') + ')', '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); } })(); })(); Reduce warnings by LucaMarconato · Pull Request #1113 · scverse/spatialdata · GitHub
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Reduce warnings - #1113

Merged
LucaMarconato merged 13 commits into
mainfrom
less-warnings
May 5, 2026
Merged

Reduce warnings#1113
LucaMarconato merged 13 commits into
mainfrom
less-warnings

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@LucaMarconato

@LucaMarconatoLucaMarconato commented May 5, 2026

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Reduce warnings, in particular:

  • Use zip(strict=True) when converting tuple chunks to dict in RasterSchema
  • Copy AnnData views before modifying .uns in TableModel.parse
  • Use explicit string obs index in AnnData construction to avoid implicit index warnings
  • Add .copy() after compute()/slice to avoid pandas SettingWithCopyWarning (CoW)
  • Remove unused docs/_templates autosummary files
  • Update tutorials submodule
  • Fix pandas CoW issues

LucaMarconatoand others added 5 commits May 5, 2026 13:59
@LucaMarconato@claude
reduce warnings and fix pandas CoW issues
24a161f
- Use zip(strict=True) when converting tuple chunks to dict in RasterSchema
- Copy AnnData views before modifying .uns in TableModel.parse
- Use explicit string obs index in AnnData construction to avoid implicit index warnings
- Add .copy() after compute()/slice to avoid pandas SettingWithCopyWarning (CoW)
- Remove unused docs/_templates autosummary files
- Update tutorials submodule
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@LucaMarconato
Merge branch 'main' into less-warnings
44dbbdf
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
0866ab6
for more information, see https://pre-commit.ci
@LucaMarconato
fix pre-commit
1fd8c0b
@LucaMarconato
Merge branch 'less-warnings' ofhttps://github.com/scverse/spatialdata…
16ce7c3
…into less-warnings
@codecov

codecovBot commented May 5, 2026•
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.87%. Comparing base (8d7f72f) to head (7df090f).
⚠️ Report is 26 commits behind head on main.

Additional details and impacted files
@@ Coverage Diff @@## main #1113 +/- ##
==========================================
- Coverage 91.93% 91.87% -0.07% 
==========================================
Files 51 51 Lines 7772 7775 +3 ==========================================
- Hits 7145 7143 -2 - Misses 627 632 +5
Files with missing linesCoverage Δ
src/spatialdata/datasets.py100.00% <100.00%> (ø)
src/spatialdata/models/models.py87.78% <100.00%> (-0.89%)⬇️

... and 1 file with indirect coverage changes

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

LucaMarconatoand others added 6 commits May 5, 2026 14:55
@LucaMarconato@claude
fix: avoid coordinate column collision in test_points_model to suppre…
da5d363
…ss INFO noise
Build the dataframe with only the coordinate columns actually needed for
each branch: source columns (A/B/C) when a coordinates mapping is provided,
target columns (x/y/z) otherwise. This prevents the rename-drop and
z-ignored-in-2D INFO messages (240 occurrences) from firing during tests.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@LucaMarconato
Merge branch 'main' into less-warnings
91734a7
@LucaMarconato@claude
fix: use pd.Categorical for feature_key column in test_points_model t…
1fe839b
…o suppress WARNING noise
The target column was a plain str Series; PointsModel.parse() converted it
to an unknown-categories dask Categorical, triggering a performance warning
on every parametrized invocation. Using pd.Categorical with known categories
up-front avoids the conversion path entirely.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@LucaMarconato@claude
fix: suppress 'not stored in most current format' UserWarning in old-…
0d9aa8c
…format tests
Use `re.match`-compatible pattern (anchored at start) and add
`@pytest.mark.filterwarnings` to standalone parametrized tests outside
`TestReadWrite` that intentionally exercise the V01 container format.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
81c47a0
for more information, see https://pre-commit.ci
@LucaMarconato@claude
refactor: simplify old-format warning suppression using pytest.mark.f…
110a6ce
…ilterwarnings
Replace verbose autouse fixtures (catch_warnings + isinstance check) with a
single @pytest.mark.filterwarnings decorator on each class/function. The
isinstance guard was unnecessary because V02 tests never emit the warning,
so the filter is a harmless no-op for them. Also removes now-unused
`import warnings` from test_format.py and test_readwrite.py, and
CurrentSpatialDataContainerFormat from test_attrs_io.py.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@LucaMarconatoLucaMarconato mentioned this pull request May 5, 2026
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@LucaMarconato

LucaMarconato commented May 5, 2026

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Recap:

  • Reduced the number of warnings in general
  • Approximately halved the numbers of warnings emitted (and not caught) during tests. ~100 left
  • Greatly reduced the number of logs (INFO, WARNING), during tests.

@LucaMarconato
LucaMarconato merged commit d0582ec into mainMay 5, 2026
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@LucaMarconato
LucaMarconato deleted the less-warnings branch May 5, 2026 16:09
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