agent-bios 0.18.0 → 0.19.0

package/compose/corpus_app.py

@@ -0,0 +1,456 @@
+#!/usr/bin/env python3
+"""Explicit Codex app discovery and per-task corpus context delivery."""
+from __future__ import annotations
+
+import argparse
+from datetime import datetime, timezone
+import hashlib
+import json
+import os
+from pathlib import Path
+import re
+import shutil
+import sys
+import tempfile
+from typing import Any
+
+try:
+    from corpus_store import CorpusStore, CorpusStoreError
+    from corpus_transaction import (TransactionError, confirmed_release, guard_pending,
+                                    reject_symlink_ancestors, transaction_lock)
+except ImportError:
+    from .corpus_store import CorpusStore, CorpusStoreError
+    from .corpus_transaction import (TransactionError, confirmed_release, guard_pending,
+                                     reject_symlink_ancestors, transaction_lock)
+
+
+SCHEMA_VERSION = 1
+BRIDGE_MEMBERS = ("SKILL.md", "agents/openai.yaml", "scripts/bridge.py",
+                  "scripts/corpus_transaction.py", "bridge.json")
+SESSION_ID = re.compile(r"[A-Za-z0-9][A-Za-z0-9_-]{0,127}\Z")
+
+
+class AppError(RuntimeError):
+    pass
+
+
+def _json_bytes(value: Any) -> bytes:
+    return (json.dumps(value, ensure_ascii=False, indent=2, sort_keys=True) + "\n").encode("utf-8")
+
+
+def _read_json(path: Path) -> dict[str, Any]:
+    reject_symlink_ancestors(path)
+    try:
+        value = json.loads(path.read_text(encoding="utf-8"))
+    except (OSError, ValueError) as exc:
+        raise AppError(f"unreadable app state: {path}") from exc
+    if not isinstance(value, dict):
+        raise AppError(f"invalid app state: {path}")
+    return value
+
+
+def _write_json(path: Path, value: dict[str, Any]) -> None:
+    reject_symlink_ancestors(path)
+    path.parent.mkdir(parents=True, exist_ok=True, mode=0o700)
+    descriptor, temporary = tempfile.mkstemp(prefix=f".{path.name}.", dir=path.parent)
+    try:
+        with os.fdopen(descriptor, "wb") as handle:
+            handle.write(_json_bytes(value))
+            handle.flush()
+            os.fsync(handle.fileno())
+        os.replace(temporary, path)
+    finally:
+        if os.path.lexists(temporary):
+            os.unlink(temporary)
+
+
+def _tree_digest(members: dict[str, bytes]) -> str:
+    digest = hashlib.sha256()
+    for relative, data in sorted(members.items()):
+        digest.update(relative.encode("utf-8") + b"\0" + data + b"\0")
+    return digest.hexdigest()
+
+
+def _roots(environ: dict[str, str] | None) -> tuple[dict[str, str], Path, Path, Path]:
+    env = dict(os.environ if environ is None else environ)
+    home = Path(env.get("HOME", str(Path.home()))).expanduser().absolute()
+    state = Path(env.get("AGENT_BIOS_STATE_DIR", str(home / ".local/share/agent-bios"))).expanduser().absolute()
+    user = Path(env.get("AGENT_BIOS_CORPUS_DIR", str(home / ".config/agent-bios/corpus"))).expanduser().absolute()
+    return env, home, state, user
+
+
+class AppBridge:
+    """Own one explicit-only skill symlink; retain immutable private generations."""
+
+    def __init__(self, repo: Path, environ: dict[str, str] | None = None):
+        self.repo = Path(repo).absolute()
+        self.env, self.home, self.state_root, self.user_root = _roots(environ)
+        self.target = self.home / ".agents/skills/agent-bios"
+        self.generations = self.state_root / "runtime/app-bridges"
+
+    def _base_config(self) -> dict[str, Any]:
+        return {"schema_version": SCHEMA_VERSION, "home": str(self.home),
+                "state_root": str(self.state_root), "user_root": str(self.user_root),
+                "discovery_path": str(self.target)}
+
+    def _config(self) -> dict[str, Any]:
+        config = self._base_config()
+        if "AGENT_LAUNCH_VENV" in self.env:
+            value = self.env["AGENT_LAUNCH_VENV"]
+            config["launch_venv"] = str(Path(value).expanduser().absolute()) if value else ""
+        else:
+            current = self._owned_target()
+            if current is not None:
+                saved = _read_json(current / "bridge.json")
+                if "launch_venv" in saved:
+                    config["launch_venv"] = saved["launch_venv"]
+        return config
+
+    def _source_members(self) -> dict[str, bytes]:
+        reject_symlink_ancestors(self.state_root)
+        guard_pending(self.state_root)
+        release = confirmed_release(self.state_root)
+        source = release / "compose/app_bridge"
+        members = {}
+        for name in BRIDGE_MEMBERS:
+            if name == "bridge.json":
+                members[name] = _json_bytes(self._config())
+                continue
+            path = release / "compose/corpus_transaction.py" if name == "scripts/corpus_transaction.py" else source / name
+            reject_symlink_ancestors(path)
+            if not path.is_file():
+                raise AppError(f"installed release has no app bridge member: {path}")
+            members[name] = path.read_bytes()
+        return members
+
+    def _owned_target(self) -> Path | None:
+        reject_symlink_ancestors(self.target.parent)
+        if not os.path.lexists(self.target):
+            return None
+        if not self.target.is_symlink():
+            raise AppError(f"preserving unowned app skill: {self.target}")
+        raw = Path(os.readlink(self.target))
+        if not raw.is_absolute() or raw.parent != self.generations or not re.fullmatch(r"[a-f0-9]{64}", raw.name):
+            raise AppError(f"preserving unowned app skill link: {self.target}")
+        reject_symlink_ancestors(raw)
+        if not raw.is_dir():
+            raise AppError(f"owned app skill generation is unavailable: {raw}")
+        paths = list(raw.rglob("*"))
+        if any(path.is_symlink() for path in paths):
+            raise AppError(f"preserving redirected app skill generation: {raw}")
+        files = {path.relative_to(raw).as_posix(): path.read_bytes() for path in paths if path.is_file()}
+        if set(files) != set(BRIDGE_MEMBERS) or _tree_digest(files) != raw.name:
+            raise AppError(f"preserving changed app skill generation: {raw}")
+        config = _read_json(raw / "bridge.json")
+        base = self._base_config()
+        if (any(config.get(key) != value for key, value in base.items())
+                or set(config) - set(base) - {"launch_venv"}
+                or ("launch_venv" in config and (not isinstance(config["launch_venv"], str)
+                    or (config["launch_venv"] and not Path(config["launch_venv"]).is_absolute())))):
+            raise AppError(f"app skill belongs to different private root settings: {self.target}")
+        return raw
+
+    def status(self) -> dict[str, Any]:
+        try:
+            target = self._owned_target()
+            return {"registered": target is not None, "discovery_path": str(self.target),
+                    "generation": str(target) if target else None, "implicit_invocation": False,
+                    "native_discovery": "unverified", "session_activation": "explicit-use-only"}
+        except (AppError, OSError, TransactionError) as exc:
+            return {"registered": False, "discovery_path": str(self.target), "needs_action": [str(exc)],
+                    "native_discovery": "unverified", "session_activation": "explicit-use-only"}
+
+    def has_owned_registration(self) -> bool:
+        """Identify our link namespace without opening unrelated skill contents."""
+        try:
+            reject_symlink_ancestors(self.target.parent)
+            if not self.target.is_symlink():
+                return False
+            target = Path(os.readlink(self.target))
+            return target.is_absolute() and target.parent == self.generations
+        except (OSError, TransactionError):
+            return False
+
+    def managed_status(self) -> dict[str, Any]:
+        """Lifecycle view: foreign native paths are outside this installer."""
+        if not self.has_owned_registration():
+            return {"registered": False, "managed": False, "discovery_path": str(self.target)}
+        return {**self.status(), "managed": True}
+
+    def register(self, dry_run: bool = False) -> dict[str, Any]:
+        reject_symlink_ancestors(self.state_root)
+        if dry_run:
+            before = self._owned_target()
+            members = self._source_members()
+            generation = self.generations / _tree_digest(members)
+            return {"registered": before is not None, "dry_run": True, "changed": before != generation,
+                    "discovery_path": str(self.target), "generation": str(generation),
+                    "implicit_invocation": False, "native_discovery": "unverified",
+                    "session_activation": "explicit-use-only"}
+        with transaction_lock(self.state_root):
+            before = self._owned_target()
+            members = self._source_members()
+            generation = self.generations / _tree_digest(members)
+            result = {"registered": True, "dry_run": False, "changed": before != generation,
+                      "discovery_path": str(self.target), "generation": str(generation),
+                      "implicit_invocation": False, "native_discovery": "unverified",
+                      "session_activation": "explicit-use-only"}
+            reject_symlink_ancestors(generation)
+            if generation.exists():
+                paths = list(generation.rglob("*"))
+                actual = {path.relative_to(generation).as_posix(): path.read_bytes()
+                          for path in paths if path.is_file() and not path.is_symlink()}
+                if any(path.is_symlink() for path in paths) or actual != members:
+                    raise AppError(f"app bridge generation collision: {generation}")
+            else:
+                self.generations.mkdir(parents=True, exist_ok=True, mode=0o700)
+                temporary = Path(tempfile.mkdtemp(prefix=".bridge-", dir=self.generations))
+                try:
+                    for relative, data in members.items():
+                        path = temporary / relative
+                        path.parent.mkdir(parents=True, exist_ok=True)
+                        path.write_bytes(data)
+                        path.chmod(0o600)
+                    os.replace(temporary, generation)
+                finally:
+                    if temporary.exists():
+                        shutil.rmtree(temporary)
+            self.target.parent.mkdir(parents=True, exist_ok=True)
+            if self._owned_target() != before:
+                raise AppError("app skill changed while preparing registration")
+            descriptor, temporary = tempfile.mkstemp(prefix=".agent-bios-link-", dir=self.target.parent)
+            os.close(descriptor)
+            os.unlink(temporary)
+            try:
+                os.symlink(str(generation), temporary)
+                os.replace(temporary, self.target)
+            finally:
+                if os.path.lexists(temporary):
+                    os.unlink(temporary)
+            return result
+
+    def unregister(self, dry_run: bool = False) -> dict[str, Any]:
+        reject_symlink_ancestors(self.state_root)
+        if dry_run or not os.path.lexists(self.target):
+            before = self._owned_target()
+            return {"registered": before is not None, "dry_run": dry_run, "changed": before is not None,
+                    "discovery_path": str(self.target), "retained_private_generations": True}
+        with transaction_lock(self.state_root):
+            before = self._owned_target()
+            if before is not None:
+                self.target.unlink()
+            return {"registered": False, "dry_run": False, "changed": before is not None,
+                    "discovery_path": str(self.target), "retained_private_generations": True}
+
+    def refresh_registration(self) -> dict[str, Any]:
+        """Refresh an existing owned registration; installation never opts in."""
+        status = self.managed_status()
+        if not status["registered"]:
+            return status
+        try:
+            return {**self.register(), "managed": True}
+        except (AppError, OSError, TransactionError) as exc:
+            return {**self.managed_status(), "needs_action": [str(exc)]}
+
+
+class AppSessions:
+    """Record returned context, separately from native launch pins and host proof."""
+
+    def __init__(self, repo: Path, environ: dict[str, str] | None = None):
+        self.repo = Path(repo).absolute()
+        self.env, self.home, self.state_root, self.user_root = _roots(environ)
+
+    def _session(self, session: str | None) -> str:
+        value = session if session is not None else self.env.get("CODEX_THREAD_ID")
+        if not isinstance(value, str) or not SESSION_ID.fullmatch(value):
+            raise AppError("app session requires CODEX_THREAD_ID or --session with a valid task id")
+        return value
+
+    def _path(self, session: str) -> Path:
+        return self.state_root / "sessions/app-context" / f"{session}.json"
+
+    def _read(self, session: str) -> dict[str, Any]:
+        path = self._path(session)
+        reject_symlink_ancestors(path)
+        if not path.exists():
+            return {"schema_version": SCHEMA_VERSION, "host": "codex", "session_id": session,
+                    "enabled": False, "deliveries": []}
+        record = _read_json(path)
+        if (record.get("schema_version") != SCHEMA_VERSION or record.get("host") != "codex"
+                or record.get("session_id") != session or not isinstance(record.get("enabled"), bool)
+                or not isinstance(record.get("deliveries"), list)):
+            raise AppError(f"invalid app session receipt: {path}")
+        for delivery in record["deliveries"]:
+            if (not isinstance(delivery, dict) or delivery.get("delivery") != "returned-as-context"
+                    or not isinstance(delivery.get("content_ref"), str)
+                    or not re.fullmatch(r"[a-f0-9]{64}", delivery["content_ref"])):
+                raise AppError(f"invalid app session delivery: {path}")
+        return record
+
+    @staticmethod
+    def _view(record: dict[str, Any]) -> dict[str, Any]:
+        delivered = bool(record["deliveries"])
+        return {**record, "ever_delivered": delivered,
+                "active_content_ref": record["deliveries"][-1]["content_ref"] if delivered and record["enabled"] else None,
+                "native_activation": False, "host_loading": "unverified",
+                "context_retracted": False,
+                "clean_exclusion_requires_new_session": delivered and not record["enabled"]}
+
+    def status(self, session: str | None = None) -> dict[str, Any]:
+        return self._view(self._read(self._session(session)))
+
+    def off(self, session: str | None = None) -> dict[str, Any]:
+        session = self._session(session)
+        reject_symlink_ancestors(self.state_root)
+        with transaction_lock(self.state_root):
+            record = self._read(session)
+            record["enabled"] = False
+            _write_json(self._path(session), record)
+            result = self._view(record)
+            result["message"] = (
+                "Corpus delivery is off. Previously returned text remains in conversation context; "
+                "start a new session for clean exclusion."
+                if record["deliveries"] else "Corpus delivery is off; this bridge has returned no corpus text to this session."
+            )
+            return result
+
+    def _snapshot(self, *, selection: list[str] | None, selection_mode: str | None,
+                  cwd: Path | None, dry_run: bool) -> dict[str, Any]:
+        reject_symlink_ancestors(self.state_root)
+        guard_pending(self.state_root)
+        release = confirmed_release(self.state_root)
+        store = CorpusStore(release, self.state_root, self.user_root)
+        if selection is not None and selection_mode is None:
+            selection_mode = "selected"
+        return store.snapshot(host="codex", selection=selection, selection_mode=selection_mode,
+                              cwd=Path(cwd or Path.cwd()).absolute(), dry_run=dry_run, native=False)
+
+    def _runtime_commands(self) -> dict[str, Any]:
+        release = confirmed_release(self.state_root)
+        bridge = AppBridge(self.repo, self.env)
+        result = {"package_root": str(release),
+                  "learn_argv": ["/bin/bash", str(release / "install.sh"), "learn"],
+                  "environment": {"AGENT_BIOS_PACKAGE_ROOT": str(release),
+                                  "AGENT_BIOS_STATE_DIR": str(self.state_root),
+                                  "AGENT_BIOS_CORPUS_DIR": str(self.user_root),
+                                  "AGENT_BIOS_PRIVATE_CORPUS": "1", "AGENT_BIOS_LEGACY_INSTALL": "0"}}
+        registered = bridge.managed_status().get("registered")
+        if "AGENT_LAUNCH_VENV" in self.env or registered:
+            config = bridge._config()
+            if "launch_venv" in config:
+                result["environment"]["AGENT_LAUNCH_VENV"] = config["launch_venv"]
+        if registered:
+            result["bridge_learn_argv"] = [sys.executable, str(bridge.target / "scripts/bridge.py"), "learn"]
+        return result
+
+    def preview(self, session: str | None = None, *, selection: list[str] | None = None,
+                selection_mode: str | None = None, cwd: Path | None = None) -> dict[str, Any]:
+        session = self._session(session)
+        if selection_mode == "none":
+            return {"session_id": session, "selection_mode": "none", "content_ref": None,
+                    "instruction_characters": 0, "delivery": "preview-only", "native_activation": False}
+        snapshot = self._snapshot(selection=selection, selection_mode=selection_mode, cwd=cwd, dry_run=True)
+        return {"session_id": session, "content_ref": snapshot["content_ref"], "revision": snapshot["revision"],
+                "instruction_characters": len(snapshot["instruction_text"]),
+                "unavailable": snapshot.get("unavailable", []), "selection": selection,
+                "selection_mode": snapshot.get("selection_mode", selection_mode),
+                "delivery": "preview-only", "native_activation": False}
+
+    def use(self, session: str | None = None, *, selection: list[str] | None = None,
+            selection_mode: str | None = None, cwd: Path | None = None,
+            expected_content_ref: str | None = None) -> dict[str, Any]:
+        session = self._session(session)
+        if selection_mode == "none":
+            return self.off(session)
+        reject_symlink_ancestors(self.state_root)
+        with transaction_lock(self.state_root):
+            record = self._read(session)
+            snapshot = self._snapshot(selection=selection, selection_mode=selection_mode, cwd=cwd, dry_run=False)
+            if expected_content_ref is not None and snapshot["content_ref"] != expected_content_ref:
+                raise AppError("corpus preview changed; preview again before using this session selection")
+            if not snapshot["instruction_text"].strip():
+                return self.off(session)
+            delivery = {"at": datetime.now(timezone.utc).isoformat(), "content_ref": snapshot["content_ref"],
+                        "snapshot_path": snapshot["path"], "revision": snapshot["revision"],
+                        "cwd": str(Path(cwd or Path.cwd()).absolute()), "delivery": "returned-as-context",
+                        "instruction_sha256": hashlib.sha256(snapshot["instruction_text"].encode("utf-8")).hexdigest()}
+            record["deliveries"].append(delivery)
+            record["enabled"] = True
+            runtime = self._runtime_commands()
+            _write_json(self._path(session), record)
+            return {**self._view(record), "delivery": "returned-as-context",
+                    "content_ref": snapshot["content_ref"], "instruction_text": snapshot["instruction_text"],
+                    "runtime": runtime,
+                    "unavailable": snapshot.get("unavailable", []),
+                    "message": "Returned the selected immutable corpus as task context. This receipt is not proof of model reading or native startup activation."}
+
+
+def build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(prog="agent-bios app", description=__doc__)
+    parser.add_argument("--repo", type=Path, default=Path(__file__).resolve().parents[1])
+    parser.add_argument("--state-dir", type=Path)
+    parser.add_argument("--user-dir", type=Path)
+    parser.add_argument("--json", action="store_true")
+    commands = parser.add_subparsers(dest="command", required=True)
+    for name in ("register", "unregister", "status"):
+        command = commands.add_parser(name)
+        if name != "status":
+            command.add_argument("--dry-run", action="store_true")
+    session = commands.add_parser("session", help="explicitly preview, use or stop corpus delivery in one app task")
+    operations = session.add_subparsers(dest="operation", required=True)
+    for name in ("preview", "use", "off", "status"):
+        command = operations.add_parser(name)
+        command.add_argument("--session", help="defaults to CODEX_THREAD_ID")
+        if name in {"preview", "use"}:
+            selection = command.add_mutually_exclusive_group()
+            selection.add_argument("--domains", help="comma-separated qualified corpus selection")
+            selection.add_argument("--no-corpus", action="store_true")
+            command.add_argument("--cwd", type=Path)
+            if name == "use":
+                command.add_argument("--expected-content-ref", help="require the exact previously previewed snapshot")
+    return parser
+
+
+def main(argv: list[str] | None = None) -> int:
+    raw = list(sys.argv[1:] if argv is None else argv)
+    as_json = "--json" in raw
+    args = build_parser().parse_args([token for token in raw if token != "--json"])
+    env = dict(os.environ)
+    if args.state_dir is not None:
+        env["AGENT_BIOS_STATE_DIR"] = str(args.state_dir)
+    if args.user_dir is not None:
+        env["AGENT_BIOS_CORPUS_DIR"] = str(args.user_dir)
+    try:
+        if args.command == "session":
+            manager = AppSessions(args.repo, env)
+            options = {}
+            if args.operation in {"preview", "use"}:
+                selected = None
+                if args.domains is not None:
+                    selected = [value.strip() for value in args.domains.split(",") if value.strip()]
+                    if not selected:
+                        raise AppError("--domains requires a nonempty corpus selection; use --no-corpus to keep corpus off")
+                options = {"selection": selected,
+                           "selection_mode": "none" if args.no_corpus else "selected" if selected is not None else None,
+                           "cwd": args.cwd}
+                if args.operation == "use":
+                    options["expected_content_ref"] = args.expected_content_ref
+            result = getattr(manager, args.operation)(session=args.session, **options)
+        else:
+            manager = AppBridge(args.repo, env)
+            options = {} if args.command == "status" else {"dry_run": args.dry_run}
+            result = getattr(manager, args.command)(**options)
+        if not as_json and isinstance(result.get("instruction_text"), str):
+            metadata = {key: value for key, value in result.items() if key != "instruction_text"}
+            print(json.dumps(metadata, ensure_ascii=False, indent=2, sort_keys=True), file=sys.stderr)
+            print(result["instruction_text"], end="")
+        else:
+            print(json.dumps(result, ensure_ascii=False, indent=2, sort_keys=True))
+        return 0
+    except (AppError, CorpusStoreError, TransactionError, OSError) as exc:
+        print(f"agent-bios app: {exc}", file=sys.stderr)
+        return 2
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())