') + ')', 'gi'); if (regex.test(text)) { found = true; var frag = document.createDocumentFragment(); var parts = text.split(regex); parts.forEach(function(part, i) { if (i % 2 === 0) { frag.appendChild(document.createTextNode(part)); } else { var span = document.createElement('span'); span.className = 'userscript-highlight'; span.textContent = part; frag.appendChild(span); } }); node.parentNode.replaceChild(frag, node); } }); } else if (node.nodeType === 1 && node.childNodes) { // element var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT']; if (!skipTags.includes(node.tagName)) { Array.from(node.childNodes).forEach(highlight); } } } highlight(document.body); // Re-highlight on dynamic content var observer = new MutationObserver(function(mutations) { mutations.forEach(function(m) { m.addedNodes.forEach(function(node) { if (node.nodeType === 1 || node.nodeType === 3) highlight(node); }); }); }); observer.observe(document.body, { childList: true, subtree: true }); })(); } } catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + ', 'i'); if (__m === '*' || __re.test(location.href)) { // Strip utm_, fbclid, gclid, etc. from all links on page (function() { var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content', 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid', 'ref', 'ref_src', 'source', 'medium', 'campaign']; function cleanUrl(url) { try { var u = new URL(url, window.location.origin); var changed = false; trackingParams.forEach(function(p) { if (u.searchParams.has(p)) { u.searchParams.delete(p); changed = true; } }); return changed ? u.toString() : url; } catch (e) { return url; } } function cleanLinks() { document.querySelectorAll('a[href]').forEach(function(a) { var clean = cleanUrl(a.href); if (clean !== a.href) a.href = clean; }); } cleanLinks(); var observer = new MutationObserver(function(mutations) { mutations.forEach(function(m) { m.addedNodes.forEach(function(node) { if (node.nodeType === 1) { if (node.tagName === 'A') cleanLinks(); node.querySelectorAll('a[href]').forEach(function(a) { var clean = cleanUrl(a.href); if (clean !== a.href) a.href = clean; }); } }); }); }); observer.observe(document.body, { childList: true, subtree: true }); })(); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + ', 'i'); if (__m === '*' || __re.test(location.href)) { // Auto-enable theater mode on YouTube (function() { function tryTheater() { var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]'); if (btn && !btn.classList.contains('activated')) { btn.click(); } } // Try immediately tryTheater(); // Try after navigation (SPA) var lastUrl = location.href; setInterval(function() { if (location.href !== lastUrl) { lastUrl = location.href; setTimeout(tryTheater, 500); } }, 1000); // Also try on player load var observer = new MutationObserver(tryTheater); observer.observe(document.body, { childList: true, subtree: true }); })(); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + ', 'i'); if (__m === '*' || __re.test(location.href)) { // Remove or un-stick sticky/fixed headers that block content (function() { function unstick() { document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) { if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') { el.style.position = 'static'; el.style.top = 'auto'; el.style.zIndex = 'auto'; } }); } unstick(); var observer = new MutationObserver(unstick); observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] }); })(); } } catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); } })(); })(); fix transform points with duplicate indices by LucaMarconato · Pull Request #1129 · scverse/spatialdata · GitHub
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fix transform points with duplicate indices - #1129

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LucaMarconato merged 3 commits into
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fix/transform-points-duplicate-indices
May 15, 2026
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fix transform points with duplicate indices#1129
LucaMarconato merged 3 commits into
mainfrom
fix/transform-points-duplicate-indices

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@LucaMarconatoLucaMarconato commented May 15, 2026

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Closes#1105

The problem is that transcripts given by spatialdata_io.xenium() have non-unique indices across partitions (no table is annotating them, so uniqueness is not necessary).

The preserves the indices upon transformation.

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LucaMarconato marked this pull request as draft May 15, 2026 11:35
@LucaMarconato@claude
Fix spatialdata_attrs lost after transform on points with duplicate i…
38c5262
…ndex
dd.from_delayed starts with empty attrs, so spatialdata_attrs (feature_key,
instance_key) was silently dropped. Copy all non-transform attrs from the
original element to restore the previous behaviour.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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LucaMarconato marked this pull request as ready for review May 15, 2026 12:25
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.28%. Comparing base (5e3b982) to head (3500317).
⚠️ Report is 15 commits behind head on main.

Additional details and impacted files
@@ Coverage Diff @@## main #1129 +/- ##
=======================================
Coverage 92.27% 92.28% =======================================
Files 51 51 Lines 7797 7804 +7 =======================================
+ Hits 7195 7202 +7 
Misses 602 602
Files with missing linesCoverage Δ
src/spatialdata/_core/operations/transform.py91.73% <100.00%> (+0.24%)⬆️
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

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LucaMarconato enabled auto-merge (squash) May 15, 2026 12:29
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LucaMarconato merged commit accf496 into mainMay 15, 2026
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LucaMarconato deleted the fix/transform-points-duplicate-indices branch May 15, 2026 12:31
@enric-bazzenric-bazz mentioned this pull request Jun 23, 2026
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Error attempting to transform xenium transcript coordinate using transform()

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