Clean up a few Python 2-isms (#586)

* CLN : Use of super

	modified:   zarr/indexing.py
	modified:   zarr/n5.py
	modified:   zarr/storage.py
	modified:   zarr/tests/test_convenience.py

* CLN : Remove coding cookies from file

utf-8 is the default source code file encoding on python 3

* CLN : Remove u-string prefixes

the string prefixes dont do anything on python 3 and are visual noise

	modified:   zarr/tests/test_core.py
	modified:   zarr/tests/test_creation.py
	modified:   zarr/tests/test_filters.py
	modified:   zarr/tests/test_hierarchy.py
	modified:   zarr/util.py

* CLN : Remove conditional

The conditional always evaluates to True on Python 3 so the rest of the
if/elif/else conditional has been removed

	modified:   zarr/storage.py

* DOC : Add an entry in release doc

	modified:   docs/release.rst

* CLN : Fix a pep8 issue

remove the import entirely and use os.replace instead of replace

	modified:   zarr/storage.py

Author: rahulporuri

docs/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 #
 # zarr documentation build configuration file, created by
 # sphinx-quickstart on Mon May  2 21:40:09 2016.

docs/release.rst

@@ -7,6 +7,10 @@ Next release
 
 * `DirectoryStore` now uses `os.scandir`, which should make listing large store
   faster, :issue:`563`
+  
+* Remove a few remaining Python 2-isms.
+  By :user:`Poruri Sai Rahul <rahulporuri>`; :issue:`393`.
+
 * Fix minor bug in `N5Store`. 
   By :user:`gsakkis`, :issue:`550`.
 

setup.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import sys
 
 from setuptools import setup

zarr/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # flake8: noqa
 from zarr.codecs import *
 from zarr.convenience import (consolidate_metadata, copy, copy_all, copy_store,

zarr/attrs.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 from collections.abc import MutableMapping
 
 from zarr.meta import parse_metadata

zarr/codecs.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # flake8: noqa
 from numcodecs import *
 from numcodecs import get_codec, Blosc, Zlib, Delta, AsType, BZ2

zarr/convenience.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Convenience functions for storing and loading data."""
 import io
 import itertools

zarr/core.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import binascii
 import hashlib
 import itertools

zarr/creation.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 from warnings import warn
 
 import numpy as np

zarr/errors.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 
 
 class MetadataError(Exception):

zarr/hierarchy.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 from collections.abc import MutableMapping
 from itertools import islice
 

zarr/indexing.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import collections
 import itertools
 import math
@@ -740,7 +739,7 @@ def __init__(self, selection, array):
         selection = np.nonzero(selection[0])
 
         # delegate the rest to superclass
-        super(MaskIndexer, self).__init__(selection, array)
+        super().__init__(selection, array)
 
 
 class VIndex(object):

zarr/meta.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import base64
 from collections.abc import Mapping
 

zarr/meta_v1.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import json
 
 import numpy as np

zarr/n5.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """This module contains a storage class and codec to support the N5 format.
 """
 import os
@@ -97,7 +96,7 @@ def __getitem__(self, key):
 
             key = invert_chunk_coords(key)
 
-        return super(N5Store, self).__getitem__(key)
+        return super().__getitem__(key)
 
     def __setitem__(self, key, value):
 
@@ -144,7 +143,7 @@ def __setitem__(self, key, value):
 
             key = invert_chunk_coords(key)
 
-        super(N5Store, self).__setitem__(key, value)
+        super().__setitem__(key, value)
 
     def __delitem__(self, key):
 
@@ -157,7 +156,7 @@ def __delitem__(self, key):
         elif is_chunk_key(key):
             key = invert_chunk_coords(key)
 
-        super(N5Store, self).__delitem__(key)
+        super().__delitem__(key)
 
     def __contains__(self, key):
 
@@ -184,7 +183,7 @@ def __contains__(self, key):
 
             key = invert_chunk_coords(key)
 
-        return super(N5Store, self).__contains__(key)
+        return super().__contains__(key)
 
     def __eq__(self, other):
         return (
@@ -200,7 +199,7 @@ def listdir(self, path=None):
         # We can't use NestedDirectoryStore's listdir, as it requires
         # array_meta_key to be present in array directories, which this store
         # doesn't provide.
-        children = super(NestedDirectoryStore, self).listdir(path=path)
+        children = super().listdir(path=path)
 
         if self._is_array(path):
 
@@ -244,7 +243,7 @@ def listdir(self, path=None):
 
     def _load_n5_attrs(self, path):
         try:
-            s = super(N5Store, self).__getitem__(path)
+            s = super().__getitem__(path)
             return json_loads(s)
         except KeyError:
             return {}

zarr/storage.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """This module contains storage classes for use with Zarr arrays and groups.
 
 Note that any object implementing the :class:`MutableMapping` interface from the
@@ -29,7 +28,7 @@
 import zipfile
 from collections import OrderedDict
 from collections.abc import MutableMapping
-from os import scandir, replace
+from os import scandir
 from pickle import PicklingError
 from threading import Lock, RLock
 from typing import Optional, Union, List, Tuple, Dict
@@ -710,7 +709,7 @@ def __init__(self, *args, **kwargs):
                       "will be removed in the future. Please use MemoryStore.",
                       DeprecationWarning,
                       stacklevel=2)
-        super(DictStore, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
 
 
 class DirectoryStore(MutableMapping):
@@ -858,7 +857,7 @@ def __setitem__(self, key, value):
             self._tofile(value, temp_path)
 
             # move temporary file into place
-            replace(temp_path, file_path)
+            os.replace(temp_path, file_path)
 
         finally:
             # clean up if temp file still exists for whatever reason
@@ -1139,7 +1138,7 @@ class TempStore(DirectoryStore):
     def __init__(self, suffix='', prefix='zarr', dir=None, normalize_keys=False):
         path = tempfile.mkdtemp(suffix=suffix, prefix=prefix, dir=dir)
         atexit.register(atexit_rmtree, path)
-        super(TempStore, self).__init__(path, normalize_keys=normalize_keys)
+        super().__init__(path, normalize_keys=normalize_keys)
 
 
 _prog_ckey = re.compile(r'^(\d+)(\.\d+)+$')
@@ -1228,23 +1227,23 @@ class NestedDirectoryStore(DirectoryStore):
     """
 
     def __init__(self, path, normalize_keys=False):
-        super(NestedDirectoryStore, self).__init__(path, normalize_keys=normalize_keys)
+        super().__init__(path, normalize_keys=normalize_keys)
 
     def __getitem__(self, key):
         key = _nested_map_ckey(key)
-        return super(NestedDirectoryStore, self).__getitem__(key)
+        return super().__getitem__(key)
 
     def __setitem__(self, key, value):
         key = _nested_map_ckey(key)
-        super(NestedDirectoryStore, self).__setitem__(key, value)
+        super().__setitem__(key, value)
 
     def __delitem__(self, key):
         key = _nested_map_ckey(key)
-        super(NestedDirectoryStore, self).__delitem__(key)
+        super().__delitem__(key)
 
     def __contains__(self, key):
         key = _nested_map_ckey(key)
-        return super(NestedDirectoryStore, self).__contains__(key)
+        return super().__contains__(key)
 
     def __eq__(self, other):
         return (
@@ -1253,7 +1252,7 @@ def __eq__(self, other):
         )
 
     def listdir(self, path=None):
-        children = super(NestedDirectoryStore, self).listdir(path=path)
+        children = super().listdir(path=path)
         if array_meta_key in children:
             # special handling of directories containing an array to map nested chunk
             # keys back to standard chunk keys

zarr/sync.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import os
 from collections import defaultdict
 from threading import Lock

zarr/tests/__init__.py

@@ -1 +0,0 @@
-# -*- coding: utf-8 -*-

zarr/tests/test_attrs.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import json
 import unittest
 

zarr/tests/test_convenience.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import atexit
 import os
 import tempfile
@@ -426,7 +425,7 @@ def check_copied_group(original, copied, without_attrs=False, expect_props=None,
 class TestCopy(unittest.TestCase):
 
     def __init__(self, *args, **kwargs):
-        super(TestCopy, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self.source_h5py = False
         self.dest_h5py = False
         self.new_source = group
@@ -715,7 +714,7 @@ def temp_h5f():
 class TestCopyHDF5ToZarr(TestCopy):
 
     def __init__(self, *args, **kwargs):
-        super(TestCopyHDF5ToZarr, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self.source_h5py = True
         self.dest_h5py = False
         self.new_source = temp_h5f
@@ -725,7 +724,7 @@ def __init__(self, *args, **kwargs):
 class TestCopyZarrToHDF5(TestCopy):
 
     def __init__(self, *args, **kwargs):
-        super(TestCopyZarrToHDF5, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self.source_h5py = False
         self.dest_h5py = True
         self.new_source = group
@@ -735,7 +734,7 @@ def __init__(self, *args, **kwargs):
 class TestCopyHDF5ToHDF5(TestCopy):
 
     def __init__(self, *args, **kwargs):
-        super(TestCopyHDF5ToHDF5, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self.source_h5py = True
         self.dest_h5py = True
         self.new_source = temp_h5f

zarr/tests/test_core.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import atexit
 import os
 import pickle
@@ -1185,12 +1184,12 @@ def test_object_arrays_vlen_text(self):
         data = np.array(greetings * 1000, dtype=object)
 
         z = self.create_array(shape=data.shape, dtype=object, object_codec=VLenUTF8())
-        z[0] = u'foo'
-        assert z[0] == u'foo'
-        z[1] = u'bar'
-        assert z[1] == u'bar'
-        z[2] = u'baz'
-        assert z[2] == u'baz'
+        z[0] = 'foo'
+        assert z[0] == 'foo'
+        z[1] = 'bar'
+        assert z[1] == 'bar'
+        z[2] = 'baz'
+        assert z[2] == 'baz'
         z[:] = data
         a = z[:]
         assert a.dtype == object
@@ -1815,7 +1814,7 @@ def test_attrs_n5_keywords(self):
         z = self.create_array(shape=(1050,), chunks=100, dtype='i4')
         for k in n5_keywords:
             with pytest.raises(ValueError):
-                z.attrs[k] = u""
+                z.attrs[k] = ""
 
     def test_compressors(self):
         compressors = [

zarr/tests/test_creation.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import atexit
 import os.path
 import shutil
@@ -148,7 +147,7 @@ def test_full():
     assert np.all(a == v)
 
     # unicode string dtype
-    v = u'xxx'
+    v = 'xxx'
     z = full(100, chunks=10, fill_value=v, dtype='U3')
     assert v == z[0]
     a = z[...]

zarr/tests/test_filters.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import numpy as np
 from numcodecs import (BZ2, AsType, Blosc, Categorize, Delta, FixedScaleOffset,
                        PackBits, Quantize, Zlib)
@@ -164,8 +163,8 @@ def test_array_with_packbits_filter():
 def test_array_with_categorize_filter():
 
     # setup
-    data = np.random.choice([u'foo', u'bar', u'baz'], size=100)
-    flt = Categorize(dtype=data.dtype, labels=[u'foo', u'bar', u'baz'])
+    data = np.random.choice(['foo', 'bar', 'baz'], size=100)
+    flt = Categorize(dtype=data.dtype, labels=['foo', 'bar', 'baz'])
     filters = [flt]
 
     for compressor in compressors:

zarr/tests/test_hierarchy.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import atexit
 import os
 import pickle
@@ -1278,14 +1277,14 @@ def test_tree():
     g5.create_dataset('baz', shape=100, chunks=10)
 
     # test root group
-    expect_bytes = textwrap.dedent(u"""\
+    expect_bytes = textwrap.dedent("""\
     /
      +-- bar
      |   +-- baz
      |   +-- quux
      |       +-- baz (100,) float64
      +-- foo""").encode()
-    expect_text = textwrap.dedent(u"""\
+    expect_text = textwrap.dedent("""\
     /
      ├── bar
      │   ├── baz
@@ -1295,19 +1294,19 @@ def test_tree():
     _check_tree(g1, expect_bytes, expect_text)
 
     # test different group
-    expect_bytes = textwrap.dedent(u"""\
+    expect_bytes = textwrap.dedent("""\
     foo""").encode()
-    expect_text = textwrap.dedent(u"""\
+    expect_text = textwrap.dedent("""\
     foo""")
     _check_tree(g2, expect_bytes, expect_text)
 
     # test different group
-    expect_bytes = textwrap.dedent(u"""\
+    expect_bytes = textwrap.dedent("""\
     bar
      +-- baz
      +-- quux
          +-- baz (100,) float64""").encode()
-    expect_text = textwrap.dedent(u"""\
+    expect_text = textwrap.dedent("""\
     bar
      ├── baz
      └── quux

zarr/tests/test_indexing.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import numpy as np
 import pytest
 from numpy.testing import assert_array_equal

zarr/tests/test_info.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import numcodecs
 
 import zarr