"""Test the numpy pickler as a replacement of the standard pickler."""
import bz2
import copy
import gzip
import io
import mmap
import os
import pickle
import random
import re
import socket
import sys
import warnings
import zlib
from contextlib import closing
from pathlib import Path
try:
import lzma
except ImportError:
lzma = None
import pytest
# numpy_pickle is not a drop-in replacement of pickle, as it takes
# filenames instead of open files as arguments.
from joblib import numpy_pickle, register_compressor
from joblib.compressor import (
_COMPRESSORS,
_LZ4_PREFIX,
LZ4_NOT_INSTALLED_ERROR,
BinaryZlibFile,
CompressorWrapper,
)
from joblib.numpy_pickle_utils import (
_IO_BUFFER_SIZE,
_detect_compressor,
_ensure_native_byte_order,
_is_numpy_array_byte_order_mismatch,
)
from joblib.test import data
from joblib.test.common import (
memory_used,
np,
with_lz4,
with_memory_profiler,
with_numpy,
without_lz4,
)
from joblib.testing import parametrize, raises, warns
###############################################################################
# Define a list of standard types.
# Borrowed from dill, initial author: Micheal McKerns:
# http://dev.danse.us/trac/pathos/browser/dill/dill_test2.py
typelist = []
# testing types
_none = None
typelist.append(_none)
_type = type
typelist.append(_type)
_bool = bool(1)
typelist.append(_bool)
_int = int(1)
typelist.append(_int)
_float = float(1)
typelist.append(_float)
_complex = complex(1)
typelist.append(_complex)
_string = str(1)
typelist.append(_string)
_tuple = ()
typelist.append(_tuple)
_list = []
typelist.append(_list)
_dict = {}
typelist.append(_dict)
_builtin = len
typelist.append(_builtin)
def _function(x):
yield x
class _class:
def _method(self):
pass
class _newclass(object):
def _method(self):
pass
typelist.append(_function)
typelist.append(_class)
typelist.append(_newclass) #
_instance = _class()
typelist.append(_instance)
_object = _newclass()
typelist.append(_object) #
###############################################################################
# Tests
@parametrize("compress", [0, 1])
@parametrize("member", typelist)
def test_standard_types(tmpdir, compress, member):
# Test pickling and saving with standard types.
filename = tmpdir.join("test.pkl").strpath
numpy_pickle.dump(member, filename, compress=compress)
_member = numpy_pickle.load(filename)
# We compare the pickled instance to the reloaded one only if it
# can be compared to a copied one
if member == copy.deepcopy(member):
assert member == _member
def test_value_error():
# Test inverting the input arguments to dump
with raises(ValueError):
numpy_pickle.dump("foo", dict())
@parametrize("wrong_compress", [-1, 10, dict()])
def test_compress_level_error(wrong_compress):
# Verify that passing an invalid compress argument raises an error.
exception_msg = 'Non valid compress level given: "{0}"'.format(wrong_compress)
with raises(ValueError) as excinfo:
numpy_pickle.dump("dummy", "foo", compress=wrong_compress)
excinfo.match(exception_msg)
@with_numpy
@parametrize("compress", [False, True, 0, 3, "zlib"])
def test_numpy_persistence(tmpdir, compress):
filename = tmpdir.join("test.pkl").strpath
rnd = np.random.RandomState(0)
a = rnd.random_sample((10, 2))
# We use 'a.T' to have a non C-contiguous array.
for index, obj in enumerate(((a,), (a.T,), (a, a), [a, a, a])):
filenames = numpy_pickle.dump(obj, filename, compress=compress)
# All is cached in one file
assert len(filenames) == 1
# Check that only one file was created
assert filenames[0] == filename
# Check that this file does exist
assert os.path.exists(filenames[0])
# Unpickle the object
obj_ = numpy_pickle.load(filename)
# Check that the items are indeed arrays
for item in obj_:
assert isinstance(item, np.ndarray)
# And finally, check that all the values are equal.
np.testing.assert_array_equal(np.array(obj), np.array(obj_))
# Now test with an array subclass
obj = np.memmap(filename + "mmap", mode="w+", shape=4, dtype=np.float64)
filenames = numpy_pickle.dump(obj, filename, compress=compress)
# All is cached in one file
assert len(filenames) == 1
obj_ = numpy_pickle.load(filename)
if type(obj) is not np.memmap and hasattr(obj, "__array_prepare__"):
# We don't reconstruct memmaps
assert isinstance(obj_, type(obj))
np.testing.assert_array_equal(obj_, obj)
# Test with an object containing multiple numpy arrays
obj = ComplexTestObject()
filenames = numpy_pickle.dump(obj, filename, compress=compress)
# All is cached in one file
assert len(filenames) == 1
obj_loaded = numpy_pickle.load(filename)
assert isinstance(obj_loaded, type(obj))
np.testing.assert_array_equal(obj_loaded.array_float, obj.array_float)
np.testing.assert_array_equal(obj_loaded.array_int, obj.array_int)
np.testing.assert_array_equal(obj_loaded.array_obj, obj.array_obj)
@with_numpy
def test_numpy_persistence_bufferred_array_compression(tmpdir):
big_array = np.ones((_IO_BUFFER_SIZE + 100), dtype=np.uint8)
filename = tmpdir.join("test.pkl").strpath
numpy_pickle.dump(big_array, filename, compress=True)
arr_reloaded = numpy_pickle.load(filename)
np.testing.assert_array_equal(big_array, arr_reloaded)
@with_numpy
def test_memmap_persistence(tmpdir):
rnd = np.random.RandomState(0)
a = rnd.random_sample(10)
filename = tmpdir.join("test1.pkl").strpath
numpy_pickle.dump(a, filename)
b = numpy_pickle.load(filename, mmap_mode="r")
assert isinstance(b, np.memmap)
# Test with an object containing multiple numpy arrays
filename = tmpdir.join("test2.pkl").strpath
obj = ComplexTestObject()
numpy_pickle.dump(obj, filename)
obj_loaded = numpy_pickle.load(filename, mmap_mode="r")
assert isinstance(obj_loaded, type(obj))
assert isinstance(obj_loaded.array_float, np.memmap)
assert not obj_loaded.array_float.flags.writeable
assert isinstance(obj_loaded.array_int, np.memmap)
assert not obj_loaded.array_int.flags.writeable
# Memory map not allowed for numpy object arrays
assert not isinstance(obj_loaded.array_obj, np.memmap)
np.testing.assert_array_equal(obj_loaded.array_float, obj.array_float)
np.testing.assert_array_equal(obj_loaded.array_int, obj.array_int)
np.testing.assert_array_equal(obj_loaded.array_obj, obj.array_obj)
# Test we can write in memmapped arrays
obj_loaded = numpy_pickle.load(filename, mmap_mode="r+")
assert obj_loaded.array_float.flags.writeable
obj_loaded.array_float[0:10] = 10.0
assert obj_loaded.array_int.flags.writeable
obj_loaded.array_int[0:10] = 10
obj_reloaded = numpy_pickle.load(filename, mmap_mode="r")
np.testing.assert_array_equal(obj_reloaded.array_float, obj_loaded.array_float)
np.testing.assert_array_equal(obj_reloaded.array_int, obj_loaded.array_int)
# Test w+ mode is caught and the mode has switched to r+
numpy_pickle.load(filename, mmap_mode="w+")
assert obj_loaded.array_int.flags.writeable
assert obj_loaded.array_int.mode == "r+"
assert obj_loaded.array_float.flags.writeable
assert obj_loaded.array_float.mode == "r+"
@with_numpy
def test_memmap_persistence_mixed_dtypes(tmpdir):
# loading datastructures that have sub-arrays with dtype=object
# should not prevent memmapping on fixed size dtype sub-arrays.
rnd = np.random.RandomState(0)
a = rnd.random_sample(10)
b = np.array([1, "b"], dtype=object)
construct = (a, b)
filename = tmpdir.join("test.pkl").strpath
numpy_pickle.dump(construct, filename)
a_clone, b_clone = numpy_pickle.load(filename, mmap_mode="r")
# the floating point array has been memory mapped
assert isinstance(a_clone, np.memmap)
# the object-dtype array has been loaded in memory
assert not isinstance(b_clone, np.memmap)
@with_numpy
def test_masked_array_persistence(tmpdir):
# The special-case picker fails, because saving masked_array
# not implemented, but it just delegates to the standard pickler.
rnd = np.random.RandomState(0)
a = rnd.random_sample(10)
a = np.ma.masked_greater(a, 0.5)
filename = tmpdir.join("test.pkl").strpath
numpy_pickle.dump(a, filename)
b = numpy_pickle.load(filename, mmap_mode="r")
assert isinstance(b, np.ma.masked_array)
@with_numpy
def test_compress_mmap_mode_warning(tmpdir):
# Test the warning in case of compress + mmap_mode
rnd = np.random.RandomState(0)
obj = rnd.random_sample(10)
this_filename = tmpdir.join("test.pkl").strpath
numpy_pickle.dump(obj, this_filename, compress=1)
with warns(UserWarning) as warninfo:
reloaded_obj = numpy_pickle.load(this_filename, mmap_mode="r+")
debug_msg = "\n".join([str(w) for w in warninfo])
warninfo = [w.message for w in warninfo]
assert not isinstance(reloaded_obj, np.memmap)
np.testing.assert_array_equal(obj, reloaded_obj)
assert len(warninfo) == 1, debug_msg
assert (
str(warninfo[0]) == 'mmap_mode "r+" is not compatible with compressed '
f'file {this_filename}. "r+" flag will be ignored.'
)
@with_numpy
@with_memory_profiler
@parametrize("compress", [True, False])
def test_memory_usage(tmpdir, compress):
# Verify memory stays within expected bounds.
filename = tmpdir.join("test.pkl").strpath
small_array = np.ones((10, 10))
big_array = np.ones(shape=100 * int(1e6), dtype=np.uint8)
for obj in (small_array, big_array):
size = obj.nbytes / 1e6
obj_filename = filename + str(np.random.randint(0, 1000))
mem_used = memory_used(numpy_pickle.dump, obj, obj_filename, compress=compress)
# The memory used to dump the object shouldn't exceed the buffer
# size used to write array chunks (16MB).
write_buf_size = _IO_BUFFER_SIZE + 16 * 1024**2 / 1e6
assert mem_used <= write_buf_size
mem_used = memory_used(numpy_pickle.load, obj_filename)
# memory used should be less than array size + buffer size used to
# read the array chunk by chunk.
read_buf_size = 32 + _IO_BUFFER_SIZE # MiB
assert mem_used < size + read_buf_size
@with_numpy
def test_compressed_pickle_dump_and_load(tmpdir):
expected_list = [
np.arange(5, dtype=np.dtype("i8")),
np.arange(5, dtype=np.dtype("f8")),
np.array([1, "abc", {"a": 1, "b": 2}], dtype="O"),
np.arange(256, dtype=np.uint8).tobytes(),
"C'est l'\xe9t\xe9 !",
]
fname = tmpdir.join("temp.pkl.gz").strpath
dumped_filenames = numpy_pickle.dump(expected_list, fname, compress=1)
assert len(dumped_filenames) == 1
result_list = numpy_pickle.load(fname)
for result, expected in zip(result_list, expected_list):
if isinstance(expected, np.ndarray):
expected = _ensure_native_byte_order(expected)
assert result.dtype == expected.dtype
np.testing.assert_equal(result, expected)
else:
assert result == expected
@with_numpy
def test_memmap_load(tmpdir):
little_endian_dtype = np.dtype("i8")
all_dtypes = (little_endian_dtype, big_endian_dtype)
le_array = np.arange(5, dtype=little_endian_dtype)
be_array = np.arange(5, dtype=big_endian_dtype)
fname = tmpdir.join("temp.pkl").strpath
numpy_pickle.dump([le_array, be_array], fname)
le_array_native_load, be_array_native_load = numpy_pickle.load(
fname, ensure_native_byte_order=True
)
assert le_array_native_load.dtype == be_array_native_load.dtype
assert le_array_native_load.dtype in all_dtypes
le_array_nonnative_load, be_array_nonnative_load = numpy_pickle.load(
fname, ensure_native_byte_order=False
)
assert le_array_nonnative_load.dtype == le_array.dtype
assert be_array_nonnative_load.dtype == be_array.dtype
def test_invalid_parameters_raise():
expected_msg = (
"Native byte ordering can only be enforced if 'mmap_mode' parameter "
"is set to None, but got 'mmap_mode=r+' instead."
)
with raises(ValueError, match=re.escape(expected_msg)):
numpy_pickle.load(
"/path/to/some/dump.pkl", ensure_native_byte_order=True, mmap_mode="r+"
)
def _check_pickle(filename, expected_list, mmap_mode=None):
"""Helper function to test joblib pickle content.
Note: currently only pickles containing an iterable are supported
by this function.
"""
version_match = re.match(r".+py(\d)(\d).+", filename)
py_version_used_for_writing = int(version_match.group(1))
py_version_to_default_pickle_protocol = {2: 2, 3: 3}
pickle_reading_protocol = py_version_to_default_pickle_protocol.get(3, 4)
pickle_writing_protocol = py_version_to_default_pickle_protocol.get(
py_version_used_for_writing, 4
)
if pickle_reading_protocol >= pickle_writing_protocol:
try:
with warnings.catch_warnings(record=True) as warninfo:
warnings.simplefilter("always")
result_list = numpy_pickle.load(filename, mmap_mode=mmap_mode)
filename_base = os.path.basename(filename)
expected_nb_deprecation_warnings = (
1 if ("_0.9" in filename_base or "_0.8.4" in filename_base) else 0
)
expected_nb_user_warnings = (
3
if (re.search("_0.1.+.pkl$", filename_base) and mmap_mode is not None)
else 0
)
expected_nb_warnings = (
expected_nb_deprecation_warnings + expected_nb_user_warnings
)
assert len(warninfo) == expected_nb_warnings, (
"Did not get the expected number of warnings. Expected "
f"{expected_nb_warnings} but got warnings: "
f"{[w.message for w in warninfo]}"
)
deprecation_warnings = [
w for w in warninfo if issubclass(w.category, DeprecationWarning)
]
user_warnings = [w for w in warninfo if issubclass(w.category, UserWarning)]
for w in deprecation_warnings:
assert (
str(w.message)
== "The file '{0}' has been generated with a joblib "
"version less than 0.10. Please regenerate this "
"pickle file.".format(filename)
)
for w in user_warnings:
escaped_filename = re.escape(filename)
assert re.search(
f"memmapped.+{escaped_filename}.+segmentation fault", str(w.message)
)
for result, expected in zip(result_list, expected_list):
if isinstance(expected, np.ndarray):
expected = _ensure_native_byte_order(expected)
assert result.dtype == expected.dtype
np.testing.assert_equal(result, expected)
else:
assert result == expected
except Exception as exc:
# When trying to read with python 3 a pickle generated
# with python 2 we expect a user-friendly error
if py_version_used_for_writing == 2:
assert isinstance(exc, ValueError)
message = (
"You may be trying to read with "
"python 3 a joblib pickle generated with python 2."
)
assert message in str(exc)
elif filename.endswith(".lz4") and with_lz4.args[0]:
assert isinstance(exc, ValueError)
assert LZ4_NOT_INSTALLED_ERROR in str(exc)
else:
raise
else:
# Pickle protocol used for writing is too high. We expect a
# "unsupported pickle protocol" error message
try:
numpy_pickle.load(filename)
raise AssertionError(
"Numpy pickle loading should have raised a ValueError exception"
)
except ValueError as e:
message = "unsupported pickle protocol: {0}".format(pickle_writing_protocol)
assert message in str(e.args)
@with_numpy
def test_joblib_pickle_across_python_versions():
# We need to be specific about dtypes in particular endianness
# because the pickles can be generated on one architecture and
# the tests run on another one. See
# https://github.com/joblib/joblib/issues/279.
expected_list = [
np.arange(5, dtype=np.dtype("i8"), ("", ">f8")]),
np.arange(3, dtype=np.dtype(">i8")),
np.arange(3, dtype=np.dtype(">f8")),
]
# Verify the byteorder mismatch is correctly detected.
for array in be_arrays:
if sys.byteorder == "big":
assert not _is_numpy_array_byte_order_mismatch(array)
else:
assert _is_numpy_array_byte_order_mismatch(array)
converted = _ensure_native_byte_order(array)
if converted.dtype.fields:
for f in converted.dtype.fields.values():
f[0].byteorder == "="
else:
assert converted.dtype.byteorder == "="
# List of numpy arrays with little endian byteorder.
le_arrays = [
np.array([(1, 2.0), (3, 4.0)], dtype=[("", " size
np.testing.assert_array_equal(obj, memmaps)
def test_register_compressor(tmpdir):
# Check that registering compressor file works.
compressor_name = "test-name"
compressor_prefix = "test-prefix"
class BinaryCompressorTestFile(io.BufferedIOBase):
pass
class BinaryCompressorTestWrapper(CompressorWrapper):
def __init__(self):
CompressorWrapper.__init__(
self, obj=BinaryCompressorTestFile, prefix=compressor_prefix
)
register_compressor(compressor_name, BinaryCompressorTestWrapper())
assert _COMPRESSORS[compressor_name].fileobj_factory == BinaryCompressorTestFile
assert _COMPRESSORS[compressor_name].prefix == compressor_prefix
# Remove this dummy compressor file from extra compressors because other
# tests might fail because of this
_COMPRESSORS.pop(compressor_name)
@parametrize("invalid_name", [1, (), {}])
def test_register_compressor_invalid_name(invalid_name):
# Test that registering an invalid compressor name is not allowed.
with raises(ValueError) as excinfo:
register_compressor(invalid_name, None)
excinfo.match("Compressor name should be a string")
def test_register_compressor_invalid_fileobj():
# Test that registering an invalid file object is not allowed.
class InvalidFileObject:
pass
class InvalidFileObjectWrapper(CompressorWrapper):
def __init__(self):
CompressorWrapper.__init__(self, obj=InvalidFileObject, prefix=b"prefix")
with raises(ValueError) as excinfo:
register_compressor("invalid", InvalidFileObjectWrapper())
excinfo.match(
"Compressor 'fileobj_factory' attribute should implement "
"the file object interface"
)
class AnotherZlibCompressorWrapper(CompressorWrapper):
def __init__(self):
CompressorWrapper.__init__(self, obj=BinaryZlibFile, prefix=b"prefix")
class StandardLibGzipCompressorWrapper(CompressorWrapper):
def __init__(self):
CompressorWrapper.__init__(self, obj=gzip.GzipFile, prefix=b"prefix")
def test_register_compressor_already_registered():
# Test registration of existing compressor files.
compressor_name = "test-name"
# register a test compressor
register_compressor(compressor_name, AnotherZlibCompressorWrapper())
with raises(ValueError) as excinfo:
register_compressor(compressor_name, StandardLibGzipCompressorWrapper())
excinfo.match("Compressor '{}' already registered.".format(compressor_name))
register_compressor(compressor_name, StandardLibGzipCompressorWrapper(), force=True)
assert compressor_name in _COMPRESSORS
assert _COMPRESSORS[compressor_name].fileobj_factory == gzip.GzipFile
# Remove this dummy compressor file from extra compressors because other
# tests might fail because of this
_COMPRESSORS.pop(compressor_name)
@with_lz4
def test_lz4_compression(tmpdir):
# Check that lz4 can be used when dependency is available.
import lz4.frame
compressor = "lz4"
assert compressor in _COMPRESSORS
assert _COMPRESSORS[compressor].fileobj_factory == lz4.frame.LZ4FrameFile
fname = tmpdir.join("test.pkl").strpath
data = "test data"
numpy_pickle.dump(data, fname, compress=compressor)
with open(fname, "rb") as f:
assert f.read(len(_LZ4_PREFIX)) == _LZ4_PREFIX
assert numpy_pickle.load(fname) == data
# Test that LZ4 is applied based on file extension
numpy_pickle.dump(data, fname + ".lz4")
with open(fname, "rb") as f:
assert f.read(len(_LZ4_PREFIX)) == _LZ4_PREFIX
assert numpy_pickle.load(fname) == data
@without_lz4
def test_lz4_compression_without_lz4(tmpdir):
# Check that lz4 cannot be used when dependency is not available.
fname = tmpdir.join("test.nolz4").strpath
data = "test data"
msg = LZ4_NOT_INSTALLED_ERROR
with raises(ValueError) as excinfo:
numpy_pickle.dump(data, fname, compress="lz4")
excinfo.match(msg)
with raises(ValueError) as excinfo:
numpy_pickle.dump(data, fname + ".lz4")
excinfo.match(msg)
protocols = [pickle.DEFAULT_PROTOCOL]
if pickle.HIGHEST_PROTOCOL != pickle.DEFAULT_PROTOCOL:
protocols.append(pickle.HIGHEST_PROTOCOL)
@with_numpy
@parametrize("protocol", protocols)
def test_memmap_alignment_padding(tmpdir, protocol):
# Test that memmaped arrays returned by numpy.load are correctly aligned
fname = tmpdir.join("test.mmap").strpath
a = np.random.randn(2)
numpy_pickle.dump(a, fname, protocol=protocol)
memmap = numpy_pickle.load(fname, mmap_mode="r")
assert isinstance(memmap, np.memmap)
np.testing.assert_array_equal(a, memmap)
assert memmap.ctypes.data % numpy_pickle.NUMPY_ARRAY_ALIGNMENT_BYTES == 0
assert memmap.flags.aligned
array_list = [
np.random.randn(2),
np.random.randn(2),
np.random.randn(2),
np.random.randn(2),
]
# On Windows OSError 22 if reusing the same path for memmap ...
fname = tmpdir.join("test1.mmap").strpath
numpy_pickle.dump(array_list, fname, protocol=protocol)
l_reloaded = numpy_pickle.load(fname, mmap_mode="r")
for idx, memmap in enumerate(l_reloaded):
assert isinstance(memmap, np.memmap)
np.testing.assert_array_equal(array_list[idx], memmap)
assert memmap.ctypes.data % numpy_pickle.NUMPY_ARRAY_ALIGNMENT_BYTES == 0
assert memmap.flags.aligned
array_dict = {
"a0": np.arange(2, dtype=np.uint8),
"a1": np.arange(3, dtype=np.uint8),
"a2": np.arange(5, dtype=np.uint8),
"a3": np.arange(7, dtype=np.uint8),
"a4": np.arange(11, dtype=np.uint8),
"a5": np.arange(13, dtype=np.uint8),
"a6": np.arange(17, dtype=np.uint8),
"a7": np.arange(19, dtype=np.uint8),
"a8": np.arange(23, dtype=np.uint8),
}
# On Windows OSError 22 if reusing the same path for memmap ...
fname = tmpdir.join("test2.mmap").strpath
numpy_pickle.dump(array_dict, fname, protocol=protocol)
d_reloaded = numpy_pickle.load(fname, mmap_mode="r")
for key, memmap in d_reloaded.items():
assert isinstance(memmap, np.memmap)
np.testing.assert_array_equal(array_dict[key], memmap)
assert memmap.ctypes.data % numpy_pickle.NUMPY_ARRAY_ALIGNMENT_BYTES == 0
assert memmap.flags.aligned