Default zarr.open to open_group if shape is not provided - #2158

Merged
jhamman merged 11 commits into
zarr-developers:v3from
agoodm:v3_open_group
Sep 27, 2024
Merged

Default zarr.open to open_group if shape is not provided#2158
jhamman merged 11 commits into
zarr-developers:v3from
agoodm:v3_open_group

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@agoodmagoodm commented Sep 8, 2024

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[Description of PR] Closes#2143

This change makes the v3 zarr.open more consistent with v2 by defaulting to open_group if shape isn't provided, which now allows for initializing a group in a non-existent path if mode="a".

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • GitHub Actions have all passed
  • Test coverage is 100% (Codecov passes)

jhamman
jhamman reviewed Sep 10, 2024
View reviewed changes
Comment threadtests/v3/test_api.py
agoodm
agoodm commented Sep 10, 2024
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Comment threadsrc/zarr/api/asynchronous.py Outdated
Comment threadtests/v3/test_api.py
@agoodm
agoodm requested a review from jhammanSeptember 12, 2024 18:03
jhamman
jhamman reviewed Sep 13, 2024
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Comment threadsrc/zarr/api/asynchronous.py Outdated
@jhammanjhamman added the V3 label Sep 13, 2024
@CzakiCzaki mentioned this pull request Sep 14, 2024
Merged
jni pushed a commit to napari/napari that referenced this pull request Sep 16, 2024
@Czaki
Blockzarr==3.0.0a4(#7271)
dd842a7
# References and relevant issues
closes#7270
# Description
as zarr-developers/zarr-python#2143 is not
resolved yet we need to block next alpha release. But there is
zarr-developers/zarr-python#2158 opened, so it
should be resolved shortly.
jhamman
jhamman approved these changes Sep 17, 2024
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This looks good @agoodm -- thanks for working out the logic in a clean way.

jhamman
jhamman reviewed Sep 27, 2024
View reviewed changes
Comment threadsrc/zarr/core/array.py Outdated
@jhamman
jhamman merged commit 1560d21 into zarr-developers:v3Sep 27, 2024
dcherian added a commit to dcherian/zarr-python that referenced this pull request Sep 27, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ae3bca5
* v3: (21 commits)
Default zarr.open to open_group if shape is not provided (zarr-developers#2158)
feat: metadata-only support for storage transformers metadata (zarr-developers#2180)
fix(async): set default concurrency to 10 tasks (zarr-developers#2256)
chore(deps): drop support for python 3.10 and numpy 1.24 (zarr-developers#2217)
feature(store): add LoggingStore wrapper (zarr-developers#2231)
Apply assorted ruff/flake8-simplify rules (SIM) (zarr-developers#2259)
Add array storage helpers (zarr-developers#2065)
Apply ruff/flake8-annotations rule ANN204 (zarr-developers#2258)
No need to run DeepSource any more - we use ruff (zarr-developers#2261)
Remove unnecessary lambda expression (zarr-developers#2260)
Enforce ruff/flake8-comprehensions rules (C4) (zarr-developers#2239)
Use `map(str, *)` in `test_accessed_chunks` (zarr-developers#2229)
Replace Gitter with Zulip (zarr-developers#2254)
Enforce ruff/flake8-pytest-style rules (PT) (zarr-developers#2236)
Fix multiple identical imports (zarr-developers#2241)
Enforce ruff/flake8-return rules (RET) (zarr-developers#2237)
Enforce ruff/flynt rules (FLY) (zarr-developers#2240)
Fix fill_value handling for complex dtypes (zarr-developers#2200)
Update V2 codec pipeline to use concrete classes (zarr-developers#2244)
Apply and enforce more ruff rules (zarr-developers#2053)
...
@psobolewskiPhDpsobolewskiPhD mentioned this pull request Sep 28, 2024
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@CzakiCzaki mentioned this pull request Oct 8, 2024
Closed
@jhammanjhamman added this to the 3.0.0.beta milestone Oct 17, 2024
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zarr.open do not allow creating group file [v3]

3 participants

@agoodm@jhamman@dstansby
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
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})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Default zarr.open to open_group if shape is not provided - #2158
Merged
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Sep 27, 2024
Merged
Default zarr.open to open_group if shape is not provided#2158
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Conversation
@agoodm
@agoodmagoodm
commented
Sep 8, 2024

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[Description of PR] Closes#2143
This change makes the v3 zarr.open more consistent with v2 by defaulting to open_group if shape isn't provided, which now allows for initializing a group in a non-existent path if mode="a".
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
jhamman
jhamman
reviewed
Sep 10, 2024
View reviewed changes
Comment threadtests/v3/test_api.py
agoodm
agoodm
commented
Sep 10, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

Comment threadtests/v3/test_api.py
@agoodm
agoodm
requested a review
from jhammanSeptember 12, 2024 18:03
jhamman
jhamman
reviewed
Sep 13, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

@jhammanjhamman
added
the 
V3

label
Sep 13, 2024
@CzakiCzaki
mentioned this pull request
Sep 14, 2024
 Merged

jni pushed a commit
to napari/napari
that referenced
this pull request
Sep 16, 2024
@Czaki
Blockzarr==3.0.0a4(#7271)
dd842a7
# References and relevant issues
closes#7270
# Description
as zarr-developers/zarr-python#2143 is not
resolved yet we need to block next alpha release. But there is
zarr-developers/zarr-python#2158 opened, so it
should be resolved shortly.
jhamman
jhamman
approved these changes
Sep 17, 2024
View reviewed changes
@jhammanjhamman
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This looks good @agoodm -- thanks for working out the logic in a clean way.
jhamman
jhamman
reviewed
Sep 27, 2024
View reviewed changes
Comment threadsrc/zarr/core/array.py
Outdated

@jhamman
jhamman
merged commit 1560d21
into
zarr-developers:v3Sep 27, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 27, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ae3bca5
* v3: (21 commits)
Default zarr.open to open_group if shape is not provided (zarr-developers#2158)
feat: metadata-only support for storage transformers metadata (zarr-developers#2180)
fix(async): set default concurrency to 10 tasks (zarr-developers#2256)
chore(deps): drop support for python 3.10 and numpy 1.24 (zarr-developers#2217)
feature(store): add LoggingStore wrapper (zarr-developers#2231)
Apply assorted ruff/flake8-simplify rules (SIM) (zarr-developers#2259)
Add array storage helpers (zarr-developers#2065)
Apply ruff/flake8-annotations rule ANN204 (zarr-developers#2258)
No need to run DeepSource any more - we use ruff (zarr-developers#2261)
Remove unnecessary lambda expression (zarr-developers#2260)
Enforce ruff/flake8-comprehensions rules (C4) (zarr-developers#2239)
Use `map(str, *)` in `test_accessed_chunks` (zarr-developers#2229)
Replace Gitter with Zulip (zarr-developers#2254)
Enforce ruff/flake8-pytest-style rules (PT) (zarr-developers#2236)
Fix multiple identical imports (zarr-developers#2241)
Enforce ruff/flake8-return rules (RET) (zarr-developers#2237)
Enforce ruff/flynt rules (FLY) (zarr-developers#2240)
Fix fill_value handling for complex dtypes (zarr-developers#2200)
Update V2 codec pipeline to use concrete classes (zarr-developers#2244)
Apply and enforce more ruff rules (zarr-developers#2053)
...
@psobolewskiPhDpsobolewskiPhD
mentioned this pull request
Sep 28, 2024
 Merged

@CzakiCzaki
mentioned this pull request
Oct 8, 2024

Closed

@jhammanjhamman
added this to the 3.0.0.beta milestone
Oct 17, 2024
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zarr.open do not allow creating group file [v3]


3 participants

@agoodm@jhamman@dstansby

, '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");
}
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Default zarr.open to open_group if shape is not provided - #2158
Merged
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Sep 27, 2024
Merged
Default zarr.open to open_group if shape is not provided#2158
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Conversation
@agoodm
@agoodmagoodm
commented
Sep 8, 2024

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[Description of PR] Closes#2143
This change makes the v3 zarr.open more consistent with v2 by defaulting to open_group if shape isn't provided, which now allows for initializing a group in a non-existent path if mode="a".
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
jhamman
jhamman
reviewed
Sep 10, 2024
View reviewed changes
Comment threadtests/v3/test_api.py
agoodm
agoodm
commented
Sep 10, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

Comment threadtests/v3/test_api.py
@agoodm
agoodm
requested a review
from jhammanSeptember 12, 2024 18:03
jhamman
jhamman
reviewed
Sep 13, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

@jhammanjhamman
added
the 
V3

label
Sep 13, 2024
@CzakiCzaki
mentioned this pull request
Sep 14, 2024
 Merged

jni pushed a commit
to napari/napari
that referenced
this pull request
Sep 16, 2024
@Czaki
Blockzarr==3.0.0a4(#7271)
dd842a7
# References and relevant issues
closes#7270
# Description
as zarr-developers/zarr-python#2143 is not
resolved yet we need to block next alpha release. But there is
zarr-developers/zarr-python#2158 opened, so it
should be resolved shortly.
jhamman
jhamman
approved these changes
Sep 17, 2024
View reviewed changes
@jhammanjhamman
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This looks good @agoodm -- thanks for working out the logic in a clean way.
jhamman
jhamman
reviewed
Sep 27, 2024
View reviewed changes
Comment threadsrc/zarr/core/array.py
Outdated

@jhamman
jhamman
merged commit 1560d21
into
zarr-developers:v3Sep 27, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 27, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ae3bca5
* v3: (21 commits)
Default zarr.open to open_group if shape is not provided (zarr-developers#2158)
feat: metadata-only support for storage transformers metadata (zarr-developers#2180)
fix(async): set default concurrency to 10 tasks (zarr-developers#2256)
chore(deps): drop support for python 3.10 and numpy 1.24 (zarr-developers#2217)
feature(store): add LoggingStore wrapper (zarr-developers#2231)
Apply assorted ruff/flake8-simplify rules (SIM) (zarr-developers#2259)
Add array storage helpers (zarr-developers#2065)
Apply ruff/flake8-annotations rule ANN204 (zarr-developers#2258)
No need to run DeepSource any more - we use ruff (zarr-developers#2261)
Remove unnecessary lambda expression (zarr-developers#2260)
Enforce ruff/flake8-comprehensions rules (C4) (zarr-developers#2239)
Use `map(str, *)` in `test_accessed_chunks` (zarr-developers#2229)
Replace Gitter with Zulip (zarr-developers#2254)
Enforce ruff/flake8-pytest-style rules (PT) (zarr-developers#2236)
Fix multiple identical imports (zarr-developers#2241)
Enforce ruff/flake8-return rules (RET) (zarr-developers#2237)
Enforce ruff/flynt rules (FLY) (zarr-developers#2240)
Fix fill_value handling for complex dtypes (zarr-developers#2200)
Update V2 codec pipeline to use concrete classes (zarr-developers#2244)
Apply and enforce more ruff rules (zarr-developers#2053)
...
@psobolewskiPhDpsobolewskiPhD
mentioned this pull request
Sep 28, 2024
 Merged

@CzakiCzaki
mentioned this pull request
Oct 8, 2024

Closed

@jhammanjhamman
added this to the 3.0.0.beta milestone
Oct 17, 2024
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Status: Done


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zarr.open do not allow creating group file [v3]


3 participants

@agoodm@jhamman@dstansby

, '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");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Default zarr.open to open_group if shape is not provided - #2158
Merged
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Sep 27, 2024
Merged
Default zarr.open to open_group if shape is not provided#2158
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Conversation
@agoodm
@agoodmagoodm
commented
Sep 8, 2024

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[Description of PR] Closes#2143
This change makes the v3 zarr.open more consistent with v2 by defaulting to open_group if shape isn't provided, which now allows for initializing a group in a non-existent path if mode="a".
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
jhamman
jhamman
reviewed
Sep 10, 2024
View reviewed changes
Comment threadtests/v3/test_api.py
agoodm
agoodm
commented
Sep 10, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

Comment threadtests/v3/test_api.py
@agoodm
agoodm
requested a review
from jhammanSeptember 12, 2024 18:03
jhamman
jhamman
reviewed
Sep 13, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

@jhammanjhamman
added
the 
V3

label
Sep 13, 2024
@CzakiCzaki
mentioned this pull request
Sep 14, 2024
 Merged

jni pushed a commit
to napari/napari
that referenced
this pull request
Sep 16, 2024
@Czaki
Blockzarr==3.0.0a4(#7271)
dd842a7
# References and relevant issues
closes#7270
# Description
as zarr-developers/zarr-python#2143 is not
resolved yet we need to block next alpha release. But there is
zarr-developers/zarr-python#2158 opened, so it
should be resolved shortly.
jhamman
jhamman
approved these changes
Sep 17, 2024
View reviewed changes
@jhammanjhamman
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This looks good @agoodm -- thanks for working out the logic in a clean way.
jhamman
jhamman
reviewed
Sep 27, 2024
View reviewed changes
Comment threadsrc/zarr/core/array.py
Outdated

@jhamman
jhamman
merged commit 1560d21
into
zarr-developers:v3Sep 27, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 27, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ae3bca5
* v3: (21 commits)
Default zarr.open to open_group if shape is not provided (zarr-developers#2158)
feat: metadata-only support for storage transformers metadata (zarr-developers#2180)
fix(async): set default concurrency to 10 tasks (zarr-developers#2256)
chore(deps): drop support for python 3.10 and numpy 1.24 (zarr-developers#2217)
feature(store): add LoggingStore wrapper (zarr-developers#2231)
Apply assorted ruff/flake8-simplify rules (SIM) (zarr-developers#2259)
Add array storage helpers (zarr-developers#2065)
Apply ruff/flake8-annotations rule ANN204 (zarr-developers#2258)
No need to run DeepSource any more - we use ruff (zarr-developers#2261)
Remove unnecessary lambda expression (zarr-developers#2260)
Enforce ruff/flake8-comprehensions rules (C4) (zarr-developers#2239)
Use `map(str, *)` in `test_accessed_chunks` (zarr-developers#2229)
Replace Gitter with Zulip (zarr-developers#2254)
Enforce ruff/flake8-pytest-style rules (PT) (zarr-developers#2236)
Fix multiple identical imports (zarr-developers#2241)
Enforce ruff/flake8-return rules (RET) (zarr-developers#2237)
Enforce ruff/flynt rules (FLY) (zarr-developers#2240)
Fix fill_value handling for complex dtypes (zarr-developers#2200)
Update V2 codec pipeline to use concrete classes (zarr-developers#2244)
Apply and enforce more ruff rules (zarr-developers#2053)
...
@psobolewskiPhDpsobolewskiPhD
mentioned this pull request
Sep 28, 2024
 Merged

@CzakiCzaki
mentioned this pull request
Oct 8, 2024

Closed

@jhammanjhamman
added this to the 3.0.0.beta milestone
Oct 17, 2024
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Zarr-Python - 3.0

Status: Done


Milestone

3.0.0.beta

Development

Successfully merging this pull request may close these issues.
zarr.open do not allow creating group file [v3]


3 participants

@agoodm@jhamman@dstansby

, '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
Default zarr.open to open_group if shape is not provided - #2158
Merged
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Sep 27, 2024
Merged
Default zarr.open to open_group if shape is not provided#2158
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Conversation
@agoodm
@agoodmagoodm
commented
Sep 8, 2024

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[Description of PR] Closes#2143
This change makes the v3 zarr.open more consistent with v2 by defaulting to open_group if shape isn't provided, which now allows for initializing a group in a non-existent path if mode="a".
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
jhamman
jhamman
reviewed
Sep 10, 2024
View reviewed changes
Comment threadtests/v3/test_api.py
agoodm
agoodm
commented
Sep 10, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

Comment threadtests/v3/test_api.py
@agoodm
agoodm
requested a review
from jhammanSeptember 12, 2024 18:03
jhamman
jhamman
reviewed
Sep 13, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

@jhammanjhamman
added
the 
V3

label
Sep 13, 2024
@CzakiCzaki
mentioned this pull request
Sep 14, 2024
 Merged

jni pushed a commit
to napari/napari
that referenced
this pull request
Sep 16, 2024
@Czaki
Blockzarr==3.0.0a4(#7271)
dd842a7
# References and relevant issues
closes#7270
# Description
as zarr-developers/zarr-python#2143 is not
resolved yet we need to block next alpha release. But there is
zarr-developers/zarr-python#2158 opened, so it
should be resolved shortly.
jhamman
jhamman
approved these changes
Sep 17, 2024
View reviewed changes
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This looks good @agoodm -- thanks for working out the logic in a clean way.
jhamman
jhamman
reviewed
Sep 27, 2024
View reviewed changes
Comment threadsrc/zarr/core/array.py
Outdated

@jhamman
jhamman
merged commit 1560d21
into
zarr-developers:v3Sep 27, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 27, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ae3bca5
* v3: (21 commits)
Default zarr.open to open_group if shape is not provided (zarr-developers#2158)
feat: metadata-only support for storage transformers metadata (zarr-developers#2180)
fix(async): set default concurrency to 10 tasks (zarr-developers#2256)
chore(deps): drop support for python 3.10 and numpy 1.24 (zarr-developers#2217)
feature(store): add LoggingStore wrapper (zarr-developers#2231)
Apply assorted ruff/flake8-simplify rules (SIM) (zarr-developers#2259)
Add array storage helpers (zarr-developers#2065)
Apply ruff/flake8-annotations rule ANN204 (zarr-developers#2258)
No need to run DeepSource any more - we use ruff (zarr-developers#2261)
Remove unnecessary lambda expression (zarr-developers#2260)
Enforce ruff/flake8-comprehensions rules (C4) (zarr-developers#2239)
Use `map(str, *)` in `test_accessed_chunks` (zarr-developers#2229)
Replace Gitter with Zulip (zarr-developers#2254)
Enforce ruff/flake8-pytest-style rules (PT) (zarr-developers#2236)
Fix multiple identical imports (zarr-developers#2241)
Enforce ruff/flake8-return rules (RET) (zarr-developers#2237)
Enforce ruff/flynt rules (FLY) (zarr-developers#2240)
Fix fill_value handling for complex dtypes (zarr-developers#2200)
Update V2 codec pipeline to use concrete classes (zarr-developers#2244)
Apply and enforce more ruff rules (zarr-developers#2053)
...
@psobolewskiPhDpsobolewskiPhD
mentioned this pull request
Sep 28, 2024
 Merged

@CzakiCzaki
mentioned this pull request
Oct 8, 2024

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@jhammanjhamman
added this to the 3.0.0.beta milestone
Oct 17, 2024
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Zarr-Python - 3.0

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zarr.open do not allow creating group file [v3]


3 participants

@agoodm@jhamman@dstansby

, '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
Default zarr.open to open_group if shape is not provided - #2158
Merged
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Sep 27, 2024
Merged
Default zarr.open to open_group if shape is not provided#2158
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Conversation
@agoodm
@agoodmagoodm
commented
Sep 8, 2024

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[Description of PR] Closes#2143
This change makes the v3 zarr.open more consistent with v2 by defaulting to open_group if shape isn't provided, which now allows for initializing a group in a non-existent path if mode="a".
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
jhamman
jhamman
reviewed
Sep 10, 2024
View reviewed changes
Comment threadtests/v3/test_api.py
agoodm
agoodm
commented
Sep 10, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

Comment threadtests/v3/test_api.py
@agoodm
agoodm
requested a review
from jhammanSeptember 12, 2024 18:03
jhamman
jhamman
reviewed
Sep 13, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

@jhammanjhamman
added
the 
V3

label
Sep 13, 2024
@CzakiCzaki
mentioned this pull request
Sep 14, 2024
 Merged

jni pushed a commit
to napari/napari
that referenced
this pull request
Sep 16, 2024
@Czaki
Blockzarr==3.0.0a4(#7271)
dd842a7
# References and relevant issues
closes#7270
# Description
as zarr-developers/zarr-python#2143 is not
resolved yet we need to block next alpha release. But there is
zarr-developers/zarr-python#2158 opened, so it
should be resolved shortly.
jhamman
jhamman
approved these changes
Sep 17, 2024
View reviewed changes
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This looks good @agoodm -- thanks for working out the logic in a clean way.
jhamman
jhamman
reviewed
Sep 27, 2024
View reviewed changes
Comment threadsrc/zarr/core/array.py
Outdated

@jhamman
jhamman
merged commit 1560d21
into
zarr-developers:v3Sep 27, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 27, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ae3bca5
* v3: (21 commits)
Default zarr.open to open_group if shape is not provided (zarr-developers#2158)
feat: metadata-only support for storage transformers metadata (zarr-developers#2180)
fix(async): set default concurrency to 10 tasks (zarr-developers#2256)
chore(deps): drop support for python 3.10 and numpy 1.24 (zarr-developers#2217)
feature(store): add LoggingStore wrapper (zarr-developers#2231)
Apply assorted ruff/flake8-simplify rules (SIM) (zarr-developers#2259)
Add array storage helpers (zarr-developers#2065)
Apply ruff/flake8-annotations rule ANN204 (zarr-developers#2258)
No need to run DeepSource any more - we use ruff (zarr-developers#2261)
Remove unnecessary lambda expression (zarr-developers#2260)
Enforce ruff/flake8-comprehensions rules (C4) (zarr-developers#2239)
Use `map(str, *)` in `test_accessed_chunks` (zarr-developers#2229)
Replace Gitter with Zulip (zarr-developers#2254)
Enforce ruff/flake8-pytest-style rules (PT) (zarr-developers#2236)
Fix multiple identical imports (zarr-developers#2241)
Enforce ruff/flake8-return rules (RET) (zarr-developers#2237)
Enforce ruff/flynt rules (FLY) (zarr-developers#2240)
Fix fill_value handling for complex dtypes (zarr-developers#2200)
Update V2 codec pipeline to use concrete classes (zarr-developers#2244)
Apply and enforce more ruff rules (zarr-developers#2053)
...
@psobolewskiPhDpsobolewskiPhD
mentioned this pull request
Sep 28, 2024
 Merged

@CzakiCzaki
mentioned this pull request
Oct 8, 2024

Closed

@jhammanjhamman
added this to the 3.0.0.beta milestone
Oct 17, 2024
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Zarr-Python - 3.0

Status: Done


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3.0.0.beta

Development

Successfully merging this pull request may close these issues.
zarr.open do not allow creating group file [v3]


3 participants

@agoodm@jhamman@dstansby

, '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
Default zarr.open to open_group if shape is not provided - #2158
Merged
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Sep 27, 2024
Merged
Default zarr.open to open_group if shape is not provided#2158
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Conversation
@agoodm
@agoodmagoodm
commented
Sep 8, 2024

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[Description of PR] Closes#2143
This change makes the v3 zarr.open more consistent with v2 by defaulting to open_group if shape isn't provided, which now allows for initializing a group in a non-existent path if mode="a".
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
jhamman
jhamman
reviewed
Sep 10, 2024
View reviewed changes
Comment threadtests/v3/test_api.py
agoodm
agoodm
commented
Sep 10, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

Comment threadtests/v3/test_api.py
@agoodm
agoodm
requested a review
from jhammanSeptember 12, 2024 18:03
jhamman
jhamman
reviewed
Sep 13, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

@jhammanjhamman
added
the 
V3

label
Sep 13, 2024
@CzakiCzaki
mentioned this pull request
Sep 14, 2024
 Merged

jni pushed a commit
to napari/napari
that referenced
this pull request
Sep 16, 2024
@Czaki
Blockzarr==3.0.0a4(#7271)
dd842a7
# References and relevant issues
closes#7270
# Description
as zarr-developers/zarr-python#2143 is not
resolved yet we need to block next alpha release. But there is
zarr-developers/zarr-python#2158 opened, so it
should be resolved shortly.
jhamman
jhamman
approved these changes
Sep 17, 2024
View reviewed changes
@jhammanjhamman
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This looks good @agoodm -- thanks for working out the logic in a clean way.
jhamman
jhamman
reviewed
Sep 27, 2024
View reviewed changes
Comment threadsrc/zarr/core/array.py
Outdated

@jhamman
jhamman
merged commit 1560d21
into
zarr-developers:v3Sep 27, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 27, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ae3bca5
* v3: (21 commits)
Default zarr.open to open_group if shape is not provided (zarr-developers#2158)
feat: metadata-only support for storage transformers metadata (zarr-developers#2180)
fix(async): set default concurrency to 10 tasks (zarr-developers#2256)
chore(deps): drop support for python 3.10 and numpy 1.24 (zarr-developers#2217)
feature(store): add LoggingStore wrapper (zarr-developers#2231)
Apply assorted ruff/flake8-simplify rules (SIM) (zarr-developers#2259)
Add array storage helpers (zarr-developers#2065)
Apply ruff/flake8-annotations rule ANN204 (zarr-developers#2258)
No need to run DeepSource any more - we use ruff (zarr-developers#2261)
Remove unnecessary lambda expression (zarr-developers#2260)
Enforce ruff/flake8-comprehensions rules (C4) (zarr-developers#2239)
Use `map(str, *)` in `test_accessed_chunks` (zarr-developers#2229)
Replace Gitter with Zulip (zarr-developers#2254)
Enforce ruff/flake8-pytest-style rules (PT) (zarr-developers#2236)
Fix multiple identical imports (zarr-developers#2241)
Enforce ruff/flake8-return rules (RET) (zarr-developers#2237)
Enforce ruff/flynt rules (FLY) (zarr-developers#2240)
Fix fill_value handling for complex dtypes (zarr-developers#2200)
Update V2 codec pipeline to use concrete classes (zarr-developers#2244)
Apply and enforce more ruff rules (zarr-developers#2053)
...
@psobolewskiPhDpsobolewskiPhD
mentioned this pull request
Sep 28, 2024
 Merged

@CzakiCzaki
mentioned this pull request
Oct 8, 2024

Closed

@jhammanjhamman
added this to the 3.0.0.beta milestone
Oct 17, 2024
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@jhammanjhammanjhamman approved these changes

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@dstansbydstansbydstansby left review comments
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Projects

Zarr-Python - 3.0

Status: Done


Milestone

3.0.0.beta

Development

Successfully merging this pull request may close these issues.
zarr.open do not allow creating group file [v3]


3 participants

@agoodm@jhamman@dstansby

, '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
Default zarr.open to open_group if shape is not provided - #2158
Merged
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Sep 27, 2024
Merged
Default zarr.open to open_group if shape is not provided#2158
jhamman merged 11 commits into
zarr-developers:v3from 
agoodm:v3_open_group
Conversation
@agoodm
@agoodmagoodm
commented
Sep 8, 2024

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[Description of PR] Closes#2143
This change makes the v3 zarr.open more consistent with v2 by defaulting to open_group if shape isn't provided, which now allows for initializing a group in a non-existent path if mode="a".
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
jhamman
jhamman
reviewed
Sep 10, 2024
View reviewed changes
Comment threadtests/v3/test_api.py
agoodm
agoodm
commented
Sep 10, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

Comment threadtests/v3/test_api.py
@agoodm
agoodm
requested a review
from jhammanSeptember 12, 2024 18:03
jhamman
jhamman
reviewed
Sep 13, 2024
View reviewed changes
Comment threadsrc/zarr/api/asynchronous.py
Outdated

@jhammanjhamman
added
the 
V3

label
Sep 13, 2024
@CzakiCzaki
mentioned this pull request
Sep 14, 2024
 Merged

jni pushed a commit
to napari/napari
that referenced
this pull request
Sep 16, 2024
@Czaki
Blockzarr==3.0.0a4(#7271)
dd842a7
# References and relevant issues
closes#7270
# Description
as zarr-developers/zarr-python#2143 is not
resolved yet we need to block next alpha release. But there is
zarr-developers/zarr-python#2158 opened, so it
should be resolved shortly.
jhamman
jhamman
approved these changes
Sep 17, 2024
View reviewed changes
@jhammanjhamman
left a comment


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This looks good @agoodm -- thanks for working out the logic in a clean way.
jhamman
jhamman
reviewed
Sep 27, 2024
View reviewed changes
Comment threadsrc/zarr/core/array.py
Outdated

@jhamman
jhamman
merged commit 1560d21
into
zarr-developers:v3Sep 27, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 27, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ae3bca5
* v3: (21 commits)
Default zarr.open to open_group if shape is not provided (zarr-developers#2158)
feat: metadata-only support for storage transformers metadata (zarr-developers#2180)
fix(async): set default concurrency to 10 tasks (zarr-developers#2256)
chore(deps): drop support for python 3.10 and numpy 1.24 (zarr-developers#2217)
feature(store): add LoggingStore wrapper (zarr-developers#2231)
Apply assorted ruff/flake8-simplify rules (SIM) (zarr-developers#2259)
Add array storage helpers (zarr-developers#2065)
Apply ruff/flake8-annotations rule ANN204 (zarr-developers#2258)
No need to run DeepSource any more - we use ruff (zarr-developers#2261)
Remove unnecessary lambda expression (zarr-developers#2260)
Enforce ruff/flake8-comprehensions rules (C4) (zarr-developers#2239)
Use `map(str, *)` in `test_accessed_chunks` (zarr-developers#2229)
Replace Gitter with Zulip (zarr-developers#2254)
Enforce ruff/flake8-pytest-style rules (PT) (zarr-developers#2236)
Fix multiple identical imports (zarr-developers#2241)
Enforce ruff/flake8-return rules (RET) (zarr-developers#2237)
Enforce ruff/flynt rules (FLY) (zarr-developers#2240)
Fix fill_value handling for complex dtypes (zarr-developers#2200)
Update V2 codec pipeline to use concrete classes (zarr-developers#2244)
Apply and enforce more ruff rules (zarr-developers#2053)
...
@psobolewskiPhDpsobolewskiPhD
mentioned this pull request
Sep 28, 2024
 Merged

@CzakiCzaki
mentioned this pull request
Oct 8, 2024

Closed

@jhammanjhamman
added this to the 3.0.0.beta milestone
Oct 17, 2024
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@jhammanjhammanjhamman approved these changes

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Zarr-Python - 3.0

Status: Done


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3.0.0.beta

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Successfully merging this pull request may close these issues.
zarr.open do not allow creating group file [v3]


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