_graph.node_link_graph(_raw, edges="links")
except TypeError:
G = json_graph.node_link_graph(_raw)
except Exception as exc:
print(f"error: could not load graph: {exc}", file=sys.stderr)
sys.exit(1)
print(
_query_graph_text(
G,
question,
mode="dfs" if use_dfs else "bfs",
depth=2,
token_budget=budget,
context_filters=context_filters,
)
)
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 = "graphify-out/graph.json"
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)
print(
format_affected(
graph,
query,
relations=relations or DEFAULT_AFFECTED_RELATIONS,
depth=depth,
)
)
elif cmd == "save-result":
# graphify save-result --question Q --answer A --type T [--nodes N1 N2 ...]
import argparse as _ap
p = _ap.ArgumentParser(prog="graphify save-result")
p.add_argument("--question", required=True)
p.add_argument("--answer", required=True)
p.add_argument("--type", dest="query_type", default="query")
p.add_argument("--nodes", nargs="*", default=[])
p.add_argument("--memory-dir", default="graphify-out/memory")
opts = p.parse_args(sys.argv[2:])
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,
)
print(f"Saved to {out}")
elif cmd == "path":
if len(sys.argv) < 4:
print(
'Usage: graphify path "<source>" "<target>" [--graph path]',
file=sys.stderr,
)
sys.exit(1)
from graphify.serve import _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:]
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)
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, tgt_nid = src_scored[0][1], tgt_scored[0][1]
# 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 in (("source", src_scored), ("target", tgt_scored)):
if len(_scored) >= 2:
_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,
)
try:
path_nodes = _nx.shortest_path(G.to_undirected(as_view=True), src_nid, tgt_nid)
except (_nx.NetworkXNoPath, _nx.NodeNotFound):
print(f"No path found between '{source_label}' and '{target_label}'.")
sys.exit(0)
hops = len(path_nodes) - 1
segments = []
from graphify.build import edge_data
for i in range(len(path_nodes) - 1):
u, v = path_nodes[i], path_nodes[i + 1]
# Check which direction the stored edge points.
if G.has_edge(u, v):
edata = edge_data(G, u, v)
forward = True
else:
edata = edge_data(G, v, u)
forward = False
rel = edata.get("relation", "")
conf = edata.get("confidence", "")
conf_str = f" [{conf}]" if conf 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))
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
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)
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', '')}")
print(f" Degree: {G.degree(nid)}")
from graphify.build import edge_data
connections: list[tuple[str, str, dict]] = [] # (direction, neighbor_id, edge_data)
for nb in G.successors(nid):
connections.append(("out", nb, edge_data(G, nid, nb)))
for nb in G.predecessors(nid):
connections.append(("in", nb, edge_data(G, nb, nid)))
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 "<--"
print(f" {arrow} {G.nodes[nb].get('label', nb)} [{rel}] [{conf}]")
if len(connections) > 20:
print(f" ... and {len(connections) - 20} more")
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
_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
_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
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 == "--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 == "--no-viz" 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
print("Loading existing graph...")
_enforce_graph_size_cap_or_exit(graph_json)
_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")
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)
cohesion = score_all(G, communities)
gods = god_nodes(G)
surprises = surprising_connections(G, communities)
out = watch_path / "graphify-out"
out.mkdir(parents=True, exist_ok=True)
labels_path = out / ".graphify_labels.json"
if labels_path.exists() and not force_relabel:
try:
labels = {int(k): v for k, v in json.loads(labels_path.read_text(encoding="utf-8")).items()}
except Exception:
labels = {cid: f"Community {cid}" for cid in communities}
elif no_label and not force_relabel:
labels = {cid: f"Community {cid}" for cid in communities}
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 with the configured backend rather than leave
# "Community N" (#1097). Degrades to placeholders if no backend/on error.
from graphify.llm import generate_community_labels
print("Labeling communities...")
# The final labels (LLM or placeholder fallback) are persisted to
# .graphify_labels.json by the unconditional write below.
labels, _ = generate_community_labels(
G, communities, backend=label_backend, gods=gods
)
questions = suggest_questions(G, communities, labels)
tokens = {"input": 0, "output": 0}
from graphify.export import _git_head as _gh
_commit = _gh()
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)
(out / "GRAPH_REPORT.md").write_text(report, encoding="utf-8")
from graphify.export import backup_if_protected as _backup
_backup(out)
to_json(G, communities, str(out / "graph.json"))
labels_path.write_text(json.dumps({str(k): v for k, v in labels.items()}, ensure_ascii=False), 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()
print(f"Done - {len(communities)} communities. GRAPH_REPORT.md and graph.json updated (--no-viz; graph.html removed).")
else:
try:
to_html(G, communities, str(html_target), community_labels=labels or None)
print(f"Done - {len(communities)} communities. GRAPH_REPORT.md, graph.json and graph.html updated.")
except ValueError as viz_err:
if html_target.exists():
html_target.unlink()
print(f"Skipped graph.html: {viz_err}")
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 == "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"
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,
)
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"))
try:
return _jg.node_link_graph(data, edges="links"), data
except TypeError:
return _jg.node_link_graph(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)
Path(_current_path).write_text(json.dumps(out_data, indent=2), encoding="utf-8")
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
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"])
try:
G = _jg.node_link_graph(data, edges="links")
except TypeError:
G = _jg.node_link_graph(data)
graphs.append(G)
merged = _nx.Graph()
for G, gp in zip(graphs, graph_paths):
repo_tag = gp.parent.parent.name # graphify-out/../ → repo dir name
prefixed = _prefix(G, repo_tag)
merged = _nx.compose(merged, prefixed)
try:
out_data = _jg.node_link_data(merged, edges="links")
except TypeError:
out_data = _jg.node_link_data(merged)
out_path.parent.mkdir(parents=True, exist_ok=True)
out_path.write_text(json.dumps(out_data, indent=2), encoding="utf-8")
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"):
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)
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"
neo4j_uri: str | None = None
neo4j_user = "neo4j"
# F-031: prefer the NEO4J_PASSWORD env var so the password never
# appears on argv (visible in `ps` output / shell history). The
# explicit --password flag still overrides it for compatibility.
neo4j_password: str | None = 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):
neo4j_uri = args[i + 1]; i += 2
elif a == "--user" and i + 1 < len(args):
neo4j_user = args[i + 1]; i += 2
elif a == "--password" and i + 1 < len(args):
neo4j_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
_enforce_graph_size_cap_or_exit(graph_path)
_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:
_to_html(G, communities, str(out_dir / "graph.html"),
community_labels=labels or None, node_limit=node_limit)
if G.number_of_nodes() <= node_limit:
print(f"graph.html written - open in any browser, no server needed")
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 neo4j_uri:
from graphify.export import push_to_neo4j as _push
if neo4j_password is None:
print("error: --password required for --push", file=sys.stderr)
sys.exit(1)
result = _push(G, uri=neo4j_uri, user=neo4j_user,
password=neo4j_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 cmd == "benchmark":
from graphify.benchmark import run_benchmark, print_benchmark
graph_path = sys.argv[2] if len(sys.argv) > 2 else "graphify-out/graph.json"
_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] [--google-workspace] [--no-cluster] "
"[--max-workers N] [--token-budget N] [--max-concurrency N] "
"[--api-timeout S]",
file=sys.stderr,
)
sys.exit(1)
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
no_cluster = False
dedup_llm = False
google_workspace = False
global_merge = 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] = []
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:]
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 == "--out" and i + 1 < len(args):
out_dir = Path(args[i + 1]); i += 2
elif a.startswith("--out="):
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 == "--google-workspace":
google_workspace = 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
else:
i += 1
_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)
# Backend resolution. If user did not pass --backend, sniff env.
# If backend was explicitly requested, validate its key is present
# and surface a clear error early — don't let extract_corpus_parallel
# raise mid-run after we've spent time on AST extraction.
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,
)
if backend is None:
backend = _detect_backend()
if backend is None:
print(
"error: no LLM API key found. 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.",
file=sys.stderr,
)
sys.exit(1)
if backend not in _BACKENDS:
print(
f"error: unknown backend '{backend}'. "
f"Available: {', '.join(sorted(_BACKENDS))}",
file=sys.stderr,
)
sys.exit(1)
if backend == "ollama":
# Fail closed with a clean message (not a deep traceback) if
# OLLAMA_BASE_URL points at a link-local/metadata address. warn=False:
# the later in-flow call owns the user-facing warning for LAN hosts.
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):
# Ollama on a loopback URL ignores auth entirely; don't block
# the run just because OLLAMA_API_KEY is unset (issue #792).
# extract_files_direct already prints a warning and substitutes
# a placeholder key in that case.
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)
# 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)
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"
incremental_mode = manifest_path.exists() and existing_graph_path.exists()
if 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=cli_excludes or None,
)
else:
print(f"[graphify extract] scanning {target}")
detection = _detect(target, google_workspace=google_workspace or None, extra_excludes=cli_excludes or None)
files_by_type = detection.get("files", {})
if incremental_mode:
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", []))
unchanged_total = sum(len(v) for v in detection.get("unchanged_files", {}).values())
else:
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 = []
unchanged_total = 0
semantic_files = doc_files + paper_files + image_files
if incremental_mode:
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"
)
else:
print(
f"[graphify extract] found {len(code_files)} code, "
f"{len(doc_files)} docs, {len(paper_files)} papers, "
f"{len(image_files)} images"
)
# 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
ast_kwargs: dict = {"cache_root": target}
if cli_max_workers is not None:
ast_kwargs["max_workers"] = cli_max_workers
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)
ast_result = {"nodes": [], "edges": [], "input_tokens": 0, "output_tokens": 0}
# Semantic extraction on docs/papers/images. Check cache first.
from graphify.cache import (
check_semantic_cache as _check_semantic_cache,
save_semantic_cache as _save_semantic_cache,
)
sem_result: dict = {
"nodes": [], "edges": [], "hyperedges": [],
"input_tokens": 0, "output_tokens": 0,
}
sem_cache_hits = 0
sem_cache_misses = 0
if semantic_files:
sem_paths_str = [str(p) for p in semantic_files]
cached_nodes, cached_edges, cached_hyperedges, uncached_paths = (
_check_semantic_cache(sem_paths_str, root=target)
)
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,
}
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}
# 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)
try:
_save_semantic_cache(
fresh.get("nodes", []),
fresh.get("edges", []),
fresh.get("hyperedges", []),
root=target,
)
except Exception as exc:
print(f"[graphify extract] warning: could not write semantic cache: {exc}", file=sys.stderr)
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)
# Merge AST + semantic. 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", [])),
"edges": list(ast_result.get("edges", [])) + list(sem_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).
_sem_extracted: set[str] = {
n.get("source_file", "") for n in sem_result.get("nodes", [])
} | {
e.get("source_file", "") for e in sem_result.get("edges", [])
}
_sem_extracted.discard("")
_sem_types = {"document", "paper", "image"}
_manifest_files = {
ftype: [f for f in flist if ftype not in _sem_types or f in _sem_extracted]
for ftype, flist in files_by_type.items()
}
if no_cluster:
# --no-cluster: dump the raw merged extraction as graph.json.
# No NetworkX, no community detection, no analysis sidecar.
from graphify.export import backup_if_protected as _backup
_backup(graphify_out)
graph_json_path.write_text(
json.dumps(merged, indent=2), encoding="utf-8"
)
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:
_save_manifest(_manifest_files, manifest_path=str(manifest_path), kind="both")
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)
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:
G = _build_merge(
[merged],
graph_path=existing_graph_path,
prune_sources=deleted_files or None,
dedup=True,
dedup_llm_backend=dedup_backend,
root=target,
)
else:
G = _build([merged], dedup=True, dedup_llm_backend=dedup_backend, root=target)
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)
cohesion = _score_all(G, communities)
try:
gods = _god_nodes(G)
except Exception:
gods = []
try:
surprises = _surprising(G, communities)
except Exception:
surprises = []
from graphify.export import backup_if_protected as _backup
_backup(graphify_out)
_to_json(G, communities, str(graph_json_path), force=True)
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"],
},
}
analysis_path.write_text(json.dumps(analysis, indent=2), encoding="utf-8")
try:
_save_manifest(_manifest_files, manifest_path=str(manifest_path), kind="both")
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:
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"
)
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"
)
elif cmd == "cache-check":
# graphify cache-check <files_from> [--root <dir>]
# Reads file paths (one per line) from <files_from>, checks semantic cache.
# 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>]", file=sys.stderr)
sys.exit(1)
files_from = Path(sys.argv[2])
root = Path(".")
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
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)
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()
for cf in chunk_files:
try:
chunk = json.loads(Path(cf).read_text(encoding="utf-8"))
except (json.JSONDecodeError, OSError) as exc:
print(f"[graphify merge-chunks] warning: skipping {cf}: {exc}", file=sys.stderr)
continue
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", []))
merged["input_tokens"] += chunk.get("input_tokens", 0)
merged["output_tokens"] += chunk.get("output_tokens", 0)
out_path.parent.mkdir(parents=True, exist_ok=True)
out_path.write_text(json.dumps(merged, ensure_ascii=False), encoding="utf-8")
print(
f"Merged {len(chunk_files)} chunks: {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)
out_path2.write_text(json.dumps(merged2, ensure_ascii=False), encoding="utf-8")
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"
main()
else:
print(f"error: unknown command '{cmd}'", file=sys.stderr)
print("Run 'graphify --help' for usage.", file=sys.stderr)
sys.exit(1)
if __name__ == "__main__":
main()
Reference in New Issue View Git Blame Copy Permalink