241 lines
8.2 KiB
Python
241 lines
8.2 KiB
Python
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"""Numpy pickle compatibility functions."""
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import pickle
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import os
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import zlib
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import inspect
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from io import BytesIO
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from .numpy_pickle_utils import _ZFILE_PREFIX
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from .numpy_pickle_utils import Unpickler
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def hex_str(an_int):
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"""Convert an int to an hexadecimal string."""
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return '{:#x}'.format(an_int)
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def asbytes(s):
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if isinstance(s, bytes):
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return s
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return s.encode('latin1')
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_MAX_LEN = len(hex_str(2 ** 64))
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_CHUNK_SIZE = 64 * 1024
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def read_zfile(file_handle):
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"""Read the z-file and return the content as a string.
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Z-files are raw data compressed with zlib used internally by joblib
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for persistence. Backward compatibility is not guaranteed. Do not
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use for external purposes.
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"""
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file_handle.seek(0)
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header_length = len(_ZFILE_PREFIX) + _MAX_LEN
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length = file_handle.read(header_length)
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length = length[len(_ZFILE_PREFIX):]
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length = int(length, 16)
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# With python2 and joblib version <= 0.8.4 compressed pickle header is one
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# character wider so we need to ignore an additional space if present.
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# Note: the first byte of the zlib data is guaranteed not to be a
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# space according to
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# https://tools.ietf.org/html/rfc6713#section-2.1
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next_byte = file_handle.read(1)
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if next_byte != b' ':
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# The zlib compressed data has started and we need to go back
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# one byte
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file_handle.seek(header_length)
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# We use the known length of the data to tell Zlib the size of the
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# buffer to allocate.
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data = zlib.decompress(file_handle.read(), 15, length)
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assert len(data) == length, (
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"Incorrect data length while decompressing %s."
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"The file could be corrupted." % file_handle)
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return data
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def write_zfile(file_handle, data, compress=1):
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"""Write the data in the given file as a Z-file.
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Z-files are raw data compressed with zlib used internally by joblib
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for persistence. Backward compatibility is not guarantied. Do not
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use for external purposes.
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"""
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file_handle.write(_ZFILE_PREFIX)
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length = hex_str(len(data))
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# Store the length of the data
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file_handle.write(asbytes(length.ljust(_MAX_LEN)))
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file_handle.write(zlib.compress(asbytes(data), compress))
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###############################################################################
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# Utility objects for persistence.
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class NDArrayWrapper(object):
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"""An object to be persisted instead of numpy arrays.
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The only thing this object does, is to carry the filename in which
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the array has been persisted, and the array subclass.
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"""
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def __init__(self, filename, subclass, allow_mmap=True):
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"""Constructor. Store the useful information for later."""
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self.filename = filename
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self.subclass = subclass
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self.allow_mmap = allow_mmap
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def read(self, unpickler):
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"""Reconstruct the array."""
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filename = os.path.join(unpickler._dirname, self.filename)
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# Load the array from the disk
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# use getattr instead of self.allow_mmap to ensure backward compat
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# with NDArrayWrapper instances pickled with joblib < 0.9.0
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allow_mmap = getattr(self, 'allow_mmap', True)
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kwargs = {}
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if allow_mmap:
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kwargs['mmap_mode'] = unpickler.mmap_mode
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if "allow_pickle" in inspect.signature(unpickler.np.load).parameters:
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# Required in numpy 1.16.3 and later to aknowledge the security
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# risk.
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kwargs["allow_pickle"] = True
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array = unpickler.np.load(filename, **kwargs)
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# Reconstruct subclasses. This does not work with old
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# versions of numpy
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if (hasattr(array, '__array_prepare__') and
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self.subclass not in (unpickler.np.ndarray,
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unpickler.np.memmap)):
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# We need to reconstruct another subclass
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new_array = unpickler.np.core.multiarray._reconstruct(
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self.subclass, (0,), 'b')
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return new_array.__array_prepare__(array)
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else:
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return array
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class ZNDArrayWrapper(NDArrayWrapper):
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"""An object to be persisted instead of numpy arrays.
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This object store the Zfile filename in which
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the data array has been persisted, and the meta information to
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retrieve it.
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The reason that we store the raw buffer data of the array and
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the meta information, rather than array representation routine
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(tobytes) is that it enables us to use completely the strided
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model to avoid memory copies (a and a.T store as fast). In
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addition saving the heavy information separately can avoid
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creating large temporary buffers when unpickling data with
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large arrays.
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"""
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def __init__(self, filename, init_args, state):
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"""Constructor. Store the useful information for later."""
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self.filename = filename
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self.state = state
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self.init_args = init_args
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def read(self, unpickler):
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"""Reconstruct the array from the meta-information and the z-file."""
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# Here we a simply reproducing the unpickling mechanism for numpy
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# arrays
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filename = os.path.join(unpickler._dirname, self.filename)
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array = unpickler.np.core.multiarray._reconstruct(*self.init_args)
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with open(filename, 'rb') as f:
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data = read_zfile(f)
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state = self.state + (data,)
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array.__setstate__(state)
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return array
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class ZipNumpyUnpickler(Unpickler):
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"""A subclass of the Unpickler to unpickle our numpy pickles."""
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dispatch = Unpickler.dispatch.copy()
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def __init__(self, filename, file_handle, mmap_mode=None):
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"""Constructor."""
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self._filename = os.path.basename(filename)
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self._dirname = os.path.dirname(filename)
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self.mmap_mode = mmap_mode
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self.file_handle = self._open_pickle(file_handle)
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Unpickler.__init__(self, self.file_handle)
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try:
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import numpy as np
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except ImportError:
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np = None
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self.np = np
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def _open_pickle(self, file_handle):
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return BytesIO(read_zfile(file_handle))
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def load_build(self):
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"""Set the state of a newly created object.
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We capture it to replace our place-holder objects,
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NDArrayWrapper, by the array we are interested in. We
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replace them directly in the stack of pickler.
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"""
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Unpickler.load_build(self)
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if isinstance(self.stack[-1], NDArrayWrapper):
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if self.np is None:
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raise ImportError("Trying to unpickle an ndarray, "
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"but numpy didn't import correctly")
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nd_array_wrapper = self.stack.pop()
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array = nd_array_wrapper.read(self)
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self.stack.append(array)
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dispatch[pickle.BUILD[0]] = load_build
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def load_compatibility(filename):
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"""Reconstruct a Python object from a file persisted with joblib.dump.
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This function ensures the compatibility with joblib old persistence format
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(<= 0.9.3).
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Parameters
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-----------
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filename: string
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The name of the file from which to load the object
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Returns
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-------
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result: any Python object
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The object stored in the file.
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See Also
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--------
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joblib.dump : function to save an object
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Notes
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-----
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This function can load numpy array files saved separately during the
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dump.
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"""
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with open(filename, 'rb') as file_handle:
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# We are careful to open the file handle early and keep it open to
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# avoid race-conditions on renames. That said, if data is stored in
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# companion files, moving the directory will create a race when
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# joblib tries to access the companion files.
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unpickler = ZipNumpyUnpickler(filename, file_handle=file_handle)
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try:
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obj = unpickler.load()
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except UnicodeDecodeError as exc:
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# More user-friendly error message
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new_exc = ValueError(
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'You may be trying to read with '
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'python 3 a joblib pickle generated with python 2. '
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'This feature is not supported by joblib.')
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new_exc.__cause__ = exc
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raise new_exc
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finally:
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if hasattr(unpickler, 'file_handle'):
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unpickler.file_handle.close()
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return obj
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