partd-1.0.0/0000755€#ô2€<ÄÎÏ0000000000013504343206013651 5ustar mrocklin00000000000000partd-1.0.0/LICENSE.txt0000644€#ô2€<ÄÎÏ0000000274113504343040015474 0ustar mrocklin00000000000000Copyright (c) 2015, Continuum Analytics, Inc. and contributors All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Neither the name of Continuum Analytics nor the names of any contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. partd-1.0.0/MANIFEST.in0000644€#ô2€<ÄÎÏ0000000020313504343040015376 0ustar mrocklin00000000000000recursive-include partd *.py include requirements.txt include setup.py include README.rst include LICENSE.txt include MANIFEST.in partd-1.0.0/PKG-INFO0000644€#ô2€<ÄÎÏ0000001172613504343206014755 0ustar mrocklin00000000000000Metadata-Version: 2.1 Name: partd Version: 1.0.0 Summary: Appendable key-value storage Home-page: http://github.com/dask/partd/ Maintainer: Matthew Rocklin Maintainer-email: mrocklin@gmail.com License: BSD Description: PartD ===== |Build Status| |Version Status| Key-value byte store with appendable values Partd stores key-value pairs. Values are raw bytes. We append on old values. Partd excels at shuffling operations. Operations ---------- PartD has two main operations, ``append`` and ``get``. Example ------- 1. Create a Partd backed by a directory:: >>> import partd >>> p = partd.File('/path/to/new/dataset/') 2. Append key-byte pairs to dataset:: >>> p.append({'x': b'Hello ', 'y': b'123'}) >>> p.append({'x': b'world!', 'y': b'456'}) 3. Get bytes associated to keys:: >>> p.get('x') # One key b'Hello world!' >>> p.get(['y', 'x']) # List of keys [b'123456', b'Hello world!'] 4. Destroy partd dataset:: >>> p.drop() That's it. Implementations --------------- We can back a partd by an in-memory dictionary:: >>> p = Dict() For larger amounts of data or to share data between processes we back a partd by a directory of files. This uses file-based locks for consistency.:: >>> p = File('/path/to/dataset/') However this can fail for many small writes. In these cases you may wish to buffer one partd with another, keeping a fixed maximum of data in the buffering partd. This writes the larger elements of the first partd to the second partd when space runs low:: >>> p = Buffer(Dict(), File(), available_memory=2e9) # 2GB memory buffer You might also want to have many distributed process write to a single partd consistently. This can be done with a server * Server Process:: >>> p = Buffer(Dict(), File(), available_memory=2e9) # 2GB memory buffer >>> s = Server(p, address='ipc://server') * Worker processes:: >>> p = Client('ipc://server') # Client machine talks to remote server Encodings and Compression ------------------------- Once we can robustly and efficiently append bytes to a partd we consider compression and encodings. This is generally available with the ``Encode`` partd, which accepts three functions, one to apply on bytes as they are written, one to apply to bytes as they are read, and one to join bytestreams. Common configurations already exist for common data and compression formats. We may wish to compress and decompress data transparently as we interact with a partd. Objects like ``BZ2``, ``Blosc``, ``ZLib`` and ``Snappy`` exist and take another partd as an argument.:: >>> p = File(...) >>> p = ZLib(p) These work exactly as before, the (de)compression happens automatically. Common data formats like Python lists, numpy arrays, and pandas dataframes are also supported out of the box.:: >>> p = File(...) >>> p = NumPy(p) >>> p.append({'x': np.array([...])}) This lets us forget about bytes and think instead in our normal data types. Composition ----------- In principle we want to compose all of these choices together 1. Write policy: ``Dict``, ``File``, ``Buffer``, ``Client`` 2. Encoding: ``Pickle``, ``Numpy``, ``Pandas``, ... 3. Compression: ``Blosc``, ``Snappy``, ... Partd objects compose by nesting. Here we make a partd that writes pickle encoded BZ2 compressed bytes directly to disk:: >>> p = Pickle(BZ2(File('foo'))) We could construct more complex systems that include compression, serialization, buffering, and remote access.:: >>> server = Server(Buffer(Dict(), File(), available_memory=2e0)) >>> client = Pickle(Snappy(Client(server.address))) >>> client.append({'x': [1, 2, 3]}) .. |Build Status| image:: https://travis-ci.org/dask/partd.png :target: https://travis-ci.org/dask/partd .. |Version Status| image:: https://img.shields.io/pypi/v/partd.svg :target: https://pypi.python.org/pypi/partd/ Platform: UNKNOWN Provides-Extra: complete partd-1.0.0/README.rst0000644€#ô2€<ÄÎÏ0000000730713504343040015343 0ustar mrocklin00000000000000PartD ===== |Build Status| |Version Status| Key-value byte store with appendable values Partd stores key-value pairs. Values are raw bytes. We append on old values. Partd excels at shuffling operations. Operations ---------- PartD has two main operations, ``append`` and ``get``. Example ------- 1. Create a Partd backed by a directory:: >>> import partd >>> p = partd.File('/path/to/new/dataset/') 2. Append key-byte pairs to dataset:: >>> p.append({'x': b'Hello ', 'y': b'123'}) >>> p.append({'x': b'world!', 'y': b'456'}) 3. Get bytes associated to keys:: >>> p.get('x') # One key b'Hello world!' >>> p.get(['y', 'x']) # List of keys [b'123456', b'Hello world!'] 4. Destroy partd dataset:: >>> p.drop() That's it. Implementations --------------- We can back a partd by an in-memory dictionary:: >>> p = Dict() For larger amounts of data or to share data between processes we back a partd by a directory of files. This uses file-based locks for consistency.:: >>> p = File('/path/to/dataset/') However this can fail for many small writes. In these cases you may wish to buffer one partd with another, keeping a fixed maximum of data in the buffering partd. This writes the larger elements of the first partd to the second partd when space runs low:: >>> p = Buffer(Dict(), File(), available_memory=2e9) # 2GB memory buffer You might also want to have many distributed process write to a single partd consistently. This can be done with a server * Server Process:: >>> p = Buffer(Dict(), File(), available_memory=2e9) # 2GB memory buffer >>> s = Server(p, address='ipc://server') * Worker processes:: >>> p = Client('ipc://server') # Client machine talks to remote server Encodings and Compression ------------------------- Once we can robustly and efficiently append bytes to a partd we consider compression and encodings. This is generally available with the ``Encode`` partd, which accepts three functions, one to apply on bytes as they are written, one to apply to bytes as they are read, and one to join bytestreams. Common configurations already exist for common data and compression formats. We may wish to compress and decompress data transparently as we interact with a partd. Objects like ``BZ2``, ``Blosc``, ``ZLib`` and ``Snappy`` exist and take another partd as an argument.:: >>> p = File(...) >>> p = ZLib(p) These work exactly as before, the (de)compression happens automatically. Common data formats like Python lists, numpy arrays, and pandas dataframes are also supported out of the box.:: >>> p = File(...) >>> p = NumPy(p) >>> p.append({'x': np.array([...])}) This lets us forget about bytes and think instead in our normal data types. Composition ----------- In principle we want to compose all of these choices together 1. Write policy: ``Dict``, ``File``, ``Buffer``, ``Client`` 2. Encoding: ``Pickle``, ``Numpy``, ``Pandas``, ... 3. Compression: ``Blosc``, ``Snappy``, ... Partd objects compose by nesting. Here we make a partd that writes pickle encoded BZ2 compressed bytes directly to disk:: >>> p = Pickle(BZ2(File('foo'))) We could construct more complex systems that include compression, serialization, buffering, and remote access.:: >>> server = Server(Buffer(Dict(), File(), available_memory=2e0)) >>> client = Pickle(Snappy(Client(server.address))) >>> client.append({'x': [1, 2, 3]}) .. |Build Status| image:: https://travis-ci.org/dask/partd.png :target: https://travis-ci.org/dask/partd .. |Version Status| image:: https://img.shields.io/pypi/v/partd.svg :target: https://pypi.python.org/pypi/partd/ partd-1.0.0/partd/0000755€#ô2€<ÄÎÏ0000000000013504343206014763 5ustar mrocklin00000000000000partd-1.0.0/partd/__init__.py0000644€#ô2€<ÄÎÏ0000000073113504343113017072 0ustar mrocklin00000000000000from __future__ import absolute_import from .file import File from .dict import Dict from .buffer import Buffer from .encode import Encode from .pickle import Pickle from .python import Python from .compressed import * from .utils import ignoring with ignoring(ImportError): from .numpy import Numpy with ignoring(ImportError): from .pandas import PandasColumns, PandasBlocks with ignoring(ImportError): from .zmq import Client, Server __version__ = '1.0.0' partd-1.0.0/partd/buffer.py0000644€#ô2€<ÄÎÏ0000000706513504343040016612 0ustar mrocklin00000000000000from .core import Interface from threading import Lock from toolz import merge_with, topk, accumulate, pluck from operator import add from bisect import bisect from collections import defaultdict from .compatibility import Queue, Empty def zero(): return 0 class Buffer(Interface): def __init__(self, fast, slow, available_memory=1e9): self.lock = Lock() self.fast = fast self.slow = slow self.available_memory = available_memory self.lengths = defaultdict(zero) self.memory_usage = 0 Interface.__init__(self) def __getstate__(self): return {'fast': self.fast, 'slow': self.slow, 'memory_usage': self.memory_usage, 'lengths': self.lengths, 'available_memory': self.available_memory} def __setstate__(self, state): Interface.__setstate__(self, state) self.lock = Lock() self.__dict__.update(state) def append(self, data, lock=True, **kwargs): if lock: self.lock.acquire() try: for k, v in data.items(): self.lengths[k] += len(v) self.memory_usage += len(v) self.fast.append(data, lock=False, **kwargs) while self.memory_usage > self.available_memory: keys = keys_to_flush(self.lengths, 0.1, maxcount=20) self.flush(keys) finally: if lock: self.lock.release() def _get(self, keys, lock=True, **kwargs): if lock: self.lock.acquire() try: result = list(map(add, self.fast.get(keys, lock=False), self.slow.get(keys, lock=False))) finally: if lock: self.lock.release() return result def _iset(self, key, value, lock=True): """ Idempotent set """ if lock: self.lock.acquire() try: self.fast.iset(key, value, lock=False) finally: if lock: self.lock.release() def _delete(self, keys, lock=True): if lock: self.lock.acquire() try: self.fast.delete(keys, lock=False) self.slow.delete(keys, lock=False) finally: if lock: self.lock.release() def drop(self): self._iset_seen.clear() self.fast.drop() self.slow.drop() def __exit__(self, *args): self.drop() def flush(self, keys=None, block=None): """ Flush keys to disk Parameters ---------- keys: list or None list of keys to flush block: bool (defaults to None) Whether or not to block until all writing is complete If no keys are given then flush all keys """ if keys is None: keys = list(self.lengths) self.slow.append(dict(zip(keys, self.fast.get(keys)))) self.fast.delete(keys) for key in keys: self.memory_usage -= self.lengths[key] del self.lengths[key] def keys_to_flush(lengths, fraction=0.1, maxcount=100000): """ Which keys to remove >>> lengths = {'a': 20, 'b': 10, 'c': 15, 'd': 15, ... 'e': 10, 'f': 25, 'g': 5} >>> keys_to_flush(lengths, 0.5) ['f', 'a'] """ top = topk(max(len(lengths) // 2, 1), lengths.items(), key=1) total = sum(lengths.values()) cutoff = min(maxcount, max(1, bisect(list(accumulate(add, pluck(1, top))), total * fraction))) result = [k for k, v in top[:cutoff]] assert result return result partd-1.0.0/partd/compatibility.py0000644€#ô2€<ÄÎÏ0000000051113504343040020177 0ustar mrocklin00000000000000from __future__ import absolute_import import sys if sys.version_info[0] == 3: from io import StringIO unicode = str import pickle from queue import Queue, Empty if sys.version_info[0] == 2: from StringIO import StringIO unicode = unicode import cPickle as pickle from Queue import Queue, Empty partd-1.0.0/partd/compressed.py0000644€#ô2€<ÄÎÏ0000000222113504343040017472 0ustar mrocklin00000000000000from .utils import ignoring from .encode import Encode from functools import partial __all__ = [] def bytes_concat(L): return b''.join(L) with ignoring(ImportError, AttributeError): # In case snappy is not installed, or another package called snappy that does not implement compress / decompress. # For example, SnapPy (https://pypi.org/project/snappy/) import snappy Snappy = partial(Encode, snappy.compress, snappy.decompress, bytes_concat) __all__.append('Snappy') with ignoring(ImportError): import zlib ZLib = partial(Encode, zlib.compress, zlib.decompress, bytes_concat) __all__.append('ZLib') with ignoring(ImportError): import bz2 BZ2 = partial(Encode, bz2.compress, bz2.decompress, bytes_concat) __all__.append('BZ2') with ignoring(ImportError): import blosc Blosc = partial(Encode, blosc.compress, blosc.decompress, bytes_concat) __all__.append('Blosc') partd-1.0.0/partd/core.py0000644€#ô2€<ÄÎÏ0000000440313504343040016262 0ustar mrocklin00000000000000from __future__ import absolute_import import os import shutil import locket import string from toolz import memoize from contextlib import contextmanager from .utils import nested_get, flatten # http://stackoverflow.com/questions/295135/turn-a-string-into-a-valid-filename-in-python valid_chars = "-_.() " + string.ascii_letters + string.digits + os.path.sep def escape_filename(fn): """ Escape text so that it is a valid filename >>> escape_filename('Foo!bar?') 'Foobar' """ return ''.join(filter(valid_chars.__contains__, fn)) def filename(path, key): return os.path.join(path, escape_filename(token(key))) def token(key): """ >>> token('hello') 'hello' >>> token(('hello', 'world')) # doctest: +SKIP 'hello/world' """ if isinstance(key, str): return key elif isinstance(key, tuple): return os.path.join(*map(token, key)) else: return str(key) class Interface(object): def __init__(self): self._iset_seen = set() def __setstate__(self, state): self.__dict__.update(state) self._iset_seen = set() def iset(self, key, value, **kwargs): if key in self._iset_seen: return else: self._iset(key, value, **kwargs) self._iset_seen.add(key) def __enter__(self): return self def __exit__(self, type, value, traceback): self.drop() def iget(self, key): return self._get([key], lock=False)[0] def get(self, keys, **kwargs): if not isinstance(keys, list): return self.get([keys], **kwargs)[0] elif any(isinstance(key, list) for key in keys): # nested case flatkeys = list(flatten(keys)) result = self.get(flatkeys, **kwargs) return nested_get(keys, dict(zip(flatkeys, result))) else: return self._get(keys, **kwargs) def delete(self, keys, **kwargs): if not isinstance(keys, list): return self._delete([keys], **kwargs) else: return self._delete(keys, **kwargs) def pop(self, keys, **kwargs): with self.partd.lock: result = self.partd.get(keys, lock=False) self.partd.delete(keys, lock=False) return result partd-1.0.0/partd/dict.py0000644€#ô2€<ÄÎÏ0000000324513504343040016260 0ustar mrocklin00000000000000from .core import Interface from threading import Lock class Dict(Interface): def __init__(self): self.lock = Lock() self.data = dict() Interface.__init__(self) def __getstate__(self): return {'data': self.data} def __setstate__(self, state): Interface.__setstate__(self, state) Dict.__init__(self) self.data = state['data'] def append(self, data, lock=True, **kwargs): if lock: self.lock.acquire() try: for k, v in data.items(): if k not in self.data: self.data[k] = [] self.data[k].append(v) finally: if lock: self.lock.release() def _get(self, keys, lock=True, **kwargs): assert isinstance(keys, (list, tuple, set)) if lock: self.lock.acquire() try: result = [b''.join(self.data.get(key, [])) for key in keys] finally: if lock: self.lock.release() return result def _iset(self, key, value, lock=True): """ Idempotent set """ if lock: self.lock.acquire() try: self.data[key] = [value] finally: if lock: self.lock.release() def _delete(self, keys, lock=True): if lock: self.lock.acquire() try: for key in keys: if key in self.data: del self.data[key] finally: if lock: self.lock.release() def drop(self): self._iset_seen.clear() self.data.clear() def __exit__(self, *args): self.drop() partd-1.0.0/partd/encode.py0000644€#ô2€<ÄÎÏ0000000240713504343040016571 0ustar mrocklin00000000000000from .core import Interface from .file import File from toolz import valmap from .utils import frame, framesplit class Encode(Interface): def __init__(self, encode, decode, join, partd=None): if not partd or isinstance(partd, str): partd = File(partd) self.partd = partd self.encode = encode self.decode = decode self.join = join Interface.__init__(self) def __getstate__(self): return self.__dict__ __setstate__ = Interface.__setstate__ def append(self, data, **kwargs): data = valmap(self.encode, data) data = valmap(frame, data) self.partd.append(data, **kwargs) def _get(self, keys, **kwargs): raw = self.partd._get(keys, **kwargs) return [self.join([self.decode(frame) for frame in framesplit(chunk)]) for chunk in raw] def delete(self, keys, **kwargs): return self.partd.delete(keys, **kwargs) def _iset(self, key, value, **kwargs): return self.partd.iset(key, frame(self.encode(value)), **kwargs) def drop(self): return self.partd.drop() @property def lock(self): return self.partd.lock def __exit__(self, *args): self.drop() self.partd.__exit__(*args) partd-1.0.0/partd/file.py0000644€#ô2€<ÄÎÏ0000000762613504343040016263 0ustar mrocklin00000000000000from __future__ import absolute_import import atexit import os import shutil import string import tempfile from .core import Interface import locket from .utils import ignoring class File(Interface): def __init__(self, path=None, dir=None): if not path: path = tempfile.mkdtemp(suffix='.partd', dir=dir) cleanup_files.append(path) self._explicitly_given_path = False else: self._explicitly_given_path = True self.path = path if not os.path.exists(path): with ignoring(OSError): os.makedirs(path) self.lock = locket.lock_file(self.filename('.lock')) Interface.__init__(self) def __getstate__(self): return {'path': self.path} def __setstate__(self, state): Interface.__setstate__(self, state) File.__init__(self, state['path']) def append(self, data, lock=True, fsync=False, **kwargs): if lock: self.lock.acquire() try: for k, v in data.items(): fn = self.filename(k) if not os.path.exists(os.path.dirname(fn)): os.makedirs(os.path.dirname(fn)) with open(fn, 'ab') as f: f.write(v) if fsync: os.fsync(f) finally: if lock: self.lock.release() def _get(self, keys, lock=True, **kwargs): assert isinstance(keys, (list, tuple, set)) if lock: self.lock.acquire() try: result = [] for key in keys: try: with open(self.filename(key), 'rb') as f: result.append(f.read()) except IOError: result.append(b'') finally: if lock: self.lock.release() return result def _iset(self, key, value, lock=True): """ Idempotent set """ fn = self.filename(key) if not os.path.exists(os.path.dirname(fn)): os.makedirs(os.path.dirname(fn)) if lock: self.lock.acquire() try: with open(self.filename(key), 'wb') as f: f.write(value) finally: if lock: self.lock.release() def _delete(self, keys, lock=True): if lock: self.lock.acquire() try: for key in keys: path = filename(self.path, key) if os.path.exists(path): os.remove(path) finally: if lock: self.lock.release() def drop(self): if os.path.exists(self.path): shutil.rmtree(self.path) self._iset_seen.clear() os.mkdir(self.path) def filename(self, key): return filename(self.path, key) def __exit__(self, *args): self.drop() os.rmdir(self.path) def __del__(self): if not self._explicitly_given_path: self.drop() os.rmdir(self.path) def filename(path, key): return os.path.join(path, escape_filename(token(key))) # http://stackoverflow.com/questions/295135/turn-a-string-into-a-valid-filename-in-python valid_chars = "-_.() " + string.ascii_letters + string.digits + os.path.sep def escape_filename(fn): """ Escape text so that it is a valid filename >>> escape_filename('Foo!bar?') 'Foobar' """ return ''.join(filter(valid_chars.__contains__, fn)) def token(key): """ >>> token('hello') 'hello' >>> token(('hello', 'world')) # doctest: +SKIP 'hello/world' """ if isinstance(key, str): return key elif isinstance(key, tuple): return os.path.join(*map(token, key)) else: return str(key) cleanup_files = list() @atexit.register def cleanup(): for fn in cleanup_files: if os.path.exists(fn): shutil.rmtree(fn) partd-1.0.0/partd/numpy.py0000644€#ô2€<ÄÎÏ0000001016513504343040016504 0ustar mrocklin00000000000000""" Store arrays We put arrays on disk as raw bytes, extending along the first dimension. Alongside each array x we ensure the value x.dtype which stores the string description of the array's dtype. """ from __future__ import absolute_import import numpy as np from toolz import valmap, identity, partial from .compatibility import pickle from .core import Interface from .file import File from .utils import frame, framesplit, suffix, ignoring def serialize_dtype(dt): """ Serialize dtype to bytes >>> serialize_dtype(np.dtype('i4')) '>> serialize_dtype(np.dtype('M8[us]')) '>> parse_dtype('i4') dtype('int32') >>> parse_dtype("[('a', 'i4')]") dtype([('a', '= (0, 5, 2): unpack_kwargs = {'raw': False} else: unpack_kwargs = {'encoding': 'utf-8'} blocks = [msgpack.unpackb(f, **unpack_kwargs) for f in framesplit(bytes)] except Exception: blocks = [pickle.loads(f) for f in framesplit(bytes)] result = np.empty(sum(map(len, blocks)), dtype='O') i = 0 for block in blocks: result[i:i + len(block)] = block i += len(block) return result else: result = np.frombuffer(bytes, dtype) if copy: result = result.copy() return result compress_text = identity decompress_text = identity compress_bytes = lambda bytes, itemsize: bytes decompress_bytes = identity with ignoring(ImportError): import blosc blosc.set_nthreads(1) compress_bytes = blosc.compress decompress_bytes = blosc.decompress compress_text = partial(blosc.compress, typesize=1) decompress_text = blosc.decompress with ignoring(ImportError): from snappy import compress as compress_text from snappy import decompress as decompress_text def compress(bytes, dtype): if dtype == 'O': return compress_text(bytes) else: return compress_bytes(bytes, dtype.itemsize) def decompress(bytes, dtype): if dtype == 'O': return decompress_text(bytes) else: return decompress_bytes(bytes) partd-1.0.0/partd/pandas.py0000644€#ô2€<ÄÎÏ0000001402213504343040016576 0ustar mrocklin00000000000000from __future__ import absolute_import from functools import partial import numpy as np import pandas as pd from pandas.core.internals import create_block_manager_from_blocks, make_block from . import numpy as pnp from .core import Interface from .compatibility import pickle from .encode import Encode from .utils import extend, framesplit, frame dumps = partial(pickle.dumps, protocol=pickle.HIGHEST_PROTOCOL) class PandasColumns(Interface): def __init__(self, partd=None): self.partd = pnp.Numpy(partd) Interface.__init__(self) def append(self, data, **kwargs): for k, df in data.items(): self.iset(extend(k, '.columns'), dumps(list(df.columns))) self.iset(extend(k, '.index-name'), dumps(df.index.name)) # TODO: don't use values, it does some work. Look at _blocks instead # pframe/cframe do this well arrays = dict((extend(k, col), df[col].values) for k, df in data.items() for col in df.columns) arrays.update(dict((extend(k, '.index'), df.index.values) for k, df in data.items())) # TODO: handle categoricals self.partd.append(arrays, **kwargs) def _get(self, keys, columns=None, **kwargs): if columns is None: columns = self.partd.partd.get([extend(k, '.columns') for k in keys], **kwargs) columns = list(map(pickle.loads, columns)) else: columns = [columns] * len(keys) index_names = self.partd.partd.get([extend(k, '.index-name') for k in keys], **kwargs) index_names = map(pickle.loads, index_names) keys = [[extend(k, '.index'), [extend(k, col) for col in cols]] for k, cols in zip(keys, columns)] arrays = self.partd.get(keys, **kwargs) return [pd.DataFrame(dict(zip(cols, arrs)), columns=cols, index=pd.Index(index, name=iname)) for iname, (index, arrs), cols in zip(index_names, arrays, columns)] def __getstate__(self): return {'partd': self.partd} def _iset(self, key, value): return self.partd._iset(key, value) def drop(self): return self.partd.drop() @property def lock(self): return self.partd.partd.lock def __exit__(self, *args): self.drop() self.partd.__exit__(self, *args) def __del__(self): self.partd.__del__() def index_to_header_bytes(ind): # These have special `__reduce__` methods, just use pickle if isinstance(ind, (pd.DatetimeIndex, pd.MultiIndex, pd.RangeIndex)): return None, dumps(ind) if isinstance(ind, pd.CategoricalIndex): cat = (ind.ordered, ind.categories) values = ind.codes else: cat = None values = ind.values header = (type(ind), ind._get_attributes_dict(), values.dtype, cat) bytes = pnp.compress(pnp.serialize(values), values.dtype) return header, bytes def index_from_header_bytes(header, bytes): if header is None: return pickle.loads(bytes) typ, attr, dtype, cat = header data = pnp.deserialize(pnp.decompress(bytes, dtype), dtype, copy=True) if cat: data = pd.Categorical.from_codes(data, cat[1], ordered=cat[0]) return typ.__new__(typ, data=data, **attr) def block_to_header_bytes(block): values = block.values try: # pandas >= 0.19 from pandas.api.types import is_datetime64tz_dtype except ImportError: from pandas.core.common import is_datetime64tz_dtype if isinstance(values, pd.Categorical): extension = ('categorical_type', (values.ordered, values.categories)) values = values.codes elif is_datetime64tz_dtype(block): extension = ('datetime64_tz_type', (block.values.tzinfo,)) values = values.view('i8') else: extension = ('numpy_type', ()) header = (block.mgr_locs.as_array, values.dtype, values.shape, extension) bytes = pnp.compress(pnp.serialize(values), values.dtype) return header, bytes def block_from_header_bytes(header, bytes): placement, dtype, shape, (extension_type, extension_values) = header values = pnp.deserialize(pnp.decompress(bytes, dtype), dtype, copy=True).reshape(shape) if extension_type == 'categorical_type': values = pd.Categorical.from_codes(values, extension_values[1], ordered=extension_values[0]) elif extension_type == 'datetime64_tz_type': tz_info = extension_values[0] values = pd.DatetimeIndex(values).tz_localize('utc').tz_convert( tz_info) return make_block(values, placement=placement) def serialize(df): """ Serialize and compress a Pandas DataFrame Uses Pandas blocks, snappy, and blosc to deconstruct an array into bytes """ col_header, col_bytes = index_to_header_bytes(df.columns) ind_header, ind_bytes = index_to_header_bytes(df.index) headers = [col_header, ind_header] bytes = [col_bytes, ind_bytes] for block in df._data.blocks: h, b = block_to_header_bytes(block) headers.append(h) bytes.append(b) frames = [dumps(headers)] + bytes return b''.join(map(frame, frames)) def deserialize(bytes): """ Deserialize and decompress bytes back to a pandas DataFrame """ frames = list(framesplit(bytes)) headers = pickle.loads(frames[0]) bytes = frames[1:] axes = [index_from_header_bytes(headers[0], bytes[0]), index_from_header_bytes(headers[1], bytes[1])] blocks = [block_from_header_bytes(h, b) for (h, b) in zip(headers[2:], bytes[2:])] return pd.DataFrame(create_block_manager_from_blocks(blocks, axes)) def join(dfs): if not dfs: return pd.DataFrame() else: return pd.concat(dfs) PandasBlocks = partial(Encode, serialize, deserialize, join) partd-1.0.0/partd/pickle.py0000644€#ô2€<ÄÎÏ0000000064413504343040016604 0ustar mrocklin00000000000000""" get/put functions that consume/produce Python lists using Pickle to serialize """ from __future__ import absolute_import from .compatibility import pickle from .encode import Encode from functools import partial def concat(lists): return sum(lists, []) Pickle = partial(Encode, partial(pickle.dumps, protocol=pickle.HIGHEST_PROTOCOL), pickle.loads, concat) partd-1.0.0/partd/python.py0000644€#ô2€<ÄÎÏ0000000170113504343040016651 0ustar mrocklin00000000000000""" get/put functions that consume/produce Python lists using msgpack or pickle to serialize. First we try msgpack (it's faster). If that fails then we default to pickle. """ from __future__ import absolute_import from .compatibility import pickle try: from pandas import msgpack except ImportError: try: import msgpack except ImportError: msgpack = False from .encode import Encode from functools import partial def dumps(x): try: return msgpack.packb(x, use_bin_type=True) except: return pickle.dumps(x, protocol=pickle.HIGHEST_PROTOCOL) def loads(x): try: if msgpack.version >= (0, 5, 2): unpack_kwargs = {'raw': False} else: unpack_kwargs = {'encoding': 'utf-8'} return msgpack.unpackb(x, **unpack_kwargs) except: return pickle.loads(x) def concat(lists): return sum(lists, []) Python = partial(Encode, dumps, loads, concat) partd-1.0.0/partd/tests/0000755€#ô2€<ÄÎÏ0000000000013504343206016125 5ustar mrocklin00000000000000partd-1.0.0/partd/tests/test_buffer.py0000644€#ô2€<ÄÎÏ0000000303013504343040020777 0ustar mrocklin00000000000000from partd.dict import Dict from partd.file import File from partd.buffer import Buffer, keys_to_flush import pickle import shutil import os def test_partd(): a = Dict() b = Dict() with Buffer(a, b, available_memory=10) as p: p.append({'x': b'Hello', 'y': b'abc'}) assert a.get(['x', 'y']) == [b'Hello', b'abc'] p.append({'x': b'World!', 'y': b'def'}) assert a.get(['x', 'y']) == [b'', b'abcdef'] assert b.get(['x', 'y']) == [b'HelloWorld!', b''] result = p.get(['y', 'x']) assert result == [b'abcdef', b'HelloWorld!'] assert p.get('z') == b'' with p.lock: # uh oh, possible deadlock result = p.get(['x'], lock=False) def test_keys_to_flush(): lengths = {'a': 20, 'b': 10, 'c': 15, 'd': 15, 'e': 10, 'f': 25, 'g': 5} assert keys_to_flush(lengths, 0.5) == ['f', 'a'] def test_pickle(): with Dict() as a: with File() as b: c = Buffer(a, b) c.append({'x': b'123'}) d = pickle.loads(pickle.dumps(c)) assert d.get('x') == c.get('x') pickled_attrs = ('memory_usage', 'lengths', 'available_memory') for attr in pickled_attrs: assert hasattr(d, attr) assert getattr(d, attr) == getattr(c, attr) # special case Dict and File -- some attrs do not pickle assert hasattr(d, 'fast') assert d.fast.data == c.fast.data assert hasattr(d, 'slow') assert d.slow.path == c.slow.path partd-1.0.0/partd/tests/test_compressed.py0000644€#ô2€<ÄÎÏ0000000133613504343040021701 0ustar mrocklin00000000000000from partd.compressed import ZLib import shutil import os import pickle def test_partd(): with ZLib() as p: p.append({'x': b'Hello', 'y': b'abc'}) p.append({'x': b'World!', 'y': b'def'}) assert os.path.exists(p.partd.filename('x')) assert os.path.exists(p.partd.filename('y')) result = p.get(['y', 'x']) assert result == [b'abcdef', b'HelloWorld!'] assert p.get('z') == b'' with p.lock: # uh oh, possible deadlock result = p.get(['x'], lock=False) assert not os.path.exists(p.partd.path) def test_pickle(): with ZLib() as p: p.append({'x': b'123'}) q = pickle.loads(pickle.dumps(p)) assert q.get('x') == b'123' partd-1.0.0/partd/tests/test_dict.py0000644€#ô2€<ÄÎÏ0000000165413504343040020463 0ustar mrocklin00000000000000from partd.dict import Dict import shutil import os def test_partd(): with Dict() as p: p.append({'x': b'Hello', 'y': b'abc'}) p.append({'x': b'World!', 'y': b'def'}) result = p.get(['y', 'x']) assert result == [b'abcdef', b'HelloWorld!'] assert p.get('z') == b'' with p.lock: # uh oh, possible deadlock result = p.get(['x'], lock=False) def test_key_tuple(): with Dict() as p: p.append({('a', 'b'): b'123'}) assert p.get(('a', 'b')) == b'123' def test_iset(): with Dict() as p: p.iset('x', b'123') assert 'x' in p._iset_seen assert 'y' not in p._iset_seen p.iset('x', b'123') p.iset('x', b'123') assert p.get('x') == b'123' def test_delete_non_existent_key(): with Dict() as p: p.append({'x': b'123'}) p.delete(['x', 'y']) assert p.get(['x', 'y']) == [b'', b''] partd-1.0.0/partd/tests/test_encode.py0000644€#ô2€<ÄÎÏ0000000127413504343040020773 0ustar mrocklin00000000000000from partd.file import File from partd.encode import Encode import zlib import shutil import os def test_partd(): with Encode(zlib.compress, zlib.decompress, b''.join) as p: p.append({'x': b'Hello', 'y': b'abc'}) p.append({'x': b'World!', 'y': b'def'}) result = p.get(['y', 'x']) assert result == [b'abcdef', b'HelloWorld!'] assert p.get('z') == b'' with p.lock: # uh oh, possible deadlock result = p.get(['x'], lock=False) def test_ensure(): with Encode(zlib.compress, zlib.decompress, b''.join) as p: p.iset('x', b'123') p.iset('x', b'123') p.iset('x', b'123') assert p.get('x') == b'123' partd-1.0.0/partd/tests/test_file.py0000644€#ô2€<ÄÎÏ0000000341013504343040020447 0ustar mrocklin00000000000000from partd.file import File import shutil import os def test_partd(): with File() as p: p.append({'x': b'Hello', 'y': b'abc'}) p.append({'x': b'World!', 'y': b'def'}) assert os.path.exists(p.filename('x')) assert os.path.exists(p.filename('y')) result = p.get(['y', 'x']) assert result == [b'abcdef', b'HelloWorld!'] assert p.get('z') == b'' with p.lock: # uh oh, possible deadlock result = p.get(['x'], lock=False) assert not os.path.exists(p.path) def test_key_tuple(): with File() as p: p.append({('a', 'b'): b'123'}) assert os.path.exists(p.filename(('a', 'b'))) def test_iset(): with File() as p: p.iset('x', b'123') assert 'x' in p._iset_seen assert 'y' not in p._iset_seen p.iset('x', b'123') p.iset('x', b'123') assert p.get('x') == b'123' def test_nested_get(): with File() as p: p.append({'x': b'1', 'y': b'2', 'z': b'3'}) assert p.get(['x', ['y', 'z']]) == [b'1', [b'2', b'3']] def test_drop(): with File() as p: p.append({'x': b'123'}) p.iset('y', b'abc') assert p.get('x') == b'123' assert p.get('y') == b'abc' p.drop() assert p.get('x') == b'' assert p.get('y') == b'' p.append({'x': b'123'}) p.iset('y', b'def') assert p.get('x') == b'123' assert p.get('y') == b'def' def test_del(): f = File() assert f.path assert os.path.exists(f.path) f.__del__() assert not os.path.exists(f.path) with File('Foo') as p: p.__del__() assert os.path.exists(p.path) def test_specify_dirname(): with File(dir=os.getcwd()) as f: assert os.getcwd() in f.path partd-1.0.0/partd/tests/test_numpy.py0000644€#ô2€<ÄÎÏ0000000445313504343040020710 0ustar mrocklin00000000000000from __future__ import absolute_import import pytest np = pytest.importorskip('numpy') # noqa import pickle import partd from partd.numpy import Numpy def test_numpy(): dt = np.dtype([('a', 'i4'), ('b', 'i2'), ('c', 'f8')]) with Numpy() as p: p.append({'a': np.array([10, 20, 30], dtype=dt['a']), 'b': np.array([ 1, 2, 3], dtype=dt['b']), 'c': np.array([.1, .2, .3], dtype=dt['c'])}) p.append({'a': np.array([70, 80, 90], dtype=dt['a']), 'b': np.array([ 7, 8, 9], dtype=dt['b']), 'c': np.array([.7, .8, .9], dtype=dt['c'])}) result = p.get(['a', 'c']) assert (result[0] == np.array([10, 20, 30, 70, 80, 90],dtype=dt['a'])).all() assert (result[1] == np.array([.1, .2, .3, .7, .8, .9],dtype=dt['c'])).all() with p.lock: # uh oh, possible deadlock result = p.get(['a'], lock=False) def test_nested(): with Numpy() as p: p.append({'x': np.array([1, 2, 3]), ('y', 1): np.array([4, 5, 6]), ('z', 'a', 3): np.array([.1, .2, .3])}) assert (p.get(('z', 'a', 3)) == np.array([.1, .2, .3])).all() def test_serialization(): with Numpy() as p: p.append({'x': np.array([1, 2, 3])}) q = pickle.loads(pickle.dumps(p)) assert (q.get('x') == [1, 2, 3]).all() array_of_lists = np.empty(3, dtype='O') array_of_lists[:] = [[1, 2], [3, 4], [5, 6]] @pytest.mark.parametrize('x', [np.array(['Alice', 'Bob', 'Charlie'], dtype='O'), array_of_lists]) def test_object_dtype(x): with Numpy() as p: p.append({'x': x}) p.append({'x': x}) assert isinstance(p.get('x'), np.ndarray) assert (p.get('x') == np.concatenate([x, x])).all() def test_datetime_types(): x = np.array(['2014-01-01T12:00:00'], dtype='M8[us]') y = np.array(['2014-01-01T12:00:00'], dtype='M8[s]') with Numpy() as p: p.append({'x': x, 'y': y}) assert p.get('x').dtype == x.dtype assert p.get('y').dtype == y.dtype def test_non_utf8_bytes(): a = np.array([b'\xc3\x28', b'\xa0\xa1', b'\xe2\x28\xa1', b'\xe2\x82\x28', b'\xf0\x28\x8c\xbc'], dtype='O') s = partd.numpy.serialize(a) assert (partd.numpy.deserialize(s, 'O') == a).all() partd-1.0.0/partd/tests/test_pandas.py0000644€#ô2€<ÄÎÏ0000000721713504343040021007 0ustar mrocklin00000000000000from __future__ import absolute_import import pytest pytest.importorskip('pandas') # noqa import numpy as np import pandas as pd import pandas.util.testing as tm import os from partd.pandas import PandasColumns, PandasBlocks, serialize, deserialize df1 = pd.DataFrame({'a': [1, 2, 3], 'b': [1., 2., 3.], 'c': ['x', 'y', 'x']}, columns=['a', 'b', 'c'], index=pd.Index([1, 2, 3], name='myindex')) df2 = pd.DataFrame({'a': [10, 20, 30], 'b': [10., 20., 30.], 'c': ['X', 'Y', 'X']}, columns=['a', 'b', 'c'], index=pd.Index([10, 20, 30], name='myindex')) def test_PandasColumns(): with PandasColumns() as p: assert os.path.exists(p.partd.partd.path) p.append({'x': df1, 'y': df2}) p.append({'x': df2, 'y': df1}) assert os.path.exists(p.partd.partd.filename('x')) assert os.path.exists(p.partd.partd.filename(('x', 'a'))) assert os.path.exists(p.partd.partd.filename(('x', '.index'))) assert os.path.exists(p.partd.partd.filename('y')) result = p.get(['y', 'x']) tm.assert_frame_equal(result[0], pd.concat([df2, df1])) tm.assert_frame_equal(result[1], pd.concat([df1, df2])) with p.lock: # uh oh, possible deadlock result = p.get(['x'], lock=False) assert not os.path.exists(p.partd.partd.path) def test_column_selection(): with PandasColumns('foo') as p: p.append({'x': df1, 'y': df2}) p.append({'x': df2, 'y': df1}) result = p.get('x', columns=['c', 'b']) tm.assert_frame_equal(result, pd.concat([df1, df2])[['c', 'b']]) def test_PandasBlocks(): with PandasBlocks() as p: assert os.path.exists(p.partd.path) p.append({'x': df1, 'y': df2}) p.append({'x': df2, 'y': df1}) assert os.path.exists(p.partd.filename('x')) assert os.path.exists(p.partd.filename('y')) result = p.get(['y', 'x']) tm.assert_frame_equal(result[0], pd.concat([df2, df1])) tm.assert_frame_equal(result[1], pd.concat([df1, df2])) with p.lock: # uh oh, possible deadlock result = p.get(['x'], lock=False) assert not os.path.exists(p.partd.path) @pytest.mark.parametrize('ordered', [False, True]) def test_serialize_categoricals(ordered): frame = pd.DataFrame({'x': [1, 2, 3, 4], 'y': pd.Categorical(['c', 'a', 'b', 'a'], ordered=ordered)}, index=pd.Categorical(['x', 'y', 'z', 'x'], ordered=ordered)) frame.index.name = 'foo' frame.columns.name = 'bar' for ind, df in [(0, frame), (1, frame.T)]: df2 = deserialize(serialize(df)) tm.assert_frame_equal(df, df2) def test_serialize_multi_index(): df = pd.DataFrame({'x': ['a', 'b', 'c', 'a', 'b', 'c'], 'y': [1, 2, 3, 4, 5, 6], 'z': [7., 8, 9, 10, 11, 12]}) df = df.groupby([df.x, df.y]).sum() df.index.name = 'foo' df.columns.name = 'bar' df2 = deserialize(serialize(df)) tm.assert_frame_equal(df, df2) @pytest.mark.parametrize('base', [ pd.Timestamp('1987-03-3T01:01:01+0001'), pd.Timestamp('1987-03-03 01:01:01-0600', tz='US/Central'), ]) def test_serialize(base): df = pd.DataFrame({'x': [ base + pd.Timedelta(seconds=i) for i in np.random.randint(0, 1000, size=10)], 'y': list(range(10)), 'z': pd.date_range('2017', periods=10)}) df2 = deserialize(serialize(df)) tm.assert_frame_equal(df, df2) partd-1.0.0/partd/tests/test_partd.py0000644€#ô2€<ÄÎÏ0000000240113504343040020641 0ustar mrocklin00000000000000from partd import File from partd.core import token, escape_filename, filename from partd import core import os import shutil from contextlib import contextmanager def test_partd(): path = 'tmp.partd' with File(path) as p: p.append({'x': b'Hello', 'y': b'abc'}) p.append({'x': b'World!', 'y': b'def'}) assert os.path.exists(p.filename('x')) assert os.path.exists(p.filename('y')) result = p.get(['y', 'x']) assert result == [b'abcdef', b'HelloWorld!'] assert p.get('z') == b'' with p.lock: # uh oh, possible deadlock result = p.get(['x'], lock=False) assert not os.path.exists(path) def test_key_tuple(): with File('foo') as p: p.append({('a', 'b'): b'123'}) assert os.path.exists(os.path.join(p.path, 'a', 'b')) def test_ensure(): with File('foo') as p: p.iset('x', b'123') p.iset('x', b'123') p.iset('x', b'123') assert p.get('x') == b'123' def test_filenames(): assert token('hello') == 'hello' assert token(('hello', 'world')) == os.path.join('hello', 'world') assert escape_filename(os.path.join('a', 'b')) == os.path.join('a', 'b') assert filename('dir', ('a', 'b')) == os.path.join('dir', 'a', 'b') partd-1.0.0/partd/tests/test_pickle.py0000644€#ô2€<ÄÎÏ0000000137213504343040021004 0ustar mrocklin00000000000000from partd.pickle import Pickle import os import shutil def test_pickle(): with Pickle() as p: p.append({'x': ['Hello', 'World!'], 'y': [1, 2, 3]}) p.append({'x': ['Alice', 'Bob!'], 'y': [4, 5, 6]}) assert os.path.exists(p.partd.filename('x')) assert os.path.exists(p.partd.filename('y')) result = p.get(['y', 'x']) assert result == [[1, 2, 3, 4, 5, 6], ['Hello', 'World!', 'Alice', 'Bob!']] with p.lock: # uh oh, possible deadlock result = p.get(['x'], lock=False) assert not os.path.exists(p.partd.path) def test_ensure(): with Pickle() as p: p.iset('x', [1, 2, 3]) p.iset('x', [1, 2, 3]) assert p.get('x') == [1, 2, 3] partd-1.0.0/partd/tests/test_python.py0000644€#ô2€<ÄÎÏ0000000037013504343040021053 0ustar mrocklin00000000000000from partd.python import dumps, loads import os import shutil from math import sin def test_pack_unpack(): data = [1, 2, b'Hello', 'Hello'] assert loads(dumps(data)) == data data = [1, 2, sin] assert loads(dumps(data)) == data partd-1.0.0/partd/tests/test_utils.py0000644€#ô2€<ÄÎÏ0000000040213504343040020666 0ustar mrocklin00000000000000from partd.utils import frame, framesplit import struct def test_frame(): assert frame(b'Hello') == struct.pack('Q', 5) + b'Hello' def test_framesplit(): L = [b'Hello', b'World!', b'123'] assert list(framesplit(b''.join(map(frame, L)))) == L partd-1.0.0/partd/tests/test_zmq.py0000644€#ô2€<ÄÎÏ0000000640513504343040020346 0ustar mrocklin00000000000000import pytest pytest.importorskip('zmq') from partd.zmq import Server, keys_to_flush, File, Client from partd import core, Dict from threading import Thread from time import sleep from contextlib import contextmanager import pickle import os import shutil def test_server(): s = Server() try: s.start() s.append({'x': b'abc', 'y': b'1234'}) s.append({'x': b'def', 'y': b'5678'}) assert s.get(['x']) == [b'abcdef'] assert s.get(['x', 'y']) == [b'abcdef', b'12345678'] assert s.get(['x']) == [b'abcdef'] finally: s.close() def dont_test_flow_control(): path = 'bar' if os.path.exists('bar'): shutil.rmtree('bar') s = Server('bar', available_memory=1, n_outstanding_writes=3, start=False) p = Client(s.address) try: listen_thread = Thread(target=s.listen) listen_thread.start() """ Don't start these threads self._write_to_disk_thread = Thread(target=self._write_to_disk) self._write_to_disk_thread.start() self._free_frozen_sockets_thread = Thread(target=self._free_frozen_sockets) self._free_frozen_sockets_thread.start() """ p.append({'x': b'12345'}) sleep(0.1) assert s._out_disk_buffer.qsize() == 1 p.append({'x': b'12345'}) p.append({'x': b'12345'}) sleep(0.1) assert s._out_disk_buffer.qsize() == 3 held_append = Thread(target=p.append, args=({'x': b'123'},)) held_append.start() sleep(0.1) assert held_append.isAlive() # held! assert not s._frozen_sockets.empty() write_to_disk_thread = Thread(target=s._write_to_disk) write_to_disk_thread.start() free_frozen_sockets_thread = Thread(target=s._free_frozen_sockets) free_frozen_sockets_thread.start() sleep(0.2) assert not held_append.isAlive() assert s._frozen_sockets.empty() finally: s.close() @contextmanager def partd_server(**kwargs): with Server(**kwargs) as server: with Client(server.address) as p: yield (p, server) def test_partd_object(): with partd_server() as (p, server): p.append({'x': b'Hello', 'y': b'abc'}) p.append({'x': b'World!', 'y': b'def'}) result = p.get(['y', 'x']) assert result == [b'abcdef', b'HelloWorld!'] def test_delete(): with partd_server() as (p, server): p.append({'x': b'Hello'}) assert p.get('x') == b'Hello' p.delete(['x']) assert p.get('x') == b'' def test_iset(): with partd_server() as (p, server): p.iset('x', b'111') p.iset('x', b'111') assert p.get('x') == b'111' def test_tuple_keys(): with partd_server() as (p, server): p.append({('x', 'y'): b'123'}) assert p.get(('x', 'y')) == b'123' def test_serialization(): with partd_server() as (p, server): p.append({'x': b'123'}) q = pickle.loads(pickle.dumps(p)) assert q.get('x') == b'123' def test_drop(): with partd_server() as (p, server): p.append({'x': b'123'}) p.drop() assert p.get('x') == b'' def dont_test_server_autocreation(): with Client() as p: p.append({'x': b'123'}) assert p.get('x') == b'123' partd-1.0.0/partd/utils.py0000644€#ô2€<ÄÎÏ0000000730613504343040016477 0ustar mrocklin00000000000000from contextlib import contextmanager import os import shutil import tempfile import struct def raises(exc, lamda): try: lamda() return False except exc: return True @contextmanager def tmpfile(extension=''): extension = '.' + extension.lstrip('.') handle, filename = tempfile.mkstemp(extension) os.close(handle) os.remove(filename) try: yield filename finally: if os.path.exists(filename): if os.path.isdir(filename): shutil.rmtree(filename) else: os.remove(filename) def frame(bytes): """ Pack the length of the bytes in front of the bytes TODO: This does a full copy. This should maybe be inlined somehow wherever this gets used instead. My laptop shows a data bandwidth of 2GB/s """ return struct.pack('Q', len(bytes)) + bytes def framesplit(bytes): """ Split buffer into frames of concatenated chunks >>> data = frame(b'Hello') + frame(b'World') >>> list(framesplit(data)) # doctest: +SKIP [b'Hello', b'World'] """ i = 0; n = len(bytes) chunks = list() while i < n: nbytes = struct.unpack('Q', bytes[i:i+8])[0] i += 8 yield bytes[i: i + nbytes] i += nbytes def partition_all(n, bytes): """ Partition bytes into evenly sized blocks The final block holds the remainder and so may not be of equal size >>> list(partition_all(2, b'Hello')) ['He', 'll', 'o'] See Also: toolz.partition_all """ if len(bytes) < n: # zero copy fast common case yield bytes else: for i in range(0, len(bytes), n): yield bytes[i: i+n] @contextmanager def ignoring(*exc): try: yield except exc: pass @contextmanager def do_nothing(*args, **kwargs): yield def nested_get(ind, coll, lazy=False): """ Get nested index from collection Examples -------- >>> nested_get(1, 'abc') 'b' >>> nested_get([1, 0], 'abc') ['b', 'a'] >>> nested_get([[1, 0], [0, 1]], 'abc') [['b', 'a'], ['a', 'b']] """ if isinstance(ind, list): if lazy: return (nested_get(i, coll, lazy=lazy) for i in ind) else: return [nested_get(i, coll, lazy=lazy) for i in ind] else: return coll[ind] def flatten(seq): """ >>> list(flatten([1])) [1] >>> list(flatten([[1, 2], [1, 2]])) [1, 2, 1, 2] >>> list(flatten([[[1], [2]], [[1], [2]]])) [1, 2, 1, 2] >>> list(flatten(((1, 2), (1, 2)))) # Don't flatten tuples [(1, 2), (1, 2)] >>> list(flatten((1, 2, [3, 4]))) # support heterogeneous [1, 2, 3, 4] """ for item in seq: if isinstance(item, list): for item2 in flatten(item): yield item2 else: yield item def suffix(key, term): """ suffix a key with a suffix Works if they key is a string or a tuple >>> suffix('x', '.dtype') 'x.dtype' >>> suffix(('a', 'b', 'c'), '.dtype') ('a', 'b', 'c.dtype') """ if isinstance(key, str): return key + term elif isinstance(key, tuple): return key[:-1] + (suffix(key[-1], term),) else: return suffix(str(key), term) def extend(key, term): """ extend a key with a another element in a tuple Works if they key is a string or a tuple >>> extend('x', '.dtype') ('x', '.dtype') >>> extend(('a', 'b', 'c'), '.dtype') ('a', 'b', 'c', '.dtype') """ if isinstance(term, tuple): pass elif isinstance(term, str): term = (term,) else: term = (str(term),) if not isinstance(key, tuple): key = (key,) return key + term partd-1.0.0/partd/zmq.py0000644€#ô2€<ÄÎÏ0000002276113504343040016150 0ustar mrocklin00000000000000from __future__ import absolute_import, print_function import zmq import logging from itertools import chain from bisect import bisect import socket from operator import add from time import sleep, time from toolz import accumulate, topk, pluck, merge, keymap import uuid from collections import defaultdict from contextlib import contextmanager from threading import Thread, Lock from datetime import datetime from multiprocessing import Process import traceback import sys from .dict import Dict from .file import File from .buffer import Buffer from . import core from .compatibility import Queue, Empty, unicode from .utils import ignoring tuple_sep = b'-|-' logger = logging.getLogger(__name__) @contextmanager def logerrors(): try: yield except Exception as e: logger.exception(e) raise class Server(object): def __init__(self, partd=None, bind=None, start=True, block=False, hostname=None): self.context = zmq.Context() if partd is None: partd = Buffer(Dict(), File()) self.partd = partd self.socket = self.context.socket(zmq.ROUTER) if hostname is None: hostname = socket.gethostname() if isinstance(bind, unicode): bind = bind.encode() if bind is None: port = self.socket.bind_to_random_port('tcp://*') else: self.socket.bind(bind) port = int(bind.split(':')[-1].rstrip('/')) self.address = ('tcp://%s:%d' % (hostname, port)).encode() self.status = 'created' self.partd.lock.acquire() self._lock = Lock() self._socket_lock = Lock() if start: self.start() if block: self.block() def start(self): if self.status != 'run': self.status = 'run' self._listen_thread = Thread(target=self.listen) self._listen_thread.start() logger.debug('Start server at %s', self.address) def block(self): """ Block until all threads close """ try: self._listen_thread.join() except AttributeError: pass def listen(self): with logerrors(): logger.debug('Start listening %s', self.address) while self.status != 'closed': if not self.socket.poll(100): continue with self._socket_lock: payload = self.socket.recv_multipart() address, command, payload = payload[0], payload[1], payload[2:] logger.debug('Server receives %s %s', address, command) if command == b'close': logger.debug('Server closes') self.ack(address) self.status = 'closed' break # self.close() elif command == b'append': keys, values = payload[::2], payload[1::2] keys = list(map(deserialize_key, keys)) data = dict(zip(keys, values)) self.partd.append(data, lock=False) logger.debug('Server appends %d keys', len(data)) self.ack(address) elif command == b'iset': key, value = payload key = deserialize_key(key) self.partd.iset(key, value, lock=False) self.ack(address) elif command == b'get': keys = list(map(deserialize_key, payload)) logger.debug('get %s', keys) result = self.get(keys) self.send_to_client(address, result) self.ack(address, flow_control=False) elif command == b'delete': keys = list(map(deserialize_key, payload)) logger.debug('delete %s', keys) self.partd.delete(keys, lock=False) self.ack(address, flow_control=False) elif command == b'syn': self.ack(address) elif command == b'drop': self.drop() self.ack(address) else: logger.debug("Unknown command: %s", command) raise ValueError("Unknown command: " + command) def send_to_client(self, address, result): with logerrors(): if not isinstance(result, list): result = [result] with self._socket_lock: self.socket.send_multipart([address] + result) def ack(self, address, flow_control=True): with logerrors(): logger.debug('Server sends ack') self.send_to_client(address, b'ack') def append(self, data): self.partd.append(data, lock=False) logger.debug('Server appends %d keys', len(data)) def drop(self): with logerrors(): self.partd.drop() def get(self, keys): with logerrors(): logger.debug('Server gets keys: %s', keys) with self._lock: result = self.partd.get(keys, lock=False) return result def close(self): logger.debug('Server closes') self.status = 'closed' self.block() with ignoring(zmq.error.ZMQError): self.socket.close(1) with ignoring(zmq.error.ZMQError): self.context.destroy(3) self.partd.lock.release() def __enter__(self): self.start() return self def __exit__(self, *args): self.close() self.partd.__exit__(*args) def keys_to_flush(lengths, fraction=0.1, maxcount=100000): """ Which keys to remove >>> lengths = {'a': 20, 'b': 10, 'c': 15, 'd': 15, ... 'e': 10, 'f': 25, 'g': 5} >>> keys_to_flush(lengths, 0.5) ['f', 'a'] """ top = topk(max(len(lengths) // 2, 1), lengths.items(), key=1) total = sum(lengths.values()) cutoff = min(maxcount, max(1, bisect(list(accumulate(add, pluck(1, top))), total * fraction))) result = [k for k, v in top[:cutoff]] assert result return result def serialize_key(key): """ >>> serialize_key('x') 'x' >>> serialize_key(('a', 'b', 1)) 'a-|-b-|-1' """ if isinstance(key, tuple): return tuple_sep.join(map(serialize_key, key)) if isinstance(key, bytes): return key if isinstance(key, str): return key.encode() return str(key).encode() def deserialize_key(text): """ >>> deserialize_key('x') 'x' >>> deserialize_key('a-|-b-|-1') ('a', 'b', '1') """ if tuple_sep in text: return tuple(text.split(tuple_sep)) else: return text from .core import Interface from .file import File class Client(Interface): def __init__(self, address=None, create_server=False, **kwargs): self.address = address self.context = zmq.Context() self.socket = self.context.socket(zmq.DEALER) logger.debug('Client connects to %s', address) self.socket.connect(address) self.send(b'syn', [], ack_required=False) self.lock = NotALock() # Server sequentializes everything Interface.__init__(self) def __getstate__(self): return {'address': self.address} def __setstate__(self, state): self.__init__(state['address']) logger.debug('Reconstruct client from pickled state') def send(self, command, payload, recv=False, ack_required=True): if ack_required: ack = self.socket.recv_multipart() assert ack == [b'ack'] logger.debug('Client sends command: %s', command) self.socket.send_multipart([command] + payload) if recv: result = self.socket.recv_multipart() else: result = None return result def _get(self, keys, lock=None): """ Lock argument is ignored. Everything is sequential (I think) """ logger.debug('Client gets %s %s', self.address, keys) keys = list(map(serialize_key, keys)) return self.send(b'get', keys, recv=True) def append(self, data, lock=None): logger.debug('Client appends %s %s', self.address, str(len(data)) + ' keys') data = keymap(serialize_key, data) payload = list(chain.from_iterable(data.items())) self.send(b'append', payload) def _delete(self, keys, lock=None): logger.debug('Client deletes %s %s', self.address, str(len(keys)) + ' keys') keys = list(map(serialize_key, keys)) self.send(b'delete', keys) def _iset(self, key, value): self.send(b'iset', [serialize_key(key), value]) def drop(self): self.send(b'drop', []) sleep(0.05) def close_server(self): self.send(b'close', []) def close(self): if hasattr(self, 'server_process'): with ignoring(zmq.error.ZMQError): self.close_server() self.server_process.join() with ignoring(zmq.error.ZMQError): self.socket.close(1) with ignoring(zmq.error.ZMQError): self.context.destroy(1) def __exit__(self, type, value, traceback): self.drop() self.close() def __del__(self): self.close() class NotALock(object): def acquire(self): pass def release(self): pass def __enter__(self): return self def __exit__(self, *args): pass partd-1.0.0/partd.egg-info/0000755€#ô2€<ÄÎÏ0000000000013504343206016455 5ustar mrocklin00000000000000partd-1.0.0/partd.egg-info/PKG-INFO0000644€#ô2€<ÄÎÏ0000001172613504343206017561 0ustar mrocklin00000000000000Metadata-Version: 2.1 Name: partd Version: 1.0.0 Summary: Appendable key-value storage Home-page: http://github.com/dask/partd/ Maintainer: Matthew Rocklin Maintainer-email: mrocklin@gmail.com License: BSD Description: PartD ===== |Build Status| |Version Status| Key-value byte store with appendable values Partd stores key-value pairs. Values are raw bytes. We append on old values. Partd excels at shuffling operations. Operations ---------- PartD has two main operations, ``append`` and ``get``. Example ------- 1. Create a Partd backed by a directory:: >>> import partd >>> p = partd.File('/path/to/new/dataset/') 2. Append key-byte pairs to dataset:: >>> p.append({'x': b'Hello ', 'y': b'123'}) >>> p.append({'x': b'world!', 'y': b'456'}) 3. Get bytes associated to keys:: >>> p.get('x') # One key b'Hello world!' >>> p.get(['y', 'x']) # List of keys [b'123456', b'Hello world!'] 4. Destroy partd dataset:: >>> p.drop() That's it. Implementations --------------- We can back a partd by an in-memory dictionary:: >>> p = Dict() For larger amounts of data or to share data between processes we back a partd by a directory of files. This uses file-based locks for consistency.:: >>> p = File('/path/to/dataset/') However this can fail for many small writes. In these cases you may wish to buffer one partd with another, keeping a fixed maximum of data in the buffering partd. This writes the larger elements of the first partd to the second partd when space runs low:: >>> p = Buffer(Dict(), File(), available_memory=2e9) # 2GB memory buffer You might also want to have many distributed process write to a single partd consistently. This can be done with a server * Server Process:: >>> p = Buffer(Dict(), File(), available_memory=2e9) # 2GB memory buffer >>> s = Server(p, address='ipc://server') * Worker processes:: >>> p = Client('ipc://server') # Client machine talks to remote server Encodings and Compression ------------------------- Once we can robustly and efficiently append bytes to a partd we consider compression and encodings. This is generally available with the ``Encode`` partd, which accepts three functions, one to apply on bytes as they are written, one to apply to bytes as they are read, and one to join bytestreams. Common configurations already exist for common data and compression formats. We may wish to compress and decompress data transparently as we interact with a partd. Objects like ``BZ2``, ``Blosc``, ``ZLib`` and ``Snappy`` exist and take another partd as an argument.:: >>> p = File(...) >>> p = ZLib(p) These work exactly as before, the (de)compression happens automatically. Common data formats like Python lists, numpy arrays, and pandas dataframes are also supported out of the box.:: >>> p = File(...) >>> p = NumPy(p) >>> p.append({'x': np.array([...])}) This lets us forget about bytes and think instead in our normal data types. Composition ----------- In principle we want to compose all of these choices together 1. Write policy: ``Dict``, ``File``, ``Buffer``, ``Client`` 2. Encoding: ``Pickle``, ``Numpy``, ``Pandas``, ... 3. Compression: ``Blosc``, ``Snappy``, ... Partd objects compose by nesting. Here we make a partd that writes pickle encoded BZ2 compressed bytes directly to disk:: >>> p = Pickle(BZ2(File('foo'))) We could construct more complex systems that include compression, serialization, buffering, and remote access.:: >>> server = Server(Buffer(Dict(), File(), available_memory=2e0)) >>> client = Pickle(Snappy(Client(server.address))) >>> client.append({'x': [1, 2, 3]}) .. |Build Status| image:: https://travis-ci.org/dask/partd.png :target: https://travis-ci.org/dask/partd .. |Version Status| image:: https://img.shields.io/pypi/v/partd.svg :target: https://pypi.python.org/pypi/partd/ Platform: UNKNOWN Provides-Extra: complete partd-1.0.0/partd.egg-info/SOURCES.txt0000644€#ô2€<ÄÎÏ0000000141013504343206020335 0ustar mrocklin00000000000000LICENSE.txt MANIFEST.in README.rst requirements.txt setup.py partd/__init__.py partd/buffer.py partd/compatibility.py partd/compressed.py partd/core.py partd/dict.py partd/encode.py partd/file.py partd/numpy.py partd/pandas.py partd/pickle.py partd/python.py partd/utils.py partd/zmq.py partd.egg-info/PKG-INFO partd.egg-info/SOURCES.txt partd.egg-info/dependency_links.txt partd.egg-info/not-zip-safe partd.egg-info/requires.txt partd.egg-info/top_level.txt partd/tests/test_buffer.py partd/tests/test_compressed.py partd/tests/test_dict.py partd/tests/test_encode.py partd/tests/test_file.py partd/tests/test_numpy.py partd/tests/test_pandas.py partd/tests/test_partd.py partd/tests/test_pickle.py partd/tests/test_python.py partd/tests/test_utils.py partd/tests/test_zmq.pypartd-1.0.0/partd.egg-info/dependency_links.txt0000644€#ô2€<ÄÎÏ0000000000113504343206022523 0ustar mrocklin00000000000000 partd-1.0.0/partd.egg-info/not-zip-safe0000644€#ô2€<ÄÎÏ0000000000113504343206020703 0ustar mrocklin00000000000000 partd-1.0.0/partd.egg-info/requires.txt0000644€#ô2€<ÄÎÏ0000000010113504343206021045 0ustar mrocklin00000000000000locket toolz [complete] numpy>=1.9.0 pandas>=0.19.0 pyzmq blosc partd-1.0.0/partd.egg-info/top_level.txt0000644€#ô2€<ÄÎÏ0000000000613504343206021203 0ustar mrocklin00000000000000partd partd-1.0.0/requirements.txt0000644€#ô2€<ÄÎÏ0000000001513504343040017125 0ustar mrocklin00000000000000locket toolz partd-1.0.0/setup.cfg0000644€#ô2€<ÄÎÏ0000000004613504343206015472 0ustar mrocklin00000000000000[egg_info] tag_build = tag_date = 0 partd-1.0.0/setup.py0000755€#ô2€<ÄÎÏ0000000131413504343101015357 0ustar mrocklin00000000000000#!/usr/bin/env python from os.path import exists from setuptools import setup setup(name='partd', version='1.0.0', description='Appendable key-value storage', url='http://github.com/dask/partd/', maintainer='Matthew Rocklin', maintainer_email='mrocklin@gmail.com', license='BSD', keywords='', packages=['partd'], install_requires=list(open('requirements.txt').read().strip().split('\n')), long_description=(open('README.rst').read() if exists('README.rst') else ''), extras_require={'complete': [ 'numpy >= 1.9.0', 'pandas >=0.19.0', 'pyzmq', 'blosc', ]}, zip_safe=False)