fix file modes - #2000

Merged
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes
Jul 26, 2024
Merged

fix file modes#2000
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes

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fixes#1978
according to docstrings of zarr.open the modes should do:

mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
Persistence mode: 'r' means read only (must exist); 'r+' means
read/write (must exist); 'a' means read/write (create if doesn't
exist); 'w' means create (overwrite if exists); 'w-' means create
(fail if exists).

this PR implements and tests this behavior, so #1978 gets fixed

@normanrznormanrz added the V3 label Jun 27, 2024
@normanrznormanrz added this to the 3.0.0 milestone Jun 27, 2024
@normanrz
normanrz requested a review from jhammanJune 27, 2024 13:12
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
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Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

@brokkoli71

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Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

good point, according to the docstrings: 'w' means create (overwrite if exists). So yes, would be probably a good idea to have a generalized Store.clear. I will have a look at that

@d-v-b

d-v-b commented Jul 2, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

@brokkoli71

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

@d-v-b

d-v-b commented Jul 3, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

There's a lot of usage for create + overwrite -- if users are rapidly iterating on something, they already created an old array, but they want to save a new array with the same name + different datatype, then the easiest way to do this is via something like an overwrite option. Handling this via array the creation flow is more ergonomic than forcing users to go through a separate API.

Don't worry too much about the performance concerns with bulk deletion for now. We should make the API convenient, then worry about performance later. I only brought delete performance up because it's something that zarr python v2 didn't deal with, which caused me some headaches.

@jhammanjhamman mentioned this pull request Jul 3, 2024
Comment threadsrc/zarr/abc/store.py Outdated
# Conflicts:
#	tests/v3/conftest.py
#	tests/v3/test_codecs.py
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this is looking great! Just a few final comments.

Comment threadtests/v3/test_api.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
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brokkoli71 requested a review from jhammanJuly 18, 2024 13:40

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One last comment and a suggestion on ensure_open that you can take or leave. Thanks again for pushing on this.

Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
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@brokkoli71 - happy to merge this if you can resolve the conflicts.

# Conflicts:
#	src/zarr/store/remote.py
@joshmoore

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Sadly still conflicting, @brokkoli71

# Conflicts:
#	src/zarr/store/core.py
#	tests/v3/test_store/test_memory.py
@normanrz
normanrz merged commit 325786a into zarr-developers:v3Jul 26, 2024
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[v3] Mode 'r+' is not working

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@brokkoli71@jhamman@d-v-b@joshmoore@normanrz
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
Skip to content

fix file modes - #2000

Merged
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes
Jul 26, 2024
Merged

fix file modes#2000
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes

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@brokkoli71

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fixes#1978
according to docstrings of zarr.open the modes should do:

mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
Persistence mode: 'r' means read only (must exist); 'r+' means
read/write (must exist); 'a' means read/write (create if doesn't
exist); 'w' means create (overwrite if exists); 'w-' means create
(fail if exists).

this PR implements and tests this behavior, so #1978 gets fixed

@normanrznormanrz added the V3 label Jun 27, 2024
@normanrznormanrz added this to the 3.0.0 milestone Jun 27, 2024
@normanrz
normanrz requested a review from jhammanJune 27, 2024 13:12
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
@jhamman

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Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

@brokkoli71

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ContributorAuthor

Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

good point, according to the docstrings: 'w' means create (overwrite if exists). So yes, would be probably a good idea to have a generalized Store.clear. I will have a look at that

@d-v-b

d-v-b commented Jul 2, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

@brokkoli71

Copy link
Copy Markdown
ContributorAuthor

I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

@d-v-b

d-v-b commented Jul 3, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

There's a lot of usage for create + overwrite -- if users are rapidly iterating on something, they already created an old array, but they want to save a new array with the same name + different datatype, then the easiest way to do this is via something like an overwrite option. Handling this via array the creation flow is more ergonomic than forcing users to go through a separate API.

Don't worry too much about the performance concerns with bulk deletion for now. We should make the API convenient, then worry about performance later. I only brought delete performance up because it's something that zarr python v2 didn't deal with, which caused me some headaches.

@jhammanjhamman mentioned this pull request Jul 3, 2024
Comment threadsrc/zarr/abc/store.py Outdated
# Conflicts:
#	tests/v3/conftest.py
#	tests/v3/test_codecs.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 5, 2024 11:53

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this is looking great! Just a few final comments.

Comment threadtests/v3/test_api.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 18, 2024 13:40

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One last comment and a suggestion on ensure_open that you can take or leave. Thanks again for pushing on this.

Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@jhamman

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@brokkoli71 - happy to merge this if you can resolve the conflicts.

# Conflicts:
#	src/zarr/store/remote.py
@joshmoore

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Sadly still conflicting, @brokkoli71

# Conflicts:
#	src/zarr/store/core.py
#	tests/v3/test_store/test_memory.py
@normanrz
normanrz merged commit 325786a into zarr-developers:v3Jul 26, 2024
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[v3] Mode 'r+' is not working

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@brokkoli71@jhamman@d-v-b@joshmoore@normanrz
, '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

fix file modes - #2000

Merged
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes
Jul 26, 2024
Merged

fix file modes#2000
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes

Conversation

@brokkoli71

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fixes#1978
according to docstrings of zarr.open the modes should do:

mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
Persistence mode: 'r' means read only (must exist); 'r+' means
read/write (must exist); 'a' means read/write (create if doesn't
exist); 'w' means create (overwrite if exists); 'w-' means create
(fail if exists).

this PR implements and tests this behavior, so #1978 gets fixed

@normanrznormanrz added the V3 label Jun 27, 2024
@normanrznormanrz added this to the 3.0.0 milestone Jun 27, 2024
@normanrz
normanrz requested a review from jhammanJune 27, 2024 13:12
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
@jhamman

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Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

@brokkoli71

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ContributorAuthor

Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

good point, according to the docstrings: 'w' means create (overwrite if exists). So yes, would be probably a good idea to have a generalized Store.clear. I will have a look at that

@d-v-b

d-v-b commented Jul 2, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

@brokkoli71

Copy link
Copy Markdown
ContributorAuthor

I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

@d-v-b

d-v-b commented Jul 3, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

There's a lot of usage for create + overwrite -- if users are rapidly iterating on something, they already created an old array, but they want to save a new array with the same name + different datatype, then the easiest way to do this is via something like an overwrite option. Handling this via array the creation flow is more ergonomic than forcing users to go through a separate API.

Don't worry too much about the performance concerns with bulk deletion for now. We should make the API convenient, then worry about performance later. I only brought delete performance up because it's something that zarr python v2 didn't deal with, which caused me some headaches.

@jhammanjhamman mentioned this pull request Jul 3, 2024
Comment threadsrc/zarr/abc/store.py Outdated
# Conflicts:
#	tests/v3/conftest.py
#	tests/v3/test_codecs.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 5, 2024 11:53

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this is looking great! Just a few final comments.

Comment threadtests/v3/test_api.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 18, 2024 13:40

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One last comment and a suggestion on ensure_open that you can take or leave. Thanks again for pushing on this.

Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@jhamman

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@brokkoli71 - happy to merge this if you can resolve the conflicts.

# Conflicts:
#	src/zarr/store/remote.py
@joshmoore

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Sadly still conflicting, @brokkoli71

# Conflicts:
#	src/zarr/store/core.py
#	tests/v3/test_store/test_memory.py
@normanrz
normanrz merged commit 325786a into zarr-developers:v3Jul 26, 2024
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[v3] Mode 'r+' is not working

5 participants

@brokkoli71@jhamman@d-v-b@joshmoore@normanrz
, '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

fix file modes - #2000

Merged
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes
Jul 26, 2024
Merged

fix file modes#2000
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes

Conversation

@brokkoli71

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fixes#1978
according to docstrings of zarr.open the modes should do:

mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
Persistence mode: 'r' means read only (must exist); 'r+' means
read/write (must exist); 'a' means read/write (create if doesn't
exist); 'w' means create (overwrite if exists); 'w-' means create
(fail if exists).

this PR implements and tests this behavior, so #1978 gets fixed

@normanrznormanrz added the V3 label Jun 27, 2024
@normanrznormanrz added this to the 3.0.0 milestone Jun 27, 2024
@normanrz
normanrz requested a review from jhammanJune 27, 2024 13:12
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
@jhamman

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Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

@brokkoli71

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ContributorAuthor

Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

good point, according to the docstrings: 'w' means create (overwrite if exists). So yes, would be probably a good idea to have a generalized Store.clear. I will have a look at that

@d-v-b

d-v-b commented Jul 2, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

@brokkoli71

Copy link
Copy Markdown
ContributorAuthor

I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

@d-v-b

d-v-b commented Jul 3, 2024

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Contributor

I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

There's a lot of usage for create + overwrite -- if users are rapidly iterating on something, they already created an old array, but they want to save a new array with the same name + different datatype, then the easiest way to do this is via something like an overwrite option. Handling this via array the creation flow is more ergonomic than forcing users to go through a separate API.

Don't worry too much about the performance concerns with bulk deletion for now. We should make the API convenient, then worry about performance later. I only brought delete performance up because it's something that zarr python v2 didn't deal with, which caused me some headaches.

@jhammanjhamman mentioned this pull request Jul 3, 2024
Comment threadsrc/zarr/abc/store.py Outdated
# Conflicts:
#	tests/v3/conftest.py
#	tests/v3/test_codecs.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 5, 2024 11:53

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this is looking great! Just a few final comments.

Comment threadtests/v3/test_api.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 18, 2024 13:40

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One last comment and a suggestion on ensure_open that you can take or leave. Thanks again for pushing on this.

Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@jhamman

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@brokkoli71 - happy to merge this if you can resolve the conflicts.

# Conflicts:
#	src/zarr/store/remote.py
@joshmoore

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Sadly still conflicting, @brokkoli71

# Conflicts:
#	src/zarr/store/core.py
#	tests/v3/test_store/test_memory.py
@normanrz
normanrz merged commit 325786a into zarr-developers:v3Jul 26, 2024
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Successfully merging this pull request may close these issues.

[v3] Mode 'r+' is not working

5 participants

@brokkoli71@jhamman@d-v-b@joshmoore@normanrz
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links"); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + '
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fix file modes - #2000

Merged
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes
Jul 26, 2024
Merged

fix file modes#2000
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes

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fixes#1978
according to docstrings of zarr.open the modes should do:

mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
Persistence mode: 'r' means read only (must exist); 'r+' means
read/write (must exist); 'a' means read/write (create if doesn't
exist); 'w' means create (overwrite if exists); 'w-' means create
(fail if exists).

this PR implements and tests this behavior, so #1978 gets fixed

@normanrznormanrz added the V3 label Jun 27, 2024
@normanrznormanrz added this to the 3.0.0 milestone Jun 27, 2024
@normanrz
normanrz requested a review from jhammanJune 27, 2024 13:12
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
@jhamman

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Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

@brokkoli71

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Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

good point, according to the docstrings: 'w' means create (overwrite if exists). So yes, would be probably a good idea to have a generalized Store.clear. I will have a look at that

@d-v-b

d-v-b commented Jul 2, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

@brokkoli71

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ContributorAuthor

I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

@d-v-b

d-v-b commented Jul 3, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

There's a lot of usage for create + overwrite -- if users are rapidly iterating on something, they already created an old array, but they want to save a new array with the same name + different datatype, then the easiest way to do this is via something like an overwrite option. Handling this via array the creation flow is more ergonomic than forcing users to go through a separate API.

Don't worry too much about the performance concerns with bulk deletion for now. We should make the API convenient, then worry about performance later. I only brought delete performance up because it's something that zarr python v2 didn't deal with, which caused me some headaches.

@jhammanjhamman mentioned this pull request Jul 3, 2024
Comment threadsrc/zarr/abc/store.py Outdated
# Conflicts:
#	tests/v3/conftest.py
#	tests/v3/test_codecs.py
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this is looking great! Just a few final comments.

Comment threadtests/v3/test_api.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 18, 2024 13:40

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One last comment and a suggestion on ensure_open that you can take or leave. Thanks again for pushing on this.

Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@jhamman

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@brokkoli71 - happy to merge this if you can resolve the conflicts.

# Conflicts:
#	src/zarr/store/remote.py
@joshmoore

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Sadly still conflicting, @brokkoli71

# Conflicts:
#	src/zarr/store/core.py
#	tests/v3/test_store/test_memory.py
@normanrz
normanrz merged commit 325786a into zarr-developers:v3Jul 26, 2024
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[v3] Mode 'r+' is not working

5 participants

@brokkoli71@jhamman@d-v-b@joshmoore@normanrz
, '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

fix file modes - #2000

Merged
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes
Jul 26, 2024
Merged

fix file modes#2000
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes

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@brokkoli71

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fixes#1978
according to docstrings of zarr.open the modes should do:

mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
Persistence mode: 'r' means read only (must exist); 'r+' means
read/write (must exist); 'a' means read/write (create if doesn't
exist); 'w' means create (overwrite if exists); 'w-' means create
(fail if exists).

this PR implements and tests this behavior, so #1978 gets fixed

@normanrznormanrz added the V3 label Jun 27, 2024
@normanrznormanrz added this to the 3.0.0 milestone Jun 27, 2024
@normanrz
normanrz requested a review from jhammanJune 27, 2024 13:12
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
@jhamman

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Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

@brokkoli71

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ContributorAuthor

Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

good point, according to the docstrings: 'w' means create (overwrite if exists). So yes, would be probably a good idea to have a generalized Store.clear. I will have a look at that

@d-v-b

d-v-b commented Jul 2, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

@brokkoli71

Copy link
Copy Markdown
ContributorAuthor

I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

@d-v-b

d-v-b commented Jul 3, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

There's a lot of usage for create + overwrite -- if users are rapidly iterating on something, they already created an old array, but they want to save a new array with the same name + different datatype, then the easiest way to do this is via something like an overwrite option. Handling this via array the creation flow is more ergonomic than forcing users to go through a separate API.

Don't worry too much about the performance concerns with bulk deletion for now. We should make the API convenient, then worry about performance later. I only brought delete performance up because it's something that zarr python v2 didn't deal with, which caused me some headaches.

@jhammanjhamman mentioned this pull request Jul 3, 2024
Comment threadsrc/zarr/abc/store.py Outdated
# Conflicts:
#	tests/v3/conftest.py
#	tests/v3/test_codecs.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 5, 2024 11:53

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this is looking great! Just a few final comments.

Comment threadtests/v3/test_api.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 18, 2024 13:40

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One last comment and a suggestion on ensure_open that you can take or leave. Thanks again for pushing on this.

Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@jhamman

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@brokkoli71 - happy to merge this if you can resolve the conflicts.

# Conflicts:
#	src/zarr/store/remote.py
@joshmoore

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Sadly still conflicting, @brokkoli71

# Conflicts:
#	src/zarr/store/core.py
#	tests/v3/test_store/test_memory.py
@normanrz
normanrz merged commit 325786a into zarr-developers:v3Jul 26, 2024
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[v3] Mode 'r+' is not working

5 participants

@brokkoli71@jhamman@d-v-b@joshmoore@normanrz
, '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

fix file modes - #2000

Merged
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes
Jul 26, 2024
Merged

fix file modes#2000
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes

Conversation

@brokkoli71

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fixes#1978
according to docstrings of zarr.open the modes should do:

mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
Persistence mode: 'r' means read only (must exist); 'r+' means
read/write (must exist); 'a' means read/write (create if doesn't
exist); 'w' means create (overwrite if exists); 'w-' means create
(fail if exists).

this PR implements and tests this behavior, so #1978 gets fixed

@normanrznormanrz added the V3 label Jun 27, 2024
@normanrznormanrz added this to the 3.0.0 milestone Jun 27, 2024
@normanrz
normanrz requested a review from jhammanJune 27, 2024 13:12
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
@jhamman

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Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

@brokkoli71

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ContributorAuthor

Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

good point, according to the docstrings: 'w' means create (overwrite if exists). So yes, would be probably a good idea to have a generalized Store.clear. I will have a look at that

@d-v-b

d-v-b commented Jul 2, 2024

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Contributor

I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

@brokkoli71

Copy link
Copy Markdown
ContributorAuthor

I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

@d-v-b

d-v-b commented Jul 3, 2024

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Contributor

I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

There's a lot of usage for create + overwrite -- if users are rapidly iterating on something, they already created an old array, but they want to save a new array with the same name + different datatype, then the easiest way to do this is via something like an overwrite option. Handling this via array the creation flow is more ergonomic than forcing users to go through a separate API.

Don't worry too much about the performance concerns with bulk deletion for now. We should make the API convenient, then worry about performance later. I only brought delete performance up because it's something that zarr python v2 didn't deal with, which caused me some headaches.

@jhammanjhamman mentioned this pull request Jul 3, 2024
Comment threadsrc/zarr/abc/store.py Outdated
# Conflicts:
#	tests/v3/conftest.py
#	tests/v3/test_codecs.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 5, 2024 11:53

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this is looking great! Just a few final comments.

Comment threadtests/v3/test_api.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 18, 2024 13:40

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One last comment and a suggestion on ensure_open that you can take or leave. Thanks again for pushing on this.

Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@jhamman

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@brokkoli71 - happy to merge this if you can resolve the conflicts.

# Conflicts:
#	src/zarr/store/remote.py
@joshmoore

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Sadly still conflicting, @brokkoli71

# Conflicts:
#	src/zarr/store/core.py
#	tests/v3/test_store/test_memory.py
@normanrz
normanrz merged commit 325786a into zarr-developers:v3Jul 26, 2024
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[v3] Mode 'r+' is not working

5 participants

@brokkoli71@jhamman@d-v-b@joshmoore@normanrz
, '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

fix file modes - #2000

Merged
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes
Jul 26, 2024
Merged

fix file modes#2000
normanrz merged 27 commits into
zarr-developers:v3from
scalableminds:fix-file-modes

Conversation

@brokkoli71

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fixes#1978
according to docstrings of zarr.open the modes should do:

mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
Persistence mode: 'r' means read only (must exist); 'r+' means
read/write (must exist); 'a' means read/write (create if doesn't
exist); 'w' means create (overwrite if exists); 'w-' means create
(fail if exists).

this PR implements and tests this behavior, so #1978 gets fixed

@normanrznormanrz added the V3 label Jun 27, 2024
@normanrznormanrz added this to the 3.0.0 milestone Jun 27, 2024
@normanrz
normanrz requested a review from jhammanJune 27, 2024 13:12
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
@jhamman

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Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

@brokkoli71

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ContributorAuthor

Thanks @brokkoli71 for picking this up. What is the expected behavior of mode='w'? Should we have a Store.clear() method that we call in these cases?

good point, according to the docstrings: 'w' means create (overwrite if exists). So yes, would be probably a good idea to have a generalized Store.clear. I will have a look at that

@d-v-b

d-v-b commented Jul 2, 2024

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I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

@brokkoli71

Copy link
Copy Markdown
ContributorAuthor

I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

@d-v-b

d-v-b commented Jul 3, 2024

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Contributor

I agree that a method for clearing a store is a good idea. Just bear in mind that this can be a performance bottleneck when deleting arrays with a lot of chunks, especially on remote storage. We should think about performance at some point.

I was wondering, if supporting mode='w' as create (overwrite if exists) is a good idea concerning the performance? what is the usecase of this mode? maybe it would be better to explicitly have a delete or clear method? or we should have a warning in the docstrings?

There's a lot of usage for create + overwrite -- if users are rapidly iterating on something, they already created an old array, but they want to save a new array with the same name + different datatype, then the easiest way to do this is via something like an overwrite option. Handling this via array the creation flow is more ergonomic than forcing users to go through a separate API.

Don't worry too much about the performance concerns with bulk deletion for now. We should make the API convenient, then worry about performance later. I only brought delete performance up because it's something that zarr python v2 didn't deal with, which caused me some headaches.

@jhammanjhamman mentioned this pull request Jul 3, 2024
Comment threadsrc/zarr/abc/store.py Outdated
# Conflicts:
#	tests/v3/conftest.py
#	tests/v3/test_codecs.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 5, 2024 11:53

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this is looking great! Just a few final comments.

Comment threadtests/v3/test_api.py Outdated
Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@brokkoli71
brokkoli71 requested a review from jhammanJuly 18, 2024 13:40

@jhammanjhamman left a comment

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One last comment and a suggestion on ensure_open that you can take or leave. Thanks again for pushing on this.

Comment threadsrc/zarr/abc/store.py Outdated
Comment threadsrc/zarr/abc/store.py
@jhamman

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@brokkoli71 - happy to merge this if you can resolve the conflicts.

# Conflicts:
#	src/zarr/store/remote.py
@joshmoore

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Sadly still conflicting, @brokkoli71

# Conflicts:
#	src/zarr/store/core.py
#	tests/v3/test_store/test_memory.py
@normanrz
normanrz merged commit 325786a into zarr-developers:v3Jul 26, 2024
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@brokkoli71@jhamman@d-v-b@joshmoore@normanrz