Fixes - #1

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TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from
TomNicholas:dtree-zarrv3-2
Mar 19, 2025
Merged

Fixes#1
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from
TomNicholas:dtree-zarrv3-2

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@TomNicholas

@TomNicholasTomNicholas commented Mar 17, 2025

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I couldn't work out how to get the permissions right so I've just opened this against your PR branch @aladinor. I plan to make some more changes tomorrow.

@TomNicholas
TomNicholas changed the base branch from main to dtree-zarrv3March 17, 2025 23:46
@TomNicholas
Merge branch 'dtree-zarrv3' into dtree-zarrv3-2
980ebb4
@TomNicholas
revert changes to test fixture
30f5bba
@TomNicholas
formatting
4d1fdb5
@TomNicholas
add decorator to parametrize over zarr formats
ecef578
@TomNicholas
ensure both versions of zarr-python and both versions of zarr-python …
c2a1f5f
…get tested
@TomNicholas
change datatree fixture to not produce values that would be fill_valu…
cde6b65
…es by default in zarr
@TomNicholas
refactor test to make expected behaviour clearer
09fad6e
@TomNicholas
fix wrongly expected behaviour - should not expect inherited variable…
77575b5
… to be written to zarr
@TomNicholas
make arrays no longer scalars to dodgepydata#10147
0a9f874
@TomNicholas
Merge branch 'dtree-zarrv3-2' ofhttps://github.com/TomNicholas/xarray…
565938b
…into dtree-zarrv3-2
@TomNicholas
fix bad merge
daf0f42
@TomNicholas
parametrize almost every test over zarr_format
84bde40
@TomNicholas
parametrize encoding test over zarr_formats
04d937c
@TomNicholas
use xfail in encoding test
765c5f0
@TomNicholas
updated expected behaviour of zarr on-disk in light ofpydata#10147
7eee31c
@TomNicholas
fully revert change to simple_datatree test fixture by considered zar…
0969422
…r's fill_value in assertion
@TomNicholas
parametrize unaligned_zarr test fixture over zarr_format
cacf419
@TomNicholas
move parametrize_over_zarr_format decorator to apply to entire test c…
1a60ebe
…lass
@TomNicholas
for now explicitly consolidate metadata in test fixture
d98abe3
@TomNicholas
correct bug in writing of consolidated metadata
2dcefe4
TomNicholas
TomNicholas commented Mar 19, 2025
View reviewed changes
Comment threadxarray/backends/zarr.py
kwargs = {}
if _zarr_v3():
# https://github.com/zarr-developers/zarr-python/pull/2113#issuecomment-2386718323
kwargs["path"] = self.zarr_group.name.lstrip("/")

@TomNicholasTomNicholasMar 19, 2025•
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FYI @TomAugspurger@jhamman and I are 95% sure that this line was unnecessary and a bug. It was causing consolidated metadata to not be written at the store root each time, and now that we changed it, it fixed various buggy behaviour we were seeing.

relevant to zarr-developers/zarr-python#2113 (comment)

@TomNicholas
TomNicholas merged commit 94f0ddc into aladinor:dtree-zarrv3Mar 19, 2025
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@TomNicholas@ianhi
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} 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
Fixes - #1
Merged
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Mar 19, 2025
Merged
Fixes#1
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Conversation
@TomNicholas
@TomNicholasTomNicholas
commented
Mar 17, 2025

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Collaborator
I couldn't work out how to get the permissions right so I've just opened this against your PR branch @aladinor. I plan to make some more changes tomorrow.
@TomNicholas
TomNicholas
changed the base branch from
main
to
dtree-zarrv3March 17, 2025 23:46
@TomNicholas
Merge branch 'dtree-zarrv3' into dtree-zarrv3-2
980ebb4
@TomNicholas
revert changes to test fixture
30f5bba
@TomNicholas
formatting
4d1fdb5
@TomNicholas
add decorator to parametrize over zarr formats
ecef578
@TomNicholas
ensure both versions of zarr-python and both versions of zarr-python …
c2a1f5f
…get tested
@TomNicholas
change datatree fixture to not produce values that would be fill_valu…
cde6b65
…es by default in zarr
@TomNicholas
refactor test to make expected behaviour clearer
09fad6e
@TomNicholas
fix wrongly expected behaviour - should not expect inherited variable…
77575b5
… to be written to zarr
@TomNicholas
make arrays no longer scalars to dodgepydata#10147
0a9f874
@TomNicholas
Merge branch 'dtree-zarrv3-2' ofhttps://github.com/TomNicholas/xarray…
565938b
…into dtree-zarrv3-2
@TomNicholas
fix bad merge
daf0f42
@TomNicholas
parametrize almost every test over zarr_format
84bde40
@TomNicholas
parametrize encoding test over zarr_formats
04d937c
@TomNicholas
use xfail in encoding test
765c5f0
@TomNicholas
updated expected behaviour of zarr on-disk in light ofpydata#10147
7eee31c
@TomNicholas
fully revert change to simple_datatree test fixture by considered zar…
0969422
…r's fill_value in assertion
@TomNicholas
parametrize unaligned_zarr test fixture over zarr_format
cacf419
@TomNicholas
move parametrize_over_zarr_format decorator to apply to entire test c…
1a60ebe
…lass
@TomNicholas
for now explicitly consolidate metadata in test fixture
d98abe3
@TomNicholas
correct bug in writing of consolidated metadata
2dcefe4
TomNicholas
TomNicholas
commented
Mar 19, 2025
View reviewed changes
Comment threadxarray/backends/zarr.py
 kwargs = {}
 if _zarr_v3():
 # https://github.com/zarr-developers/zarr-python/pull/2113#issuecomment-2386718323
 kwargs["path"] = self.zarr_group.name.lstrip("/")
@TomNicholasTomNicholasMar 19, 2025•

edited

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FYI @TomAugspurger@jhamman and I are 95% sure that this line was unnecessary and a bug. It was causing consolidated metadata to not be written at the store root each time, and now that we changed it, it fixed various buggy behaviour we were seeing.
relevant to zarr-developers/zarr-python#2113 (comment)
@TomNicholas
TomNicholas
merged commit 94f0ddc
into
aladinor:dtree-zarrv3Mar 19, 2025
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@TomNicholas@ianhi

, '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
Fixes - #1
Merged
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Mar 19, 2025
Merged
Fixes#1
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Conversation
@TomNicholas
@TomNicholasTomNicholas
commented
Mar 17, 2025

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Collaborator
I couldn't work out how to get the permissions right so I've just opened this against your PR branch @aladinor. I plan to make some more changes tomorrow.
@TomNicholas
TomNicholas
changed the base branch from
main
to
dtree-zarrv3March 17, 2025 23:46
@TomNicholas
Merge branch 'dtree-zarrv3' into dtree-zarrv3-2
980ebb4
@TomNicholas
revert changes to test fixture
30f5bba
@TomNicholas
formatting
4d1fdb5
@TomNicholas
add decorator to parametrize over zarr formats
ecef578
@TomNicholas
ensure both versions of zarr-python and both versions of zarr-python …
c2a1f5f
…get tested
@TomNicholas
change datatree fixture to not produce values that would be fill_valu…
cde6b65
…es by default in zarr
@TomNicholas
refactor test to make expected behaviour clearer
09fad6e
@TomNicholas
fix wrongly expected behaviour - should not expect inherited variable…
77575b5
… to be written to zarr
@TomNicholas
make arrays no longer scalars to dodgepydata#10147
0a9f874
@TomNicholas
Merge branch 'dtree-zarrv3-2' ofhttps://github.com/TomNicholas/xarray…
565938b
…into dtree-zarrv3-2
@TomNicholas
fix bad merge
daf0f42
@TomNicholas
parametrize almost every test over zarr_format
84bde40
@TomNicholas
parametrize encoding test over zarr_formats
04d937c
@TomNicholas
use xfail in encoding test
765c5f0
@TomNicholas
updated expected behaviour of zarr on-disk in light ofpydata#10147
7eee31c
@TomNicholas
fully revert change to simple_datatree test fixture by considered zar…
0969422
…r's fill_value in assertion
@TomNicholas
parametrize unaligned_zarr test fixture over zarr_format
cacf419
@TomNicholas
move parametrize_over_zarr_format decorator to apply to entire test c…
1a60ebe
…lass
@TomNicholas
for now explicitly consolidate metadata in test fixture
d98abe3
@TomNicholas
correct bug in writing of consolidated metadata
2dcefe4
TomNicholas
TomNicholas
commented
Mar 19, 2025
View reviewed changes
Comment threadxarray/backends/zarr.py
 kwargs = {}
 if _zarr_v3():
 # https://github.com/zarr-developers/zarr-python/pull/2113#issuecomment-2386718323
 kwargs["path"] = self.zarr_group.name.lstrip("/")
@TomNicholasTomNicholasMar 19, 2025•

edited

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FYI @TomAugspurger@jhamman and I are 95% sure that this line was unnecessary and a bug. It was causing consolidated metadata to not be written at the store root each time, and now that we changed it, it fixed various buggy behaviour we were seeing.
relevant to zarr-developers/zarr-python#2113 (comment)
@TomNicholas
TomNicholas
merged commit 94f0ddc
into
aladinor:dtree-zarrv3Mar 19, 2025
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@TomNicholas@ianhi

, '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
Fixes - #1
Merged
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Mar 19, 2025
Merged
Fixes#1
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Conversation
@TomNicholas
@TomNicholasTomNicholas
commented
Mar 17, 2025

Copy link


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Collaborator
I couldn't work out how to get the permissions right so I've just opened this against your PR branch @aladinor. I plan to make some more changes tomorrow.
@TomNicholas
TomNicholas
changed the base branch from
main
to
dtree-zarrv3March 17, 2025 23:46
@TomNicholas
Merge branch 'dtree-zarrv3' into dtree-zarrv3-2
980ebb4
@TomNicholas
revert changes to test fixture
30f5bba
@TomNicholas
formatting
4d1fdb5
@TomNicholas
add decorator to parametrize over zarr formats
ecef578
@TomNicholas
ensure both versions of zarr-python and both versions of zarr-python …
c2a1f5f
…get tested
@TomNicholas
change datatree fixture to not produce values that would be fill_valu…
cde6b65
…es by default in zarr
@TomNicholas
refactor test to make expected behaviour clearer
09fad6e
@TomNicholas
fix wrongly expected behaviour - should not expect inherited variable…
77575b5
… to be written to zarr
@TomNicholas
make arrays no longer scalars to dodgepydata#10147
0a9f874
@TomNicholas
Merge branch 'dtree-zarrv3-2' ofhttps://github.com/TomNicholas/xarray…
565938b
…into dtree-zarrv3-2
@TomNicholas
fix bad merge
daf0f42
@TomNicholas
parametrize almost every test over zarr_format
84bde40
@TomNicholas
parametrize encoding test over zarr_formats
04d937c
@TomNicholas
use xfail in encoding test
765c5f0
@TomNicholas
updated expected behaviour of zarr on-disk in light ofpydata#10147
7eee31c
@TomNicholas
fully revert change to simple_datatree test fixture by considered zar…
0969422
…r's fill_value in assertion
@TomNicholas
parametrize unaligned_zarr test fixture over zarr_format
cacf419
@TomNicholas
move parametrize_over_zarr_format decorator to apply to entire test c…
1a60ebe
…lass
@TomNicholas
for now explicitly consolidate metadata in test fixture
d98abe3
@TomNicholas
correct bug in writing of consolidated metadata
2dcefe4
TomNicholas
TomNicholas
commented
Mar 19, 2025
View reviewed changes
Comment threadxarray/backends/zarr.py
 kwargs = {}
 if _zarr_v3():
 # https://github.com/zarr-developers/zarr-python/pull/2113#issuecomment-2386718323
 kwargs["path"] = self.zarr_group.name.lstrip("/")
@TomNicholasTomNicholasMar 19, 2025•

edited

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FYI @TomAugspurger@jhamman and I are 95% sure that this line was unnecessary and a bug. It was causing consolidated metadata to not be written at the store root each time, and now that we changed it, it fixed various buggy behaviour we were seeing.
relevant to zarr-developers/zarr-python#2113 (comment)
@TomNicholas
TomNicholas
merged commit 94f0ddc
into
aladinor:dtree-zarrv3Mar 19, 2025
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2 participants

@TomNicholas@ianhi

, '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
Fixes - #1
Merged
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Mar 19, 2025
Merged
Fixes#1
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Conversation
@TomNicholas
@TomNicholasTomNicholas
commented
Mar 17, 2025

Copy link


Copy Markdown

Collaborator
I couldn't work out how to get the permissions right so I've just opened this against your PR branch @aladinor. I plan to make some more changes tomorrow.
@TomNicholas
TomNicholas
changed the base branch from
main
to
dtree-zarrv3March 17, 2025 23:46
@TomNicholas
Merge branch 'dtree-zarrv3' into dtree-zarrv3-2
980ebb4
@TomNicholas
revert changes to test fixture
30f5bba
@TomNicholas
formatting
4d1fdb5
@TomNicholas
add decorator to parametrize over zarr formats
ecef578
@TomNicholas
ensure both versions of zarr-python and both versions of zarr-python …
c2a1f5f
…get tested
@TomNicholas
change datatree fixture to not produce values that would be fill_valu…
cde6b65
…es by default in zarr
@TomNicholas
refactor test to make expected behaviour clearer
09fad6e
@TomNicholas
fix wrongly expected behaviour - should not expect inherited variable…
77575b5
… to be written to zarr
@TomNicholas
make arrays no longer scalars to dodgepydata#10147
0a9f874
@TomNicholas
Merge branch 'dtree-zarrv3-2' ofhttps://github.com/TomNicholas/xarray…
565938b
…into dtree-zarrv3-2
@TomNicholas
fix bad merge
daf0f42
@TomNicholas
parametrize almost every test over zarr_format
84bde40
@TomNicholas
parametrize encoding test over zarr_formats
04d937c
@TomNicholas
use xfail in encoding test
765c5f0
@TomNicholas
updated expected behaviour of zarr on-disk in light ofpydata#10147
7eee31c
@TomNicholas
fully revert change to simple_datatree test fixture by considered zar…
0969422
…r's fill_value in assertion
@TomNicholas
parametrize unaligned_zarr test fixture over zarr_format
cacf419
@TomNicholas
move parametrize_over_zarr_format decorator to apply to entire test c…
1a60ebe
…lass
@TomNicholas
for now explicitly consolidate metadata in test fixture
d98abe3
@TomNicholas
correct bug in writing of consolidated metadata
2dcefe4
TomNicholas
TomNicholas
commented
Mar 19, 2025
View reviewed changes
Comment threadxarray/backends/zarr.py
 kwargs = {}
 if _zarr_v3():
 # https://github.com/zarr-developers/zarr-python/pull/2113#issuecomment-2386718323
 kwargs["path"] = self.zarr_group.name.lstrip("/")
@TomNicholasTomNicholasMar 19, 2025•

edited

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FYI @TomAugspurger@jhamman and I are 95% sure that this line was unnecessary and a bug. It was causing consolidated metadata to not be written at the store root each time, and now that we changed it, it fixed various buggy behaviour we were seeing.
relevant to zarr-developers/zarr-python#2113 (comment)
@TomNicholas
TomNicholas
merged commit 94f0ddc
into
aladinor:dtree-zarrv3Mar 19, 2025
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@TomNicholas@ianhi

, '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
Fixes - #1
Merged
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Mar 19, 2025
Merged
Fixes#1
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Conversation
@TomNicholas
@TomNicholasTomNicholas
commented
Mar 17, 2025

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I couldn't work out how to get the permissions right so I've just opened this against your PR branch @aladinor. I plan to make some more changes tomorrow.
@TomNicholas
TomNicholas
changed the base branch from
main
to
dtree-zarrv3March 17, 2025 23:46
@TomNicholas
Merge branch 'dtree-zarrv3' into dtree-zarrv3-2
980ebb4
@TomNicholas
revert changes to test fixture
30f5bba
@TomNicholas
formatting
4d1fdb5
@TomNicholas
add decorator to parametrize over zarr formats
ecef578
@TomNicholas
ensure both versions of zarr-python and both versions of zarr-python …
c2a1f5f
…get tested
@TomNicholas
change datatree fixture to not produce values that would be fill_valu…
cde6b65
…es by default in zarr
@TomNicholas
refactor test to make expected behaviour clearer
09fad6e
@TomNicholas
fix wrongly expected behaviour - should not expect inherited variable…
77575b5
… to be written to zarr
@TomNicholas
make arrays no longer scalars to dodgepydata#10147
0a9f874
@TomNicholas
Merge branch 'dtree-zarrv3-2' ofhttps://github.com/TomNicholas/xarray…
565938b
…into dtree-zarrv3-2
@TomNicholas
fix bad merge
daf0f42
@TomNicholas
parametrize almost every test over zarr_format
84bde40
@TomNicholas
parametrize encoding test over zarr_formats
04d937c
@TomNicholas
use xfail in encoding test
765c5f0
@TomNicholas
updated expected behaviour of zarr on-disk in light ofpydata#10147
7eee31c
@TomNicholas
fully revert change to simple_datatree test fixture by considered zar…
0969422
…r's fill_value in assertion
@TomNicholas
parametrize unaligned_zarr test fixture over zarr_format
cacf419
@TomNicholas
move parametrize_over_zarr_format decorator to apply to entire test c…
1a60ebe
…lass
@TomNicholas
for now explicitly consolidate metadata in test fixture
d98abe3
@TomNicholas
correct bug in writing of consolidated metadata
2dcefe4
TomNicholas
TomNicholas
commented
Mar 19, 2025
View reviewed changes
Comment threadxarray/backends/zarr.py
 kwargs = {}
 if _zarr_v3():
 # https://github.com/zarr-developers/zarr-python/pull/2113#issuecomment-2386718323
 kwargs["path"] = self.zarr_group.name.lstrip("/")
@TomNicholasTomNicholasMar 19, 2025•

edited

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FYI @TomAugspurger@jhamman and I are 95% sure that this line was unnecessary and a bug. It was causing consolidated metadata to not be written at the store root each time, and now that we changed it, it fixed various buggy behaviour we were seeing.
relevant to zarr-developers/zarr-python#2113 (comment)
@TomNicholas
TomNicholas
merged commit 94f0ddc
into
aladinor:dtree-zarrv3Mar 19, 2025
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2 participants

@TomNicholas@ianhi

, '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
Fixes - #1
Merged
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Mar 19, 2025
Merged
Fixes#1
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Conversation
@TomNicholas
@TomNicholasTomNicholas
commented
Mar 17, 2025

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Collaborator
I couldn't work out how to get the permissions right so I've just opened this against your PR branch @aladinor. I plan to make some more changes tomorrow.
@TomNicholas
TomNicholas
changed the base branch from
main
to
dtree-zarrv3March 17, 2025 23:46
@TomNicholas
Merge branch 'dtree-zarrv3' into dtree-zarrv3-2
980ebb4
@TomNicholas
revert changes to test fixture
30f5bba
@TomNicholas
formatting
4d1fdb5
@TomNicholas
add decorator to parametrize over zarr formats
ecef578
@TomNicholas
ensure both versions of zarr-python and both versions of zarr-python …
c2a1f5f
…get tested
@TomNicholas
change datatree fixture to not produce values that would be fill_valu…
cde6b65
…es by default in zarr
@TomNicholas
refactor test to make expected behaviour clearer
09fad6e
@TomNicholas
fix wrongly expected behaviour - should not expect inherited variable…
77575b5
… to be written to zarr
@TomNicholas
make arrays no longer scalars to dodgepydata#10147
0a9f874
@TomNicholas
Merge branch 'dtree-zarrv3-2' ofhttps://github.com/TomNicholas/xarray…
565938b
…into dtree-zarrv3-2
@TomNicholas
fix bad merge
daf0f42
@TomNicholas
parametrize almost every test over zarr_format
84bde40
@TomNicholas
parametrize encoding test over zarr_formats
04d937c
@TomNicholas
use xfail in encoding test
765c5f0
@TomNicholas
updated expected behaviour of zarr on-disk in light ofpydata#10147
7eee31c
@TomNicholas
fully revert change to simple_datatree test fixture by considered zar…
0969422
…r's fill_value in assertion
@TomNicholas
parametrize unaligned_zarr test fixture over zarr_format
cacf419
@TomNicholas
move parametrize_over_zarr_format decorator to apply to entire test c…
1a60ebe
…lass
@TomNicholas
for now explicitly consolidate metadata in test fixture
d98abe3
@TomNicholas
correct bug in writing of consolidated metadata
2dcefe4
TomNicholas
TomNicholas
commented
Mar 19, 2025
View reviewed changes
Comment threadxarray/backends/zarr.py
 kwargs = {}
 if _zarr_v3():
 # https://github.com/zarr-developers/zarr-python/pull/2113#issuecomment-2386718323
 kwargs["path"] = self.zarr_group.name.lstrip("/")
@TomNicholasTomNicholasMar 19, 2025•

edited

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FYI @TomAugspurger@jhamman and I are 95% sure that this line was unnecessary and a bug. It was causing consolidated metadata to not be written at the store root each time, and now that we changed it, it fixed various buggy behaviour we were seeing.
relevant to zarr-developers/zarr-python#2113 (comment)
@TomNicholas
TomNicholas
merged commit 94f0ddc
into
aladinor:dtree-zarrv3Mar 19, 2025
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2 participants

@TomNicholas@ianhi

, '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
Fixes - #1
Merged
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Mar 19, 2025
Merged
Fixes#1
TomNicholas merged 34 commits into
aladinor:dtree-zarrv3from 
TomNicholas:dtree-zarrv3-2
Conversation
@TomNicholas
@TomNicholasTomNicholas
commented
Mar 17, 2025

Copy link


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Collaborator
I couldn't work out how to get the permissions right so I've just opened this against your PR branch @aladinor. I plan to make some more changes tomorrow.
@TomNicholas
TomNicholas
changed the base branch from
main
to
dtree-zarrv3March 17, 2025 23:46
@TomNicholas
Merge branch 'dtree-zarrv3' into dtree-zarrv3-2
980ebb4
@TomNicholas
revert changes to test fixture
30f5bba
@TomNicholas
formatting
4d1fdb5
@TomNicholas
add decorator to parametrize over zarr formats
ecef578
@TomNicholas
ensure both versions of zarr-python and both versions of zarr-python …
c2a1f5f
…get tested
@TomNicholas
change datatree fixture to not produce values that would be fill_valu…
cde6b65
…es by default in zarr
@TomNicholas
refactor test to make expected behaviour clearer
09fad6e
@TomNicholas
fix wrongly expected behaviour - should not expect inherited variable…
77575b5
… to be written to zarr
@TomNicholas
make arrays no longer scalars to dodgepydata#10147
0a9f874
@TomNicholas
Merge branch 'dtree-zarrv3-2' ofhttps://github.com/TomNicholas/xarray…
565938b
…into dtree-zarrv3-2
@TomNicholas
fix bad merge
daf0f42
@TomNicholas
parametrize almost every test over zarr_format
84bde40
@TomNicholas
parametrize encoding test over zarr_formats
04d937c
@TomNicholas
use xfail in encoding test
765c5f0
@TomNicholas
updated expected behaviour of zarr on-disk in light ofpydata#10147
7eee31c
@TomNicholas
fully revert change to simple_datatree test fixture by considered zar…
0969422
…r's fill_value in assertion
@TomNicholas
parametrize unaligned_zarr test fixture over zarr_format
cacf419
@TomNicholas
move parametrize_over_zarr_format decorator to apply to entire test c…
1a60ebe
…lass
@TomNicholas
for now explicitly consolidate metadata in test fixture
d98abe3
@TomNicholas
correct bug in writing of consolidated metadata
2dcefe4
TomNicholas
TomNicholas
commented
Mar 19, 2025
View reviewed changes
Comment threadxarray/backends/zarr.py
 kwargs = {}
 if _zarr_v3():
 # https://github.com/zarr-developers/zarr-python/pull/2113#issuecomment-2386718323
 kwargs["path"] = self.zarr_group.name.lstrip("/")
@TomNicholasTomNicholasMar 19, 2025•

edited

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FYI @TomAugspurger@jhamman and I are 95% sure that this line was unnecessary and a bug. It was causing consolidated metadata to not be written at the store root each time, and now that we changed it, it fixed various buggy behaviour we were seeing.
relevant to zarr-developers/zarr-python#2113 (comment)
@TomNicholas
TomNicholas
merged commit 94f0ddc
into
aladinor:dtree-zarrv3Mar 19, 2025
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2 participants

@TomNicholas@ianhi