def debug_shell(user_ns, user_global_ns, traceback=None, execWrapper=None):
ipshell = None
try:
import IPython
have_ipython = True
except ImportError:
have_ipython = False
if not ipshell and traceback and have_ipython:
try:
from IPython.core.debugger import Pdb
from IPython.terminal.debugger import TerminalPdb
from IPython.terminal.ipapp import TerminalIPythonApp
ipapp = TerminalIPythonApp.instance()
ipapp.interact = False # Avoid output (banner, prints)
ipapp.initialize(argv=[])
def_colors = ipapp.shell.colors
pdb_obj = TerminalPdb(def_colors)
pdb_obj.botframe = None # not sure. exception otherwise at quit
ipshell = lambda: pdb_obj.interaction(None, traceback=traceback)
except Exception:
print("IPython Pdb exception:")
better_exchook(*sys.exc_info(), autodebugshell=False)
if not ipshell and have_ipython:
try:
import IPython
import IPython.terminal.embed
class DummyMod(object):
pass
module = DummyMod()
module.__dict__ = user_global_ns
module.__name__ = "_DummyMod"
if "__name__" not in user_ns:
user_ns = user_ns.copy()
user_ns["__name__"] = "_DummyUserNsMod"
ipshell = IPython.terminal.embed.InteractiveShellEmbed.instance(
user_ns=user_ns, user_module=module)
except Exception:
print("IPython not available:")
better_exchook(*sys.exc_info(), autodebugshell=False)
else:
if execWrapper:
old = ipshell.run_code
ipshell.run_code = lambda code: execWrapper(lambda: old(code))
if ipshell:
ipshell()
else:
print("Use simple debug shell:")
if traceback:
import pdb
pdb.post_mortem(traceback)
else:
simple_debug_shell(user_global_ns, user_ns)
def debug_shell(user_ns, user_global_ns, traceback=None, execWrapper=None):
ipshell = None
try:
import IPython
have_ipython = True
except ImportError:
have_ipython = False
if not ipshell and traceback and have_ipython:
try:
from IPython.core.debugger import Pdb
from IPython.terminal.debugger import TerminalPdb
from IPython.terminal.ipapp import TerminalIPythonApp
ipapp = TerminalIPythonApp.instance()
ipapp.interact = False # Avoid output (banner, prints)
ipapp.initialize(argv=[])
def_colors = ipapp.shell.colors
pdb_obj = TerminalPdb(def_colors)
pdb_obj.botframe = None # not sure. exception otherwise at quit
ipshell = lambda: pdb_obj.interaction(None, traceback=traceback)
except Exception:
print("IPython Pdb exception:")
better_exchook(*sys.exc_info(), autodebugshell=False)
if not ipshell and have_ipython:
try:
import IPython
import IPython.terminal.embed
class DummyMod(object): pass
module = DummyMod()
module.__dict__ = user_global_ns
module.__name__ = "_DummyMod"
if "__name__" not in user_ns:
user_ns = user_ns.copy()
user_ns["__name__"] = "_DummyUserNsMod"
ipshell = IPython.terminal.embed.InteractiveShellEmbed.instance(
user_ns=user_ns, user_module=module)
except Exception:
print("IPython not available:")
better_exchook(*sys.exc_info(), autodebugshell=False)
else:
if execWrapper:
old = ipshell.run_code
ipshell.run_code = lambda code: execWrapper(lambda: old(code))
if ipshell:
ipshell()
else:
print("Use simple debug shell:")
if traceback:
import pdb
pdb.post_mortem(traceback)
else:
simple_debug_shell(user_global_ns, user_ns)
def debug(self, kind='ipdb'):
"""
Run callable in debug mode.
Parameters
----------
kind : str ('ipdb' or 'pdb')
Which debugger to use 'ipdb' for IPython debugger or 'pdb' for
debugger from the standard library
Notes
-----
Be careful when debugging tasks. If the task has run
successfully, you overwrite products but don't save the
updated source code, your DAG will enter an inconsistent state where
the metadata won't match the overwritten product.
"""
opts = {'ipdb', 'pdb'}
if kind not in opts:
raise ValueError('"kind" must be one of {}, got: "{}"'.format(
opts, kind))
if self.exec_status == TaskStatus.WaitingRender:
raise TaskBuildError('Error in task "{}". '
'Cannot call task.debug() on a task that has '
'not been '
'rendered, call DAG.render() first'.format(
self.name))
if 'upstream' in self.params and self._unserializer:
params = _unserialize_params(self.params, self._unserializer)
else:
params = self.params.to_dict()
if self._serializer:
params.pop('product')
if kind == 'ipdb':
try:
# this seems to only work in a Terminal
ipdb = TerminalPdb()
except AttributeError:
# this works in a Jupyter notebook
ipdb = Pdb()
ipdb.runcall(self.source.primitive, **params)
elif kind == 'pdb':
pdb.runcall(self.source.primitive, **params)
def dispatch_line(self, frame):
"""Handle line action and return the next line callback."""
callback = TerminalPdb.dispatch_line(self, frame)
# If the ipdb session ended, don't return a callback for the next line
if self.stoplineno == -1:
return None
return callback
def debug(self, kind='ipdb'):
"""
Opens the notebook (with injected parameters) in debug mode in a
temporary location
Parameters
----------
kind : str, default='ipdb'
Debugger to use, 'ipdb' to use line-by-line IPython debugger,
'pdb' to use line-by-line Python debugger or 'pm' to to
post-portem debugging using IPython
Notes
-----
Be careful when debugging tasks. If the task has run
successfully, you overwrite products but don't save the
updated source code, your DAG will enter an inconsistent state where
the metadata won't match the overwritten product.
"""
if self.source.language != 'python':
raise NotImplementedError(
'debug is not implemented for "{}" '
'notebooks, only python is supported'.format(
self.source.language))
opts = {'ipdb', 'pdb', 'pm'}
if kind not in opts:
raise ValueError('kind must be one of {}'.format(opts))
nb = _read_rendered_notebook(self.source.nb_str_rendered)
fd, tmp_path = tempfile.mkstemp(suffix='.py')
os.close(fd)
code = jupytext.writes(nb, version=nbformat.NO_CONVERT, fmt='py')
Path(tmp_path).write_text(code)
if kind == 'pm':
# post-mortem debugging
try:
subprocess.run(['ipython', tmp_path, '--pdb'])
finally:
Path(tmp_path).unlink()
else:
if kind == 'ipdb':
from IPython.terminal.debugger import TerminalPdb, Pdb
code = compile(source=code, filename=tmp_path, mode='exec')
try:
# this seems to only work in a Terminal
debugger = TerminalPdb()
except AttributeError:
# this works in a Jupyter notebook
debugger = Pdb()
elif kind == 'pdb':
debugger = pdb
try:
debugger.run(code)
finally:
Path(tmp_path).unlink()
import os
import time
import re
import pandas as pd
import warnings
import numpy as np
from spykshrk.franklab.data_containers import DataFrameClass
from abc import ABCMeta, abstractmethod
try:
from IPython.terminal.debugger import TerminalPdb
bp = TerminalPdb(color_scheme='linux').set_trace
except AttributeError as err:
# print('Warning: Attribute Error ({}), disabling IPython TerminalPdb.'.format(err))
bp = lambda: None
idx = pd.IndexSlice
class FrankFileFormatError(RuntimeError):
pass
class FrankFileFormatWarning(RuntimeWarning):
pass
class FrankHDFFormatError(RuntimeError):
pass
from struct import unpack
import numpy as np
import pandas as pd
from scipy.io import loadmat
import spykshrk.franklab.filterframework_util as ff_util
from spykshrk.franklab.data_containers import RippleTimes, UnitTime
from spykshrk.realtime.datatypes import LFPPoint, LinearPosPoint, SpikePoint
from spykshrk.franklab.errors import DataReadError, DataContentError, ConfigurationError
idx = pd.IndexSlice
try:
from IPython.terminal.debugger import TerminalPdb
bp = TerminalPdb().set_trace
except AttributeError as err:
#print('Warning: Attribute Error ({}), disabling IPython TerminalPdb.'.format(err))
bp = lambda: None
# setup pandas string/print format for debugging/interactive
pd.set_option('float_format', '{:,.1f}'.format)
pd.set_option('display.max_rows', 20)
pd.set_option('display.width', 120)
# Constant variable definitions
TIMESTAMP_SCALE = 10000 # factor to convert timestamp to s
class AnimalInfo:
""" animalinfo - stores details of the single animal to process and generates
def __init__(self, exc_info, *args, **kwargs):
TerminalPdb.__init__(self, *args, **kwargs)
self.exc_info = exc_info