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bioagent-bench/.venv/lib/python3.14/site-packages/anyio/__init__.py

@@ -0,0 +1,111 @@
+from __future__ import annotations
+
+from ._core._contextmanagers import AsyncContextManagerMixin as AsyncContextManagerMixin
+from ._core._contextmanagers import ContextManagerMixin as ContextManagerMixin
+from ._core._eventloop import current_time as current_time
+from ._core._eventloop import get_all_backends as get_all_backends
+from ._core._eventloop import get_available_backends as get_available_backends
+from ._core._eventloop import get_cancelled_exc_class as get_cancelled_exc_class
+from ._core._eventloop import run as run
+from ._core._eventloop import sleep as sleep
+from ._core._eventloop import sleep_forever as sleep_forever
+from ._core._eventloop import sleep_until as sleep_until
+from ._core._exceptions import BrokenResourceError as BrokenResourceError
+from ._core._exceptions import BrokenWorkerInterpreter as BrokenWorkerInterpreter
+from ._core._exceptions import BrokenWorkerProcess as BrokenWorkerProcess
+from ._core._exceptions import BusyResourceError as BusyResourceError
+from ._core._exceptions import ClosedResourceError as ClosedResourceError
+from ._core._exceptions import ConnectionFailed as ConnectionFailed
+from ._core._exceptions import DelimiterNotFound as DelimiterNotFound
+from ._core._exceptions import EndOfStream as EndOfStream
+from ._core._exceptions import IncompleteRead as IncompleteRead
+from ._core._exceptions import NoEventLoopError as NoEventLoopError
+from ._core._exceptions import RunFinishedError as RunFinishedError
+from ._core._exceptions import TypedAttributeLookupError as TypedAttributeLookupError
+from ._core._exceptions import WouldBlock as WouldBlock
+from ._core._fileio import AsyncFile as AsyncFile
+from ._core._fileio import Path as Path
+from ._core._fileio import open_file as open_file
+from ._core._fileio import wrap_file as wrap_file
+from ._core._resources import aclose_forcefully as aclose_forcefully
+from ._core._signals import open_signal_receiver as open_signal_receiver
+from ._core._sockets import TCPConnectable as TCPConnectable
+from ._core._sockets import UNIXConnectable as UNIXConnectable
+from ._core._sockets import as_connectable as as_connectable
+from ._core._sockets import connect_tcp as connect_tcp
+from ._core._sockets import connect_unix as connect_unix
+from ._core._sockets import create_connected_udp_socket as create_connected_udp_socket
+from ._core._sockets import (
+    create_connected_unix_datagram_socket as create_connected_unix_datagram_socket,
+)
+from ._core._sockets import create_tcp_listener as create_tcp_listener
+from ._core._sockets import create_udp_socket as create_udp_socket
+from ._core._sockets import create_unix_datagram_socket as create_unix_datagram_socket
+from ._core._sockets import create_unix_listener as create_unix_listener
+from ._core._sockets import getaddrinfo as getaddrinfo
+from ._core._sockets import getnameinfo as getnameinfo
+from ._core._sockets import notify_closing as notify_closing
+from ._core._sockets import wait_readable as wait_readable
+from ._core._sockets import wait_socket_readable as wait_socket_readable
+from ._core._sockets import wait_socket_writable as wait_socket_writable
+from ._core._sockets import wait_writable as wait_writable
+from ._core._streams import create_memory_object_stream as create_memory_object_stream
+from ._core._subprocesses import open_process as open_process
+from ._core._subprocesses import run_process as run_process
+from ._core._synchronization import CapacityLimiter as CapacityLimiter
+from ._core._synchronization import (
+    CapacityLimiterStatistics as CapacityLimiterStatistics,
+)
+from ._core._synchronization import Condition as Condition
+from ._core._synchronization import ConditionStatistics as ConditionStatistics
+from ._core._synchronization import Event as Event
+from ._core._synchronization import EventStatistics as EventStatistics
+from ._core._synchronization import Lock as Lock
+from ._core._synchronization import LockStatistics as LockStatistics
+from ._core._synchronization import ResourceGuard as ResourceGuard
+from ._core._synchronization import Semaphore as Semaphore
+from ._core._synchronization import SemaphoreStatistics as SemaphoreStatistics
+from ._core._tasks import TASK_STATUS_IGNORED as TASK_STATUS_IGNORED
+from ._core._tasks import CancelScope as CancelScope
+from ._core._tasks import create_task_group as create_task_group
+from ._core._tasks import current_effective_deadline as current_effective_deadline
+from ._core._tasks import fail_after as fail_after
+from ._core._tasks import move_on_after as move_on_after
+from ._core._tempfile import NamedTemporaryFile as NamedTemporaryFile
+from ._core._tempfile import SpooledTemporaryFile as SpooledTemporaryFile
+from ._core._tempfile import TemporaryDirectory as TemporaryDirectory
+from ._core._tempfile import TemporaryFile as TemporaryFile
+from ._core._tempfile import gettempdir as gettempdir
+from ._core._tempfile import gettempdirb as gettempdirb
+from ._core._tempfile import mkdtemp as mkdtemp
+from ._core._tempfile import mkstemp as mkstemp
+from ._core._testing import TaskInfo as TaskInfo
+from ._core._testing import get_current_task as get_current_task
+from ._core._testing import get_running_tasks as get_running_tasks
+from ._core._testing import wait_all_tasks_blocked as wait_all_tasks_blocked
+from ._core._typedattr import TypedAttributeProvider as TypedAttributeProvider
+from ._core._typedattr import TypedAttributeSet as TypedAttributeSet
+from ._core._typedattr import typed_attribute as typed_attribute
+
+# Re-export imports so they look like they live directly in this package
+for __value in list(locals().values()):
+    if getattr(__value, "__module__", "").startswith("anyio."):
+        __value.__module__ = __name__
+
+
+del __value
+
+
+def __getattr__(attr: str) -> type[BrokenWorkerInterpreter]:
+    """Support deprecated aliases."""
+    if attr == "BrokenWorkerIntepreter":
+        import warnings
+
+        warnings.warn(
+            "The 'BrokenWorkerIntepreter' alias is deprecated, use 'BrokenWorkerInterpreter' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return BrokenWorkerInterpreter
+
+    raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_backends/_trio.py

@@ -0,0 +1,1343 @@
+from __future__ import annotations
+
+import array
+import math
+import os
+import socket
+import sys
+import types
+import weakref
+from collections.abc import (
+    AsyncGenerator,
+    AsyncIterator,
+    Awaitable,
+    Callable,
+    Collection,
+    Coroutine,
+    Iterable,
+    Sequence,
+)
+from contextlib import AbstractContextManager
+from dataclasses import dataclass
+from io import IOBase
+from os import PathLike
+from signal import Signals
+from socket import AddressFamily, SocketKind
+from types import TracebackType
+from typing import (
+    IO,
+    TYPE_CHECKING,
+    Any,
+    Generic,
+    NoReturn,
+    ParamSpec,
+    TypeVar,
+    cast,
+    overload,
+)
+
+import trio.from_thread
+import trio.lowlevel
+from outcome import Error, Outcome, Value
+from trio.lowlevel import (
+    current_root_task,
+    current_task,
+    notify_closing,
+    wait_readable,
+    wait_writable,
+)
+from trio.socket import SocketType as TrioSocketType
+from trio.to_thread import run_sync
+
+from .. import (
+    CapacityLimiterStatistics,
+    EventStatistics,
+    LockStatistics,
+    RunFinishedError,
+    TaskInfo,
+    WouldBlock,
+    abc,
+)
+from .._core._eventloop import claim_worker_thread
+from .._core._exceptions import (
+    BrokenResourceError,
+    BusyResourceError,
+    ClosedResourceError,
+    EndOfStream,
+)
+from .._core._sockets import convert_ipv6_sockaddr
+from .._core._streams import create_memory_object_stream
+from .._core._synchronization import (
+    CapacityLimiter as BaseCapacityLimiter,
+)
+from .._core._synchronization import Event as BaseEvent
+from .._core._synchronization import Lock as BaseLock
+from .._core._synchronization import (
+    ResourceGuard,
+    SemaphoreStatistics,
+)
+from .._core._synchronization import Semaphore as BaseSemaphore
+from .._core._tasks import CancelScope as BaseCancelScope
+from ..abc import IPSockAddrType, UDPPacketType, UNIXDatagramPacketType
+from ..abc._eventloop import AsyncBackend, StrOrBytesPath
+from ..streams.memory import MemoryObjectSendStream
+
+if TYPE_CHECKING:
+    from _typeshed import FileDescriptorLike
+
+if sys.version_info >= (3, 11):
+    from typing import TypeVarTuple, Unpack
+else:
+    from exceptiongroup import BaseExceptionGroup
+    from typing_extensions import TypeVarTuple, Unpack
+
+T = TypeVar("T")
+T_Retval = TypeVar("T_Retval")
+T_SockAddr = TypeVar("T_SockAddr", str, IPSockAddrType)
+PosArgsT = TypeVarTuple("PosArgsT")
+P = ParamSpec("P")
+
+
+#
+# Event loop
+#
+
+RunVar = trio.lowlevel.RunVar
+
+
+#
+# Timeouts and cancellation
+#
+
+
+class CancelScope(BaseCancelScope):
+    def __new__(
+        cls, original: trio.CancelScope | None = None, **kwargs: object
+    ) -> CancelScope:
+        return object.__new__(cls)
+
+    def __init__(self, original: trio.CancelScope | None = None, **kwargs: Any) -> None:
+        self.__original = original or trio.CancelScope(**kwargs)
+
+    def __enter__(self) -> CancelScope:
+        self.__original.__enter__()
+        return self
+
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> bool:
+        return self.__original.__exit__(exc_type, exc_val, exc_tb)
+
+    def cancel(self, reason: str | None = None) -> None:
+        self.__original.cancel(reason)
+
+    @property
+    def deadline(self) -> float:
+        return self.__original.deadline
+
+    @deadline.setter
+    def deadline(self, value: float) -> None:
+        self.__original.deadline = value
+
+    @property
+    def cancel_called(self) -> bool:
+        return self.__original.cancel_called
+
+    @property
+    def cancelled_caught(self) -> bool:
+        return self.__original.cancelled_caught
+
+    @property
+    def shield(self) -> bool:
+        return self.__original.shield
+
+    @shield.setter
+    def shield(self, value: bool) -> None:
+        self.__original.shield = value
+
+
+#
+# Task groups
+#
+
+
+class TaskGroup(abc.TaskGroup):
+    def __init__(self) -> None:
+        self._active = False
+        self._nursery_manager = trio.open_nursery(strict_exception_groups=True)
+        self.cancel_scope = None  # type: ignore[assignment]
+
+    async def __aenter__(self) -> TaskGroup:
+        self._active = True
+        self._nursery = await self._nursery_manager.__aenter__()
+        self.cancel_scope = CancelScope(self._nursery.cancel_scope)
+        return self
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> bool:
+        try:
+            # trio.Nursery.__exit__ returns bool; .open_nursery has wrong type
+            return await self._nursery_manager.__aexit__(exc_type, exc_val, exc_tb)  # type: ignore[return-value]
+        except BaseExceptionGroup as exc:
+            if not exc.split(trio.Cancelled)[1]:
+                raise trio.Cancelled._create() from exc
+
+            raise
+        finally:
+            del exc_val, exc_tb
+            self._active = False
+
+    def start_soon(
+        self,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[Any]],
+        *args: Unpack[PosArgsT],
+        name: object = None,
+    ) -> None:
+        if not self._active:
+            raise RuntimeError(
+                "This task group is not active; no new tasks can be started."
+            )
+
+        self._nursery.start_soon(func, *args, name=name)
+
+    async def start(
+        self, func: Callable[..., Awaitable[Any]], *args: object, name: object = None
+    ) -> Any:
+        if not self._active:
+            raise RuntimeError(
+                "This task group is not active; no new tasks can be started."
+            )
+
+        return await self._nursery.start(func, *args, name=name)
+
+
+#
+# Subprocesses
+#
+
+
+@dataclass(eq=False)
+class ReceiveStreamWrapper(abc.ByteReceiveStream):
+    _stream: trio.abc.ReceiveStream
+
+    async def receive(self, max_bytes: int | None = None) -> bytes:
+        try:
+            data = await self._stream.receive_some(max_bytes)
+        except trio.ClosedResourceError as exc:
+            raise ClosedResourceError from exc.__cause__
+        except trio.BrokenResourceError as exc:
+            raise BrokenResourceError from exc.__cause__
+
+        if data:
+            return bytes(data)
+        else:
+            raise EndOfStream
+
+    async def aclose(self) -> None:
+        await self._stream.aclose()
+
+
+@dataclass(eq=False)
+class SendStreamWrapper(abc.ByteSendStream):
+    _stream: trio.abc.SendStream
+
+    async def send(self, item: bytes) -> None:
+        try:
+            await self._stream.send_all(item)
+        except trio.ClosedResourceError as exc:
+            raise ClosedResourceError from exc.__cause__
+        except trio.BrokenResourceError as exc:
+            raise BrokenResourceError from exc.__cause__
+
+    async def aclose(self) -> None:
+        await self._stream.aclose()
+
+
+@dataclass(eq=False)
+class Process(abc.Process):
+    _process: trio.Process
+    _stdin: abc.ByteSendStream | None
+    _stdout: abc.ByteReceiveStream | None
+    _stderr: abc.ByteReceiveStream | None
+
+    async def aclose(self) -> None:
+        with CancelScope(shield=True):
+            if self._stdin:
+                await self._stdin.aclose()
+            if self._stdout:
+                await self._stdout.aclose()
+            if self._stderr:
+                await self._stderr.aclose()
+
+        try:
+            await self.wait()
+        except BaseException:
+            self.kill()
+            with CancelScope(shield=True):
+                await self.wait()
+            raise
+
+    async def wait(self) -> int:
+        return await self._process.wait()
+
+    def terminate(self) -> None:
+        self._process.terminate()
+
+    def kill(self) -> None:
+        self._process.kill()
+
+    def send_signal(self, signal: Signals) -> None:
+        self._process.send_signal(signal)
+
+    @property
+    def pid(self) -> int:
+        return self._process.pid
+
+    @property
+    def returncode(self) -> int | None:
+        return self._process.returncode
+
+    @property
+    def stdin(self) -> abc.ByteSendStream | None:
+        return self._stdin
+
+    @property
+    def stdout(self) -> abc.ByteReceiveStream | None:
+        return self._stdout
+
+    @property
+    def stderr(self) -> abc.ByteReceiveStream | None:
+        return self._stderr
+
+
+class _ProcessPoolShutdownInstrument(trio.abc.Instrument):
+    def after_run(self) -> None:
+        super().after_run()
+
+
+current_default_worker_process_limiter: trio.lowlevel.RunVar = RunVar(
+    "current_default_worker_process_limiter"
+)
+
+
+async def _shutdown_process_pool(workers: set[abc.Process]) -> None:
+    try:
+        await trio.sleep(math.inf)
+    except trio.Cancelled:
+        for process in workers:
+            if process.returncode is None:
+                process.kill()
+
+        with CancelScope(shield=True):
+            for process in workers:
+                await process.aclose()
+
+
+#
+# Sockets and networking
+#
+
+
+class _TrioSocketMixin(Generic[T_SockAddr]):
+    def __init__(self, trio_socket: TrioSocketType) -> None:
+        self._trio_socket = trio_socket
+        self._closed = False
+
+    def _check_closed(self) -> None:
+        if self._closed:
+            raise ClosedResourceError
+        if self._trio_socket.fileno() < 0:
+            raise BrokenResourceError
+
+    @property
+    def _raw_socket(self) -> socket.socket:
+        return self._trio_socket._sock  # type: ignore[attr-defined]
+
+    async def aclose(self) -> None:
+        if self._trio_socket.fileno() >= 0:
+            self._closed = True
+            self._trio_socket.close()
+
+    def _convert_socket_error(self, exc: BaseException) -> NoReturn:
+        if isinstance(exc, trio.ClosedResourceError):
+            raise ClosedResourceError from exc
+        elif self._trio_socket.fileno() < 0 and self._closed:
+            raise ClosedResourceError from None
+        elif isinstance(exc, OSError):
+            raise BrokenResourceError from exc
+        else:
+            raise exc
+
+
+class SocketStream(_TrioSocketMixin, abc.SocketStream):
+    def __init__(self, trio_socket: TrioSocketType) -> None:
+        super().__init__(trio_socket)
+        self._receive_guard = ResourceGuard("reading from")
+        self._send_guard = ResourceGuard("writing to")
+
+    async def receive(self, max_bytes: int = 65536) -> bytes:
+        with self._receive_guard:
+            try:
+                data = await self._trio_socket.recv(max_bytes)
+            except BaseException as exc:
+                self._convert_socket_error(exc)
+
+            if data:
+                return data
+            else:
+                raise EndOfStream
+
+    async def send(self, item: bytes) -> None:
+        with self._send_guard:
+            view = memoryview(item)
+            while view:
+                try:
+                    bytes_sent = await self._trio_socket.send(view)
+                except BaseException as exc:
+                    self._convert_socket_error(exc)
+
+                view = view[bytes_sent:]
+
+    async def send_eof(self) -> None:
+        self._trio_socket.shutdown(socket.SHUT_WR)
+
+
+class UNIXSocketStream(SocketStream, abc.UNIXSocketStream):
+    async def receive_fds(self, msglen: int, maxfds: int) -> tuple[bytes, list[int]]:
+        if not isinstance(msglen, int) or msglen < 0:
+            raise ValueError("msglen must be a non-negative integer")
+        if not isinstance(maxfds, int) or maxfds < 1:
+            raise ValueError("maxfds must be a positive integer")
+
+        fds = array.array("i")
+        await trio.lowlevel.checkpoint()
+        with self._receive_guard:
+            while True:
+                try:
+                    message, ancdata, flags, addr = await self._trio_socket.recvmsg(
+                        msglen, socket.CMSG_LEN(maxfds * fds.itemsize)
+                    )
+                except BaseException as exc:
+                    self._convert_socket_error(exc)
+                else:
+                    if not message and not ancdata:
+                        raise EndOfStream
+
+                    break
+
+        for cmsg_level, cmsg_type, cmsg_data in ancdata:
+            if cmsg_level != socket.SOL_SOCKET or cmsg_type != socket.SCM_RIGHTS:
+                raise RuntimeError(
+                    f"Received unexpected ancillary data; message = {message!r}, "
+                    f"cmsg_level = {cmsg_level}, cmsg_type = {cmsg_type}"
+                )
+
+            fds.frombytes(cmsg_data[: len(cmsg_data) - (len(cmsg_data) % fds.itemsize)])
+
+        return message, list(fds)
+
+    async def send_fds(self, message: bytes, fds: Collection[int | IOBase]) -> None:
+        if not message:
+            raise ValueError("message must not be empty")
+        if not fds:
+            raise ValueError("fds must not be empty")
+
+        filenos: list[int] = []
+        for fd in fds:
+            if isinstance(fd, int):
+                filenos.append(fd)
+            elif isinstance(fd, IOBase):
+                filenos.append(fd.fileno())
+
+        fdarray = array.array("i", filenos)
+        await trio.lowlevel.checkpoint()
+        with self._send_guard:
+            while True:
+                try:
+                    await self._trio_socket.sendmsg(
+                        [message],
+                        [
+                            (
+                                socket.SOL_SOCKET,
+                                socket.SCM_RIGHTS,
+                                fdarray,
+                            )
+                        ],
+                    )
+                    break
+                except BaseException as exc:
+                    self._convert_socket_error(exc)
+
+
+class TCPSocketListener(_TrioSocketMixin, abc.SocketListener):
+    def __init__(self, raw_socket: socket.socket):
+        super().__init__(trio.socket.from_stdlib_socket(raw_socket))
+        self._accept_guard = ResourceGuard("accepting connections from")
+
+    async def accept(self) -> SocketStream:
+        with self._accept_guard:
+            try:
+                trio_socket, _addr = await self._trio_socket.accept()
+            except BaseException as exc:
+                self._convert_socket_error(exc)
+
+        trio_socket.setsockopt(socket.IPPROTO_TCP, socket.TCP_NODELAY, 1)
+        return SocketStream(trio_socket)
+
+
+class UNIXSocketListener(_TrioSocketMixin, abc.SocketListener):
+    def __init__(self, raw_socket: socket.socket):
+        super().__init__(trio.socket.from_stdlib_socket(raw_socket))
+        self._accept_guard = ResourceGuard("accepting connections from")
+
+    async def accept(self) -> UNIXSocketStream:
+        with self._accept_guard:
+            try:
+                trio_socket, _addr = await self._trio_socket.accept()
+            except BaseException as exc:
+                self._convert_socket_error(exc)
+
+        return UNIXSocketStream(trio_socket)
+
+
+class UDPSocket(_TrioSocketMixin[IPSockAddrType], abc.UDPSocket):
+    def __init__(self, trio_socket: TrioSocketType) -> None:
+        super().__init__(trio_socket)
+        self._receive_guard = ResourceGuard("reading from")
+        self._send_guard = ResourceGuard("writing to")
+
+    async def receive(self) -> tuple[bytes, IPSockAddrType]:
+        with self._receive_guard:
+            try:
+                data, addr = await self._trio_socket.recvfrom(65536)
+                return data, convert_ipv6_sockaddr(addr)
+            except BaseException as exc:
+                self._convert_socket_error(exc)
+
+    async def send(self, item: UDPPacketType) -> None:
+        with self._send_guard:
+            try:
+                await self._trio_socket.sendto(*item)
+            except BaseException as exc:
+                self._convert_socket_error(exc)
+
+
+class ConnectedUDPSocket(_TrioSocketMixin[IPSockAddrType], abc.ConnectedUDPSocket):
+    def __init__(self, trio_socket: TrioSocketType) -> None:
+        super().__init__(trio_socket)
+        self._receive_guard = ResourceGuard("reading from")
+        self._send_guard = ResourceGuard("writing to")
+
+    async def receive(self) -> bytes:
+        with self._receive_guard:
+            try:
+                return await self._trio_socket.recv(65536)
+            except BaseException as exc:
+                self._convert_socket_error(exc)
+
+    async def send(self, item: bytes) -> None:
+        with self._send_guard:
+            try:
+                await self._trio_socket.send(item)
+            except BaseException as exc:
+                self._convert_socket_error(exc)
+
+
+class UNIXDatagramSocket(_TrioSocketMixin[str], abc.UNIXDatagramSocket):
+    def __init__(self, trio_socket: TrioSocketType) -> None:
+        super().__init__(trio_socket)
+        self._receive_guard = ResourceGuard("reading from")
+        self._send_guard = ResourceGuard("writing to")
+
+    async def receive(self) -> UNIXDatagramPacketType:
+        with self._receive_guard:
+            try:
+                data, addr = await self._trio_socket.recvfrom(65536)
+                return data, addr
+            except BaseException as exc:
+                self._convert_socket_error(exc)
+
+    async def send(self, item: UNIXDatagramPacketType) -> None:
+        with self._send_guard:
+            try:
+                await self._trio_socket.sendto(*item)
+            except BaseException as exc:
+                self._convert_socket_error(exc)
+
+
+class ConnectedUNIXDatagramSocket(
+    _TrioSocketMixin[str], abc.ConnectedUNIXDatagramSocket
+):
+    def __init__(self, trio_socket: TrioSocketType) -> None:
+        super().__init__(trio_socket)
+        self._receive_guard = ResourceGuard("reading from")
+        self._send_guard = ResourceGuard("writing to")
+
+    async def receive(self) -> bytes:
+        with self._receive_guard:
+            try:
+                return await self._trio_socket.recv(65536)
+            except BaseException as exc:
+                self._convert_socket_error(exc)
+
+    async def send(self, item: bytes) -> None:
+        with self._send_guard:
+            try:
+                await self._trio_socket.send(item)
+            except BaseException as exc:
+                self._convert_socket_error(exc)
+
+
+#
+# Synchronization
+#
+
+
+class Event(BaseEvent):
+    def __new__(cls) -> Event:
+        return object.__new__(cls)
+
+    def __init__(self) -> None:
+        self.__original = trio.Event()
+
+    def is_set(self) -> bool:
+        return self.__original.is_set()
+
+    async def wait(self) -> None:
+        return await self.__original.wait()
+
+    def statistics(self) -> EventStatistics:
+        orig_statistics = self.__original.statistics()
+        return EventStatistics(tasks_waiting=orig_statistics.tasks_waiting)
+
+    def set(self) -> None:
+        self.__original.set()
+
+
+class Lock(BaseLock):
+    def __new__(cls, *, fast_acquire: bool = False) -> Lock:
+        return object.__new__(cls)
+
+    def __init__(self, *, fast_acquire: bool = False) -> None:
+        self._fast_acquire = fast_acquire
+        self.__original = trio.Lock()
+
+    @staticmethod
+    def _convert_runtime_error_msg(exc: RuntimeError) -> None:
+        if exc.args == ("attempt to re-acquire an already held Lock",):
+            exc.args = ("Attempted to acquire an already held Lock",)
+
+    async def acquire(self) -> None:
+        if not self._fast_acquire:
+            try:
+                await self.__original.acquire()
+            except RuntimeError as exc:
+                self._convert_runtime_error_msg(exc)
+                raise
+
+            return
+
+        # This is the "fast path" where we don't let other tasks run
+        await trio.lowlevel.checkpoint_if_cancelled()
+        try:
+            self.__original.acquire_nowait()
+        except trio.WouldBlock:
+            await self.__original._lot.park()
+        except RuntimeError as exc:
+            self._convert_runtime_error_msg(exc)
+            raise
+
+    def acquire_nowait(self) -> None:
+        try:
+            self.__original.acquire_nowait()
+        except trio.WouldBlock:
+            raise WouldBlock from None
+        except RuntimeError as exc:
+            self._convert_runtime_error_msg(exc)
+            raise
+
+    def locked(self) -> bool:
+        return self.__original.locked()
+
+    def release(self) -> None:
+        self.__original.release()
+
+    def statistics(self) -> LockStatistics:
+        orig_statistics = self.__original.statistics()
+        owner = TrioTaskInfo(orig_statistics.owner) if orig_statistics.owner else None
+        return LockStatistics(
+            orig_statistics.locked, owner, orig_statistics.tasks_waiting
+        )
+
+
+class Semaphore(BaseSemaphore):
+    def __new__(
+        cls,
+        initial_value: int,
+        *,
+        max_value: int | None = None,
+        fast_acquire: bool = False,
+    ) -> Semaphore:
+        return object.__new__(cls)
+
+    def __init__(
+        self,
+        initial_value: int,
+        *,
+        max_value: int | None = None,
+        fast_acquire: bool = False,
+    ) -> None:
+        super().__init__(initial_value, max_value=max_value, fast_acquire=fast_acquire)
+        self.__original = trio.Semaphore(initial_value, max_value=max_value)
+
+    async def acquire(self) -> None:
+        if not self._fast_acquire:
+            await self.__original.acquire()
+            return
+
+        # This is the "fast path" where we don't let other tasks run
+        await trio.lowlevel.checkpoint_if_cancelled()
+        try:
+            self.__original.acquire_nowait()
+        except trio.WouldBlock:
+            await self.__original._lot.park()
+
+    def acquire_nowait(self) -> None:
+        try:
+            self.__original.acquire_nowait()
+        except trio.WouldBlock:
+            raise WouldBlock from None
+
+    @property
+    def max_value(self) -> int | None:
+        return self.__original.max_value
+
+    @property
+    def value(self) -> int:
+        return self.__original.value
+
+    def release(self) -> None:
+        self.__original.release()
+
+    def statistics(self) -> SemaphoreStatistics:
+        orig_statistics = self.__original.statistics()
+        return SemaphoreStatistics(orig_statistics.tasks_waiting)
+
+
+class CapacityLimiter(BaseCapacityLimiter):
+    def __new__(
+        cls,
+        total_tokens: float | None = None,
+        *,
+        original: trio.CapacityLimiter | None = None,
+    ) -> CapacityLimiter:
+        return object.__new__(cls)
+
+    def __init__(
+        self,
+        total_tokens: float | None = None,
+        *,
+        original: trio.CapacityLimiter | None = None,
+    ) -> None:
+        if original is not None:
+            self.__original = original
+        else:
+            assert total_tokens is not None
+            self.__original = trio.CapacityLimiter(total_tokens)
+
+    async def __aenter__(self) -> None:
+        return await self.__original.__aenter__()
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        await self.__original.__aexit__(exc_type, exc_val, exc_tb)
+
+    @property
+    def total_tokens(self) -> float:
+        return self.__original.total_tokens
+
+    @total_tokens.setter
+    def total_tokens(self, value: float) -> None:
+        self.__original.total_tokens = value
+
+    @property
+    def borrowed_tokens(self) -> int:
+        return self.__original.borrowed_tokens
+
+    @property
+    def available_tokens(self) -> float:
+        return self.__original.available_tokens
+
+    def acquire_nowait(self) -> None:
+        self.__original.acquire_nowait()
+
+    def acquire_on_behalf_of_nowait(self, borrower: object) -> None:
+        self.__original.acquire_on_behalf_of_nowait(borrower)
+
+    async def acquire(self) -> None:
+        await self.__original.acquire()
+
+    async def acquire_on_behalf_of(self, borrower: object) -> None:
+        await self.__original.acquire_on_behalf_of(borrower)
+
+    def release(self) -> None:
+        return self.__original.release()
+
+    def release_on_behalf_of(self, borrower: object) -> None:
+        return self.__original.release_on_behalf_of(borrower)
+
+    def statistics(self) -> CapacityLimiterStatistics:
+        orig = self.__original.statistics()
+        return CapacityLimiterStatistics(
+            borrowed_tokens=orig.borrowed_tokens,
+            total_tokens=orig.total_tokens,
+            borrowers=tuple(orig.borrowers),
+            tasks_waiting=orig.tasks_waiting,
+        )
+
+
+_capacity_limiter_wrapper: trio.lowlevel.RunVar = RunVar("_capacity_limiter_wrapper")
+
+
+#
+# Signal handling
+#
+
+
+class _SignalReceiver:
+    _iterator: AsyncIterator[int]
+
+    def __init__(self, signals: tuple[Signals, ...]):
+        self._signals = signals
+
+    def __enter__(self) -> _SignalReceiver:
+        self._cm = trio.open_signal_receiver(*self._signals)
+        self._iterator = self._cm.__enter__()
+        return self
+
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> bool | None:
+        return self._cm.__exit__(exc_type, exc_val, exc_tb)
+
+    def __aiter__(self) -> _SignalReceiver:
+        return self
+
+    async def __anext__(self) -> Signals:
+        signum = await self._iterator.__anext__()
+        return Signals(signum)
+
+
+#
+# Testing and debugging
+#
+
+
+class TestRunner(abc.TestRunner):
+    def __init__(self, **options: Any) -> None:
+        from queue import Queue
+
+        self._call_queue: Queue[Callable[[], object]] = Queue()
+        self._send_stream: MemoryObjectSendStream | None = None
+        self._options = options
+
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: types.TracebackType | None,
+    ) -> None:
+        if self._send_stream:
+            self._send_stream.close()
+            while self._send_stream is not None:
+                self._call_queue.get()()
+
+    async def _run_tests_and_fixtures(self) -> None:
+        self._send_stream, receive_stream = create_memory_object_stream(1)
+        with receive_stream:
+            async for coro, outcome_holder in receive_stream:
+                try:
+                    retval = await coro
+                except BaseException as exc:
+                    outcome_holder.append(Error(exc))
+                else:
+                    outcome_holder.append(Value(retval))
+
+    def _main_task_finished(self, outcome: object) -> None:
+        self._send_stream = None
+
+    def _call_in_runner_task(
+        self,
+        func: Callable[P, Awaitable[T_Retval]],
+        /,
+        *args: P.args,
+        **kwargs: P.kwargs,
+    ) -> T_Retval:
+        if self._send_stream is None:
+            trio.lowlevel.start_guest_run(
+                self._run_tests_and_fixtures,
+                run_sync_soon_threadsafe=self._call_queue.put,
+                done_callback=self._main_task_finished,
+                **self._options,
+            )
+            while self._send_stream is None:
+                self._call_queue.get()()
+
+        outcome_holder: list[Outcome] = []
+        self._send_stream.send_nowait((func(*args, **kwargs), outcome_holder))
+        while not outcome_holder:
+            self._call_queue.get()()
+
+        return outcome_holder[0].unwrap()
+
+    def run_asyncgen_fixture(
+        self,
+        fixture_func: Callable[..., AsyncGenerator[T_Retval, Any]],
+        kwargs: dict[str, Any],
+    ) -> Iterable[T_Retval]:
+        asyncgen = fixture_func(**kwargs)
+        fixturevalue: T_Retval = self._call_in_runner_task(asyncgen.asend, None)
+
+        yield fixturevalue
+
+        try:
+            self._call_in_runner_task(asyncgen.asend, None)
+        except StopAsyncIteration:
+            pass
+        else:
+            self._call_in_runner_task(asyncgen.aclose)
+            raise RuntimeError("Async generator fixture did not stop")
+
+    def run_fixture(
+        self,
+        fixture_func: Callable[..., Coroutine[Any, Any, T_Retval]],
+        kwargs: dict[str, Any],
+    ) -> T_Retval:
+        return self._call_in_runner_task(fixture_func, **kwargs)
+
+    def run_test(
+        self, test_func: Callable[..., Coroutine[Any, Any, Any]], kwargs: dict[str, Any]
+    ) -> None:
+        self._call_in_runner_task(test_func, **kwargs)
+
+
+class TrioTaskInfo(TaskInfo):
+    def __init__(self, task: trio.lowlevel.Task):
+        parent_id = None
+        if task.parent_nursery and task.parent_nursery.parent_task:
+            parent_id = id(task.parent_nursery.parent_task)
+
+        super().__init__(id(task), parent_id, task.name, task.coro)
+        self._task = weakref.proxy(task)
+
+    def has_pending_cancellation(self) -> bool:
+        try:
+            return self._task._cancel_status.effectively_cancelled
+        except ReferenceError:
+            # If the task is no longer around, it surely doesn't have a cancellation
+            # pending
+            return False
+
+
+class TrioBackend(AsyncBackend):
+    @classmethod
+    def run(
+        cls,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval]],
+        args: tuple[Unpack[PosArgsT]],
+        kwargs: dict[str, Any],
+        options: dict[str, Any],
+    ) -> T_Retval:
+        return trio.run(func, *args)
+
+    @classmethod
+    def current_token(cls) -> object:
+        return trio.lowlevel.current_trio_token()
+
+    @classmethod
+    def current_time(cls) -> float:
+        return trio.current_time()
+
+    @classmethod
+    def cancelled_exception_class(cls) -> type[BaseException]:
+        return trio.Cancelled
+
+    @classmethod
+    async def checkpoint(cls) -> None:
+        await trio.lowlevel.checkpoint()
+
+    @classmethod
+    async def checkpoint_if_cancelled(cls) -> None:
+        await trio.lowlevel.checkpoint_if_cancelled()
+
+    @classmethod
+    async def cancel_shielded_checkpoint(cls) -> None:
+        await trio.lowlevel.cancel_shielded_checkpoint()
+
+    @classmethod
+    async def sleep(cls, delay: float) -> None:
+        await trio.sleep(delay)
+
+    @classmethod
+    def create_cancel_scope(
+        cls, *, deadline: float = math.inf, shield: bool = False
+    ) -> abc.CancelScope:
+        return CancelScope(deadline=deadline, shield=shield)
+
+    @classmethod
+    def current_effective_deadline(cls) -> float:
+        return trio.current_effective_deadline()
+
+    @classmethod
+    def create_task_group(cls) -> abc.TaskGroup:
+        return TaskGroup()
+
+    @classmethod
+    def create_event(cls) -> abc.Event:
+        return Event()
+
+    @classmethod
+    def create_lock(cls, *, fast_acquire: bool) -> Lock:
+        return Lock(fast_acquire=fast_acquire)
+
+    @classmethod
+    def create_semaphore(
+        cls,
+        initial_value: int,
+        *,
+        max_value: int | None = None,
+        fast_acquire: bool = False,
+    ) -> abc.Semaphore:
+        return Semaphore(initial_value, max_value=max_value, fast_acquire=fast_acquire)
+
+    @classmethod
+    def create_capacity_limiter(cls, total_tokens: float) -> CapacityLimiter:
+        return CapacityLimiter(total_tokens)
+
+    @classmethod
+    async def run_sync_in_worker_thread(
+        cls,
+        func: Callable[[Unpack[PosArgsT]], T_Retval],
+        args: tuple[Unpack[PosArgsT]],
+        abandon_on_cancel: bool = False,
+        limiter: abc.CapacityLimiter | None = None,
+    ) -> T_Retval:
+        def wrapper() -> T_Retval:
+            with claim_worker_thread(TrioBackend, token):
+                return func(*args)
+
+        token = TrioBackend.current_token()
+        return await run_sync(
+            wrapper,
+            abandon_on_cancel=abandon_on_cancel,
+            limiter=cast(trio.CapacityLimiter, limiter),
+        )
+
+    @classmethod
+    def check_cancelled(cls) -> None:
+        trio.from_thread.check_cancelled()
+
+    @classmethod
+    def run_async_from_thread(
+        cls,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval]],
+        args: tuple[Unpack[PosArgsT]],
+        token: object,
+    ) -> T_Retval:
+        trio_token = cast("trio.lowlevel.TrioToken | None", token)
+        try:
+            return trio.from_thread.run(func, *args, trio_token=trio_token)
+        except trio.RunFinishedError:
+            raise RunFinishedError from None
+
+    @classmethod
+    def run_sync_from_thread(
+        cls,
+        func: Callable[[Unpack[PosArgsT]], T_Retval],
+        args: tuple[Unpack[PosArgsT]],
+        token: object,
+    ) -> T_Retval:
+        trio_token = cast("trio.lowlevel.TrioToken | None", token)
+        try:
+            return trio.from_thread.run_sync(func, *args, trio_token=trio_token)
+        except trio.RunFinishedError:
+            raise RunFinishedError from None
+
+    @classmethod
+    async def open_process(
+        cls,
+        command: StrOrBytesPath | Sequence[StrOrBytesPath],
+        *,
+        stdin: int | IO[Any] | None,
+        stdout: int | IO[Any] | None,
+        stderr: int | IO[Any] | None,
+        **kwargs: Any,
+    ) -> Process:
+        def convert_item(item: StrOrBytesPath) -> str:
+            str_or_bytes = os.fspath(item)
+            if isinstance(str_or_bytes, str):
+                return str_or_bytes
+            else:
+                return os.fsdecode(str_or_bytes)
+
+        if isinstance(command, (str, bytes, PathLike)):
+            process = await trio.lowlevel.open_process(
+                convert_item(command),
+                stdin=stdin,
+                stdout=stdout,
+                stderr=stderr,
+                shell=True,
+                **kwargs,
+            )
+        else:
+            process = await trio.lowlevel.open_process(
+                [convert_item(item) for item in command],
+                stdin=stdin,
+                stdout=stdout,
+                stderr=stderr,
+                shell=False,
+                **kwargs,
+            )
+
+        stdin_stream = SendStreamWrapper(process.stdin) if process.stdin else None
+        stdout_stream = ReceiveStreamWrapper(process.stdout) if process.stdout else None
+        stderr_stream = ReceiveStreamWrapper(process.stderr) if process.stderr else None
+        return Process(process, stdin_stream, stdout_stream, stderr_stream)
+
+    @classmethod
+    def setup_process_pool_exit_at_shutdown(cls, workers: set[abc.Process]) -> None:
+        trio.lowlevel.spawn_system_task(_shutdown_process_pool, workers)
+
+    @classmethod
+    async def connect_tcp(
+        cls, host: str, port: int, local_address: IPSockAddrType | None = None
+    ) -> SocketStream:
+        family = socket.AF_INET6 if ":" in host else socket.AF_INET
+        trio_socket = trio.socket.socket(family)
+        trio_socket.setsockopt(socket.IPPROTO_TCP, socket.TCP_NODELAY, 1)
+        if local_address:
+            await trio_socket.bind(local_address)
+
+        try:
+            await trio_socket.connect((host, port))
+        except BaseException:
+            trio_socket.close()
+            raise
+
+        return SocketStream(trio_socket)
+
+    @classmethod
+    async def connect_unix(cls, path: str | bytes) -> abc.UNIXSocketStream:
+        trio_socket = trio.socket.socket(socket.AF_UNIX)
+        try:
+            await trio_socket.connect(path)
+        except BaseException:
+            trio_socket.close()
+            raise
+
+        return UNIXSocketStream(trio_socket)
+
+    @classmethod
+    def create_tcp_listener(cls, sock: socket.socket) -> abc.SocketListener:
+        return TCPSocketListener(sock)
+
+    @classmethod
+    def create_unix_listener(cls, sock: socket.socket) -> abc.SocketListener:
+        return UNIXSocketListener(sock)
+
+    @classmethod
+    async def create_udp_socket(
+        cls,
+        family: socket.AddressFamily,
+        local_address: IPSockAddrType | None,
+        remote_address: IPSockAddrType | None,
+        reuse_port: bool,
+    ) -> UDPSocket | ConnectedUDPSocket:
+        trio_socket = trio.socket.socket(family=family, type=socket.SOCK_DGRAM)
+
+        if reuse_port:
+            trio_socket.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEPORT, 1)
+
+        if local_address:
+            await trio_socket.bind(local_address)
+
+        if remote_address:
+            await trio_socket.connect(remote_address)
+            return ConnectedUDPSocket(trio_socket)
+        else:
+            return UDPSocket(trio_socket)
+
+    @classmethod
+    @overload
+    async def create_unix_datagram_socket(
+        cls, raw_socket: socket.socket, remote_path: None
+    ) -> abc.UNIXDatagramSocket: ...
+
+    @classmethod
+    @overload
+    async def create_unix_datagram_socket(
+        cls, raw_socket: socket.socket, remote_path: str | bytes
+    ) -> abc.ConnectedUNIXDatagramSocket: ...
+
+    @classmethod
+    async def create_unix_datagram_socket(
+        cls, raw_socket: socket.socket, remote_path: str | bytes | None
+    ) -> abc.UNIXDatagramSocket | abc.ConnectedUNIXDatagramSocket:
+        trio_socket = trio.socket.from_stdlib_socket(raw_socket)
+
+        if remote_path:
+            await trio_socket.connect(remote_path)
+            return ConnectedUNIXDatagramSocket(trio_socket)
+        else:
+            return UNIXDatagramSocket(trio_socket)
+
+    @classmethod
+    async def getaddrinfo(
+        cls,
+        host: bytes | str | None,
+        port: str | int | None,
+        *,
+        family: int | AddressFamily = 0,
+        type: int | SocketKind = 0,
+        proto: int = 0,
+        flags: int = 0,
+    ) -> Sequence[
+        tuple[
+            AddressFamily,
+            SocketKind,
+            int,
+            str,
+            tuple[str, int] | tuple[str, int, int, int] | tuple[int, bytes],
+        ]
+    ]:
+        return await trio.socket.getaddrinfo(host, port, family, type, proto, flags)
+
+    @classmethod
+    async def getnameinfo(
+        cls, sockaddr: IPSockAddrType, flags: int = 0
+    ) -> tuple[str, str]:
+        return await trio.socket.getnameinfo(sockaddr, flags)
+
+    @classmethod
+    async def wait_readable(cls, obj: FileDescriptorLike) -> None:
+        try:
+            await wait_readable(obj)
+        except trio.ClosedResourceError as exc:
+            raise ClosedResourceError().with_traceback(exc.__traceback__) from None
+        except trio.BusyResourceError:
+            raise BusyResourceError("reading from") from None
+
+    @classmethod
+    async def wait_writable(cls, obj: FileDescriptorLike) -> None:
+        try:
+            await wait_writable(obj)
+        except trio.ClosedResourceError as exc:
+            raise ClosedResourceError().with_traceback(exc.__traceback__) from None
+        except trio.BusyResourceError:
+            raise BusyResourceError("writing to") from None
+
+    @classmethod
+    def notify_closing(cls, obj: FileDescriptorLike) -> None:
+        notify_closing(obj)
+
+    @classmethod
+    async def wrap_listener_socket(cls, sock: socket.socket) -> abc.SocketListener:
+        return TCPSocketListener(sock)
+
+    @classmethod
+    async def wrap_stream_socket(cls, sock: socket.socket) -> SocketStream:
+        trio_sock = trio.socket.from_stdlib_socket(sock)
+        return SocketStream(trio_sock)
+
+    @classmethod
+    async def wrap_unix_stream_socket(cls, sock: socket.socket) -> UNIXSocketStream:
+        trio_sock = trio.socket.from_stdlib_socket(sock)
+        return UNIXSocketStream(trio_sock)
+
+    @classmethod
+    async def wrap_udp_socket(cls, sock: socket.socket) -> UDPSocket:
+        trio_sock = trio.socket.from_stdlib_socket(sock)
+        return UDPSocket(trio_sock)
+
+    @classmethod
+    async def wrap_connected_udp_socket(cls, sock: socket.socket) -> ConnectedUDPSocket:
+        trio_sock = trio.socket.from_stdlib_socket(sock)
+        return ConnectedUDPSocket(trio_sock)
+
+    @classmethod
+    async def wrap_unix_datagram_socket(cls, sock: socket.socket) -> UNIXDatagramSocket:
+        trio_sock = trio.socket.from_stdlib_socket(sock)
+        return UNIXDatagramSocket(trio_sock)
+
+    @classmethod
+    async def wrap_connected_unix_datagram_socket(
+        cls, sock: socket.socket
+    ) -> ConnectedUNIXDatagramSocket:
+        trio_sock = trio.socket.from_stdlib_socket(sock)
+        return ConnectedUNIXDatagramSocket(trio_sock)
+
+    @classmethod
+    def current_default_thread_limiter(cls) -> CapacityLimiter:
+        try:
+            return _capacity_limiter_wrapper.get()
+        except LookupError:
+            limiter = CapacityLimiter(
+                original=trio.to_thread.current_default_thread_limiter()
+            )
+            _capacity_limiter_wrapper.set(limiter)
+            return limiter
+
+    @classmethod
+    def open_signal_receiver(
+        cls, *signals: Signals
+    ) -> AbstractContextManager[AsyncIterator[Signals]]:
+        return _SignalReceiver(signals)
+
+    @classmethod
+    def get_current_task(cls) -> TaskInfo:
+        task = current_task()
+        return TrioTaskInfo(task)
+
+    @classmethod
+    def get_running_tasks(cls) -> Sequence[TaskInfo]:
+        root_task = current_root_task()
+        assert root_task
+        task_infos = [TrioTaskInfo(root_task)]
+        nurseries = root_task.child_nurseries
+        while nurseries:
+            new_nurseries: list[trio.Nursery] = []
+            for nursery in nurseries:
+                for task in nursery.child_tasks:
+                    task_infos.append(TrioTaskInfo(task))
+                    new_nurseries.extend(task.child_nurseries)
+
+            nurseries = new_nurseries
+
+        return task_infos
+
+    @classmethod
+    async def wait_all_tasks_blocked(cls) -> None:
+        from trio.testing import wait_all_tasks_blocked
+
+        await wait_all_tasks_blocked()
+
+    @classmethod
+    def create_test_runner(cls, options: dict[str, Any]) -> TestRunner:
+        return TestRunner(**options)
+
+
+backend_class = TrioBackend

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_asyncio_selector_thread.py

@@ -0,0 +1,167 @@
+from __future__ import annotations
+
+import asyncio
+import socket
+import threading
+from collections.abc import Callable
+from selectors import EVENT_READ, EVENT_WRITE, DefaultSelector
+from typing import TYPE_CHECKING, Any
+
+if TYPE_CHECKING:
+    from _typeshed import FileDescriptorLike
+
+_selector_lock = threading.Lock()
+_selector: Selector | None = None
+
+
+class Selector:
+    def __init__(self) -> None:
+        self._thread = threading.Thread(target=self.run, name="AnyIO socket selector")
+        self._selector = DefaultSelector()
+        self._send, self._receive = socket.socketpair()
+        self._send.setblocking(False)
+        self._receive.setblocking(False)
+        # This somewhat reduces the amount of memory wasted queueing up data
+        # for wakeups. With these settings, maximum number of 1-byte sends
+        # before getting BlockingIOError:
+        #   Linux 4.8: 6
+        #   macOS (darwin 15.5): 1
+        #   Windows 10: 525347
+        # Windows you're weird. (And on Windows setting SNDBUF to 0 makes send
+        # blocking, even on non-blocking sockets, so don't do that.)
+        self._receive.setsockopt(socket.SOL_SOCKET, socket.SO_RCVBUF, 1)
+        self._send.setsockopt(socket.SOL_SOCKET, socket.SO_SNDBUF, 1)
+        # On Windows this is a TCP socket so this might matter. On other
+        # platforms this fails b/c AF_UNIX sockets aren't actually TCP.
+        try:
+            self._send.setsockopt(socket.IPPROTO_TCP, socket.TCP_NODELAY, 1)
+        except OSError:
+            pass
+
+        self._selector.register(self._receive, EVENT_READ)
+        self._closed = False
+
+    def start(self) -> None:
+        self._thread.start()
+        threading._register_atexit(self._stop)  # type: ignore[attr-defined]
+
+    def _stop(self) -> None:
+        global _selector
+        self._closed = True
+        self._notify_self()
+        self._send.close()
+        self._thread.join()
+        self._selector.unregister(self._receive)
+        self._receive.close()
+        self._selector.close()
+        _selector = None
+        assert not self._selector.get_map(), (
+            "selector still has registered file descriptors after shutdown"
+        )
+
+    def _notify_self(self) -> None:
+        try:
+            self._send.send(b"\x00")
+        except BlockingIOError:
+            pass
+
+    def add_reader(self, fd: FileDescriptorLike, callback: Callable[[], Any]) -> None:
+        loop = asyncio.get_running_loop()
+        try:
+            key = self._selector.get_key(fd)
+        except KeyError:
+            self._selector.register(fd, EVENT_READ, {EVENT_READ: (loop, callback)})
+        else:
+            if EVENT_READ in key.data:
+                raise ValueError(
+                    "this file descriptor is already registered for reading"
+                )
+
+            key.data[EVENT_READ] = loop, callback
+            self._selector.modify(fd, key.events | EVENT_READ, key.data)
+
+        self._notify_self()
+
+    def add_writer(self, fd: FileDescriptorLike, callback: Callable[[], Any]) -> None:
+        loop = asyncio.get_running_loop()
+        try:
+            key = self._selector.get_key(fd)
+        except KeyError:
+            self._selector.register(fd, EVENT_WRITE, {EVENT_WRITE: (loop, callback)})
+        else:
+            if EVENT_WRITE in key.data:
+                raise ValueError(
+                    "this file descriptor is already registered for writing"
+                )
+
+            key.data[EVENT_WRITE] = loop, callback
+            self._selector.modify(fd, key.events | EVENT_WRITE, key.data)
+
+        self._notify_self()
+
+    def remove_reader(self, fd: FileDescriptorLike) -> bool:
+        try:
+            key = self._selector.get_key(fd)
+        except KeyError:
+            return False
+
+        if new_events := key.events ^ EVENT_READ:
+            del key.data[EVENT_READ]
+            self._selector.modify(fd, new_events, key.data)
+        else:
+            self._selector.unregister(fd)
+
+        return True
+
+    def remove_writer(self, fd: FileDescriptorLike) -> bool:
+        try:
+            key = self._selector.get_key(fd)
+        except KeyError:
+            return False
+
+        if new_events := key.events ^ EVENT_WRITE:
+            del key.data[EVENT_WRITE]
+            self._selector.modify(fd, new_events, key.data)
+        else:
+            self._selector.unregister(fd)
+
+        return True
+
+    def run(self) -> None:
+        while not self._closed:
+            for key, events in self._selector.select():
+                if key.fileobj is self._receive:
+                    try:
+                        while self._receive.recv(4096):
+                            pass
+                    except BlockingIOError:
+                        pass
+
+                    continue
+
+                if events & EVENT_READ:
+                    loop, callback = key.data[EVENT_READ]
+                    self.remove_reader(key.fd)
+                    try:
+                        loop.call_soon_threadsafe(callback)
+                    except RuntimeError:
+                        pass  # the loop was already closed
+
+                if events & EVENT_WRITE:
+                    loop, callback = key.data[EVENT_WRITE]
+                    self.remove_writer(key.fd)
+                    try:
+                        loop.call_soon_threadsafe(callback)
+                    except RuntimeError:
+                        pass  # the loop was already closed
+
+
+def get_selector() -> Selector:
+    global _selector
+
+    with _selector_lock:
+        if _selector is None:
+            _selector = Selector()
+            _selector.start()
+
+        return _selector

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_contextmanagers.py

@@ -0,0 +1,200 @@
+from __future__ import annotations
+
+from abc import abstractmethod
+from contextlib import AbstractAsyncContextManager, AbstractContextManager
+from inspect import isasyncgen, iscoroutine, isgenerator
+from types import TracebackType
+from typing import Protocol, TypeVar, cast, final
+
+_T_co = TypeVar("_T_co", covariant=True)
+_ExitT_co = TypeVar("_ExitT_co", covariant=True, bound="bool | None")
+
+
+class _SupportsCtxMgr(Protocol[_T_co, _ExitT_co]):
+    def __contextmanager__(self) -> AbstractContextManager[_T_co, _ExitT_co]: ...
+
+
+class _SupportsAsyncCtxMgr(Protocol[_T_co, _ExitT_co]):
+    def __asynccontextmanager__(
+        self,
+    ) -> AbstractAsyncContextManager[_T_co, _ExitT_co]: ...
+
+
+class ContextManagerMixin:
+    """
+    Mixin class providing context manager functionality via a generator-based
+    implementation.
+
+    This class allows you to implement a context manager via :meth:`__contextmanager__`
+    which should return a generator. The mechanics are meant to mirror those of
+    :func:`@contextmanager <contextlib.contextmanager>`.
+
+    .. note:: Classes using this mix-in are not reentrant as context managers, meaning
+        that once you enter it, you can't re-enter before first exiting it.
+
+    .. seealso:: :doc:`contextmanagers`
+    """
+
+    __cm: AbstractContextManager[object, bool | None] | None = None
+
+    @final
+    def __enter__(self: _SupportsCtxMgr[_T_co, bool | None]) -> _T_co:
+        # Needed for mypy to assume self still has the __cm member
+        assert isinstance(self, ContextManagerMixin)
+        if self.__cm is not None:
+            raise RuntimeError(
+                f"this {self.__class__.__qualname__} has already been entered"
+            )
+
+        cm = self.__contextmanager__()
+        if not isinstance(cm, AbstractContextManager):
+            if isgenerator(cm):
+                raise TypeError(
+                    "__contextmanager__() returned a generator object instead of "
+                    "a context manager. Did you forget to add the @contextmanager "
+                    "decorator?"
+                )
+
+            raise TypeError(
+                f"__contextmanager__() did not return a context manager object, "
+                f"but {cm.__class__!r}"
+            )
+
+        if cm is self:
+            raise TypeError(
+                f"{self.__class__.__qualname__}.__contextmanager__() returned "
+                f"self. Did you forget to add the @contextmanager decorator and a "
+                f"'yield' statement?"
+            )
+
+        value = cm.__enter__()
+        self.__cm = cm
+        return value
+
+    @final
+    def __exit__(
+        self: _SupportsCtxMgr[object, _ExitT_co],
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> _ExitT_co:
+        # Needed for mypy to assume self still has the __cm member
+        assert isinstance(self, ContextManagerMixin)
+        if self.__cm is None:
+            raise RuntimeError(
+                f"this {self.__class__.__qualname__} has not been entered yet"
+            )
+
+        # Prevent circular references
+        cm = self.__cm
+        del self.__cm
+
+        return cast(_ExitT_co, cm.__exit__(exc_type, exc_val, exc_tb))
+
+    @abstractmethod
+    def __contextmanager__(self) -> AbstractContextManager[object, bool | None]:
+        """
+        Implement your context manager logic here.
+
+        This method **must** be decorated with
+        :func:`@contextmanager <contextlib.contextmanager>`.
+
+        .. note:: Remember that the ``yield`` will raise any exception raised in the
+            enclosed context block, so use a ``finally:`` block to clean up resources!
+
+        :return: a context manager object
+        """
+
+
+class AsyncContextManagerMixin:
+    """
+    Mixin class providing async context manager functionality via a generator-based
+    implementation.
+
+    This class allows you to implement a context manager via
+    :meth:`__asynccontextmanager__`. The mechanics are meant to mirror those of
+    :func:`@asynccontextmanager <contextlib.asynccontextmanager>`.
+
+    .. note:: Classes using this mix-in are not reentrant as context managers, meaning
+        that once you enter it, you can't re-enter before first exiting it.
+
+    .. seealso:: :doc:`contextmanagers`
+    """
+
+    __cm: AbstractAsyncContextManager[object, bool | None] | None = None
+
+    @final
+    async def __aenter__(self: _SupportsAsyncCtxMgr[_T_co, bool | None]) -> _T_co:
+        # Needed for mypy to assume self still has the __cm member
+        assert isinstance(self, AsyncContextManagerMixin)
+        if self.__cm is not None:
+            raise RuntimeError(
+                f"this {self.__class__.__qualname__} has already been entered"
+            )
+
+        cm = self.__asynccontextmanager__()
+        if not isinstance(cm, AbstractAsyncContextManager):
+            if isasyncgen(cm):
+                raise TypeError(
+                    "__asynccontextmanager__() returned an async generator instead of "
+                    "an async context manager. Did you forget to add the "
+                    "@asynccontextmanager decorator?"
+                )
+            elif iscoroutine(cm):
+                cm.close()
+                raise TypeError(
+                    "__asynccontextmanager__() returned a coroutine object instead of "
+                    "an async context manager. Did you forget to add the "
+                    "@asynccontextmanager decorator and a 'yield' statement?"
+                )
+
+            raise TypeError(
+                f"__asynccontextmanager__() did not return an async context manager, "
+                f"but {cm.__class__!r}"
+            )
+
+        if cm is self:
+            raise TypeError(
+                f"{self.__class__.__qualname__}.__asynccontextmanager__() returned "
+                f"self. Did you forget to add the @asynccontextmanager decorator and a "
+                f"'yield' statement?"
+            )
+
+        value = await cm.__aenter__()
+        self.__cm = cm
+        return value
+
+    @final
+    async def __aexit__(
+        self: _SupportsAsyncCtxMgr[object, _ExitT_co],
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> _ExitT_co:
+        assert isinstance(self, AsyncContextManagerMixin)
+        if self.__cm is None:
+            raise RuntimeError(
+                f"this {self.__class__.__qualname__} has not been entered yet"
+            )
+
+        # Prevent circular references
+        cm = self.__cm
+        del self.__cm
+
+        return cast(_ExitT_co, await cm.__aexit__(exc_type, exc_val, exc_tb))
+
+    @abstractmethod
+    def __asynccontextmanager__(
+        self,
+    ) -> AbstractAsyncContextManager[object, bool | None]:
+        """
+        Implement your async context manager logic here.
+
+        This method **must** be decorated with
+        :func:`@asynccontextmanager <contextlib.asynccontextmanager>`.
+
+        .. note:: Remember that the ``yield`` will raise any exception raised in the
+            enclosed context block, so use a ``finally:`` block to clean up resources!
+
+        :return: an async context manager object
+        """

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_eventloop.py

@@ -0,0 +1,234 @@
+from __future__ import annotations
+
+import math
+import sys
+import threading
+from collections.abc import Awaitable, Callable, Generator
+from contextlib import contextmanager
+from contextvars import Token
+from importlib import import_module
+from typing import TYPE_CHECKING, Any, TypeVar
+
+from ._exceptions import NoEventLoopError
+
+if sys.version_info >= (3, 11):
+    from typing import TypeVarTuple, Unpack
+else:
+    from typing_extensions import TypeVarTuple, Unpack
+
+sniffio: Any
+try:
+    import sniffio
+except ModuleNotFoundError:
+    sniffio = None
+
+if TYPE_CHECKING:
+    from ..abc import AsyncBackend
+
+# This must be updated when new backends are introduced
+BACKENDS = "asyncio", "trio"
+
+T_Retval = TypeVar("T_Retval")
+PosArgsT = TypeVarTuple("PosArgsT")
+
+threadlocals = threading.local()
+loaded_backends: dict[str, type[AsyncBackend]] = {}
+
+
+def run(
+    func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval]],
+    *args: Unpack[PosArgsT],
+    backend: str = "asyncio",
+    backend_options: dict[str, Any] | None = None,
+) -> T_Retval:
+    """
+    Run the given coroutine function in an asynchronous event loop.
+
+    The current thread must not be already running an event loop.
+
+    :param func: a coroutine function
+    :param args: positional arguments to ``func``
+    :param backend: name of the asynchronous event loop implementation – currently
+        either ``asyncio`` or ``trio``
+    :param backend_options: keyword arguments to call the backend ``run()``
+        implementation with (documented :ref:`here <backend options>`)
+    :return: the return value of the coroutine function
+    :raises RuntimeError: if an asynchronous event loop is already running in this
+        thread
+    :raises LookupError: if the named backend is not found
+
+    """
+    if asynclib_name := current_async_library():
+        raise RuntimeError(f"Already running {asynclib_name} in this thread")
+
+    try:
+        async_backend = get_async_backend(backend)
+    except ImportError as exc:
+        raise LookupError(f"No such backend: {backend}") from exc
+
+    token = None
+    if asynclib_name is None:
+        # Since we're in control of the event loop, we can cache the name of the async
+        # library
+        token = set_current_async_library(backend)
+
+    try:
+        backend_options = backend_options or {}
+        return async_backend.run(func, args, {}, backend_options)
+    finally:
+        reset_current_async_library(token)
+
+
+async def sleep(delay: float) -> None:
+    """
+    Pause the current task for the specified duration.
+
+    :param delay: the duration, in seconds
+
+    """
+    return await get_async_backend().sleep(delay)
+
+
+async def sleep_forever() -> None:
+    """
+    Pause the current task until it's cancelled.
+
+    This is a shortcut for ``sleep(math.inf)``.
+
+    .. versionadded:: 3.1
+
+    """
+    await sleep(math.inf)
+
+
+async def sleep_until(deadline: float) -> None:
+    """
+    Pause the current task until the given time.
+
+    :param deadline: the absolute time to wake up at (according to the internal
+        monotonic clock of the event loop)
+
+    .. versionadded:: 3.1
+
+    """
+    now = current_time()
+    await sleep(max(deadline - now, 0))
+
+
+def current_time() -> float:
+    """
+    Return the current value of the event loop's internal clock.
+
+    :return: the clock value (seconds)
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    return get_async_backend().current_time()
+
+
+def get_all_backends() -> tuple[str, ...]:
+    """Return a tuple of the names of all built-in backends."""
+    return BACKENDS
+
+
+def get_available_backends() -> tuple[str, ...]:
+    """
+    Test for the availability of built-in backends.
+
+    :return a tuple of the built-in backend names that were successfully imported
+
+    .. versionadded:: 4.12
+
+    """
+    available_backends: list[str] = []
+    for backend_name in get_all_backends():
+        try:
+            get_async_backend(backend_name)
+        except ImportError:
+            continue
+
+        available_backends.append(backend_name)
+
+    return tuple(available_backends)
+
+
+def get_cancelled_exc_class() -> type[BaseException]:
+    """
+    Return the current async library's cancellation exception class.
+
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    return get_async_backend().cancelled_exception_class()
+
+
+#
+# Private API
+#
+
+
+@contextmanager
+def claim_worker_thread(
+    backend_class: type[AsyncBackend], token: object
+) -> Generator[Any, None, None]:
+    from ..lowlevel import EventLoopToken
+
+    threadlocals.current_token = EventLoopToken(backend_class, token)
+    try:
+        yield
+    finally:
+        del threadlocals.current_token
+
+
+def get_async_backend(asynclib_name: str | None = None) -> type[AsyncBackend]:
+    if asynclib_name is None:
+        asynclib_name = current_async_library()
+        if not asynclib_name:
+            raise NoEventLoopError(
+                f"Not currently running on any asynchronous event loop. "
+                f"Available async backends: {', '.join(get_all_backends())}"
+            )
+
+    # We use our own dict instead of sys.modules to get the already imported back-end
+    # class because the appropriate modules in sys.modules could potentially be only
+    # partially initialized
+    try:
+        return loaded_backends[asynclib_name]
+    except KeyError:
+        module = import_module(f"anyio._backends._{asynclib_name}")
+        loaded_backends[asynclib_name] = module.backend_class
+        return module.backend_class
+
+
+def current_async_library() -> str | None:
+    if sniffio is None:
+        # If sniffio is not installed, we assume we're either running asyncio or nothing
+        import asyncio
+
+        try:
+            asyncio.get_running_loop()
+            return "asyncio"
+        except RuntimeError:
+            pass
+    else:
+        try:
+            return sniffio.current_async_library()
+        except sniffio.AsyncLibraryNotFoundError:
+            pass
+
+    return None
+
+
+def set_current_async_library(asynclib_name: str | None) -> Token | None:
+    # no-op if sniffio is not installed
+    if sniffio is None:
+        return None
+
+    return sniffio.current_async_library_cvar.set(asynclib_name)
+
+
+def reset_current_async_library(token: Token | None) -> None:
+    if token is not None:
+        sniffio.current_async_library_cvar.reset(token)

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_exceptions.py

@@ -0,0 +1,156 @@
+from __future__ import annotations
+
+import sys
+from collections.abc import Generator
+from textwrap import dedent
+from typing import Any
+
+if sys.version_info < (3, 11):
+    from exceptiongroup import BaseExceptionGroup
+
+
+class BrokenResourceError(Exception):
+    """
+    Raised when trying to use a resource that has been rendered unusable due to external
+    causes (e.g. a send stream whose peer has disconnected).
+    """
+
+
+class BrokenWorkerProcess(Exception):
+    """
+    Raised by :meth:`~anyio.to_process.run_sync` if the worker process terminates abruptly or
+    otherwise misbehaves.
+    """
+
+
+class BrokenWorkerInterpreter(Exception):
+    """
+    Raised by :meth:`~anyio.to_interpreter.run_sync` if an unexpected exception is
+    raised in the subinterpreter.
+    """
+
+    def __init__(self, excinfo: Any):
+        # This was adapted from concurrent.futures.interpreter.ExecutionFailed
+        msg = excinfo.formatted
+        if not msg:
+            if excinfo.type and excinfo.msg:
+                msg = f"{excinfo.type.__name__}: {excinfo.msg}"
+            else:
+                msg = excinfo.type.__name__ or excinfo.msg
+
+        super().__init__(msg)
+        self.excinfo = excinfo
+
+    def __str__(self) -> str:
+        try:
+            formatted = self.excinfo.errdisplay
+        except Exception:
+            return super().__str__()
+        else:
+            return dedent(
+                f"""
+                {super().__str__()}
+
+                Uncaught in the interpreter:
+
+                {formatted}
+                """.strip()
+            )
+
+
+class BusyResourceError(Exception):
+    """
+    Raised when two tasks are trying to read from or write to the same resource
+    concurrently.
+    """
+
+    def __init__(self, action: str):
+        super().__init__(f"Another task is already {action} this resource")
+
+
+class ClosedResourceError(Exception):
+    """Raised when trying to use a resource that has been closed."""
+
+
+class ConnectionFailed(OSError):
+    """
+    Raised when a connection attempt fails.
+
+    .. note:: This class inherits from :exc:`OSError` for backwards compatibility.
+    """
+
+
+def iterate_exceptions(
+    exception: BaseException,
+) -> Generator[BaseException, None, None]:
+    if isinstance(exception, BaseExceptionGroup):
+        for exc in exception.exceptions:
+            yield from iterate_exceptions(exc)
+    else:
+        yield exception
+
+
+class DelimiterNotFound(Exception):
+    """
+    Raised during
+    :meth:`~anyio.streams.buffered.BufferedByteReceiveStream.receive_until` if the
+    maximum number of bytes has been read without the delimiter being found.
+    """
+
+    def __init__(self, max_bytes: int) -> None:
+        super().__init__(
+            f"The delimiter was not found among the first {max_bytes} bytes"
+        )
+
+
+class EndOfStream(Exception):
+    """
+    Raised when trying to read from a stream that has been closed from the other end.
+    """
+
+
+class IncompleteRead(Exception):
+    """
+    Raised during
+    :meth:`~anyio.streams.buffered.BufferedByteReceiveStream.receive_exactly` or
+    :meth:`~anyio.streams.buffered.BufferedByteReceiveStream.receive_until` if the
+    connection is closed before the requested amount of bytes has been read.
+    """
+
+    def __init__(self) -> None:
+        super().__init__(
+            "The stream was closed before the read operation could be completed"
+        )
+
+
+class TypedAttributeLookupError(LookupError):
+    """
+    Raised by :meth:`~anyio.TypedAttributeProvider.extra` when the given typed attribute
+    is not found and no default value has been given.
+    """
+
+
+class WouldBlock(Exception):
+    """Raised by ``X_nowait`` functions if ``X()`` would block."""
+
+
+class NoEventLoopError(RuntimeError):
+    """
+    Raised by several functions that require an event loop to be running in the current
+    thread when there is no running event loop.
+
+    This is also raised by :func:`.from_thread.run` and :func:`.from_thread.run_sync`
+    if not calling from an AnyIO worker thread, and no ``token`` was passed.
+    """
+
+
+class RunFinishedError(RuntimeError):
+    """
+    Raised by :func:`.from_thread.run` and :func:`.from_thread.run_sync` if the event
+    loop associated with the explicitly passed token has already finished.
+    """
+
+    def __init__(self) -> None:
+        super().__init__(
+            "The event loop associated with the given token has already finished"
+        )

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_fileio.py

@@ -0,0 +1,799 @@
+from __future__ import annotations
+
+import os
+import pathlib
+import sys
+from collections.abc import (
+    AsyncIterator,
+    Callable,
+    Iterable,
+    Iterator,
+    Sequence,
+)
+from dataclasses import dataclass
+from functools import partial
+from os import PathLike
+from typing import (
+    IO,
+    TYPE_CHECKING,
+    Any,
+    AnyStr,
+    ClassVar,
+    Final,
+    Generic,
+    overload,
+)
+
+from .. import to_thread
+from ..abc import AsyncResource
+
+if TYPE_CHECKING:
+    from types import ModuleType
+
+    from _typeshed import OpenBinaryMode, OpenTextMode, ReadableBuffer, WriteableBuffer
+else:
+    ReadableBuffer = OpenBinaryMode = OpenTextMode = WriteableBuffer = object
+
+
+class AsyncFile(AsyncResource, Generic[AnyStr]):
+    """
+    An asynchronous file object.
+
+    This class wraps a standard file object and provides async friendly versions of the
+    following blocking methods (where available on the original file object):
+
+    * read
+    * read1
+    * readline
+    * readlines
+    * readinto
+    * readinto1
+    * write
+    * writelines
+    * truncate
+    * seek
+    * tell
+    * flush
+
+    All other methods are directly passed through.
+
+    This class supports the asynchronous context manager protocol which closes the
+    underlying file at the end of the context block.
+
+    This class also supports asynchronous iteration::
+
+        async with await open_file(...) as f:
+            async for line in f:
+                print(line)
+    """
+
+    def __init__(self, fp: IO[AnyStr]) -> None:
+        self._fp: Any = fp
+
+    def __getattr__(self, name: str) -> object:
+        return getattr(self._fp, name)
+
+    @property
+    def wrapped(self) -> IO[AnyStr]:
+        """The wrapped file object."""
+        return self._fp
+
+    async def __aiter__(self) -> AsyncIterator[AnyStr]:
+        while True:
+            line = await self.readline()
+            if line:
+                yield line
+            else:
+                break
+
+    async def aclose(self) -> None:
+        return await to_thread.run_sync(self._fp.close)
+
+    async def read(self, size: int = -1) -> AnyStr:
+        return await to_thread.run_sync(self._fp.read, size)
+
+    async def read1(self: AsyncFile[bytes], size: int = -1) -> bytes:
+        return await to_thread.run_sync(self._fp.read1, size)
+
+    async def readline(self) -> AnyStr:
+        return await to_thread.run_sync(self._fp.readline)
+
+    async def readlines(self) -> list[AnyStr]:
+        return await to_thread.run_sync(self._fp.readlines)
+
+    async def readinto(self: AsyncFile[bytes], b: WriteableBuffer) -> int:
+        return await to_thread.run_sync(self._fp.readinto, b)
+
+    async def readinto1(self: AsyncFile[bytes], b: WriteableBuffer) -> int:
+        return await to_thread.run_sync(self._fp.readinto1, b)
+
+    @overload
+    async def write(self: AsyncFile[bytes], b: ReadableBuffer) -> int: ...
+
+    @overload
+    async def write(self: AsyncFile[str], b: str) -> int: ...
+
+    async def write(self, b: ReadableBuffer | str) -> int:
+        return await to_thread.run_sync(self._fp.write, b)
+
+    @overload
+    async def writelines(
+        self: AsyncFile[bytes], lines: Iterable[ReadableBuffer]
+    ) -> None: ...
+
+    @overload
+    async def writelines(self: AsyncFile[str], lines: Iterable[str]) -> None: ...
+
+    async def writelines(self, lines: Iterable[ReadableBuffer] | Iterable[str]) -> None:
+        return await to_thread.run_sync(self._fp.writelines, lines)
+
+    async def truncate(self, size: int | None = None) -> int:
+        return await to_thread.run_sync(self._fp.truncate, size)
+
+    async def seek(self, offset: int, whence: int | None = os.SEEK_SET) -> int:
+        return await to_thread.run_sync(self._fp.seek, offset, whence)
+
+    async def tell(self) -> int:
+        return await to_thread.run_sync(self._fp.tell)
+
+    async def flush(self) -> None:
+        return await to_thread.run_sync(self._fp.flush)
+
+
+@overload
+async def open_file(
+    file: str | PathLike[str] | int,
+    mode: OpenBinaryMode,
+    buffering: int = ...,
+    encoding: str | None = ...,
+    errors: str | None = ...,
+    newline: str | None = ...,
+    closefd: bool = ...,
+    opener: Callable[[str, int], int] | None = ...,
+) -> AsyncFile[bytes]: ...
+
+
+@overload
+async def open_file(
+    file: str | PathLike[str] | int,
+    mode: OpenTextMode = ...,
+    buffering: int = ...,
+    encoding: str | None = ...,
+    errors: str | None = ...,
+    newline: str | None = ...,
+    closefd: bool = ...,
+    opener: Callable[[str, int], int] | None = ...,
+) -> AsyncFile[str]: ...
+
+
+async def open_file(
+    file: str | PathLike[str] | int,
+    mode: str = "r",
+    buffering: int = -1,
+    encoding: str | None = None,
+    errors: str | None = None,
+    newline: str | None = None,
+    closefd: bool = True,
+    opener: Callable[[str, int], int] | None = None,
+) -> AsyncFile[Any]:
+    """
+    Open a file asynchronously.
+
+    The arguments are exactly the same as for the builtin :func:`open`.
+
+    :return: an asynchronous file object
+
+    """
+    fp = await to_thread.run_sync(
+        open, file, mode, buffering, encoding, errors, newline, closefd, opener
+    )
+    return AsyncFile(fp)
+
+
+def wrap_file(file: IO[AnyStr]) -> AsyncFile[AnyStr]:
+    """
+    Wrap an existing file as an asynchronous file.
+
+    :param file: an existing file-like object
+    :return: an asynchronous file object
+
+    """
+    return AsyncFile(file)
+
+
+@dataclass(eq=False)
+class _PathIterator(AsyncIterator["Path"]):
+    iterator: Iterator[PathLike[str]]
+
+    async def __anext__(self) -> Path:
+        nextval = await to_thread.run_sync(
+            next, self.iterator, None, abandon_on_cancel=True
+        )
+        if nextval is None:
+            raise StopAsyncIteration from None
+
+        return Path(nextval)
+
+
+class Path:
+    """
+    An asynchronous version of :class:`pathlib.Path`.
+
+    This class cannot be substituted for :class:`pathlib.Path` or
+    :class:`pathlib.PurePath`, but it is compatible with the :class:`os.PathLike`
+    interface.
+
+    It implements the Python 3.10 version of :class:`pathlib.Path` interface, except for
+    the deprecated :meth:`~pathlib.Path.link_to` method.
+
+    Some methods may be unavailable or have limited functionality, based on the Python
+    version:
+
+    * :meth:`~pathlib.Path.copy` (available on Python 3.14 or later)
+    * :meth:`~pathlib.Path.copy_into` (available on Python 3.14 or later)
+    * :meth:`~pathlib.Path.from_uri` (available on Python 3.13 or later)
+    * :meth:`~pathlib.PurePath.full_match` (available on Python 3.13 or later)
+    * :attr:`~pathlib.Path.info` (available on Python 3.14 or later)
+    * :meth:`~pathlib.Path.is_junction` (available on Python 3.12 or later)
+    * :meth:`~pathlib.PurePath.match` (the ``case_sensitive`` parameter is only
+      available on Python 3.13 or later)
+    * :meth:`~pathlib.Path.move` (available on Python 3.14 or later)
+    * :meth:`~pathlib.Path.move_into` (available on Python 3.14 or later)
+    * :meth:`~pathlib.PurePath.relative_to` (the ``walk_up`` parameter is only available
+      on Python 3.12 or later)
+    * :meth:`~pathlib.Path.walk` (available on Python 3.12 or later)
+
+    Any methods that do disk I/O need to be awaited on. These methods are:
+
+    * :meth:`~pathlib.Path.absolute`
+    * :meth:`~pathlib.Path.chmod`
+    * :meth:`~pathlib.Path.cwd`
+    * :meth:`~pathlib.Path.exists`
+    * :meth:`~pathlib.Path.expanduser`
+    * :meth:`~pathlib.Path.group`
+    * :meth:`~pathlib.Path.hardlink_to`
+    * :meth:`~pathlib.Path.home`
+    * :meth:`~pathlib.Path.is_block_device`
+    * :meth:`~pathlib.Path.is_char_device`
+    * :meth:`~pathlib.Path.is_dir`
+    * :meth:`~pathlib.Path.is_fifo`
+    * :meth:`~pathlib.Path.is_file`
+    * :meth:`~pathlib.Path.is_junction`
+    * :meth:`~pathlib.Path.is_mount`
+    * :meth:`~pathlib.Path.is_socket`
+    * :meth:`~pathlib.Path.is_symlink`
+    * :meth:`~pathlib.Path.lchmod`
+    * :meth:`~pathlib.Path.lstat`
+    * :meth:`~pathlib.Path.mkdir`
+    * :meth:`~pathlib.Path.open`
+    * :meth:`~pathlib.Path.owner`
+    * :meth:`~pathlib.Path.read_bytes`
+    * :meth:`~pathlib.Path.read_text`
+    * :meth:`~pathlib.Path.readlink`
+    * :meth:`~pathlib.Path.rename`
+    * :meth:`~pathlib.Path.replace`
+    * :meth:`~pathlib.Path.resolve`
+    * :meth:`~pathlib.Path.rmdir`
+    * :meth:`~pathlib.Path.samefile`
+    * :meth:`~pathlib.Path.stat`
+    * :meth:`~pathlib.Path.symlink_to`
+    * :meth:`~pathlib.Path.touch`
+    * :meth:`~pathlib.Path.unlink`
+    * :meth:`~pathlib.Path.walk`
+    * :meth:`~pathlib.Path.write_bytes`
+    * :meth:`~pathlib.Path.write_text`
+
+    Additionally, the following methods return an async iterator yielding
+    :class:`~.Path` objects:
+
+    * :meth:`~pathlib.Path.glob`
+    * :meth:`~pathlib.Path.iterdir`
+    * :meth:`~pathlib.Path.rglob`
+    """
+
+    __slots__ = "_path", "__weakref__"
+
+    __weakref__: Any
+
+    def __init__(self, *args: str | PathLike[str]) -> None:
+        self._path: Final[pathlib.Path] = pathlib.Path(*args)
+
+    def __fspath__(self) -> str:
+        return self._path.__fspath__()
+
+    if sys.version_info >= (3, 15):
+
+        def __vfspath__(self) -> str:
+            return self._path.__vfspath__()
+
+    def __str__(self) -> str:
+        return self._path.__str__()
+
+    def __repr__(self) -> str:
+        return f"{self.__class__.__name__}({self.as_posix()!r})"
+
+    def __bytes__(self) -> bytes:
+        return self._path.__bytes__()
+
+    def __hash__(self) -> int:
+        return self._path.__hash__()
+
+    def __eq__(self, other: object) -> bool:
+        target = other._path if isinstance(other, Path) else other
+        return self._path.__eq__(target)
+
+    def __lt__(self, other: pathlib.PurePath | Path) -> bool:
+        target = other._path if isinstance(other, Path) else other
+        return self._path.__lt__(target)
+
+    def __le__(self, other: pathlib.PurePath | Path) -> bool:
+        target = other._path if isinstance(other, Path) else other
+        return self._path.__le__(target)
+
+    def __gt__(self, other: pathlib.PurePath | Path) -> bool:
+        target = other._path if isinstance(other, Path) else other
+        return self._path.__gt__(target)
+
+    def __ge__(self, other: pathlib.PurePath | Path) -> bool:
+        target = other._path if isinstance(other, Path) else other
+        return self._path.__ge__(target)
+
+    def __truediv__(self, other: str | PathLike[str]) -> Path:
+        return Path(self._path / other)
+
+    def __rtruediv__(self, other: str | PathLike[str]) -> Path:
+        return Path(other) / self
+
+    @property
+    def parts(self) -> tuple[str, ...]:
+        return self._path.parts
+
+    @property
+    def drive(self) -> str:
+        return self._path.drive
+
+    @property
+    def root(self) -> str:
+        return self._path.root
+
+    @property
+    def anchor(self) -> str:
+        return self._path.anchor
+
+    @property
+    def parents(self) -> Sequence[Path]:
+        return tuple(Path(p) for p in self._path.parents)
+
+    @property
+    def parent(self) -> Path:
+        return Path(self._path.parent)
+
+    @property
+    def name(self) -> str:
+        return self._path.name
+
+    @property
+    def suffix(self) -> str:
+        return self._path.suffix
+
+    @property
+    def suffixes(self) -> list[str]:
+        return self._path.suffixes
+
+    @property
+    def stem(self) -> str:
+        return self._path.stem
+
+    async def absolute(self) -> Path:
+        path = await to_thread.run_sync(self._path.absolute)
+        return Path(path)
+
+    def as_posix(self) -> str:
+        return self._path.as_posix()
+
+    def as_uri(self) -> str:
+        return self._path.as_uri()
+
+    if sys.version_info >= (3, 13):
+        parser: ClassVar[ModuleType] = pathlib.Path.parser
+
+        @classmethod
+        def from_uri(cls, uri: str) -> Path:
+            return Path(pathlib.Path.from_uri(uri))
+
+        def full_match(
+            self, path_pattern: str, *, case_sensitive: bool | None = None
+        ) -> bool:
+            return self._path.full_match(path_pattern, case_sensitive=case_sensitive)
+
+        def match(
+            self, path_pattern: str, *, case_sensitive: bool | None = None
+        ) -> bool:
+            return self._path.match(path_pattern, case_sensitive=case_sensitive)
+    else:
+
+        def match(self, path_pattern: str) -> bool:
+            return self._path.match(path_pattern)
+
+    if sys.version_info >= (3, 14):
+
+        @property
+        def info(self) -> Any:  # TODO: add return type annotation when Typeshed gets it
+            return self._path.info
+
+        async def copy(
+            self,
+            target: str | os.PathLike[str],
+            *,
+            follow_symlinks: bool = True,
+            preserve_metadata: bool = False,
+        ) -> Path:
+            func = partial(
+                self._path.copy,
+                follow_symlinks=follow_symlinks,
+                preserve_metadata=preserve_metadata,
+            )
+            return Path(await to_thread.run_sync(func, pathlib.Path(target)))
+
+        async def copy_into(
+            self,
+            target_dir: str | os.PathLike[str],
+            *,
+            follow_symlinks: bool = True,
+            preserve_metadata: bool = False,
+        ) -> Path:
+            func = partial(
+                self._path.copy_into,
+                follow_symlinks=follow_symlinks,
+                preserve_metadata=preserve_metadata,
+            )
+            return Path(await to_thread.run_sync(func, pathlib.Path(target_dir)))
+
+        async def move(self, target: str | os.PathLike[str]) -> Path:
+            # Upstream does not handle anyio.Path properly as a PathLike
+            target = pathlib.Path(target)
+            return Path(await to_thread.run_sync(self._path.move, target))
+
+        async def move_into(
+            self,
+            target_dir: str | os.PathLike[str],
+        ) -> Path:
+            return Path(await to_thread.run_sync(self._path.move_into, target_dir))
+
+    def is_relative_to(self, other: str | PathLike[str]) -> bool:
+        try:
+            self.relative_to(other)
+            return True
+        except ValueError:
+            return False
+
+    async def chmod(self, mode: int, *, follow_symlinks: bool = True) -> None:
+        func = partial(os.chmod, follow_symlinks=follow_symlinks)
+        return await to_thread.run_sync(func, self._path, mode)
+
+    @classmethod
+    async def cwd(cls) -> Path:
+        path = await to_thread.run_sync(pathlib.Path.cwd)
+        return cls(path)
+
+    async def exists(self) -> bool:
+        return await to_thread.run_sync(self._path.exists, abandon_on_cancel=True)
+
+    async def expanduser(self) -> Path:
+        return Path(
+            await to_thread.run_sync(self._path.expanduser, abandon_on_cancel=True)
+        )
+
+    if sys.version_info < (3, 12):
+        # Python 3.11 and earlier
+        def glob(self, pattern: str) -> AsyncIterator[Path]:
+            gen = self._path.glob(pattern)
+            return _PathIterator(gen)
+    elif (3, 12) <= sys.version_info < (3, 13):
+        # changed in Python 3.12:
+        # - The case_sensitive parameter was added.
+        def glob(
+            self,
+            pattern: str,
+            *,
+            case_sensitive: bool | None = None,
+        ) -> AsyncIterator[Path]:
+            gen = self._path.glob(pattern, case_sensitive=case_sensitive)
+            return _PathIterator(gen)
+    elif sys.version_info >= (3, 13):
+        # Changed in Python 3.13:
+        # - The recurse_symlinks parameter was added.
+        # - The pattern parameter accepts a path-like object.
+        def glob(  # type: ignore[misc] # mypy doesn't allow for differing signatures in a conditional block
+            self,
+            pattern: str | PathLike[str],
+            *,
+            case_sensitive: bool | None = None,
+            recurse_symlinks: bool = False,
+        ) -> AsyncIterator[Path]:
+            gen = self._path.glob(
+                pattern,  # type: ignore[arg-type]
+                case_sensitive=case_sensitive,
+                recurse_symlinks=recurse_symlinks,
+            )
+            return _PathIterator(gen)
+
+    async def group(self) -> str:
+        return await to_thread.run_sync(self._path.group, abandon_on_cancel=True)
+
+    async def hardlink_to(
+        self, target: str | bytes | PathLike[str] | PathLike[bytes]
+    ) -> None:
+        if isinstance(target, Path):
+            target = target._path
+
+        await to_thread.run_sync(os.link, target, self)
+
+    @classmethod
+    async def home(cls) -> Path:
+        home_path = await to_thread.run_sync(pathlib.Path.home)
+        return cls(home_path)
+
+    def is_absolute(self) -> bool:
+        return self._path.is_absolute()
+
+    async def is_block_device(self) -> bool:
+        return await to_thread.run_sync(
+            self._path.is_block_device, abandon_on_cancel=True
+        )
+
+    async def is_char_device(self) -> bool:
+        return await to_thread.run_sync(
+            self._path.is_char_device, abandon_on_cancel=True
+        )
+
+    async def is_dir(self) -> bool:
+        return await to_thread.run_sync(self._path.is_dir, abandon_on_cancel=True)
+
+    async def is_fifo(self) -> bool:
+        return await to_thread.run_sync(self._path.is_fifo, abandon_on_cancel=True)
+
+    async def is_file(self) -> bool:
+        return await to_thread.run_sync(self._path.is_file, abandon_on_cancel=True)
+
+    if sys.version_info >= (3, 12):
+
+        async def is_junction(self) -> bool:
+            return await to_thread.run_sync(self._path.is_junction)
+
+    async def is_mount(self) -> bool:
+        return await to_thread.run_sync(
+            os.path.ismount, self._path, abandon_on_cancel=True
+        )
+
+    if sys.version_info < (3, 15):
+
+        def is_reserved(self) -> bool:
+            return self._path.is_reserved()
+
+    async def is_socket(self) -> bool:
+        return await to_thread.run_sync(self._path.is_socket, abandon_on_cancel=True)
+
+    async def is_symlink(self) -> bool:
+        return await to_thread.run_sync(self._path.is_symlink, abandon_on_cancel=True)
+
+    async def iterdir(self) -> AsyncIterator[Path]:
+        gen = (
+            self._path.iterdir()
+            if sys.version_info < (3, 13)
+            else await to_thread.run_sync(self._path.iterdir, abandon_on_cancel=True)
+        )
+        async for path in _PathIterator(gen):
+            yield path
+
+    def joinpath(self, *args: str | PathLike[str]) -> Path:
+        return Path(self._path.joinpath(*args))
+
+    async def lchmod(self, mode: int) -> None:
+        await to_thread.run_sync(self._path.lchmod, mode)
+
+    async def lstat(self) -> os.stat_result:
+        return await to_thread.run_sync(self._path.lstat, abandon_on_cancel=True)
+
+    async def mkdir(
+        self, mode: int = 0o777, parents: bool = False, exist_ok: bool = False
+    ) -> None:
+        await to_thread.run_sync(self._path.mkdir, mode, parents, exist_ok)
+
+    @overload
+    async def open(
+        self,
+        mode: OpenBinaryMode,
+        buffering: int = ...,
+        encoding: str | None = ...,
+        errors: str | None = ...,
+        newline: str | None = ...,
+    ) -> AsyncFile[bytes]: ...
+
+    @overload
+    async def open(
+        self,
+        mode: OpenTextMode = ...,
+        buffering: int = ...,
+        encoding: str | None = ...,
+        errors: str | None = ...,
+        newline: str | None = ...,
+    ) -> AsyncFile[str]: ...
+
+    async def open(
+        self,
+        mode: str = "r",
+        buffering: int = -1,
+        encoding: str | None = None,
+        errors: str | None = None,
+        newline: str | None = None,
+    ) -> AsyncFile[Any]:
+        fp = await to_thread.run_sync(
+            self._path.open, mode, buffering, encoding, errors, newline
+        )
+        return AsyncFile(fp)
+
+    async def owner(self) -> str:
+        return await to_thread.run_sync(self._path.owner, abandon_on_cancel=True)
+
+    async def read_bytes(self) -> bytes:
+        return await to_thread.run_sync(self._path.read_bytes)
+
+    async def read_text(
+        self, encoding: str | None = None, errors: str | None = None
+    ) -> str:
+        return await to_thread.run_sync(self._path.read_text, encoding, errors)
+
+    if sys.version_info >= (3, 12):
+
+        def relative_to(
+            self, *other: str | PathLike[str], walk_up: bool = False
+        ) -> Path:
+            # relative_to() should work with any PathLike but it doesn't
+            others = [pathlib.Path(other) for other in other]
+            return Path(self._path.relative_to(*others, walk_up=walk_up))
+
+    else:
+
+        def relative_to(self, *other: str | PathLike[str]) -> Path:
+            return Path(self._path.relative_to(*other))
+
+    async def readlink(self) -> Path:
+        target = await to_thread.run_sync(os.readlink, self._path)
+        return Path(target)
+
+    async def rename(self, target: str | pathlib.PurePath | Path) -> Path:
+        if isinstance(target, Path):
+            target = target._path
+
+        await to_thread.run_sync(self._path.rename, target)
+        return Path(target)
+
+    async def replace(self, target: str | pathlib.PurePath | Path) -> Path:
+        if isinstance(target, Path):
+            target = target._path
+
+        await to_thread.run_sync(self._path.replace, target)
+        return Path(target)
+
+    async def resolve(self, strict: bool = False) -> Path:
+        func = partial(self._path.resolve, strict=strict)
+        return Path(await to_thread.run_sync(func, abandon_on_cancel=True))
+
+    if sys.version_info < (3, 12):
+        # Pre Python 3.12
+        def rglob(self, pattern: str) -> AsyncIterator[Path]:
+            gen = self._path.rglob(pattern)
+            return _PathIterator(gen)
+    elif (3, 12) <= sys.version_info < (3, 13):
+        # Changed in Python 3.12:
+        # - The case_sensitive parameter was added.
+        def rglob(
+            self, pattern: str, *, case_sensitive: bool | None = None
+        ) -> AsyncIterator[Path]:
+            gen = self._path.rglob(pattern, case_sensitive=case_sensitive)
+            return _PathIterator(gen)
+    elif sys.version_info >= (3, 13):
+        # Changed in Python 3.13:
+        # - The recurse_symlinks parameter was added.
+        # - The pattern parameter accepts a path-like object.
+        def rglob(  # type: ignore[misc] # mypy doesn't allow for differing signatures in a conditional block
+            self,
+            pattern: str | PathLike[str],
+            *,
+            case_sensitive: bool | None = None,
+            recurse_symlinks: bool = False,
+        ) -> AsyncIterator[Path]:
+            gen = self._path.rglob(
+                pattern,  # type: ignore[arg-type]
+                case_sensitive=case_sensitive,
+                recurse_symlinks=recurse_symlinks,
+            )
+            return _PathIterator(gen)
+
+    async def rmdir(self) -> None:
+        await to_thread.run_sync(self._path.rmdir)
+
+    async def samefile(self, other_path: str | PathLike[str]) -> bool:
+        if isinstance(other_path, Path):
+            other_path = other_path._path
+
+        return await to_thread.run_sync(
+            self._path.samefile, other_path, abandon_on_cancel=True
+        )
+
+    async def stat(self, *, follow_symlinks: bool = True) -> os.stat_result:
+        func = partial(os.stat, follow_symlinks=follow_symlinks)
+        return await to_thread.run_sync(func, self._path, abandon_on_cancel=True)
+
+    async def symlink_to(
+        self,
+        target: str | bytes | PathLike[str] | PathLike[bytes],
+        target_is_directory: bool = False,
+    ) -> None:
+        if isinstance(target, Path):
+            target = target._path
+
+        await to_thread.run_sync(self._path.symlink_to, target, target_is_directory)
+
+    async def touch(self, mode: int = 0o666, exist_ok: bool = True) -> None:
+        await to_thread.run_sync(self._path.touch, mode, exist_ok)
+
+    async def unlink(self, missing_ok: bool = False) -> None:
+        try:
+            await to_thread.run_sync(self._path.unlink)
+        except FileNotFoundError:
+            if not missing_ok:
+                raise
+
+    if sys.version_info >= (3, 12):
+
+        async def walk(
+            self,
+            top_down: bool = True,
+            on_error: Callable[[OSError], object] | None = None,
+            follow_symlinks: bool = False,
+        ) -> AsyncIterator[tuple[Path, list[str], list[str]]]:
+            def get_next_value() -> tuple[pathlib.Path, list[str], list[str]] | None:
+                try:
+                    return next(gen)
+                except StopIteration:
+                    return None
+
+            gen = self._path.walk(top_down, on_error, follow_symlinks)
+            while True:
+                value = await to_thread.run_sync(get_next_value)
+                if value is None:
+                    return
+
+                root, dirs, paths = value
+                yield Path(root), dirs, paths
+
+    def with_name(self, name: str) -> Path:
+        return Path(self._path.with_name(name))
+
+    def with_stem(self, stem: str) -> Path:
+        return Path(self._path.with_name(stem + self._path.suffix))
+
+    def with_suffix(self, suffix: str) -> Path:
+        return Path(self._path.with_suffix(suffix))
+
+    def with_segments(self, *pathsegments: str | PathLike[str]) -> Path:
+        return Path(*pathsegments)
+
+    async def write_bytes(self, data: bytes) -> int:
+        return await to_thread.run_sync(self._path.write_bytes, data)
+
+    async def write_text(
+        self,
+        data: str,
+        encoding: str | None = None,
+        errors: str | None = None,
+        newline: str | None = None,
+    ) -> int:
+        return await to_thread.run_sync(
+            self._path.write_text, data, encoding, errors, newline
+        )
+
+
+PathLike.register(Path)

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_resources.py

@@ -0,0 +1,18 @@
+from __future__ import annotations
+
+from ..abc import AsyncResource
+from ._tasks import CancelScope
+
+
+async def aclose_forcefully(resource: AsyncResource) -> None:
+    """
+    Close an asynchronous resource in a cancelled scope.
+
+    Doing this closes the resource without waiting on anything.
+
+    :param resource: the resource to close
+
+    """
+    with CancelScope() as scope:
+        scope.cancel()
+        await resource.aclose()

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_signals.py

@@ -0,0 +1,29 @@
+from __future__ import annotations
+
+from collections.abc import AsyncIterator
+from contextlib import AbstractContextManager
+from signal import Signals
+
+from ._eventloop import get_async_backend
+
+
+def open_signal_receiver(
+    *signals: Signals,
+) -> AbstractContextManager[AsyncIterator[Signals]]:
+    """
+    Start receiving operating system signals.
+
+    :param signals: signals to receive (e.g. ``signal.SIGINT``)
+    :return: an asynchronous context manager for an asynchronous iterator which yields
+        signal numbers
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    .. warning:: Windows does not support signals natively so it is best to avoid
+        relying on this in cross-platform applications.
+
+    .. warning:: On asyncio, this permanently replaces any previous signal handler for
+        the given signals, as set via :meth:`~asyncio.loop.add_signal_handler`.
+
+    """
+    return get_async_backend().open_signal_receiver(*signals)

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_sockets.py

@@ -0,0 +1,1003 @@
+from __future__ import annotations
+
+import errno
+import os
+import socket
+import ssl
+import stat
+import sys
+from collections.abc import Awaitable
+from dataclasses import dataclass
+from ipaddress import IPv4Address, IPv6Address, ip_address
+from os import PathLike, chmod
+from socket import AddressFamily, SocketKind
+from typing import TYPE_CHECKING, Any, Literal, cast, overload
+
+from .. import ConnectionFailed, to_thread
+from ..abc import (
+    ByteStreamConnectable,
+    ConnectedUDPSocket,
+    ConnectedUNIXDatagramSocket,
+    IPAddressType,
+    IPSockAddrType,
+    SocketListener,
+    SocketStream,
+    UDPSocket,
+    UNIXDatagramSocket,
+    UNIXSocketStream,
+)
+from ..streams.stapled import MultiListener
+from ..streams.tls import TLSConnectable, TLSStream
+from ._eventloop import get_async_backend
+from ._resources import aclose_forcefully
+from ._synchronization import Event
+from ._tasks import create_task_group, move_on_after
+
+if TYPE_CHECKING:
+    from _typeshed import FileDescriptorLike
+else:
+    FileDescriptorLike = object
+
+if sys.version_info < (3, 11):
+    from exceptiongroup import ExceptionGroup
+
+if sys.version_info >= (3, 12):
+    from typing import override
+else:
+    from typing_extensions import override
+
+if sys.version_info < (3, 13):
+    from typing_extensions import deprecated
+else:
+    from warnings import deprecated
+
+IPPROTO_IPV6 = getattr(socket, "IPPROTO_IPV6", 41)  # https://bugs.python.org/issue29515
+
+AnyIPAddressFamily = Literal[
+    AddressFamily.AF_UNSPEC, AddressFamily.AF_INET, AddressFamily.AF_INET6
+]
+IPAddressFamily = Literal[AddressFamily.AF_INET, AddressFamily.AF_INET6]
+
+
+# tls_hostname given
+@overload
+async def connect_tcp(
+    remote_host: IPAddressType,
+    remote_port: int,
+    *,
+    local_host: IPAddressType | None = ...,
+    ssl_context: ssl.SSLContext | None = ...,
+    tls_standard_compatible: bool = ...,
+    tls_hostname: str,
+    happy_eyeballs_delay: float = ...,
+) -> TLSStream: ...
+
+
+# ssl_context given
+@overload
+async def connect_tcp(
+    remote_host: IPAddressType,
+    remote_port: int,
+    *,
+    local_host: IPAddressType | None = ...,
+    ssl_context: ssl.SSLContext,
+    tls_standard_compatible: bool = ...,
+    tls_hostname: str | None = ...,
+    happy_eyeballs_delay: float = ...,
+) -> TLSStream: ...
+
+
+# tls=True
+@overload
+async def connect_tcp(
+    remote_host: IPAddressType,
+    remote_port: int,
+    *,
+    local_host: IPAddressType | None = ...,
+    tls: Literal[True],
+    ssl_context: ssl.SSLContext | None = ...,
+    tls_standard_compatible: bool = ...,
+    tls_hostname: str | None = ...,
+    happy_eyeballs_delay: float = ...,
+) -> TLSStream: ...
+
+
+# tls=False
+@overload
+async def connect_tcp(
+    remote_host: IPAddressType,
+    remote_port: int,
+    *,
+    local_host: IPAddressType | None = ...,
+    tls: Literal[False],
+    ssl_context: ssl.SSLContext | None = ...,
+    tls_standard_compatible: bool = ...,
+    tls_hostname: str | None = ...,
+    happy_eyeballs_delay: float = ...,
+) -> SocketStream: ...
+
+
+# No TLS arguments
+@overload
+async def connect_tcp(
+    remote_host: IPAddressType,
+    remote_port: int,
+    *,
+    local_host: IPAddressType | None = ...,
+    happy_eyeballs_delay: float = ...,
+) -> SocketStream: ...
+
+
+async def connect_tcp(
+    remote_host: IPAddressType,
+    remote_port: int,
+    *,
+    local_host: IPAddressType | None = None,
+    tls: bool = False,
+    ssl_context: ssl.SSLContext | None = None,
+    tls_standard_compatible: bool = True,
+    tls_hostname: str | None = None,
+    happy_eyeballs_delay: float = 0.25,
+) -> SocketStream | TLSStream:
+    """
+    Connect to a host using the TCP protocol.
+
+    This function implements the stateless version of the Happy Eyeballs algorithm (RFC
+    6555). If ``remote_host`` is a host name that resolves to multiple IP addresses,
+    each one is tried until one connection attempt succeeds. If the first attempt does
+    not connected within 250 milliseconds, a second attempt is started using the next
+    address in the list, and so on. On IPv6 enabled systems, an IPv6 address (if
+    available) is tried first.
+
+    When the connection has been established, a TLS handshake will be done if either
+    ``ssl_context`` or ``tls_hostname`` is not ``None``, or if ``tls`` is ``True``.
+
+    :param remote_host: the IP address or host name to connect to
+    :param remote_port: port on the target host to connect to
+    :param local_host: the interface address or name to bind the socket to before
+        connecting
+    :param tls: ``True`` to do a TLS handshake with the connected stream and return a
+        :class:`~anyio.streams.tls.TLSStream` instead
+    :param ssl_context: the SSL context object to use (if omitted, a default context is
+        created)
+    :param tls_standard_compatible: If ``True``, performs the TLS shutdown handshake
+        before closing the stream and requires that the server does this as well.
+        Otherwise, :exc:`~ssl.SSLEOFError` may be raised during reads from the stream.
+        Some protocols, such as HTTP, require this option to be ``False``.
+        See :meth:`~ssl.SSLContext.wrap_socket` for details.
+    :param tls_hostname: host name to check the server certificate against (defaults to
+        the value of ``remote_host``)
+    :param happy_eyeballs_delay: delay (in seconds) before starting the next connection
+        attempt
+    :return: a socket stream object if no TLS handshake was done, otherwise a TLS stream
+    :raises ConnectionFailed: if the connection fails
+
+    """
+    # Placed here due to https://github.com/python/mypy/issues/7057
+    connected_stream: SocketStream | None = None
+
+    async def try_connect(remote_host: str, event: Event) -> None:
+        nonlocal connected_stream
+        try:
+            stream = await asynclib.connect_tcp(remote_host, remote_port, local_address)
+        except OSError as exc:
+            oserrors.append(exc)
+            return
+        else:
+            if connected_stream is None:
+                connected_stream = stream
+                tg.cancel_scope.cancel()
+            else:
+                await stream.aclose()
+        finally:
+            event.set()
+
+    asynclib = get_async_backend()
+    local_address: IPSockAddrType | None = None
+    family = socket.AF_UNSPEC
+    if local_host:
+        gai_res = await getaddrinfo(str(local_host), None)
+        family, *_, local_address = gai_res[0]
+
+    target_host = str(remote_host)
+    try:
+        addr_obj = ip_address(remote_host)
+    except ValueError:
+        addr_obj = None
+
+    if addr_obj is not None:
+        if isinstance(addr_obj, IPv6Address):
+            target_addrs = [(socket.AF_INET6, addr_obj.compressed)]
+        else:
+            target_addrs = [(socket.AF_INET, addr_obj.compressed)]
+    else:
+        # getaddrinfo() will raise an exception if name resolution fails
+        gai_res = await getaddrinfo(
+            target_host, remote_port, family=family, type=socket.SOCK_STREAM
+        )
+
+        # Organize the list so that the first address is an IPv6 address (if available)
+        # and the second one is an IPv4 addresses. The rest can be in whatever order.
+        v6_found = v4_found = False
+        target_addrs = []
+        for af, *_, sa in gai_res:
+            if af == socket.AF_INET6 and not v6_found:
+                v6_found = True
+                target_addrs.insert(0, (af, sa[0]))
+            elif af == socket.AF_INET and not v4_found and v6_found:
+                v4_found = True
+                target_addrs.insert(1, (af, sa[0]))
+            else:
+                target_addrs.append((af, sa[0]))
+
+    oserrors: list[OSError] = []
+    try:
+        async with create_task_group() as tg:
+            for _af, addr in target_addrs:
+                event = Event()
+                tg.start_soon(try_connect, addr, event)
+                with move_on_after(happy_eyeballs_delay):
+                    await event.wait()
+
+        if connected_stream is None:
+            cause = (
+                oserrors[0]
+                if len(oserrors) == 1
+                else ExceptionGroup("multiple connection attempts failed", oserrors)
+            )
+            raise OSError("All connection attempts failed") from cause
+    finally:
+        oserrors.clear()
+
+    if tls or tls_hostname or ssl_context:
+        try:
+            return await TLSStream.wrap(
+                connected_stream,
+                server_side=False,
+                hostname=tls_hostname or str(remote_host),
+                ssl_context=ssl_context,
+                standard_compatible=tls_standard_compatible,
+            )
+        except BaseException:
+            await aclose_forcefully(connected_stream)
+            raise
+
+    return connected_stream
+
+
+async def connect_unix(path: str | bytes | PathLike[Any]) -> UNIXSocketStream:
+    """
+    Connect to the given UNIX socket.
+
+    Not available on Windows.
+
+    :param path: path to the socket
+    :return: a socket stream object
+    :raises ConnectionFailed: if the connection fails
+
+    """
+    path = os.fspath(path)
+    return await get_async_backend().connect_unix(path)
+
+
+async def create_tcp_listener(
+    *,
+    local_host: IPAddressType | None = None,
+    local_port: int = 0,
+    family: AnyIPAddressFamily = socket.AddressFamily.AF_UNSPEC,
+    backlog: int = 65536,
+    reuse_port: bool = False,
+) -> MultiListener[SocketStream]:
+    """
+    Create a TCP socket listener.
+
+    :param local_port: port number to listen on
+    :param local_host: IP address of the interface to listen on. If omitted, listen on
+        all IPv4 and IPv6 interfaces. To listen on all interfaces on a specific address
+        family, use ``0.0.0.0`` for IPv4 or ``::`` for IPv6.
+    :param family: address family (used if ``local_host`` was omitted)
+    :param backlog: maximum number of queued incoming connections (up to a maximum of
+        2**16, or 65536)
+    :param reuse_port: ``True`` to allow multiple sockets to bind to the same
+        address/port (not supported on Windows)
+    :return: a multi-listener object containing one or more socket listeners
+    :raises OSError: if there's an error creating a socket, or binding to one or more
+        interfaces failed
+
+    """
+    asynclib = get_async_backend()
+    backlog = min(backlog, 65536)
+    local_host = str(local_host) if local_host is not None else None
+
+    def setup_raw_socket(
+        fam: AddressFamily,
+        bind_addr: tuple[str, int] | tuple[str, int, int, int],
+        *,
+        v6only: bool = True,
+    ) -> socket.socket:
+        sock = socket.socket(fam)
+        try:
+            sock.setblocking(False)
+
+            if fam == AddressFamily.AF_INET6:
+                sock.setsockopt(IPPROTO_IPV6, socket.IPV6_V6ONLY, v6only)
+
+            # For Windows, enable exclusive address use. For others, enable address
+            # reuse.
+            if sys.platform == "win32":
+                sock.setsockopt(socket.SOL_SOCKET, socket.SO_EXCLUSIVEADDRUSE, 1)
+            else:
+                sock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
+
+            if reuse_port:
+                sock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEPORT, 1)
+
+            # Workaround for #554
+            if fam == socket.AF_INET6 and "%" in bind_addr[0]:
+                addr, scope_id = bind_addr[0].split("%", 1)
+                bind_addr = (addr, bind_addr[1], 0, int(scope_id))
+
+            sock.bind(bind_addr)
+            sock.listen(backlog)
+        except BaseException:
+            sock.close()
+            raise
+
+        return sock
+
+    # We passing type=0 on non-Windows platforms as a workaround for a uvloop bug
+    # where we don't get the correct scope ID for IPv6 link-local addresses when passing
+    # type=socket.SOCK_STREAM to getaddrinfo():
+    # https://github.com/MagicStack/uvloop/issues/539
+    gai_res = await getaddrinfo(
+        local_host,
+        local_port,
+        family=family,
+        type=socket.SOCK_STREAM if sys.platform == "win32" else 0,
+        flags=socket.AI_PASSIVE | socket.AI_ADDRCONFIG,
+    )
+
+    # The set comprehension is here to work around a glibc bug:
+    # https://sourceware.org/bugzilla/show_bug.cgi?id=14969
+    sockaddrs = sorted({res for res in gai_res if res[1] == SocketKind.SOCK_STREAM})
+
+    # Special case for dual-stack binding on the "any" interface
+    if (
+        local_host is None
+        and family == AddressFamily.AF_UNSPEC
+        and socket.has_dualstack_ipv6()
+        and any(fam == AddressFamily.AF_INET6 for fam, *_ in gai_res)
+    ):
+        raw_socket = setup_raw_socket(
+            AddressFamily.AF_INET6, ("::", local_port), v6only=False
+        )
+        listener = asynclib.create_tcp_listener(raw_socket)
+        return MultiListener([listener])
+
+    errors: list[OSError] = []
+    try:
+        for _ in range(len(sockaddrs)):
+            listeners: list[SocketListener] = []
+            bound_ephemeral_port = local_port
+            try:
+                for fam, *_, sockaddr in sockaddrs:
+                    sockaddr = sockaddr[0], bound_ephemeral_port, *sockaddr[2:]
+                    raw_socket = setup_raw_socket(fam, sockaddr)
+
+                    # Store the assigned port if an ephemeral port was requested, so
+                    # we'll bind to the same port on all interfaces
+                    if local_port == 0 and len(gai_res) > 1:
+                        bound_ephemeral_port = raw_socket.getsockname()[1]
+
+                    listeners.append(asynclib.create_tcp_listener(raw_socket))
+            except BaseException as exc:
+                for listener in listeners:
+                    await listener.aclose()
+
+                # If an ephemeral port was requested but binding the assigned port
+                # failed for another interface, rotate the address list and try again
+                if (
+                    isinstance(exc, OSError)
+                    and exc.errno == errno.EADDRINUSE
+                    and local_port == 0
+                    and bound_ephemeral_port
+                ):
+                    errors.append(exc)
+                    sockaddrs.append(sockaddrs.pop(0))
+                    continue
+
+                raise
+
+            return MultiListener(listeners)
+
+        raise OSError(
+            f"Could not create {len(sockaddrs)} listeners with a consistent port"
+        ) from ExceptionGroup("Several bind attempts failed", errors)
+    finally:
+        del errors  # Prevent reference cycles
+
+
+async def create_unix_listener(
+    path: str | bytes | PathLike[Any],
+    *,
+    mode: int | None = None,
+    backlog: int = 65536,
+) -> SocketListener:
+    """
+    Create a UNIX socket listener.
+
+    Not available on Windows.
+
+    :param path: path of the socket
+    :param mode: permissions to set on the socket
+    :param backlog: maximum number of queued incoming connections (up to a maximum of
+        2**16, or 65536)
+    :return: a listener object
+
+    .. versionchanged:: 3.0
+        If a socket already exists on the file system in the given path, it will be
+        removed first.
+
+    """
+    backlog = min(backlog, 65536)
+    raw_socket = await setup_unix_local_socket(path, mode, socket.SOCK_STREAM)
+    try:
+        raw_socket.listen(backlog)
+        return get_async_backend().create_unix_listener(raw_socket)
+    except BaseException:
+        raw_socket.close()
+        raise
+
+
+async def create_udp_socket(
+    family: AnyIPAddressFamily = AddressFamily.AF_UNSPEC,
+    *,
+    local_host: IPAddressType | None = None,
+    local_port: int = 0,
+    reuse_port: bool = False,
+) -> UDPSocket:
+    """
+    Create a UDP socket.
+
+    If ``port`` has been given, the socket will be bound to this port on the local
+    machine, making this socket suitable for providing UDP based services.
+
+    :param family: address family (``AF_INET`` or ``AF_INET6``) – automatically
+        determined from ``local_host`` if omitted
+    :param local_host: IP address or host name of the local interface to bind to
+    :param local_port: local port to bind to
+    :param reuse_port: ``True`` to allow multiple sockets to bind to the same
+        address/port (not supported on Windows)
+    :return: a UDP socket
+
+    """
+    if family is AddressFamily.AF_UNSPEC and not local_host:
+        raise ValueError('Either "family" or "local_host" must be given')
+
+    if local_host:
+        gai_res = await getaddrinfo(
+            str(local_host),
+            local_port,
+            family=family,
+            type=socket.SOCK_DGRAM,
+            flags=socket.AI_PASSIVE | socket.AI_ADDRCONFIG,
+        )
+        family = cast(AnyIPAddressFamily, gai_res[0][0])
+        local_address = gai_res[0][-1]
+    elif family is AddressFamily.AF_INET6:
+        local_address = ("::", 0)
+    else:
+        local_address = ("0.0.0.0", 0)
+
+    sock = await get_async_backend().create_udp_socket(
+        family, local_address, None, reuse_port
+    )
+    return cast(UDPSocket, sock)
+
+
+async def create_connected_udp_socket(
+    remote_host: IPAddressType,
+    remote_port: int,
+    *,
+    family: AnyIPAddressFamily = AddressFamily.AF_UNSPEC,
+    local_host: IPAddressType | None = None,
+    local_port: int = 0,
+    reuse_port: bool = False,
+) -> ConnectedUDPSocket:
+    """
+    Create a connected UDP socket.
+
+    Connected UDP sockets can only communicate with the specified remote host/port, an
+    any packets sent from other sources are dropped.
+
+    :param remote_host: remote host to set as the default target
+    :param remote_port: port on the remote host to set as the default target
+    :param family: address family (``AF_INET`` or ``AF_INET6``) – automatically
+        determined from ``local_host`` or ``remote_host`` if omitted
+    :param local_host: IP address or host name of the local interface to bind to
+    :param local_port: local port to bind to
+    :param reuse_port: ``True`` to allow multiple sockets to bind to the same
+        address/port (not supported on Windows)
+    :return: a connected UDP socket
+
+    """
+    local_address = None
+    if local_host:
+        gai_res = await getaddrinfo(
+            str(local_host),
+            local_port,
+            family=family,
+            type=socket.SOCK_DGRAM,
+            flags=socket.AI_PASSIVE | socket.AI_ADDRCONFIG,
+        )
+        family = cast(AnyIPAddressFamily, gai_res[0][0])
+        local_address = gai_res[0][-1]
+
+    gai_res = await getaddrinfo(
+        str(remote_host), remote_port, family=family, type=socket.SOCK_DGRAM
+    )
+    family = cast(AnyIPAddressFamily, gai_res[0][0])
+    remote_address = gai_res[0][-1]
+
+    sock = await get_async_backend().create_udp_socket(
+        family, local_address, remote_address, reuse_port
+    )
+    return cast(ConnectedUDPSocket, sock)
+
+
+async def create_unix_datagram_socket(
+    *,
+    local_path: None | str | bytes | PathLike[Any] = None,
+    local_mode: int | None = None,
+) -> UNIXDatagramSocket:
+    """
+    Create a UNIX datagram socket.
+
+    Not available on Windows.
+
+    If ``local_path`` has been given, the socket will be bound to this path, making this
+    socket suitable for receiving datagrams from other processes. Other processes can
+    send datagrams to this socket only if ``local_path`` is set.
+
+    If a socket already exists on the file system in the ``local_path``, it will be
+    removed first.
+
+    :param local_path: the path on which to bind to
+    :param local_mode: permissions to set on the local socket
+    :return: a UNIX datagram socket
+
+    """
+    raw_socket = await setup_unix_local_socket(
+        local_path, local_mode, socket.SOCK_DGRAM
+    )
+    return await get_async_backend().create_unix_datagram_socket(raw_socket, None)
+
+
+async def create_connected_unix_datagram_socket(
+    remote_path: str | bytes | PathLike[Any],
+    *,
+    local_path: None | str | bytes | PathLike[Any] = None,
+    local_mode: int | None = None,
+) -> ConnectedUNIXDatagramSocket:
+    """
+    Create a connected UNIX datagram socket.
+
+    Connected datagram sockets can only communicate with the specified remote path.
+
+    If ``local_path`` has been given, the socket will be bound to this path, making
+    this socket suitable for receiving datagrams from other processes. Other processes
+    can send datagrams to this socket only if ``local_path`` is set.
+
+    If a socket already exists on the file system in the ``local_path``, it will be
+    removed first.
+
+    :param remote_path: the path to set as the default target
+    :param local_path: the path on which to bind to
+    :param local_mode: permissions to set on the local socket
+    :return: a connected UNIX datagram socket
+
+    """
+    remote_path = os.fspath(remote_path)
+    raw_socket = await setup_unix_local_socket(
+        local_path, local_mode, socket.SOCK_DGRAM
+    )
+    return await get_async_backend().create_unix_datagram_socket(
+        raw_socket, remote_path
+    )
+
+
+async def getaddrinfo(
+    host: bytes | str | None,
+    port: str | int | None,
+    *,
+    family: int | AddressFamily = 0,
+    type: int | SocketKind = 0,
+    proto: int = 0,
+    flags: int = 0,
+) -> list[tuple[AddressFamily, SocketKind, int, str, tuple[str, int]]]:
+    """
+    Look up a numeric IP address given a host name.
+
+    Internationalized domain names are translated according to the (non-transitional)
+    IDNA 2008 standard.
+
+    .. note:: 4-tuple IPv6 socket addresses are automatically converted to 2-tuples of
+        (host, port), unlike what :func:`socket.getaddrinfo` does.
+
+    :param host: host name
+    :param port: port number
+    :param family: socket family (`'AF_INET``, ...)
+    :param type: socket type (``SOCK_STREAM``, ...)
+    :param proto: protocol number
+    :param flags: flags to pass to upstream ``getaddrinfo()``
+    :return: list of tuples containing (family, type, proto, canonname, sockaddr)
+
+    .. seealso:: :func:`socket.getaddrinfo`
+
+    """
+    # Handle unicode hostnames
+    if isinstance(host, str):
+        try:
+            encoded_host: bytes | None = host.encode("ascii")
+        except UnicodeEncodeError:
+            import idna
+
+            encoded_host = idna.encode(host, uts46=True)
+    else:
+        encoded_host = host
+
+    gai_res = await get_async_backend().getaddrinfo(
+        encoded_host, port, family=family, type=type, proto=proto, flags=flags
+    )
+    return [
+        (family, type, proto, canonname, convert_ipv6_sockaddr(sockaddr))
+        for family, type, proto, canonname, sockaddr in gai_res
+        # filter out IPv6 results when IPv6 is disabled
+        if not isinstance(sockaddr[0], int)
+    ]
+
+
+def getnameinfo(sockaddr: IPSockAddrType, flags: int = 0) -> Awaitable[tuple[str, str]]:
+    """
+    Look up the host name of an IP address.
+
+    :param sockaddr: socket address (e.g. (ipaddress, port) for IPv4)
+    :param flags: flags to pass to upstream ``getnameinfo()``
+    :return: a tuple of (host name, service name)
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    .. seealso:: :func:`socket.getnameinfo`
+
+    """
+    return get_async_backend().getnameinfo(sockaddr, flags)
+
+
+@deprecated("This function is deprecated; use `wait_readable` instead")
+def wait_socket_readable(sock: socket.socket) -> Awaitable[None]:
+    """
+    .. deprecated:: 4.7.0
+       Use :func:`wait_readable` instead.
+
+    Wait until the given socket has data to be read.
+
+    .. warning:: Only use this on raw sockets that have not been wrapped by any higher
+        level constructs like socket streams!
+
+    :param sock: a socket object
+    :raises ~anyio.ClosedResourceError: if the socket was closed while waiting for the
+        socket to become readable
+    :raises ~anyio.BusyResourceError: if another task is already waiting for the socket
+        to become readable
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    return get_async_backend().wait_readable(sock.fileno())
+
+
+@deprecated("This function is deprecated; use `wait_writable` instead")
+def wait_socket_writable(sock: socket.socket) -> Awaitable[None]:
+    """
+    .. deprecated:: 4.7.0
+       Use :func:`wait_writable` instead.
+
+    Wait until the given socket can be written to.
+
+    This does **NOT** work on Windows when using the asyncio backend with a proactor
+    event loop (default on py3.8+).
+
+    .. warning:: Only use this on raw sockets that have not been wrapped by any higher
+        level constructs like socket streams!
+
+    :param sock: a socket object
+    :raises ~anyio.ClosedResourceError: if the socket was closed while waiting for the
+        socket to become writable
+    :raises ~anyio.BusyResourceError: if another task is already waiting for the socket
+        to become writable
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    return get_async_backend().wait_writable(sock.fileno())
+
+
+def wait_readable(obj: FileDescriptorLike) -> Awaitable[None]:
+    """
+    Wait until the given object has data to be read.
+
+    On Unix systems, ``obj`` must either be an integer file descriptor, or else an
+    object with a ``.fileno()`` method which returns an integer file descriptor. Any
+    kind of file descriptor can be passed, though the exact semantics will depend on
+    your kernel. For example, this probably won't do anything useful for on-disk files.
+
+    On Windows systems, ``obj`` must either be an integer ``SOCKET`` handle, or else an
+    object with a ``.fileno()`` method which returns an integer ``SOCKET`` handle. File
+    descriptors aren't supported, and neither are handles that refer to anything besides
+    a ``SOCKET``.
+
+    On backends where this functionality is not natively provided (asyncio
+    ``ProactorEventLoop`` on Windows), it is provided using a separate selector thread
+    which is set to shut down when the interpreter shuts down.
+
+    .. warning:: Don't use this on raw sockets that have been wrapped by any higher
+        level constructs like socket streams!
+
+    :param obj: an object with a ``.fileno()`` method or an integer handle
+    :raises ~anyio.ClosedResourceError: if the object was closed while waiting for the
+        object to become readable
+    :raises ~anyio.BusyResourceError: if another task is already waiting for the object
+        to become readable
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    return get_async_backend().wait_readable(obj)
+
+
+def wait_writable(obj: FileDescriptorLike) -> Awaitable[None]:
+    """
+    Wait until the given object can be written to.
+
+    :param obj: an object with a ``.fileno()`` method or an integer handle
+    :raises ~anyio.ClosedResourceError: if the object was closed while waiting for the
+        object to become writable
+    :raises ~anyio.BusyResourceError: if another task is already waiting for the object
+        to become writable
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    .. seealso:: See the documentation of :func:`wait_readable` for the definition of
+       ``obj`` and notes on backend compatibility.
+
+    .. warning:: Don't use this on raw sockets that have been wrapped by any higher
+        level constructs like socket streams!
+
+    """
+    return get_async_backend().wait_writable(obj)
+
+
+def notify_closing(obj: FileDescriptorLike) -> None:
+    """
+    Call this before closing a file descriptor (on Unix) or socket (on
+    Windows). This will cause any `wait_readable` or `wait_writable`
+    calls on the given object to immediately wake up and raise
+    `~anyio.ClosedResourceError`.
+
+    This doesn't actually close the object – you still have to do that
+    yourself afterwards. Also, you want to be careful to make sure no
+    new tasks start waiting on the object in between when you call this
+    and when it's actually closed. So to close something properly, you
+    usually want to do these steps in order:
+
+    1. Explicitly mark the object as closed, so that any new attempts
+       to use it will abort before they start.
+    2. Call `notify_closing` to wake up any already-existing users.
+    3. Actually close the object.
+
+    It's also possible to do them in a different order if that's more
+    convenient, *but only if* you make sure not to have any checkpoints in
+    between the steps. This way they all happen in a single atomic
+    step, so other tasks won't be able to tell what order they happened
+    in anyway.
+
+    :param obj: an object with a ``.fileno()`` method or an integer handle
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    get_async_backend().notify_closing(obj)
+
+
+#
+# Private API
+#
+
+
+def convert_ipv6_sockaddr(
+    sockaddr: tuple[str, int, int, int] | tuple[str, int],
+) -> tuple[str, int]:
+    """
+    Convert a 4-tuple IPv6 socket address to a 2-tuple (address, port) format.
+
+    If the scope ID is nonzero, it is added to the address, separated with ``%``.
+    Otherwise the flow id and scope id are simply cut off from the tuple.
+    Any other kinds of socket addresses are returned as-is.
+
+    :param sockaddr: the result of :meth:`~socket.socket.getsockname`
+    :return: the converted socket address
+
+    """
+    # This is more complicated than it should be because of MyPy
+    if isinstance(sockaddr, tuple) and len(sockaddr) == 4:
+        host, port, flowinfo, scope_id = sockaddr
+        if scope_id:
+            # PyPy (as of v7.3.11) leaves the interface name in the result, so
+            # we discard it and only get the scope ID from the end
+            # (https://foss.heptapod.net/pypy/pypy/-/issues/3938)
+            host = host.split("%")[0]
+
+            # Add scope_id to the address
+            return f"{host}%{scope_id}", port
+        else:
+            return host, port
+    else:
+        return sockaddr
+
+
+async def setup_unix_local_socket(
+    path: None | str | bytes | PathLike[Any],
+    mode: int | None,
+    socktype: int,
+) -> socket.socket:
+    """
+    Create a UNIX local socket object, deleting the socket at the given path if it
+    exists.
+
+    Not available on Windows.
+
+    :param path: path of the socket
+    :param mode: permissions to set on the socket
+    :param socktype: socket.SOCK_STREAM or socket.SOCK_DGRAM
+
+    """
+    path_str: str | None
+    if path is not None:
+        path_str = os.fsdecode(path)
+
+        # Linux abstract namespace sockets aren't backed by a concrete file so skip stat call
+        if not path_str.startswith("\0"):
+            # Copied from pathlib...
+            try:
+                stat_result = os.stat(path)
+            except OSError as e:
+                if e.errno not in (
+                    errno.ENOENT,
+                    errno.ENOTDIR,
+                    errno.EBADF,
+                    errno.ELOOP,
+                ):
+                    raise
+            else:
+                if stat.S_ISSOCK(stat_result.st_mode):
+                    os.unlink(path)
+    else:
+        path_str = None
+
+    raw_socket = socket.socket(socket.AF_UNIX, socktype)
+    raw_socket.setblocking(False)
+
+    if path_str is not None:
+        try:
+            await to_thread.run_sync(raw_socket.bind, path_str, abandon_on_cancel=True)
+            if mode is not None:
+                await to_thread.run_sync(chmod, path_str, mode, abandon_on_cancel=True)
+        except BaseException:
+            raw_socket.close()
+            raise
+
+    return raw_socket
+
+
+@dataclass
+class TCPConnectable(ByteStreamConnectable):
+    """
+    Connects to a TCP server at the given host and port.
+
+    :param host: host name or IP address of the server
+    :param port: TCP port number of the server
+    """
+
+    host: str | IPv4Address | IPv6Address
+    port: int
+
+    def __post_init__(self) -> None:
+        if self.port < 1 or self.port > 65535:
+            raise ValueError("TCP port number out of range")
+
+    @override
+    async def connect(self) -> SocketStream:
+        try:
+            return await connect_tcp(self.host, self.port)
+        except OSError as exc:
+            raise ConnectionFailed(
+                f"error connecting to {self.host}:{self.port}: {exc}"
+            ) from exc
+
+
+@dataclass
+class UNIXConnectable(ByteStreamConnectable):
+    """
+    Connects to a UNIX domain socket at the given path.
+
+    :param path: the file system path of the socket
+    """
+
+    path: str | bytes | PathLike[str] | PathLike[bytes]
+
+    @override
+    async def connect(self) -> UNIXSocketStream:
+        try:
+            return await connect_unix(self.path)
+        except OSError as exc:
+            raise ConnectionFailed(f"error connecting to {self.path!r}: {exc}") from exc
+
+
+def as_connectable(
+    remote: ByteStreamConnectable
+    | tuple[str | IPv4Address | IPv6Address, int]
+    | str
+    | bytes
+    | PathLike[str],
+    /,
+    *,
+    tls: bool = False,
+    ssl_context: ssl.SSLContext | None = None,
+    tls_hostname: str | None = None,
+    tls_standard_compatible: bool = True,
+) -> ByteStreamConnectable:
+    """
+    Return a byte stream connectable from the given object.
+
+    If a bytestream connectable is given, it is returned unchanged.
+    If a tuple of (host, port) is given, a TCP connectable is returned.
+    If a string or bytes path is given, a UNIX connectable is returned.
+
+    If ``tls=True``, the connectable will be wrapped in a
+    :class:`~.streams.tls.TLSConnectable`.
+
+    :param remote: a connectable, a tuple of (host, port) or a path to a UNIX socket
+    :param tls: if ``True``, wrap the plaintext connectable in a
+        :class:`~.streams.tls.TLSConnectable`, using the provided TLS settings)
+    :param ssl_context: if ``tls=True``, the SSLContext object to use  (if not provided,
+        a secure default will be created)
+    :param tls_hostname: if ``tls=True``, host name of the server to use for checking
+        the server certificate (defaults to the host portion of the address for TCP
+        connectables)
+    :param tls_standard_compatible: if ``False`` and ``tls=True``, makes the TLS stream
+        skip the closing handshake when closing the connection, so it won't raise an
+        exception if the server does the same
+
+    """
+    connectable: TCPConnectable | UNIXConnectable | TLSConnectable
+    if isinstance(remote, ByteStreamConnectable):
+        return remote
+    elif isinstance(remote, tuple) and len(remote) == 2:
+        connectable = TCPConnectable(*remote)
+    elif isinstance(remote, (str, bytes, PathLike)):
+        connectable = UNIXConnectable(remote)
+    else:
+        raise TypeError(f"cannot convert {remote!r} to a connectable")
+
+    if tls:
+        if not tls_hostname and isinstance(connectable, TCPConnectable):
+            tls_hostname = str(connectable.host)
+
+        connectable = TLSConnectable(
+            connectable,
+            ssl_context=ssl_context,
+            hostname=tls_hostname,
+            standard_compatible=tls_standard_compatible,
+        )
+
+    return connectable

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_streams.py

@@ -0,0 +1,52 @@
+from __future__ import annotations
+
+import math
+from typing import TypeVar
+from warnings import warn
+
+from ..streams.memory import (
+    MemoryObjectReceiveStream,
+    MemoryObjectSendStream,
+    _MemoryObjectStreamState,
+)
+
+T_Item = TypeVar("T_Item")
+
+
+class create_memory_object_stream(
+    tuple[MemoryObjectSendStream[T_Item], MemoryObjectReceiveStream[T_Item]],
+):
+    """
+    Create a memory object stream.
+
+    The stream's item type can be annotated like
+    :func:`create_memory_object_stream[T_Item]`.
+
+    :param max_buffer_size: number of items held in the buffer until ``send()`` starts
+        blocking
+    :param item_type: old way of marking the streams with the right generic type for
+        static typing (does nothing on AnyIO 4)
+
+        .. deprecated:: 4.0
+          Use ``create_memory_object_stream[YourItemType](...)`` instead.
+    :return: a tuple of (send stream, receive stream)
+
+    """
+
+    def __new__(  # type: ignore[misc]
+        cls, max_buffer_size: float = 0, item_type: object = None
+    ) -> tuple[MemoryObjectSendStream[T_Item], MemoryObjectReceiveStream[T_Item]]:
+        if max_buffer_size != math.inf and not isinstance(max_buffer_size, int):
+            raise ValueError("max_buffer_size must be either an integer or math.inf")
+        if max_buffer_size < 0:
+            raise ValueError("max_buffer_size cannot be negative")
+        if item_type is not None:
+            warn(
+                "The item_type argument has been deprecated in AnyIO 4.0. "
+                "Use create_memory_object_stream[YourItemType](...) instead.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+
+        state = _MemoryObjectStreamState[T_Item](max_buffer_size)
+        return (MemoryObjectSendStream(state), MemoryObjectReceiveStream(state))

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_subprocesses.py

@@ -0,0 +1,196 @@
+from __future__ import annotations
+
+from collections.abc import AsyncIterable, Iterable, Mapping, Sequence
+from io import BytesIO
+from os import PathLike
+from subprocess import PIPE, CalledProcessError, CompletedProcess
+from typing import IO, Any, TypeAlias, cast
+
+from ..abc import Process
+from ._eventloop import get_async_backend
+from ._tasks import create_task_group
+
+StrOrBytesPath: TypeAlias = str | bytes | PathLike[str] | PathLike[bytes]
+
+
+async def run_process(
+    command: StrOrBytesPath | Sequence[StrOrBytesPath],
+    *,
+    input: bytes | None = None,
+    stdin: int | IO[Any] | None = None,
+    stdout: int | IO[Any] | None = PIPE,
+    stderr: int | IO[Any] | None = PIPE,
+    check: bool = True,
+    cwd: StrOrBytesPath | None = None,
+    env: Mapping[str, str] | None = None,
+    startupinfo: Any = None,
+    creationflags: int = 0,
+    start_new_session: bool = False,
+    pass_fds: Sequence[int] = (),
+    user: str | int | None = None,
+    group: str | int | None = None,
+    extra_groups: Iterable[str | int] | None = None,
+    umask: int = -1,
+) -> CompletedProcess[bytes]:
+    """
+    Run an external command in a subprocess and wait until it completes.
+
+    .. seealso:: :func:`subprocess.run`
+
+    :param command: either a string to pass to the shell, or an iterable of strings
+        containing the executable name or path and its arguments
+    :param input: bytes passed to the standard input of the subprocess
+    :param stdin: one of :data:`subprocess.PIPE`, :data:`subprocess.DEVNULL`,
+        a file-like object, or `None`; ``input`` overrides this
+    :param stdout: one of :data:`subprocess.PIPE`, :data:`subprocess.DEVNULL`,
+        a file-like object, or `None`
+    :param stderr: one of :data:`subprocess.PIPE`, :data:`subprocess.DEVNULL`,
+        :data:`subprocess.STDOUT`, a file-like object, or `None`
+    :param check: if ``True``, raise :exc:`~subprocess.CalledProcessError` if the
+        process terminates with a return code other than 0
+    :param cwd: If not ``None``, change the working directory to this before running the
+        command
+    :param env: if not ``None``, this mapping replaces the inherited environment
+        variables from the parent process
+    :param startupinfo: an instance of :class:`subprocess.STARTUPINFO` that can be used
+        to specify process startup parameters (Windows only)
+    :param creationflags: flags that can be used to control the creation of the
+        subprocess (see :class:`subprocess.Popen` for the specifics)
+    :param start_new_session: if ``true`` the setsid() system call will be made in the
+        child process prior to the execution of the subprocess. (POSIX only)
+    :param pass_fds: sequence of file descriptors to keep open between the parent and
+        child processes. (POSIX only)
+    :param user: effective user to run the process as (Python >= 3.9, POSIX only)
+    :param group: effective group to run the process as (Python >= 3.9, POSIX only)
+    :param extra_groups: supplementary groups to set in the subprocess (Python >= 3.9,
+        POSIX only)
+    :param umask: if not negative, this umask is applied in the child process before
+        running the given command (Python >= 3.9, POSIX only)
+    :return: an object representing the completed process
+    :raises ~subprocess.CalledProcessError: if ``check`` is ``True`` and the process
+        exits with a nonzero return code
+
+    """
+
+    async def drain_stream(stream: AsyncIterable[bytes], index: int) -> None:
+        buffer = BytesIO()
+        async for chunk in stream:
+            buffer.write(chunk)
+
+        stream_contents[index] = buffer.getvalue()
+
+    if stdin is not None and input is not None:
+        raise ValueError("only one of stdin and input is allowed")
+
+    async with await open_process(
+        command,
+        stdin=PIPE if input else stdin,
+        stdout=stdout,
+        stderr=stderr,
+        cwd=cwd,
+        env=env,
+        startupinfo=startupinfo,
+        creationflags=creationflags,
+        start_new_session=start_new_session,
+        pass_fds=pass_fds,
+        user=user,
+        group=group,
+        extra_groups=extra_groups,
+        umask=umask,
+    ) as process:
+        stream_contents: list[bytes | None] = [None, None]
+        async with create_task_group() as tg:
+            if process.stdout:
+                tg.start_soon(drain_stream, process.stdout, 0)
+
+            if process.stderr:
+                tg.start_soon(drain_stream, process.stderr, 1)
+
+            if process.stdin and input:
+                await process.stdin.send(input)
+                await process.stdin.aclose()
+
+            await process.wait()
+
+    output, errors = stream_contents
+    if check and process.returncode != 0:
+        raise CalledProcessError(cast(int, process.returncode), command, output, errors)
+
+    return CompletedProcess(command, cast(int, process.returncode), output, errors)
+
+
+async def open_process(
+    command: StrOrBytesPath | Sequence[StrOrBytesPath],
+    *,
+    stdin: int | IO[Any] | None = PIPE,
+    stdout: int | IO[Any] | None = PIPE,
+    stderr: int | IO[Any] | None = PIPE,
+    cwd: StrOrBytesPath | None = None,
+    env: Mapping[str, str] | None = None,
+    startupinfo: Any = None,
+    creationflags: int = 0,
+    start_new_session: bool = False,
+    pass_fds: Sequence[int] = (),
+    user: str | int | None = None,
+    group: str | int | None = None,
+    extra_groups: Iterable[str | int] | None = None,
+    umask: int = -1,
+) -> Process:
+    """
+    Start an external command in a subprocess.
+
+    .. seealso:: :class:`subprocess.Popen`
+
+    :param command: either a string to pass to the shell, or an iterable of strings
+        containing the executable name or path and its arguments
+    :param stdin: one of :data:`subprocess.PIPE`, :data:`subprocess.DEVNULL`, a
+        file-like object, or ``None``
+    :param stdout: one of :data:`subprocess.PIPE`, :data:`subprocess.DEVNULL`,
+        a file-like object, or ``None``
+    :param stderr: one of :data:`subprocess.PIPE`, :data:`subprocess.DEVNULL`,
+        :data:`subprocess.STDOUT`, a file-like object, or ``None``
+    :param cwd: If not ``None``, the working directory is changed before executing
+    :param env: If env is not ``None``, it must be a mapping that defines the
+        environment variables for the new process
+    :param creationflags: flags that can be used to control the creation of the
+        subprocess (see :class:`subprocess.Popen` for the specifics)
+    :param startupinfo: an instance of :class:`subprocess.STARTUPINFO` that can be used
+        to specify process startup parameters (Windows only)
+    :param start_new_session: if ``true`` the setsid() system call will be made in the
+        child process prior to the execution of the subprocess. (POSIX only)
+    :param pass_fds: sequence of file descriptors to keep open between the parent and
+        child processes. (POSIX only)
+    :param user: effective user to run the process as (POSIX only)
+    :param group: effective group to run the process as (POSIX only)
+    :param extra_groups: supplementary groups to set in the subprocess (POSIX only)
+    :param umask: if not negative, this umask is applied in the child process before
+        running the given command (POSIX only)
+    :return: an asynchronous process object
+
+    """
+    kwargs: dict[str, Any] = {}
+    if user is not None:
+        kwargs["user"] = user
+
+    if group is not None:
+        kwargs["group"] = group
+
+    if extra_groups is not None:
+        kwargs["extra_groups"] = group
+
+    if umask >= 0:
+        kwargs["umask"] = umask
+
+    return await get_async_backend().open_process(
+        command,
+        stdin=stdin,
+        stdout=stdout,
+        stderr=stderr,
+        cwd=cwd,
+        env=env,
+        startupinfo=startupinfo,
+        creationflags=creationflags,
+        start_new_session=start_new_session,
+        pass_fds=pass_fds,
+        **kwargs,
+    )

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_synchronization.py

@@ -0,0 +1,757 @@
+from __future__ import annotations
+
+import math
+from collections import deque
+from collections.abc import Callable
+from dataclasses import dataclass
+from types import TracebackType
+from typing import TypeVar
+
+from ..lowlevel import checkpoint_if_cancelled
+from ._eventloop import get_async_backend
+from ._exceptions import BusyResourceError, NoEventLoopError
+from ._tasks import CancelScope
+from ._testing import TaskInfo, get_current_task
+
+T = TypeVar("T")
+
+
+@dataclass(frozen=True)
+class EventStatistics:
+    """
+    :ivar int tasks_waiting: number of tasks waiting on :meth:`~.Event.wait`
+    """
+
+    tasks_waiting: int
+
+
+@dataclass(frozen=True)
+class CapacityLimiterStatistics:
+    """
+    :ivar int borrowed_tokens: number of tokens currently borrowed by tasks
+    :ivar float total_tokens: total number of available tokens
+    :ivar tuple borrowers: tasks or other objects currently holding tokens borrowed from
+        this limiter
+    :ivar int tasks_waiting: number of tasks waiting on
+        :meth:`~.CapacityLimiter.acquire` or
+        :meth:`~.CapacityLimiter.acquire_on_behalf_of`
+    """
+
+    borrowed_tokens: int
+    total_tokens: float
+    borrowers: tuple[object, ...]
+    tasks_waiting: int
+
+
+@dataclass(frozen=True)
+class LockStatistics:
+    """
+    :ivar bool locked: flag indicating if this lock is locked or not
+    :ivar ~anyio.TaskInfo owner: task currently holding the lock (or ``None`` if the
+        lock is not held by any task)
+    :ivar int tasks_waiting: number of tasks waiting on :meth:`~.Lock.acquire`
+    """
+
+    locked: bool
+    owner: TaskInfo | None
+    tasks_waiting: int
+
+
+@dataclass(frozen=True)
+class ConditionStatistics:
+    """
+    :ivar int tasks_waiting: number of tasks blocked on :meth:`~.Condition.wait`
+    :ivar ~anyio.LockStatistics lock_statistics: statistics of the underlying
+        :class:`~.Lock`
+    """
+
+    tasks_waiting: int
+    lock_statistics: LockStatistics
+
+
+@dataclass(frozen=True)
+class SemaphoreStatistics:
+    """
+    :ivar int tasks_waiting: number of tasks waiting on :meth:`~.Semaphore.acquire`
+
+    """
+
+    tasks_waiting: int
+
+
+class Event:
+    def __new__(cls) -> Event:
+        try:
+            return get_async_backend().create_event()
+        except NoEventLoopError:
+            return EventAdapter()
+
+    def set(self) -> None:
+        """Set the flag, notifying all listeners."""
+        raise NotImplementedError
+
+    def is_set(self) -> bool:
+        """Return ``True`` if the flag is set, ``False`` if not."""
+        raise NotImplementedError
+
+    async def wait(self) -> None:
+        """
+        Wait until the flag has been set.
+
+        If the flag has already been set when this method is called, it returns
+        immediately.
+
+        """
+        raise NotImplementedError
+
+    def statistics(self) -> EventStatistics:
+        """Return statistics about the current state of this event."""
+        raise NotImplementedError
+
+
+class EventAdapter(Event):
+    _internal_event: Event | None = None
+    _is_set: bool = False
+
+    def __new__(cls) -> EventAdapter:
+        return object.__new__(cls)
+
+    @property
+    def _event(self) -> Event:
+        if self._internal_event is None:
+            self._internal_event = get_async_backend().create_event()
+            if self._is_set:
+                self._internal_event.set()
+
+        return self._internal_event
+
+    def set(self) -> None:
+        if self._internal_event is None:
+            self._is_set = True
+        else:
+            self._event.set()
+
+    def is_set(self) -> bool:
+        if self._internal_event is None:
+            return self._is_set
+
+        return self._internal_event.is_set()
+
+    async def wait(self) -> None:
+        await self._event.wait()
+
+    def statistics(self) -> EventStatistics:
+        if self._internal_event is None:
+            return EventStatistics(tasks_waiting=0)
+
+        return self._internal_event.statistics()
+
+
+class Lock:
+    def __new__(cls, *, fast_acquire: bool = False) -> Lock:
+        try:
+            return get_async_backend().create_lock(fast_acquire=fast_acquire)
+        except NoEventLoopError:
+            return LockAdapter(fast_acquire=fast_acquire)
+
+    async def __aenter__(self) -> None:
+        await self.acquire()
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        self.release()
+
+    async def acquire(self) -> None:
+        """Acquire the lock."""
+        raise NotImplementedError
+
+    def acquire_nowait(self) -> None:
+        """
+        Acquire the lock, without blocking.
+
+        :raises ~anyio.WouldBlock: if the operation would block
+
+        """
+        raise NotImplementedError
+
+    def release(self) -> None:
+        """Release the lock."""
+        raise NotImplementedError
+
+    def locked(self) -> bool:
+        """Return True if the lock is currently held."""
+        raise NotImplementedError
+
+    def statistics(self) -> LockStatistics:
+        """
+        Return statistics about the current state of this lock.
+
+        .. versionadded:: 3.0
+        """
+        raise NotImplementedError
+
+
+class LockAdapter(Lock):
+    _internal_lock: Lock | None = None
+
+    def __new__(cls, *, fast_acquire: bool = False) -> LockAdapter:
+        return object.__new__(cls)
+
+    def __init__(self, *, fast_acquire: bool = False):
+        self._fast_acquire = fast_acquire
+
+    @property
+    def _lock(self) -> Lock:
+        if self._internal_lock is None:
+            self._internal_lock = get_async_backend().create_lock(
+                fast_acquire=self._fast_acquire
+            )
+
+        return self._internal_lock
+
+    async def __aenter__(self) -> None:
+        await self._lock.acquire()
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        if self._internal_lock is not None:
+            self._internal_lock.release()
+
+    async def acquire(self) -> None:
+        """Acquire the lock."""
+        await self._lock.acquire()
+
+    def acquire_nowait(self) -> None:
+        """
+        Acquire the lock, without blocking.
+
+        :raises ~anyio.WouldBlock: if the operation would block
+
+        """
+        self._lock.acquire_nowait()
+
+    def release(self) -> None:
+        """Release the lock."""
+        self._lock.release()
+
+    def locked(self) -> bool:
+        """Return True if the lock is currently held."""
+        return self._lock.locked()
+
+    def statistics(self) -> LockStatistics:
+        """
+        Return statistics about the current state of this lock.
+
+        .. versionadded:: 3.0
+
+        """
+        if self._internal_lock is None:
+            return LockStatistics(False, None, 0)
+
+        return self._internal_lock.statistics()
+
+
+class Condition:
+    _owner_task: TaskInfo | None = None
+
+    def __init__(self, lock: Lock | None = None):
+        self._lock = lock or Lock()
+        self._waiters: deque[Event] = deque()
+
+    async def __aenter__(self) -> None:
+        await self.acquire()
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        self.release()
+
+    def _check_acquired(self) -> None:
+        if self._owner_task != get_current_task():
+            raise RuntimeError("The current task is not holding the underlying lock")
+
+    async def acquire(self) -> None:
+        """Acquire the underlying lock."""
+        await self._lock.acquire()
+        self._owner_task = get_current_task()
+
+    def acquire_nowait(self) -> None:
+        """
+        Acquire the underlying lock, without blocking.
+
+        :raises ~anyio.WouldBlock: if the operation would block
+
+        """
+        self._lock.acquire_nowait()
+        self._owner_task = get_current_task()
+
+    def release(self) -> None:
+        """Release the underlying lock."""
+        self._lock.release()
+
+    def locked(self) -> bool:
+        """Return True if the lock is set."""
+        return self._lock.locked()
+
+    def notify(self, n: int = 1) -> None:
+        """Notify exactly n listeners."""
+        self._check_acquired()
+        for _ in range(n):
+            try:
+                event = self._waiters.popleft()
+            except IndexError:
+                break
+
+            event.set()
+
+    def notify_all(self) -> None:
+        """Notify all the listeners."""
+        self._check_acquired()
+        for event in self._waiters:
+            event.set()
+
+        self._waiters.clear()
+
+    async def wait(self) -> None:
+        """Wait for a notification."""
+        await checkpoint_if_cancelled()
+        self._check_acquired()
+        event = Event()
+        self._waiters.append(event)
+        self.release()
+        try:
+            await event.wait()
+        except BaseException:
+            if not event.is_set():
+                self._waiters.remove(event)
+            elif self._waiters:
+                # This task was notified by could not act on it, so pass
+                # it on to the next task
+                self._waiters.popleft().set()
+
+            raise
+        finally:
+            with CancelScope(shield=True):
+                await self.acquire()
+
+    async def wait_for(self, predicate: Callable[[], T]) -> T:
+        """
+        Wait until a predicate becomes true.
+
+        :param predicate: a callable that returns a truthy value when the condition is
+            met
+        :return: the result of the predicate
+
+        .. versionadded:: 4.11.0
+
+        """
+        while not (result := predicate()):
+            await self.wait()
+
+        return result
+
+    def statistics(self) -> ConditionStatistics:
+        """
+        Return statistics about the current state of this condition.
+
+        .. versionadded:: 3.0
+        """
+        return ConditionStatistics(len(self._waiters), self._lock.statistics())
+
+
+class Semaphore:
+    def __new__(
+        cls,
+        initial_value: int,
+        *,
+        max_value: int | None = None,
+        fast_acquire: bool = False,
+    ) -> Semaphore:
+        try:
+            return get_async_backend().create_semaphore(
+                initial_value, max_value=max_value, fast_acquire=fast_acquire
+            )
+        except NoEventLoopError:
+            return SemaphoreAdapter(initial_value, max_value=max_value)
+
+    def __init__(
+        self,
+        initial_value: int,
+        *,
+        max_value: int | None = None,
+        fast_acquire: bool = False,
+    ):
+        if not isinstance(initial_value, int):
+            raise TypeError("initial_value must be an integer")
+        if initial_value < 0:
+            raise ValueError("initial_value must be >= 0")
+        if max_value is not None:
+            if not isinstance(max_value, int):
+                raise TypeError("max_value must be an integer or None")
+            if max_value < initial_value:
+                raise ValueError(
+                    "max_value must be equal to or higher than initial_value"
+                )
+
+        self._fast_acquire = fast_acquire
+
+    async def __aenter__(self) -> Semaphore:
+        await self.acquire()
+        return self
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        self.release()
+
+    async def acquire(self) -> None:
+        """Decrement the semaphore value, blocking if necessary."""
+        raise NotImplementedError
+
+    def acquire_nowait(self) -> None:
+        """
+        Acquire the underlying lock, without blocking.
+
+        :raises ~anyio.WouldBlock: if the operation would block
+
+        """
+        raise NotImplementedError
+
+    def release(self) -> None:
+        """Increment the semaphore value."""
+        raise NotImplementedError
+
+    @property
+    def value(self) -> int:
+        """The current value of the semaphore."""
+        raise NotImplementedError
+
+    @property
+    def max_value(self) -> int | None:
+        """The maximum value of the semaphore."""
+        raise NotImplementedError
+
+    def statistics(self) -> SemaphoreStatistics:
+        """
+        Return statistics about the current state of this semaphore.
+
+        .. versionadded:: 3.0
+        """
+        raise NotImplementedError
+
+
+class SemaphoreAdapter(Semaphore):
+    _internal_semaphore: Semaphore | None = None
+
+    def __new__(
+        cls,
+        initial_value: int,
+        *,
+        max_value: int | None = None,
+        fast_acquire: bool = False,
+    ) -> SemaphoreAdapter:
+        return object.__new__(cls)
+
+    def __init__(
+        self,
+        initial_value: int,
+        *,
+        max_value: int | None = None,
+        fast_acquire: bool = False,
+    ) -> None:
+        super().__init__(initial_value, max_value=max_value, fast_acquire=fast_acquire)
+        self._initial_value = initial_value
+        self._max_value = max_value
+
+    @property
+    def _semaphore(self) -> Semaphore:
+        if self._internal_semaphore is None:
+            self._internal_semaphore = get_async_backend().create_semaphore(
+                self._initial_value, max_value=self._max_value
+            )
+
+        return self._internal_semaphore
+
+    async def acquire(self) -> None:
+        await self._semaphore.acquire()
+
+    def acquire_nowait(self) -> None:
+        self._semaphore.acquire_nowait()
+
+    def release(self) -> None:
+        self._semaphore.release()
+
+    @property
+    def value(self) -> int:
+        if self._internal_semaphore is None:
+            return self._initial_value
+
+        return self._semaphore.value
+
+    @property
+    def max_value(self) -> int | None:
+        return self._max_value
+
+    def statistics(self) -> SemaphoreStatistics:
+        if self._internal_semaphore is None:
+            return SemaphoreStatistics(tasks_waiting=0)
+
+        return self._semaphore.statistics()
+
+
+class CapacityLimiter:
+    def __new__(cls, total_tokens: float) -> CapacityLimiter:
+        try:
+            return get_async_backend().create_capacity_limiter(total_tokens)
+        except NoEventLoopError:
+            return CapacityLimiterAdapter(total_tokens)
+
+    async def __aenter__(self) -> None:
+        raise NotImplementedError
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        raise NotImplementedError
+
+    @property
+    def total_tokens(self) -> float:
+        """
+        The total number of tokens available for borrowing.
+
+        This is a read-write property. If the total number of tokens is increased, the
+        proportionate number of tasks waiting on this limiter will be granted their
+        tokens.
+
+        .. versionchanged:: 3.0
+            The property is now writable.
+        .. versionchanged:: 4.12
+            The value can now be set to 0.
+
+        """
+        raise NotImplementedError
+
+    @total_tokens.setter
+    def total_tokens(self, value: float) -> None:
+        raise NotImplementedError
+
+    @property
+    def borrowed_tokens(self) -> int:
+        """The number of tokens that have currently been borrowed."""
+        raise NotImplementedError
+
+    @property
+    def available_tokens(self) -> float:
+        """The number of tokens currently available to be borrowed"""
+        raise NotImplementedError
+
+    def acquire_nowait(self) -> None:
+        """
+        Acquire a token for the current task without waiting for one to become
+        available.
+
+        :raises ~anyio.WouldBlock: if there are no tokens available for borrowing
+
+        """
+        raise NotImplementedError
+
+    def acquire_on_behalf_of_nowait(self, borrower: object) -> None:
+        """
+        Acquire a token without waiting for one to become available.
+
+        :param borrower: the entity borrowing a token
+        :raises ~anyio.WouldBlock: if there are no tokens available for borrowing
+
+        """
+        raise NotImplementedError
+
+    async def acquire(self) -> None:
+        """
+        Acquire a token for the current task, waiting if necessary for one to become
+        available.
+
+        """
+        raise NotImplementedError
+
+    async def acquire_on_behalf_of(self, borrower: object) -> None:
+        """
+        Acquire a token, waiting if necessary for one to become available.
+
+        :param borrower: the entity borrowing a token
+
+        """
+        raise NotImplementedError
+
+    def release(self) -> None:
+        """
+        Release the token held by the current task.
+
+        :raises RuntimeError: if the current task has not borrowed a token from this
+            limiter.
+
+        """
+        raise NotImplementedError
+
+    def release_on_behalf_of(self, borrower: object) -> None:
+        """
+        Release the token held by the given borrower.
+
+        :raises RuntimeError: if the borrower has not borrowed a token from this
+            limiter.
+
+        """
+        raise NotImplementedError
+
+    def statistics(self) -> CapacityLimiterStatistics:
+        """
+        Return statistics about the current state of this limiter.
+
+        .. versionadded:: 3.0
+
+        """
+        raise NotImplementedError
+
+
+class CapacityLimiterAdapter(CapacityLimiter):
+    _internal_limiter: CapacityLimiter | None = None
+
+    def __new__(cls, total_tokens: float) -> CapacityLimiterAdapter:
+        return object.__new__(cls)
+
+    def __init__(self, total_tokens: float) -> None:
+        self.total_tokens = total_tokens
+
+    @property
+    def _limiter(self) -> CapacityLimiter:
+        if self._internal_limiter is None:
+            self._internal_limiter = get_async_backend().create_capacity_limiter(
+                self._total_tokens
+            )
+
+        return self._internal_limiter
+
+    async def __aenter__(self) -> None:
+        await self._limiter.__aenter__()
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        return await self._limiter.__aexit__(exc_type, exc_val, exc_tb)
+
+    @property
+    def total_tokens(self) -> float:
+        if self._internal_limiter is None:
+            return self._total_tokens
+
+        return self._internal_limiter.total_tokens
+
+    @total_tokens.setter
+    def total_tokens(self, value: float) -> None:
+        if not isinstance(value, int) and value is not math.inf:
+            raise TypeError("total_tokens must be an int or math.inf")
+        elif value < 1:
+            raise ValueError("total_tokens must be >= 1")
+
+        if self._internal_limiter is None:
+            self._total_tokens = value
+            return
+
+        self._limiter.total_tokens = value
+
+    @property
+    def borrowed_tokens(self) -> int:
+        if self._internal_limiter is None:
+            return 0
+
+        return self._internal_limiter.borrowed_tokens
+
+    @property
+    def available_tokens(self) -> float:
+        if self._internal_limiter is None:
+            return self._total_tokens
+
+        return self._internal_limiter.available_tokens
+
+    def acquire_nowait(self) -> None:
+        self._limiter.acquire_nowait()
+
+    def acquire_on_behalf_of_nowait(self, borrower: object) -> None:
+        self._limiter.acquire_on_behalf_of_nowait(borrower)
+
+    async def acquire(self) -> None:
+        await self._limiter.acquire()
+
+    async def acquire_on_behalf_of(self, borrower: object) -> None:
+        await self._limiter.acquire_on_behalf_of(borrower)
+
+    def release(self) -> None:
+        self._limiter.release()
+
+    def release_on_behalf_of(self, borrower: object) -> None:
+        self._limiter.release_on_behalf_of(borrower)
+
+    def statistics(self) -> CapacityLimiterStatistics:
+        if self._internal_limiter is None:
+            return CapacityLimiterStatistics(
+                borrowed_tokens=0,
+                total_tokens=self.total_tokens,
+                borrowers=(),
+                tasks_waiting=0,
+            )
+
+        return self._internal_limiter.statistics()
+
+
+class ResourceGuard:
+    """
+    A context manager for ensuring that a resource is only used by a single task at a
+    time.
+
+    Entering this context manager while the previous has not exited it yet will trigger
+    :exc:`BusyResourceError`.
+
+    :param action: the action to guard against (visible in the :exc:`BusyResourceError`
+        when triggered, e.g. "Another task is already {action} this resource")
+
+    .. versionadded:: 4.1
+    """
+
+    __slots__ = "action", "_guarded"
+
+    def __init__(self, action: str = "using"):
+        self.action: str = action
+        self._guarded = False
+
+    def __enter__(self) -> None:
+        if self._guarded:
+            raise BusyResourceError(self.action)
+
+        self._guarded = True
+
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        self._guarded = False

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_tasks.py

@@ -0,0 +1,173 @@
+from __future__ import annotations
+
+import math
+from collections.abc import Generator
+from contextlib import contextmanager
+from types import TracebackType
+
+from ..abc._tasks import TaskGroup, TaskStatus
+from ._eventloop import get_async_backend
+
+
+class _IgnoredTaskStatus(TaskStatus[object]):
+    def started(self, value: object = None) -> None:
+        pass
+
+
+TASK_STATUS_IGNORED = _IgnoredTaskStatus()
+
+
+class CancelScope:
+    """
+    Wraps a unit of work that can be made separately cancellable.
+
+    :param deadline: The time (clock value) when this scope is cancelled automatically
+    :param shield: ``True`` to shield the cancel scope from external cancellation
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+    """
+
+    def __new__(
+        cls, *, deadline: float = math.inf, shield: bool = False
+    ) -> CancelScope:
+        return get_async_backend().create_cancel_scope(shield=shield, deadline=deadline)
+
+    def cancel(self, reason: str | None = None) -> None:
+        """
+        Cancel this scope immediately.
+
+        :param reason: a message describing the reason for the cancellation
+
+        """
+        raise NotImplementedError
+
+    @property
+    def deadline(self) -> float:
+        """
+        The time (clock value) when this scope is cancelled automatically.
+
+        Will be ``float('inf')`` if no timeout has been set.
+
+        """
+        raise NotImplementedError
+
+    @deadline.setter
+    def deadline(self, value: float) -> None:
+        raise NotImplementedError
+
+    @property
+    def cancel_called(self) -> bool:
+        """``True`` if :meth:`cancel` has been called."""
+        raise NotImplementedError
+
+    @property
+    def cancelled_caught(self) -> bool:
+        """
+        ``True`` if this scope suppressed a cancellation exception it itself raised.
+
+        This is typically used to check if any work was interrupted, or to see if the
+        scope was cancelled due to its deadline being reached. The value will, however,
+        only be ``True`` if the cancellation was triggered by the scope itself (and not
+        an outer scope).
+
+        """
+        raise NotImplementedError
+
+    @property
+    def shield(self) -> bool:
+        """
+        ``True`` if this scope is shielded from external cancellation.
+
+        While a scope is shielded, it will not receive cancellations from outside.
+
+        """
+        raise NotImplementedError
+
+    @shield.setter
+    def shield(self, value: bool) -> None:
+        raise NotImplementedError
+
+    def __enter__(self) -> CancelScope:
+        raise NotImplementedError
+
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> bool:
+        raise NotImplementedError
+
+
+@contextmanager
+def fail_after(
+    delay: float | None, shield: bool = False
+) -> Generator[CancelScope, None, None]:
+    """
+    Create a context manager which raises a :class:`TimeoutError` if does not finish in
+    time.
+
+    :param delay: maximum allowed time (in seconds) before raising the exception, or
+        ``None`` to disable the timeout
+    :param shield: ``True`` to shield the cancel scope from external cancellation
+    :return: a context manager that yields a cancel scope
+    :rtype: :class:`~typing.ContextManager`\\[:class:`~anyio.CancelScope`\\]
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    current_time = get_async_backend().current_time
+    deadline = (current_time() + delay) if delay is not None else math.inf
+    with get_async_backend().create_cancel_scope(
+        deadline=deadline, shield=shield
+    ) as cancel_scope:
+        yield cancel_scope
+
+    if cancel_scope.cancelled_caught and current_time() >= cancel_scope.deadline:
+        raise TimeoutError
+
+
+def move_on_after(delay: float | None, shield: bool = False) -> CancelScope:
+    """
+    Create a cancel scope with a deadline that expires after the given delay.
+
+    :param delay: maximum allowed time (in seconds) before exiting the context block, or
+        ``None`` to disable the timeout
+    :param shield: ``True`` to shield the cancel scope from external cancellation
+    :return: a cancel scope
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    deadline = (
+        (get_async_backend().current_time() + delay) if delay is not None else math.inf
+    )
+    return get_async_backend().create_cancel_scope(deadline=deadline, shield=shield)
+
+
+def current_effective_deadline() -> float:
+    """
+    Return the nearest deadline among all the cancel scopes effective for the current
+    task.
+
+    :return: a clock value from the event loop's internal clock (or ``float('inf')`` if
+        there is no deadline in effect, or ``float('-inf')`` if the current scope has
+        been cancelled)
+    :rtype: float
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    return get_async_backend().current_effective_deadline()
+
+
+def create_task_group() -> TaskGroup:
+    """
+    Create a task group.
+
+    :return: a task group
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    return get_async_backend().create_task_group()

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_tempfile.py

@@ -0,0 +1,613 @@
+from __future__ import annotations
+
+import os
+import sys
+import tempfile
+from collections.abc import Iterable
+from io import BytesIO, TextIOWrapper
+from types import TracebackType
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    AnyStr,
+    Generic,
+    overload,
+)
+
+from .. import to_thread
+from .._core._fileio import AsyncFile
+from ..lowlevel import checkpoint_if_cancelled
+
+if TYPE_CHECKING:
+    from _typeshed import OpenBinaryMode, OpenTextMode, ReadableBuffer, WriteableBuffer
+
+
+class TemporaryFile(Generic[AnyStr]):
+    """
+    An asynchronous temporary file that is automatically created and cleaned up.
+
+    This class provides an asynchronous context manager interface to a temporary file.
+    The file is created using Python's standard `tempfile.TemporaryFile` function in a
+    background thread, and is wrapped as an asynchronous file using `AsyncFile`.
+
+    :param mode: The mode in which the file is opened. Defaults to "w+b".
+    :param buffering: The buffering policy (-1 means the default buffering).
+    :param encoding: The encoding used to decode or encode the file. Only applicable in
+        text mode.
+    :param newline: Controls how universal newlines mode works (only applicable in text
+        mode).
+    :param suffix: The suffix for the temporary file name.
+    :param prefix: The prefix for the temporary file name.
+    :param dir: The directory in which the temporary file is created.
+    :param errors: The error handling scheme used for encoding/decoding errors.
+    """
+
+    _async_file: AsyncFile[AnyStr]
+
+    @overload
+    def __init__(
+        self: TemporaryFile[bytes],
+        mode: OpenBinaryMode = ...,
+        buffering: int = ...,
+        encoding: str | None = ...,
+        newline: str | None = ...,
+        suffix: str | None = ...,
+        prefix: str | None = ...,
+        dir: str | None = ...,
+        *,
+        errors: str | None = ...,
+    ): ...
+    @overload
+    def __init__(
+        self: TemporaryFile[str],
+        mode: OpenTextMode,
+        buffering: int = ...,
+        encoding: str | None = ...,
+        newline: str | None = ...,
+        suffix: str | None = ...,
+        prefix: str | None = ...,
+        dir: str | None = ...,
+        *,
+        errors: str | None = ...,
+    ): ...
+
+    def __init__(
+        self,
+        mode: OpenTextMode | OpenBinaryMode = "w+b",
+        buffering: int = -1,
+        encoding: str | None = None,
+        newline: str | None = None,
+        suffix: str | None = None,
+        prefix: str | None = None,
+        dir: str | None = None,
+        *,
+        errors: str | None = None,
+    ) -> None:
+        self.mode = mode
+        self.buffering = buffering
+        self.encoding = encoding
+        self.newline = newline
+        self.suffix: str | None = suffix
+        self.prefix: str | None = prefix
+        self.dir: str | None = dir
+        self.errors = errors
+
+    async def __aenter__(self) -> AsyncFile[AnyStr]:
+        fp = await to_thread.run_sync(
+            lambda: tempfile.TemporaryFile(
+                self.mode,
+                self.buffering,
+                self.encoding,
+                self.newline,
+                self.suffix,
+                self.prefix,
+                self.dir,
+                errors=self.errors,
+            )
+        )
+        self._async_file = AsyncFile(fp)
+        return self._async_file
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_value: BaseException | None,
+        traceback: TracebackType | None,
+    ) -> None:
+        await self._async_file.aclose()
+
+
+class NamedTemporaryFile(Generic[AnyStr]):
+    """
+    An asynchronous named temporary file that is automatically created and cleaned up.
+
+    This class provides an asynchronous context manager for a temporary file with a
+    visible name in the file system. It uses Python's standard
+    :func:`~tempfile.NamedTemporaryFile` function and wraps the file object with
+    :class:`AsyncFile` for asynchronous operations.
+
+    :param mode: The mode in which the file is opened. Defaults to "w+b".
+    :param buffering: The buffering policy (-1 means the default buffering).
+    :param encoding: The encoding used to decode or encode the file. Only applicable in
+        text mode.
+    :param newline: Controls how universal newlines mode works (only applicable in text
+        mode).
+    :param suffix: The suffix for the temporary file name.
+    :param prefix: The prefix for the temporary file name.
+    :param dir: The directory in which the temporary file is created.
+    :param delete: Whether to delete the file when it is closed.
+    :param errors: The error handling scheme used for encoding/decoding errors.
+    :param delete_on_close: (Python 3.12+) Whether to delete the file on close.
+    """
+
+    _async_file: AsyncFile[AnyStr]
+
+    @overload
+    def __init__(
+        self: NamedTemporaryFile[bytes],
+        mode: OpenBinaryMode = ...,
+        buffering: int = ...,
+        encoding: str | None = ...,
+        newline: str | None = ...,
+        suffix: str | None = ...,
+        prefix: str | None = ...,
+        dir: str | None = ...,
+        delete: bool = ...,
+        *,
+        errors: str | None = ...,
+        delete_on_close: bool = ...,
+    ): ...
+    @overload
+    def __init__(
+        self: NamedTemporaryFile[str],
+        mode: OpenTextMode,
+        buffering: int = ...,
+        encoding: str | None = ...,
+        newline: str | None = ...,
+        suffix: str | None = ...,
+        prefix: str | None = ...,
+        dir: str | None = ...,
+        delete: bool = ...,
+        *,
+        errors: str | None = ...,
+        delete_on_close: bool = ...,
+    ): ...
+
+    def __init__(
+        self,
+        mode: OpenBinaryMode | OpenTextMode = "w+b",
+        buffering: int = -1,
+        encoding: str | None = None,
+        newline: str | None = None,
+        suffix: str | None = None,
+        prefix: str | None = None,
+        dir: str | None = None,
+        delete: bool = True,
+        *,
+        errors: str | None = None,
+        delete_on_close: bool = True,
+    ) -> None:
+        self._params: dict[str, Any] = {
+            "mode": mode,
+            "buffering": buffering,
+            "encoding": encoding,
+            "newline": newline,
+            "suffix": suffix,
+            "prefix": prefix,
+            "dir": dir,
+            "delete": delete,
+            "errors": errors,
+        }
+        if sys.version_info >= (3, 12):
+            self._params["delete_on_close"] = delete_on_close
+
+    async def __aenter__(self) -> AsyncFile[AnyStr]:
+        fp = await to_thread.run_sync(
+            lambda: tempfile.NamedTemporaryFile(**self._params)
+        )
+        self._async_file = AsyncFile(fp)
+        return self._async_file
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_value: BaseException | None,
+        traceback: TracebackType | None,
+    ) -> None:
+        await self._async_file.aclose()
+
+
+class SpooledTemporaryFile(AsyncFile[AnyStr]):
+    """
+    An asynchronous spooled temporary file that starts in memory and is spooled to disk.
+
+    This class provides an asynchronous interface to a spooled temporary file, much like
+    Python's standard :class:`~tempfile.SpooledTemporaryFile`. It supports asynchronous
+    write operations and provides a method to force a rollover to disk.
+
+    :param max_size: Maximum size in bytes before the file is rolled over to disk.
+    :param mode: The mode in which the file is opened. Defaults to "w+b".
+    :param buffering: The buffering policy (-1 means the default buffering).
+    :param encoding: The encoding used to decode or encode the file (text mode only).
+    :param newline: Controls how universal newlines mode works (text mode only).
+    :param suffix: The suffix for the temporary file name.
+    :param prefix: The prefix for the temporary file name.
+    :param dir: The directory in which the temporary file is created.
+    :param errors: The error handling scheme used for encoding/decoding errors.
+    """
+
+    _rolled: bool = False
+
+    @overload
+    def __init__(
+        self: SpooledTemporaryFile[bytes],
+        max_size: int = ...,
+        mode: OpenBinaryMode = ...,
+        buffering: int = ...,
+        encoding: str | None = ...,
+        newline: str | None = ...,
+        suffix: str | None = ...,
+        prefix: str | None = ...,
+        dir: str | None = ...,
+        *,
+        errors: str | None = ...,
+    ): ...
+    @overload
+    def __init__(
+        self: SpooledTemporaryFile[str],
+        max_size: int = ...,
+        mode: OpenTextMode = ...,
+        buffering: int = ...,
+        encoding: str | None = ...,
+        newline: str | None = ...,
+        suffix: str | None = ...,
+        prefix: str | None = ...,
+        dir: str | None = ...,
+        *,
+        errors: str | None = ...,
+    ): ...
+
+    def __init__(
+        self,
+        max_size: int = 0,
+        mode: OpenBinaryMode | OpenTextMode = "w+b",
+        buffering: int = -1,
+        encoding: str | None = None,
+        newline: str | None = None,
+        suffix: str | None = None,
+        prefix: str | None = None,
+        dir: str | None = None,
+        *,
+        errors: str | None = None,
+    ) -> None:
+        self._tempfile_params: dict[str, Any] = {
+            "mode": mode,
+            "buffering": buffering,
+            "encoding": encoding,
+            "newline": newline,
+            "suffix": suffix,
+            "prefix": prefix,
+            "dir": dir,
+            "errors": errors,
+        }
+        self._max_size = max_size
+        if "b" in mode:
+            super().__init__(BytesIO())  # type: ignore[arg-type]
+        else:
+            super().__init__(
+                TextIOWrapper(  # type: ignore[arg-type]
+                    BytesIO(),
+                    encoding=encoding,
+                    errors=errors,
+                    newline=newline,
+                    write_through=True,
+                )
+            )
+
+    async def aclose(self) -> None:
+        if not self._rolled:
+            self._fp.close()
+            return
+
+        await super().aclose()
+
+    async def _check(self) -> None:
+        if self._rolled or self._fp.tell() <= self._max_size:
+            return
+
+        await self.rollover()
+
+    async def rollover(self) -> None:
+        if self._rolled:
+            return
+
+        self._rolled = True
+        buffer = self._fp
+        buffer.seek(0)
+        self._fp = await to_thread.run_sync(
+            lambda: tempfile.TemporaryFile(**self._tempfile_params)
+        )
+        await self.write(buffer.read())
+        buffer.close()
+
+    @property
+    def closed(self) -> bool:
+        return self._fp.closed
+
+    async def read(self, size: int = -1) -> AnyStr:
+        if not self._rolled:
+            await checkpoint_if_cancelled()
+            return self._fp.read(size)
+
+        return await super().read(size)  # type: ignore[return-value]
+
+    async def read1(self: SpooledTemporaryFile[bytes], size: int = -1) -> bytes:
+        if not self._rolled:
+            await checkpoint_if_cancelled()
+            return self._fp.read1(size)
+
+        return await super().read1(size)
+
+    async def readline(self) -> AnyStr:
+        if not self._rolled:
+            await checkpoint_if_cancelled()
+            return self._fp.readline()
+
+        return await super().readline()  # type: ignore[return-value]
+
+    async def readlines(self) -> list[AnyStr]:
+        if not self._rolled:
+            await checkpoint_if_cancelled()
+            return self._fp.readlines()
+
+        return await super().readlines()  # type: ignore[return-value]
+
+    async def readinto(self: SpooledTemporaryFile[bytes], b: WriteableBuffer) -> int:
+        if not self._rolled:
+            await checkpoint_if_cancelled()
+            self._fp.readinto(b)
+
+        return await super().readinto(b)
+
+    async def readinto1(self: SpooledTemporaryFile[bytes], b: WriteableBuffer) -> int:
+        if not self._rolled:
+            await checkpoint_if_cancelled()
+            self._fp.readinto(b)
+
+        return await super().readinto1(b)
+
+    async def seek(self, offset: int, whence: int | None = os.SEEK_SET) -> int:
+        if not self._rolled:
+            await checkpoint_if_cancelled()
+            return self._fp.seek(offset, whence)
+
+        return await super().seek(offset, whence)
+
+    async def tell(self) -> int:
+        if not self._rolled:
+            await checkpoint_if_cancelled()
+            return self._fp.tell()
+
+        return await super().tell()
+
+    async def truncate(self, size: int | None = None) -> int:
+        if not self._rolled:
+            await checkpoint_if_cancelled()
+            return self._fp.truncate(size)
+
+        return await super().truncate(size)
+
+    @overload
+    async def write(self: SpooledTemporaryFile[bytes], b: ReadableBuffer) -> int: ...
+    @overload
+    async def write(self: SpooledTemporaryFile[str], b: str) -> int: ...
+
+    async def write(self, b: ReadableBuffer | str) -> int:
+        """
+        Asynchronously write data to the spooled temporary file.
+
+        If the file has not yet been rolled over, the data is written synchronously,
+        and a rollover is triggered if the size exceeds the maximum size.
+
+        :param s: The data to write.
+        :return: The number of bytes written.
+        :raises RuntimeError: If the underlying file is not initialized.
+
+        """
+        if not self._rolled:
+            await checkpoint_if_cancelled()
+            result = self._fp.write(b)
+            await self._check()
+            return result
+
+        return await super().write(b)  # type: ignore[misc]
+
+    @overload
+    async def writelines(
+        self: SpooledTemporaryFile[bytes], lines: Iterable[ReadableBuffer]
+    ) -> None: ...
+    @overload
+    async def writelines(
+        self: SpooledTemporaryFile[str], lines: Iterable[str]
+    ) -> None: ...
+
+    async def writelines(self, lines: Iterable[str] | Iterable[ReadableBuffer]) -> None:
+        """
+        Asynchronously write a list of lines to the spooled temporary file.
+
+        If the file has not yet been rolled over, the lines are written synchronously,
+        and a rollover is triggered if the size exceeds the maximum size.
+
+        :param lines: An iterable of lines to write.
+        :raises RuntimeError: If the underlying file is not initialized.
+
+        """
+        if not self._rolled:
+            await checkpoint_if_cancelled()
+            result = self._fp.writelines(lines)
+            await self._check()
+            return result
+
+        return await super().writelines(lines)  # type: ignore[misc]
+
+
+class TemporaryDirectory(Generic[AnyStr]):
+    """
+    An asynchronous temporary directory that is created and cleaned up automatically.
+
+    This class provides an asynchronous context manager for creating a temporary
+    directory. It wraps Python's standard :class:`~tempfile.TemporaryDirectory` to
+    perform directory creation and cleanup operations in a background thread.
+
+    :param suffix: Suffix to be added to the temporary directory name.
+    :param prefix: Prefix to be added to the temporary directory name.
+    :param dir: The parent directory where the temporary directory is created.
+    :param ignore_cleanup_errors: Whether to ignore errors during cleanup
+    :param delete: Whether to delete the directory upon closing (Python 3.12+).
+    """
+
+    def __init__(
+        self,
+        suffix: AnyStr | None = None,
+        prefix: AnyStr | None = None,
+        dir: AnyStr | None = None,
+        *,
+        ignore_cleanup_errors: bool = False,
+        delete: bool = True,
+    ) -> None:
+        self.suffix: AnyStr | None = suffix
+        self.prefix: AnyStr | None = prefix
+        self.dir: AnyStr | None = dir
+        self.ignore_cleanup_errors = ignore_cleanup_errors
+        self.delete = delete
+
+        self._tempdir: tempfile.TemporaryDirectory | None = None
+
+    async def __aenter__(self) -> str:
+        params: dict[str, Any] = {
+            "suffix": self.suffix,
+            "prefix": self.prefix,
+            "dir": self.dir,
+            "ignore_cleanup_errors": self.ignore_cleanup_errors,
+        }
+        if sys.version_info >= (3, 12):
+            params["delete"] = self.delete
+
+        self._tempdir = await to_thread.run_sync(
+            lambda: tempfile.TemporaryDirectory(**params)
+        )
+        return await to_thread.run_sync(self._tempdir.__enter__)
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_value: BaseException | None,
+        traceback: TracebackType | None,
+    ) -> None:
+        if self._tempdir is not None:
+            await to_thread.run_sync(
+                self._tempdir.__exit__, exc_type, exc_value, traceback
+            )
+
+    async def cleanup(self) -> None:
+        if self._tempdir is not None:
+            await to_thread.run_sync(self._tempdir.cleanup)
+
+
+@overload
+async def mkstemp(
+    suffix: str | None = None,
+    prefix: str | None = None,
+    dir: str | None = None,
+    text: bool = False,
+) -> tuple[int, str]: ...
+
+
+@overload
+async def mkstemp(
+    suffix: bytes | None = None,
+    prefix: bytes | None = None,
+    dir: bytes | None = None,
+    text: bool = False,
+) -> tuple[int, bytes]: ...
+
+
+async def mkstemp(
+    suffix: AnyStr | None = None,
+    prefix: AnyStr | None = None,
+    dir: AnyStr | None = None,
+    text: bool = False,
+) -> tuple[int, str | bytes]:
+    """
+    Asynchronously create a temporary file and return an OS-level handle and the file
+    name.
+
+    This function wraps `tempfile.mkstemp` and executes it in a background thread.
+
+    :param suffix: Suffix to be added to the file name.
+    :param prefix: Prefix to be added to the file name.
+    :param dir: Directory in which the temporary file is created.
+    :param text: Whether the file is opened in text mode.
+    :return: A tuple containing the file descriptor and the file name.
+
+    """
+    return await to_thread.run_sync(tempfile.mkstemp, suffix, prefix, dir, text)
+
+
+@overload
+async def mkdtemp(
+    suffix: str | None = None,
+    prefix: str | None = None,
+    dir: str | None = None,
+) -> str: ...
+
+
+@overload
+async def mkdtemp(
+    suffix: bytes | None = None,
+    prefix: bytes | None = None,
+    dir: bytes | None = None,
+) -> bytes: ...
+
+
+async def mkdtemp(
+    suffix: AnyStr | None = None,
+    prefix: AnyStr | None = None,
+    dir: AnyStr | None = None,
+) -> str | bytes:
+    """
+    Asynchronously create a temporary directory and return its path.
+
+    This function wraps `tempfile.mkdtemp` and executes it in a background thread.
+
+    :param suffix: Suffix to be added to the directory name.
+    :param prefix: Prefix to be added to the directory name.
+    :param dir: Parent directory where the temporary directory is created.
+    :return: The path of the created temporary directory.
+
+    """
+    return await to_thread.run_sync(tempfile.mkdtemp, suffix, prefix, dir)
+
+
+async def gettempdir() -> str:
+    """
+    Asynchronously return the name of the directory used for temporary files.
+
+    This function wraps `tempfile.gettempdir` and executes it in a background thread.
+
+    :return: The path of the temporary directory as a string.
+
+    """
+    return await to_thread.run_sync(tempfile.gettempdir)
+
+
+async def gettempdirb() -> bytes:
+    """
+    Asynchronously return the name of the directory used for temporary files in bytes.
+
+    This function wraps `tempfile.gettempdirb` and executes it in a background thread.
+
+    :return: The path of the temporary directory as bytes.
+
+    """
+    return await to_thread.run_sync(tempfile.gettempdirb)

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_testing.py

@@ -0,0 +1,82 @@
+from __future__ import annotations
+
+from collections.abc import Awaitable, Generator
+from typing import Any, cast
+
+from ._eventloop import get_async_backend
+
+
+class TaskInfo:
+    """
+    Represents an asynchronous task.
+
+    :ivar int id: the unique identifier of the task
+    :ivar parent_id: the identifier of the parent task, if any
+    :vartype parent_id: Optional[int]
+    :ivar str name: the description of the task (if any)
+    :ivar ~collections.abc.Coroutine coro: the coroutine object of the task
+    """
+
+    __slots__ = "_name", "id", "parent_id", "name", "coro"
+
+    def __init__(
+        self,
+        id: int,
+        parent_id: int | None,
+        name: str | None,
+        coro: Generator[Any, Any, Any] | Awaitable[Any],
+    ):
+        func = get_current_task
+        self._name = f"{func.__module__}.{func.__qualname__}"
+        self.id: int = id
+        self.parent_id: int | None = parent_id
+        self.name: str | None = name
+        self.coro: Generator[Any, Any, Any] | Awaitable[Any] = coro
+
+    def __eq__(self, other: object) -> bool:
+        if isinstance(other, TaskInfo):
+            return self.id == other.id
+
+        return NotImplemented
+
+    def __hash__(self) -> int:
+        return hash(self.id)
+
+    def __repr__(self) -> str:
+        return f"{self.__class__.__name__}(id={self.id!r}, name={self.name!r})"
+
+    def has_pending_cancellation(self) -> bool:
+        """
+        Return ``True`` if the task has a cancellation pending, ``False`` otherwise.
+
+        """
+        return False
+
+
+def get_current_task() -> TaskInfo:
+    """
+    Return the current task.
+
+    :return: a representation of the current task
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    return get_async_backend().get_current_task()
+
+
+def get_running_tasks() -> list[TaskInfo]:
+    """
+    Return a list of running tasks in the current event loop.
+
+    :return: a list of task info objects
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    return cast("list[TaskInfo]", get_async_backend().get_running_tasks())
+
+
+async def wait_all_tasks_blocked() -> None:
+    """Wait until all other tasks are waiting for something."""
+    await get_async_backend().wait_all_tasks_blocked()

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/_core/_typedattr.py

@@ -0,0 +1,81 @@
+from __future__ import annotations
+
+from collections.abc import Callable, Mapping
+from typing import Any, TypeVar, final, overload
+
+from ._exceptions import TypedAttributeLookupError
+
+T_Attr = TypeVar("T_Attr")
+T_Default = TypeVar("T_Default")
+undefined = object()
+
+
+def typed_attribute() -> Any:
+    """Return a unique object, used to mark typed attributes."""
+    return object()
+
+
+class TypedAttributeSet:
+    """
+    Superclass for typed attribute collections.
+
+    Checks that every public attribute of every subclass has a type annotation.
+    """
+
+    def __init_subclass__(cls) -> None:
+        annotations: dict[str, Any] = getattr(cls, "__annotations__", {})
+        for attrname in dir(cls):
+            if not attrname.startswith("_") and attrname not in annotations:
+                raise TypeError(
+                    f"Attribute {attrname!r} is missing its type annotation"
+                )
+
+        super().__init_subclass__()
+
+
+class TypedAttributeProvider:
+    """Base class for classes that wish to provide typed extra attributes."""
+
+    @property
+    def extra_attributes(self) -> Mapping[T_Attr, Callable[[], T_Attr]]:
+        """
+        A mapping of the extra attributes to callables that return the corresponding
+        values.
+
+        If the provider wraps another provider, the attributes from that wrapper should
+        also be included in the returned mapping (but the wrapper may override the
+        callables from the wrapped instance).
+
+        """
+        return {}
+
+    @overload
+    def extra(self, attribute: T_Attr) -> T_Attr: ...
+
+    @overload
+    def extra(self, attribute: T_Attr, default: T_Default) -> T_Attr | T_Default: ...
+
+    @final
+    def extra(self, attribute: Any, default: object = undefined) -> object:
+        """
+        extra(attribute, default=undefined)
+
+        Return the value of the given typed extra attribute.
+
+        :param attribute: the attribute (member of a :class:`~TypedAttributeSet`) to
+            look for
+        :param default: the value that should be returned if no value is found for the
+            attribute
+        :raises ~anyio.TypedAttributeLookupError: if the search failed and no default
+            value was given
+
+        """
+        try:
+            getter = self.extra_attributes[attribute]
+        except KeyError:
+            if default is undefined:
+                raise TypedAttributeLookupError("Attribute not found") from None
+            else:
+                return default
+
+        return getter()

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/abc/__init__.py

@@ -0,0 +1,58 @@
+from __future__ import annotations
+
+from ._eventloop import AsyncBackend as AsyncBackend
+from ._resources import AsyncResource as AsyncResource
+from ._sockets import ConnectedUDPSocket as ConnectedUDPSocket
+from ._sockets import ConnectedUNIXDatagramSocket as ConnectedUNIXDatagramSocket
+from ._sockets import IPAddressType as IPAddressType
+from ._sockets import IPSockAddrType as IPSockAddrType
+from ._sockets import SocketAttribute as SocketAttribute
+from ._sockets import SocketListener as SocketListener
+from ._sockets import SocketStream as SocketStream
+from ._sockets import UDPPacketType as UDPPacketType
+from ._sockets import UDPSocket as UDPSocket
+from ._sockets import UNIXDatagramPacketType as UNIXDatagramPacketType
+from ._sockets import UNIXDatagramSocket as UNIXDatagramSocket
+from ._sockets import UNIXSocketStream as UNIXSocketStream
+from ._streams import AnyByteReceiveStream as AnyByteReceiveStream
+from ._streams import AnyByteSendStream as AnyByteSendStream
+from ._streams import AnyByteStream as AnyByteStream
+from ._streams import AnyByteStreamConnectable as AnyByteStreamConnectable
+from ._streams import AnyUnreliableByteReceiveStream as AnyUnreliableByteReceiveStream
+from ._streams import AnyUnreliableByteSendStream as AnyUnreliableByteSendStream
+from ._streams import AnyUnreliableByteStream as AnyUnreliableByteStream
+from ._streams import ByteReceiveStream as ByteReceiveStream
+from ._streams import ByteSendStream as ByteSendStream
+from ._streams import ByteStream as ByteStream
+from ._streams import ByteStreamConnectable as ByteStreamConnectable
+from ._streams import Listener as Listener
+from ._streams import ObjectReceiveStream as ObjectReceiveStream
+from ._streams import ObjectSendStream as ObjectSendStream
+from ._streams import ObjectStream as ObjectStream
+from ._streams import ObjectStreamConnectable as ObjectStreamConnectable
+from ._streams import UnreliableObjectReceiveStream as UnreliableObjectReceiveStream
+from ._streams import UnreliableObjectSendStream as UnreliableObjectSendStream
+from ._streams import UnreliableObjectStream as UnreliableObjectStream
+from ._subprocesses import Process as Process
+from ._tasks import TaskGroup as TaskGroup
+from ._tasks import TaskStatus as TaskStatus
+from ._testing import TestRunner as TestRunner
+
+# Re-exported here, for backwards compatibility
+# isort: off
+from .._core._synchronization import (
+    CapacityLimiter as CapacityLimiter,
+    Condition as Condition,
+    Event as Event,
+    Lock as Lock,
+    Semaphore as Semaphore,
+)
+from .._core._tasks import CancelScope as CancelScope
+from ..from_thread import BlockingPortal as BlockingPortal
+
+# Re-export imports so they look like they live directly in this package
+for __value in list(locals().values()):
+    if getattr(__value, "__module__", "").startswith("anyio.abc."):
+        __value.__module__ = __name__
+
+del __value

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/abc/_eventloop.py

@@ -0,0 +1,409 @@
+from __future__ import annotations
+
+import math
+import sys
+from abc import ABCMeta, abstractmethod
+from collections.abc import AsyncIterator, Awaitable, Callable, Sequence
+from contextlib import AbstractContextManager
+from os import PathLike
+from signal import Signals
+from socket import AddressFamily, SocketKind, socket
+from typing import (
+    IO,
+    TYPE_CHECKING,
+    Any,
+    TypeAlias,
+    TypeVar,
+    overload,
+)
+
+if sys.version_info >= (3, 11):
+    from typing import TypeVarTuple, Unpack
+else:
+    from typing_extensions import TypeVarTuple, Unpack
+
+if TYPE_CHECKING:
+    from _typeshed import FileDescriptorLike
+
+    from .._core._synchronization import CapacityLimiter, Event, Lock, Semaphore
+    from .._core._tasks import CancelScope
+    from .._core._testing import TaskInfo
+    from ._sockets import (
+        ConnectedUDPSocket,
+        ConnectedUNIXDatagramSocket,
+        IPSockAddrType,
+        SocketListener,
+        SocketStream,
+        UDPSocket,
+        UNIXDatagramSocket,
+        UNIXSocketStream,
+    )
+    from ._subprocesses import Process
+    from ._tasks import TaskGroup
+    from ._testing import TestRunner
+
+T_Retval = TypeVar("T_Retval")
+PosArgsT = TypeVarTuple("PosArgsT")
+StrOrBytesPath: TypeAlias = str | bytes | PathLike[str] | PathLike[bytes]
+
+
+class AsyncBackend(metaclass=ABCMeta):
+    @classmethod
+    @abstractmethod
+    def run(
+        cls,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval]],
+        args: tuple[Unpack[PosArgsT]],
+        kwargs: dict[str, Any],
+        options: dict[str, Any],
+    ) -> T_Retval:
+        """
+        Run the given coroutine function in an asynchronous event loop.
+
+        The current thread must not be already running an event loop.
+
+        :param func: a coroutine function
+        :param args: positional arguments to ``func``
+        :param kwargs: positional arguments to ``func``
+        :param options: keyword arguments to call the backend ``run()`` implementation
+            with
+        :return: the return value of the coroutine function
+        """
+
+    @classmethod
+    @abstractmethod
+    def current_token(cls) -> object:
+        """
+        Return an object that allows other threads to run code inside the event loop.
+
+        :return: a token object, specific to the event loop running in the current
+            thread
+        """
+
+    @classmethod
+    @abstractmethod
+    def current_time(cls) -> float:
+        """
+        Return the current value of the event loop's internal clock.
+
+        :return: the clock value (seconds)
+        """
+
+    @classmethod
+    @abstractmethod
+    def cancelled_exception_class(cls) -> type[BaseException]:
+        """Return the exception class that is raised in a task if it's cancelled."""
+
+    @classmethod
+    @abstractmethod
+    async def checkpoint(cls) -> None:
+        """
+        Check if the task has been cancelled, and allow rescheduling of other tasks.
+
+        This is effectively the same as running :meth:`checkpoint_if_cancelled` and then
+        :meth:`cancel_shielded_checkpoint`.
+        """
+
+    @classmethod
+    async def checkpoint_if_cancelled(cls) -> None:
+        """
+        Check if the current task group has been cancelled.
+
+        This will check if the task has been cancelled, but will not allow other tasks
+        to be scheduled if not.
+
+        """
+        if cls.current_effective_deadline() == -math.inf:
+            await cls.checkpoint()
+
+    @classmethod
+    async def cancel_shielded_checkpoint(cls) -> None:
+        """
+        Allow the rescheduling of other tasks.
+
+        This will give other tasks the opportunity to run, but without checking if the
+        current task group has been cancelled, unlike with :meth:`checkpoint`.
+
+        """
+        with cls.create_cancel_scope(shield=True):
+            await cls.sleep(0)
+
+    @classmethod
+    @abstractmethod
+    async def sleep(cls, delay: float) -> None:
+        """
+        Pause the current task for the specified duration.
+
+        :param delay: the duration, in seconds
+        """
+
+    @classmethod
+    @abstractmethod
+    def create_cancel_scope(
+        cls, *, deadline: float = math.inf, shield: bool = False
+    ) -> CancelScope:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def current_effective_deadline(cls) -> float:
+        """
+        Return the nearest deadline among all the cancel scopes effective for the
+        current task.
+
+        :return:
+            - a clock value from the event loop's internal clock
+            - ``inf`` if there is no deadline in effect
+            - ``-inf`` if the current scope has been cancelled
+        :rtype: float
+        """
+
+    @classmethod
+    @abstractmethod
+    def create_task_group(cls) -> TaskGroup:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def create_event(cls) -> Event:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def create_lock(cls, *, fast_acquire: bool) -> Lock:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def create_semaphore(
+        cls,
+        initial_value: int,
+        *,
+        max_value: int | None = None,
+        fast_acquire: bool = False,
+    ) -> Semaphore:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def create_capacity_limiter(cls, total_tokens: float) -> CapacityLimiter:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def run_sync_in_worker_thread(
+        cls,
+        func: Callable[[Unpack[PosArgsT]], T_Retval],
+        args: tuple[Unpack[PosArgsT]],
+        abandon_on_cancel: bool = False,
+        limiter: CapacityLimiter | None = None,
+    ) -> T_Retval:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def check_cancelled(cls) -> None:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def run_async_from_thread(
+        cls,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval]],
+        args: tuple[Unpack[PosArgsT]],
+        token: object,
+    ) -> T_Retval:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def run_sync_from_thread(
+        cls,
+        func: Callable[[Unpack[PosArgsT]], T_Retval],
+        args: tuple[Unpack[PosArgsT]],
+        token: object,
+    ) -> T_Retval:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def open_process(
+        cls,
+        command: StrOrBytesPath | Sequence[StrOrBytesPath],
+        *,
+        stdin: int | IO[Any] | None,
+        stdout: int | IO[Any] | None,
+        stderr: int | IO[Any] | None,
+        **kwargs: Any,
+    ) -> Process:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def setup_process_pool_exit_at_shutdown(cls, workers: set[Process]) -> None:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def connect_tcp(
+        cls, host: str, port: int, local_address: IPSockAddrType | None = None
+    ) -> SocketStream:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def connect_unix(cls, path: str | bytes) -> UNIXSocketStream:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def create_tcp_listener(cls, sock: socket) -> SocketListener:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def create_unix_listener(cls, sock: socket) -> SocketListener:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def create_udp_socket(
+        cls,
+        family: AddressFamily,
+        local_address: IPSockAddrType | None,
+        remote_address: IPSockAddrType | None,
+        reuse_port: bool,
+    ) -> UDPSocket | ConnectedUDPSocket:
+        pass
+
+    @classmethod
+    @overload
+    async def create_unix_datagram_socket(
+        cls, raw_socket: socket, remote_path: None
+    ) -> UNIXDatagramSocket: ...
+
+    @classmethod
+    @overload
+    async def create_unix_datagram_socket(
+        cls, raw_socket: socket, remote_path: str | bytes
+    ) -> ConnectedUNIXDatagramSocket: ...
+
+    @classmethod
+    @abstractmethod
+    async def create_unix_datagram_socket(
+        cls, raw_socket: socket, remote_path: str | bytes | None
+    ) -> UNIXDatagramSocket | ConnectedUNIXDatagramSocket:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def getaddrinfo(
+        cls,
+        host: bytes | str | None,
+        port: str | int | None,
+        *,
+        family: int | AddressFamily = 0,
+        type: int | SocketKind = 0,
+        proto: int = 0,
+        flags: int = 0,
+    ) -> Sequence[
+        tuple[
+            AddressFamily,
+            SocketKind,
+            int,
+            str,
+            tuple[str, int] | tuple[str, int, int, int] | tuple[int, bytes],
+        ]
+    ]:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def getnameinfo(
+        cls, sockaddr: IPSockAddrType, flags: int = 0
+    ) -> tuple[str, str]:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def wait_readable(cls, obj: FileDescriptorLike) -> None:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def wait_writable(cls, obj: FileDescriptorLike) -> None:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def notify_closing(cls, obj: FileDescriptorLike) -> None:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def wrap_listener_socket(cls, sock: socket) -> SocketListener:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def wrap_stream_socket(cls, sock: socket) -> SocketStream:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def wrap_unix_stream_socket(cls, sock: socket) -> UNIXSocketStream:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def wrap_udp_socket(cls, sock: socket) -> UDPSocket:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def wrap_connected_udp_socket(cls, sock: socket) -> ConnectedUDPSocket:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def wrap_unix_datagram_socket(cls, sock: socket) -> UNIXDatagramSocket:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def wrap_connected_unix_datagram_socket(
+        cls, sock: socket
+    ) -> ConnectedUNIXDatagramSocket:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def current_default_thread_limiter(cls) -> CapacityLimiter:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def open_signal_receiver(
+        cls, *signals: Signals
+    ) -> AbstractContextManager[AsyncIterator[Signals]]:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def get_current_task(cls) -> TaskInfo:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def get_running_tasks(cls) -> Sequence[TaskInfo]:
+        pass
+
+    @classmethod
+    @abstractmethod
+    async def wait_all_tasks_blocked(cls) -> None:
+        pass
+
+    @classmethod
+    @abstractmethod
+    def create_test_runner(cls, options: dict[str, Any]) -> TestRunner:
+        pass

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/abc/_resources.py

@@ -0,0 +1,33 @@
+from __future__ import annotations
+
+from abc import ABCMeta, abstractmethod
+from types import TracebackType
+from typing import TypeVar
+
+T = TypeVar("T")
+
+
+class AsyncResource(metaclass=ABCMeta):
+    """
+    Abstract base class for all closeable asynchronous resources.
+
+    Works as an asynchronous context manager which returns the instance itself on enter,
+    and calls :meth:`aclose` on exit.
+    """
+
+    __slots__ = ()
+
+    async def __aenter__(self: T) -> T:
+        return self
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        await self.aclose()
+
+    @abstractmethod
+    async def aclose(self) -> None:
+        """Close the resource."""

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/abc/_sockets.py

@@ -0,0 +1,399 @@
+from __future__ import annotations
+
+import errno
+import socket
+from abc import abstractmethod
+from collections.abc import Callable, Collection, Mapping
+from contextlib import AsyncExitStack
+from io import IOBase
+from ipaddress import IPv4Address, IPv6Address
+from socket import AddressFamily
+from typing import Any, TypeAlias, TypeVar
+
+from .._core._eventloop import get_async_backend
+from .._core._typedattr import (
+    TypedAttributeProvider,
+    TypedAttributeSet,
+    typed_attribute,
+)
+from ._streams import ByteStream, Listener, UnreliableObjectStream
+from ._tasks import TaskGroup
+
+IPAddressType: TypeAlias = str | IPv4Address | IPv6Address
+IPSockAddrType: TypeAlias = tuple[str, int]
+SockAddrType: TypeAlias = IPSockAddrType | str
+UDPPacketType: TypeAlias = tuple[bytes, IPSockAddrType]
+UNIXDatagramPacketType: TypeAlias = tuple[bytes, str]
+T_Retval = TypeVar("T_Retval")
+
+
+def _validate_socket(
+    sock_or_fd: socket.socket | int,
+    sock_type: socket.SocketKind,
+    addr_family: socket.AddressFamily = socket.AF_UNSPEC,
+    *,
+    require_connected: bool = False,
+    require_bound: bool = False,
+) -> socket.socket:
+    if isinstance(sock_or_fd, int):
+        try:
+            sock = socket.socket(fileno=sock_or_fd)
+        except OSError as exc:
+            if exc.errno == errno.ENOTSOCK:
+                raise ValueError(
+                    "the file descriptor does not refer to a socket"
+                ) from exc
+            elif require_connected:
+                raise ValueError("the socket must be connected") from exc
+            elif require_bound:
+                raise ValueError("the socket must be bound to a local address") from exc
+            else:
+                raise
+    elif isinstance(sock_or_fd, socket.socket):
+        sock = sock_or_fd
+    else:
+        raise TypeError(
+            f"expected an int or socket, got {type(sock_or_fd).__qualname__} instead"
+        )
+
+    try:
+        if require_connected:
+            try:
+                sock.getpeername()
+            except OSError as exc:
+                raise ValueError("the socket must be connected") from exc
+
+        if require_bound:
+            try:
+                if sock.family in (socket.AF_INET, socket.AF_INET6):
+                    bound_addr = sock.getsockname()[1]
+                else:
+                    bound_addr = sock.getsockname()
+            except OSError:
+                bound_addr = None
+
+            if not bound_addr:
+                raise ValueError("the socket must be bound to a local address")
+
+        if addr_family != socket.AF_UNSPEC and sock.family != addr_family:
+            raise ValueError(
+                f"address family mismatch: expected {addr_family.name}, got "
+                f"{sock.family.name}"
+            )
+
+        if sock.type != sock_type:
+            raise ValueError(
+                f"socket type mismatch: expected {sock_type.name}, got {sock.type.name}"
+            )
+    except BaseException:
+        # Avoid ResourceWarning from the locally constructed socket object
+        if isinstance(sock_or_fd, int):
+            sock.detach()
+
+        raise
+
+    sock.setblocking(False)
+    return sock
+
+
+class SocketAttribute(TypedAttributeSet):
+    """
+    .. attribute:: family
+        :type: socket.AddressFamily
+
+        the address family of the underlying socket
+
+    .. attribute:: local_address
+        :type: tuple[str, int] | str
+
+        the local address the underlying socket is connected to
+
+    .. attribute:: local_port
+        :type: int
+
+        for IP based sockets, the local port the underlying socket is bound to
+
+    .. attribute:: raw_socket
+        :type: socket.socket
+
+        the underlying stdlib socket object
+
+    .. attribute:: remote_address
+        :type: tuple[str, int] | str
+
+        the remote address the underlying socket is connected to
+
+    .. attribute:: remote_port
+        :type: int
+
+        for IP based sockets, the remote port the underlying socket is connected to
+    """
+
+    family: AddressFamily = typed_attribute()
+    local_address: SockAddrType = typed_attribute()
+    local_port: int = typed_attribute()
+    raw_socket: socket.socket = typed_attribute()
+    remote_address: SockAddrType = typed_attribute()
+    remote_port: int = typed_attribute()
+
+
+class _SocketProvider(TypedAttributeProvider):
+    @property
+    def extra_attributes(self) -> Mapping[Any, Callable[[], Any]]:
+        from .._core._sockets import convert_ipv6_sockaddr as convert
+
+        attributes: dict[Any, Callable[[], Any]] = {
+            SocketAttribute.family: lambda: self._raw_socket.family,
+            SocketAttribute.local_address: lambda: convert(
+                self._raw_socket.getsockname()
+            ),
+            SocketAttribute.raw_socket: lambda: self._raw_socket,
+        }
+        try:
+            peername: tuple[str, int] | None = convert(self._raw_socket.getpeername())
+        except OSError:
+            peername = None
+
+        # Provide the remote address for connected sockets
+        if peername is not None:
+            attributes[SocketAttribute.remote_address] = lambda: peername
+
+        # Provide local and remote ports for IP based sockets
+        if self._raw_socket.family in (AddressFamily.AF_INET, AddressFamily.AF_INET6):
+            attributes[SocketAttribute.local_port] = lambda: (
+                self._raw_socket.getsockname()[1]
+            )
+            if peername is not None:
+                remote_port = peername[1]
+                attributes[SocketAttribute.remote_port] = lambda: remote_port
+
+        return attributes
+
+    @property
+    @abstractmethod
+    def _raw_socket(self) -> socket.socket:
+        pass
+
+
+class SocketStream(ByteStream, _SocketProvider):
+    """
+    Transports bytes over a socket.
+
+    Supports all relevant extra attributes from :class:`~SocketAttribute`.
+    """
+
+    @classmethod
+    async def from_socket(cls, sock_or_fd: socket.socket | int) -> SocketStream:
+        """
+        Wrap an existing socket object or file descriptor as a socket stream.
+
+        The newly created socket wrapper takes ownership of the socket being passed in.
+        The existing socket must already be connected.
+
+        :param sock_or_fd: a socket object or file descriptor
+        :return: a socket stream
+
+        """
+        sock = _validate_socket(sock_or_fd, socket.SOCK_STREAM, require_connected=True)
+        return await get_async_backend().wrap_stream_socket(sock)
+
+
+class UNIXSocketStream(SocketStream):
+    @classmethod
+    async def from_socket(cls, sock_or_fd: socket.socket | int) -> UNIXSocketStream:
+        """
+        Wrap an existing socket object or file descriptor as a UNIX socket stream.
+
+        The newly created socket wrapper takes ownership of the socket being passed in.
+        The existing socket must already be connected.
+
+        :param sock_or_fd: a socket object or file descriptor
+        :return: a UNIX socket stream
+
+        """
+        sock = _validate_socket(
+            sock_or_fd, socket.SOCK_STREAM, socket.AF_UNIX, require_connected=True
+        )
+        return await get_async_backend().wrap_unix_stream_socket(sock)
+
+    @abstractmethod
+    async def send_fds(self, message: bytes, fds: Collection[int | IOBase]) -> None:
+        """
+        Send file descriptors along with a message to the peer.
+
+        :param message: a non-empty bytestring
+        :param fds: a collection of files (either numeric file descriptors or open file
+            or socket objects)
+        """
+
+    @abstractmethod
+    async def receive_fds(self, msglen: int, maxfds: int) -> tuple[bytes, list[int]]:
+        """
+        Receive file descriptors along with a message from the peer.
+
+        :param msglen: length of the message to expect from the peer
+        :param maxfds: maximum number of file descriptors to expect from the peer
+        :return: a tuple of (message, file descriptors)
+        """
+
+
+class SocketListener(Listener[SocketStream], _SocketProvider):
+    """
+    Listens to incoming socket connections.
+
+    Supports all relevant extra attributes from :class:`~SocketAttribute`.
+    """
+
+    @classmethod
+    async def from_socket(
+        cls,
+        sock_or_fd: socket.socket | int,
+    ) -> SocketListener:
+        """
+        Wrap an existing socket object or file descriptor as a socket listener.
+
+        The newly created listener takes ownership of the socket being passed in.
+
+        :param sock_or_fd: a socket object or file descriptor
+        :return: a socket listener
+
+        """
+        sock = _validate_socket(sock_or_fd, socket.SOCK_STREAM, require_bound=True)
+        return await get_async_backend().wrap_listener_socket(sock)
+
+    @abstractmethod
+    async def accept(self) -> SocketStream:
+        """Accept an incoming connection."""
+
+    async def serve(
+        self,
+        handler: Callable[[SocketStream], Any],
+        task_group: TaskGroup | None = None,
+    ) -> None:
+        from .. import create_task_group
+
+        async with AsyncExitStack() as stack:
+            if task_group is None:
+                task_group = await stack.enter_async_context(create_task_group())
+
+            while True:
+                stream = await self.accept()
+                task_group.start_soon(handler, stream)
+
+
+class UDPSocket(UnreliableObjectStream[UDPPacketType], _SocketProvider):
+    """
+    Represents an unconnected UDP socket.
+
+    Supports all relevant extra attributes from :class:`~SocketAttribute`.
+    """
+
+    @classmethod
+    async def from_socket(cls, sock_or_fd: socket.socket | int) -> UDPSocket:
+        """
+        Wrap an existing socket object or file descriptor as a UDP socket.
+
+        The newly created socket wrapper takes ownership of the socket being passed in.
+        The existing socket must be bound to a local address.
+
+        :param sock_or_fd: a socket object or file descriptor
+        :return: a UDP socket
+
+        """
+        sock = _validate_socket(sock_or_fd, socket.SOCK_DGRAM, require_bound=True)
+        return await get_async_backend().wrap_udp_socket(sock)
+
+    async def sendto(self, data: bytes, host: str, port: int) -> None:
+        """
+        Alias for :meth:`~.UnreliableObjectSendStream.send` ((data, (host, port))).
+
+        """
+        return await self.send((data, (host, port)))
+
+
+class ConnectedUDPSocket(UnreliableObjectStream[bytes], _SocketProvider):
+    """
+    Represents an connected UDP socket.
+
+    Supports all relevant extra attributes from :class:`~SocketAttribute`.
+    """
+
+    @classmethod
+    async def from_socket(cls, sock_or_fd: socket.socket | int) -> ConnectedUDPSocket:
+        """
+        Wrap an existing socket object or file descriptor as a connected UDP socket.
+
+        The newly created socket wrapper takes ownership of the socket being passed in.
+        The existing socket must already be connected.
+
+        :param sock_or_fd: a socket object or file descriptor
+        :return: a connected UDP socket
+
+        """
+        sock = _validate_socket(
+            sock_or_fd,
+            socket.SOCK_DGRAM,
+            require_connected=True,
+        )
+        return await get_async_backend().wrap_connected_udp_socket(sock)
+
+
+class UNIXDatagramSocket(
+    UnreliableObjectStream[UNIXDatagramPacketType], _SocketProvider
+):
+    """
+    Represents an unconnected Unix datagram socket.
+
+    Supports all relevant extra attributes from :class:`~SocketAttribute`.
+    """
+
+    @classmethod
+    async def from_socket(
+        cls,
+        sock_or_fd: socket.socket | int,
+    ) -> UNIXDatagramSocket:
+        """
+        Wrap an existing socket object or file descriptor as a UNIX datagram
+        socket.
+
+        The newly created socket wrapper takes ownership of the socket being passed in.
+
+        :param sock_or_fd: a socket object or file descriptor
+        :return: a UNIX datagram socket
+
+        """
+        sock = _validate_socket(sock_or_fd, socket.SOCK_DGRAM, socket.AF_UNIX)
+        return await get_async_backend().wrap_unix_datagram_socket(sock)
+
+    async def sendto(self, data: bytes, path: str) -> None:
+        """Alias for :meth:`~.UnreliableObjectSendStream.send` ((data, path))."""
+        return await self.send((data, path))
+
+
+class ConnectedUNIXDatagramSocket(UnreliableObjectStream[bytes], _SocketProvider):
+    """
+    Represents a connected Unix datagram socket.
+
+    Supports all relevant extra attributes from :class:`~SocketAttribute`.
+    """
+
+    @classmethod
+    async def from_socket(
+        cls,
+        sock_or_fd: socket.socket | int,
+    ) -> ConnectedUNIXDatagramSocket:
+        """
+        Wrap an existing socket object or file descriptor as a connected UNIX datagram
+        socket.
+
+        The newly created socket wrapper takes ownership of the socket being passed in.
+        The existing socket must already be connected.
+
+        :param sock_or_fd: a socket object or file descriptor
+        :return: a connected UNIX datagram socket
+
+        """
+        sock = _validate_socket(
+            sock_or_fd, socket.SOCK_DGRAM, socket.AF_UNIX, require_connected=True
+        )
+        return await get_async_backend().wrap_connected_unix_datagram_socket(sock)

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/abc/_streams.py

@@ -0,0 +1,233 @@
+from __future__ import annotations
+
+from abc import ABCMeta, abstractmethod
+from collections.abc import Callable
+from typing import Any, Generic, TypeAlias, TypeVar
+
+from .._core._exceptions import EndOfStream
+from .._core._typedattr import TypedAttributeProvider
+from ._resources import AsyncResource
+from ._tasks import TaskGroup
+
+T_Item = TypeVar("T_Item")
+T_co = TypeVar("T_co", covariant=True)
+T_contra = TypeVar("T_contra", contravariant=True)
+
+
+class UnreliableObjectReceiveStream(
+    Generic[T_co], AsyncResource, TypedAttributeProvider
+):
+    """
+    An interface for receiving objects.
+
+    This interface makes no guarantees that the received messages arrive in the order in
+    which they were sent, or that no messages are missed.
+
+    Asynchronously iterating over objects of this type will yield objects matching the
+    given type parameter.
+    """
+
+    def __aiter__(self) -> UnreliableObjectReceiveStream[T_co]:
+        return self
+
+    async def __anext__(self) -> T_co:
+        try:
+            return await self.receive()
+        except EndOfStream:
+            raise StopAsyncIteration from None
+
+    @abstractmethod
+    async def receive(self) -> T_co:
+        """
+        Receive the next item.
+
+        :raises ~anyio.ClosedResourceError: if the receive stream has been explicitly
+            closed
+        :raises ~anyio.EndOfStream: if this stream has been closed from the other end
+        :raises ~anyio.BrokenResourceError: if this stream has been rendered unusable
+            due to external causes
+        """
+
+
+class UnreliableObjectSendStream(
+    Generic[T_contra], AsyncResource, TypedAttributeProvider
+):
+    """
+    An interface for sending objects.
+
+    This interface makes no guarantees that the messages sent will reach the
+    recipient(s) in the same order in which they were sent, or at all.
+    """
+
+    @abstractmethod
+    async def send(self, item: T_contra) -> None:
+        """
+        Send an item to the peer(s).
+
+        :param item: the item to send
+        :raises ~anyio.ClosedResourceError: if the send stream has been explicitly
+            closed
+        :raises ~anyio.BrokenResourceError: if this stream has been rendered unusable
+            due to external causes
+        """
+
+
+class UnreliableObjectStream(
+    UnreliableObjectReceiveStream[T_Item], UnreliableObjectSendStream[T_Item]
+):
+    """
+    A bidirectional message stream which does not guarantee the order or reliability of
+    message delivery.
+    """
+
+
+class ObjectReceiveStream(UnreliableObjectReceiveStream[T_co]):
+    """
+    A receive message stream which guarantees that messages are received in the same
+    order in which they were sent, and that no messages are missed.
+    """
+
+
+class ObjectSendStream(UnreliableObjectSendStream[T_contra]):
+    """
+    A send message stream which guarantees that messages are delivered in the same order
+    in which they were sent, without missing any messages in the middle.
+    """
+
+
+class ObjectStream(
+    ObjectReceiveStream[T_Item],
+    ObjectSendStream[T_Item],
+    UnreliableObjectStream[T_Item],
+):
+    """
+    A bidirectional message stream which guarantees the order and reliability of message
+    delivery.
+    """
+
+    @abstractmethod
+    async def send_eof(self) -> None:
+        """
+        Send an end-of-file indication to the peer.
+
+        You should not try to send any further data to this stream after calling this
+        method. This method is idempotent (does nothing on successive calls).
+        """
+
+
+class ByteReceiveStream(AsyncResource, TypedAttributeProvider):
+    """
+    An interface for receiving bytes from a single peer.
+
+    Iterating this byte stream will yield a byte string of arbitrary length, but no more
+    than 65536 bytes.
+    """
+
+    def __aiter__(self) -> ByteReceiveStream:
+        return self
+
+    async def __anext__(self) -> bytes:
+        try:
+            return await self.receive()
+        except EndOfStream:
+            raise StopAsyncIteration from None
+
+    @abstractmethod
+    async def receive(self, max_bytes: int = 65536) -> bytes:
+        """
+        Receive at most ``max_bytes`` bytes from the peer.
+
+        .. note:: Implementers of this interface should not return an empty
+            :class:`bytes` object, and users should ignore them.
+
+        :param max_bytes: maximum number of bytes to receive
+        :return: the received bytes
+        :raises ~anyio.EndOfStream: if this stream has been closed from the other end
+        """
+
+
+class ByteSendStream(AsyncResource, TypedAttributeProvider):
+    """An interface for sending bytes to a single peer."""
+
+    @abstractmethod
+    async def send(self, item: bytes) -> None:
+        """
+        Send the given bytes to the peer.
+
+        :param item: the bytes to send
+        """
+
+
+class ByteStream(ByteReceiveStream, ByteSendStream):
+    """A bidirectional byte stream."""
+
+    @abstractmethod
+    async def send_eof(self) -> None:
+        """
+        Send an end-of-file indication to the peer.
+
+        You should not try to send any further data to this stream after calling this
+        method. This method is idempotent (does nothing on successive calls).
+        """
+
+
+#: Type alias for all unreliable bytes-oriented receive streams.
+AnyUnreliableByteReceiveStream: TypeAlias = (
+    UnreliableObjectReceiveStream[bytes] | ByteReceiveStream
+)
+#: Type alias for all unreliable bytes-oriented send streams.
+AnyUnreliableByteSendStream: TypeAlias = (
+    UnreliableObjectSendStream[bytes] | ByteSendStream
+)
+#: Type alias for all unreliable bytes-oriented streams.
+AnyUnreliableByteStream: TypeAlias = UnreliableObjectStream[bytes] | ByteStream
+#: Type alias for all bytes-oriented receive streams.
+AnyByteReceiveStream: TypeAlias = ObjectReceiveStream[bytes] | ByteReceiveStream
+#: Type alias for all bytes-oriented send streams.
+AnyByteSendStream: TypeAlias = ObjectSendStream[bytes] | ByteSendStream
+#: Type alias for all bytes-oriented streams.
+AnyByteStream: TypeAlias = ObjectStream[bytes] | ByteStream
+
+
+class Listener(Generic[T_co], AsyncResource, TypedAttributeProvider):
+    """An interface for objects that let you accept incoming connections."""
+
+    @abstractmethod
+    async def serve(
+        self, handler: Callable[[T_co], Any], task_group: TaskGroup | None = None
+    ) -> None:
+        """
+        Accept incoming connections as they come in and start tasks to handle them.
+
+        :param handler: a callable that will be used to handle each accepted connection
+        :param task_group: the task group that will be used to start tasks for handling
+            each accepted connection (if omitted, an ad-hoc task group will be created)
+        """
+
+
+class ObjectStreamConnectable(Generic[T_co], metaclass=ABCMeta):
+    @abstractmethod
+    async def connect(self) -> ObjectStream[T_co]:
+        """
+        Connect to the remote endpoint.
+
+        :return: an object stream connected to the remote end
+        :raises ConnectionFailed: if the connection fails
+        """
+
+
+class ByteStreamConnectable(metaclass=ABCMeta):
+    @abstractmethod
+    async def connect(self) -> ByteStream:
+        """
+        Connect to the remote endpoint.
+
+        :return: a bytestream connected to the remote end
+        :raises ConnectionFailed: if the connection fails
+        """
+
+
+#: Type alias for all connectables returning bytestreams or bytes-oriented object streams
+AnyByteStreamConnectable: TypeAlias = (
+    ObjectStreamConnectable[bytes] | ByteStreamConnectable
+)

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/abc/_subprocesses.py

@@ -0,0 +1,79 @@
+from __future__ import annotations
+
+from abc import abstractmethod
+from signal import Signals
+
+from ._resources import AsyncResource
+from ._streams import ByteReceiveStream, ByteSendStream
+
+
+class Process(AsyncResource):
+    """An asynchronous version of :class:`subprocess.Popen`."""
+
+    @abstractmethod
+    async def wait(self) -> int:
+        """
+        Wait until the process exits.
+
+        :return: the exit code of the process
+        """
+
+    @abstractmethod
+    def terminate(self) -> None:
+        """
+        Terminates the process, gracefully if possible.
+
+        On Windows, this calls ``TerminateProcess()``.
+        On POSIX systems, this sends ``SIGTERM`` to the process.
+
+        .. seealso:: :meth:`subprocess.Popen.terminate`
+        """
+
+    @abstractmethod
+    def kill(self) -> None:
+        """
+        Kills the process.
+
+        On Windows, this calls ``TerminateProcess()``.
+        On POSIX systems, this sends ``SIGKILL`` to the process.
+
+        .. seealso:: :meth:`subprocess.Popen.kill`
+        """
+
+    @abstractmethod
+    def send_signal(self, signal: Signals) -> None:
+        """
+        Send a signal to the subprocess.
+
+        .. seealso:: :meth:`subprocess.Popen.send_signal`
+
+        :param signal: the signal number (e.g. :data:`signal.SIGHUP`)
+        """
+
+    @property
+    @abstractmethod
+    def pid(self) -> int:
+        """The process ID of the process."""
+
+    @property
+    @abstractmethod
+    def returncode(self) -> int | None:
+        """
+        The return code of the process. If the process has not yet terminated, this will
+        be ``None``.
+        """
+
+    @property
+    @abstractmethod
+    def stdin(self) -> ByteSendStream | None:
+        """The stream for the standard input of the process."""
+
+    @property
+    @abstractmethod
+    def stdout(self) -> ByteReceiveStream | None:
+        """The stream for the standard output of the process."""
+
+    @property
+    @abstractmethod
+    def stderr(self) -> ByteReceiveStream | None:
+        """The stream for the standard error output of the process."""

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/abc/_tasks.py

@@ -0,0 +1,117 @@
+from __future__ import annotations
+
+import sys
+from abc import ABCMeta, abstractmethod
+from collections.abc import Awaitable, Callable
+from types import TracebackType
+from typing import TYPE_CHECKING, Any, Protocol, overload
+
+if sys.version_info >= (3, 13):
+    from typing import TypeVar
+else:
+    from typing_extensions import TypeVar
+
+if sys.version_info >= (3, 11):
+    from typing import TypeVarTuple, Unpack
+else:
+    from typing_extensions import TypeVarTuple, Unpack
+
+if TYPE_CHECKING:
+    from .._core._tasks import CancelScope
+
+T_Retval = TypeVar("T_Retval")
+T_contra = TypeVar("T_contra", contravariant=True, default=None)
+PosArgsT = TypeVarTuple("PosArgsT")
+
+
+class TaskStatus(Protocol[T_contra]):
+    @overload
+    def started(self: TaskStatus[None]) -> None: ...
+
+    @overload
+    def started(self, value: T_contra) -> None: ...
+
+    def started(self, value: T_contra | None = None) -> None:
+        """
+        Signal that the task has started.
+
+        :param value: object passed back to the starter of the task
+        """
+
+
+class TaskGroup(metaclass=ABCMeta):
+    """
+    Groups several asynchronous tasks together.
+
+    :ivar cancel_scope: the cancel scope inherited by all child tasks
+    :vartype cancel_scope: CancelScope
+
+    .. note:: On asyncio, support for eager task factories is considered to be
+        **experimental**. In particular, they don't follow the usual semantics of new
+        tasks being scheduled on the next iteration of the event loop, and may thus
+        cause unexpected behavior in code that wasn't written with such semantics in
+        mind.
+    """
+
+    cancel_scope: CancelScope
+
+    @abstractmethod
+    def start_soon(
+        self,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[Any]],
+        *args: Unpack[PosArgsT],
+        name: object = None,
+    ) -> None:
+        """
+        Start a new task in this task group.
+
+        :param func: a coroutine function
+        :param args: positional arguments to call the function with
+        :param name: name of the task, for the purposes of introspection and debugging
+
+        .. versionadded:: 3.0
+        """
+
+    @abstractmethod
+    async def start(
+        self,
+        func: Callable[..., Awaitable[Any]],
+        *args: object,
+        name: object = None,
+    ) -> Any:
+        """
+        Start a new task and wait until it signals for readiness.
+
+        The target callable must accept a keyword argument ``task_status`` (of type
+        :class:`TaskStatus`). Awaiting on this method will return whatever was passed to
+        ``task_status.started()`` (``None`` by default).
+
+        .. note:: The :class:`TaskStatus` class is generic, and the type argument should
+            indicate the type of the value that will be passed to
+            ``task_status.started()``.
+
+        :param func: a coroutine function that accepts the ``task_status`` keyword
+            argument
+        :param args: positional arguments to call the function with
+        :param name: an optional name for the task, for introspection and debugging
+        :return: the value passed to ``task_status.started()``
+        :raises RuntimeError: if the task finishes without calling
+            ``task_status.started()``
+
+        .. seealso:: :ref:`start_initialize`
+
+        .. versionadded:: 3.0
+        """
+
+    @abstractmethod
+    async def __aenter__(self) -> TaskGroup:
+        """Enter the task group context and allow starting new tasks."""
+
+    @abstractmethod
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> bool:
+        """Exit the task group context waiting for all tasks to finish."""

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/abc/_testing.py

@@ -0,0 +1,65 @@
+from __future__ import annotations
+
+import types
+from abc import ABCMeta, abstractmethod
+from collections.abc import AsyncGenerator, Callable, Coroutine, Iterable
+from typing import Any, TypeVar
+
+_T = TypeVar("_T")
+
+
+class TestRunner(metaclass=ABCMeta):
+    """
+    Encapsulates a running event loop. Every call made through this object will use the
+    same event loop.
+    """
+
+    def __enter__(self) -> TestRunner:
+        return self
+
+    @abstractmethod
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: types.TracebackType | None,
+    ) -> bool | None: ...
+
+    @abstractmethod
+    def run_asyncgen_fixture(
+        self,
+        fixture_func: Callable[..., AsyncGenerator[_T, Any]],
+        kwargs: dict[str, Any],
+    ) -> Iterable[_T]:
+        """
+        Run an async generator fixture.
+
+        :param fixture_func: the fixture function
+        :param kwargs: keyword arguments to call the fixture function with
+        :return: an iterator yielding the value yielded from the async generator
+        """
+
+    @abstractmethod
+    def run_fixture(
+        self,
+        fixture_func: Callable[..., Coroutine[Any, Any, _T]],
+        kwargs: dict[str, Any],
+    ) -> _T:
+        """
+        Run an async fixture.
+
+        :param fixture_func: the fixture function
+        :param kwargs: keyword arguments to call the fixture function with
+        :return: the return value of the fixture function
+        """
+
+    @abstractmethod
+    def run_test(
+        self, test_func: Callable[..., Coroutine[Any, Any, Any]], kwargs: dict[str, Any]
+    ) -> None:
+        """
+        Run an async test function.
+
+        :param test_func: the test function
+        :param kwargs: keyword arguments to call the test function with
+        """

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/from_thread.py

@@ -0,0 +1,578 @@
+from __future__ import annotations
+
+__all__ = (
+    "BlockingPortal",
+    "BlockingPortalProvider",
+    "check_cancelled",
+    "run",
+    "run_sync",
+    "start_blocking_portal",
+)
+
+import sys
+from collections.abc import Awaitable, Callable, Generator
+from concurrent.futures import Future
+from contextlib import (
+    AbstractAsyncContextManager,
+    AbstractContextManager,
+    contextmanager,
+)
+from dataclasses import dataclass, field
+from functools import partial
+from inspect import isawaitable
+from threading import Lock, Thread, current_thread, get_ident
+from types import TracebackType
+from typing import (
+    Any,
+    Generic,
+    TypeVar,
+    cast,
+    overload,
+)
+
+from ._core._eventloop import (
+    get_cancelled_exc_class,
+    threadlocals,
+)
+from ._core._eventloop import run as run_eventloop
+from ._core._exceptions import NoEventLoopError
+from ._core._synchronization import Event
+from ._core._tasks import CancelScope, create_task_group
+from .abc._tasks import TaskStatus
+from .lowlevel import EventLoopToken, current_token
+
+if sys.version_info >= (3, 11):
+    from typing import TypeVarTuple, Unpack
+else:
+    from typing_extensions import TypeVarTuple, Unpack
+
+T_Retval = TypeVar("T_Retval")
+T_co = TypeVar("T_co", covariant=True)
+PosArgsT = TypeVarTuple("PosArgsT")
+
+
+def _token_or_error(token: EventLoopToken | None) -> EventLoopToken:
+    if token is not None:
+        return token
+
+    try:
+        return threadlocals.current_token
+    except AttributeError:
+        raise NoEventLoopError(
+            "Not running inside an AnyIO worker thread, and no event loop token was "
+            "provided"
+        ) from None
+
+
+def run(
+    func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval]],
+    *args: Unpack[PosArgsT],
+    token: EventLoopToken | None = None,
+) -> T_Retval:
+    """
+    Call a coroutine function from a worker thread.
+
+    :param func: a coroutine function
+    :param args: positional arguments for the callable
+    :param token: an event loop token to use to get back to the event loop thread
+        (required if calling this function from outside an AnyIO worker thread)
+    :return: the return value of the coroutine function
+    :raises MissingTokenError: if no token was provided and called from outside an
+        AnyIO worker thread
+    :raises RunFinishedError: if the event loop tied to ``token`` is no longer running
+
+    .. versionchanged:: 4.11.0
+        Added the ``token`` parameter.
+
+    """
+    explicit_token = token is not None
+    token = _token_or_error(token)
+    return token.backend_class.run_async_from_thread(
+        func, args, token=token.native_token if explicit_token else None
+    )
+
+
+def run_sync(
+    func: Callable[[Unpack[PosArgsT]], T_Retval],
+    *args: Unpack[PosArgsT],
+    token: EventLoopToken | None = None,
+) -> T_Retval:
+    """
+    Call a function in the event loop thread from a worker thread.
+
+    :param func: a callable
+    :param args: positional arguments for the callable
+    :param token: an event loop token to use to get back to the event loop thread
+        (required if calling this function from outside an AnyIO worker thread)
+    :return: the return value of the callable
+    :raises MissingTokenError: if no token was provided and called from outside an
+        AnyIO worker thread
+    :raises RunFinishedError: if the event loop tied to ``token`` is no longer running
+
+    .. versionchanged:: 4.11.0
+        Added the ``token`` parameter.
+
+    """
+    explicit_token = token is not None
+    token = _token_or_error(token)
+    return token.backend_class.run_sync_from_thread(
+        func, args, token=token.native_token if explicit_token else None
+    )
+
+
+class _BlockingAsyncContextManager(Generic[T_co], AbstractContextManager):
+    _enter_future: Future[T_co]
+    _exit_future: Future[bool | None]
+    _exit_event: Event
+    _exit_exc_info: tuple[
+        type[BaseException] | None, BaseException | None, TracebackType | None
+    ] = (None, None, None)
+
+    def __init__(
+        self, async_cm: AbstractAsyncContextManager[T_co], portal: BlockingPortal
+    ):
+        self._async_cm = async_cm
+        self._portal = portal
+
+    async def run_async_cm(self) -> bool | None:
+        try:
+            self._exit_event = Event()
+            value = await self._async_cm.__aenter__()
+        except BaseException as exc:
+            self._enter_future.set_exception(exc)
+            raise
+        else:
+            self._enter_future.set_result(value)
+
+        try:
+            # Wait for the sync context manager to exit.
+            # This next statement can raise `get_cancelled_exc_class()` if
+            # something went wrong in a task group in this async context
+            # manager.
+            await self._exit_event.wait()
+        finally:
+            # In case of cancellation, it could be that we end up here before
+            # `_BlockingAsyncContextManager.__exit__` is called, and an
+            # `_exit_exc_info` has been set.
+            result = await self._async_cm.__aexit__(*self._exit_exc_info)
+
+        return result
+
+    def __enter__(self) -> T_co:
+        self._enter_future = Future()
+        self._exit_future = self._portal.start_task_soon(self.run_async_cm)
+        return self._enter_future.result()
+
+    def __exit__(
+        self,
+        __exc_type: type[BaseException] | None,
+        __exc_value: BaseException | None,
+        __traceback: TracebackType | None,
+    ) -> bool | None:
+        self._exit_exc_info = __exc_type, __exc_value, __traceback
+        self._portal.call(self._exit_event.set)
+        return self._exit_future.result()
+
+
+class _BlockingPortalTaskStatus(TaskStatus):
+    def __init__(self, future: Future):
+        self._future = future
+
+    def started(self, value: object = None) -> None:
+        self._future.set_result(value)
+
+
+class BlockingPortal:
+    """
+    An object that lets external threads run code in an asynchronous event loop.
+
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+    """
+
+    def __init__(self) -> None:
+        self._token = current_token()
+        self._event_loop_thread_id: int | None = get_ident()
+        self._stop_event = Event()
+        self._task_group = create_task_group()
+
+    async def __aenter__(self) -> BlockingPortal:
+        await self._task_group.__aenter__()
+        return self
+
+    async def __aexit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> bool:
+        await self.stop()
+        return await self._task_group.__aexit__(exc_type, exc_val, exc_tb)
+
+    def _check_running(self) -> None:
+        if self._event_loop_thread_id is None:
+            raise RuntimeError("This portal is not running")
+        if self._event_loop_thread_id == get_ident():
+            raise RuntimeError(
+                "This method cannot be called from the event loop thread"
+            )
+
+    async def sleep_until_stopped(self) -> None:
+        """Sleep until :meth:`stop` is called."""
+        await self._stop_event.wait()
+
+    async def stop(self, cancel_remaining: bool = False) -> None:
+        """
+        Signal the portal to shut down.
+
+        This marks the portal as no longer accepting new calls and exits from
+        :meth:`sleep_until_stopped`.
+
+        :param cancel_remaining: ``True`` to cancel all the remaining tasks, ``False``
+            to let them finish before returning
+
+        """
+        self._event_loop_thread_id = None
+        self._stop_event.set()
+        if cancel_remaining:
+            self._task_group.cancel_scope.cancel("the blocking portal is shutting down")
+
+    async def _call_func(
+        self,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval] | T_Retval],
+        args: tuple[Unpack[PosArgsT]],
+        kwargs: dict[str, Any],
+        future: Future[T_Retval],
+    ) -> None:
+        def callback(f: Future[T_Retval]) -> None:
+            if f.cancelled():
+                if self._event_loop_thread_id == get_ident():
+                    scope.cancel("the future was cancelled")
+                elif self._event_loop_thread_id is not None:
+                    self.call(scope.cancel, "the future was cancelled")
+
+        try:
+            retval_or_awaitable = func(*args, **kwargs)
+            if isawaitable(retval_or_awaitable):
+                with CancelScope() as scope:
+                    future.add_done_callback(callback)
+                    retval = await retval_or_awaitable
+            else:
+                retval = retval_or_awaitable
+        except get_cancelled_exc_class():
+            future.cancel()
+            future.set_running_or_notify_cancel()
+        except BaseException as exc:
+            if not future.cancelled():
+                future.set_exception(exc)
+
+            # Let base exceptions fall through
+            if not isinstance(exc, Exception):
+                raise
+        else:
+            if not future.cancelled():
+                future.set_result(retval)
+        finally:
+            scope = None  # type: ignore[assignment]
+
+    def _spawn_task_from_thread(
+        self,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval] | T_Retval],
+        args: tuple[Unpack[PosArgsT]],
+        kwargs: dict[str, Any],
+        name: object,
+        future: Future[T_Retval],
+    ) -> None:
+        """
+        Spawn a new task using the given callable.
+
+        :param func: a callable
+        :param args: positional arguments to be passed to the callable
+        :param kwargs: keyword arguments to be passed to the callable
+        :param name: name of the task (will be coerced to a string if not ``None``)
+        :param future: a future that will resolve to the return value of the callable,
+            or the exception raised during its execution
+
+        """
+        run_sync(
+            partial(self._task_group.start_soon, name=name),
+            self._call_func,
+            func,
+            args,
+            kwargs,
+            future,
+            token=self._token,
+        )
+
+    @overload
+    def call(
+        self,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval]],
+        *args: Unpack[PosArgsT],
+    ) -> T_Retval: ...
+
+    @overload
+    def call(
+        self, func: Callable[[Unpack[PosArgsT]], T_Retval], *args: Unpack[PosArgsT]
+    ) -> T_Retval: ...
+
+    def call(
+        self,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval] | T_Retval],
+        *args: Unpack[PosArgsT],
+    ) -> T_Retval:
+        """
+        Call the given function in the event loop thread.
+
+        If the callable returns a coroutine object, it is awaited on.
+
+        :param func: any callable
+        :raises RuntimeError: if the portal is not running or if this method is called
+            from within the event loop thread
+
+        """
+        return cast(T_Retval, self.start_task_soon(func, *args).result())
+
+    @overload
+    def start_task_soon(
+        self,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval]],
+        *args: Unpack[PosArgsT],
+        name: object = None,
+    ) -> Future[T_Retval]: ...
+
+    @overload
+    def start_task_soon(
+        self,
+        func: Callable[[Unpack[PosArgsT]], T_Retval],
+        *args: Unpack[PosArgsT],
+        name: object = None,
+    ) -> Future[T_Retval]: ...
+
+    def start_task_soon(
+        self,
+        func: Callable[[Unpack[PosArgsT]], Awaitable[T_Retval] | T_Retval],
+        *args: Unpack[PosArgsT],
+        name: object = None,
+    ) -> Future[T_Retval]:
+        """
+        Start a task in the portal's task group.
+
+        The task will be run inside a cancel scope which can be cancelled by cancelling
+        the returned future.
+
+        :param func: the target function
+        :param args: positional arguments passed to ``func``
+        :param name: name of the task (will be coerced to a string if not ``None``)
+        :return: a future that resolves with the return value of the callable if the
+            task completes successfully, or with the exception raised in the task
+        :raises RuntimeError: if the portal is not running or if this method is called
+            from within the event loop thread
+        :rtype: concurrent.futures.Future[T_Retval]
+
+        .. versionadded:: 3.0
+
+        """
+        self._check_running()
+        f: Future[T_Retval] = Future()
+        self._spawn_task_from_thread(func, args, {}, name, f)
+        return f
+
+    def start_task(
+        self,
+        func: Callable[..., Awaitable[T_Retval]],
+        *args: object,
+        name: object = None,
+    ) -> tuple[Future[T_Retval], Any]:
+        """
+        Start a task in the portal's task group and wait until it signals for readiness.
+
+        This method works the same way as :meth:`.abc.TaskGroup.start`.
+
+        :param func: the target function
+        :param args: positional arguments passed to ``func``
+        :param name: name of the task (will be coerced to a string if not ``None``)
+        :return: a tuple of (future, task_status_value) where the ``task_status_value``
+            is the value passed to ``task_status.started()`` from within the target
+            function
+        :rtype: tuple[concurrent.futures.Future[T_Retval], Any]
+
+        .. versionadded:: 3.0
+
+        """
+
+        def task_done(future: Future[T_Retval]) -> None:
+            if not task_status_future.done():
+                if future.cancelled():
+                    task_status_future.cancel()
+                elif future.exception():
+                    task_status_future.set_exception(future.exception())
+                else:
+                    exc = RuntimeError(
+                        "Task exited without calling task_status.started()"
+                    )
+                    task_status_future.set_exception(exc)
+
+        self._check_running()
+        task_status_future: Future = Future()
+        task_status = _BlockingPortalTaskStatus(task_status_future)
+        f: Future = Future()
+        f.add_done_callback(task_done)
+        self._spawn_task_from_thread(func, args, {"task_status": task_status}, name, f)
+        return f, task_status_future.result()
+
+    def wrap_async_context_manager(
+        self, cm: AbstractAsyncContextManager[T_co]
+    ) -> AbstractContextManager[T_co]:
+        """
+        Wrap an async context manager as a synchronous context manager via this portal.
+
+        Spawns a task that will call both ``__aenter__()`` and ``__aexit__()``, stopping
+        in the middle until the synchronous context manager exits.
+
+        :param cm: an asynchronous context manager
+        :return: a synchronous context manager
+
+        .. versionadded:: 2.1
+
+        """
+        return _BlockingAsyncContextManager(cm, self)
+
+
+@dataclass
+class BlockingPortalProvider:
+    """
+    A manager for a blocking portal. Used as a context manager. The first thread to
+    enter this context manager causes a blocking portal to be started with the specific
+    parameters, and the last thread to exit causes the portal to be shut down. Thus,
+    there will be exactly one blocking portal running in this context as long as at
+    least one thread has entered this context manager.
+
+    The parameters are the same as for :func:`~anyio.run`.
+
+    :param backend: name of the backend
+    :param backend_options: backend options
+
+    .. versionadded:: 4.4
+    """
+
+    backend: str = "asyncio"
+    backend_options: dict[str, Any] | None = None
+    _lock: Lock = field(init=False, default_factory=Lock)
+    _leases: int = field(init=False, default=0)
+    _portal: BlockingPortal = field(init=False)
+    _portal_cm: AbstractContextManager[BlockingPortal] | None = field(
+        init=False, default=None
+    )
+
+    def __enter__(self) -> BlockingPortal:
+        with self._lock:
+            if self._portal_cm is None:
+                self._portal_cm = start_blocking_portal(
+                    self.backend, self.backend_options
+                )
+                self._portal = self._portal_cm.__enter__()
+
+            self._leases += 1
+            return self._portal
+
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        portal_cm: AbstractContextManager[BlockingPortal] | None = None
+        with self._lock:
+            assert self._portal_cm
+            assert self._leases > 0
+            self._leases -= 1
+            if not self._leases:
+                portal_cm = self._portal_cm
+                self._portal_cm = None
+                del self._portal
+
+        if portal_cm:
+            portal_cm.__exit__(None, None, None)
+
+
+@contextmanager
+def start_blocking_portal(
+    backend: str = "asyncio",
+    backend_options: dict[str, Any] | None = None,
+    *,
+    name: str | None = None,
+) -> Generator[BlockingPortal, Any, None]:
+    """
+    Start a new event loop in a new thread and run a blocking portal in its main task.
+
+    The parameters are the same as for :func:`~anyio.run`.
+
+    :param backend: name of the backend
+    :param backend_options: backend options
+    :param name: name of the thread
+    :return: a context manager that yields a blocking portal
+
+    .. versionchanged:: 3.0
+        Usage as a context manager is now required.
+
+    """
+
+    async def run_portal() -> None:
+        async with BlockingPortal() as portal_:
+            if name is None:
+                current_thread().name = f"{backend}-portal-{id(portal_):x}"
+
+            future.set_result(portal_)
+            await portal_.sleep_until_stopped()
+
+    def run_blocking_portal() -> None:
+        if future.set_running_or_notify_cancel():
+            try:
+                run_eventloop(
+                    run_portal, backend=backend, backend_options=backend_options
+                )
+            except BaseException as exc:
+                if not future.done():
+                    future.set_exception(exc)
+
+    future: Future[BlockingPortal] = Future()
+    thread = Thread(target=run_blocking_portal, daemon=True, name=name)
+    thread.start()
+    try:
+        cancel_remaining_tasks = False
+        portal = future.result()
+        try:
+            yield portal
+        except BaseException:
+            cancel_remaining_tasks = True
+            raise
+        finally:
+            try:
+                portal.call(portal.stop, cancel_remaining_tasks)
+            except RuntimeError:
+                pass
+    finally:
+        thread.join()
+
+
+def check_cancelled() -> None:
+    """
+    Check if the cancel scope of the host task's running the current worker thread has
+    been cancelled.
+
+    If the host task's current cancel scope has indeed been cancelled, the
+    backend-specific cancellation exception will be raised.
+
+    :raises RuntimeError: if the current thread was not spawned by
+        :func:`.to_thread.run_sync`
+
+    """
+    try:
+        token: EventLoopToken = threadlocals.current_token
+    except AttributeError:
+        raise NoEventLoopError(
+            "This function can only be called inside an AnyIO worker thread"
+        ) from None
+
+    token.backend_class.check_cancelled()

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/functools.py

@@ -0,0 +1,409 @@
+from __future__ import annotations
+
+__all__ = (
+    "AsyncCacheInfo",
+    "AsyncCacheParameters",
+    "AsyncLRUCacheWrapper",
+    "cache",
+    "lru_cache",
+    "reduce",
+)
+
+import functools
+import sys
+from collections import OrderedDict
+from collections.abc import (
+    AsyncIterable,
+    Awaitable,
+    Callable,
+    Coroutine,
+    Hashable,
+    Iterable,
+)
+from functools import update_wrapper
+from inspect import iscoroutinefunction
+from typing import (
+    Any,
+    Generic,
+    NamedTuple,
+    TypedDict,
+    TypeVar,
+    cast,
+    final,
+    overload,
+)
+from weakref import WeakKeyDictionary
+
+from ._core._eventloop import current_time
+from ._core._synchronization import Lock
+from .lowlevel import RunVar, checkpoint
+
+if sys.version_info >= (3, 11):
+    from typing import ParamSpec
+else:
+    from typing_extensions import ParamSpec
+
+T = TypeVar("T")
+S = TypeVar("S")
+P = ParamSpec("P")
+lru_cache_items: RunVar[
+    WeakKeyDictionary[
+        AsyncLRUCacheWrapper[Any, Any],
+        OrderedDict[
+            Hashable,
+            tuple[_InitialMissingType, Lock, float | None]
+            | tuple[Any, None, float | None],
+        ],
+    ]
+] = RunVar("lru_cache_items")
+
+
+class _InitialMissingType:
+    pass
+
+
+initial_missing: _InitialMissingType = _InitialMissingType()
+
+
+class AsyncCacheInfo(NamedTuple):
+    hits: int
+    misses: int
+    maxsize: int | None
+    currsize: int
+    ttl: int | None
+
+
+class AsyncCacheParameters(TypedDict):
+    maxsize: int | None
+    typed: bool
+    always_checkpoint: bool
+    ttl: int | None
+
+
+class _LRUMethodWrapper(Generic[T]):
+    def __init__(self, wrapper: AsyncLRUCacheWrapper[..., T], instance: object):
+        self.__wrapper = wrapper
+        self.__instance = instance
+
+    def cache_info(self) -> AsyncCacheInfo:
+        return self.__wrapper.cache_info()
+
+    def cache_parameters(self) -> AsyncCacheParameters:
+        return self.__wrapper.cache_parameters()
+
+    def cache_clear(self) -> None:
+        self.__wrapper.cache_clear()
+
+    async def __call__(self, *args: Any, **kwargs: Any) -> T:
+        if self.__instance is None:
+            return await self.__wrapper(*args, **kwargs)
+
+        return await self.__wrapper(self.__instance, *args, **kwargs)
+
+
+@final
+class AsyncLRUCacheWrapper(Generic[P, T]):
+    def __init__(
+        self,
+        func: Callable[P, Awaitable[T]],
+        maxsize: int | None,
+        typed: bool,
+        always_checkpoint: bool,
+        ttl: int | None,
+    ):
+        self.__wrapped__ = func
+        self._hits: int = 0
+        self._misses: int = 0
+        self._maxsize = max(maxsize, 0) if maxsize is not None else None
+        self._currsize: int = 0
+        self._typed = typed
+        self._always_checkpoint = always_checkpoint
+        self._ttl = ttl
+        update_wrapper(self, func)
+
+    def cache_info(self) -> AsyncCacheInfo:
+        return AsyncCacheInfo(
+            self._hits, self._misses, self._maxsize, self._currsize, self._ttl
+        )
+
+    def cache_parameters(self) -> AsyncCacheParameters:
+        return {
+            "maxsize": self._maxsize,
+            "typed": self._typed,
+            "always_checkpoint": self._always_checkpoint,
+            "ttl": self._ttl,
+        }
+
+    def cache_clear(self) -> None:
+        if cache := lru_cache_items.get(None):
+            cache.pop(self, None)
+            self._hits = self._misses = self._currsize = 0
+
+    async def __call__(self, *args: P.args, **kwargs: P.kwargs) -> T:
+        # Easy case first: if maxsize == 0, no caching is done
+        if self._maxsize == 0:
+            value = await self.__wrapped__(*args, **kwargs)
+            self._misses += 1
+            return value
+
+        # The key is constructed as a flat tuple to avoid memory overhead
+        key: tuple[Any, ...] = args
+        if kwargs:
+            # initial_missing is used as a separator
+            key += (initial_missing,) + sum(kwargs.items(), ())
+
+        if self._typed:
+            key += tuple(type(arg) for arg in args)
+            if kwargs:
+                key += (initial_missing,) + tuple(type(val) for val in kwargs.values())
+
+        try:
+            cache = lru_cache_items.get()
+        except LookupError:
+            cache = WeakKeyDictionary()
+            lru_cache_items.set(cache)
+
+        try:
+            cache_entry = cache[self]
+        except KeyError:
+            cache_entry = cache[self] = OrderedDict()
+
+        cached_value: T | _InitialMissingType
+        try:
+            cached_value, lock, expires_at = cache_entry[key]
+        except KeyError:
+            # We're the first task to call this function
+            cached_value, lock, expires_at = (
+                initial_missing,
+                Lock(fast_acquire=not self._always_checkpoint),
+                None,
+            )
+            cache_entry[key] = cached_value, lock, expires_at
+
+        if lock is None:
+            if expires_at is not None and current_time() >= expires_at:
+                self._currsize -= 1
+                cached_value, lock, expires_at = (
+                    initial_missing,
+                    Lock(fast_acquire=not self._always_checkpoint),
+                    None,
+                )
+                cache_entry[key] = cached_value, lock, expires_at
+            else:
+                # The value was already cached
+                self._hits += 1
+                cache_entry.move_to_end(key)
+                if self._always_checkpoint:
+                    await checkpoint()
+
+                return cast(T, cached_value)
+
+        async with lock:
+            # Check if another task filled the cache while we acquired the lock
+            if (cached_value := cache_entry[key][0]) is initial_missing:
+                self._misses += 1
+                if self._maxsize is not None and self._currsize >= self._maxsize:
+                    cache_entry.popitem(last=False)
+                else:
+                    self._currsize += 1
+
+                value = await self.__wrapped__(*args, **kwargs)
+                expires_at = (
+                    current_time() + self._ttl if self._ttl is not None else None
+                )
+                cache_entry[key] = value, None, expires_at
+            else:
+                # Another task filled the cache while we were waiting for the lock
+                self._hits += 1
+                cache_entry.move_to_end(key)
+                value = cast(T, cached_value)
+
+        return value
+
+    def __get__(
+        self, instance: object, owner: type | None = None
+    ) -> _LRUMethodWrapper[T]:
+        wrapper = _LRUMethodWrapper(self, instance)
+        update_wrapper(wrapper, self.__wrapped__)
+        return wrapper
+
+
+class _LRUCacheWrapper(Generic[T]):
+    def __init__(
+        self, maxsize: int | None, typed: bool, always_checkpoint: bool, ttl: int | None
+    ):
+        self._maxsize = maxsize
+        self._typed = typed
+        self._always_checkpoint = always_checkpoint
+        self._ttl = ttl
+
+    @overload
+    def __call__(  # type: ignore[overload-overlap]
+        self, func: Callable[P, Coroutine[Any, Any, T]], /
+    ) -> AsyncLRUCacheWrapper[P, T]: ...
+
+    @overload
+    def __call__(
+        self, func: Callable[..., T], /
+    ) -> functools._lru_cache_wrapper[T]: ...
+
+    def __call__(
+        self, f: Callable[P, Coroutine[Any, Any, T]] | Callable[..., T], /
+    ) -> AsyncLRUCacheWrapper[P, T] | functools._lru_cache_wrapper[T]:
+        if iscoroutinefunction(f):
+            return AsyncLRUCacheWrapper(
+                f, self._maxsize, self._typed, self._always_checkpoint, self._ttl
+            )
+
+        return functools.lru_cache(maxsize=self._maxsize, typed=self._typed)(f)  # type: ignore[arg-type]
+
+
+@overload
+def cache(  # type: ignore[overload-overlap]
+    func: Callable[P, Coroutine[Any, Any, T]], /
+) -> AsyncLRUCacheWrapper[P, T]: ...
+
+
+@overload
+def cache(func: Callable[..., T], /) -> functools._lru_cache_wrapper[T]: ...
+
+
+def cache(
+    func: Callable[..., T] | Callable[P, Coroutine[Any, Any, T]], /
+) -> AsyncLRUCacheWrapper[P, T] | functools._lru_cache_wrapper[T]:
+    """
+    A convenient shortcut for :func:`lru_cache` with ``maxsize=None``.
+
+    This is the asynchronous equivalent to :func:`functools.cache`.
+
+    """
+    return lru_cache(maxsize=None)(func)
+
+
+@overload
+def lru_cache(
+    *,
+    maxsize: int | None = ...,
+    typed: bool = ...,
+    always_checkpoint: bool = ...,
+    ttl: int | None = ...,
+) -> _LRUCacheWrapper[Any]: ...
+
+
+@overload
+def lru_cache(  # type: ignore[overload-overlap]
+    func: Callable[P, Coroutine[Any, Any, T]], /
+) -> AsyncLRUCacheWrapper[P, T]: ...
+
+
+@overload
+def lru_cache(func: Callable[..., T], /) -> functools._lru_cache_wrapper[T]: ...
+
+
+def lru_cache(
+    func: Callable[P, Coroutine[Any, Any, T]] | Callable[..., T] | None = None,
+    /,
+    *,
+    maxsize: int | None = 128,
+    typed: bool = False,
+    always_checkpoint: bool = False,
+    ttl: int | None = None,
+) -> (
+    AsyncLRUCacheWrapper[P, T] | functools._lru_cache_wrapper[T] | _LRUCacheWrapper[Any]
+):
+    """
+    An asynchronous version of :func:`functools.lru_cache`.
+
+    If a synchronous function is passed, the standard library
+    :func:`functools.lru_cache` is applied instead.
+
+    :param always_checkpoint: if ``True``, every call to the cached function will be
+        guaranteed to yield control to the event loop at least once
+    :param ttl: time in seconds after which to invalidate cache entries
+
+    .. note:: Caches and locks are managed on a per-event loop basis.
+
+    """
+    if func is None:
+        return _LRUCacheWrapper[Any](maxsize, typed, always_checkpoint, ttl)
+
+    if not callable(func):
+        raise TypeError("the first argument must be callable")
+
+    return _LRUCacheWrapper[T](maxsize, typed, always_checkpoint, ttl)(func)
+
+
+@overload
+async def reduce(
+    function: Callable[[T, S], Awaitable[T]],
+    iterable: Iterable[S] | AsyncIterable[S],
+    /,
+    initial: T,
+) -> T: ...
+
+
+@overload
+async def reduce(
+    function: Callable[[T, T], Awaitable[T]],
+    iterable: Iterable[T] | AsyncIterable[T],
+    /,
+) -> T: ...
+
+
+async def reduce(  # type: ignore[misc]
+    function: Callable[[T, T], Awaitable[T]] | Callable[[T, S], Awaitable[T]],
+    iterable: Iterable[T] | Iterable[S] | AsyncIterable[T] | AsyncIterable[S],
+    /,
+    initial: T | _InitialMissingType = initial_missing,
+) -> T:
+    """
+    Asynchronous version of :func:`functools.reduce`.
+
+    :param function: a coroutine function that takes two arguments: the accumulated
+        value and the next element from the iterable
+    :param iterable: an iterable or async iterable
+    :param initial: the initial value (if missing, the first element of the iterable is
+        used as the initial value)
+
+    """
+    element: Any
+    function_called = False
+    if isinstance(iterable, AsyncIterable):
+        async_it = iterable.__aiter__()
+        if initial is initial_missing:
+            try:
+                value = cast(T, await async_it.__anext__())
+            except StopAsyncIteration:
+                raise TypeError(
+                    "reduce() of empty sequence with no initial value"
+                ) from None
+        else:
+            value = cast(T, initial)
+
+        async for element in async_it:
+            value = await function(value, element)
+            function_called = True
+    elif isinstance(iterable, Iterable):
+        it = iter(iterable)
+        if initial is initial_missing:
+            try:
+                value = cast(T, next(it))
+            except StopIteration:
+                raise TypeError(
+                    "reduce() of empty sequence with no initial value"
+                ) from None
+        else:
+            value = cast(T, initial)
+
+        for element in it:
+            value = await function(value, element)
+            function_called = True
+    else:
+        raise TypeError("reduce() argument 2 must be an iterable or async iterable")
+
+    # Make sure there is at least one checkpoint, even if an empty iterable and an
+    # initial value were given
+    if not function_called:
+        await checkpoint()
+
+    return value

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/lowlevel.py

@@ -0,0 +1,196 @@
+from __future__ import annotations
+
+__all__ = (
+    "EventLoopToken",
+    "RunvarToken",
+    "RunVar",
+    "checkpoint",
+    "checkpoint_if_cancelled",
+    "cancel_shielded_checkpoint",
+    "current_token",
+)
+
+import enum
+from dataclasses import dataclass
+from types import TracebackType
+from typing import Any, Generic, Literal, TypeVar, final, overload
+from weakref import WeakKeyDictionary
+
+from ._core._eventloop import get_async_backend
+from .abc import AsyncBackend
+
+T = TypeVar("T")
+D = TypeVar("D")
+
+
+async def checkpoint() -> None:
+    """
+    Check for cancellation and allow the scheduler to switch to another task.
+
+    Equivalent to (but more efficient than)::
+
+        await checkpoint_if_cancelled()
+        await cancel_shielded_checkpoint()
+
+    .. versionadded:: 3.0
+
+    """
+    await get_async_backend().checkpoint()
+
+
+async def checkpoint_if_cancelled() -> None:
+    """
+    Enter a checkpoint if the enclosing cancel scope has been cancelled.
+
+    This does not allow the scheduler to switch to a different task.
+
+    .. versionadded:: 3.0
+
+    """
+    await get_async_backend().checkpoint_if_cancelled()
+
+
+async def cancel_shielded_checkpoint() -> None:
+    """
+    Allow the scheduler to switch to another task but without checking for cancellation.
+
+    Equivalent to (but potentially more efficient than)::
+
+        with CancelScope(shield=True):
+            await checkpoint()
+
+    .. versionadded:: 3.0
+
+    """
+    await get_async_backend().cancel_shielded_checkpoint()
+
+
+@final
+@dataclass(frozen=True, repr=False)
+class EventLoopToken:
+    """
+    An opaque object that holds a reference to an event loop.
+
+    .. versionadded:: 4.11.0
+    """
+
+    backend_class: type[AsyncBackend]
+    native_token: object
+
+
+def current_token() -> EventLoopToken:
+    """
+    Return a token object that can be used to call code in the current event loop from
+    another thread.
+
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    .. versionadded:: 4.11.0
+
+    """
+    backend_class = get_async_backend()
+    raw_token = backend_class.current_token()
+    return EventLoopToken(backend_class, raw_token)
+
+
+_run_vars: WeakKeyDictionary[object, dict[RunVar[Any], Any]] = WeakKeyDictionary()
+
+
+class _NoValueSet(enum.Enum):
+    NO_VALUE_SET = enum.auto()
+
+
+class RunvarToken(Generic[T]):
+    __slots__ = "_var", "_value", "_redeemed"
+
+    def __init__(self, var: RunVar[T], value: T | Literal[_NoValueSet.NO_VALUE_SET]):
+        self._var = var
+        self._value: T | Literal[_NoValueSet.NO_VALUE_SET] = value
+        self._redeemed = False
+
+    def __enter__(self) -> RunvarToken[T]:
+        return self
+
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        self._var.reset(self)
+
+
+class RunVar(Generic[T]):
+    """
+    Like a :class:`~contextvars.ContextVar`, except scoped to the running event loop.
+
+    Can be used as a context manager, Just like :class:`~contextvars.ContextVar`, that
+    will reset the variable to its previous value when the context block is exited.
+    """
+
+    __slots__ = "_name", "_default"
+
+    NO_VALUE_SET: Literal[_NoValueSet.NO_VALUE_SET] = _NoValueSet.NO_VALUE_SET
+
+    def __init__(
+        self, name: str, default: T | Literal[_NoValueSet.NO_VALUE_SET] = NO_VALUE_SET
+    ):
+        self._name = name
+        self._default = default
+
+    @property
+    def _current_vars(self) -> dict[RunVar[T], T]:
+        native_token = current_token().native_token
+        try:
+            return _run_vars[native_token]
+        except KeyError:
+            run_vars = _run_vars[native_token] = {}
+            return run_vars
+
+    @overload
+    def get(self, default: D) -> T | D: ...
+
+    @overload
+    def get(self) -> T: ...
+
+    def get(
+        self, default: D | Literal[_NoValueSet.NO_VALUE_SET] = NO_VALUE_SET
+    ) -> T | D:
+        try:
+            return self._current_vars[self]
+        except KeyError:
+            if default is not RunVar.NO_VALUE_SET:
+                return default
+            elif self._default is not RunVar.NO_VALUE_SET:
+                return self._default
+
+        raise LookupError(
+            f'Run variable "{self._name}" has no value and no default set'
+        )
+
+    def set(self, value: T) -> RunvarToken[T]:
+        current_vars = self._current_vars
+        token = RunvarToken(self, current_vars.get(self, RunVar.NO_VALUE_SET))
+        current_vars[self] = value
+        return token
+
+    def reset(self, token: RunvarToken[T]) -> None:
+        if token._var is not self:
+            raise ValueError("This token does not belong to this RunVar")
+
+        if token._redeemed:
+            raise ValueError("This token has already been used")
+
+        if token._value is _NoValueSet.NO_VALUE_SET:
+            try:
+                del self._current_vars[self]
+            except KeyError:
+                pass
+        else:
+            self._current_vars[self] = token._value
+
+        token._redeemed = True
+
+    def __repr__(self) -> str:
+        return f"<RunVar name={self._name!r}>"

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/pytest_plugin.py

@@ -0,0 +1,363 @@
+from __future__ import annotations
+
+import dataclasses
+import socket
+import sys
+from collections.abc import Callable, Generator, Iterator
+from contextlib import ExitStack, contextmanager
+from inspect import isasyncgenfunction, iscoroutinefunction, ismethod
+from typing import Any, cast
+
+import pytest
+from _pytest.fixtures import FuncFixtureInfo, SubRequest
+from _pytest.outcomes import Exit
+from _pytest.python import CallSpec2
+from _pytest.scope import Scope
+
+from . import get_available_backends
+from ._core._eventloop import (
+    current_async_library,
+    get_async_backend,
+    reset_current_async_library,
+    set_current_async_library,
+)
+from ._core._exceptions import iterate_exceptions
+from .abc import TestRunner
+
+if sys.version_info < (3, 11):
+    from exceptiongroup import ExceptionGroup
+
+_current_runner: TestRunner | None = None
+_runner_stack: ExitStack | None = None
+_runner_leases = 0
+
+
+def extract_backend_and_options(backend: object) -> tuple[str, dict[str, Any]]:
+    if isinstance(backend, str):
+        return backend, {}
+    elif isinstance(backend, tuple) and len(backend) == 2:
+        if isinstance(backend[0], str) and isinstance(backend[1], dict):
+            return cast(tuple[str, dict[str, Any]], backend)
+
+    raise TypeError("anyio_backend must be either a string or tuple of (string, dict)")
+
+
+@contextmanager
+def get_runner(
+    backend_name: str, backend_options: dict[str, Any]
+) -> Iterator[TestRunner]:
+    global _current_runner, _runner_leases, _runner_stack
+    if _current_runner is None:
+        asynclib = get_async_backend(backend_name)
+        _runner_stack = ExitStack()
+        if current_async_library() is None:
+            # Since we're in control of the event loop, we can cache the name of the
+            # async library
+            token = set_current_async_library(backend_name)
+            _runner_stack.callback(reset_current_async_library, token)
+
+        backend_options = backend_options or {}
+        _current_runner = _runner_stack.enter_context(
+            asynclib.create_test_runner(backend_options)
+        )
+
+    _runner_leases += 1
+    try:
+        yield _current_runner
+    finally:
+        _runner_leases -= 1
+        if not _runner_leases:
+            assert _runner_stack is not None
+            _runner_stack.close()
+            _runner_stack = _current_runner = None
+
+
+def pytest_addoption(parser: pytest.Parser) -> None:
+    parser.addini(
+        "anyio_mode",
+        default="strict",
+        help='AnyIO plugin mode (either "strict" or "auto")',
+    )
+
+
+def pytest_configure(config: pytest.Config) -> None:
+    config.addinivalue_line(
+        "markers",
+        "anyio: mark the (coroutine function) test to be run asynchronously via anyio.",
+    )
+    if (
+        config.getini("anyio_mode") == "auto"
+        and config.pluginmanager.has_plugin("asyncio")
+        and config.getini("asyncio_mode") == "auto"
+    ):
+        config.issue_config_time_warning(
+            pytest.PytestConfigWarning(
+                "AnyIO auto mode has been enabled together with pytest-asyncio auto "
+                "mode. This may cause unexpected behavior."
+            ),
+            1,
+        )
+
+
+@pytest.hookimpl(hookwrapper=True)
+def pytest_fixture_setup(fixturedef: Any, request: Any) -> Generator[Any]:
+    def wrapper(anyio_backend: Any, request: SubRequest, **kwargs: Any) -> Any:
+        # Rebind any fixture methods to the request instance
+        if (
+            request.instance
+            and ismethod(func)
+            and type(func.__self__) is type(request.instance)
+        ):
+            local_func = func.__func__.__get__(request.instance)
+        else:
+            local_func = func
+
+        backend_name, backend_options = extract_backend_and_options(anyio_backend)
+        if has_backend_arg:
+            kwargs["anyio_backend"] = anyio_backend
+
+        if has_request_arg:
+            kwargs["request"] = request
+
+        with get_runner(backend_name, backend_options) as runner:
+            if isasyncgenfunction(local_func):
+                yield from runner.run_asyncgen_fixture(local_func, kwargs)
+            else:
+                yield runner.run_fixture(local_func, kwargs)
+
+    # Only apply this to coroutine functions and async generator functions in requests
+    # that involve the anyio_backend fixture
+    func = fixturedef.func
+    if isasyncgenfunction(func) or iscoroutinefunction(func):
+        if "anyio_backend" in request.fixturenames:
+            fixturedef.func = wrapper
+            original_argname = fixturedef.argnames
+
+            if not (has_backend_arg := "anyio_backend" in fixturedef.argnames):
+                fixturedef.argnames += ("anyio_backend",)
+
+            if not (has_request_arg := "request" in fixturedef.argnames):
+                fixturedef.argnames += ("request",)
+
+            try:
+                return (yield)
+            finally:
+                fixturedef.func = func
+                fixturedef.argnames = original_argname
+
+    return (yield)
+
+
+@pytest.hookimpl(tryfirst=True)
+def pytest_pycollect_makeitem(
+    collector: pytest.Module | pytest.Class, name: str, obj: object
+) -> None:
+    if collector.istestfunction(obj, name):
+        inner_func = obj.hypothesis.inner_test if hasattr(obj, "hypothesis") else obj
+        if iscoroutinefunction(inner_func):
+            anyio_auto_mode = collector.config.getini("anyio_mode") == "auto"
+            marker = collector.get_closest_marker("anyio")
+            own_markers = getattr(obj, "pytestmark", ())
+            if (
+                anyio_auto_mode
+                or marker
+                or any(marker.name == "anyio" for marker in own_markers)
+            ):
+                pytest.mark.usefixtures("anyio_backend")(obj)
+
+
+def pytest_collection_finish(session: pytest.Session) -> None:
+    for i, item in reversed(list(enumerate(session.items))):
+        if (
+            isinstance(item, pytest.Function)
+            and iscoroutinefunction(item.function)
+            and item.get_closest_marker("anyio") is not None
+            and "anyio_backend" not in item.fixturenames
+        ):
+            new_items = []
+            try:
+                cs_fields = {f.name for f in dataclasses.fields(CallSpec2)}
+            except TypeError:
+                cs_fields = set()
+
+            for param_index, backend in enumerate(get_available_backends()):
+                if "_arg2scope" in cs_fields:  # pytest >= 8
+                    callspec = CallSpec2(
+                        params={"anyio_backend": backend},
+                        indices={"anyio_backend": param_index},
+                        _arg2scope={"anyio_backend": Scope.Module},
+                        _idlist=[backend],
+                        marks=[],
+                    )
+                else:  # pytest 7.x
+                    callspec = CallSpec2(  # type: ignore[call-arg]
+                        funcargs={},
+                        params={"anyio_backend": backend},
+                        indices={"anyio_backend": param_index},
+                        arg2scope={"anyio_backend": Scope.Module},
+                        idlist=[backend],
+                        marks=[],
+                    )
+
+                fi = item._fixtureinfo
+                new_names_closure = list(fi.names_closure)
+                if "anyio_backend" not in new_names_closure:
+                    new_names_closure.append("anyio_backend")
+
+                new_fixtureinfo = FuncFixtureInfo(
+                    argnames=fi.argnames,
+                    initialnames=fi.initialnames,
+                    names_closure=new_names_closure,
+                    name2fixturedefs=fi.name2fixturedefs,
+                )
+                new_item = pytest.Function.from_parent(
+                    item.parent,
+                    name=f"{item.originalname}[{backend}]",
+                    callspec=callspec,
+                    callobj=item.obj,
+                    fixtureinfo=new_fixtureinfo,
+                    keywords=item.keywords,
+                    originalname=item.originalname,
+                )
+                new_items.append(new_item)
+
+            session.items[i : i + 1] = new_items
+
+
+@pytest.hookimpl(tryfirst=True)
+def pytest_pyfunc_call(pyfuncitem: Any) -> bool | None:
+    def run_with_hypothesis(**kwargs: Any) -> None:
+        with get_runner(backend_name, backend_options) as runner:
+            runner.run_test(original_func, kwargs)
+
+    backend = pyfuncitem.funcargs.get("anyio_backend")
+    if backend:
+        backend_name, backend_options = extract_backend_and_options(backend)
+
+        if hasattr(pyfuncitem.obj, "hypothesis"):
+            # Wrap the inner test function unless it's already wrapped
+            original_func = pyfuncitem.obj.hypothesis.inner_test
+            if original_func.__qualname__ != run_with_hypothesis.__qualname__:
+                if iscoroutinefunction(original_func):
+                    pyfuncitem.obj.hypothesis.inner_test = run_with_hypothesis
+
+            return None
+
+        if iscoroutinefunction(pyfuncitem.obj):
+            funcargs = pyfuncitem.funcargs
+            testargs = {arg: funcargs[arg] for arg in pyfuncitem._fixtureinfo.argnames}
+            with get_runner(backend_name, backend_options) as runner:
+                try:
+                    runner.run_test(pyfuncitem.obj, testargs)
+                except ExceptionGroup as excgrp:
+                    for exc in iterate_exceptions(excgrp):
+                        if isinstance(exc, (Exit, KeyboardInterrupt, SystemExit)):
+                            raise exc from excgrp
+
+                    raise
+
+            return True
+
+    return None
+
+
+@pytest.fixture(scope="module", params=get_available_backends())
+def anyio_backend(request: Any) -> Any:
+    return request.param
+
+
+@pytest.fixture
+def anyio_backend_name(anyio_backend: Any) -> str:
+    if isinstance(anyio_backend, str):
+        return anyio_backend
+    else:
+        return anyio_backend[0]
+
+
+@pytest.fixture
+def anyio_backend_options(anyio_backend: Any) -> dict[str, Any]:
+    if isinstance(anyio_backend, str):
+        return {}
+    else:
+        return anyio_backend[1]
+
+
+class FreePortFactory:
+    """
+    Manages port generation based on specified socket kind, ensuring no duplicate
+    ports are generated.
+
+    This class provides functionality for generating available free ports on the
+    system. It is initialized with a specific socket kind and can generate ports
+    for given address families while avoiding reuse of previously generated ports.
+
+    Users should not instantiate this class directly, but use the
+    ``free_tcp_port_factory`` and ``free_udp_port_factory`` fixtures instead. For simple
+    uses cases, ``free_tcp_port`` and ``free_udp_port`` can be used instead.
+    """
+
+    def __init__(self, kind: socket.SocketKind) -> None:
+        self._kind = kind
+        self._generated = set[int]()
+
+    @property
+    def kind(self) -> socket.SocketKind:
+        """
+        The type of socket connection (e.g., :data:`~socket.SOCK_STREAM` or
+        :data:`~socket.SOCK_DGRAM`) used to bind for checking port availability
+
+        """
+        return self._kind
+
+    def __call__(self, family: socket.AddressFamily | None = None) -> int:
+        """
+        Return an unbound port for the given address family.
+
+        :param family: if omitted, both IPv4 and IPv6 addresses will be tried
+        :return: a port number
+
+        """
+        if family is not None:
+            families = [family]
+        else:
+            families = [socket.AF_INET]
+            if socket.has_ipv6:
+                families.append(socket.AF_INET6)
+
+        while True:
+            port = 0
+            with ExitStack() as stack:
+                for family in families:
+                    sock = stack.enter_context(socket.socket(family, self._kind))
+                    addr = "::1" if family == socket.AF_INET6 else "127.0.0.1"
+                    try:
+                        sock.bind((addr, port))
+                    except OSError:
+                        break
+
+                    if not port:
+                        port = sock.getsockname()[1]
+                else:
+                    if port not in self._generated:
+                        self._generated.add(port)
+                        return port
+
+
+@pytest.fixture(scope="session")
+def free_tcp_port_factory() -> FreePortFactory:
+    return FreePortFactory(socket.SOCK_STREAM)
+
+
+@pytest.fixture(scope="session")
+def free_udp_port_factory() -> FreePortFactory:
+    return FreePortFactory(socket.SOCK_DGRAM)
+
+
+@pytest.fixture
+def free_tcp_port(free_tcp_port_factory: Callable[[], int]) -> int:
+    return free_tcp_port_factory()
+
+
+@pytest.fixture
+def free_udp_port(free_udp_port_factory: Callable[[], int]) -> int:
+    return free_udp_port_factory()

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/streams/buffered.py

@@ -0,0 +1,188 @@
+from __future__ import annotations
+
+__all__ = (
+    "BufferedByteReceiveStream",
+    "BufferedByteStream",
+    "BufferedConnectable",
+)
+
+import sys
+from collections.abc import Callable, Iterable, Mapping
+from dataclasses import dataclass, field
+from typing import Any, SupportsIndex
+
+from .. import ClosedResourceError, DelimiterNotFound, EndOfStream, IncompleteRead
+from ..abc import (
+    AnyByteReceiveStream,
+    AnyByteStream,
+    AnyByteStreamConnectable,
+    ByteReceiveStream,
+    ByteStream,
+    ByteStreamConnectable,
+)
+
+if sys.version_info >= (3, 12):
+    from typing import override
+else:
+    from typing_extensions import override
+
+
+@dataclass(eq=False)
+class BufferedByteReceiveStream(ByteReceiveStream):
+    """
+    Wraps any bytes-based receive stream and uses a buffer to provide sophisticated
+    receiving capabilities in the form of a byte stream.
+    """
+
+    receive_stream: AnyByteReceiveStream
+    _buffer: bytearray = field(init=False, default_factory=bytearray)
+    _closed: bool = field(init=False, default=False)
+
+    async def aclose(self) -> None:
+        await self.receive_stream.aclose()
+        self._closed = True
+
+    @property
+    def buffer(self) -> bytes:
+        """The bytes currently in the buffer."""
+        return bytes(self._buffer)
+
+    @property
+    def extra_attributes(self) -> Mapping[Any, Callable[[], Any]]:
+        return self.receive_stream.extra_attributes
+
+    def feed_data(self, data: Iterable[SupportsIndex], /) -> None:
+        """
+        Append data directly into the buffer.
+
+        Any data in the buffer will be consumed by receive operations before receiving
+        anything from the wrapped stream.
+
+        :param data: the data to append to the buffer (can be bytes or anything else
+            that supports ``__index__()``)
+
+        """
+        self._buffer.extend(data)
+
+    async def receive(self, max_bytes: int = 65536) -> bytes:
+        if self._closed:
+            raise ClosedResourceError
+
+        if self._buffer:
+            chunk = bytes(self._buffer[:max_bytes])
+            del self._buffer[:max_bytes]
+            return chunk
+        elif isinstance(self.receive_stream, ByteReceiveStream):
+            return await self.receive_stream.receive(max_bytes)
+        else:
+            # With a bytes-oriented object stream, we need to handle any surplus bytes
+            # we get from the receive() call
+            chunk = await self.receive_stream.receive()
+            if len(chunk) > max_bytes:
+                # Save the surplus bytes in the buffer
+                self._buffer.extend(chunk[max_bytes:])
+                return chunk[:max_bytes]
+            else:
+                return chunk
+
+    async def receive_exactly(self, nbytes: int) -> bytes:
+        """
+        Read exactly the given amount of bytes from the stream.
+
+        :param nbytes: the number of bytes to read
+        :return: the bytes read
+        :raises ~anyio.IncompleteRead: if the stream was closed before the requested
+            amount of bytes could be read from the stream
+
+        """
+        while True:
+            remaining = nbytes - len(self._buffer)
+            if remaining <= 0:
+                retval = self._buffer[:nbytes]
+                del self._buffer[:nbytes]
+                return bytes(retval)
+
+            try:
+                if isinstance(self.receive_stream, ByteReceiveStream):
+                    chunk = await self.receive_stream.receive(remaining)
+                else:
+                    chunk = await self.receive_stream.receive()
+            except EndOfStream as exc:
+                raise IncompleteRead from exc
+
+            self._buffer.extend(chunk)
+
+    async def receive_until(self, delimiter: bytes, max_bytes: int) -> bytes:
+        """
+        Read from the stream until the delimiter is found or max_bytes have been read.
+
+        :param delimiter: the marker to look for in the stream
+        :param max_bytes: maximum number of bytes that will be read before raising
+            :exc:`~anyio.DelimiterNotFound`
+        :return: the bytes read (not including the delimiter)
+        :raises ~anyio.IncompleteRead: if the stream was closed before the delimiter
+            was found
+        :raises ~anyio.DelimiterNotFound: if the delimiter is not found within the
+            bytes read up to the maximum allowed
+
+        """
+        delimiter_size = len(delimiter)
+        offset = 0
+        while True:
+            # Check if the delimiter can be found in the current buffer
+            index = self._buffer.find(delimiter, offset)
+            if index >= 0:
+                found = self._buffer[:index]
+                del self._buffer[: index + len(delimiter) :]
+                return bytes(found)
+
+            # Check if the buffer is already at or over the limit
+            if len(self._buffer) >= max_bytes:
+                raise DelimiterNotFound(max_bytes)
+
+            # Read more data into the buffer from the socket
+            try:
+                data = await self.receive_stream.receive()
+            except EndOfStream as exc:
+                raise IncompleteRead from exc
+
+            # Move the offset forward and add the new data to the buffer
+            offset = max(len(self._buffer) - delimiter_size + 1, 0)
+            self._buffer.extend(data)
+
+
+class BufferedByteStream(BufferedByteReceiveStream, ByteStream):
+    """
+    A full-duplex variant of :class:`BufferedByteReceiveStream`. All writes are passed
+    through to the wrapped stream as-is.
+    """
+
+    def __init__(self, stream: AnyByteStream):
+        """
+        :param stream: the stream to be wrapped
+
+        """
+        super().__init__(stream)
+        self._stream = stream
+
+    @override
+    async def send_eof(self) -> None:
+        await self._stream.send_eof()
+
+    @override
+    async def send(self, item: bytes) -> None:
+        await self._stream.send(item)
+
+
+class BufferedConnectable(ByteStreamConnectable):
+    def __init__(self, connectable: AnyByteStreamConnectable):
+        """
+        :param connectable: the connectable to wrap
+
+        """
+        self.connectable = connectable
+
+    @override
+    async def connect(self) -> BufferedByteStream:
+        stream = await self.connectable.connect()
+        return BufferedByteStream(stream)

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/streams/file.py

@@ -0,0 +1,154 @@
+from __future__ import annotations
+
+__all__ = (
+    "FileReadStream",
+    "FileStreamAttribute",
+    "FileWriteStream",
+)
+
+from collections.abc import Callable, Mapping
+from io import SEEK_SET, UnsupportedOperation
+from os import PathLike
+from pathlib import Path
+from typing import IO, Any
+
+from .. import (
+    BrokenResourceError,
+    ClosedResourceError,
+    EndOfStream,
+    TypedAttributeSet,
+    to_thread,
+    typed_attribute,
+)
+from ..abc import ByteReceiveStream, ByteSendStream
+
+
+class FileStreamAttribute(TypedAttributeSet):
+    #: the open file descriptor
+    file: IO[bytes] = typed_attribute()
+    #: the path of the file on the file system, if available (file must be a real file)
+    path: Path = typed_attribute()
+    #: the file number, if available (file must be a real file or a TTY)
+    fileno: int = typed_attribute()
+
+
+class _BaseFileStream:
+    def __init__(self, file: IO[bytes]):
+        self._file = file
+
+    async def aclose(self) -> None:
+        await to_thread.run_sync(self._file.close)
+
+    @property
+    def extra_attributes(self) -> Mapping[Any, Callable[[], Any]]:
+        attributes: dict[Any, Callable[[], Any]] = {
+            FileStreamAttribute.file: lambda: self._file,
+        }
+
+        if hasattr(self._file, "name"):
+            attributes[FileStreamAttribute.path] = lambda: Path(self._file.name)
+
+        try:
+            self._file.fileno()
+        except UnsupportedOperation:
+            pass
+        else:
+            attributes[FileStreamAttribute.fileno] = lambda: self._file.fileno()
+
+        return attributes
+
+
+class FileReadStream(_BaseFileStream, ByteReceiveStream):
+    """
+    A byte stream that reads from a file in the file system.
+
+    :param file: a file that has been opened for reading in binary mode
+
+    .. versionadded:: 3.0
+    """
+
+    @classmethod
+    async def from_path(cls, path: str | PathLike[str]) -> FileReadStream:
+        """
+        Create a file read stream by opening the given file.
+
+        :param path: path of the file to read from
+
+        """
+        file = await to_thread.run_sync(Path(path).open, "rb")
+        return cls(file)
+
+    async def receive(self, max_bytes: int = 65536) -> bytes:
+        try:
+            data = await to_thread.run_sync(self._file.read, max_bytes)
+        except ValueError:
+            raise ClosedResourceError from None
+        except OSError as exc:
+            raise BrokenResourceError from exc
+
+        if data:
+            return data
+        else:
+            raise EndOfStream
+
+    async def seek(self, position: int, whence: int = SEEK_SET) -> int:
+        """
+        Seek the file to the given position.
+
+        .. seealso:: :meth:`io.IOBase.seek`
+
+        .. note:: Not all file descriptors are seekable.
+
+        :param position: position to seek the file to
+        :param whence: controls how ``position`` is interpreted
+        :return: the new absolute position
+        :raises OSError: if the file is not seekable
+
+        """
+        return await to_thread.run_sync(self._file.seek, position, whence)
+
+    async def tell(self) -> int:
+        """
+        Return the current stream position.
+
+        .. note:: Not all file descriptors are seekable.
+
+        :return: the current absolute position
+        :raises OSError: if the file is not seekable
+
+        """
+        return await to_thread.run_sync(self._file.tell)
+
+
+class FileWriteStream(_BaseFileStream, ByteSendStream):
+    """
+    A byte stream that writes to a file in the file system.
+
+    :param file: a file that has been opened for writing in binary mode
+
+    .. versionadded:: 3.0
+    """
+
+    @classmethod
+    async def from_path(
+        cls, path: str | PathLike[str], append: bool = False
+    ) -> FileWriteStream:
+        """
+        Create a file write stream by opening the given file for writing.
+
+        :param path: path of the file to write to
+        :param append: if ``True``, open the file for appending; if ``False``, any
+            existing file at the given path will be truncated
+
+        """
+        mode = "ab" if append else "wb"
+        file = await to_thread.run_sync(Path(path).open, mode)
+        return cls(file)
+
+    async def send(self, item: bytes) -> None:
+        try:
+            await to_thread.run_sync(self._file.write, item)
+        except ValueError:
+            raise ClosedResourceError from None
+        except OSError as exc:
+            raise BrokenResourceError from exc

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/streams/memory.py

@@ -0,0 +1,325 @@
+from __future__ import annotations
+
+__all__ = (
+    "MemoryObjectReceiveStream",
+    "MemoryObjectSendStream",
+    "MemoryObjectStreamStatistics",
+)
+
+import warnings
+from collections import OrderedDict, deque
+from dataclasses import dataclass, field
+from types import TracebackType
+from typing import Generic, NamedTuple, TypeVar
+
+from .. import (
+    BrokenResourceError,
+    ClosedResourceError,
+    EndOfStream,
+    WouldBlock,
+)
+from .._core._testing import TaskInfo, get_current_task
+from ..abc import Event, ObjectReceiveStream, ObjectSendStream
+from ..lowlevel import checkpoint
+
+T_Item = TypeVar("T_Item")
+T_co = TypeVar("T_co", covariant=True)
+T_contra = TypeVar("T_contra", contravariant=True)
+
+
+class MemoryObjectStreamStatistics(NamedTuple):
+    current_buffer_used: int  #: number of items stored in the buffer
+    #: maximum number of items that can be stored on this stream (or :data:`math.inf`)
+    max_buffer_size: float
+    open_send_streams: int  #: number of unclosed clones of the send stream
+    open_receive_streams: int  #: number of unclosed clones of the receive stream
+    #: number of tasks blocked on :meth:`MemoryObjectSendStream.send`
+    tasks_waiting_send: int
+    #: number of tasks blocked on :meth:`MemoryObjectReceiveStream.receive`
+    tasks_waiting_receive: int
+
+
+@dataclass(eq=False)
+class _MemoryObjectItemReceiver(Generic[T_Item]):
+    task_info: TaskInfo = field(init=False, default_factory=get_current_task)
+    item: T_Item = field(init=False)
+
+    def __repr__(self) -> str:
+        # When item is not defined, we get following error with default __repr__:
+        # AttributeError: 'MemoryObjectItemReceiver' object has no attribute 'item'
+        item = getattr(self, "item", None)
+        return f"{self.__class__.__name__}(task_info={self.task_info}, item={item!r})"
+
+
+@dataclass(eq=False)
+class _MemoryObjectStreamState(Generic[T_Item]):
+    max_buffer_size: float = field()
+    buffer: deque[T_Item] = field(init=False, default_factory=deque)
+    open_send_channels: int = field(init=False, default=0)
+    open_receive_channels: int = field(init=False, default=0)
+    waiting_receivers: OrderedDict[Event, _MemoryObjectItemReceiver[T_Item]] = field(
+        init=False, default_factory=OrderedDict
+    )
+    waiting_senders: OrderedDict[Event, T_Item] = field(
+        init=False, default_factory=OrderedDict
+    )
+
+    def statistics(self) -> MemoryObjectStreamStatistics:
+        return MemoryObjectStreamStatistics(
+            len(self.buffer),
+            self.max_buffer_size,
+            self.open_send_channels,
+            self.open_receive_channels,
+            len(self.waiting_senders),
+            len(self.waiting_receivers),
+        )
+
+
+@dataclass(eq=False)
+class MemoryObjectReceiveStream(Generic[T_co], ObjectReceiveStream[T_co]):
+    _state: _MemoryObjectStreamState[T_co]
+    _closed: bool = field(init=False, default=False)
+
+    def __post_init__(self) -> None:
+        self._state.open_receive_channels += 1
+
+    def receive_nowait(self) -> T_co:
+        """
+        Receive the next item if it can be done without waiting.
+
+        :return: the received item
+        :raises ~anyio.ClosedResourceError: if this send stream has been closed
+        :raises ~anyio.EndOfStream: if the buffer is empty and this stream has been
+            closed from the sending end
+        :raises ~anyio.WouldBlock: if there are no items in the buffer and no tasks
+            waiting to send
+
+        """
+        if self._closed:
+            raise ClosedResourceError
+
+        if self._state.waiting_senders:
+            # Get the item from the next sender
+            send_event, item = self._state.waiting_senders.popitem(last=False)
+            self._state.buffer.append(item)
+            send_event.set()
+
+        if self._state.buffer:
+            return self._state.buffer.popleft()
+        elif not self._state.open_send_channels:
+            raise EndOfStream
+
+        raise WouldBlock
+
+    async def receive(self) -> T_co:
+        await checkpoint()
+        try:
+            return self.receive_nowait()
+        except WouldBlock:
+            # Add ourselves in the queue
+            receive_event = Event()
+            receiver = _MemoryObjectItemReceiver[T_co]()
+            self._state.waiting_receivers[receive_event] = receiver
+
+            try:
+                await receive_event.wait()
+            finally:
+                self._state.waiting_receivers.pop(receive_event, None)
+
+            try:
+                return receiver.item
+            except AttributeError:
+                raise EndOfStream from None
+
+    def clone(self) -> MemoryObjectReceiveStream[T_co]:
+        """
+        Create a clone of this receive stream.
+
+        Each clone can be closed separately. Only when all clones have been closed will
+        the receiving end of the memory stream be considered closed by the sending ends.
+
+        :return: the cloned stream
+
+        """
+        if self._closed:
+            raise ClosedResourceError
+
+        return MemoryObjectReceiveStream(_state=self._state)
+
+    def close(self) -> None:
+        """
+        Close the stream.
+
+        This works the exact same way as :meth:`aclose`, but is provided as a special
+        case for the benefit of synchronous callbacks.
+
+        """
+        if not self._closed:
+            self._closed = True
+            self._state.open_receive_channels -= 1
+            if self._state.open_receive_channels == 0:
+                send_events = list(self._state.waiting_senders.keys())
+                for event in send_events:
+                    event.set()
+
+    async def aclose(self) -> None:
+        self.close()
+
+    def statistics(self) -> MemoryObjectStreamStatistics:
+        """
+        Return statistics about the current state of this stream.
+
+        .. versionadded:: 3.0
+        """
+        return self._state.statistics()
+
+    def __enter__(self) -> MemoryObjectReceiveStream[T_co]:
+        return self
+
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        self.close()
+
+    def __del__(self) -> None:
+        if not self._closed:
+            warnings.warn(
+                f"Unclosed <{self.__class__.__name__} at {id(self):x}>",
+                ResourceWarning,
+                stacklevel=1,
+                source=self,
+            )
+
+
+@dataclass(eq=False)
+class MemoryObjectSendStream(Generic[T_contra], ObjectSendStream[T_contra]):
+    _state: _MemoryObjectStreamState[T_contra]
+    _closed: bool = field(init=False, default=False)
+
+    def __post_init__(self) -> None:
+        self._state.open_send_channels += 1
+
+    def send_nowait(self, item: T_contra) -> None:
+        """
+        Send an item immediately if it can be done without waiting.
+
+        :param item: the item to send
+        :raises ~anyio.ClosedResourceError: if this send stream has been closed
+        :raises ~anyio.BrokenResourceError: if the stream has been closed from the
+            receiving end
+        :raises ~anyio.WouldBlock: if the buffer is full and there are no tasks waiting
+            to receive
+
+        """
+        if self._closed:
+            raise ClosedResourceError
+        if not self._state.open_receive_channels:
+            raise BrokenResourceError
+
+        while self._state.waiting_receivers:
+            receive_event, receiver = self._state.waiting_receivers.popitem(last=False)
+            if not receiver.task_info.has_pending_cancellation():
+                receiver.item = item
+                receive_event.set()
+                return
+
+        if len(self._state.buffer) < self._state.max_buffer_size:
+            self._state.buffer.append(item)
+        else:
+            raise WouldBlock
+
+    async def send(self, item: T_contra) -> None:
+        """
+        Send an item to the stream.
+
+        If the buffer is full, this method blocks until there is again room in the
+        buffer or the item can be sent directly to a receiver.
+
+        :param item: the item to send
+        :raises ~anyio.ClosedResourceError: if this send stream has been closed
+        :raises ~anyio.BrokenResourceError: if the stream has been closed from the
+            receiving end
+
+        """
+        await checkpoint()
+        try:
+            self.send_nowait(item)
+        except WouldBlock:
+            # Wait until there's someone on the receiving end
+            send_event = Event()
+            self._state.waiting_senders[send_event] = item
+            try:
+                await send_event.wait()
+            except BaseException:
+                self._state.waiting_senders.pop(send_event, None)
+                raise
+
+            if send_event in self._state.waiting_senders:
+                del self._state.waiting_senders[send_event]
+                raise BrokenResourceError from None
+
+    def clone(self) -> MemoryObjectSendStream[T_contra]:
+        """
+        Create a clone of this send stream.
+
+        Each clone can be closed separately. Only when all clones have been closed will
+        the sending end of the memory stream be considered closed by the receiving ends.
+
+        :return: the cloned stream
+
+        """
+        if self._closed:
+            raise ClosedResourceError
+
+        return MemoryObjectSendStream(_state=self._state)
+
+    def close(self) -> None:
+        """
+        Close the stream.
+
+        This works the exact same way as :meth:`aclose`, but is provided as a special
+        case for the benefit of synchronous callbacks.
+
+        """
+        if not self._closed:
+            self._closed = True
+            self._state.open_send_channels -= 1
+            if self._state.open_send_channels == 0:
+                receive_events = list(self._state.waiting_receivers.keys())
+                self._state.waiting_receivers.clear()
+                for event in receive_events:
+                    event.set()
+
+    async def aclose(self) -> None:
+        self.close()
+
+    def statistics(self) -> MemoryObjectStreamStatistics:
+        """
+        Return statistics about the current state of this stream.
+
+        .. versionadded:: 3.0
+        """
+        return self._state.statistics()
+
+    def __enter__(self) -> MemoryObjectSendStream[T_contra]:
+        return self
+
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_val: BaseException | None,
+        exc_tb: TracebackType | None,
+    ) -> None:
+        self.close()
+
+    def __del__(self) -> None:
+        if not self._closed:
+            warnings.warn(
+                f"Unclosed <{self.__class__.__name__} at {id(self):x}>",
+                ResourceWarning,
+                stacklevel=1,
+                source=self,
+            )

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/streams/stapled.py

@@ -0,0 +1,147 @@
+from __future__ import annotations
+
+__all__ = (
+    "MultiListener",
+    "StapledByteStream",
+    "StapledObjectStream",
+)
+
+from collections.abc import Callable, Mapping, Sequence
+from dataclasses import dataclass
+from typing import Any, Generic, TypeVar
+
+from ..abc import (
+    ByteReceiveStream,
+    ByteSendStream,
+    ByteStream,
+    Listener,
+    ObjectReceiveStream,
+    ObjectSendStream,
+    ObjectStream,
+    TaskGroup,
+)
+
+T_Item = TypeVar("T_Item")
+T_Stream = TypeVar("T_Stream")
+
+
+@dataclass(eq=False)
+class StapledByteStream(ByteStream):
+    """
+    Combines two byte streams into a single, bidirectional byte stream.
+
+    Extra attributes will be provided from both streams, with the receive stream
+    providing the values in case of a conflict.
+
+    :param ByteSendStream send_stream: the sending byte stream
+    :param ByteReceiveStream receive_stream: the receiving byte stream
+    """
+
+    send_stream: ByteSendStream
+    receive_stream: ByteReceiveStream
+
+    async def receive(self, max_bytes: int = 65536) -> bytes:
+        return await self.receive_stream.receive(max_bytes)
+
+    async def send(self, item: bytes) -> None:
+        await self.send_stream.send(item)
+
+    async def send_eof(self) -> None:
+        await self.send_stream.aclose()
+
+    async def aclose(self) -> None:
+        await self.send_stream.aclose()
+        await self.receive_stream.aclose()
+
+    @property
+    def extra_attributes(self) -> Mapping[Any, Callable[[], Any]]:
+        return {
+            **self.send_stream.extra_attributes,
+            **self.receive_stream.extra_attributes,
+        }
+
+
+@dataclass(eq=False)
+class StapledObjectStream(Generic[T_Item], ObjectStream[T_Item]):
+    """
+    Combines two object streams into a single, bidirectional object stream.
+
+    Extra attributes will be provided from both streams, with the receive stream
+    providing the values in case of a conflict.
+
+    :param ObjectSendStream send_stream: the sending object stream
+    :param ObjectReceiveStream receive_stream: the receiving object stream
+    """
+
+    send_stream: ObjectSendStream[T_Item]
+    receive_stream: ObjectReceiveStream[T_Item]
+
+    async def receive(self) -> T_Item:
+        return await self.receive_stream.receive()
+
+    async def send(self, item: T_Item) -> None:
+        await self.send_stream.send(item)
+
+    async def send_eof(self) -> None:
+        await self.send_stream.aclose()
+
+    async def aclose(self) -> None:
+        await self.send_stream.aclose()
+        await self.receive_stream.aclose()
+
+    @property
+    def extra_attributes(self) -> Mapping[Any, Callable[[], Any]]:
+        return {
+            **self.send_stream.extra_attributes,
+            **self.receive_stream.extra_attributes,
+        }
+
+
+@dataclass(eq=False)
+class MultiListener(Generic[T_Stream], Listener[T_Stream]):
+    """
+    Combines multiple listeners into one, serving connections from all of them at once.
+
+    Any MultiListeners in the given collection of listeners will have their listeners
+    moved into this one.
+
+    Extra attributes are provided from each listener, with each successive listener
+    overriding any conflicting attributes from the previous one.
+
+    :param listeners: listeners to serve
+    :type listeners: Sequence[Listener[T_Stream]]
+    """
+
+    listeners: Sequence[Listener[T_Stream]]
+
+    def __post_init__(self) -> None:
+        listeners: list[Listener[T_Stream]] = []
+        for listener in self.listeners:
+            if isinstance(listener, MultiListener):
+                listeners.extend(listener.listeners)
+                del listener.listeners[:]  # type: ignore[attr-defined]
+            else:
+                listeners.append(listener)
+
+        self.listeners = listeners
+
+    async def serve(
+        self, handler: Callable[[T_Stream], Any], task_group: TaskGroup | None = None
+    ) -> None:
+        from .. import create_task_group
+
+        async with create_task_group() as tg:
+            for listener in self.listeners:
+                tg.start_soon(listener.serve, handler, task_group)
+
+    async def aclose(self) -> None:
+        for listener in self.listeners:
+            await listener.aclose()
+
+    @property
+    def extra_attributes(self) -> Mapping[Any, Callable[[], Any]]:
+        attributes: dict = {}
+        for listener in self.listeners:
+            attributes.update(listener.extra_attributes)
+
+        return attributes

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/streams/text.py

@@ -0,0 +1,176 @@
+from __future__ import annotations
+
+__all__ = (
+    "TextConnectable",
+    "TextReceiveStream",
+    "TextSendStream",
+    "TextStream",
+)
+
+import codecs
+import sys
+from collections.abc import Callable, Mapping
+from dataclasses import InitVar, dataclass, field
+from typing import Any
+
+from ..abc import (
+    AnyByteReceiveStream,
+    AnyByteSendStream,
+    AnyByteStream,
+    AnyByteStreamConnectable,
+    ObjectReceiveStream,
+    ObjectSendStream,
+    ObjectStream,
+    ObjectStreamConnectable,
+)
+
+if sys.version_info >= (3, 12):
+    from typing import override
+else:
+    from typing_extensions import override
+
+
+@dataclass(eq=False)
+class TextReceiveStream(ObjectReceiveStream[str]):
+    """
+    Stream wrapper that decodes bytes to strings using the given encoding.
+
+    Decoding is done using :class:`~codecs.IncrementalDecoder` which returns any
+    completely received unicode characters as soon as they come in.
+
+    :param transport_stream: any bytes-based receive stream
+    :param encoding: character encoding to use for decoding bytes to strings (defaults
+        to ``utf-8``)
+    :param errors: handling scheme for decoding errors (defaults to ``strict``; see the
+        `codecs module documentation`_ for a comprehensive list of options)
+
+    .. _codecs module documentation:
+        https://docs.python.org/3/library/codecs.html#codec-objects
+    """
+
+    transport_stream: AnyByteReceiveStream
+    encoding: InitVar[str] = "utf-8"
+    errors: InitVar[str] = "strict"
+    _decoder: codecs.IncrementalDecoder = field(init=False)
+
+    def __post_init__(self, encoding: str, errors: str) -> None:
+        decoder_class = codecs.getincrementaldecoder(encoding)
+        self._decoder = decoder_class(errors=errors)
+
+    async def receive(self) -> str:
+        while True:
+            chunk = await self.transport_stream.receive()
+            decoded = self._decoder.decode(chunk)
+            if decoded:
+                return decoded
+
+    async def aclose(self) -> None:
+        await self.transport_stream.aclose()
+        self._decoder.reset()
+
+    @property
+    def extra_attributes(self) -> Mapping[Any, Callable[[], Any]]:
+        return self.transport_stream.extra_attributes
+
+
+@dataclass(eq=False)
+class TextSendStream(ObjectSendStream[str]):
+    """
+    Sends strings to the wrapped stream as bytes using the given encoding.
+
+    :param AnyByteSendStream transport_stream: any bytes-based send stream
+    :param str encoding: character encoding to use for encoding strings to bytes
+        (defaults to ``utf-8``)
+    :param str errors: handling scheme for encoding errors (defaults to ``strict``; see
+        the `codecs module documentation`_ for a comprehensive list of options)
+
+    .. _codecs module documentation:
+        https://docs.python.org/3/library/codecs.html#codec-objects
+    """
+
+    transport_stream: AnyByteSendStream
+    encoding: InitVar[str] = "utf-8"
+    errors: str = "strict"
+    _encoder: Callable[..., tuple[bytes, int]] = field(init=False)
+
+    def __post_init__(self, encoding: str) -> None:
+        self._encoder = codecs.getencoder(encoding)
+
+    async def send(self, item: str) -> None:
+        encoded = self._encoder(item, self.errors)[0]
+        await self.transport_stream.send(encoded)
+
+    async def aclose(self) -> None:
+        await self.transport_stream.aclose()
+
+    @property
+    def extra_attributes(self) -> Mapping[Any, Callable[[], Any]]:
+        return self.transport_stream.extra_attributes
+
+
+@dataclass(eq=False)
+class TextStream(ObjectStream[str]):
+    """
+    A bidirectional stream that decodes bytes to strings on receive and encodes strings
+    to bytes on send.
+
+    Extra attributes will be provided from both streams, with the receive stream
+    providing the values in case of a conflict.
+
+    :param AnyByteStream transport_stream: any bytes-based stream
+    :param str encoding: character encoding to use for encoding/decoding strings to/from
+        bytes (defaults to ``utf-8``)
+    :param str errors: handling scheme for encoding errors (defaults to ``strict``; see
+        the `codecs module documentation`_ for a comprehensive list of options)
+
+    .. _codecs module documentation:
+        https://docs.python.org/3/library/codecs.html#codec-objects
+    """
+
+    transport_stream: AnyByteStream
+    encoding: InitVar[str] = "utf-8"
+    errors: InitVar[str] = "strict"
+    _receive_stream: TextReceiveStream = field(init=False)
+    _send_stream: TextSendStream = field(init=False)
+
+    def __post_init__(self, encoding: str, errors: str) -> None:
+        self._receive_stream = TextReceiveStream(
+            self.transport_stream, encoding=encoding, errors=errors
+        )
+        self._send_stream = TextSendStream(
+            self.transport_stream, encoding=encoding, errors=errors
+        )
+
+    async def receive(self) -> str:
+        return await self._receive_stream.receive()
+
+    async def send(self, item: str) -> None:
+        await self._send_stream.send(item)
+
+    async def send_eof(self) -> None:
+        await self.transport_stream.send_eof()
+
+    async def aclose(self) -> None:
+        await self._send_stream.aclose()
+        await self._receive_stream.aclose()
+
+    @property
+    def extra_attributes(self) -> Mapping[Any, Callable[[], Any]]:
+        return {
+            **self._send_stream.extra_attributes,
+            **self._receive_stream.extra_attributes,
+        }
+
+
+class TextConnectable(ObjectStreamConnectable[str]):
+    def __init__(self, connectable: AnyByteStreamConnectable):
+        """
+        :param connectable: the bytestream endpoint to wrap
+
+        """
+        self.connectable = connectable
+
+    @override
+    async def connect(self) -> TextStream:
+        stream = await self.connectable.connect()
+        return TextStream(stream)

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/streams/tls.py

@@ -0,0 +1,421 @@
+from __future__ import annotations
+
+__all__ = (
+    "TLSAttribute",
+    "TLSConnectable",
+    "TLSListener",
+    "TLSStream",
+)
+
+import logging
+import re
+import ssl
+import sys
+from collections.abc import Callable, Mapping
+from dataclasses import dataclass
+from functools import wraps
+from ssl import SSLContext
+from typing import Any, TypeAlias, TypeVar
+
+from .. import (
+    BrokenResourceError,
+    EndOfStream,
+    aclose_forcefully,
+    get_cancelled_exc_class,
+    to_thread,
+)
+from .._core._typedattr import TypedAttributeSet, typed_attribute
+from ..abc import (
+    AnyByteStream,
+    AnyByteStreamConnectable,
+    ByteStream,
+    ByteStreamConnectable,
+    Listener,
+    TaskGroup,
+)
+
+if sys.version_info >= (3, 11):
+    from typing import TypeVarTuple, Unpack
+else:
+    from typing_extensions import TypeVarTuple, Unpack
+
+if sys.version_info >= (3, 12):
+    from typing import override
+else:
+    from typing_extensions import override
+
+T_Retval = TypeVar("T_Retval")
+PosArgsT = TypeVarTuple("PosArgsT")
+_PCTRTT: TypeAlias = tuple[tuple[str, str], ...]
+_PCTRTTT: TypeAlias = tuple[_PCTRTT, ...]
+
+
+class TLSAttribute(TypedAttributeSet):
+    """Contains Transport Layer Security related attributes."""
+
+    #: the selected ALPN protocol
+    alpn_protocol: str | None = typed_attribute()
+    #: the channel binding for type ``tls-unique``
+    channel_binding_tls_unique: bytes = typed_attribute()
+    #: the selected cipher
+    cipher: tuple[str, str, int] = typed_attribute()
+    #: the peer certificate in dictionary form (see :meth:`ssl.SSLSocket.getpeercert`
+    # for more information)
+    peer_certificate: None | (dict[str, str | _PCTRTTT | _PCTRTT]) = typed_attribute()
+    #: the peer certificate in binary form
+    peer_certificate_binary: bytes | None = typed_attribute()
+    #: ``True`` if this is the server side of the connection
+    server_side: bool = typed_attribute()
+    #: ciphers shared by the client during the TLS handshake (``None`` if this is the
+    #: client side)
+    shared_ciphers: list[tuple[str, str, int]] | None = typed_attribute()
+    #: the :class:`~ssl.SSLObject` used for encryption
+    ssl_object: ssl.SSLObject = typed_attribute()
+    #: ``True`` if this stream does (and expects) a closing TLS handshake when the
+    #: stream is being closed
+    standard_compatible: bool = typed_attribute()
+    #: the TLS protocol version (e.g. ``TLSv1.2``)
+    tls_version: str = typed_attribute()
+
+
+@dataclass(eq=False)
+class TLSStream(ByteStream):
+    """
+    A stream wrapper that encrypts all sent data and decrypts received data.
+
+    This class has no public initializer; use :meth:`wrap` instead.
+    All extra attributes from :class:`~TLSAttribute` are supported.
+
+    :var AnyByteStream transport_stream: the wrapped stream
+
+    """
+
+    transport_stream: AnyByteStream
+    standard_compatible: bool
+    _ssl_object: ssl.SSLObject
+    _read_bio: ssl.MemoryBIO
+    _write_bio: ssl.MemoryBIO
+
+    @classmethod
+    async def wrap(
+        cls,
+        transport_stream: AnyByteStream,
+        *,
+        server_side: bool | None = None,
+        hostname: str | None = None,
+        ssl_context: ssl.SSLContext | None = None,
+        standard_compatible: bool = True,
+    ) -> TLSStream:
+        """
+        Wrap an existing stream with Transport Layer Security.
+
+        This performs a TLS handshake with the peer.
+
+        :param transport_stream: a bytes-transporting stream to wrap
+        :param server_side: ``True`` if this is the server side of the connection,
+            ``False`` if this is the client side (if omitted, will be set to ``False``
+            if ``hostname`` has been provided, ``False`` otherwise). Used only to create
+            a default context when an explicit context has not been provided.
+        :param hostname: host name of the peer (if host name checking is desired)
+        :param ssl_context: the SSLContext object to use (if not provided, a secure
+            default will be created)
+        :param standard_compatible: if ``False``, skip the closing handshake when
+            closing the connection, and don't raise an exception if the peer does the
+            same
+        :raises ~ssl.SSLError: if the TLS handshake fails
+
+        """
+        if server_side is None:
+            server_side = not hostname
+
+        if not ssl_context:
+            purpose = (
+                ssl.Purpose.CLIENT_AUTH if server_side else ssl.Purpose.SERVER_AUTH
+            )
+            ssl_context = ssl.create_default_context(purpose)
+
+            # Re-enable detection of unexpected EOFs if it was disabled by Python
+            if hasattr(ssl, "OP_IGNORE_UNEXPECTED_EOF"):
+                ssl_context.options &= ~ssl.OP_IGNORE_UNEXPECTED_EOF
+
+        bio_in = ssl.MemoryBIO()
+        bio_out = ssl.MemoryBIO()
+
+        # External SSLContext implementations may do blocking I/O in wrap_bio(),
+        # but the standard library implementation won't
+        if type(ssl_context) is ssl.SSLContext:
+            ssl_object = ssl_context.wrap_bio(
+                bio_in, bio_out, server_side=server_side, server_hostname=hostname
+            )
+        else:
+            ssl_object = await to_thread.run_sync(
+                ssl_context.wrap_bio,
+                bio_in,
+                bio_out,
+                server_side,
+                hostname,
+                None,
+            )
+
+        wrapper = cls(
+            transport_stream=transport_stream,
+            standard_compatible=standard_compatible,
+            _ssl_object=ssl_object,
+            _read_bio=bio_in,
+            _write_bio=bio_out,
+        )
+        await wrapper._call_sslobject_method(ssl_object.do_handshake)
+        return wrapper
+
+    async def _call_sslobject_method(
+        self, func: Callable[[Unpack[PosArgsT]], T_Retval], *args: Unpack[PosArgsT]
+    ) -> T_Retval:
+        while True:
+            try:
+                result = func(*args)
+            except ssl.SSLWantReadError:
+                try:
+                    # Flush any pending writes first
+                    if self._write_bio.pending:
+                        await self.transport_stream.send(self._write_bio.read())
+
+                    data = await self.transport_stream.receive()
+                except EndOfStream:
+                    self._read_bio.write_eof()
+                except OSError as exc:
+                    self._read_bio.write_eof()
+                    self._write_bio.write_eof()
+                    raise BrokenResourceError from exc
+                else:
+                    self._read_bio.write(data)
+            except ssl.SSLWantWriteError:
+                await self.transport_stream.send(self._write_bio.read())
+            except ssl.SSLSyscallError as exc:
+                self._read_bio.write_eof()
+                self._write_bio.write_eof()
+                raise BrokenResourceError from exc
+            except ssl.SSLError as exc:
+                self._read_bio.write_eof()
+                self._write_bio.write_eof()
+                if isinstance(exc, ssl.SSLEOFError) or (
+                    exc.strerror and "UNEXPECTED_EOF_WHILE_READING" in exc.strerror
+                ):
+                    if self.standard_compatible:
+                        raise BrokenResourceError from exc
+                    else:
+                        raise EndOfStream from None
+
+                raise
+            else:
+                # Flush any pending writes first
+                if self._write_bio.pending:
+                    await self.transport_stream.send(self._write_bio.read())
+
+                return result
+
+    async def unwrap(self) -> tuple[AnyByteStream, bytes]:
+        """
+        Does the TLS closing handshake.
+
+        :return: a tuple of (wrapped byte stream, bytes left in the read buffer)
+
+        """
+        await self._call_sslobject_method(self._ssl_object.unwrap)
+        self._read_bio.write_eof()
+        self._write_bio.write_eof()
+        return self.transport_stream, self._read_bio.read()
+
+    async def aclose(self) -> None:
+        if self.standard_compatible:
+            try:
+                await self.unwrap()
+            except BaseException:
+                await aclose_forcefully(self.transport_stream)
+                raise
+
+        await self.transport_stream.aclose()
+
+    async def receive(self, max_bytes: int = 65536) -> bytes:
+        data = await self._call_sslobject_method(self._ssl_object.read, max_bytes)
+        if not data:
+            raise EndOfStream
+
+        return data
+
+    async def send(self, item: bytes) -> None:
+        await self._call_sslobject_method(self._ssl_object.write, item)
+
+    async def send_eof(self) -> None:
+        tls_version = self.extra(TLSAttribute.tls_version)
+        match = re.match(r"TLSv(\d+)(?:\.(\d+))?", tls_version)
+        if match:
+            major, minor = int(match.group(1)), int(match.group(2) or 0)
+            if (major, minor) < (1, 3):
+                raise NotImplementedError(
+                    f"send_eof() requires at least TLSv1.3; current "
+                    f"session uses {tls_version}"
+                )
+
+        raise NotImplementedError(
+            "send_eof() has not yet been implemented for TLS streams"
+        )
+
+    @property
+    def extra_attributes(self) -> Mapping[Any, Callable[[], Any]]:
+        return {
+            **self.transport_stream.extra_attributes,
+            TLSAttribute.alpn_protocol: self._ssl_object.selected_alpn_protocol,
+            TLSAttribute.channel_binding_tls_unique: (
+                self._ssl_object.get_channel_binding
+            ),
+            TLSAttribute.cipher: self._ssl_object.cipher,
+            TLSAttribute.peer_certificate: lambda: self._ssl_object.getpeercert(False),
+            TLSAttribute.peer_certificate_binary: lambda: self._ssl_object.getpeercert(
+                True
+            ),
+            TLSAttribute.server_side: lambda: self._ssl_object.server_side,
+            TLSAttribute.shared_ciphers: lambda: (
+                self._ssl_object.shared_ciphers()
+                if self._ssl_object.server_side
+                else None
+            ),
+            TLSAttribute.standard_compatible: lambda: self.standard_compatible,
+            TLSAttribute.ssl_object: lambda: self._ssl_object,
+            TLSAttribute.tls_version: self._ssl_object.version,
+        }
+
+
+@dataclass(eq=False)
+class TLSListener(Listener[TLSStream]):
+    """
+    A convenience listener that wraps another listener and auto-negotiates a TLS session
+    on every accepted connection.
+
+    If the TLS handshake times out or raises an exception,
+    :meth:`handle_handshake_error` is called to do whatever post-mortem processing is
+    deemed necessary.
+
+    Supports only the :attr:`~TLSAttribute.standard_compatible` extra attribute.
+
+    :param Listener listener: the listener to wrap
+    :param ssl_context: the SSL context object
+    :param standard_compatible: a flag passed through to :meth:`TLSStream.wrap`
+    :param handshake_timeout: time limit for the TLS handshake
+        (passed to :func:`~anyio.fail_after`)
+    """
+
+    listener: Listener[Any]
+    ssl_context: ssl.SSLContext
+    standard_compatible: bool = True
+    handshake_timeout: float = 30
+
+    @staticmethod
+    async def handle_handshake_error(exc: BaseException, stream: AnyByteStream) -> None:
+        """
+        Handle an exception raised during the TLS handshake.
+
+        This method does 3 things:
+
+        #. Forcefully closes the original stream
+        #. Logs the exception (unless it was a cancellation exception) using the
+           ``anyio.streams.tls`` logger
+        #. Reraises the exception if it was a base exception or a cancellation exception
+
+        :param exc: the exception
+        :param stream: the original stream
+
+        """
+        await aclose_forcefully(stream)
+
+        # Log all except cancellation exceptions
+        if not isinstance(exc, get_cancelled_exc_class()):
+            # CPython (as of 3.11.5) returns incorrect `sys.exc_info()` here when using
+            # any asyncio implementation, so we explicitly pass the exception to log
+            # (https://github.com/python/cpython/issues/108668). Trio does not have this
+            # issue because it works around the CPython bug.
+            logging.getLogger(__name__).exception(
+                "Error during TLS handshake", exc_info=exc
+            )
+
+        # Only reraise base exceptions and cancellation exceptions
+        if not isinstance(exc, Exception) or isinstance(exc, get_cancelled_exc_class()):
+            raise
+
+    async def serve(
+        self,
+        handler: Callable[[TLSStream], Any],
+        task_group: TaskGroup | None = None,
+    ) -> None:
+        @wraps(handler)
+        async def handler_wrapper(stream: AnyByteStream) -> None:
+            from .. import fail_after
+
+            try:
+                with fail_after(self.handshake_timeout):
+                    wrapped_stream = await TLSStream.wrap(
+                        stream,
+                        ssl_context=self.ssl_context,
+                        standard_compatible=self.standard_compatible,
+                    )
+            except BaseException as exc:
+                await self.handle_handshake_error(exc, stream)
+            else:
+                await handler(wrapped_stream)
+
+        await self.listener.serve(handler_wrapper, task_group)
+
+    async def aclose(self) -> None:
+        await self.listener.aclose()
+
+    @property
+    def extra_attributes(self) -> Mapping[Any, Callable[[], Any]]:
+        return {
+            TLSAttribute.standard_compatible: lambda: self.standard_compatible,
+        }
+
+
+class TLSConnectable(ByteStreamConnectable):
+    """
+    Wraps another connectable and does TLS negotiation after a successful connection.
+
+    :param connectable: the connectable to wrap
+    :param hostname: host name of the server (if host name checking is desired)
+    :param ssl_context: the SSLContext object to use (if not provided, a secure default
+        will be created)
+    :param standard_compatible: if ``False``, skip the closing handshake when closing
+        the connection, and don't raise an exception if the server does the same
+    """
+
+    def __init__(
+        self,
+        connectable: AnyByteStreamConnectable,
+        *,
+        hostname: str | None = None,
+        ssl_context: ssl.SSLContext | None = None,
+        standard_compatible: bool = True,
+    ) -> None:
+        self.connectable = connectable
+        self.ssl_context: SSLContext = ssl_context or ssl.create_default_context(
+            ssl.Purpose.SERVER_AUTH
+        )
+        if not isinstance(self.ssl_context, ssl.SSLContext):
+            raise TypeError(
+                "ssl_context must be an instance of ssl.SSLContext, not "
+                f"{type(self.ssl_context).__name__}"
+            )
+        self.hostname = hostname
+        self.standard_compatible = standard_compatible
+
+    @override
+    async def connect(self) -> TLSStream:
+        stream = await self.connectable.connect()
+        try:
+            return await TLSStream.wrap(
+                stream,
+                hostname=self.hostname,
+                ssl_context=self.ssl_context,
+                standard_compatible=self.standard_compatible,
+            )
+        except BaseException:
+            await aclose_forcefully(stream)
+            raise

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/to_interpreter.py

@@ -0,0 +1,246 @@
+from __future__ import annotations
+
+__all__ = (
+    "run_sync",
+    "current_default_interpreter_limiter",
+)
+
+import atexit
+import os
+import sys
+from collections import deque
+from collections.abc import Callable
+from typing import Any, Final, TypeVar
+
+from . import current_time, to_thread
+from ._core._exceptions import BrokenWorkerInterpreter
+from ._core._synchronization import CapacityLimiter
+from .lowlevel import RunVar
+
+if sys.version_info >= (3, 11):
+    from typing import TypeVarTuple, Unpack
+else:
+    from typing_extensions import TypeVarTuple, Unpack
+
+if sys.version_info >= (3, 14):
+    from concurrent.interpreters import ExecutionFailed, create
+
+    def _interp_call(
+        func: Callable[..., Any], args: tuple[Any, ...]
+    ) -> tuple[Any, bool]:
+        try:
+            retval = func(*args)
+        except BaseException as exc:
+            return exc, True
+        else:
+            return retval, False
+
+    class _Worker:
+        last_used: float = 0
+
+        def __init__(self) -> None:
+            self._interpreter = create()
+
+        def destroy(self) -> None:
+            self._interpreter.close()
+
+        def call(
+            self,
+            func: Callable[..., T_Retval],
+            args: tuple[Any, ...],
+        ) -> T_Retval:
+            try:
+                res, is_exception = self._interpreter.call(_interp_call, func, args)
+            except ExecutionFailed as exc:
+                raise BrokenWorkerInterpreter(exc.excinfo) from exc
+
+            if is_exception:
+                raise res
+
+            return res
+elif sys.version_info >= (3, 13):
+    import _interpqueues
+    import _interpreters
+
+    UNBOUND: Final = 2  # I have no clue how this works, but it was used in the stdlib
+    FMT_UNPICKLED: Final = 0
+    FMT_PICKLED: Final = 1
+    QUEUE_PICKLE_ARGS: Final = (FMT_PICKLED, UNBOUND)
+    QUEUE_UNPICKLE_ARGS: Final = (FMT_UNPICKLED, UNBOUND)
+
+    _run_func = compile(
+        """
+import _interpqueues
+from _interpreters import NotShareableError
+from pickle import loads, dumps, HIGHEST_PROTOCOL
+
+QUEUE_PICKLE_ARGS = (1, 2)
+QUEUE_UNPICKLE_ARGS = (0, 2)
+
+item = _interpqueues.get(queue_id)[0]
+try:
+    func, args = loads(item)
+    retval = func(*args)
+except BaseException as exc:
+    is_exception = True
+    retval = exc
+else:
+    is_exception = False
+
+try:
+    _interpqueues.put(queue_id, (retval, is_exception), *QUEUE_UNPICKLE_ARGS)
+except NotShareableError:
+    retval = dumps(retval, HIGHEST_PROTOCOL)
+    _interpqueues.put(queue_id, (retval, is_exception), *QUEUE_PICKLE_ARGS)
+    """,
+        "<string>",
+        "exec",
+    )
+
+    class _Worker:
+        last_used: float = 0
+
+        def __init__(self) -> None:
+            self._interpreter_id = _interpreters.create()
+            self._queue_id = _interpqueues.create(1, *QUEUE_UNPICKLE_ARGS)
+            _interpreters.set___main___attrs(
+                self._interpreter_id, {"queue_id": self._queue_id}
+            )
+
+        def destroy(self) -> None:
+            _interpqueues.destroy(self._queue_id)
+            _interpreters.destroy(self._interpreter_id)
+
+        def call(
+            self,
+            func: Callable[..., T_Retval],
+            args: tuple[Any, ...],
+        ) -> T_Retval:
+            import pickle
+
+            item = pickle.dumps((func, args), pickle.HIGHEST_PROTOCOL)
+            _interpqueues.put(self._queue_id, item, *QUEUE_PICKLE_ARGS)
+            exc_info = _interpreters.exec(self._interpreter_id, _run_func)
+            if exc_info:
+                raise BrokenWorkerInterpreter(exc_info)
+
+            res = _interpqueues.get(self._queue_id)
+            (res, is_exception), fmt = res[:2]
+            if fmt == FMT_PICKLED:
+                res = pickle.loads(res)
+
+            if is_exception:
+                raise res
+
+            return res
+else:
+
+    class _Worker:
+        last_used: float = 0
+
+        def __init__(self) -> None:
+            raise RuntimeError("subinterpreters require at least Python 3.13")
+
+        def call(
+            self,
+            func: Callable[..., T_Retval],
+            args: tuple[Any, ...],
+        ) -> T_Retval:
+            raise NotImplementedError
+
+        def destroy(self) -> None:
+            pass
+
+
+DEFAULT_CPU_COUNT: Final = 8  # this is just an arbitrarily selected value
+MAX_WORKER_IDLE_TIME = (
+    30  # seconds a subinterpreter can be idle before becoming eligible for pruning
+)
+
+T_Retval = TypeVar("T_Retval")
+PosArgsT = TypeVarTuple("PosArgsT")
+
+_idle_workers = RunVar[deque[_Worker]]("_available_workers")
+_default_interpreter_limiter = RunVar[CapacityLimiter]("_default_interpreter_limiter")
+
+
+def _stop_workers(workers: deque[_Worker]) -> None:
+    for worker in workers:
+        worker.destroy()
+
+    workers.clear()
+
+
+async def run_sync(
+    func: Callable[[Unpack[PosArgsT]], T_Retval],
+    *args: Unpack[PosArgsT],
+    limiter: CapacityLimiter | None = None,
+) -> T_Retval:
+    """
+    Call the given function with the given arguments in a subinterpreter.
+
+    .. warning:: On Python 3.13, the :mod:`concurrent.interpreters` module was not yet
+        available, so the code path for that Python version relies on an undocumented,
+        private API. As such, it is recommended to not rely on this function for anything
+        mission-critical on Python 3.13.
+
+    :param func: a callable
+    :param args: the positional arguments for the callable
+    :param limiter: capacity limiter to use to limit the total number of subinterpreters
+        running (if omitted, the default limiter is used)
+    :return: the result of the call
+    :raises BrokenWorkerInterpreter: if there's an internal error in a subinterpreter
+
+    """
+    if limiter is None:
+        limiter = current_default_interpreter_limiter()
+
+    try:
+        idle_workers = _idle_workers.get()
+    except LookupError:
+        idle_workers = deque()
+        _idle_workers.set(idle_workers)
+        atexit.register(_stop_workers, idle_workers)
+
+    async with limiter:
+        try:
+            worker = idle_workers.pop()
+        except IndexError:
+            worker = _Worker()
+
+    try:
+        return await to_thread.run_sync(
+            worker.call,
+            func,
+            args,
+            limiter=limiter,
+        )
+    finally:
+        # Prune workers that have been idle for too long
+        now = current_time()
+        while idle_workers:
+            if now - idle_workers[0].last_used <= MAX_WORKER_IDLE_TIME:
+                break
+
+            await to_thread.run_sync(idle_workers.popleft().destroy, limiter=limiter)
+
+        worker.last_used = current_time()
+        idle_workers.append(worker)
+
+
+def current_default_interpreter_limiter() -> CapacityLimiter:
+    """
+    Return the capacity limiter used by default to limit the number of concurrently
+    running subinterpreters.
+
+    Defaults to the number of CPU cores.
+
+    :return: a capacity limiter object
+
+    """
+    try:
+        return _default_interpreter_limiter.get()
+    except LookupError:
+        limiter = CapacityLimiter(os.cpu_count() or DEFAULT_CPU_COUNT)
+        _default_interpreter_limiter.set(limiter)
+        return limiter

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/to_process.py

@@ -0,0 +1,266 @@
+from __future__ import annotations
+
+__all__ = (
+    "current_default_process_limiter",
+    "process_worker",
+    "run_sync",
+)
+
+import os
+import pickle
+import subprocess
+import sys
+from collections import deque
+from collections.abc import Callable
+from importlib.util import module_from_spec, spec_from_file_location
+from typing import TypeVar, cast
+
+from ._core._eventloop import current_time, get_async_backend, get_cancelled_exc_class
+from ._core._exceptions import BrokenWorkerProcess
+from ._core._subprocesses import open_process
+from ._core._synchronization import CapacityLimiter
+from ._core._tasks import CancelScope, fail_after
+from .abc import ByteReceiveStream, ByteSendStream, Process
+from .lowlevel import RunVar, checkpoint_if_cancelled
+from .streams.buffered import BufferedByteReceiveStream
+
+if sys.version_info >= (3, 11):
+    from typing import TypeVarTuple, Unpack
+else:
+    from typing_extensions import TypeVarTuple, Unpack
+
+WORKER_MAX_IDLE_TIME = 300  # 5 minutes
+
+T_Retval = TypeVar("T_Retval")
+PosArgsT = TypeVarTuple("PosArgsT")
+
+_process_pool_workers: RunVar[set[Process]] = RunVar("_process_pool_workers")
+_process_pool_idle_workers: RunVar[deque[tuple[Process, float]]] = RunVar(
+    "_process_pool_idle_workers"
+)
+_default_process_limiter: RunVar[CapacityLimiter] = RunVar("_default_process_limiter")
+
+
+async def run_sync(  # type: ignore[return]
+    func: Callable[[Unpack[PosArgsT]], T_Retval],
+    *args: Unpack[PosArgsT],
+    cancellable: bool = False,
+    limiter: CapacityLimiter | None = None,
+) -> T_Retval:
+    """
+    Call the given function with the given arguments in a worker process.
+
+    If the ``cancellable`` option is enabled and the task waiting for its completion is
+    cancelled, the worker process running it will be abruptly terminated using SIGKILL
+    (or ``terminateProcess()`` on Windows).
+
+    :param func: a callable
+    :param args: positional arguments for the callable
+    :param cancellable: ``True`` to allow cancellation of the operation while it's
+        running
+    :param limiter: capacity limiter to use to limit the total amount of processes
+        running (if omitted, the default limiter is used)
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+    :return: an awaitable that yields the return value of the function.
+
+    """
+
+    async def send_raw_command(pickled_cmd: bytes) -> object:
+        try:
+            await stdin.send(pickled_cmd)
+            response = await buffered.receive_until(b"\n", 50)
+            status, length = response.split(b" ")
+            if status not in (b"RETURN", b"EXCEPTION"):
+                raise RuntimeError(
+                    f"Worker process returned unexpected response: {response!r}"
+                )
+
+            pickled_response = await buffered.receive_exactly(int(length))
+        except BaseException as exc:
+            workers.discard(process)
+            try:
+                process.kill()
+                with CancelScope(shield=True):
+                    await process.aclose()
+            except ProcessLookupError:
+                pass
+
+            if isinstance(exc, get_cancelled_exc_class()):
+                raise
+            else:
+                raise BrokenWorkerProcess from exc
+
+        retval = pickle.loads(pickled_response)
+        if status == b"EXCEPTION":
+            assert isinstance(retval, BaseException)
+            raise retval
+        else:
+            return retval
+
+    # First pickle the request before trying to reserve a worker process
+    await checkpoint_if_cancelled()
+    request = pickle.dumps(("run", func, args), protocol=pickle.HIGHEST_PROTOCOL)
+
+    # If this is the first run in this event loop thread, set up the necessary variables
+    try:
+        workers = _process_pool_workers.get()
+        idle_workers = _process_pool_idle_workers.get()
+    except LookupError:
+        workers = set()
+        idle_workers = deque()
+        _process_pool_workers.set(workers)
+        _process_pool_idle_workers.set(idle_workers)
+        get_async_backend().setup_process_pool_exit_at_shutdown(workers)
+
+    async with limiter or current_default_process_limiter():
+        # Pop processes from the pool (starting from the most recently used) until we
+        # find one that hasn't exited yet
+        process: Process
+        while idle_workers:
+            process, idle_since = idle_workers.pop()
+            if process.returncode is None:
+                stdin = cast(ByteSendStream, process.stdin)
+                buffered = BufferedByteReceiveStream(
+                    cast(ByteReceiveStream, process.stdout)
+                )
+
+                # Prune any other workers that have been idle for WORKER_MAX_IDLE_TIME
+                # seconds or longer
+                now = current_time()
+                killed_processes: list[Process] = []
+                while idle_workers:
+                    if now - idle_workers[0][1] < WORKER_MAX_IDLE_TIME:
+                        break
+
+                    process_to_kill, idle_since = idle_workers.popleft()
+                    process_to_kill.kill()
+                    workers.remove(process_to_kill)
+                    killed_processes.append(process_to_kill)
+
+                with CancelScope(shield=True):
+                    for killed_process in killed_processes:
+                        await killed_process.aclose()
+
+                break
+
+            workers.remove(process)
+        else:
+            command = [sys.executable, "-u", "-m", __name__]
+            process = await open_process(
+                command, stdin=subprocess.PIPE, stdout=subprocess.PIPE
+            )
+            try:
+                stdin = cast(ByteSendStream, process.stdin)
+                buffered = BufferedByteReceiveStream(
+                    cast(ByteReceiveStream, process.stdout)
+                )
+                with fail_after(20):
+                    message = await buffered.receive(6)
+
+                if message != b"READY\n":
+                    raise BrokenWorkerProcess(
+                        f"Worker process returned unexpected response: {message!r}"
+                    )
+
+                main_module_path = getattr(sys.modules["__main__"], "__file__", None)
+                pickled = pickle.dumps(
+                    ("init", sys.path, main_module_path),
+                    protocol=pickle.HIGHEST_PROTOCOL,
+                )
+                await send_raw_command(pickled)
+            except (BrokenWorkerProcess, get_cancelled_exc_class()):
+                raise
+            except BaseException as exc:
+                process.kill()
+                raise BrokenWorkerProcess(
+                    "Error during worker process initialization"
+                ) from exc
+
+            workers.add(process)
+
+        with CancelScope(shield=not cancellable):
+            try:
+                return cast(T_Retval, await send_raw_command(request))
+            finally:
+                if process in workers:
+                    idle_workers.append((process, current_time()))
+
+
+def current_default_process_limiter() -> CapacityLimiter:
+    """
+    Return the capacity limiter that is used by default to limit the number of worker
+    processes.
+
+    :return: a capacity limiter object
+
+    """
+    try:
+        return _default_process_limiter.get()
+    except LookupError:
+        limiter = CapacityLimiter(os.cpu_count() or 2)
+        _default_process_limiter.set(limiter)
+        return limiter
+
+
+def process_worker() -> None:
+    # Redirect standard streams to os.devnull so that user code won't interfere with the
+    # parent-worker communication
+    stdin = sys.stdin
+    stdout = sys.stdout
+    sys.stdin = open(os.devnull)
+    sys.stdout = open(os.devnull, "w")
+
+    stdout.buffer.write(b"READY\n")
+    while True:
+        retval = exception = None
+        try:
+            command, *args = pickle.load(stdin.buffer)
+        except EOFError:
+            return
+        except BaseException as exc:
+            exception = exc
+        else:
+            if command == "run":
+                func, args = args
+                try:
+                    retval = func(*args)
+                except BaseException as exc:
+                    exception = exc
+            elif command == "init":
+                main_module_path: str | None
+                sys.path, main_module_path = args
+                del sys.modules["__main__"]
+                if main_module_path and os.path.isfile(main_module_path):
+                    # Load the parent's main module but as __mp_main__ instead of
+                    # __main__ (like multiprocessing does) to avoid infinite recursion
+                    try:
+                        spec = spec_from_file_location("__mp_main__", main_module_path)
+                        if spec and spec.loader:
+                            main = module_from_spec(spec)
+                            spec.loader.exec_module(main)
+                            sys.modules["__main__"] = main
+                    except BaseException as exc:
+                        exception = exc
+        try:
+            if exception is not None:
+                status = b"EXCEPTION"
+                pickled = pickle.dumps(exception, pickle.HIGHEST_PROTOCOL)
+            else:
+                status = b"RETURN"
+                pickled = pickle.dumps(retval, pickle.HIGHEST_PROTOCOL)
+        except BaseException as exc:
+            exception = exc
+            status = b"EXCEPTION"
+            pickled = pickle.dumps(exc, pickle.HIGHEST_PROTOCOL)
+
+        stdout.buffer.write(b"%s %d\n" % (status, len(pickled)))
+        stdout.buffer.write(pickled)
+
+        # Respect SIGTERM
+        if isinstance(exception, SystemExit):
+            raise exception
+
+
+if __name__ == "__main__":
+    process_worker()

bioagent-bench/.venv/lib/python3.14/site-packages/anyio/to_thread.py

@@ -0,0 +1,78 @@
+from __future__ import annotations
+
+__all__ = (
+    "run_sync",
+    "current_default_thread_limiter",
+)
+
+import sys
+from collections.abc import Callable
+from typing import TypeVar
+from warnings import warn
+
+from ._core._eventloop import get_async_backend
+from .abc import CapacityLimiter
+
+if sys.version_info >= (3, 11):
+    from typing import TypeVarTuple, Unpack
+else:
+    from typing_extensions import TypeVarTuple, Unpack
+
+T_Retval = TypeVar("T_Retval")
+PosArgsT = TypeVarTuple("PosArgsT")
+
+
+async def run_sync(
+    func: Callable[[Unpack[PosArgsT]], T_Retval],
+    *args: Unpack[PosArgsT],
+    abandon_on_cancel: bool = False,
+    cancellable: bool | None = None,
+    limiter: CapacityLimiter | None = None,
+) -> T_Retval:
+    """
+    Call the given function with the given arguments in a worker thread.
+
+    If the ``abandon_on_cancel`` option is enabled and the task waiting for its
+    completion is cancelled, the thread will still run its course but its
+    return value (or any raised exception) will be ignored.
+
+    :param func: a callable
+    :param args: positional arguments for the callable
+    :param abandon_on_cancel: ``True`` to abandon the thread (leaving it to run
+        unchecked on own) if the host task is cancelled, ``False`` to ignore
+        cancellations in the host task until the operation has completed in the worker
+        thread
+    :param cancellable: deprecated alias of ``abandon_on_cancel``; will override
+        ``abandon_on_cancel`` if both parameters are passed
+    :param limiter: capacity limiter to use to limit the total amount of threads running
+        (if omitted, the default limiter is used)
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+    :return: an awaitable that yields the return value of the function.
+
+    """
+    if cancellable is not None:
+        abandon_on_cancel = cancellable
+        warn(
+            "The `cancellable=` keyword argument to `anyio.to_thread.run_sync` is "
+            "deprecated since AnyIO 4.1.0; use `abandon_on_cancel=` instead",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+
+    return await get_async_backend().run_sync_in_worker_thread(
+        func, args, abandon_on_cancel=abandon_on_cancel, limiter=limiter
+    )
+
+
+def current_default_thread_limiter() -> CapacityLimiter:
+    """
+    Return the capacity limiter that is used by default to limit the number of
+    concurrent threads.
+
+    :return: a capacity limiter object
+    :raises NoEventLoopError: if no supported asynchronous event loop is running in the
+        current thread
+
+    """
+    return get_async_backend().current_default_thread_limiter()

bioagent-bench/.venv/lib/python3.14/site-packages/certifi-2026.4.22.dist-info/INSTALLER

@@ -0,0 +1 @@
+uv

bioagent-bench/.venv/lib/python3.14/site-packages/certifi-2026.4.22.dist-info/METADATA

@@ -0,0 +1,78 @@
+Metadata-Version: 2.4
+Name: certifi
+Version: 2026.4.22
+Summary: Python package for providing Mozilla's CA Bundle.
+Home-page: https://github.com/certifi/python-certifi
+Author: Kenneth Reitz
+Author-email: me@kennethreitz.com
+License: MPL-2.0
+Project-URL: Source, https://github.com/certifi/python-certifi
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.7
+License-File: LICENSE
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: requires-python
+Dynamic: summary
+
+Certifi: Python SSL Certificates
+================================
+
+Certifi provides Mozilla's carefully curated collection of Root Certificates for
+validating the trustworthiness of SSL certificates while verifying the identity
+of TLS hosts. It has been extracted from the `Requests`_ project.
+
+Installation
+------------
+
+``certifi`` is available on PyPI. Simply install it with ``pip``::
+
+    $ pip install certifi
+
+Usage
+-----
+
+To reference the installed certificate authority (CA) bundle, you can use the
+built-in function::
+
+    >>> import certifi
+
+    >>> certifi.where()
+    '/usr/local/lib/python3.7/site-packages/certifi/cacert.pem'
+
+Or from the command line::
+
+    $ python -m certifi
+    /usr/local/lib/python3.7/site-packages/certifi/cacert.pem
+
+Enjoy!
+
+.. _`Requests`: https://requests.readthedocs.io/en/master/
+
+Addition/Removal of Certificates
+--------------------------------
+
+Certifi does not support any addition/removal or other modification of the
+CA trust store content. This project is intended to provide a reliable and
+highly portable root of trust to python deployments. Look to upstream projects
+for methods to use alternate trust.

bioagent-bench/.venv/lib/python3.14/site-packages/certifi-2026.4.22.dist-info/RECORD

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+certifi-2026.4.22.dist-info/METADATA,sha256=Ttb_6cy-0FBGq3v_ICTNPKcXKVs2i-0f4gpz42W8QVo,2474
+certifi-2026.4.22.dist-info/RECORD,,
+certifi-2026.4.22.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+certifi-2026.4.22.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+certifi-2026.4.22.dist-info/licenses/LICENSE,sha256=6TcW2mucDVpKHfYP5pWzcPBpVgPSH2-D8FPkLPwQyvc,989
+certifi-2026.4.22.dist-info/top_level.txt,sha256=KMu4vUCfsjLrkPbSNdgdekS-pVJzBAJFO__nI8NF6-U,8
+certifi/__init__.py,sha256=iBJYWtxRGHMaO1S73pWYpFn962WQ4ldof2GkfMSREJM,94
+certifi/__main__.py,sha256=xBBoj905TUWBLRGANOcf7oi6e-3dMP4cEoG9OyMs11g,243
+certifi/cacert.pem,sha256=Fr4_b-sVQIGV3P46oade-dty9ka5brvv3Gj1YlX3mfg,238641
+certifi/core.py,sha256=XFXycndG5pf37ayeF8N32HUuDafsyhkVMbO4BAPWHa0,3394
+certifi/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0

bioagent-bench/.venv/lib/python3.14/site-packages/certifi-2026.4.22.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

bioagent-bench/.venv/lib/python3.14/site-packages/certifi-2026.4.22.dist-info/licenses/LICENSE

@@ -0,0 +1,20 @@
+This package contains a modified version of ca-bundle.crt:
+
+ca-bundle.crt -- Bundle of CA Root Certificates
+
+This is a bundle of X.509 certificates of public Certificate Authorities
+(CA). These were automatically extracted from Mozilla's root certificates
+file (certdata.txt).  This file can be found in the mozilla source tree:
+https://hg.mozilla.org/mozilla-central/file/tip/security/nss/lib/ckfw/builtins/certdata.txt
+It contains the certificates in PEM format and therefore
+can be directly used with curl / libcurl / php_curl, or with
+an Apache+mod_ssl webserver for SSL client authentication.
+Just configure this file as the SSLCACertificateFile.#
+
+***** BEGIN LICENSE BLOCK *****
+This Source Code Form is subject to the terms of the Mozilla Public License,
+v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain
+one at http://mozilla.org/MPL/2.0/.
+
+***** END LICENSE BLOCK *****
+@(#) $RCSfile: certdata.txt,v $ $Revision: 1.80 $ $Date: 2011/11/03 15:11:58 $

bioagent-bench/.venv/lib/python3.14/site-packages/certifi-2026.4.22.dist-info/top_level.txt

@@ -0,0 +1 @@
+certifi