RFC: Optionally support memory-mapping DirectoryStore values#377

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jakirkham wants to merge 9 commits into from
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RFC: Optionally support memory-mapping DirectoryStore values #377

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a860a32
Compare test data's content generally
jakirkham May 6, 2019
8f7d342
Optionally memory-mapping data in `DirectoryStore`
jakirkham May 6, 2019
9099032
Add `memmap` flag to `DirectoryStore` subclasses
jakirkham May 6, 2019
960453f
Test memory-mapping support in `DirectoryStore`
jakirkham May 6, 2019
d177b41
Implement `pop` and `popitem` for `DirectoryStore`
jakirkham May 6, 2019
9e4e679
Coerce NumPy `memmap` object to a `memoryview`
jakirkham May 6, 2019
ad88587
Simplify `DirectoryStore`'s `pop` method
jakirkham May 6, 2019
60470bd
Use `pop` in `popitem` implementation
jakirkham May 6, 2019
08f98dd
Override `pop` in `NestedDirectoryStore`
jakirkham May 6, 2019
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46 changes: 39 additions & 7 deletions zarr/storage.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@
import glob
import warnings

import numpy as np

from zarr.util import (json_loads, normalize_shape, normalize_chunks, normalize_order,
normalize_storage_path, buffer_size,
Expand DownExpand Up@@ -709,20 +710,24 @@ class DirectoryStore(MutableMapping):

"""

def __init__(self, path):
def __init__(self, path, memmap=False):

# guard conditions
path = os.path.abspath(path)
if os.path.exists(path) and not os.path.isdir(path):
err_fspath_exists_notdir(path)

self.path = path
self.memmap = memmap

def __getitem__(self, key):
filepath = os.path.join(self.path, key)
if os.path.isfile(filepath):
with open(filepath, 'rb') as f:
return f.read()
if self.memmap:
return memoryview(np.memmap(filepath, mode='r'))
else:
with open(filepath, 'rb') as f:
return f.read()
else:
raise KeyError(key)

Expand DownExpand Up@@ -805,6 +810,29 @@ def __iter__(self):
def __len__(self):
return sum(1 for _ in self.keys())

__marker = object()

def pop(self, key, default=__marker):
filepath = os.path.join(self.path, key)
if os.path.isfile(filepath):
with open(filepath, 'rb') as f:
value = f.read()
os.remove(filepath)
return value
elif default is self.__marker:
raise KeyError(key)
else:
return default

def popitem(self):
try:
key = next(self.keys())
except StopIteration:
raise KeyError("Store empty")
else:
value = self.pop(key)
return (key, value)

def dir_path(self, path=None):
store_path = normalize_storage_path(path)
dir_path = self.path
Expand DownExpand Up@@ -896,10 +924,10 @@ class TempStore(DirectoryStore):
"""

# noinspection PyShadowingBuiltins
def __init__(self, suffix='', prefix='zarr', dir=None):
def __init__(self, suffix='', prefix='zarr', dir=None, memmap=False):
path = tempfile.mkdtemp(suffix=suffix, prefix=prefix, dir=dir)
atexit.register(atexit_rmtree, path)
super(TempStore, self).__init__(path)
super(TempStore, self).__init__(path, memmap=memmap)


_prog_ckey = re.compile(r'^(\d+)(\.\d+)+$')
Expand DownExpand Up@@ -982,8 +1010,8 @@ class NestedDirectoryStore(DirectoryStore):

"""

def __init__(self, path):
super(NestedDirectoryStore, self).__init__(path)
def __init__(self, path, memmap=False):
super(NestedDirectoryStore, self).__init__(path, memmap=memmap)

def __getitem__(self, key):
key = _nested_map_ckey(key)
Expand All@@ -1007,6 +1035,10 @@ def __eq__(self, other):
self.path == other.path
)

def pop(self, key, *args, **kwargs):
key = _nested_map_ckey(key)
return super(NestedDirectoryStore, self).pop(key, *args, **kwargs)

def listdir(self, path=None):
children = super(NestedDirectoryStore, self).listdir(path=path)
if array_meta_key in children:
Expand Down
36 changes: 23 additions & 13 deletions zarr/tests/test_storage.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -21,6 +21,7 @@
except ImportError: # pragma: no cover
asb = None

from numcodecs.compat import ensure_bytes

from zarr.storage import (init_array, array_meta_key, attrs_key, DictStore,
DirectoryStore, ZipStore, init_group, group_meta_key,
Expand DownExpand Up@@ -65,7 +66,7 @@ def test_get_set_del_contains(self):
store['foo']
store['foo'] = b'bar'
assert 'foo' in store
assert b'bar' == store['foo']
assert b'bar' == ensure_bytes(store['foo'])

# test __delitem__ (optional)
try:
Expand DownExpand Up@@ -103,10 +104,10 @@ def test_pop(self):
store['baz'] = b'qux'
assert len(store) == 2
v = store.pop('foo')
assert v == b'bar'
assert ensure_bytes(v) == b'bar'
assert len(store) == 1
v = store.pop('baz')
assert v == b'qux'
assert ensure_bytes(v) == b'qux'
assert len(store) == 0
with pytest.raises(KeyError):
store.pop('xxx')
Expand All@@ -122,7 +123,7 @@ def test_popitem(self):
store['foo'] = b'bar'
k, v = store.popitem()
assert k == 'foo'
assert v == b'bar'
assert ensure_bytes(v) == b'bar'
assert len(store) == 0
with pytest.raises(KeyError):
store.popitem()
Expand All@@ -141,8 +142,8 @@ def test_update(self):
assert 'foo' not in store
assert 'baz' not in store
store.update(foo=b'bar', baz=b'quux')
assert b'bar' == store['foo']
assert b'quux' == store['baz']
assert b'bar' == ensure_bytes(store['foo'])
assert b'quux' == ensure_bytes(store['baz'])

def test_iterators(self):
store = self.create_store()
Expand All@@ -164,9 +165,9 @@ def test_iterators(self):
assert 4 == len(store)
assert {'a', 'b', 'c/d', 'c/e/f'} == set(store)
assert {'a', 'b', 'c/d', 'c/e/f'} == set(store.keys())
assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(store.values())
assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(map(ensure_bytes, store.values()))
assert ({('a', b'aaa'), ('b', b'bbb'), ('c/d', b'ddd'), ('c/e/f', b'fff')} ==
set(store.items()))
set(map(lambda kv: (kv[0], ensure_bytes(kv[1])), store.items())))

def test_pickle(self):

Expand All@@ -190,8 +191,8 @@ def test_pickle(self):
# verify
assert n == len(store2)
assert keys == sorted(store2.keys())
assert b'bar' == store2['foo']
assert b'quux' == store2['baz']
assert b'bar' == ensure_bytes(store2['foo'])
assert b'quux' == ensure_bytes(store2['baz'])

def test_getsize(self):
store = self.create_store()
Expand DownExpand Up@@ -671,10 +672,10 @@ def setdel_hierarchy_checks(store):
# test __setitem__ overwrite level
store['x/y/z'] = b'xxx'
store['x/y'] = b'yyy'
assert b'yyy' == store['x/y']
assert b'yyy' == ensure_bytes(store['x/y'])
assert 'x/y/z' not in store
store['x'] = b'zzz'
assert b'zzz' == store['x']
assert b'zzz' == ensure_bytes(store['x'])
assert 'x/y' not in store

# test __delitem__ overwrite level
Expand DownExpand Up@@ -736,13 +737,22 @@ def test_pickle_ext(self):
# check point to same underlying directory
assert 'xxx' not in store
store2['xxx'] = b'yyy'
assert b'yyy' == store['xxx']
assert b'yyy' == ensure_bytes(store['xxx'])

def test_setdel(self):
store = self.create_store()
setdel_hierarchy_checks(store)


class TestDirectoryStoreMemmap(TestDirectoryStore, unittest.TestCase):

def create_store(self):
path = tempfile.mkdtemp()
atexit.register(atexit_rmtree, path)
store = DirectoryStore(path, memmap=True)
return store


class TestNestedDirectoryStore(TestDirectoryStore, unittest.TestCase):

def create_store(self):
Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
RFC: Optionally support memory-mapping DirectoryStore values#377

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 Closed

jakirkham
wants to merge
9
commits into

from

 Closed


RFC: Optionally support memory-mapping DirectoryStore values
#377
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a860a32

Compare test data's content generally


jakirkham May 6, 2019
8f7d342

Optionally memory-mapping data in `DirectoryStore`


jakirkham May 6, 2019
9099032

Add `memmap` flag to `DirectoryStore` subclasses


jakirkham May 6, 2019
960453f

Test memory-mapping support in `DirectoryStore`


jakirkham May 6, 2019
d177b41

Implement `pop` and `popitem` for `DirectoryStore`


jakirkham May 6, 2019
9e4e679

Coerce NumPy `memmap` object to a `memoryview`


jakirkham May 6, 2019
ad88587

Simplify `DirectoryStore`'s `pop` method


jakirkham May 6, 2019
60470bd

Use `pop` in `popitem` implementation


jakirkham May 6, 2019
08f98dd

Override `pop` in `NestedDirectoryStore`


jakirkham May 6, 2019

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46 changes: 39 additions & 7 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@
import glob
import warnings

import numpy as np

from zarr.util import (json_loads, normalize_shape, normalize_chunks, normalize_order,
 normalize_storage_path, buffer_size,
Expand DownExpand Up@@ -709,20 +710,24 @@ class DirectoryStore(MutableMapping):

 """

 def __init__(self, path):
 def __init__(self, path, memmap=False):

 # guard conditions
 path = os.path.abspath(path)
 if os.path.exists(path) and not os.path.isdir(path):
 err_fspath_exists_notdir(path)

 self.path = path
 self.memmap = memmap

 def __getitem__(self, key):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 return f.read()
 if self.memmap:
 return memoryview(np.memmap(filepath, mode='r'))
 else:
 with open(filepath, 'rb') as f:
 return f.read()
 else:
 raise KeyError(key)

Expand DownExpand Up@@ -805,6 +810,29 @@ def __iter__(self):
 def __len__(self):
 return sum(1 for _ in self.keys())

 __marker = object()

 def pop(self, key, default=__marker):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 value = f.read()
 os.remove(filepath)
 return value
 elif default is self.__marker:
 raise KeyError(key)
 else:
 return default

 def popitem(self):
 try:
 key = next(self.keys())
 except StopIteration:
 raise KeyError("Store empty")
 else:
 value = self.pop(key)
 return (key, value)

 def dir_path(self, path=None):
 store_path = normalize_storage_path(path)
 dir_path = self.path
Expand DownExpand Up@@ -896,10 +924,10 @@ class TempStore(DirectoryStore):
 """

 # noinspection PyShadowingBuiltins
 def __init__(self, suffix='', prefix='zarr', dir=None):
 def __init__(self, suffix='', prefix='zarr', dir=None, memmap=False):
 path = tempfile.mkdtemp(suffix=suffix, prefix=prefix, dir=dir)
 atexit.register(atexit_rmtree, path)
 super(TempStore, self).__init__(path)
 super(TempStore, self).__init__(path, memmap=memmap)


_prog_ckey = re.compile(r'^(\d+)(\.\d+)+$')
Expand DownExpand Up@@ -982,8 +1010,8 @@ class NestedDirectoryStore(DirectoryStore):

 """

 def __init__(self, path):
 super(NestedDirectoryStore, self).__init__(path)
 def __init__(self, path, memmap=False):
 super(NestedDirectoryStore, self).__init__(path, memmap=memmap)

 def __getitem__(self, key):
 key = _nested_map_ckey(key)
Expand All@@ -1007,6 +1035,10 @@ def __eq__(self, other):
 self.path == other.path
 )

 def pop(self, key, *args, **kwargs):
 key = _nested_map_ckey(key)
 return super(NestedDirectoryStore, self).pop(key, *args, **kwargs)

 def listdir(self, path=None):
 children = super(NestedDirectoryStore, self).listdir(path=path)
 if array_meta_key in children:
Expand Down

36 changes: 23 additions & 13 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,6 +21,7 @@
except ImportError: # pragma: no cover
 asb = None

from numcodecs.compat import ensure_bytes

from zarr.storage import (init_array, array_meta_key, attrs_key, DictStore,
 DirectoryStore, ZipStore, init_group, group_meta_key,
Expand DownExpand Up@@ -65,7 +66,7 @@ def test_get_set_del_contains(self):
 store['foo']
 store['foo'] = b'bar'
 assert 'foo' in store
 assert b'bar' == store['foo']
 assert b'bar' == ensure_bytes(store['foo'])

 # test __delitem__ (optional)
 try:
Expand DownExpand Up@@ -103,10 +104,10 @@ def test_pop(self):
 store['baz'] = b'qux'
 assert len(store) == 2
 v = store.pop('foo')
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 1
 v = store.pop('baz')
 assert v == b'qux'
 assert ensure_bytes(v) == b'qux'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.pop('xxx')
Expand All@@ -122,7 +123,7 @@ def test_popitem(self):
 store['foo'] = b'bar'
 k, v = store.popitem()
 assert k == 'foo'
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.popitem()
Expand All@@ -141,8 +142,8 @@ def test_update(self):
 assert 'foo' not in store
 assert 'baz' not in store
 store.update(foo=b'bar', baz=b'quux')
 assert b'bar' == store['foo']
 assert b'quux' == store['baz']
 assert b'bar' == ensure_bytes(store['foo'])
 assert b'quux' == ensure_bytes(store['baz'])

 def test_iterators(self):
 store = self.create_store()
Expand All@@ -164,9 +165,9 @@ def test_iterators(self):
 assert 4 == len(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store.keys())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(store.values())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(map(ensure_bytes, store.values()))
 assert ({('a', b'aaa'), ('b', b'bbb'), ('c/d', b'ddd'), ('c/e/f', b'fff')} ==
 set(store.items()))
 set(map(lambda kv: (kv[0], ensure_bytes(kv[1])), store.items())))

 def test_pickle(self):

Expand All@@ -190,8 +191,8 @@ def test_pickle(self):
 # verify
 assert n == len(store2)
 assert keys == sorted(store2.keys())
 assert b'bar' == store2['foo']
 assert b'quux' == store2['baz']
 assert b'bar' == ensure_bytes(store2['foo'])
 assert b'quux' == ensure_bytes(store2['baz'])

 def test_getsize(self):
 store = self.create_store()
Expand DownExpand Up@@ -671,10 +672,10 @@ def setdel_hierarchy_checks(store):
 # test __setitem__ overwrite level
 store['x/y/z'] = b'xxx'
 store['x/y'] = b'yyy'
 assert b'yyy' == store['x/y']
 assert b'yyy' == ensure_bytes(store['x/y'])
 assert 'x/y/z' not in store
 store['x'] = b'zzz'
 assert b'zzz' == store['x']
 assert b'zzz' == ensure_bytes(store['x'])
 assert 'x/y' not in store

 # test __delitem__ overwrite level
Expand DownExpand Up@@ -736,13 +737,22 @@ def test_pickle_ext(self):
 # check point to same underlying directory
 assert 'xxx' not in store
 store2['xxx'] = b'yyy'
 assert b'yyy' == store['xxx']
 assert b'yyy' == ensure_bytes(store['xxx'])

 def test_setdel(self):
 store = self.create_store()
 setdel_hierarchy_checks(store)


class TestDirectoryStoreMemmap(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = DirectoryStore(path, memmap=True)
 return store


class TestNestedDirectoryStore(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
RFC: Optionally support memory-mapping DirectoryStore values#377

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Closed

jakirkham
wants to merge
9
commits into

from

 Closed


RFC: Optionally support memory-mapping DirectoryStore values
#377
Show file tree
Hide file tree
 Changes from all commits
Commits

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9 commits


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Hold shift + click to select a range
a860a32

Compare test data's content generally


jakirkham May 6, 2019
8f7d342

Optionally memory-mapping data in `DirectoryStore`


jakirkham May 6, 2019
9099032

Add `memmap` flag to `DirectoryStore` subclasses


jakirkham May 6, 2019
960453f

Test memory-mapping support in `DirectoryStore`


jakirkham May 6, 2019
d177b41

Implement `pop` and `popitem` for `DirectoryStore`


jakirkham May 6, 2019
9e4e679

Coerce NumPy `memmap` object to a `memoryview`


jakirkham May 6, 2019
ad88587

Simplify `DirectoryStore`'s `pop` method


jakirkham May 6, 2019
60470bd

Use `pop` in `popitem` implementation


jakirkham May 6, 2019
08f98dd

Override `pop` in `NestedDirectoryStore`


jakirkham May 6, 2019

File filter

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46 changes: 39 additions & 7 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@
import glob
import warnings

import numpy as np

from zarr.util import (json_loads, normalize_shape, normalize_chunks, normalize_order,
 normalize_storage_path, buffer_size,
Expand DownExpand Up@@ -709,20 +710,24 @@ class DirectoryStore(MutableMapping):

 """

 def __init__(self, path):
 def __init__(self, path, memmap=False):

 # guard conditions
 path = os.path.abspath(path)
 if os.path.exists(path) and not os.path.isdir(path):
 err_fspath_exists_notdir(path)

 self.path = path
 self.memmap = memmap

 def __getitem__(self, key):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 return f.read()
 if self.memmap:
 return memoryview(np.memmap(filepath, mode='r'))
 else:
 with open(filepath, 'rb') as f:
 return f.read()
 else:
 raise KeyError(key)

Expand DownExpand Up@@ -805,6 +810,29 @@ def __iter__(self):
 def __len__(self):
 return sum(1 for _ in self.keys())

 __marker = object()

 def pop(self, key, default=__marker):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 value = f.read()
 os.remove(filepath)
 return value
 elif default is self.__marker:
 raise KeyError(key)
 else:
 return default

 def popitem(self):
 try:
 key = next(self.keys())
 except StopIteration:
 raise KeyError("Store empty")
 else:
 value = self.pop(key)
 return (key, value)

 def dir_path(self, path=None):
 store_path = normalize_storage_path(path)
 dir_path = self.path
Expand DownExpand Up@@ -896,10 +924,10 @@ class TempStore(DirectoryStore):
 """

 # noinspection PyShadowingBuiltins
 def __init__(self, suffix='', prefix='zarr', dir=None):
 def __init__(self, suffix='', prefix='zarr', dir=None, memmap=False):
 path = tempfile.mkdtemp(suffix=suffix, prefix=prefix, dir=dir)
 atexit.register(atexit_rmtree, path)
 super(TempStore, self).__init__(path)
 super(TempStore, self).__init__(path, memmap=memmap)


_prog_ckey = re.compile(r'^(\d+)(\.\d+)+$')
Expand DownExpand Up@@ -982,8 +1010,8 @@ class NestedDirectoryStore(DirectoryStore):

 """

 def __init__(self, path):
 super(NestedDirectoryStore, self).__init__(path)
 def __init__(self, path, memmap=False):
 super(NestedDirectoryStore, self).__init__(path, memmap=memmap)

 def __getitem__(self, key):
 key = _nested_map_ckey(key)
Expand All@@ -1007,6 +1035,10 @@ def __eq__(self, other):
 self.path == other.path
 )

 def pop(self, key, *args, **kwargs):
 key = _nested_map_ckey(key)
 return super(NestedDirectoryStore, self).pop(key, *args, **kwargs)

 def listdir(self, path=None):
 children = super(NestedDirectoryStore, self).listdir(path=path)
 if array_meta_key in children:
Expand Down

36 changes: 23 additions & 13 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,6 +21,7 @@
except ImportError: # pragma: no cover
 asb = None

from numcodecs.compat import ensure_bytes

from zarr.storage import (init_array, array_meta_key, attrs_key, DictStore,
 DirectoryStore, ZipStore, init_group, group_meta_key,
Expand DownExpand Up@@ -65,7 +66,7 @@ def test_get_set_del_contains(self):
 store['foo']
 store['foo'] = b'bar'
 assert 'foo' in store
 assert b'bar' == store['foo']
 assert b'bar' == ensure_bytes(store['foo'])

 # test __delitem__ (optional)
 try:
Expand DownExpand Up@@ -103,10 +104,10 @@ def test_pop(self):
 store['baz'] = b'qux'
 assert len(store) == 2
 v = store.pop('foo')
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 1
 v = store.pop('baz')
 assert v == b'qux'
 assert ensure_bytes(v) == b'qux'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.pop('xxx')
Expand All@@ -122,7 +123,7 @@ def test_popitem(self):
 store['foo'] = b'bar'
 k, v = store.popitem()
 assert k == 'foo'
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.popitem()
Expand All@@ -141,8 +142,8 @@ def test_update(self):
 assert 'foo' not in store
 assert 'baz' not in store
 store.update(foo=b'bar', baz=b'quux')
 assert b'bar' == store['foo']
 assert b'quux' == store['baz']
 assert b'bar' == ensure_bytes(store['foo'])
 assert b'quux' == ensure_bytes(store['baz'])

 def test_iterators(self):
 store = self.create_store()
Expand All@@ -164,9 +165,9 @@ def test_iterators(self):
 assert 4 == len(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store.keys())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(store.values())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(map(ensure_bytes, store.values()))
 assert ({('a', b'aaa'), ('b', b'bbb'), ('c/d', b'ddd'), ('c/e/f', b'fff')} ==
 set(store.items()))
 set(map(lambda kv: (kv[0], ensure_bytes(kv[1])), store.items())))

 def test_pickle(self):

Expand All@@ -190,8 +191,8 @@ def test_pickle(self):
 # verify
 assert n == len(store2)
 assert keys == sorted(store2.keys())
 assert b'bar' == store2['foo']
 assert b'quux' == store2['baz']
 assert b'bar' == ensure_bytes(store2['foo'])
 assert b'quux' == ensure_bytes(store2['baz'])

 def test_getsize(self):
 store = self.create_store()
Expand DownExpand Up@@ -671,10 +672,10 @@ def setdel_hierarchy_checks(store):
 # test __setitem__ overwrite level
 store['x/y/z'] = b'xxx'
 store['x/y'] = b'yyy'
 assert b'yyy' == store['x/y']
 assert b'yyy' == ensure_bytes(store['x/y'])
 assert 'x/y/z' not in store
 store['x'] = b'zzz'
 assert b'zzz' == store['x']
 assert b'zzz' == ensure_bytes(store['x'])
 assert 'x/y' not in store

 # test __delitem__ overwrite level
Expand DownExpand Up@@ -736,13 +737,22 @@ def test_pickle_ext(self):
 # check point to same underlying directory
 assert 'xxx' not in store
 store2['xxx'] = b'yyy'
 assert b'yyy' == store['xxx']
 assert b'yyy' == ensure_bytes(store['xxx'])

 def test_setdel(self):
 store = self.create_store()
 setdel_hierarchy_checks(store)


class TestDirectoryStoreMemmap(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = DirectoryStore(path, memmap=True)
 return store


class TestNestedDirectoryStore(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
RFC: Optionally support memory-mapping DirectoryStore values#377

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 Closed

jakirkham
wants to merge
9
commits into

from

 Closed


RFC: Optionally support memory-mapping DirectoryStore values
#377
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a860a32

Compare test data's content generally


jakirkham May 6, 2019
8f7d342

Optionally memory-mapping data in `DirectoryStore`


jakirkham May 6, 2019
9099032

Add `memmap` flag to `DirectoryStore` subclasses


jakirkham May 6, 2019
960453f

Test memory-mapping support in `DirectoryStore`


jakirkham May 6, 2019
d177b41

Implement `pop` and `popitem` for `DirectoryStore`


jakirkham May 6, 2019
9e4e679

Coerce NumPy `memmap` object to a `memoryview`


jakirkham May 6, 2019
ad88587

Simplify `DirectoryStore`'s `pop` method


jakirkham May 6, 2019
60470bd

Use `pop` in `popitem` implementation


jakirkham May 6, 2019
08f98dd

Override `pop` in `NestedDirectoryStore`


jakirkham May 6, 2019

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46 changes: 39 additions & 7 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@
import glob
import warnings

import numpy as np

from zarr.util import (json_loads, normalize_shape, normalize_chunks, normalize_order,
 normalize_storage_path, buffer_size,
Expand DownExpand Up@@ -709,20 +710,24 @@ class DirectoryStore(MutableMapping):

 """

 def __init__(self, path):
 def __init__(self, path, memmap=False):

 # guard conditions
 path = os.path.abspath(path)
 if os.path.exists(path) and not os.path.isdir(path):
 err_fspath_exists_notdir(path)

 self.path = path
 self.memmap = memmap

 def __getitem__(self, key):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 return f.read()
 if self.memmap:
 return memoryview(np.memmap(filepath, mode='r'))
 else:
 with open(filepath, 'rb') as f:
 return f.read()
 else:
 raise KeyError(key)

Expand DownExpand Up@@ -805,6 +810,29 @@ def __iter__(self):
 def __len__(self):
 return sum(1 for _ in self.keys())

 __marker = object()

 def pop(self, key, default=__marker):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 value = f.read()
 os.remove(filepath)
 return value
 elif default is self.__marker:
 raise KeyError(key)
 else:
 return default

 def popitem(self):
 try:
 key = next(self.keys())
 except StopIteration:
 raise KeyError("Store empty")
 else:
 value = self.pop(key)
 return (key, value)

 def dir_path(self, path=None):
 store_path = normalize_storage_path(path)
 dir_path = self.path
Expand DownExpand Up@@ -896,10 +924,10 @@ class TempStore(DirectoryStore):
 """

 # noinspection PyShadowingBuiltins
 def __init__(self, suffix='', prefix='zarr', dir=None):
 def __init__(self, suffix='', prefix='zarr', dir=None, memmap=False):
 path = tempfile.mkdtemp(suffix=suffix, prefix=prefix, dir=dir)
 atexit.register(atexit_rmtree, path)
 super(TempStore, self).__init__(path)
 super(TempStore, self).__init__(path, memmap=memmap)


_prog_ckey = re.compile(r'^(\d+)(\.\d+)+$')
Expand DownExpand Up@@ -982,8 +1010,8 @@ class NestedDirectoryStore(DirectoryStore):

 """

 def __init__(self, path):
 super(NestedDirectoryStore, self).__init__(path)
 def __init__(self, path, memmap=False):
 super(NestedDirectoryStore, self).__init__(path, memmap=memmap)

 def __getitem__(self, key):
 key = _nested_map_ckey(key)
Expand All@@ -1007,6 +1035,10 @@ def __eq__(self, other):
 self.path == other.path
 )

 def pop(self, key, *args, **kwargs):
 key = _nested_map_ckey(key)
 return super(NestedDirectoryStore, self).pop(key, *args, **kwargs)

 def listdir(self, path=None):
 children = super(NestedDirectoryStore, self).listdir(path=path)
 if array_meta_key in children:
Expand Down

36 changes: 23 additions & 13 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,6 +21,7 @@
except ImportError: # pragma: no cover
 asb = None

from numcodecs.compat import ensure_bytes

from zarr.storage import (init_array, array_meta_key, attrs_key, DictStore,
 DirectoryStore, ZipStore, init_group, group_meta_key,
Expand DownExpand Up@@ -65,7 +66,7 @@ def test_get_set_del_contains(self):
 store['foo']
 store['foo'] = b'bar'
 assert 'foo' in store
 assert b'bar' == store['foo']
 assert b'bar' == ensure_bytes(store['foo'])

 # test __delitem__ (optional)
 try:
Expand DownExpand Up@@ -103,10 +104,10 @@ def test_pop(self):
 store['baz'] = b'qux'
 assert len(store) == 2
 v = store.pop('foo')
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 1
 v = store.pop('baz')
 assert v == b'qux'
 assert ensure_bytes(v) == b'qux'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.pop('xxx')
Expand All@@ -122,7 +123,7 @@ def test_popitem(self):
 store['foo'] = b'bar'
 k, v = store.popitem()
 assert k == 'foo'
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.popitem()
Expand All@@ -141,8 +142,8 @@ def test_update(self):
 assert 'foo' not in store
 assert 'baz' not in store
 store.update(foo=b'bar', baz=b'quux')
 assert b'bar' == store['foo']
 assert b'quux' == store['baz']
 assert b'bar' == ensure_bytes(store['foo'])
 assert b'quux' == ensure_bytes(store['baz'])

 def test_iterators(self):
 store = self.create_store()
Expand All@@ -164,9 +165,9 @@ def test_iterators(self):
 assert 4 == len(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store.keys())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(store.values())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(map(ensure_bytes, store.values()))
 assert ({('a', b'aaa'), ('b', b'bbb'), ('c/d', b'ddd'), ('c/e/f', b'fff')} ==
 set(store.items()))
 set(map(lambda kv: (kv[0], ensure_bytes(kv[1])), store.items())))

 def test_pickle(self):

Expand All@@ -190,8 +191,8 @@ def test_pickle(self):
 # verify
 assert n == len(store2)
 assert keys == sorted(store2.keys())
 assert b'bar' == store2['foo']
 assert b'quux' == store2['baz']
 assert b'bar' == ensure_bytes(store2['foo'])
 assert b'quux' == ensure_bytes(store2['baz'])

 def test_getsize(self):
 store = self.create_store()
Expand DownExpand Up@@ -671,10 +672,10 @@ def setdel_hierarchy_checks(store):
 # test __setitem__ overwrite level
 store['x/y/z'] = b'xxx'
 store['x/y'] = b'yyy'
 assert b'yyy' == store['x/y']
 assert b'yyy' == ensure_bytes(store['x/y'])
 assert 'x/y/z' not in store
 store['x'] = b'zzz'
 assert b'zzz' == store['x']
 assert b'zzz' == ensure_bytes(store['x'])
 assert 'x/y' not in store

 # test __delitem__ overwrite level
Expand DownExpand Up@@ -736,13 +737,22 @@ def test_pickle_ext(self):
 # check point to same underlying directory
 assert 'xxx' not in store
 store2['xxx'] = b'yyy'
 assert b'yyy' == store['xxx']
 assert b'yyy' == ensure_bytes(store['xxx'])

 def test_setdel(self):
 store = self.create_store()
 setdel_hierarchy_checks(store)


class TestDirectoryStoreMemmap(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = DirectoryStore(path, memmap=True)
 return store


class TestNestedDirectoryStore(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
RFC: Optionally support memory-mapping DirectoryStore values#377

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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Sign in
to your account

 Closed

jakirkham
wants to merge
9
commits into

from

 Closed


RFC: Optionally support memory-mapping DirectoryStore values
#377
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a860a32

Compare test data's content generally


jakirkham May 6, 2019
8f7d342

Optionally memory-mapping data in `DirectoryStore`


jakirkham May 6, 2019
9099032

Add `memmap` flag to `DirectoryStore` subclasses


jakirkham May 6, 2019
960453f

Test memory-mapping support in `DirectoryStore`


jakirkham May 6, 2019
d177b41

Implement `pop` and `popitem` for `DirectoryStore`


jakirkham May 6, 2019
9e4e679

Coerce NumPy `memmap` object to a `memoryview`


jakirkham May 6, 2019
ad88587

Simplify `DirectoryStore`'s `pop` method


jakirkham May 6, 2019
60470bd

Use `pop` in `popitem` implementation


jakirkham May 6, 2019
08f98dd

Override `pop` in `NestedDirectoryStore`


jakirkham May 6, 2019

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46 changes: 39 additions & 7 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@
import glob
import warnings

import numpy as np

from zarr.util import (json_loads, normalize_shape, normalize_chunks, normalize_order,
 normalize_storage_path, buffer_size,
Expand DownExpand Up@@ -709,20 +710,24 @@ class DirectoryStore(MutableMapping):

 """

 def __init__(self, path):
 def __init__(self, path, memmap=False):

 # guard conditions
 path = os.path.abspath(path)
 if os.path.exists(path) and not os.path.isdir(path):
 err_fspath_exists_notdir(path)

 self.path = path
 self.memmap = memmap

 def __getitem__(self, key):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 return f.read()
 if self.memmap:
 return memoryview(np.memmap(filepath, mode='r'))
 else:
 with open(filepath, 'rb') as f:
 return f.read()
 else:
 raise KeyError(key)

Expand DownExpand Up@@ -805,6 +810,29 @@ def __iter__(self):
 def __len__(self):
 return sum(1 for _ in self.keys())

 __marker = object()

 def pop(self, key, default=__marker):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 value = f.read()
 os.remove(filepath)
 return value
 elif default is self.__marker:
 raise KeyError(key)
 else:
 return default

 def popitem(self):
 try:
 key = next(self.keys())
 except StopIteration:
 raise KeyError("Store empty")
 else:
 value = self.pop(key)
 return (key, value)

 def dir_path(self, path=None):
 store_path = normalize_storage_path(path)
 dir_path = self.path
Expand DownExpand Up@@ -896,10 +924,10 @@ class TempStore(DirectoryStore):
 """

 # noinspection PyShadowingBuiltins
 def __init__(self, suffix='', prefix='zarr', dir=None):
 def __init__(self, suffix='', prefix='zarr', dir=None, memmap=False):
 path = tempfile.mkdtemp(suffix=suffix, prefix=prefix, dir=dir)
 atexit.register(atexit_rmtree, path)
 super(TempStore, self).__init__(path)
 super(TempStore, self).__init__(path, memmap=memmap)


_prog_ckey = re.compile(r'^(\d+)(\.\d+)+$')
Expand DownExpand Up@@ -982,8 +1010,8 @@ class NestedDirectoryStore(DirectoryStore):

 """

 def __init__(self, path):
 super(NestedDirectoryStore, self).__init__(path)
 def __init__(self, path, memmap=False):
 super(NestedDirectoryStore, self).__init__(path, memmap=memmap)

 def __getitem__(self, key):
 key = _nested_map_ckey(key)
Expand All@@ -1007,6 +1035,10 @@ def __eq__(self, other):
 self.path == other.path
 )

 def pop(self, key, *args, **kwargs):
 key = _nested_map_ckey(key)
 return super(NestedDirectoryStore, self).pop(key, *args, **kwargs)

 def listdir(self, path=None):
 children = super(NestedDirectoryStore, self).listdir(path=path)
 if array_meta_key in children:
Expand Down

36 changes: 23 additions & 13 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,6 +21,7 @@
except ImportError: # pragma: no cover
 asb = None

from numcodecs.compat import ensure_bytes

from zarr.storage import (init_array, array_meta_key, attrs_key, DictStore,
 DirectoryStore, ZipStore, init_group, group_meta_key,
Expand DownExpand Up@@ -65,7 +66,7 @@ def test_get_set_del_contains(self):
 store['foo']
 store['foo'] = b'bar'
 assert 'foo' in store
 assert b'bar' == store['foo']
 assert b'bar' == ensure_bytes(store['foo'])

 # test __delitem__ (optional)
 try:
Expand DownExpand Up@@ -103,10 +104,10 @@ def test_pop(self):
 store['baz'] = b'qux'
 assert len(store) == 2
 v = store.pop('foo')
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 1
 v = store.pop('baz')
 assert v == b'qux'
 assert ensure_bytes(v) == b'qux'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.pop('xxx')
Expand All@@ -122,7 +123,7 @@ def test_popitem(self):
 store['foo'] = b'bar'
 k, v = store.popitem()
 assert k == 'foo'
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.popitem()
Expand All@@ -141,8 +142,8 @@ def test_update(self):
 assert 'foo' not in store
 assert 'baz' not in store
 store.update(foo=b'bar', baz=b'quux')
 assert b'bar' == store['foo']
 assert b'quux' == store['baz']
 assert b'bar' == ensure_bytes(store['foo'])
 assert b'quux' == ensure_bytes(store['baz'])

 def test_iterators(self):
 store = self.create_store()
Expand All@@ -164,9 +165,9 @@ def test_iterators(self):
 assert 4 == len(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store.keys())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(store.values())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(map(ensure_bytes, store.values()))
 assert ({('a', b'aaa'), ('b', b'bbb'), ('c/d', b'ddd'), ('c/e/f', b'fff')} ==
 set(store.items()))
 set(map(lambda kv: (kv[0], ensure_bytes(kv[1])), store.items())))

 def test_pickle(self):

Expand All@@ -190,8 +191,8 @@ def test_pickle(self):
 # verify
 assert n == len(store2)
 assert keys == sorted(store2.keys())
 assert b'bar' == store2['foo']
 assert b'quux' == store2['baz']
 assert b'bar' == ensure_bytes(store2['foo'])
 assert b'quux' == ensure_bytes(store2['baz'])

 def test_getsize(self):
 store = self.create_store()
Expand DownExpand Up@@ -671,10 +672,10 @@ def setdel_hierarchy_checks(store):
 # test __setitem__ overwrite level
 store['x/y/z'] = b'xxx'
 store['x/y'] = b'yyy'
 assert b'yyy' == store['x/y']
 assert b'yyy' == ensure_bytes(store['x/y'])
 assert 'x/y/z' not in store
 store['x'] = b'zzz'
 assert b'zzz' == store['x']
 assert b'zzz' == ensure_bytes(store['x'])
 assert 'x/y' not in store

 # test __delitem__ overwrite level
Expand DownExpand Up@@ -736,13 +737,22 @@ def test_pickle_ext(self):
 # check point to same underlying directory
 assert 'xxx' not in store
 store2['xxx'] = b'yyy'
 assert b'yyy' == store['xxx']
 assert b'yyy' == ensure_bytes(store['xxx'])

 def test_setdel(self):
 store = self.create_store()
 setdel_hierarchy_checks(store)


class TestDirectoryStoreMemmap(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = DirectoryStore(path, memmap=True)
 return store


class TestNestedDirectoryStore(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
RFC: Optionally support memory-mapping DirectoryStore values#377

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 Closed

jakirkham
wants to merge
9
commits into

from

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RFC: Optionally support memory-mapping DirectoryStore values
#377
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a860a32

Compare test data's content generally


jakirkham May 6, 2019
8f7d342

Optionally memory-mapping data in `DirectoryStore`


jakirkham May 6, 2019
9099032

Add `memmap` flag to `DirectoryStore` subclasses


jakirkham May 6, 2019
960453f

Test memory-mapping support in `DirectoryStore`


jakirkham May 6, 2019
d177b41

Implement `pop` and `popitem` for `DirectoryStore`


jakirkham May 6, 2019
9e4e679

Coerce NumPy `memmap` object to a `memoryview`


jakirkham May 6, 2019
ad88587

Simplify `DirectoryStore`'s `pop` method


jakirkham May 6, 2019
60470bd

Use `pop` in `popitem` implementation


jakirkham May 6, 2019
08f98dd

Override `pop` in `NestedDirectoryStore`


jakirkham May 6, 2019

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46 changes: 39 additions & 7 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@
import glob
import warnings

import numpy as np

from zarr.util import (json_loads, normalize_shape, normalize_chunks, normalize_order,
 normalize_storage_path, buffer_size,
Expand DownExpand Up@@ -709,20 +710,24 @@ class DirectoryStore(MutableMapping):

 """

 def __init__(self, path):
 def __init__(self, path, memmap=False):

 # guard conditions
 path = os.path.abspath(path)
 if os.path.exists(path) and not os.path.isdir(path):
 err_fspath_exists_notdir(path)

 self.path = path
 self.memmap = memmap

 def __getitem__(self, key):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 return f.read()
 if self.memmap:
 return memoryview(np.memmap(filepath, mode='r'))
 else:
 with open(filepath, 'rb') as f:
 return f.read()
 else:
 raise KeyError(key)

Expand DownExpand Up@@ -805,6 +810,29 @@ def __iter__(self):
 def __len__(self):
 return sum(1 for _ in self.keys())

 __marker = object()

 def pop(self, key, default=__marker):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 value = f.read()
 os.remove(filepath)
 return value
 elif default is self.__marker:
 raise KeyError(key)
 else:
 return default

 def popitem(self):
 try:
 key = next(self.keys())
 except StopIteration:
 raise KeyError("Store empty")
 else:
 value = self.pop(key)
 return (key, value)

 def dir_path(self, path=None):
 store_path = normalize_storage_path(path)
 dir_path = self.path
Expand DownExpand Up@@ -896,10 +924,10 @@ class TempStore(DirectoryStore):
 """

 # noinspection PyShadowingBuiltins
 def __init__(self, suffix='', prefix='zarr', dir=None):
 def __init__(self, suffix='', prefix='zarr', dir=None, memmap=False):
 path = tempfile.mkdtemp(suffix=suffix, prefix=prefix, dir=dir)
 atexit.register(atexit_rmtree, path)
 super(TempStore, self).__init__(path)
 super(TempStore, self).__init__(path, memmap=memmap)


_prog_ckey = re.compile(r'^(\d+)(\.\d+)+$')
Expand DownExpand Up@@ -982,8 +1010,8 @@ class NestedDirectoryStore(DirectoryStore):

 """

 def __init__(self, path):
 super(NestedDirectoryStore, self).__init__(path)
 def __init__(self, path, memmap=False):
 super(NestedDirectoryStore, self).__init__(path, memmap=memmap)

 def __getitem__(self, key):
 key = _nested_map_ckey(key)
Expand All@@ -1007,6 +1035,10 @@ def __eq__(self, other):
 self.path == other.path
 )

 def pop(self, key, *args, **kwargs):
 key = _nested_map_ckey(key)
 return super(NestedDirectoryStore, self).pop(key, *args, **kwargs)

 def listdir(self, path=None):
 children = super(NestedDirectoryStore, self).listdir(path=path)
 if array_meta_key in children:
Expand Down

36 changes: 23 additions & 13 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,6 +21,7 @@
except ImportError: # pragma: no cover
 asb = None

from numcodecs.compat import ensure_bytes

from zarr.storage import (init_array, array_meta_key, attrs_key, DictStore,
 DirectoryStore, ZipStore, init_group, group_meta_key,
Expand DownExpand Up@@ -65,7 +66,7 @@ def test_get_set_del_contains(self):
 store['foo']
 store['foo'] = b'bar'
 assert 'foo' in store
 assert b'bar' == store['foo']
 assert b'bar' == ensure_bytes(store['foo'])

 # test __delitem__ (optional)
 try:
Expand DownExpand Up@@ -103,10 +104,10 @@ def test_pop(self):
 store['baz'] = b'qux'
 assert len(store) == 2
 v = store.pop('foo')
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 1
 v = store.pop('baz')
 assert v == b'qux'
 assert ensure_bytes(v) == b'qux'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.pop('xxx')
Expand All@@ -122,7 +123,7 @@ def test_popitem(self):
 store['foo'] = b'bar'
 k, v = store.popitem()
 assert k == 'foo'
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.popitem()
Expand All@@ -141,8 +142,8 @@ def test_update(self):
 assert 'foo' not in store
 assert 'baz' not in store
 store.update(foo=b'bar', baz=b'quux')
 assert b'bar' == store['foo']
 assert b'quux' == store['baz']
 assert b'bar' == ensure_bytes(store['foo'])
 assert b'quux' == ensure_bytes(store['baz'])

 def test_iterators(self):
 store = self.create_store()
Expand All@@ -164,9 +165,9 @@ def test_iterators(self):
 assert 4 == len(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store.keys())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(store.values())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(map(ensure_bytes, store.values()))
 assert ({('a', b'aaa'), ('b', b'bbb'), ('c/d', b'ddd'), ('c/e/f', b'fff')} ==
 set(store.items()))
 set(map(lambda kv: (kv[0], ensure_bytes(kv[1])), store.items())))

 def test_pickle(self):

Expand All@@ -190,8 +191,8 @@ def test_pickle(self):
 # verify
 assert n == len(store2)
 assert keys == sorted(store2.keys())
 assert b'bar' == store2['foo']
 assert b'quux' == store2['baz']
 assert b'bar' == ensure_bytes(store2['foo'])
 assert b'quux' == ensure_bytes(store2['baz'])

 def test_getsize(self):
 store = self.create_store()
Expand DownExpand Up@@ -671,10 +672,10 @@ def setdel_hierarchy_checks(store):
 # test __setitem__ overwrite level
 store['x/y/z'] = b'xxx'
 store['x/y'] = b'yyy'
 assert b'yyy' == store['x/y']
 assert b'yyy' == ensure_bytes(store['x/y'])
 assert 'x/y/z' not in store
 store['x'] = b'zzz'
 assert b'zzz' == store['x']
 assert b'zzz' == ensure_bytes(store['x'])
 assert 'x/y' not in store

 # test __delitem__ overwrite level
Expand DownExpand Up@@ -736,13 +737,22 @@ def test_pickle_ext(self):
 # check point to same underlying directory
 assert 'xxx' not in store
 store2['xxx'] = b'yyy'
 assert b'yyy' == store['xxx']
 assert b'yyy' == ensure_bytes(store['xxx'])

 def test_setdel(self):
 store = self.create_store()
 setdel_hierarchy_checks(store)


class TestDirectoryStoreMemmap(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = DirectoryStore(path, memmap=True)
 return store


class TestNestedDirectoryStore(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
RFC: Optionally support memory-mapping DirectoryStore values#377

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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 Closed

jakirkham
wants to merge
9
commits into

from

 Closed


RFC: Optionally support memory-mapping DirectoryStore values
#377
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a860a32

Compare test data's content generally


jakirkham May 6, 2019
8f7d342

Optionally memory-mapping data in `DirectoryStore`


jakirkham May 6, 2019
9099032

Add `memmap` flag to `DirectoryStore` subclasses


jakirkham May 6, 2019
960453f

Test memory-mapping support in `DirectoryStore`


jakirkham May 6, 2019
d177b41

Implement `pop` and `popitem` for `DirectoryStore`


jakirkham May 6, 2019
9e4e679

Coerce NumPy `memmap` object to a `memoryview`


jakirkham May 6, 2019
ad88587

Simplify `DirectoryStore`'s `pop` method


jakirkham May 6, 2019
60470bd

Use `pop` in `popitem` implementation


jakirkham May 6, 2019
08f98dd

Override `pop` in `NestedDirectoryStore`


jakirkham May 6, 2019

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46 changes: 39 additions & 7 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@
import glob
import warnings

import numpy as np

from zarr.util import (json_loads, normalize_shape, normalize_chunks, normalize_order,
 normalize_storage_path, buffer_size,
Expand DownExpand Up@@ -709,20 +710,24 @@ class DirectoryStore(MutableMapping):

 """

 def __init__(self, path):
 def __init__(self, path, memmap=False):

 # guard conditions
 path = os.path.abspath(path)
 if os.path.exists(path) and not os.path.isdir(path):
 err_fspath_exists_notdir(path)

 self.path = path
 self.memmap = memmap

 def __getitem__(self, key):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 return f.read()
 if self.memmap:
 return memoryview(np.memmap(filepath, mode='r'))
 else:
 with open(filepath, 'rb') as f:
 return f.read()
 else:
 raise KeyError(key)

Expand DownExpand Up@@ -805,6 +810,29 @@ def __iter__(self):
 def __len__(self):
 return sum(1 for _ in self.keys())

 __marker = object()

 def pop(self, key, default=__marker):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 value = f.read()
 os.remove(filepath)
 return value
 elif default is self.__marker:
 raise KeyError(key)
 else:
 return default

 def popitem(self):
 try:
 key = next(self.keys())
 except StopIteration:
 raise KeyError("Store empty")
 else:
 value = self.pop(key)
 return (key, value)

 def dir_path(self, path=None):
 store_path = normalize_storage_path(path)
 dir_path = self.path
Expand DownExpand Up@@ -896,10 +924,10 @@ class TempStore(DirectoryStore):
 """

 # noinspection PyShadowingBuiltins
 def __init__(self, suffix='', prefix='zarr', dir=None):
 def __init__(self, suffix='', prefix='zarr', dir=None, memmap=False):
 path = tempfile.mkdtemp(suffix=suffix, prefix=prefix, dir=dir)
 atexit.register(atexit_rmtree, path)
 super(TempStore, self).__init__(path)
 super(TempStore, self).__init__(path, memmap=memmap)


_prog_ckey = re.compile(r'^(\d+)(\.\d+)+$')
Expand DownExpand Up@@ -982,8 +1010,8 @@ class NestedDirectoryStore(DirectoryStore):

 """

 def __init__(self, path):
 super(NestedDirectoryStore, self).__init__(path)
 def __init__(self, path, memmap=False):
 super(NestedDirectoryStore, self).__init__(path, memmap=memmap)

 def __getitem__(self, key):
 key = _nested_map_ckey(key)
Expand All@@ -1007,6 +1035,10 @@ def __eq__(self, other):
 self.path == other.path
 )

 def pop(self, key, *args, **kwargs):
 key = _nested_map_ckey(key)
 return super(NestedDirectoryStore, self).pop(key, *args, **kwargs)

 def listdir(self, path=None):
 children = super(NestedDirectoryStore, self).listdir(path=path)
 if array_meta_key in children:
Expand Down

36 changes: 23 additions & 13 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -21,6 +21,7 @@
except ImportError: # pragma: no cover
 asb = None

from numcodecs.compat import ensure_bytes

from zarr.storage import (init_array, array_meta_key, attrs_key, DictStore,
 DirectoryStore, ZipStore, init_group, group_meta_key,
Expand DownExpand Up@@ -65,7 +66,7 @@ def test_get_set_del_contains(self):
 store['foo']
 store['foo'] = b'bar'
 assert 'foo' in store
 assert b'bar' == store['foo']
 assert b'bar' == ensure_bytes(store['foo'])

 # test __delitem__ (optional)
 try:
Expand DownExpand Up@@ -103,10 +104,10 @@ def test_pop(self):
 store['baz'] = b'qux'
 assert len(store) == 2
 v = store.pop('foo')
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 1
 v = store.pop('baz')
 assert v == b'qux'
 assert ensure_bytes(v) == b'qux'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.pop('xxx')
Expand All@@ -122,7 +123,7 @@ def test_popitem(self):
 store['foo'] = b'bar'
 k, v = store.popitem()
 assert k == 'foo'
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.popitem()
Expand All@@ -141,8 +142,8 @@ def test_update(self):
 assert 'foo' not in store
 assert 'baz' not in store
 store.update(foo=b'bar', baz=b'quux')
 assert b'bar' == store['foo']
 assert b'quux' == store['baz']
 assert b'bar' == ensure_bytes(store['foo'])
 assert b'quux' == ensure_bytes(store['baz'])

 def test_iterators(self):
 store = self.create_store()
Expand All@@ -164,9 +165,9 @@ def test_iterators(self):
 assert 4 == len(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store.keys())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(store.values())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(map(ensure_bytes, store.values()))
 assert ({('a', b'aaa'), ('b', b'bbb'), ('c/d', b'ddd'), ('c/e/f', b'fff')} ==
 set(store.items()))
 set(map(lambda kv: (kv[0], ensure_bytes(kv[1])), store.items())))

 def test_pickle(self):

Expand All@@ -190,8 +191,8 @@ def test_pickle(self):
 # verify
 assert n == len(store2)
 assert keys == sorted(store2.keys())
 assert b'bar' == store2['foo']
 assert b'quux' == store2['baz']
 assert b'bar' == ensure_bytes(store2['foo'])
 assert b'quux' == ensure_bytes(store2['baz'])

 def test_getsize(self):
 store = self.create_store()
Expand DownExpand Up@@ -671,10 +672,10 @@ def setdel_hierarchy_checks(store):
 # test __setitem__ overwrite level
 store['x/y/z'] = b'xxx'
 store['x/y'] = b'yyy'
 assert b'yyy' == store['x/y']
 assert b'yyy' == ensure_bytes(store['x/y'])
 assert 'x/y/z' not in store
 store['x'] = b'zzz'
 assert b'zzz' == store['x']
 assert b'zzz' == ensure_bytes(store['x'])
 assert 'x/y' not in store

 # test __delitem__ overwrite level
Expand DownExpand Up@@ -736,13 +737,22 @@ def test_pickle_ext(self):
 # check point to same underlying directory
 assert 'xxx' not in store
 store2['xxx'] = b'yyy'
 assert b'yyy' == store['xxx']
 assert b'yyy' == ensure_bytes(store['xxx'])

 def test_setdel(self):
 store = self.create_store()
 setdel_hierarchy_checks(store)


class TestDirectoryStoreMemmap(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = DirectoryStore(path, memmap=True)
 return store


class TestNestedDirectoryStore(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
RFC: Optionally support memory-mapping DirectoryStore values#377

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Closed

jakirkham
wants to merge
9
commits into

from

 Closed


RFC: Optionally support memory-mapping DirectoryStore values
#377
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a860a32

Compare test data's content generally


jakirkham May 6, 2019
8f7d342

Optionally memory-mapping data in `DirectoryStore`


jakirkham May 6, 2019
9099032

Add `memmap` flag to `DirectoryStore` subclasses


jakirkham May 6, 2019
960453f

Test memory-mapping support in `DirectoryStore`


jakirkham May 6, 2019
d177b41

Implement `pop` and `popitem` for `DirectoryStore`


jakirkham May 6, 2019
9e4e679

Coerce NumPy `memmap` object to a `memoryview`


jakirkham May 6, 2019
ad88587

Simplify `DirectoryStore`'s `pop` method


jakirkham May 6, 2019
60470bd

Use `pop` in `popitem` implementation


jakirkham May 6, 2019
08f98dd

Override `pop` in `NestedDirectoryStore`


jakirkham May 6, 2019

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46 changes: 39 additions & 7 deletions
zarr/storage.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@
import glob
import warnings

import numpy as np

from zarr.util import (json_loads, normalize_shape, normalize_chunks, normalize_order,
 normalize_storage_path, buffer_size,
Expand DownExpand Up@@ -709,20 +710,24 @@ class DirectoryStore(MutableMapping):

 """

 def __init__(self, path):
 def __init__(self, path, memmap=False):

 # guard conditions
 path = os.path.abspath(path)
 if os.path.exists(path) and not os.path.isdir(path):
 err_fspath_exists_notdir(path)

 self.path = path
 self.memmap = memmap

 def __getitem__(self, key):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 return f.read()
 if self.memmap:
 return memoryview(np.memmap(filepath, mode='r'))
 else:
 with open(filepath, 'rb') as f:
 return f.read()
 else:
 raise KeyError(key)

Expand DownExpand Up@@ -805,6 +810,29 @@ def __iter__(self):
 def __len__(self):
 return sum(1 for _ in self.keys())

 __marker = object()

 def pop(self, key, default=__marker):
 filepath = os.path.join(self.path, key)
 if os.path.isfile(filepath):
 with open(filepath, 'rb') as f:
 value = f.read()
 os.remove(filepath)
 return value
 elif default is self.__marker:
 raise KeyError(key)
 else:
 return default

 def popitem(self):
 try:
 key = next(self.keys())
 except StopIteration:
 raise KeyError("Store empty")
 else:
 value = self.pop(key)
 return (key, value)

 def dir_path(self, path=None):
 store_path = normalize_storage_path(path)
 dir_path = self.path
Expand DownExpand Up@@ -896,10 +924,10 @@ class TempStore(DirectoryStore):
 """

 # noinspection PyShadowingBuiltins
 def __init__(self, suffix='', prefix='zarr', dir=None):
 def __init__(self, suffix='', prefix='zarr', dir=None, memmap=False):
 path = tempfile.mkdtemp(suffix=suffix, prefix=prefix, dir=dir)
 atexit.register(atexit_rmtree, path)
 super(TempStore, self).__init__(path)
 super(TempStore, self).__init__(path, memmap=memmap)


_prog_ckey = re.compile(r'^(\d+)(\.\d+)+$')
Expand DownExpand Up@@ -982,8 +1010,8 @@ class NestedDirectoryStore(DirectoryStore):

 """

 def __init__(self, path):
 super(NestedDirectoryStore, self).__init__(path)
 def __init__(self, path, memmap=False):
 super(NestedDirectoryStore, self).__init__(path, memmap=memmap)

 def __getitem__(self, key):
 key = _nested_map_ckey(key)
Expand All@@ -1007,6 +1035,10 @@ def __eq__(self, other):
 self.path == other.path
 )

 def pop(self, key, *args, **kwargs):
 key = _nested_map_ckey(key)
 return super(NestedDirectoryStore, self).pop(key, *args, **kwargs)

 def listdir(self, path=None):
 children = super(NestedDirectoryStore, self).listdir(path=path)
 if array_meta_key in children:
Expand Down

36 changes: 23 additions & 13 deletions
zarr/tests/test_storage.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -21,6 +21,7 @@
except ImportError: # pragma: no cover
 asb = None

from numcodecs.compat import ensure_bytes

from zarr.storage import (init_array, array_meta_key, attrs_key, DictStore,
 DirectoryStore, ZipStore, init_group, group_meta_key,
Expand DownExpand Up@@ -65,7 +66,7 @@ def test_get_set_del_contains(self):
 store['foo']
 store['foo'] = b'bar'
 assert 'foo' in store
 assert b'bar' == store['foo']
 assert b'bar' == ensure_bytes(store['foo'])

 # test __delitem__ (optional)
 try:
Expand DownExpand Up@@ -103,10 +104,10 @@ def test_pop(self):
 store['baz'] = b'qux'
 assert len(store) == 2
 v = store.pop('foo')
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 1
 v = store.pop('baz')
 assert v == b'qux'
 assert ensure_bytes(v) == b'qux'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.pop('xxx')
Expand All@@ -122,7 +123,7 @@ def test_popitem(self):
 store['foo'] = b'bar'
 k, v = store.popitem()
 assert k == 'foo'
 assert v == b'bar'
 assert ensure_bytes(v) == b'bar'
 assert len(store) == 0
 with pytest.raises(KeyError):
 store.popitem()
Expand All@@ -141,8 +142,8 @@ def test_update(self):
 assert 'foo' not in store
 assert 'baz' not in store
 store.update(foo=b'bar', baz=b'quux')
 assert b'bar' == store['foo']
 assert b'quux' == store['baz']
 assert b'bar' == ensure_bytes(store['foo'])
 assert b'quux' == ensure_bytes(store['baz'])

 def test_iterators(self):
 store = self.create_store()
Expand All@@ -164,9 +165,9 @@ def test_iterators(self):
 assert 4 == len(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store)
 assert {'a', 'b', 'c/d', 'c/e/f'} == set(store.keys())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(store.values())
 assert {b'aaa', b'bbb', b'ddd', b'fff'} == set(map(ensure_bytes, store.values()))
 assert ({('a', b'aaa'), ('b', b'bbb'), ('c/d', b'ddd'), ('c/e/f', b'fff')} ==
 set(store.items()))
 set(map(lambda kv: (kv[0], ensure_bytes(kv[1])), store.items())))

 def test_pickle(self):

Expand All@@ -190,8 +191,8 @@ def test_pickle(self):
 # verify
 assert n == len(store2)
 assert keys == sorted(store2.keys())
 assert b'bar' == store2['foo']
 assert b'quux' == store2['baz']
 assert b'bar' == ensure_bytes(store2['foo'])
 assert b'quux' == ensure_bytes(store2['baz'])

 def test_getsize(self):
 store = self.create_store()
Expand DownExpand Up@@ -671,10 +672,10 @@ def setdel_hierarchy_checks(store):
 # test __setitem__ overwrite level
 store['x/y/z'] = b'xxx'
 store['x/y'] = b'yyy'
 assert b'yyy' == store['x/y']
 assert b'yyy' == ensure_bytes(store['x/y'])
 assert 'x/y/z' not in store
 store['x'] = b'zzz'
 assert b'zzz' == store['x']
 assert b'zzz' == ensure_bytes(store['x'])
 assert 'x/y' not in store

 # test __delitem__ overwrite level
Expand DownExpand Up@@ -736,13 +737,22 @@ def test_pickle_ext(self):
 # check point to same underlying directory
 assert 'xxx' not in store
 store2['xxx'] = b'yyy'
 assert b'yyy' == store['xxx']
 assert b'yyy' == ensure_bytes(store['xxx'])

 def test_setdel(self):
 store = self.create_store()
 setdel_hierarchy_checks(store)


class TestDirectoryStoreMemmap(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
 path = tempfile.mkdtemp()
 atexit.register(atexit_rmtree, path)
 store = DirectoryStore(path, memmap=True)
 return store


class TestNestedDirectoryStore(TestDirectoryStore, unittest.TestCase):

 def create_store(self):
Expand Down