Simplify text handling in DB Stores - #670

Merged
Carreau merged 4 commits into
zarr-developers:masterfrom
jakirkham:simp_txt_coding_db_stores
Dec 3, 2020
Merged

Simplify text handling in DB Stores#670
Carreau merged 4 commits into
zarr-developers:masterfrom
jakirkham:simp_txt_coding_db_stores

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@jakirkhamjakirkham commented Dec 3, 2020

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Fixes#669

LMDBStore had its own way of handling text before ensure_text was added to Numcodecs. With that utility function now available, we can simplify this a bit and avoid some subtleties of the LMDB implementation.

Similarly DBMStore had some of its own text handling issues that can be solved the same way.

Finally inline all str.encode calls to make it clearer what is happening in both LMDBStore and DBMStore.

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
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

@jakirkhamjakirkham mentioned this pull request Dec 3, 2020
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@jakirkhamjakirkham changed the title Simp text handling in DB StoresSimplify text handling in DB StoresDec 3, 2020
@Carreau

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Would that bump the minimum version of lmdb ?

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Codecov Report

Merging #670 (ed1ffca) into master (a5dfc3b) will not change coverage.
The diff coverage is 100.00%.

@@ Coverage Diff @@## master #670 +/- ##
=========================================
Coverage 100.00% 100.00% =========================================
Files 27 27 Lines 10094 10087 -7 =========================================
- Hits 10094 10087 -7
Impacted FilesCoverage Δ
zarr/storage.py100.00% <100.00%> (ø)

@jakirkham

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Would that bump the minimum version of lmdb ?

Shouldn't affect it.

Basically ensure_text leverages the Python Buffer Protocol to coerce the data (bytes or other object) to a NumPy array without copying. Effectively this normalizes the data we are working with so we don't need to know about LMDB Buffer objects or whatever other object might come up ( MongoDB had a similar issue #401 ). Then we perform the decode step on the NumPy array, which we already know to work.

@CarreauCarreau added this to the v2.7 milestone Dec 3, 2020
@Carreau

Carreau commented Dec 3, 2020

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Thanks for the explanation; let's get that in.

@Carreau
Carreau merged commit 1464d90 into zarr-developers:masterDec 3, 2020
@jakirkham
jakirkham deleted the simp_txt_coding_db_stores branch December 3, 2020 23:23
@jakirkham

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Thanks Matthias! 😄

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Failures on Python 3.10

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Simplify text handling in DB Stores - #670
Merged
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Dec 3, 2020
Merged
Simplify text handling in DB Stores#670
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
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@jakirkham
@jakirkhamjakirkham
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Dec 3, 2020

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Fixes#669
LMDBStore had its own way of handling text before ensure_text was added to Numcodecs. With that utility function now available, we can simplify this a bit and avoid some subtleties of the LMDB implementation.
Similarly DBMStore had some of its own text handling issues that can be solved the same way.
Finally inline all str.encode calls to make it clearer what is happening in both LMDBStore and DBMStore.
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
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020

Closed

@jakirkhamjakirkham
changed the title
Simp text handling in DB StoresSimplify text handling in DB StoresDec 3, 2020
@Carreau
Carreau
commented
Dec 3, 2020

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Would that bump the minimum version of lmdb ?
@codecov
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Dec 3, 2020•

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Codecov Report
Merging #670 (ed1ffca) into master (a5dfc3b) will not change coverage.

The diff coverage is 100.00%.
@@ Coverage Diff @@## master #670 +/- ##
=========================================
Coverage 100.00% 100.00% =========================================
Files 27 27 Lines 10094 10087 -7 =========================================
- Hits 10094 10087 -7 
Impacted FilesCoverage Δ
zarr/storage.py100.00% <100.00%> (ø)
@jakirkham
jakirkham
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Dec 3, 2020

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Would that bump the minimum version of lmdb ?
Shouldn't affect it.
Basically ensure_text leverages the Python Buffer Protocol to coerce the data (bytes or other object) to a NumPy array without copying. Effectively this normalizes the data we are working with so we don't need to know about LMDB Buffer objects or whatever other object might come up ( MongoDB had a similar issue #401 ). Then we perform the decode step on the NumPy array, which we already know to work.
@CarreauCarreau
added this to the v2.7 milestone
Dec 3, 2020
@Carreau
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Thanks for the explanation; let's get that in.
@Carreau
Carreau
merged commit 1464d90
into
zarr-developers:masterDec 3, 2020
@jakirkham
jakirkham
deleted the

simp_txt_coding_db_stores

branch
December 3, 2020 23:23
@jakirkham
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Thanks Matthias! 😄
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Failures on Python 3.10


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@jakirkham@Carreau

, '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
Simplify text handling in DB Stores - #670
Merged
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Dec 3, 2020
Merged
Simplify text handling in DB Stores#670
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Conversation
@jakirkham
@jakirkhamjakirkham
commented
Dec 3, 2020

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Fixes#669
LMDBStore had its own way of handling text before ensure_text was added to Numcodecs. With that utility function now available, we can simplify this a bit and avoid some subtleties of the LMDB implementation.
Similarly DBMStore had some of its own text handling issues that can be solved the same way.
Finally inline all str.encode calls to make it clearer what is happening in both LMDBStore and DBMStore.
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
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020

Closed

@jakirkhamjakirkham
changed the title
Simp text handling in DB StoresSimplify text handling in DB StoresDec 3, 2020
@Carreau
Carreau
commented
Dec 3, 2020

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Would that bump the minimum version of lmdb ?
@codecov
codecovBot
commented
Dec 3, 2020•

edited

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Codecov Report
Merging #670 (ed1ffca) into master (a5dfc3b) will not change coverage.

The diff coverage is 100.00%.
@@ Coverage Diff @@## master #670 +/- ##
=========================================
Coverage 100.00% 100.00% =========================================
Files 27 27 Lines 10094 10087 -7 =========================================
- Hits 10094 10087 -7 
Impacted FilesCoverage Δ
zarr/storage.py100.00% <100.00%> (ø)
@jakirkham
jakirkham
commented
Dec 3, 2020

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Would that bump the minimum version of lmdb ?
Shouldn't affect it.
Basically ensure_text leverages the Python Buffer Protocol to coerce the data (bytes or other object) to a NumPy array without copying. Effectively this normalizes the data we are working with so we don't need to know about LMDB Buffer objects or whatever other object might come up ( MongoDB had a similar issue #401 ). Then we perform the decode step on the NumPy array, which we already know to work.
@CarreauCarreau
added this to the v2.7 milestone
Dec 3, 2020
@Carreau
Carreau
commented
Dec 3, 2020

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Thanks for the explanation; let's get that in.
@Carreau
Carreau
merged commit 1464d90
into
zarr-developers:masterDec 3, 2020
@jakirkham
jakirkham
deleted the

simp_txt_coding_db_stores

branch
December 3, 2020 23:23
@jakirkham
jakirkham
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Thanks Matthias! 😄
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Failures on Python 3.10


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@jakirkham@Carreau

, '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
Simplify text handling in DB Stores - #670
Merged
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Dec 3, 2020
Merged
Simplify text handling in DB Stores#670
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Conversation
@jakirkham
@jakirkhamjakirkham
commented
Dec 3, 2020

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Fixes#669
LMDBStore had its own way of handling text before ensure_text was added to Numcodecs. With that utility function now available, we can simplify this a bit and avoid some subtleties of the LMDB implementation.
Similarly DBMStore had some of its own text handling issues that can be solved the same way.
Finally inline all str.encode calls to make it clearer what is happening in both LMDBStore and DBMStore.
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
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020

Closed

@jakirkhamjakirkham
changed the title
Simp text handling in DB StoresSimplify text handling in DB StoresDec 3, 2020
@Carreau
Carreau
commented
Dec 3, 2020

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Would that bump the minimum version of lmdb ?
@codecov
codecovBot
commented
Dec 3, 2020•

edited

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Codecov Report
Merging #670 (ed1ffca) into master (a5dfc3b) will not change coverage.

The diff coverage is 100.00%.
@@ Coverage Diff @@## master #670 +/- ##
=========================================
Coverage 100.00% 100.00% =========================================
Files 27 27 Lines 10094 10087 -7 =========================================
- Hits 10094 10087 -7 
Impacted FilesCoverage Δ
zarr/storage.py100.00% <100.00%> (ø)
@jakirkham
jakirkham
commented
Dec 3, 2020

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MemberAuthor
Would that bump the minimum version of lmdb ?
Shouldn't affect it.
Basically ensure_text leverages the Python Buffer Protocol to coerce the data (bytes or other object) to a NumPy array without copying. Effectively this normalizes the data we are working with so we don't need to know about LMDB Buffer objects or whatever other object might come up ( MongoDB had a similar issue #401 ). Then we perform the decode step on the NumPy array, which we already know to work.
@CarreauCarreau
added this to the v2.7 milestone
Dec 3, 2020
@Carreau
Carreau
commented
Dec 3, 2020

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Thanks for the explanation; let's get that in.
@Carreau
Carreau
merged commit 1464d90
into
zarr-developers:masterDec 3, 2020
@jakirkham
jakirkham
deleted the

simp_txt_coding_db_stores

branch
December 3, 2020 23:23
@jakirkham
jakirkham
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Thanks Matthias! 😄
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Failures on Python 3.10


2 participants

@jakirkham@Carreau

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

Skip to content
Simplify text handling in DB Stores - #670
Merged
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Dec 3, 2020
Merged
Simplify text handling in DB Stores#670
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Conversation
@jakirkham
@jakirkhamjakirkham
commented
Dec 3, 2020

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Fixes#669
LMDBStore had its own way of handling text before ensure_text was added to Numcodecs. With that utility function now available, we can simplify this a bit and avoid some subtleties of the LMDB implementation.
Similarly DBMStore had some of its own text handling issues that can be solved the same way.
Finally inline all str.encode calls to make it clearer what is happening in both LMDBStore and DBMStore.
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
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020

Closed

@jakirkhamjakirkham
changed the title
Simp text handling in DB StoresSimplify text handling in DB StoresDec 3, 2020
@Carreau
Carreau
commented
Dec 3, 2020

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Would that bump the minimum version of lmdb ?
@codecov
codecovBot
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Dec 3, 2020•

edited

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Codecov Report
Merging #670 (ed1ffca) into master (a5dfc3b) will not change coverage.

The diff coverage is 100.00%.
@@ Coverage Diff @@## master #670 +/- ##
=========================================
Coverage 100.00% 100.00% =========================================
Files 27 27 Lines 10094 10087 -7 =========================================
- Hits 10094 10087 -7 
Impacted FilesCoverage Δ
zarr/storage.py100.00% <100.00%> (ø)
@jakirkham
jakirkham
commented
Dec 3, 2020

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MemberAuthor
Would that bump the minimum version of lmdb ?
Shouldn't affect it.
Basically ensure_text leverages the Python Buffer Protocol to coerce the data (bytes or other object) to a NumPy array without copying. Effectively this normalizes the data we are working with so we don't need to know about LMDB Buffer objects or whatever other object might come up ( MongoDB had a similar issue #401 ). Then we perform the decode step on the NumPy array, which we already know to work.
@CarreauCarreau
added this to the v2.7 milestone
Dec 3, 2020
@Carreau
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commented
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Thanks for the explanation; let's get that in.
@Carreau
Carreau
merged commit 1464d90
into
zarr-developers:masterDec 3, 2020
@jakirkham
jakirkham
deleted the

simp_txt_coding_db_stores

branch
December 3, 2020 23:23
@jakirkham
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Thanks Matthias! 😄
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@CarreauCarreauCarreau approved these changes
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Successfully merging this pull request may close these issues.

Failures on Python 3.10


2 participants

@jakirkham@Carreau

, '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
Simplify text handling in DB Stores - #670
Merged
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Dec 3, 2020
Merged
Simplify text handling in DB Stores#670
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Conversation
@jakirkham
@jakirkhamjakirkham
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Dec 3, 2020

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Fixes#669
LMDBStore had its own way of handling text before ensure_text was added to Numcodecs. With that utility function now available, we can simplify this a bit and avoid some subtleties of the LMDB implementation.
Similarly DBMStore had some of its own text handling issues that can be solved the same way.
Finally inline all str.encode calls to make it clearer what is happening in both LMDBStore and DBMStore.
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
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020

Closed

@jakirkhamjakirkham
changed the title
Simp text handling in DB StoresSimplify text handling in DB StoresDec 3, 2020
@Carreau
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Dec 3, 2020

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Would that bump the minimum version of lmdb ?
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Dec 3, 2020•

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Codecov Report
Merging #670 (ed1ffca) into master (a5dfc3b) will not change coverage.

The diff coverage is 100.00%.
@@ Coverage Diff @@## master #670 +/- ##
=========================================
Coverage 100.00% 100.00% =========================================
Files 27 27 Lines 10094 10087 -7 =========================================
- Hits 10094 10087 -7 
Impacted FilesCoverage Δ
zarr/storage.py100.00% <100.00%> (ø)
@jakirkham
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Would that bump the minimum version of lmdb ?
Shouldn't affect it.
Basically ensure_text leverages the Python Buffer Protocol to coerce the data (bytes or other object) to a NumPy array without copying. Effectively this normalizes the data we are working with so we don't need to know about LMDB Buffer objects or whatever other object might come up ( MongoDB had a similar issue #401 ). Then we perform the decode step on the NumPy array, which we already know to work.
@CarreauCarreau
added this to the v2.7 milestone
Dec 3, 2020
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Thanks for the explanation; let's get that in.
@Carreau
Carreau
merged commit 1464d90
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zarr-developers:masterDec 3, 2020
@jakirkham
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December 3, 2020 23:23
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Thanks Matthias! 😄
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Failures on Python 3.10


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, '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
Simplify text handling in DB Stores - #670
Merged
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Dec 3, 2020
Merged
Simplify text handling in DB Stores#670
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Conversation
@jakirkham
@jakirkhamjakirkham
commented
Dec 3, 2020

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Fixes#669
LMDBStore had its own way of handling text before ensure_text was added to Numcodecs. With that utility function now available, we can simplify this a bit and avoid some subtleties of the LMDB implementation.
Similarly DBMStore had some of its own text handling issues that can be solved the same way.
Finally inline all str.encode calls to make it clearer what is happening in both LMDBStore and DBMStore.
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
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020

Closed

@jakirkhamjakirkham
changed the title
Simp text handling in DB StoresSimplify text handling in DB StoresDec 3, 2020
@Carreau
Carreau
commented
Dec 3, 2020

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Would that bump the minimum version of lmdb ?
@codecov
codecovBot
commented
Dec 3, 2020•

edited

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Codecov Report
Merging #670 (ed1ffca) into master (a5dfc3b) will not change coverage.

The diff coverage is 100.00%.
@@ Coverage Diff @@## master #670 +/- ##
=========================================
Coverage 100.00% 100.00% =========================================
Files 27 27 Lines 10094 10087 -7 =========================================
- Hits 10094 10087 -7 
Impacted FilesCoverage Δ
zarr/storage.py100.00% <100.00%> (ø)
@jakirkham
jakirkham
commented
Dec 3, 2020

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Would that bump the minimum version of lmdb ?
Shouldn't affect it.
Basically ensure_text leverages the Python Buffer Protocol to coerce the data (bytes or other object) to a NumPy array without copying. Effectively this normalizes the data we are working with so we don't need to know about LMDB Buffer objects or whatever other object might come up ( MongoDB had a similar issue #401 ). Then we perform the decode step on the NumPy array, which we already know to work.
@CarreauCarreau
added this to the v2.7 milestone
Dec 3, 2020
@Carreau
Carreau
commented
Dec 3, 2020

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Thanks for the explanation; let's get that in.
@Carreau
Carreau
merged commit 1464d90
into
zarr-developers:masterDec 3, 2020
@jakirkham
jakirkham
deleted the

simp_txt_coding_db_stores

branch
December 3, 2020 23:23
@jakirkham
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Thanks Matthias! 😄
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@CarreauCarreauCarreau approved these changes
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Failures on Python 3.10


2 participants

@jakirkham@Carreau

, '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
Simplify text handling in DB Stores - #670
Merged
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Dec 3, 2020
Merged
Simplify text handling in DB Stores#670
Carreau merged 4 commits into
zarr-developers:masterfrom 
jakirkham:simp_txt_coding_db_stores
Conversation
@jakirkham
@jakirkhamjakirkham
commented
Dec 3, 2020

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Fixes#669
LMDBStore had its own way of handling text before ensure_text was added to Numcodecs. With that utility function now available, we can simplify this a bit and avoid some subtleties of the LMDB implementation.
Similarly DBMStore had some of its own text handling issues that can be solved the same way.
Finally inline all str.encode calls to make it clearer what is happening in both LMDBStore and DBMStore.
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
  •  AppVeyor and Travis CI passes
  •  Test coverage is 100% (Coveralls passes)
@jakirkhamjakirkham
mentioned this pull request
Dec 3, 2020

Closed

@jakirkhamjakirkham
changed the title
Simp text handling in DB StoresSimplify text handling in DB StoresDec 3, 2020
@Carreau
Carreau
commented
Dec 3, 2020

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Contributor
Would that bump the minimum version of lmdb ?
@codecov
codecovBot
commented
Dec 3, 2020•

edited

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Codecov Report
Merging #670 (ed1ffca) into master (a5dfc3b) will not change coverage.

The diff coverage is 100.00%.
@@ Coverage Diff @@## master #670 +/- ##
=========================================
Coverage 100.00% 100.00% =========================================
Files 27 27 Lines 10094 10087 -7 =========================================
- Hits 10094 10087 -7 
Impacted FilesCoverage Δ
zarr/storage.py100.00% <100.00%> (ø)
@jakirkham
jakirkham
commented
Dec 3, 2020

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MemberAuthor
Would that bump the minimum version of lmdb ?
Shouldn't affect it.
Basically ensure_text leverages the Python Buffer Protocol to coerce the data (bytes or other object) to a NumPy array without copying. Effectively this normalizes the data we are working with so we don't need to know about LMDB Buffer objects or whatever other object might come up ( MongoDB had a similar issue #401 ). Then we perform the decode step on the NumPy array, which we already know to work.
@CarreauCarreau
added this to the v2.7 milestone
Dec 3, 2020
@Carreau
Carreau
commented
Dec 3, 2020

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Thanks for the explanation; let's get that in.
@Carreau
Carreau
merged commit 1464d90
into
zarr-developers:masterDec 3, 2020
@jakirkham
jakirkham
deleted the

simp_txt_coding_db_stores

branch
December 3, 2020 23:23
@jakirkham
jakirkham
commented
Dec 3, 2020

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Thanks Matthias! 😄
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1 more reviewer

@CarreauCarreauCarreau approved these changes
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Successfully merging this pull request may close these issues.

Failures on Python 3.10


2 participants

@jakirkham@Carreau