Accept dictionaries for store argument - #2164

Merged
jhamman merged 3 commits into
zarr-developers:v3from
TomAugspurger:feature/dict-store
Sep 12, 2024
Merged

Accept dictionaries for store argument#2164
jhamman merged 3 commits into
zarr-developers:v3from
TomAugspurger:feature/dict-store

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@TomAugspurger

@TomAugspurgerTomAugspurger commented Sep 9, 2024•
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This updates how we handle a plain dictionary provided to open_group and friends so that the following works:

group = await zarr.api.asynchronous.open_group(store={}, mode="w")

The dictionary is interpreted as the store_dict argument of zarr.store.MemoryStore. This effectively mirrors the behavior of zarr-python v2, and I think doesn't introduce an ambiguity. Previously a TypeError was raised.

This change will make it slightly easier to get xarray's test suite running with zarr v3.

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 commented Sep 11, 2024

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After thinking a bit more about this, I'm a bit concerned that we may not be ready for a generic MutableMapping in the MemoryStore. What would happen if we tossed a zict.LMDB into the constructor? I suspect things would mostly work but maybe not?

@TomAugspurger

TomAugspurger commented Sep 11, 2024

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I'm not sure how much faith to put in it, but the fact that mypy allows it gives me some comfort.

@d-v-b

d-v-b commented Sep 11, 2024

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If we accept anything that implements MutableMapping here, then there's no guarantee that the store is actually in memory, since the __getitem__ and __setitem__ operations could be running arbitrary IO-ful code. This seems fine with me, as long as users know what they are getting into, and maybe a useful bridge for users who want some v2-style store behavior (but maybe a better name for the store would be MutableMappingStore?)

@TomAugspurger

TomAugspurger commented Sep 11, 2024

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Ah, I see, the concern is specifically around the isinstance at https://github.com/zarr-developers/zarr-python/pull/2164/files#diff-9a2583a58394683284176a2d2db4df1e8ffafce4f34edc7a176c625863815518R99.

In that case, yes, I think we should narrow it to just accept dictionaries, where there's no ambiguity about whether a MemoryStore is appropriate.

@jhamman
jhamman merged commit c62294e into zarr-developers:v3Sep 12, 2024
dcherian added a commit to dcherian/zarr-python that referenced this pull request Sep 16, 2024
@dcherian
Merge branch 'v3' into fix-hypothesis-complex-warning
a8de6d6
* v3:
fix: opening a group with unspecified format finds either v2 or v3 (zarr-developers#2183)
test: check that store, array, and group classes are serializable (zarr-developers#2006)
feature(store): V3 ZipStore (zarr-developers#2078)
More typing fixes for tests (zarr-developers#2173)
refactor: split metadata into v2 and v3 modules (zarr-developers#2163)
Accept dictionaries for `store` argument (zarr-developers#2164)
Simplify mypy config for tests (zarr-developers#2156)
Fixed path segment duplication in open_array (zarr-developers#2167)
Fixed test warnings (zarr-developers#2168)
chore: update pre-commit hooks (zarr-developers#2165)
Ensure that store_dict used for empty dicts (zarr-developers#2162)
Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (zarr-developers#2160)
dstansby pushed a commit to dstansby/zarr-python that referenced this pull request Sep 17, 2024
@TomAugspurger@dstansby
Accept dictionaries forstoreargument (zarr-developers#2164)
29b83f0
* Accept dictionaries for `store`
* fixup doc build warnings
* Only support dictionaries
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@TomAugspurger@jhamman@d-v-b
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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})();
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try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Accept dictionaries for store argument - #2164
Merged
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Sep 12, 2024
Merged
Accept dictionaries for store argument#2164
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Conversation
@TomAugspurger
@TomAugspurgerTomAugspurger
commented
Sep 9, 2024•

edited

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This updates how we handle a plain dictionary provided to open_group and friends so that the following works:
group = await zarr.api.asynchronous.open_group(store={}, mode="w")
The dictionary is interpreted as the store_dict argument of zarr.store.MemoryStore. This effectively mirrors the behavior of zarr-python v2, and I think doesn't introduce an ambiguity. Previously a TypeError was raised.
This change will make it slightly easier to get xarray's test suite running with zarr v3.
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
commented
Sep 11, 2024

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After thinking a bit more about this, I'm a bit concerned that we may not be ready for a generic MutableMapping in the MemoryStore. What would happen if we tossed a zict.LMDB into the constructor? I suspect things would mostly work but maybe not?
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

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I'm not sure how much faith to put in it, but the fact that mypy allows it gives me some comfort.
@d-v-b
d-v-b
commented
Sep 11, 2024

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If we accept anything that implements MutableMapping here, then there's no guarantee that the store is actually in memory, since the __getitem__ and __setitem__ operations could be running arbitrary IO-ful code. This seems fine with me, as long as users know what they are getting into, and maybe a useful bridge for users who want some v2-style store behavior (but maybe a better name for the store would be MutableMappingStore?)
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

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Ah, I see, the concern is specifically around the isinstance at https://github.com/zarr-developers/zarr-python/pull/2164/files#diff-9a2583a58394683284176a2d2db4df1e8ffafce4f34edc7a176c625863815518R99.
In that case, yes, I think we should narrow it to just accept dictionaries, where there's no ambiguity about whether a MemoryStore is appropriate.
@jhamman
jhamman
merged commit c62294e
into
zarr-developers:v3Sep 12, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 16, 2024
@dcherian
Merge branch 'v3' into fix-hypothesis-complex-warning
a8de6d6
* v3:
fix: opening a group with unspecified format finds either v2 or v3 (zarr-developers#2183)
test: check that store, array, and group classes are serializable (zarr-developers#2006)
feature(store): V3 ZipStore (zarr-developers#2078)
More typing fixes for tests (zarr-developers#2173)
refactor: split metadata into v2 and v3 modules (zarr-developers#2163)
Accept dictionaries for `store` argument (zarr-developers#2164)
Simplify mypy config for tests (zarr-developers#2156)
Fixed path segment duplication in open_array (zarr-developers#2167)
Fixed test warnings (zarr-developers#2168)
chore: update pre-commit hooks (zarr-developers#2165)
Ensure that store_dict used for empty dicts (zarr-developers#2162)
Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (zarr-developers#2160)
dstansby pushed a commit
to dstansby/zarr-python
that referenced
this pull request
Sep 17, 2024
@TomAugspurger@dstansby
Accept dictionaries forstoreargument (zarr-developers#2164)
29b83f0
* Accept dictionaries for `store`
* fixup doc build warnings
* Only support dictionaries
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@TomAugspurger@jhamman@d-v-b

, 'i');
if (__m === '*' || __re.test(location.href)) {
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Accept dictionaries for store argument - #2164
Merged
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Sep 12, 2024
Merged
Accept dictionaries for store argument#2164
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Conversation
@TomAugspurger
@TomAugspurgerTomAugspurger
commented
Sep 9, 2024•

edited

Loading

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Contributor
This updates how we handle a plain dictionary provided to open_group and friends so that the following works:
group = await zarr.api.asynchronous.open_group(store={}, mode="w")
The dictionary is interpreted as the store_dict argument of zarr.store.MemoryStore. This effectively mirrors the behavior of zarr-python v2, and I think doesn't introduce an ambiguity. Previously a TypeError was raised.
This change will make it slightly easier to get xarray's test suite running with zarr v3.
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
commented
Sep 11, 2024

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Member
After thinking a bit more about this, I'm a bit concerned that we may not be ready for a generic MutableMapping in the MemoryStore. What would happen if we tossed a zict.LMDB into the constructor? I suspect things would mostly work but maybe not?
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

Copy link


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ContributorAuthor
I'm not sure how much faith to put in it, but the fact that mypy allows it gives me some comfort.
@d-v-b
d-v-b
commented
Sep 11, 2024

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If we accept anything that implements MutableMapping here, then there's no guarantee that the store is actually in memory, since the __getitem__ and __setitem__ operations could be running arbitrary IO-ful code. This seems fine with me, as long as users know what they are getting into, and maybe a useful bridge for users who want some v2-style store behavior (but maybe a better name for the store would be MutableMappingStore?)
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

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ContributorAuthor
Ah, I see, the concern is specifically around the isinstance at https://github.com/zarr-developers/zarr-python/pull/2164/files#diff-9a2583a58394683284176a2d2db4df1e8ffafce4f34edc7a176c625863815518R99.
In that case, yes, I think we should narrow it to just accept dictionaries, where there's no ambiguity about whether a MemoryStore is appropriate.
@jhamman
jhamman
merged commit c62294e
into
zarr-developers:v3Sep 12, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 16, 2024
@dcherian
Merge branch 'v3' into fix-hypothesis-complex-warning
a8de6d6
* v3:
fix: opening a group with unspecified format finds either v2 or v3 (zarr-developers#2183)
test: check that store, array, and group classes are serializable (zarr-developers#2006)
feature(store): V3 ZipStore (zarr-developers#2078)
More typing fixes for tests (zarr-developers#2173)
refactor: split metadata into v2 and v3 modules (zarr-developers#2163)
Accept dictionaries for `store` argument (zarr-developers#2164)
Simplify mypy config for tests (zarr-developers#2156)
Fixed path segment duplication in open_array (zarr-developers#2167)
Fixed test warnings (zarr-developers#2168)
chore: update pre-commit hooks (zarr-developers#2165)
Ensure that store_dict used for empty dicts (zarr-developers#2162)
Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (zarr-developers#2160)
dstansby pushed a commit
to dstansby/zarr-python
that referenced
this pull request
Sep 17, 2024
@TomAugspurger@dstansby
Accept dictionaries forstoreargument (zarr-developers#2164)
29b83f0
* Accept dictionaries for `store`
* fixup doc build warnings
* Only support dictionaries
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@d-v-bd-v-bd-v-b approved these changes

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@TomAugspurger@jhamman@d-v-b

, '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
Accept dictionaries for store argument - #2164
Merged
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Sep 12, 2024
Merged
Accept dictionaries for store argument#2164
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Conversation
@TomAugspurger
@TomAugspurgerTomAugspurger
commented
Sep 9, 2024•

edited

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This updates how we handle a plain dictionary provided to open_group and friends so that the following works:
group = await zarr.api.asynchronous.open_group(store={}, mode="w")
The dictionary is interpreted as the store_dict argument of zarr.store.MemoryStore. This effectively mirrors the behavior of zarr-python v2, and I think doesn't introduce an ambiguity. Previously a TypeError was raised.
This change will make it slightly easier to get xarray's test suite running with zarr v3.
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
commented
Sep 11, 2024

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After thinking a bit more about this, I'm a bit concerned that we may not be ready for a generic MutableMapping in the MemoryStore. What would happen if we tossed a zict.LMDB into the constructor? I suspect things would mostly work but maybe not?
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

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ContributorAuthor
I'm not sure how much faith to put in it, but the fact that mypy allows it gives me some comfort.
@d-v-b
d-v-b
commented
Sep 11, 2024

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If we accept anything that implements MutableMapping here, then there's no guarantee that the store is actually in memory, since the __getitem__ and __setitem__ operations could be running arbitrary IO-ful code. This seems fine with me, as long as users know what they are getting into, and maybe a useful bridge for users who want some v2-style store behavior (but maybe a better name for the store would be MutableMappingStore?)
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

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ContributorAuthor
Ah, I see, the concern is specifically around the isinstance at https://github.com/zarr-developers/zarr-python/pull/2164/files#diff-9a2583a58394683284176a2d2db4df1e8ffafce4f34edc7a176c625863815518R99.
In that case, yes, I think we should narrow it to just accept dictionaries, where there's no ambiguity about whether a MemoryStore is appropriate.
@jhamman
jhamman
merged commit c62294e
into
zarr-developers:v3Sep 12, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 16, 2024
@dcherian
Merge branch 'v3' into fix-hypothesis-complex-warning
a8de6d6
* v3:
fix: opening a group with unspecified format finds either v2 or v3 (zarr-developers#2183)
test: check that store, array, and group classes are serializable (zarr-developers#2006)
feature(store): V3 ZipStore (zarr-developers#2078)
More typing fixes for tests (zarr-developers#2173)
refactor: split metadata into v2 and v3 modules (zarr-developers#2163)
Accept dictionaries for `store` argument (zarr-developers#2164)
Simplify mypy config for tests (zarr-developers#2156)
Fixed path segment duplication in open_array (zarr-developers#2167)
Fixed test warnings (zarr-developers#2168)
chore: update pre-commit hooks (zarr-developers#2165)
Ensure that store_dict used for empty dicts (zarr-developers#2162)
Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (zarr-developers#2160)
dstansby pushed a commit
to dstansby/zarr-python
that referenced
this pull request
Sep 17, 2024
@TomAugspurger@dstansby
Accept dictionaries forstoreargument (zarr-developers#2164)
29b83f0
* Accept dictionaries for `store`
* fixup doc build warnings
* Only support dictionaries
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@d-v-bd-v-bd-v-b approved these changes

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@TomAugspurger@jhamman@d-v-b

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

Skip to content
Accept dictionaries for store argument - #2164
Merged
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Sep 12, 2024
Merged
Accept dictionaries for store argument#2164
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Conversation
@TomAugspurger
@TomAugspurgerTomAugspurger
commented
Sep 9, 2024•

edited

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This updates how we handle a plain dictionary provided to open_group and friends so that the following works:
group = await zarr.api.asynchronous.open_group(store={}, mode="w")
The dictionary is interpreted as the store_dict argument of zarr.store.MemoryStore. This effectively mirrors the behavior of zarr-python v2, and I think doesn't introduce an ambiguity. Previously a TypeError was raised.
This change will make it slightly easier to get xarray's test suite running with zarr v3.
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
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Sep 11, 2024

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After thinking a bit more about this, I'm a bit concerned that we may not be ready for a generic MutableMapping in the MemoryStore. What would happen if we tossed a zict.LMDB into the constructor? I suspect things would mostly work but maybe not?
@TomAugspurger
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Sep 11, 2024

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I'm not sure how much faith to put in it, but the fact that mypy allows it gives me some comfort.
@d-v-b
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Sep 11, 2024

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If we accept anything that implements MutableMapping here, then there's no guarantee that the store is actually in memory, since the __getitem__ and __setitem__ operations could be running arbitrary IO-ful code. This seems fine with me, as long as users know what they are getting into, and maybe a useful bridge for users who want some v2-style store behavior (but maybe a better name for the store would be MutableMappingStore?)
@TomAugspurger
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Sep 11, 2024

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Ah, I see, the concern is specifically around the isinstance at https://github.com/zarr-developers/zarr-python/pull/2164/files#diff-9a2583a58394683284176a2d2db4df1e8ffafce4f34edc7a176c625863815518R99.
In that case, yes, I think we should narrow it to just accept dictionaries, where there's no ambiguity about whether a MemoryStore is appropriate.
@jhamman
jhamman
merged commit c62294e
into
zarr-developers:v3Sep 12, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 16, 2024
@dcherian
Merge branch 'v3' into fix-hypothesis-complex-warning
a8de6d6
* v3:
fix: opening a group with unspecified format finds either v2 or v3 (zarr-developers#2183)
test: check that store, array, and group classes are serializable (zarr-developers#2006)
feature(store): V3 ZipStore (zarr-developers#2078)
More typing fixes for tests (zarr-developers#2173)
refactor: split metadata into v2 and v3 modules (zarr-developers#2163)
Accept dictionaries for `store` argument (zarr-developers#2164)
Simplify mypy config for tests (zarr-developers#2156)
Fixed path segment duplication in open_array (zarr-developers#2167)
Fixed test warnings (zarr-developers#2168)
chore: update pre-commit hooks (zarr-developers#2165)
Ensure that store_dict used for empty dicts (zarr-developers#2162)
Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (zarr-developers#2160)
dstansby pushed a commit
to dstansby/zarr-python
that referenced
this pull request
Sep 17, 2024
@TomAugspurger@dstansby
Accept dictionaries forstoreargument (zarr-developers#2164)
29b83f0
* Accept dictionaries for `store`
* fixup doc build warnings
* Only support dictionaries
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, '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
Accept dictionaries for store argument - #2164
Merged
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Sep 12, 2024
Merged
Accept dictionaries for store argument#2164
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Conversation
@TomAugspurger
@TomAugspurgerTomAugspurger
commented
Sep 9, 2024•

edited

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This updates how we handle a plain dictionary provided to open_group and friends so that the following works:
group = await zarr.api.asynchronous.open_group(store={}, mode="w")
The dictionary is interpreted as the store_dict argument of zarr.store.MemoryStore. This effectively mirrors the behavior of zarr-python v2, and I think doesn't introduce an ambiguity. Previously a TypeError was raised.
This change will make it slightly easier to get xarray's test suite running with zarr v3.
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
commented
Sep 11, 2024

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After thinking a bit more about this, I'm a bit concerned that we may not be ready for a generic MutableMapping in the MemoryStore. What would happen if we tossed a zict.LMDB into the constructor? I suspect things would mostly work but maybe not?
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

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I'm not sure how much faith to put in it, but the fact that mypy allows it gives me some comfort.
@d-v-b
d-v-b
commented
Sep 11, 2024

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If we accept anything that implements MutableMapping here, then there's no guarantee that the store is actually in memory, since the __getitem__ and __setitem__ operations could be running arbitrary IO-ful code. This seems fine with me, as long as users know what they are getting into, and maybe a useful bridge for users who want some v2-style store behavior (but maybe a better name for the store would be MutableMappingStore?)
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

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Ah, I see, the concern is specifically around the isinstance at https://github.com/zarr-developers/zarr-python/pull/2164/files#diff-9a2583a58394683284176a2d2db4df1e8ffafce4f34edc7a176c625863815518R99.
In that case, yes, I think we should narrow it to just accept dictionaries, where there's no ambiguity about whether a MemoryStore is appropriate.
@jhamman
jhamman
merged commit c62294e
into
zarr-developers:v3Sep 12, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 16, 2024
@dcherian
Merge branch 'v3' into fix-hypothesis-complex-warning
a8de6d6
* v3:
fix: opening a group with unspecified format finds either v2 or v3 (zarr-developers#2183)
test: check that store, array, and group classes are serializable (zarr-developers#2006)
feature(store): V3 ZipStore (zarr-developers#2078)
More typing fixes for tests (zarr-developers#2173)
refactor: split metadata into v2 and v3 modules (zarr-developers#2163)
Accept dictionaries for `store` argument (zarr-developers#2164)
Simplify mypy config for tests (zarr-developers#2156)
Fixed path segment duplication in open_array (zarr-developers#2167)
Fixed test warnings (zarr-developers#2168)
chore: update pre-commit hooks (zarr-developers#2165)
Ensure that store_dict used for empty dicts (zarr-developers#2162)
Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (zarr-developers#2160)
dstansby pushed a commit
to dstansby/zarr-python
that referenced
this pull request
Sep 17, 2024
@TomAugspurger@dstansby
Accept dictionaries forstoreargument (zarr-developers#2164)
29b83f0
* Accept dictionaries for `store`
* fixup doc build warnings
* Only support dictionaries
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@TomAugspurger@jhamman@d-v-b

, '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
Accept dictionaries for store argument - #2164
Merged
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Sep 12, 2024
Merged
Accept dictionaries for store argument#2164
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Conversation
@TomAugspurger
@TomAugspurgerTomAugspurger
commented
Sep 9, 2024•

edited

Loading

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Contributor
This updates how we handle a plain dictionary provided to open_group and friends so that the following works:
group = await zarr.api.asynchronous.open_group(store={}, mode="w")
The dictionary is interpreted as the store_dict argument of zarr.store.MemoryStore. This effectively mirrors the behavior of zarr-python v2, and I think doesn't introduce an ambiguity. Previously a TypeError was raised.
This change will make it slightly easier to get xarray's test suite running with zarr v3.
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
commented
Sep 11, 2024

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After thinking a bit more about this, I'm a bit concerned that we may not be ready for a generic MutableMapping in the MemoryStore. What would happen if we tossed a zict.LMDB into the constructor? I suspect things would mostly work but maybe not?
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

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ContributorAuthor
I'm not sure how much faith to put in it, but the fact that mypy allows it gives me some comfort.
@d-v-b
d-v-b
commented
Sep 11, 2024

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If we accept anything that implements MutableMapping here, then there's no guarantee that the store is actually in memory, since the __getitem__ and __setitem__ operations could be running arbitrary IO-ful code. This seems fine with me, as long as users know what they are getting into, and maybe a useful bridge for users who want some v2-style store behavior (but maybe a better name for the store would be MutableMappingStore?)
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

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ContributorAuthor
Ah, I see, the concern is specifically around the isinstance at https://github.com/zarr-developers/zarr-python/pull/2164/files#diff-9a2583a58394683284176a2d2db4df1e8ffafce4f34edc7a176c625863815518R99.
In that case, yes, I think we should narrow it to just accept dictionaries, where there's no ambiguity about whether a MemoryStore is appropriate.
@jhamman
jhamman
merged commit c62294e
into
zarr-developers:v3Sep 12, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 16, 2024
@dcherian
Merge branch 'v3' into fix-hypothesis-complex-warning
a8de6d6
* v3:
fix: opening a group with unspecified format finds either v2 or v3 (zarr-developers#2183)
test: check that store, array, and group classes are serializable (zarr-developers#2006)
feature(store): V3 ZipStore (zarr-developers#2078)
More typing fixes for tests (zarr-developers#2173)
refactor: split metadata into v2 and v3 modules (zarr-developers#2163)
Accept dictionaries for `store` argument (zarr-developers#2164)
Simplify mypy config for tests (zarr-developers#2156)
Fixed path segment duplication in open_array (zarr-developers#2167)
Fixed test warnings (zarr-developers#2168)
chore: update pre-commit hooks (zarr-developers#2165)
Ensure that store_dict used for empty dicts (zarr-developers#2162)
Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (zarr-developers#2160)
dstansby pushed a commit
to dstansby/zarr-python
that referenced
this pull request
Sep 17, 2024
@TomAugspurger@dstansby
Accept dictionaries forstoreargument (zarr-developers#2164)
29b83f0
* Accept dictionaries for `store`
* fixup doc build warnings
* Only support dictionaries
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@d-v-bd-v-bd-v-b approved these changes

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3 participants

@TomAugspurger@jhamman@d-v-b

, '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
Accept dictionaries for store argument - #2164
Merged
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Sep 12, 2024
Merged
Accept dictionaries for store argument#2164
jhamman merged 3 commits into
zarr-developers:v3from 
TomAugspurger:feature/dict-store
Conversation
@TomAugspurger
@TomAugspurgerTomAugspurger
commented
Sep 9, 2024•

edited

Loading

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Contributor
This updates how we handle a plain dictionary provided to open_group and friends so that the following works:
group = await zarr.api.asynchronous.open_group(store={}, mode="w")
The dictionary is interpreted as the store_dict argument of zarr.store.MemoryStore. This effectively mirrors the behavior of zarr-python v2, and I think doesn't introduce an ambiguity. Previously a TypeError was raised.
This change will make it slightly easier to get xarray's test suite running with zarr v3.
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
commented
Sep 11, 2024

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After thinking a bit more about this, I'm a bit concerned that we may not be ready for a generic MutableMapping in the MemoryStore. What would happen if we tossed a zict.LMDB into the constructor? I suspect things would mostly work but maybe not?
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

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ContributorAuthor
I'm not sure how much faith to put in it, but the fact that mypy allows it gives me some comfort.
@d-v-b
d-v-b
commented
Sep 11, 2024

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If we accept anything that implements MutableMapping here, then there's no guarantee that the store is actually in memory, since the __getitem__ and __setitem__ operations could be running arbitrary IO-ful code. This seems fine with me, as long as users know what they are getting into, and maybe a useful bridge for users who want some v2-style store behavior (but maybe a better name for the store would be MutableMappingStore?)
@TomAugspurger
TomAugspurger
commented
Sep 11, 2024

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ContributorAuthor
Ah, I see, the concern is specifically around the isinstance at https://github.com/zarr-developers/zarr-python/pull/2164/files#diff-9a2583a58394683284176a2d2db4df1e8ffafce4f34edc7a176c625863815518R99.
In that case, yes, I think we should narrow it to just accept dictionaries, where there's no ambiguity about whether a MemoryStore is appropriate.
@jhamman
jhamman
merged commit c62294e
into
zarr-developers:v3Sep 12, 2024
dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 16, 2024
@dcherian
Merge branch 'v3' into fix-hypothesis-complex-warning
a8de6d6
* v3:
fix: opening a group with unspecified format finds either v2 or v3 (zarr-developers#2183)
test: check that store, array, and group classes are serializable (zarr-developers#2006)
feature(store): V3 ZipStore (zarr-developers#2078)
More typing fixes for tests (zarr-developers#2173)
refactor: split metadata into v2 and v3 modules (zarr-developers#2163)
Accept dictionaries for `store` argument (zarr-developers#2164)
Simplify mypy config for tests (zarr-developers#2156)
Fixed path segment duplication in open_array (zarr-developers#2167)
Fixed test warnings (zarr-developers#2168)
chore: update pre-commit hooks (zarr-developers#2165)
Ensure that store_dict used for empty dicts (zarr-developers#2162)
Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (zarr-developers#2160)
dstansby pushed a commit
to dstansby/zarr-python
that referenced
this pull request
Sep 17, 2024
@TomAugspurger@dstansby
Accept dictionaries forstoreargument (zarr-developers#2164)
29b83f0
* Accept dictionaries for `store`
* fixup doc build warnings
* Only support dictionaries
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@d-v-bd-v-bd-v-b approved these changes

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3 participants

@TomAugspurger@jhamman@d-v-b