Pins distributed; better categorical handing for points parser - #1061

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Pins distributed; better categorical handing for points parser#1061
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Minor change

The latest daskdistributed cannot be used with the second latest dask (the latest dask is not supported because it's not supported in ome-zarr-py). This PR adds an upper bound.

Main change

Improves performance of points parsing by eliminating superfluous conversions to categorical for columns that are not the feature_key column. Also warns the user that converting a column to categorical prior to parsing (by preserving the known status of the categories), improves performance.

Tested with Xenium data (performance of point parsing improves ~20x for ~100 million transcripts): .

@LucaMarconatoLucaMarconato mentioned this pull request Feb 3, 2026
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@LucaMarconatoLucaMarconato changed the title Improve handling of categoricals for feature_key in pointsPins distributed; better categorical handing for points parserFeb 3, 2026
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✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.24%. Comparing base (db34783) to head (9b60a23).
⚠️ Report is 17 commits behind head on main.

Additional details and impacted files
@@ Coverage Diff @@## main #1061 +/- ##
==========================================
+ Coverage 92.21% 92.24% +0.02% 
==========================================
Files 49 49 Lines 7593 7594 +1 ==========================================
+ Hits 7002 7005 +3 + Misses 591 589 -2
Files with missing linesCoverage Δ
src/spatialdata/models/models.py88.99% <100.00%> (+0.38%)⬆️
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@LucaMarconato
LucaMarconato merged commit 3cdf3d8 into mainFeb 3, 2026
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LucaMarconato deleted the performance/points-parsing branch February 3, 2026 17:54
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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" + '

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Pins distributed; better categorical handing for points parser - #1061
Merged
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
Feb 3, 2026
Merged
Pins distributed; better categorical handing for points parser#1061
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
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@LucaMarconatoLucaMarconato
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Minor change
The latest daskdistributed cannot be used with the second latest dask (the latest dask is not supported because it's not supported in ome-zarr-py). This PR adds an upper bound.
Main change
Improves performance of points parsing by eliminating superfluous conversions to categorical for columns that are not the feature_key column. Also warns the user that converting a column to categorical prior to parsing (by preserving the known status of the categories), improves performance.
Tested with Xenium data (performance of point parsing improves ~20x for ~100 million transcripts): .
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 3, 2026
 Merged

@LucaMarconatoLucaMarconato
changed the title
Improve handling of categoricals for feature_key in pointsPins distributed; better categorical handing for points parserFeb 3, 2026
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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.24%. Comparing base (db34783) to head (9b60a23).
⚠️ Report is 17 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1061 +/- ##
==========================================
+ Coverage 92.21% 92.24% +0.02% 
==========================================
Files 49 49 Lines 7593 7594 +1 ==========================================
+ Hits 7002 7005 +3 + Misses 591 589 -2 
Files with missing linesCoverage Δ
src/spatialdata/models/models.py88.99% <100.00%> (+0.38%)⬆️
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
LucaMarconato
merged commit 3cdf3d8
into
mainFeb 3, 2026

9 checks passed

@LucaMarconato
LucaMarconato
deleted the

performance/points-parsing

branch
February 3, 2026 17:54
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, '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('^' + ".*" + '

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Pins distributed; better categorical handing for points parser - #1061
Merged
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
Feb 3, 2026
Merged
Pins distributed; better categorical handing for points parser#1061
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
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@LucaMarconatoLucaMarconato
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Minor change
The latest daskdistributed cannot be used with the second latest dask (the latest dask is not supported because it's not supported in ome-zarr-py). This PR adds an upper bound.
Main change
Improves performance of points parsing by eliminating superfluous conversions to categorical for columns that are not the feature_key column. Also warns the user that converting a column to categorical prior to parsing (by preserving the known status of the categories), improves performance.
Tested with Xenium data (performance of point parsing improves ~20x for ~100 million transcripts): .
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 3, 2026
 Merged

@LucaMarconatoLucaMarconato
changed the title
Improve handling of categoricals for feature_key in pointsPins distributed; better categorical handing for points parserFeb 3, 2026
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edited

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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.24%. Comparing base (db34783) to head (9b60a23).
⚠️ Report is 17 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1061 +/- ##
==========================================
+ Coverage 92.21% 92.24% +0.02% 
==========================================
Files 49 49 Lines 7593 7594 +1 ==========================================
+ Hits 7002 7005 +3 + Misses 591 589 -2 
Files with missing linesCoverage Δ
src/spatialdata/models/models.py88.99% <100.00%> (+0.38%)⬆️
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
LucaMarconato
merged commit 3cdf3d8
into
mainFeb 3, 2026

9 checks passed

@LucaMarconato
LucaMarconato
deleted the

performance/points-parsing

branch
February 3, 2026 17:54
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, '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
Pins distributed; better categorical handing for points parser - #1061
Merged
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
Feb 3, 2026
Merged
Pins distributed; better categorical handing for points parser#1061
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
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@LucaMarconatoLucaMarconato
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Minor change
The latest daskdistributed cannot be used with the second latest dask (the latest dask is not supported because it's not supported in ome-zarr-py). This PR adds an upper bound.
Main change
Improves performance of points parsing by eliminating superfluous conversions to categorical for columns that are not the feature_key column. Also warns the user that converting a column to categorical prior to parsing (by preserving the known status of the categories), improves performance.
Tested with Xenium data (performance of point parsing improves ~20x for ~100 million transcripts): .
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 3, 2026
 Merged

@LucaMarconatoLucaMarconato
changed the title
Improve handling of categoricals for feature_key in pointsPins distributed; better categorical handing for points parserFeb 3, 2026
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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.24%. Comparing base (db34783) to head (9b60a23).
⚠️ Report is 17 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1061 +/- ##
==========================================
+ Coverage 92.21% 92.24% +0.02% 
==========================================
Files 49 49 Lines 7593 7594 +1 ==========================================
+ Hits 7002 7005 +3 + Misses 591 589 -2 
Files with missing linesCoverage Δ
src/spatialdata/models/models.py88.99% <100.00%> (+0.38%)⬆️
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
LucaMarconato
merged commit 3cdf3d8
into
mainFeb 3, 2026

9 checks passed

@LucaMarconato
LucaMarconato
deleted the

performance/points-parsing

branch
February 3, 2026 17:54
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, '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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Pins distributed; better categorical handing for points parser - #1061
Merged
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
Feb 3, 2026
Merged
Pins distributed; better categorical handing for points parser#1061
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
Conversation
@LucaMarconato
@LucaMarconatoLucaMarconato
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edited

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Minor change
The latest daskdistributed cannot be used with the second latest dask (the latest dask is not supported because it's not supported in ome-zarr-py). This PR adds an upper bound.
Main change
Improves performance of points parsing by eliminating superfluous conversions to categorical for columns that are not the feature_key column. Also warns the user that converting a column to categorical prior to parsing (by preserving the known status of the categories), improves performance.
Tested with Xenium data (performance of point parsing improves ~20x for ~100 million transcripts): .
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 3, 2026
 Merged

@LucaMarconatoLucaMarconato
changed the title
Improve handling of categoricals for feature_key in pointsPins distributed; better categorical handing for points parserFeb 3, 2026
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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.24%. Comparing base (db34783) to head (9b60a23).
⚠️ Report is 17 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1061 +/- ##
==========================================
+ Coverage 92.21% 92.24% +0.02% 
==========================================
Files 49 49 Lines 7593 7594 +1 ==========================================
+ Hits 7002 7005 +3 + Misses 591 589 -2 
Files with missing linesCoverage Δ
src/spatialdata/models/models.py88.99% <100.00%> (+0.38%)⬆️
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
LucaMarconato
merged commit 3cdf3d8
into
mainFeb 3, 2026

9 checks passed

@LucaMarconato
LucaMarconato
deleted the

performance/points-parsing

branch
February 3, 2026 17:54
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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('^' + ".*" + '

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Pins distributed; better categorical handing for points parser - #1061
Merged
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
Feb 3, 2026
Merged
Pins distributed; better categorical handing for points parser#1061
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
Conversation
@LucaMarconato
@LucaMarconatoLucaMarconato
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Minor change
The latest daskdistributed cannot be used with the second latest dask (the latest dask is not supported because it's not supported in ome-zarr-py). This PR adds an upper bound.
Main change
Improves performance of points parsing by eliminating superfluous conversions to categorical for columns that are not the feature_key column. Also warns the user that converting a column to categorical prior to parsing (by preserving the known status of the categories), improves performance.
Tested with Xenium data (performance of point parsing improves ~20x for ~100 million transcripts): .
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 3, 2026
 Merged

@LucaMarconatoLucaMarconato
changed the title
Improve handling of categoricals for feature_key in pointsPins distributed; better categorical handing for points parserFeb 3, 2026
@codecov
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edited

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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.24%. Comparing base (db34783) to head (9b60a23).
⚠️ Report is 17 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1061 +/- ##
==========================================
+ Coverage 92.21% 92.24% +0.02% 
==========================================
Files 49 49 Lines 7593 7594 +1 ==========================================
+ Hits 7002 7005 +3 + Misses 591 589 -2 
Files with missing linesCoverage Δ
src/spatialdata/models/models.py88.99% <100.00%> (+0.38%)⬆️
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
LucaMarconato
merged commit 3cdf3d8
into
mainFeb 3, 2026

9 checks passed

@LucaMarconato
LucaMarconato
deleted the

performance/points-parsing

branch
February 3, 2026 17:54
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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
Pins distributed; better categorical handing for points parser - #1061
Merged
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
Feb 3, 2026
Merged
Pins distributed; better categorical handing for points parser#1061
LucaMarconato merged 2 commits into
mainfrom 
performance/points-parsing
Conversation
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Minor change
The latest daskdistributed cannot be used with the second latest dask (the latest dask is not supported because it's not supported in ome-zarr-py). This PR adds an upper bound.
Main change
Improves performance of points parsing by eliminating superfluous conversions to categorical for columns that are not the feature_key column. Also warns the user that converting a column to categorical prior to parsing (by preserving the known status of the categories), improves performance.
Tested with Xenium data (performance of point parsing improves ~20x for ~100 million transcripts): .
@LucaMarconatoLucaMarconato
mentioned this pull request
Feb 3, 2026
 Merged

@LucaMarconatoLucaMarconato
changed the title
Improve handling of categoricals for feature_key in pointsPins distributed; better categorical handing for points parserFeb 3, 2026
@codecov
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commented
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edited

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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.24%. Comparing base (db34783) to head (9b60a23).
⚠️ Report is 17 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1061 +/- ##
==========================================
+ Coverage 92.21% 92.24% +0.02% 
==========================================
Files 49 49 Lines 7593 7594 +1 ==========================================
+ Hits 7002 7005 +3 + Misses 591 589 -2 
Files with missing linesCoverage Δ
src/spatialdata/models/models.py88.99% <100.00%> (+0.38%)⬆️
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Pins distributed; better categorical handing for points parser - #1061
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performance/points-parsing
Feb 3, 2026
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Pins distributed; better categorical handing for points parser#1061
LucaMarconato merged 2 commits into
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performance/points-parsing
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Minor change
The latest daskdistributed cannot be used with the second latest dask (the latest dask is not supported because it's not supported in ome-zarr-py). This PR adds an upper bound.
Main change
Improves performance of points parsing by eliminating superfluous conversions to categorical for columns that are not the feature_key column. Also warns the user that converting a column to categorical prior to parsing (by preserving the known status of the categories), improves performance.
Tested with Xenium data (performance of point parsing improves ~20x for ~100 million transcripts): .
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Improve handling of categoricals for feature_key in pointsPins distributed; better categorical handing for points parserFeb 3, 2026
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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.24%. Comparing base (db34783) to head (9b60a23).
⚠️ Report is 17 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1061 +/- ##
==========================================
+ Coverage 92.21% 92.24% +0.02% 
==========================================
Files 49 49 Lines 7593 7594 +1 ==========================================
+ Hits 7002 7005 +3 + Misses 591 589 -2 
Files with missing linesCoverage Δ
src/spatialdata/models/models.py88.99% <100.00%> (+0.38%)⬆️
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@LucaMarconato
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merged commit 3cdf3d8
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mainFeb 3, 2026

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@LucaMarconato
LucaMarconato
deleted the

performance/points-parsing

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February 3, 2026 17:54
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