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1083 lines
39 KiB
1083 lines
39 KiB
4 years ago
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import atexit
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import collections
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import datetime
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import base64
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import signal
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from textwrap import dedent
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from async_generator import asynccontextmanager
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from contextlib import contextmanager
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from time import monotonic
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from queue import Empty
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import asyncio
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import typing as t
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from traitlets.config.configurable import LoggingConfigurable
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from traitlets import List, Unicode, Bool, Enum, Any, Type, Dict, Integer, default
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from nbformat import NotebookNode
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from nbformat.v4 import output_from_msg
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from jupyter_client import KernelManager
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from jupyter_client.client import KernelClient
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from .exceptions import (
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CellControlSignal,
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CellTimeoutError,
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DeadKernelError,
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CellExecutionComplete,
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CellExecutionError
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)
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from .util import run_sync, ensure_async
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from .output_widget import OutputWidget
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def timestamp() -> str:
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return datetime.datetime.utcnow().isoformat() + 'Z'
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class NotebookClient(LoggingConfigurable):
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"""
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Encompasses a Client for executing cells in a notebook
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"""
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timeout: int = Integer(
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None,
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allow_none=True,
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help=dedent(
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"""
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The time to wait (in seconds) for output from executions.
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If a cell execution takes longer, a TimeoutError is raised.
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``None`` or ``-1`` will disable the timeout. If ``timeout_func`` is set,
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it overrides ``timeout``.
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"""
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),
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).tag(config=True)
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timeout_func: t.Any = Any(
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default_value=None,
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allow_none=True,
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help=dedent(
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"""
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A callable which, when given the cell source as input,
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returns the time to wait (in seconds) for output from cell
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executions. If a cell execution takes longer, a TimeoutError
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is raised.
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Returning ``None`` or ``-1`` will disable the timeout for the cell.
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Not setting ``timeout_func`` will cause the preprocessor to
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default to using the ``timeout`` trait for all cells. The
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``timeout_func`` trait overrides ``timeout`` if it is not ``None``.
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"""
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),
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).tag(config=True)
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interrupt_on_timeout: bool = Bool(
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False,
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help=dedent(
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"""
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If execution of a cell times out, interrupt the kernel and
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continue executing other cells rather than throwing an error and
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stopping.
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"""
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),
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).tag(config=True)
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startup_timeout: int = Integer(
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60,
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help=dedent(
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"""
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The time to wait (in seconds) for the kernel to start.
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If kernel startup takes longer, a RuntimeError is
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raised.
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"""
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),
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).tag(config=True)
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allow_errors: bool = Bool(
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False,
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help=dedent(
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"""
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If ``False`` (default), when a cell raises an error the
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execution is stopped and a `CellExecutionError`
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is raised.
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If ``True``, execution errors are ignored and the execution
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is continued until the end of the notebook. Output from
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exceptions is included in the cell output in both cases.
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"""
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),
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).tag(config=True)
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force_raise_errors: bool = Bool(
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False,
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help=dedent(
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"""
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If False (default), errors from executing the notebook can be
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allowed with a ``raises-exception`` tag on a single cell, or the
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``allow_errors`` configurable option for all cells. An allowed error
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will be recorded in notebook output, and execution will continue.
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If an error occurs when it is not explicitly allowed, a
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`CellExecutionError` will be raised.
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If True, `CellExecutionError` will be raised for any error that occurs
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while executing the notebook. This overrides both the
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``allow_errors`` option and the ``raises-exception`` cell tag.
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"""
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),
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).tag(config=True)
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extra_arguments: t.List = List(Unicode()).tag(config=True)
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kernel_name: str = Unicode(
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'',
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help=dedent(
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"""
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Name of kernel to use to execute the cells.
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If not set, use the kernel_spec embedded in the notebook.
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"""
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),
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).tag(config=True)
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raise_on_iopub_timeout: bool = Bool(
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False,
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help=dedent(
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"""
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If ``False`` (default), then the kernel will continue waiting for
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iopub messages until it receives a kernel idle message, or until a
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timeout occurs, at which point the currently executing cell will be
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skipped. If ``True``, then an error will be raised after the first
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timeout. This option generally does not need to be used, but may be
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useful in contexts where there is the possibility of executing
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notebooks with memory-consuming infinite loops.
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"""
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),
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).tag(config=True)
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store_widget_state: bool = Bool(
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True,
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help=dedent(
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"""
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If ``True`` (default), then the state of the Jupyter widgets created
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at the kernel will be stored in the metadata of the notebook.
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"""
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),
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).tag(config=True)
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record_timing: bool = Bool(
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True,
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help=dedent(
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"""
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If ``True`` (default), then the execution timings of each cell will
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be stored in the metadata of the notebook.
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"""
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),
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).tag(config=True)
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iopub_timeout: int = Integer(
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4,
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allow_none=False,
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help=dedent(
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"""
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The time to wait (in seconds) for IOPub output. This generally
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doesn't need to be set, but on some slow networks (such as CI
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systems) the default timeout might not be long enough to get all
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messages.
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"""
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),
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).tag(config=True)
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shell_timeout_interval: int = Integer(
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5,
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allow_none=False,
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help=dedent(
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"""
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The time to wait (in seconds) for Shell output before retrying.
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This generally doesn't need to be set, but if one needs to check
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for dead kernels at a faster rate this can help.
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"""
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),
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).tag(config=True)
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shutdown_kernel = Enum(
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['graceful', 'immediate'],
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default_value='graceful',
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help=dedent(
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"""
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If ``graceful`` (default), then the kernel is given time to clean
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up after executing all cells, e.g., to execute its ``atexit`` hooks.
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If ``immediate``, then the kernel is signaled to immediately
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terminate.
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"""
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),
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).tag(config=True)
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ipython_hist_file: str = Unicode(
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default_value=':memory:',
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help="""Path to file to use for SQLite history database for an IPython kernel.
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The specific value ``:memory:`` (including the colon
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at both end but not the back ticks), avoids creating a history file. Otherwise, IPython
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will create a history file for each kernel.
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When running kernels simultaneously (e.g. via multiprocessing) saving history a single
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SQLite file can result in database errors, so using ``:memory:`` is recommended in
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non-interactive contexts.
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""",
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).tag(config=True)
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kernel_manager_class: KernelManager = Type(config=True, help='The kernel manager class to use.')
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@default('kernel_manager_class')
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def _kernel_manager_class_default(self) -> KernelManager:
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"""Use a dynamic default to avoid importing jupyter_client at startup"""
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from jupyter_client import AsyncKernelManager
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return AsyncKernelManager
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_display_id_map: t.Dict[str, t.Dict] = Dict(
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help=dedent(
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"""
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mapping of locations of outputs with a given display_id
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tracks cell index and output index within cell.outputs for
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each appearance of the display_id
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{
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'display_id': {
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cell_idx: [output_idx,]
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}
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}
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"""
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)
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)
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display_data_priority: t.List = List(
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[
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'text/html',
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'application/pdf',
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'text/latex',
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'image/svg+xml',
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'image/png',
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'image/jpeg',
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'text/markdown',
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'text/plain',
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],
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help="""
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An ordered list of preferred output type, the first
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encountered will usually be used when converting discarding
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the others.
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""",
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).tag(config=True)
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resources: t.Dict = Dict(
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help=dedent(
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"""
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Additional resources used in the conversion process. For example,
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passing ``{'metadata': {'path': run_path}}`` sets the
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execution path to ``run_path``.
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"""
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)
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)
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def __init__(
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self,
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nb: NotebookNode,
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km: t.Optional[KernelManager] = None,
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**kw) -> None:
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"""Initializes the execution manager.
|
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Parameters
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----------
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nb : NotebookNode
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Notebook being executed.
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||
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km : KernelManager (optional)
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Optional kernel manager. If none is provided, a kernel manager will
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be created.
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||
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"""
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super().__init__(**kw)
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self.nb: NotebookNode = nb
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self.km: t.Optional[KernelManager] = km
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self.owns_km: bool = km is None # whether the NotebookClient owns the kernel manager
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self.kc: t.Optional[KernelClient] = None
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self.reset_execution_trackers()
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self.widget_registry: t.Dict[str, t.Dict] = {
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'@jupyter-widgets/output': {
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'OutputModel': OutputWidget
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}
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}
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# comm_open_handlers should return an object with a .handle_msg(msg) method or None
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self.comm_open_handlers: t.Dict[str, t.Any] = {
|
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'jupyter.widget': self.on_comm_open_jupyter_widget
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}
|
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|
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|
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def reset_execution_trackers(self) -> None:
|
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"""Resets any per-execution trackers.
|
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"""
|
||
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self.task_poll_for_reply: t.Optional[asyncio.Future] = None
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self.code_cells_executed = 0
|
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self._display_id_map = {}
|
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self.widget_state: t.Dict[str, t.Dict] = {}
|
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self.widget_buffers: t.Dict[str, t.List[t.Dict[str, str]]] = {}
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# maps to list of hooks, where the last is used, this is used
|
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|
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# to support nested use of output widgets.
|
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|
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self.output_hook_stack: t.Any = collections.defaultdict(list)
|
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|
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# our front-end mimicing Output widgets
|
||
|
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self.comm_objects: t.Dict[str, t.Any] = {}
|
||
|
|
|
||
|
|
def create_kernel_manager(self) -> KernelManager:
|
||
|
|
"""Creates a new kernel manager.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
km : KernelManager
|
||
|
|
Kernel manager whose client class is asynchronous.
|
||
|
|
"""
|
||
|
|
if not self.kernel_name:
|
||
|
|
kn = self.nb.metadata.get('kernelspec', {}).get('name')
|
||
|
|
if kn is not None:
|
||
|
|
self.kernel_name = kn
|
||
|
|
|
||
|
|
if not self.kernel_name:
|
||
|
|
self.km = self.kernel_manager_class(config=self.config)
|
||
|
|
else:
|
||
|
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self.km = self.kernel_manager_class(kernel_name=self.kernel_name, config=self.config)
|
||
|
|
self.km.client_class = 'jupyter_client.asynchronous.AsyncKernelClient'
|
||
|
|
return self.km
|
||
|
|
|
||
|
|
async def _async_cleanup_kernel(self) -> None:
|
||
|
|
assert self.km is not None
|
||
|
|
now = self.shutdown_kernel == "immediate"
|
||
|
|
try:
|
||
|
|
# Queue the manager to kill the process, and recover gracefully if it's already dead.
|
||
|
|
if await ensure_async(self.km.is_alive()):
|
||
|
|
await ensure_async(self.km.shutdown_kernel(now=now))
|
||
|
|
except RuntimeError as e:
|
||
|
|
# The error isn't specialized, so we have to check the message
|
||
|
|
if 'No kernel is running!' not in str(e):
|
||
|
|
raise
|
||
|
|
finally:
|
||
|
|
# Remove any state left over even if we failed to stop the kernel
|
||
|
|
await ensure_async(self.km.cleanup_resources())
|
||
|
|
if getattr(self, "kc") and self.kc is not None:
|
||
|
|
await ensure_async(self.kc.stop_channels())
|
||
|
|
self.kc = None
|
||
|
|
self.km = None
|
||
|
|
|
||
|
|
_cleanup_kernel = run_sync(_async_cleanup_kernel)
|
||
|
|
|
||
|
|
async def async_start_new_kernel(self, **kwargs) -> None:
|
||
|
|
"""Creates a new kernel.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
kwargs :
|
||
|
|
Any options for ``self.kernel_manager_class.start_kernel()``. Because
|
||
|
|
that defaults to AsyncKernelManager, this will likely include options
|
||
|
|
accepted by ``AsyncKernelManager.start_kernel()``, which includes ``cwd``.
|
||
|
|
"""
|
||
|
|
assert self.km is not None
|
||
|
|
resource_path = self.resources.get('metadata', {}).get('path') or None
|
||
|
|
if resource_path and 'cwd' not in kwargs:
|
||
|
|
kwargs["cwd"] = resource_path
|
||
|
|
|
||
|
|
has_history_manager_arg = any(
|
||
|
|
arg.startswith('--HistoryManager.hist_file') for arg in self.extra_arguments)
|
||
|
|
if (hasattr(self.km, 'ipykernel')
|
||
|
|
and self.km.ipykernel
|
||
|
|
and self.ipython_hist_file
|
||
|
|
and not has_history_manager_arg):
|
||
|
|
self.extra_arguments += ['--HistoryManager.hist_file={}'.format(self.ipython_hist_file)]
|
||
|
|
|
||
|
|
await ensure_async(self.km.start_kernel(extra_arguments=self.extra_arguments, **kwargs))
|
||
|
|
|
||
|
|
start_new_kernel = run_sync(async_start_new_kernel)
|
||
|
|
|
||
|
|
async def async_start_new_kernel_client(self) -> KernelClient:
|
||
|
|
"""Creates a new kernel client.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
kc : KernelClient
|
||
|
|
Kernel client as created by the kernel manager ``km``.
|
||
|
|
"""
|
||
|
|
assert self.km is not None
|
||
|
|
self.kc = self.km.client()
|
||
|
|
await ensure_async(self.kc.start_channels())
|
||
|
|
try:
|
||
|
|
await ensure_async(self.kc.wait_for_ready(timeout=self.startup_timeout))
|
||
|
|
except RuntimeError:
|
||
|
|
await self._async_cleanup_kernel()
|
||
|
|
raise
|
||
|
|
self.kc.allow_stdin = False
|
||
|
|
return self.kc
|
||
|
|
|
||
|
|
start_new_kernel_client = run_sync(async_start_new_kernel_client)
|
||
|
|
|
||
|
|
@contextmanager
|
||
|
|
def setup_kernel(self, **kwargs) -> t.Generator:
|
||
|
|
"""
|
||
|
|
Context manager for setting up the kernel to execute a notebook.
|
||
|
|
|
||
|
|
The assigns the Kernel Manager (``self.km``) if missing and Kernel Client(``self.kc``).
|
||
|
|
|
||
|
|
When control returns from the yield it stops the client's zmq channels, and shuts
|
||
|
|
down the kernel.
|
||
|
|
"""
|
||
|
|
# by default, cleanup the kernel client if we own the kernel manager
|
||
|
|
# and keep it alive if we don't
|
||
|
|
cleanup_kc = kwargs.pop('cleanup_kc', self.owns_km)
|
||
|
|
|
||
|
|
# Can't use run_until_complete on an asynccontextmanager function :(
|
||
|
|
if self.km is None:
|
||
|
|
self.km = self.create_kernel_manager()
|
||
|
|
|
||
|
|
if not self.km.has_kernel:
|
||
|
|
self.start_new_kernel(**kwargs)
|
||
|
|
self.start_new_kernel_client()
|
||
|
|
try:
|
||
|
|
yield
|
||
|
|
finally:
|
||
|
|
if cleanup_kc:
|
||
|
|
self._cleanup_kernel()
|
||
|
|
|
||
|
|
@asynccontextmanager
|
||
|
|
async def async_setup_kernel(self, **kwargs) -> t.AsyncGenerator:
|
||
|
|
"""
|
||
|
|
Context manager for setting up the kernel to execute a notebook.
|
||
|
|
|
||
|
|
This assigns the Kernel Manager (``self.km``) if missing and Kernel Client(``self.kc``).
|
||
|
|
|
||
|
|
When control returns from the yield it stops the client's zmq channels, and shuts
|
||
|
|
down the kernel.
|
||
|
|
|
||
|
|
Handlers for SIGINT and SIGTERM are also added to cleanup in case of unexpected shutdown.
|
||
|
|
"""
|
||
|
|
# by default, cleanup the kernel client if we own the kernel manager
|
||
|
|
# and keep it alive if we don't
|
||
|
|
cleanup_kc = kwargs.pop('cleanup_kc', self.owns_km)
|
||
|
|
if self.km is None:
|
||
|
|
self.km = self.create_kernel_manager()
|
||
|
|
|
||
|
|
# self._cleanup_kernel uses run_async, which ensures the ioloop is running again.
|
||
|
|
# This is necessary as the ioloop has stopped once atexit fires.
|
||
|
|
atexit.register(self._cleanup_kernel)
|
||
|
|
|
||
|
|
def on_signal():
|
||
|
|
asyncio.ensure_future(self._async_cleanup_kernel())
|
||
|
|
atexit.unregister(self._cleanup_kernel)
|
||
|
|
|
||
|
|
loop = asyncio.get_event_loop()
|
||
|
|
try:
|
||
|
|
loop.add_signal_handler(signal.SIGINT, on_signal)
|
||
|
|
loop.add_signal_handler(signal.SIGTERM, on_signal)
|
||
|
|
except (NotImplementedError, RuntimeError):
|
||
|
|
# NotImplementedError: Windows does not support signals.
|
||
|
|
# RuntimeError: Raised when add_signal_handler is called outside the main thread
|
||
|
|
pass
|
||
|
|
|
||
|
|
if not self.km.has_kernel:
|
||
|
|
await self.async_start_new_kernel(**kwargs)
|
||
|
|
await self.async_start_new_kernel_client()
|
||
|
|
try:
|
||
|
|
yield
|
||
|
|
finally:
|
||
|
|
if cleanup_kc:
|
||
|
|
await self._async_cleanup_kernel()
|
||
|
|
|
||
|
|
atexit.unregister(self._cleanup_kernel)
|
||
|
|
try:
|
||
|
|
loop.remove_signal_handler(signal.SIGINT)
|
||
|
|
loop.remove_signal_handler(signal.SIGTERM)
|
||
|
|
except (NotImplementedError, RuntimeError):
|
||
|
|
pass
|
||
|
|
|
||
|
|
async def async_execute(
|
||
|
|
self,
|
||
|
|
reset_kc: bool = False,
|
||
|
|
**kwargs) -> NotebookNode:
|
||
|
|
"""
|
||
|
|
Executes each code cell.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
kwargs :
|
||
|
|
Any option for ``self.kernel_manager_class.start_kernel()``. Because
|
||
|
|
that defaults to AsyncKernelManager, this will likely include options
|
||
|
|
accepted by ``jupyter_client.AsyncKernelManager.start_kernel()``,
|
||
|
|
which includes ``cwd``.
|
||
|
|
|
||
|
|
``reset_kc`` if True, the kernel client will be reset and a new one
|
||
|
|
will be created (default: False).
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
nb : NotebookNode
|
||
|
|
The executed notebook.
|
||
|
|
"""
|
||
|
|
if reset_kc and self.owns_km:
|
||
|
|
await self._async_cleanup_kernel()
|
||
|
|
self.reset_execution_trackers()
|
||
|
|
|
||
|
|
async with self.async_setup_kernel(**kwargs):
|
||
|
|
assert self.kc is not None
|
||
|
|
self.log.info("Executing notebook with kernel: %s" % self.kernel_name)
|
||
|
|
msg_id = await ensure_async(self.kc.kernel_info())
|
||
|
|
info_msg = await self.async_wait_for_reply(msg_id)
|
||
|
|
if info_msg is not None:
|
||
|
|
if 'language_info' in info_msg['content']:
|
||
|
|
self.nb.metadata['language_info'] = info_msg['content']['language_info']
|
||
|
|
else:
|
||
|
|
raise RuntimeError(
|
||
|
|
'Kernel info received message content has no "language_info" key. '
|
||
|
|
'Content is:\n' + str(info_msg['content'])
|
||
|
|
)
|
||
|
|
for index, cell in enumerate(self.nb.cells):
|
||
|
|
# Ignore `'execution_count' in content` as it's always 1
|
||
|
|
# when store_history is False
|
||
|
|
await self.async_execute_cell(
|
||
|
|
cell, index, execution_count=self.code_cells_executed + 1
|
||
|
|
)
|
||
|
|
self.set_widgets_metadata()
|
||
|
|
|
||
|
|
return self.nb
|
||
|
|
|
||
|
|
execute = run_sync(async_execute)
|
||
|
|
|
||
|
|
def set_widgets_metadata(self) -> None:
|
||
|
|
if self.widget_state:
|
||
|
|
self.nb.metadata.widgets = {
|
||
|
|
'application/vnd.jupyter.widget-state+json': {
|
||
|
|
'state': {
|
||
|
|
model_id: self._serialize_widget_state(state)
|
||
|
|
for model_id, state in self.widget_state.items()
|
||
|
|
if '_model_name' in state
|
||
|
|
},
|
||
|
|
'version_major': 2,
|
||
|
|
'version_minor': 0,
|
||
|
|
}
|
||
|
|
}
|
||
|
|
for key, widget in self.nb.metadata.widgets[
|
||
|
|
'application/vnd.jupyter.widget-state+json'
|
||
|
|
]['state'].items():
|
||
|
|
buffers = self.widget_buffers.get(key)
|
||
|
|
if buffers:
|
||
|
|
widget['buffers'] = buffers
|
||
|
|
|
||
|
|
def _update_display_id(
|
||
|
|
self,
|
||
|
|
display_id: str,
|
||
|
|
msg: t.Dict) -> None:
|
||
|
|
"""Update outputs with a given display_id"""
|
||
|
|
if display_id not in self._display_id_map:
|
||
|
|
self.log.debug("display id %r not in %s", display_id, self._display_id_map)
|
||
|
|
return
|
||
|
|
|
||
|
|
if msg['header']['msg_type'] == 'update_display_data':
|
||
|
|
msg['header']['msg_type'] = 'display_data'
|
||
|
|
|
||
|
|
try:
|
||
|
|
out = output_from_msg(msg)
|
||
|
|
except ValueError:
|
||
|
|
self.log.error("unhandled iopub msg: " + msg['msg_type'])
|
||
|
|
return
|
||
|
|
|
||
|
|
for cell_idx, output_indices in self._display_id_map[display_id].items():
|
||
|
|
cell = self.nb['cells'][cell_idx]
|
||
|
|
outputs = cell['outputs']
|
||
|
|
for output_idx in output_indices:
|
||
|
|
outputs[output_idx]['data'] = out['data']
|
||
|
|
outputs[output_idx]['metadata'] = out['metadata']
|
||
|
|
|
||
|
|
async def _async_poll_for_reply(
|
||
|
|
self,
|
||
|
|
msg_id: str,
|
||
|
|
cell: NotebookNode,
|
||
|
|
timeout: t.Optional[int],
|
||
|
|
task_poll_output_msg: asyncio.Future,
|
||
|
|
task_poll_kernel_alive: asyncio.Future) -> t.Dict:
|
||
|
|
|
||
|
|
assert self.kc is not None
|
||
|
|
new_timeout: t.Optional[float] = None
|
||
|
|
if timeout is not None:
|
||
|
|
deadline = monotonic() + timeout
|
||
|
|
new_timeout = float(timeout)
|
||
|
|
while True:
|
||
|
|
try:
|
||
|
|
msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout))
|
||
|
|
if msg['parent_header'].get('msg_id') == msg_id:
|
||
|
|
if self.record_timing:
|
||
|
|
cell['metadata']['execution']['shell.execute_reply'] = timestamp()
|
||
|
|
try:
|
||
|
|
await asyncio.wait_for(task_poll_output_msg, self.iopub_timeout)
|
||
|
|
except (asyncio.TimeoutError, Empty):
|
||
|
|
if self.raise_on_iopub_timeout:
|
||
|
|
task_poll_kernel_alive.cancel()
|
||
|
|
raise CellTimeoutError.error_from_timeout_and_cell(
|
||
|
|
"Timeout waiting for IOPub output", self.iopub_timeout, cell
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
self.log.warning("Timeout waiting for IOPub output")
|
||
|
|
task_poll_kernel_alive.cancel()
|
||
|
|
return msg
|
||
|
|
else:
|
||
|
|
if new_timeout is not None:
|
||
|
|
new_timeout = max(0, deadline - monotonic())
|
||
|
|
except Empty:
|
||
|
|
# received no message, check if kernel is still alive
|
||
|
|
assert timeout is not None
|
||
|
|
task_poll_kernel_alive.cancel()
|
||
|
|
await self._async_check_alive()
|
||
|
|
await self._async_handle_timeout(timeout, cell)
|
||
|
|
|
||
|
|
async def _async_poll_output_msg(
|
||
|
|
self,
|
||
|
|
parent_msg_id: str,
|
||
|
|
cell: NotebookNode,
|
||
|
|
cell_index: int) -> None:
|
||
|
|
|
||
|
|
assert self.kc is not None
|
||
|
|
while True:
|
||
|
|
msg = await ensure_async(self.kc.iopub_channel.get_msg(timeout=None))
|
||
|
|
if msg['parent_header'].get('msg_id') == parent_msg_id:
|
||
|
|
try:
|
||
|
|
# Will raise CellExecutionComplete when completed
|
||
|
|
self.process_message(msg, cell, cell_index)
|
||
|
|
except CellExecutionComplete:
|
||
|
|
return
|
||
|
|
|
||
|
|
async def _async_poll_kernel_alive(self) -> None:
|
||
|
|
while True:
|
||
|
|
await asyncio.sleep(1)
|
||
|
|
try:
|
||
|
|
await self._async_check_alive()
|
||
|
|
except DeadKernelError:
|
||
|
|
assert self.task_poll_for_reply is not None
|
||
|
|
self.task_poll_for_reply.cancel()
|
||
|
|
return
|
||
|
|
|
||
|
|
def _get_timeout(self, cell: t.Optional[NotebookNode]) -> int:
|
||
|
|
if self.timeout_func is not None and cell is not None:
|
||
|
|
timeout = self.timeout_func(cell)
|
||
|
|
else:
|
||
|
|
timeout = self.timeout
|
||
|
|
|
||
|
|
if not timeout or timeout < 0:
|
||
|
|
timeout = None
|
||
|
|
|
||
|
|
return timeout
|
||
|
|
|
||
|
|
async def _async_handle_timeout(
|
||
|
|
self,
|
||
|
|
timeout: int,
|
||
|
|
cell: t.Optional[NotebookNode] = None) -> None:
|
||
|
|
|
||
|
|
self.log.error("Timeout waiting for execute reply (%is)." % timeout)
|
||
|
|
if self.interrupt_on_timeout:
|
||
|
|
self.log.error("Interrupting kernel")
|
||
|
|
assert self.km is not None
|
||
|
|
await ensure_async(self.km.interrupt_kernel())
|
||
|
|
else:
|
||
|
|
raise CellTimeoutError.error_from_timeout_and_cell(
|
||
|
|
"Cell execution timed out", timeout, cell
|
||
|
|
)
|
||
|
|
|
||
|
|
async def _async_check_alive(self) -> None:
|
||
|
|
assert self.kc is not None
|
||
|
|
if not await ensure_async(self.kc.is_alive()):
|
||
|
|
self.log.error("Kernel died while waiting for execute reply.")
|
||
|
|
raise DeadKernelError("Kernel died")
|
||
|
|
|
||
|
|
async def async_wait_for_reply(
|
||
|
|
self,
|
||
|
|
msg_id: str,
|
||
|
|
cell: t.Optional[NotebookNode] = None) -> t.Optional[t.Dict]:
|
||
|
|
|
||
|
|
assert self.kc is not None
|
||
|
|
# wait for finish, with timeout
|
||
|
|
timeout = self._get_timeout(cell)
|
||
|
|
cummulative_time = 0
|
||
|
|
while True:
|
||
|
|
try:
|
||
|
|
msg = await ensure_async(
|
||
|
|
self.kc.shell_channel.get_msg(
|
||
|
|
timeout=self.shell_timeout_interval
|
||
|
|
)
|
||
|
|
)
|
||
|
|
except Empty:
|
||
|
|
await self._async_check_alive()
|
||
|
|
cummulative_time += self.shell_timeout_interval
|
||
|
|
if timeout and cummulative_time > timeout:
|
||
|
|
await self._async_async_handle_timeout(timeout, cell)
|
||
|
|
break
|
||
|
|
else:
|
||
|
|
if msg['parent_header'].get('msg_id') == msg_id:
|
||
|
|
return msg
|
||
|
|
return None
|
||
|
|
|
||
|
|
wait_for_reply = run_sync(async_wait_for_reply)
|
||
|
|
# Backwards compatability naming for papermill
|
||
|
|
_wait_for_reply = wait_for_reply
|
||
|
|
|
||
|
|
def _passed_deadline(self, deadline: int) -> bool:
|
||
|
|
if deadline is not None and deadline - monotonic() <= 0:
|
||
|
|
return True
|
||
|
|
return False
|
||
|
|
|
||
|
|
def _check_raise_for_error(
|
||
|
|
self,
|
||
|
|
cell: NotebookNode,
|
||
|
|
exec_reply: t.Optional[t.Dict]) -> None:
|
||
|
|
|
||
|
|
cell_allows_errors = self.allow_errors or "raises-exception" in cell.metadata.get(
|
||
|
|
"tags", []
|
||
|
|
)
|
||
|
|
|
||
|
|
if self.force_raise_errors or not cell_allows_errors:
|
||
|
|
if (exec_reply is not None) and exec_reply['content']['status'] == 'error':
|
||
|
|
raise CellExecutionError.from_cell_and_msg(cell, exec_reply['content'])
|
||
|
|
|
||
|
|
async def async_execute_cell(
|
||
|
|
self,
|
||
|
|
cell: NotebookNode,
|
||
|
|
cell_index: int,
|
||
|
|
execution_count: t.Optional[int] = None,
|
||
|
|
store_history: bool = True) -> NotebookNode:
|
||
|
|
"""
|
||
|
|
Executes a single code cell.
|
||
|
|
|
||
|
|
To execute all cells see :meth:`execute`.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
cell : nbformat.NotebookNode
|
||
|
|
The cell which is currently being processed.
|
||
|
|
cell_index : int
|
||
|
|
The position of the cell within the notebook object.
|
||
|
|
execution_count : int
|
||
|
|
The execution count to be assigned to the cell (default: Use kernel response)
|
||
|
|
store_history : bool
|
||
|
|
Determines if history should be stored in the kernel (default: False).
|
||
|
|
Specific to ipython kernels, which can store command histories.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
output : dict
|
||
|
|
The execution output payload (or None for no output).
|
||
|
|
|
||
|
|
Raises
|
||
|
|
------
|
||
|
|
CellExecutionError
|
||
|
|
If execution failed and should raise an exception, this will be raised
|
||
|
|
with defaults about the failure.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
cell : NotebookNode
|
||
|
|
The cell which was just processed.
|
||
|
|
"""
|
||
|
|
assert self.kc is not None
|
||
|
|
if cell.cell_type != 'code' or not cell.source.strip():
|
||
|
|
self.log.debug("Skipping non-executing cell %s", cell_index)
|
||
|
|
return cell
|
||
|
|
|
||
|
|
if self.record_timing and 'execution' not in cell['metadata']:
|
||
|
|
cell['metadata']['execution'] = {}
|
||
|
|
|
||
|
|
self.log.debug("Executing cell:\n%s", cell.source)
|
||
|
|
parent_msg_id = await ensure_async(
|
||
|
|
self.kc.execute(
|
||
|
|
cell.source,
|
||
|
|
store_history=store_history,
|
||
|
|
stop_on_error=not self.allow_errors
|
||
|
|
)
|
||
|
|
)
|
||
|
|
# We launched a code cell to execute
|
||
|
|
self.code_cells_executed += 1
|
||
|
|
exec_timeout = self._get_timeout(cell)
|
||
|
|
|
||
|
|
cell.outputs = []
|
||
|
|
self.clear_before_next_output = False
|
||
|
|
|
||
|
|
task_poll_kernel_alive = asyncio.ensure_future(
|
||
|
|
self._async_poll_kernel_alive()
|
||
|
|
)
|
||
|
|
task_poll_output_msg = asyncio.ensure_future(
|
||
|
|
self._async_poll_output_msg(parent_msg_id, cell, cell_index)
|
||
|
|
)
|
||
|
|
self.task_poll_for_reply = asyncio.ensure_future(
|
||
|
|
self._async_poll_for_reply(
|
||
|
|
parent_msg_id, cell, exec_timeout, task_poll_output_msg, task_poll_kernel_alive
|
||
|
|
)
|
||
|
|
)
|
||
|
|
try:
|
||
|
|
exec_reply = await self.task_poll_for_reply
|
||
|
|
except asyncio.CancelledError:
|
||
|
|
# can only be cancelled by task_poll_kernel_alive when the kernel is dead
|
||
|
|
task_poll_output_msg.cancel()
|
||
|
|
raise DeadKernelError("Kernel died")
|
||
|
|
except Exception as e:
|
||
|
|
# Best effort to cancel request if it hasn't been resolved
|
||
|
|
try:
|
||
|
|
# Check if the task_poll_output is doing the raising for us
|
||
|
|
if not isinstance(e, CellControlSignal):
|
||
|
|
task_poll_output_msg.cancel()
|
||
|
|
finally:
|
||
|
|
raise
|
||
|
|
|
||
|
|
if execution_count:
|
||
|
|
cell['execution_count'] = execution_count
|
||
|
|
self._check_raise_for_error(cell, exec_reply)
|
||
|
|
self.nb['cells'][cell_index] = cell
|
||
|
|
return cell
|
||
|
|
|
||
|
|
execute_cell = run_sync(async_execute_cell)
|
||
|
|
|
||
|
|
def process_message(
|
||
|
|
self,
|
||
|
|
msg: t.Dict,
|
||
|
|
cell: NotebookNode,
|
||
|
|
cell_index: int) -> t.Optional[t.List]:
|
||
|
|
"""
|
||
|
|
Processes a kernel message, updates cell state, and returns the
|
||
|
|
resulting output object that was appended to cell.outputs.
|
||
|
|
|
||
|
|
The input argument *cell* is modified in-place.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
msg : dict
|
||
|
|
The kernel message being processed.
|
||
|
|
cell : nbformat.NotebookNode
|
||
|
|
The cell which is currently being processed.
|
||
|
|
cell_index : int
|
||
|
|
The position of the cell within the notebook object.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
output : dict
|
||
|
|
The execution output payload (or None for no output).
|
||
|
|
|
||
|
|
Raises
|
||
|
|
------
|
||
|
|
CellExecutionComplete
|
||
|
|
Once a message arrives which indicates computation completeness.
|
||
|
|
|
||
|
|
"""
|
||
|
|
msg_type = msg['msg_type']
|
||
|
|
self.log.debug("msg_type: %s", msg_type)
|
||
|
|
content = msg['content']
|
||
|
|
self.log.debug("content: %s", content)
|
||
|
|
|
||
|
|
display_id = content.get('transient', {}).get('display_id', None)
|
||
|
|
if display_id and msg_type in {'execute_result', 'display_data', 'update_display_data'}:
|
||
|
|
self._update_display_id(display_id, msg)
|
||
|
|
|
||
|
|
# set the prompt number for the input and the output
|
||
|
|
if 'execution_count' in content:
|
||
|
|
cell['execution_count'] = content['execution_count']
|
||
|
|
|
||
|
|
if self.record_timing:
|
||
|
|
if msg_type == 'status':
|
||
|
|
if content['execution_state'] == 'idle':
|
||
|
|
cell['metadata']['execution']['iopub.status.idle'] = timestamp()
|
||
|
|
elif content['execution_state'] == 'busy':
|
||
|
|
cell['metadata']['execution']['iopub.status.busy'] = timestamp()
|
||
|
|
elif msg_type == 'execute_input':
|
||
|
|
cell['metadata']['execution']['iopub.execute_input'] = timestamp()
|
||
|
|
|
||
|
|
if msg_type == 'status':
|
||
|
|
if content['execution_state'] == 'idle':
|
||
|
|
raise CellExecutionComplete()
|
||
|
|
elif msg_type == 'clear_output':
|
||
|
|
self.clear_output(cell.outputs, msg, cell_index)
|
||
|
|
elif msg_type.startswith('comm'):
|
||
|
|
self.handle_comm_msg(cell.outputs, msg, cell_index)
|
||
|
|
# Check for remaining messages we don't process
|
||
|
|
elif msg_type not in ['execute_input', 'update_display_data']:
|
||
|
|
# Assign output as our processed "result"
|
||
|
|
return self.output(cell.outputs, msg, display_id, cell_index)
|
||
|
|
return None
|
||
|
|
|
||
|
|
def output(
|
||
|
|
self,
|
||
|
|
outs: t.List,
|
||
|
|
msg: t.Dict,
|
||
|
|
display_id: str,
|
||
|
|
cell_index: int) -> t.Optional[t.List]:
|
||
|
|
|
||
|
|
msg_type = msg['msg_type']
|
||
|
|
|
||
|
|
parent_msg_id = msg['parent_header'].get('msg_id')
|
||
|
|
if self.output_hook_stack[parent_msg_id]:
|
||
|
|
# if we have a hook registered, it will overrride our
|
||
|
|
# default output behaviour (e.g. OutputWidget)
|
||
|
|
hook = self.output_hook_stack[parent_msg_id][-1]
|
||
|
|
hook.output(outs, msg, display_id, cell_index)
|
||
|
|
return None
|
||
|
|
|
||
|
|
try:
|
||
|
|
out = output_from_msg(msg)
|
||
|
|
except ValueError:
|
||
|
|
self.log.error("unhandled iopub msg: " + msg_type)
|
||
|
|
return None
|
||
|
|
|
||
|
|
if self.clear_before_next_output:
|
||
|
|
self.log.debug('Executing delayed clear_output')
|
||
|
|
outs[:] = []
|
||
|
|
self.clear_display_id_mapping(cell_index)
|
||
|
|
self.clear_before_next_output = False
|
||
|
|
|
||
|
|
if display_id:
|
||
|
|
# record output index in:
|
||
|
|
# _display_id_map[display_id][cell_idx]
|
||
|
|
cell_map = self._display_id_map.setdefault(display_id, {})
|
||
|
|
output_idx_list = cell_map.setdefault(cell_index, [])
|
||
|
|
output_idx_list.append(len(outs))
|
||
|
|
|
||
|
|
outs.append(out)
|
||
|
|
|
||
|
|
return out
|
||
|
|
|
||
|
|
def clear_output(
|
||
|
|
self,
|
||
|
|
outs: t.List,
|
||
|
|
msg: t.Dict,
|
||
|
|
cell_index: int) -> None:
|
||
|
|
|
||
|
|
content = msg['content']
|
||
|
|
|
||
|
|
parent_msg_id = msg['parent_header'].get('msg_id')
|
||
|
|
if self.output_hook_stack[parent_msg_id]:
|
||
|
|
# if we have a hook registered, it will overrride our
|
||
|
|
# default clear_output behaviour (e.g. OutputWidget)
|
||
|
|
hook = self.output_hook_stack[parent_msg_id][-1]
|
||
|
|
hook.clear_output(outs, msg, cell_index)
|
||
|
|
return
|
||
|
|
|
||
|
|
if content.get('wait'):
|
||
|
|
self.log.debug('Wait to clear output')
|
||
|
|
self.clear_before_next_output = True
|
||
|
|
else:
|
||
|
|
self.log.debug('Immediate clear output')
|
||
|
|
outs[:] = []
|
||
|
|
self.clear_display_id_mapping(cell_index)
|
||
|
|
|
||
|
|
def clear_display_id_mapping(
|
||
|
|
self,
|
||
|
|
cell_index: int) -> None:
|
||
|
|
|
||
|
|
for display_id, cell_map in self._display_id_map.items():
|
||
|
|
if cell_index in cell_map:
|
||
|
|
cell_map[cell_index] = []
|
||
|
|
|
||
|
|
def handle_comm_msg(
|
||
|
|
self,
|
||
|
|
outs: t.List,
|
||
|
|
msg: t.Dict,
|
||
|
|
cell_index: int) -> None:
|
||
|
|
|
||
|
|
content = msg['content']
|
||
|
|
data = content['data']
|
||
|
|
if self.store_widget_state and 'state' in data: # ignore custom msg'es
|
||
|
|
self.widget_state.setdefault(content['comm_id'], {}).update(data['state'])
|
||
|
|
if 'buffer_paths' in data and data['buffer_paths']:
|
||
|
|
self.widget_buffers[content['comm_id']] = self._get_buffer_data(msg)
|
||
|
|
# There are cases where we need to mimic a frontend, to get similar behaviour as
|
||
|
|
# when using the Output widget from Jupyter lab/notebook
|
||
|
|
if msg['msg_type'] == 'comm_open':
|
||
|
|
target = msg['content'].get('target_name')
|
||
|
|
handler = self.comm_open_handlers.get(target)
|
||
|
|
if handler:
|
||
|
|
comm_id = msg['content']['comm_id']
|
||
|
|
comm_object = handler(msg)
|
||
|
|
if comm_object:
|
||
|
|
self.comm_objects[comm_id] = comm_object
|
||
|
|
else:
|
||
|
|
self.log.warning(f'No handler found for comm target {target!r}')
|
||
|
|
elif msg['msg_type'] == 'comm_msg':
|
||
|
|
content = msg['content']
|
||
|
|
comm_id = msg['content']['comm_id']
|
||
|
|
if comm_id in self.comm_objects:
|
||
|
|
self.comm_objects[comm_id].handle_msg(msg)
|
||
|
|
|
||
|
|
def _serialize_widget_state(self, state: t.Dict) -> t.Dict[str, t.Any]:
|
||
|
|
"""Serialize a widget state, following format in @jupyter-widgets/schema."""
|
||
|
|
return {
|
||
|
|
'model_name': state.get('_model_name'),
|
||
|
|
'model_module': state.get('_model_module'),
|
||
|
|
'model_module_version': state.get('_model_module_version'),
|
||
|
|
'state': state,
|
||
|
|
}
|
||
|
|
|
||
|
|
def _get_buffer_data(self, msg: t.Dict) -> t.List[t.Dict[str, str]]:
|
||
|
|
encoded_buffers = []
|
||
|
|
paths = msg['content']['data']['buffer_paths']
|
||
|
|
buffers = msg['buffers']
|
||
|
|
for path, buffer in zip(paths, buffers):
|
||
|
|
encoded_buffers.append(
|
||
|
|
{
|
||
|
|
'data': base64.b64encode(buffer).decode('utf-8'),
|
||
|
|
'encoding': 'base64',
|
||
|
|
'path': path,
|
||
|
|
}
|
||
|
|
)
|
||
|
|
return encoded_buffers
|
||
|
|
|
||
|
|
def register_output_hook(
|
||
|
|
self,
|
||
|
|
msg_id: str,
|
||
|
|
hook: OutputWidget) -> None:
|
||
|
|
"""Registers an override object that handles output/clear_output instead.
|
||
|
|
|
||
|
|
Multiple hooks can be registered, where the last one will be used (stack based)
|
||
|
|
"""
|
||
|
|
# mimics
|
||
|
|
# https://jupyterlab.github.io/jupyterlab/services/interfaces/kernel.ikernelconnection.html#registermessagehook
|
||
|
|
self.output_hook_stack[msg_id].append(hook)
|
||
|
|
|
||
|
|
def remove_output_hook(
|
||
|
|
self,
|
||
|
|
msg_id: str,
|
||
|
|
hook: OutputWidget) -> None:
|
||
|
|
"""Unregisters an override object that handles output/clear_output instead"""
|
||
|
|
# mimics
|
||
|
|
# https://jupyterlab.github.io/jupyterlab/services/interfaces/kernel.ikernelconnection.html#removemessagehook
|
||
|
|
removed_hook = self.output_hook_stack[msg_id].pop()
|
||
|
|
assert removed_hook == hook
|
||
|
|
|
||
|
|
def on_comm_open_jupyter_widget(self, msg: t.Dict):
|
||
|
|
content = msg['content']
|
||
|
|
data = content['data']
|
||
|
|
state = data['state']
|
||
|
|
comm_id = msg['content']['comm_id']
|
||
|
|
module = self.widget_registry.get(state['_model_module'])
|
||
|
|
if module:
|
||
|
|
widget_class = module.get(state['_model_name'])
|
||
|
|
if widget_class:
|
||
|
|
return widget_class(comm_id, state, self.kc, self)
|
||
|
|
|
||
|
|
|
||
|
|
def execute(
|
||
|
|
nb: NotebookNode,
|
||
|
|
cwd: t.Optional[str] = None,
|
||
|
|
km: t.Optional[KernelManager] = None,
|
||
|
|
**kwargs) -> NotebookClient:
|
||
|
|
"""Execute a notebook's code, updating outputs within the notebook object.
|
||
|
|
|
||
|
|
This is a convenient wrapper around NotebookClient. It returns the
|
||
|
|
modified notebook object.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
nb : NotebookNode
|
||
|
|
The notebook object to be executed
|
||
|
|
cwd : str, optional
|
||
|
|
If supplied, the kernel will run in this directory
|
||
|
|
km : AsyncKernelManager, optional
|
||
|
|
If supplied, the specified kernel manager will be used for code execution.
|
||
|
|
kwargs :
|
||
|
|
Any other options for ExecutePreprocessor, e.g. timeout, kernel_name
|
||
|
|
"""
|
||
|
|
resources = {}
|
||
|
|
if cwd is not None:
|
||
|
|
resources['metadata'] = {'path': cwd}
|
||
|
|
return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
|