Try to converge on internal types consistency.#574

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Try to converge on internal types consistency. #574

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5 changes: 5 additions & 0 deletions docs/release.rst
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,11 @@ Release notes
Next release
------------

* For consistency across stores, the `ConsolidatedMetadataStore` will return
bytes instead of objects for metadata. Internally zarr tries to be more type
stable and attempt to always pass bytes-likes object when storing objects on
stores.

* Fix minor bug in `N5Store`.
By :user:`gsakkis`, :issue:`550`.

Expand Down
2 changes: 1 addition & 1 deletion zarr/core.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -1489,7 +1489,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):
chunk[selection] = value

# encode and store
cdata = self._encode_chunk(chunk)
cdata = ensure_bytes(self._encode_chunk(chunk))

@alimanfooalimanfooJul 9, 2020

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N.B., ensuring bytes may introduce a memory copy, which may be unnecessary. Memory copies can noticeably affect performance. Ensuring we have something that supports the buffer interface would be better.

self.chunk_store[ckey] = cdata

def _set_basic_selection_nd(self, selection, value, fields=None):
Expand Down
10 changes: 8 additions & 2 deletions zarr/storage.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@
from zarr.meta import encode_array_metadata, encode_group_metadata
from zarr.util import (buffer_size, json_loads, nolock, normalize_chunks,
normalize_dtype, normalize_fill_value, normalize_order,
normalize_shape, normalize_storage_path)
normalize_shape, normalize_storage_path, json_dumps)

__doctest_requires__ = {
('RedisStore', 'RedisStore.*'): ['redis'],
Expand DownExpand Up@@ -2479,6 +2479,10 @@ class ConsolidatedMetadataStore(MutableMapping):

.. versionadded:: 2.3

.. versionchanged:: 2.5

__getitem__ will now return bytes for metadata for consistency across stores.

.. note:: This is an experimental feature.

Parameters
Expand DownExpand Up@@ -2507,7 +2511,9 @@ def __init__(self, store, metadata_key='.zmetadata'):
consolidated_format)

# decode metadata
self.meta_store = meta['metadata']
self.meta_store = {}
for k, v in meta["metadata"].items():
self.meta_store[k] = json_dumps(v)
Comment on lines +2514 to +2516

@alimanfooalimanfooJul 9, 2020

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FWIW this was originally how this worked, but this introduces an extra unnecessary JSON encode/decode round trip into the processing of consolidated metadata. In practice that may not be a performance issue, but it seemed awkward to have this extra JSON encode/decode if it wasn't necessary. Hence I introduced a special case which avoided the necessity for this, see the parse_metadata function in the original PR.


def __getitem__(self, key):
return self.meta_store[key]
Expand Down
6 changes: 0 additions & 6 deletions zarr/tests/test_convenience.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -697,12 +697,6 @@ def test_logging(self):
copy(source['foo'], dest, dry_run=True, log=True)


try:
import h5py
except ImportError: # pragma: no cover
h5py = None


def temp_h5f():
h5py = pytest.importorskip("h5py")
fn = tempfile.mktemp()
Expand Down
8 changes: 4 additions & 4 deletions zarr/tests/test_meta.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -424,15 +424,15 @@ def test_encode_decode_dtype():
def test_decode_group():

# typical
b = '''{
b = b'''{
"zarr_format": %s
}''' % ZARR_FORMAT
}''' % str(ZARR_FORMAT).encode()
meta = decode_group_metadata(b)
assert ZARR_FORMAT == meta['zarr_format']

# unsupported format
b = '''{
b = b'''{
"zarr_format": %s
}''' % (ZARR_FORMAT - 1)
}''' % str(ZARR_FORMAT - 1).encode()
with pytest.raises(MetadataError):
decode_group_metadata(b)
28 changes: 22 additions & 6 deletions zarr/tests/test_storage.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -30,6 +30,7 @@
attrs_key, default_compressor, getsize,
group_meta_key, init_array, init_group, migrate_1to2)
from zarr.tests.util import CountingDict, skip_test_env_var
from zarr.util import json_dumps


@contextmanager
Expand DownExpand Up@@ -1627,11 +1628,26 @@ def test_read_write(self):
# setup store with consolidated metdata
store = dict()
consolidated = {
'zarr_consolidated_format': 1,
'metadata': {
'foo': 'bar',
'baz': 42,
}
"zarr_consolidated_format": 1,
"metadata": {
".zgroup": {"zarr_format": 2},
"g2/arr/.zarray": {
"chunks": [5, 5],
"compressor": {
"blocksize": 0,
"clevel": 5,
"cname": "lz4",
"id": "blosc",
"shuffle": 1,
},
"dtype": "<f8",
"fill_value": 0.0,
"filters": None,
"order": "C",
"shape": [20, 20],
"zarr_format": 2,
},
},
}
store['.zmetadata'] = json.dumps(consolidated).encode()

Expand All@@ -1641,7 +1657,7 @@ def test_read_write(self):
# test __contains__, __getitem__
for key, value in consolidated['metadata'].items():
assert key in cs
assert value == cs[key]
assert json_dumps(value) == cs[key]

# test __delitem__, __setitem__
with pytest.raises(PermissionError):
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" + '

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Try to converge on internal types consistency.#574

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Try to converge on internal types consistency.
#574
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5 changes: 5 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,11 @@ Release notes
Next release
------------

* For consistency across stores, the `ConsolidatedMetadataStore` will return
 bytes instead of objects for metadata. Internally zarr tries to be more type
 stable and attempt to always pass bytes-likes object when storing objects on
 stores.

* Fix minor bug in `N5Store`. 
 By :user:`gsakkis`, :issue:`550`.

Expand Down

2 changes: 1 addition & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1489,7 +1489,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):
 chunk[selection] = value

 # encode and store
 cdata = self._encode_chunk(chunk)
 cdata = ensure_bytes(self._encode_chunk(chunk))
@alimanfooalimanfooJul 9, 2020

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Copy Markdown

Member
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

N.B., ensuring bytes may introduce a memory copy, which may be unnecessary. Memory copies can noticeably affect performance. Ensuring we have something that supports the buffer interface would be better.
 self.chunk_store[ckey] = cdata

 def _set_basic_selection_nd(self, selection, value, fields=None):
Expand Down

10 changes: 8 additions & 2 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@
from zarr.meta import encode_array_metadata, encode_group_metadata
from zarr.util import (buffer_size, json_loads, nolock, normalize_chunks,
 normalize_dtype, normalize_fill_value, normalize_order,
 normalize_shape, normalize_storage_path)
 normalize_shape, normalize_storage_path, json_dumps)

__doctest_requires__ = {
 ('RedisStore', 'RedisStore.*'): ['redis'],
Expand DownExpand Up@@ -2479,6 +2479,10 @@ class ConsolidatedMetadataStore(MutableMapping):

 .. versionadded:: 2.3

 .. versionchanged:: 2.5

 __getitem__ will now return bytes for metadata for consistency across stores.

 .. note:: This is an experimental feature.

 Parameters
Expand DownExpand Up@@ -2507,7 +2511,9 @@ def __init__(self, store, metadata_key='.zmetadata'):
 consolidated_format)

 # decode metadata
 self.meta_store = meta['metadata']
 self.meta_store = {}
 for k, v in meta["metadata"].items():
 self.meta_store[k] = json_dumps(v)

Comment on lines

+2514
 to 
+2516

@alimanfooalimanfooJul 9, 2020

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Choose a reason for hiding this comment

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FWIW this was originally how this worked, but this introduces an extra unnecessary JSON encode/decode round trip into the processing of consolidated metadata. In practice that may not be a performance issue, but it seemed awkward to have this extra JSON encode/decode if it wasn't necessary. Hence I introduced a special case which avoided the necessity for this, see the parse_metadata function in the original PR.

 def __getitem__(self, key):
 return self.meta_store[key]
Expand Down

6 changes: 0 additions & 6 deletions
zarr/tests/test_convenience.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -697,12 +697,6 @@ def test_logging(self):
 copy(source['foo'], dest, dry_run=True, log=True)


try:
 import h5py
except ImportError: # pragma: no cover
 h5py = None


def temp_h5f():
 h5py = pytest.importorskip("h5py")
 fn = tempfile.mktemp()
Expand Down

8 changes: 4 additions & 4 deletions
zarr/tests/test_meta.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -424,15 +424,15 @@ def test_encode_decode_dtype():
def test_decode_group():

 # typical
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % ZARR_FORMAT
 }''' % str(ZARR_FORMAT).encode()
 meta = decode_group_metadata(b)
 assert ZARR_FORMAT == meta['zarr_format']

 # unsupported format
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % (ZARR_FORMAT - 1)
 }''' % str(ZARR_FORMAT - 1).encode()
 with pytest.raises(MetadataError):
 decode_group_metadata(b)

28 changes: 22 additions & 6 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -30,6 +30,7 @@
 attrs_key, default_compressor, getsize,
 group_meta_key, init_array, init_group, migrate_1to2)
from zarr.tests.util import CountingDict, skip_test_env_var
from zarr.util import json_dumps


@contextmanager
Expand DownExpand Up@@ -1627,11 +1628,26 @@ def test_read_write(self):
 # setup store with consolidated metdata
 store = dict()
 consolidated = {
 'zarr_consolidated_format': 1,
 'metadata': {
 'foo': 'bar',
 'baz': 42,
 }
 "zarr_consolidated_format": 1,
 "metadata": {
 ".zgroup": {"zarr_format": 2},
 "g2/arr/.zarray": {
 "chunks": [5, 5],
 "compressor": {
 "blocksize": 0,
 "clevel": 5,
 "cname": "lz4",
 "id": "blosc",
 "shuffle": 1,
 },
 "dtype": "<f8",
 "fill_value": 0.0,
 "filters": None,
 "order": "C",
 "shape": [20, 20],
 "zarr_format": 2,
 },
 },
 }
 store['.zmetadata'] = json.dumps(consolidated).encode()

Expand All@@ -1641,7 +1657,7 @@ def test_read_write(self):
 # test __contains__, __getitem__
 for key, value in consolidated['metadata'].items():
 assert key in cs
 assert value == cs[key]
 assert json_dumps(value) == cs[key]

 # test __delitem__, __setitem__
 with pytest.raises(PermissionError):
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('^' + ".*" + '

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Try to converge on internal types consistency.#574

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 Closed

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Try to converge on internal types consistency.
#574
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5 changes: 5 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,11 @@ Release notes
Next release
------------

* For consistency across stores, the `ConsolidatedMetadataStore` will return
 bytes instead of objects for metadata. Internally zarr tries to be more type
 stable and attempt to always pass bytes-likes object when storing objects on
 stores.

* Fix minor bug in `N5Store`. 
 By :user:`gsakkis`, :issue:`550`.

Expand Down

2 changes: 1 addition & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1489,7 +1489,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):
 chunk[selection] = value

 # encode and store
 cdata = self._encode_chunk(chunk)
 cdata = ensure_bytes(self._encode_chunk(chunk))
@alimanfooalimanfooJul 9, 2020

Copy link


Copy Markdown

Member
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

N.B., ensuring bytes may introduce a memory copy, which may be unnecessary. Memory copies can noticeably affect performance. Ensuring we have something that supports the buffer interface would be better.
 self.chunk_store[ckey] = cdata

 def _set_basic_selection_nd(self, selection, value, fields=None):
Expand Down

10 changes: 8 additions & 2 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@
from zarr.meta import encode_array_metadata, encode_group_metadata
from zarr.util import (buffer_size, json_loads, nolock, normalize_chunks,
 normalize_dtype, normalize_fill_value, normalize_order,
 normalize_shape, normalize_storage_path)
 normalize_shape, normalize_storage_path, json_dumps)

__doctest_requires__ = {
 ('RedisStore', 'RedisStore.*'): ['redis'],
Expand DownExpand Up@@ -2479,6 +2479,10 @@ class ConsolidatedMetadataStore(MutableMapping):

 .. versionadded:: 2.3

 .. versionchanged:: 2.5

 __getitem__ will now return bytes for metadata for consistency across stores.

 .. note:: This is an experimental feature.

 Parameters
Expand DownExpand Up@@ -2507,7 +2511,9 @@ def __init__(self, store, metadata_key='.zmetadata'):
 consolidated_format)

 # decode metadata
 self.meta_store = meta['metadata']
 self.meta_store = {}
 for k, v in meta["metadata"].items():
 self.meta_store[k] = json_dumps(v)

Comment on lines

+2514
 to 
+2516

@alimanfooalimanfooJul 9, 2020

Copy link


Copy Markdown

Member
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

FWIW this was originally how this worked, but this introduces an extra unnecessary JSON encode/decode round trip into the processing of consolidated metadata. In practice that may not be a performance issue, but it seemed awkward to have this extra JSON encode/decode if it wasn't necessary. Hence I introduced a special case which avoided the necessity for this, see the parse_metadata function in the original PR.

 def __getitem__(self, key):
 return self.meta_store[key]
Expand Down

6 changes: 0 additions & 6 deletions
zarr/tests/test_convenience.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -697,12 +697,6 @@ def test_logging(self):
 copy(source['foo'], dest, dry_run=True, log=True)


try:
 import h5py
except ImportError: # pragma: no cover
 h5py = None


def temp_h5f():
 h5py = pytest.importorskip("h5py")
 fn = tempfile.mktemp()
Expand Down

8 changes: 4 additions & 4 deletions
zarr/tests/test_meta.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -424,15 +424,15 @@ def test_encode_decode_dtype():
def test_decode_group():

 # typical
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % ZARR_FORMAT
 }''' % str(ZARR_FORMAT).encode()
 meta = decode_group_metadata(b)
 assert ZARR_FORMAT == meta['zarr_format']

 # unsupported format
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % (ZARR_FORMAT - 1)
 }''' % str(ZARR_FORMAT - 1).encode()
 with pytest.raises(MetadataError):
 decode_group_metadata(b)

28 changes: 22 additions & 6 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -30,6 +30,7 @@
 attrs_key, default_compressor, getsize,
 group_meta_key, init_array, init_group, migrate_1to2)
from zarr.tests.util import CountingDict, skip_test_env_var
from zarr.util import json_dumps


@contextmanager
Expand DownExpand Up@@ -1627,11 +1628,26 @@ def test_read_write(self):
 # setup store with consolidated metdata
 store = dict()
 consolidated = {
 'zarr_consolidated_format': 1,
 'metadata': {
 'foo': 'bar',
 'baz': 42,
 }
 "zarr_consolidated_format": 1,
 "metadata": {
 ".zgroup": {"zarr_format": 2},
 "g2/arr/.zarray": {
 "chunks": [5, 5],
 "compressor": {
 "blocksize": 0,
 "clevel": 5,
 "cname": "lz4",
 "id": "blosc",
 "shuffle": 1,
 },
 "dtype": "<f8",
 "fill_value": 0.0,
 "filters": None,
 "order": "C",
 "shape": [20, 20],
 "zarr_format": 2,
 },
 },
 }
 store['.zmetadata'] = json.dumps(consolidated).encode()

Expand All@@ -1641,7 +1657,7 @@ def test_read_write(self):
 # test __contains__, __getitem__
 for key, value in consolidated['metadata'].items():
 assert key in cs
 assert value == cs[key]
 assert json_dumps(value) == cs[key]

 # test __delitem__, __setitem__
 with pytest.raises(PermissionError):
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
Try to converge on internal types consistency.#574

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Already on GitHub?
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 Closed

Carreau
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commit into

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 Closed


Try to converge on internal types consistency.
#574
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5 changes: 5 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,11 @@ Release notes
Next release
------------

* For consistency across stores, the `ConsolidatedMetadataStore` will return
 bytes instead of objects for metadata. Internally zarr tries to be more type
 stable and attempt to always pass bytes-likes object when storing objects on
 stores.

* Fix minor bug in `N5Store`. 
 By :user:`gsakkis`, :issue:`550`.

Expand Down

2 changes: 1 addition & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1489,7 +1489,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):
 chunk[selection] = value

 # encode and store
 cdata = self._encode_chunk(chunk)
 cdata = ensure_bytes(self._encode_chunk(chunk))
@alimanfooalimanfooJul 9, 2020

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N.B., ensuring bytes may introduce a memory copy, which may be unnecessary. Memory copies can noticeably affect performance. Ensuring we have something that supports the buffer interface would be better.
 self.chunk_store[ckey] = cdata

 def _set_basic_selection_nd(self, selection, value, fields=None):
Expand Down

10 changes: 8 additions & 2 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@
from zarr.meta import encode_array_metadata, encode_group_metadata
from zarr.util import (buffer_size, json_loads, nolock, normalize_chunks,
 normalize_dtype, normalize_fill_value, normalize_order,
 normalize_shape, normalize_storage_path)
 normalize_shape, normalize_storage_path, json_dumps)

__doctest_requires__ = {
 ('RedisStore', 'RedisStore.*'): ['redis'],
Expand DownExpand Up@@ -2479,6 +2479,10 @@ class ConsolidatedMetadataStore(MutableMapping):

 .. versionadded:: 2.3

 .. versionchanged:: 2.5

 __getitem__ will now return bytes for metadata for consistency across stores.

 .. note:: This is an experimental feature.

 Parameters
Expand DownExpand Up@@ -2507,7 +2511,9 @@ def __init__(self, store, metadata_key='.zmetadata'):
 consolidated_format)

 # decode metadata
 self.meta_store = meta['metadata']
 self.meta_store = {}
 for k, v in meta["metadata"].items():
 self.meta_store[k] = json_dumps(v)

Comment on lines

+2514
 to 
+2516

@alimanfooalimanfooJul 9, 2020

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FWIW this was originally how this worked, but this introduces an extra unnecessary JSON encode/decode round trip into the processing of consolidated metadata. In practice that may not be a performance issue, but it seemed awkward to have this extra JSON encode/decode if it wasn't necessary. Hence I introduced a special case which avoided the necessity for this, see the parse_metadata function in the original PR.

 def __getitem__(self, key):
 return self.meta_store[key]
Expand Down

6 changes: 0 additions & 6 deletions
zarr/tests/test_convenience.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -697,12 +697,6 @@ def test_logging(self):
 copy(source['foo'], dest, dry_run=True, log=True)


try:
 import h5py
except ImportError: # pragma: no cover
 h5py = None


def temp_h5f():
 h5py = pytest.importorskip("h5py")
 fn = tempfile.mktemp()
Expand Down

8 changes: 4 additions & 4 deletions
zarr/tests/test_meta.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -424,15 +424,15 @@ def test_encode_decode_dtype():
def test_decode_group():

 # typical
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % ZARR_FORMAT
 }''' % str(ZARR_FORMAT).encode()
 meta = decode_group_metadata(b)
 assert ZARR_FORMAT == meta['zarr_format']

 # unsupported format
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % (ZARR_FORMAT - 1)
 }''' % str(ZARR_FORMAT - 1).encode()
 with pytest.raises(MetadataError):
 decode_group_metadata(b)

28 changes: 22 additions & 6 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -30,6 +30,7 @@
 attrs_key, default_compressor, getsize,
 group_meta_key, init_array, init_group, migrate_1to2)
from zarr.tests.util import CountingDict, skip_test_env_var
from zarr.util import json_dumps


@contextmanager
Expand DownExpand Up@@ -1627,11 +1628,26 @@ def test_read_write(self):
 # setup store with consolidated metdata
 store = dict()
 consolidated = {
 'zarr_consolidated_format': 1,
 'metadata': {
 'foo': 'bar',
 'baz': 42,
 }
 "zarr_consolidated_format": 1,
 "metadata": {
 ".zgroup": {"zarr_format": 2},
 "g2/arr/.zarray": {
 "chunks": [5, 5],
 "compressor": {
 "blocksize": 0,
 "clevel": 5,
 "cname": "lz4",
 "id": "blosc",
 "shuffle": 1,
 },
 "dtype": "<f8",
 "fill_value": 0.0,
 "filters": None,
 "order": "C",
 "shape": [20, 20],
 "zarr_format": 2,
 },
 },
 }
 store['.zmetadata'] = json.dumps(consolidated).encode()

Expand All@@ -1641,7 +1657,7 @@ def test_read_write(self):
 # test __contains__, __getitem__
 for key, value in consolidated['metadata'].items():
 assert key in cs
 assert value == cs[key]
 assert json_dumps(value) == cs[key]

 # test __delitem__, __setitem__
 with pytest.raises(PermissionError):
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" + '

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Try to converge on internal types consistency.
#574
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5 changes: 5 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,11 @@ Release notes
Next release
------------

* For consistency across stores, the `ConsolidatedMetadataStore` will return
 bytes instead of objects for metadata. Internally zarr tries to be more type
 stable and attempt to always pass bytes-likes object when storing objects on
 stores.

* Fix minor bug in `N5Store`. 
 By :user:`gsakkis`, :issue:`550`.

Expand Down

2 changes: 1 addition & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1489,7 +1489,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):
 chunk[selection] = value

 # encode and store
 cdata = self._encode_chunk(chunk)
 cdata = ensure_bytes(self._encode_chunk(chunk))
@alimanfooalimanfooJul 9, 2020

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Member
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The reason will be displayed to describe this comment to others. Learn more.

N.B., ensuring bytes may introduce a memory copy, which may be unnecessary. Memory copies can noticeably affect performance. Ensuring we have something that supports the buffer interface would be better.
 self.chunk_store[ckey] = cdata

 def _set_basic_selection_nd(self, selection, value, fields=None):
Expand Down

10 changes: 8 additions & 2 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@
from zarr.meta import encode_array_metadata, encode_group_metadata
from zarr.util import (buffer_size, json_loads, nolock, normalize_chunks,
 normalize_dtype, normalize_fill_value, normalize_order,
 normalize_shape, normalize_storage_path)
 normalize_shape, normalize_storage_path, json_dumps)

__doctest_requires__ = {
 ('RedisStore', 'RedisStore.*'): ['redis'],
Expand DownExpand Up@@ -2479,6 +2479,10 @@ class ConsolidatedMetadataStore(MutableMapping):

 .. versionadded:: 2.3

 .. versionchanged:: 2.5

 __getitem__ will now return bytes for metadata for consistency across stores.

 .. note:: This is an experimental feature.

 Parameters
Expand DownExpand Up@@ -2507,7 +2511,9 @@ def __init__(self, store, metadata_key='.zmetadata'):
 consolidated_format)

 # decode metadata
 self.meta_store = meta['metadata']
 self.meta_store = {}
 for k, v in meta["metadata"].items():
 self.meta_store[k] = json_dumps(v)

Comment on lines

+2514
 to 
+2516

@alimanfooalimanfooJul 9, 2020

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Choose a reason for hiding this comment

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FWIW this was originally how this worked, but this introduces an extra unnecessary JSON encode/decode round trip into the processing of consolidated metadata. In practice that may not be a performance issue, but it seemed awkward to have this extra JSON encode/decode if it wasn't necessary. Hence I introduced a special case which avoided the necessity for this, see the parse_metadata function in the original PR.

 def __getitem__(self, key):
 return self.meta_store[key]
Expand Down

6 changes: 0 additions & 6 deletions
zarr/tests/test_convenience.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -697,12 +697,6 @@ def test_logging(self):
 copy(source['foo'], dest, dry_run=True, log=True)


try:
 import h5py
except ImportError: # pragma: no cover
 h5py = None


def temp_h5f():
 h5py = pytest.importorskip("h5py")
 fn = tempfile.mktemp()
Expand Down

8 changes: 4 additions & 4 deletions
zarr/tests/test_meta.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -424,15 +424,15 @@ def test_encode_decode_dtype():
def test_decode_group():

 # typical
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % ZARR_FORMAT
 }''' % str(ZARR_FORMAT).encode()
 meta = decode_group_metadata(b)
 assert ZARR_FORMAT == meta['zarr_format']

 # unsupported format
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % (ZARR_FORMAT - 1)
 }''' % str(ZARR_FORMAT - 1).encode()
 with pytest.raises(MetadataError):
 decode_group_metadata(b)

28 changes: 22 additions & 6 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -30,6 +30,7 @@
 attrs_key, default_compressor, getsize,
 group_meta_key, init_array, init_group, migrate_1to2)
from zarr.tests.util import CountingDict, skip_test_env_var
from zarr.util import json_dumps


@contextmanager
Expand DownExpand Up@@ -1627,11 +1628,26 @@ def test_read_write(self):
 # setup store with consolidated metdata
 store = dict()
 consolidated = {
 'zarr_consolidated_format': 1,
 'metadata': {
 'foo': 'bar',
 'baz': 42,
 }
 "zarr_consolidated_format": 1,
 "metadata": {
 ".zgroup": {"zarr_format": 2},
 "g2/arr/.zarray": {
 "chunks": [5, 5],
 "compressor": {
 "blocksize": 0,
 "clevel": 5,
 "cname": "lz4",
 "id": "blosc",
 "shuffle": 1,
 },
 "dtype": "<f8",
 "fill_value": 0.0,
 "filters": None,
 "order": "C",
 "shape": [20, 20],
 "zarr_format": 2,
 },
 },
 }
 store['.zmetadata'] = json.dumps(consolidated).encode()

Expand All@@ -1641,7 +1657,7 @@ def test_read_write(self):
 # test __contains__, __getitem__
 for key, value in consolidated['metadata'].items():
 assert key in cs
 assert value == cs[key]
 assert json_dumps(value) == cs[key]

 # test __delitem__, __setitem__
 with pytest.raises(PermissionError):
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
Try to converge on internal types consistency.#574

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 Closed

Carreau
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 Closed


Try to converge on internal types consistency.
#574
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5 changes: 5 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,11 @@ Release notes
Next release
------------

* For consistency across stores, the `ConsolidatedMetadataStore` will return
 bytes instead of objects for metadata. Internally zarr tries to be more type
 stable and attempt to always pass bytes-likes object when storing objects on
 stores.

* Fix minor bug in `N5Store`. 
 By :user:`gsakkis`, :issue:`550`.

Expand Down

2 changes: 1 addition & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1489,7 +1489,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):
 chunk[selection] = value

 # encode and store
 cdata = self._encode_chunk(chunk)
 cdata = ensure_bytes(self._encode_chunk(chunk))
@alimanfooalimanfooJul 9, 2020

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Member
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

N.B., ensuring bytes may introduce a memory copy, which may be unnecessary. Memory copies can noticeably affect performance. Ensuring we have something that supports the buffer interface would be better.
 self.chunk_store[ckey] = cdata

 def _set_basic_selection_nd(self, selection, value, fields=None):
Expand Down

10 changes: 8 additions & 2 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@
from zarr.meta import encode_array_metadata, encode_group_metadata
from zarr.util import (buffer_size, json_loads, nolock, normalize_chunks,
 normalize_dtype, normalize_fill_value, normalize_order,
 normalize_shape, normalize_storage_path)
 normalize_shape, normalize_storage_path, json_dumps)

__doctest_requires__ = {
 ('RedisStore', 'RedisStore.*'): ['redis'],
Expand DownExpand Up@@ -2479,6 +2479,10 @@ class ConsolidatedMetadataStore(MutableMapping):

 .. versionadded:: 2.3

 .. versionchanged:: 2.5

 __getitem__ will now return bytes for metadata for consistency across stores.

 .. note:: This is an experimental feature.

 Parameters
Expand DownExpand Up@@ -2507,7 +2511,9 @@ def __init__(self, store, metadata_key='.zmetadata'):
 consolidated_format)

 # decode metadata
 self.meta_store = meta['metadata']
 self.meta_store = {}
 for k, v in meta["metadata"].items():
 self.meta_store[k] = json_dumps(v)

Comment on lines

+2514
 to 
+2516

@alimanfooalimanfooJul 9, 2020

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Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

FWIW this was originally how this worked, but this introduces an extra unnecessary JSON encode/decode round trip into the processing of consolidated metadata. In practice that may not be a performance issue, but it seemed awkward to have this extra JSON encode/decode if it wasn't necessary. Hence I introduced a special case which avoided the necessity for this, see the parse_metadata function in the original PR.

 def __getitem__(self, key):
 return self.meta_store[key]
Expand Down

6 changes: 0 additions & 6 deletions
zarr/tests/test_convenience.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -697,12 +697,6 @@ def test_logging(self):
 copy(source['foo'], dest, dry_run=True, log=True)


try:
 import h5py
except ImportError: # pragma: no cover
 h5py = None


def temp_h5f():
 h5py = pytest.importorskip("h5py")
 fn = tempfile.mktemp()
Expand Down

8 changes: 4 additions & 4 deletions
zarr/tests/test_meta.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -424,15 +424,15 @@ def test_encode_decode_dtype():
def test_decode_group():

 # typical
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % ZARR_FORMAT
 }''' % str(ZARR_FORMAT).encode()
 meta = decode_group_metadata(b)
 assert ZARR_FORMAT == meta['zarr_format']

 # unsupported format
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % (ZARR_FORMAT - 1)
 }''' % str(ZARR_FORMAT - 1).encode()
 with pytest.raises(MetadataError):
 decode_group_metadata(b)

28 changes: 22 additions & 6 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -30,6 +30,7 @@
 attrs_key, default_compressor, getsize,
 group_meta_key, init_array, init_group, migrate_1to2)
from zarr.tests.util import CountingDict, skip_test_env_var
from zarr.util import json_dumps


@contextmanager
Expand DownExpand Up@@ -1627,11 +1628,26 @@ def test_read_write(self):
 # setup store with consolidated metdata
 store = dict()
 consolidated = {
 'zarr_consolidated_format': 1,
 'metadata': {
 'foo': 'bar',
 'baz': 42,
 }
 "zarr_consolidated_format": 1,
 "metadata": {
 ".zgroup": {"zarr_format": 2},
 "g2/arr/.zarray": {
 "chunks": [5, 5],
 "compressor": {
 "blocksize": 0,
 "clevel": 5,
 "cname": "lz4",
 "id": "blosc",
 "shuffle": 1,
 },
 "dtype": "<f8",
 "fill_value": 0.0,
 "filters": None,
 "order": "C",
 "shape": [20, 20],
 "zarr_format": 2,
 },
 },
 }
 store['.zmetadata'] = json.dumps(consolidated).encode()

Expand All@@ -1641,7 +1657,7 @@ def test_read_write(self):
 # test __contains__, __getitem__
 for key, value in consolidated['metadata'].items():
 assert key in cs
 assert value == cs[key]
 assert json_dumps(value) == cs[key]

 # test __delitem__, __setitem__
 with pytest.raises(PermissionError):
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
Try to converge on internal types consistency.#574

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 Closed

Carreau
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Try to converge on internal types consistency.
#574
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5 changes: 5 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,11 @@ Release notes
Next release
------------

* For consistency across stores, the `ConsolidatedMetadataStore` will return
 bytes instead of objects for metadata. Internally zarr tries to be more type
 stable and attempt to always pass bytes-likes object when storing objects on
 stores.

* Fix minor bug in `N5Store`. 
 By :user:`gsakkis`, :issue:`550`.

Expand Down

2 changes: 1 addition & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1489,7 +1489,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):
 chunk[selection] = value

 # encode and store
 cdata = self._encode_chunk(chunk)
 cdata = ensure_bytes(self._encode_chunk(chunk))
@alimanfooalimanfooJul 9, 2020

Copy link


Copy Markdown

Member
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

N.B., ensuring bytes may introduce a memory copy, which may be unnecessary. Memory copies can noticeably affect performance. Ensuring we have something that supports the buffer interface would be better.
 self.chunk_store[ckey] = cdata

 def _set_basic_selection_nd(self, selection, value, fields=None):
Expand Down

10 changes: 8 additions & 2 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@
from zarr.meta import encode_array_metadata, encode_group_metadata
from zarr.util import (buffer_size, json_loads, nolock, normalize_chunks,
 normalize_dtype, normalize_fill_value, normalize_order,
 normalize_shape, normalize_storage_path)
 normalize_shape, normalize_storage_path, json_dumps)

__doctest_requires__ = {
 ('RedisStore', 'RedisStore.*'): ['redis'],
Expand DownExpand Up@@ -2479,6 +2479,10 @@ class ConsolidatedMetadataStore(MutableMapping):

 .. versionadded:: 2.3

 .. versionchanged:: 2.5

 __getitem__ will now return bytes for metadata for consistency across stores.

 .. note:: This is an experimental feature.

 Parameters
Expand DownExpand Up@@ -2507,7 +2511,9 @@ def __init__(self, store, metadata_key='.zmetadata'):
 consolidated_format)

 # decode metadata
 self.meta_store = meta['metadata']
 self.meta_store = {}
 for k, v in meta["metadata"].items():
 self.meta_store[k] = json_dumps(v)

Comment on lines

+2514
 to 
+2516

@alimanfooalimanfooJul 9, 2020

Copy link


Copy Markdown

Member
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

FWIW this was originally how this worked, but this introduces an extra unnecessary JSON encode/decode round trip into the processing of consolidated metadata. In practice that may not be a performance issue, but it seemed awkward to have this extra JSON encode/decode if it wasn't necessary. Hence I introduced a special case which avoided the necessity for this, see the parse_metadata function in the original PR.

 def __getitem__(self, key):
 return self.meta_store[key]
Expand Down

6 changes: 0 additions & 6 deletions
zarr/tests/test_convenience.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -697,12 +697,6 @@ def test_logging(self):
 copy(source['foo'], dest, dry_run=True, log=True)


try:
 import h5py
except ImportError: # pragma: no cover
 h5py = None


def temp_h5f():
 h5py = pytest.importorskip("h5py")
 fn = tempfile.mktemp()
Expand Down

8 changes: 4 additions & 4 deletions
zarr/tests/test_meta.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -424,15 +424,15 @@ def test_encode_decode_dtype():
def test_decode_group():

 # typical
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % ZARR_FORMAT
 }''' % str(ZARR_FORMAT).encode()
 meta = decode_group_metadata(b)
 assert ZARR_FORMAT == meta['zarr_format']

 # unsupported format
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % (ZARR_FORMAT - 1)
 }''' % str(ZARR_FORMAT - 1).encode()
 with pytest.raises(MetadataError):
 decode_group_metadata(b)

28 changes: 22 additions & 6 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -30,6 +30,7 @@
 attrs_key, default_compressor, getsize,
 group_meta_key, init_array, init_group, migrate_1to2)
from zarr.tests.util import CountingDict, skip_test_env_var
from zarr.util import json_dumps


@contextmanager
Expand DownExpand Up@@ -1627,11 +1628,26 @@ def test_read_write(self):
 # setup store with consolidated metdata
 store = dict()
 consolidated = {
 'zarr_consolidated_format': 1,
 'metadata': {
 'foo': 'bar',
 'baz': 42,
 }
 "zarr_consolidated_format": 1,
 "metadata": {
 ".zgroup": {"zarr_format": 2},
 "g2/arr/.zarray": {
 "chunks": [5, 5],
 "compressor": {
 "blocksize": 0,
 "clevel": 5,
 "cname": "lz4",
 "id": "blosc",
 "shuffle": 1,
 },
 "dtype": "<f8",
 "fill_value": 0.0,
 "filters": None,
 "order": "C",
 "shape": [20, 20],
 "zarr_format": 2,
 },
 },
 }
 store['.zmetadata'] = json.dumps(consolidated).encode()

Expand All@@ -1641,7 +1657,7 @@ def test_read_write(self):
 # test __contains__, __getitem__
 for key, value in consolidated['metadata'].items():
 assert key in cs
 assert value == cs[key]
 assert json_dumps(value) == cs[key]

 # test __delitem__, __setitem__
 with pytest.raises(PermissionError):
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); }
})();
})();

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Try to converge on internal types consistency.
#574
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5 changes: 5 additions & 0 deletions
docs/release.rst

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,11 @@ Release notes
Next release
------------

* For consistency across stores, the `ConsolidatedMetadataStore` will return
 bytes instead of objects for metadata. Internally zarr tries to be more type
 stable and attempt to always pass bytes-likes object when storing objects on
 stores.

* Fix minor bug in `N5Store`. 
 By :user:`gsakkis`, :issue:`550`.

Expand Down

2 changes: 1 addition & 1 deletion
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1489,7 +1489,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):
 chunk[selection] = value

 # encode and store
 cdata = self._encode_chunk(chunk)
 cdata = ensure_bytes(self._encode_chunk(chunk))
@alimanfooalimanfooJul 9, 2020

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N.B., ensuring bytes may introduce a memory copy, which may be unnecessary. Memory copies can noticeably affect performance. Ensuring we have something that supports the buffer interface would be better.
 self.chunk_store[ckey] = cdata

 def _set_basic_selection_nd(self, selection, value, fields=None):
Expand Down

10 changes: 8 additions & 2 deletions
zarr/storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@
from zarr.meta import encode_array_metadata, encode_group_metadata
from zarr.util import (buffer_size, json_loads, nolock, normalize_chunks,
 normalize_dtype, normalize_fill_value, normalize_order,
 normalize_shape, normalize_storage_path)
 normalize_shape, normalize_storage_path, json_dumps)

__doctest_requires__ = {
 ('RedisStore', 'RedisStore.*'): ['redis'],
Expand DownExpand Up@@ -2479,6 +2479,10 @@ class ConsolidatedMetadataStore(MutableMapping):

 .. versionadded:: 2.3

 .. versionchanged:: 2.5

 __getitem__ will now return bytes for metadata for consistency across stores.

 .. note:: This is an experimental feature.

 Parameters
Expand DownExpand Up@@ -2507,7 +2511,9 @@ def __init__(self, store, metadata_key='.zmetadata'):
 consolidated_format)

 # decode metadata
 self.meta_store = meta['metadata']
 self.meta_store = {}
 for k, v in meta["metadata"].items():
 self.meta_store[k] = json_dumps(v)

Comment on lines

+2514
 to 
+2516

@alimanfooalimanfooJul 9, 2020

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FWIW this was originally how this worked, but this introduces an extra unnecessary JSON encode/decode round trip into the processing of consolidated metadata. In practice that may not be a performance issue, but it seemed awkward to have this extra JSON encode/decode if it wasn't necessary. Hence I introduced a special case which avoided the necessity for this, see the parse_metadata function in the original PR.

 def __getitem__(self, key):
 return self.meta_store[key]
Expand Down

6 changes: 0 additions & 6 deletions
zarr/tests/test_convenience.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -697,12 +697,6 @@ def test_logging(self):
 copy(source['foo'], dest, dry_run=True, log=True)


try:
 import h5py
except ImportError: # pragma: no cover
 h5py = None


def temp_h5f():
 h5py = pytest.importorskip("h5py")
 fn = tempfile.mktemp()
Expand Down

8 changes: 4 additions & 4 deletions
zarr/tests/test_meta.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -424,15 +424,15 @@ def test_encode_decode_dtype():
def test_decode_group():

 # typical
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % ZARR_FORMAT
 }''' % str(ZARR_FORMAT).encode()
 meta = decode_group_metadata(b)
 assert ZARR_FORMAT == meta['zarr_format']

 # unsupported format
 b = '''{
 b = b'''{
 "zarr_format": %s
 }''' % (ZARR_FORMAT - 1)
 }''' % str(ZARR_FORMAT - 1).encode()
 with pytest.raises(MetadataError):
 decode_group_metadata(b)

28 changes: 22 additions & 6 deletions
zarr/tests/test_storage.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -30,6 +30,7 @@
 attrs_key, default_compressor, getsize,
 group_meta_key, init_array, init_group, migrate_1to2)
from zarr.tests.util import CountingDict, skip_test_env_var
from zarr.util import json_dumps


@contextmanager
Expand DownExpand Up@@ -1627,11 +1628,26 @@ def test_read_write(self):
 # setup store with consolidated metdata
 store = dict()
 consolidated = {
 'zarr_consolidated_format': 1,
 'metadata': {
 'foo': 'bar',
 'baz': 42,
 }
 "zarr_consolidated_format": 1,
 "metadata": {
 ".zgroup": {"zarr_format": 2},
 "g2/arr/.zarray": {
 "chunks": [5, 5],
 "compressor": {
 "blocksize": 0,
 "clevel": 5,
 "cname": "lz4",
 "id": "blosc",
 "shuffle": 1,
 },
 "dtype": "<f8",
 "fill_value": 0.0,
 "filters": None,
 "order": "C",
 "shape": [20, 20],
 "zarr_format": 2,
 },
 },
 }
 store['.zmetadata'] = json.dumps(consolidated).encode()

Expand All@@ -1641,7 +1657,7 @@ def test_read_write(self):
 # test __contains__, __getitem__
 for key, value in consolidated['metadata'].items():
 assert key in cs
 assert value == cs[key]
 assert json_dumps(value) == cs[key]

 # test __delitem__, __setitem__
 with pytest.raises(PermissionError):
Expand Down