Io/hot fix by LucaMarconato · Pull Request #138 · scverse/spatialdata

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 contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert Uh oh! There was an error while loading. Please reload this page. scverse /spatialdataPublic Notifications You must be signed in to change notification settings Fork 93 Star 387 Code Issues263 Pull requests17 Discussions Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights Io/hot fix#138 New issue Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Sign up for GitHub By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails. Already on GitHub? Sign in to your account Merged LucaMarconato merged 23 commits into main from io/hot_fixMar 2, 2023 Conversation 74 Commits 23 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged Io/hot fix #138 Show file tree Hide file tree Changes from all commits Commits Show all changes 23 commits Select commit Hold shift + click to select a range 5953adb wip (all tests passes) LucaMarconato Feb 14, 2023e34d602 Merge branch 'old_legacy_code' into io/hot_fix LucaMarconato Feb 14, 2023ff8ea87 merged with most recent pr LucaMarconato Feb 14, 202347d240f adedd TODO for improving performance LucaMarconato Feb 14, 2023572a4c6 added safety assert before calling rmtree LucaMarconato Feb 14, 2023ed3a37f fixed a performance detail that I had left as a TODO LucaMarconato Feb 15, 20231e6a08f removed shutil usage from .write() LucaMarconato Feb 16, 20236200757 removed _called_from_write parameter LucaMarconato Feb 16, 20239c55ec8 removed all the other shutil usages LucaMarconato Feb 16, 2023e52d1df [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 16, 20238dc1a94 added docstrings for landmark-based align funcs; slighly modified them LucaMarconato Feb 16, 2023c3ea935 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Feb 16, 2023a04987d better tests for landmark-based alignment LucaMarconato Feb 16, 2023823b871 using Path instead of str LucaMarconato Feb 16, 2023e097dbf AnnData.concatenate -> ad.concat LucaMarconato Feb 16, 20235aa93a9 Apply suggestions from code review LucaMarconato Feb 22, 2023d5ed060 Merge branch 'main' into io/hot_fix LucaMarconato Feb 22, 2023fd6cddb removed tmpdir based atomic update/save LucaMarconato Feb 27, 20235ad85cc Merge branch 'main' into io/hot_fix giovp Mar 2, 2023f2e5ef3 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Mar 2, 2023584ad9d Apply suggestions from code review LucaMarconato Mar 2, 202316c4801 added os.path.realpath(); implemented giovp suggestions after review LucaMarconato Mar 2, 2023a775f67 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Mar 2, 2023 File filter Filter by extension Filter by extension .py (5) All 1 file type selected Viewed files Clear filters Conversations Failed to load comments. Loading Uh oh! There was an error while loading. Please reload this page. Jump to Jump to file Failed to load files. Loading Uh oh! There was an error while loading. Please reload this page. Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace spatialdata/_core/_spatialdata.py _spatialdata.py spatialdata/_io/read.py read.py spatialdata/utils.py utils.py tests/_io/test_readwrite.py test_readwrite.py tests/test_utils.py test_utils.py There are no files selected for viewing Loading Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 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Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , '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 contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert Uh oh! There was an error while loading. Please reload this page. scverse /spatialdataPublic Notifications You must be signed in to change notification settings Fork 93 Star 387 Code Issues263 Pull requests17 Discussions Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights Io/hot fix#138 New issue Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Sign up for GitHub By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails. Already on GitHub? Sign in to your account Merged LucaMarconato merged 23 commits into main from io/hot_fixMar 2, 2023 Conversation 74 Commits 23 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged Io/hot fix #138 Show file tree Hide file tree Changes from all commits Commits Show all changes 23 commits Select commit Hold shift + click to select a range 5953adb wip (all tests passes) LucaMarconato Feb 14, 2023e34d602 Merge branch 'old_legacy_code' into io/hot_fix LucaMarconato Feb 14, 2023ff8ea87 merged with most recent pr LucaMarconato Feb 14, 202347d240f adedd TODO for improving performance LucaMarconato Feb 14, 2023572a4c6 added safety assert before calling rmtree LucaMarconato Feb 14, 2023ed3a37f fixed a performance detail that I had left as a TODO LucaMarconato Feb 15, 20231e6a08f removed shutil usage from .write() LucaMarconato Feb 16, 20236200757 removed _called_from_write parameter LucaMarconato Feb 16, 20239c55ec8 removed all the other shutil usages LucaMarconato Feb 16, 2023e52d1df [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 16, 20238dc1a94 added docstrings for landmark-based align funcs; slighly modified them LucaMarconato Feb 16, 2023c3ea935 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Feb 16, 2023a04987d better tests for landmark-based alignment LucaMarconato Feb 16, 2023823b871 using Path instead of str LucaMarconato Feb 16, 2023e097dbf AnnData.concatenate -> ad.concat LucaMarconato Feb 16, 20235aa93a9 Apply suggestions from code review LucaMarconato Feb 22, 2023d5ed060 Merge branch 'main' into io/hot_fix LucaMarconato Feb 22, 2023fd6cddb removed tmpdir based atomic update/save LucaMarconato Feb 27, 20235ad85cc Merge branch 'main' into io/hot_fix giovp Mar 2, 2023f2e5ef3 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Mar 2, 2023584ad9d Apply suggestions from code review LucaMarconato Mar 2, 202316c4801 added os.path.realpath(); implemented giovp suggestions after review LucaMarconato Mar 2, 2023a775f67 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Mar 2, 2023 File filter Filter by extension Filter by extension .py (5) All 1 file type selected Viewed files Clear filters Conversations Failed to load comments. Loading Uh oh! There was an error while loading. Please reload this page. Jump to Jump to file Failed to load files. Loading Uh oh! There was an error while loading. Please reload this page. Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace spatialdata/_core/_spatialdata.py _spatialdata.py spatialdata/_io/read.py read.py spatialdata/utils.py utils.py tests/_io/test_readwrite.py test_readwrite.py tests/test_utils.py test_utils.py There are no files selected for viewing Loading Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later. Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , '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 contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert Uh oh! There was an error while loading. Please reload this page. scverse /spatialdataPublic Notifications You must be signed in to change notification settings Fork 93 Star 387 Code Issues263 Pull requests17 Discussions Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights Io/hot fix#138 New issue Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Sign up for GitHub By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails. Already on GitHub? Sign in to your account Merged LucaMarconato merged 23 commits into main from io/hot_fixMar 2, 2023 Conversation 74 Commits 23 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged Io/hot fix #138 Show file tree Hide file tree Changes from all commits Commits Show all changes 23 commits Select commit Hold shift + click to select a range 5953adb wip (all tests passes) LucaMarconato Feb 14, 2023e34d602 Merge branch 'old_legacy_code' into io/hot_fix LucaMarconato Feb 14, 2023ff8ea87 merged with most recent pr LucaMarconato Feb 14, 202347d240f adedd TODO for improving performance LucaMarconato Feb 14, 2023572a4c6 added safety assert before calling rmtree LucaMarconato Feb 14, 2023ed3a37f fixed a performance detail that I had left as a TODO LucaMarconato Feb 15, 20231e6a08f removed shutil usage from .write() LucaMarconato Feb 16, 20236200757 removed _called_from_write parameter LucaMarconato Feb 16, 20239c55ec8 removed all the other shutil usages LucaMarconato Feb 16, 2023e52d1df [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 16, 20238dc1a94 added docstrings for landmark-based align funcs; slighly modified them LucaMarconato Feb 16, 2023c3ea935 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Feb 16, 2023a04987d better tests for landmark-based alignment LucaMarconato Feb 16, 2023823b871 using Path instead of str LucaMarconato Feb 16, 2023e097dbf AnnData.concatenate -> ad.concat LucaMarconato Feb 16, 20235aa93a9 Apply suggestions from code review LucaMarconato Feb 22, 2023d5ed060 Merge branch 'main' into io/hot_fix LucaMarconato Feb 22, 2023fd6cddb removed tmpdir based atomic update/save LucaMarconato Feb 27, 20235ad85cc Merge branch 'main' into io/hot_fix giovp Mar 2, 2023f2e5ef3 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Mar 2, 2023584ad9d Apply suggestions from code review LucaMarconato Mar 2, 202316c4801 added os.path.realpath(); implemented giovp suggestions after review LucaMarconato Mar 2, 2023a775f67 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Mar 2, 2023 File filter Filter by extension Filter by extension .py (5) All 1 file type selected Viewed files Clear filters Conversations Failed to load comments. Loading Uh oh! There was an error while loading. Please reload this page. Jump to Jump to file Failed to load files. Loading Uh oh! There was an error while loading. Please reload this page. Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace spatialdata/_core/_spatialdata.py _spatialdata.py spatialdata/_io/read.py read.py spatialdata/utils.py utils.py tests/_io/test_readwrite.py test_readwrite.py tests/test_utils.py test_utils.py There are no files selected for viewing Loading Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later. Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , '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 contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert Uh oh! There was an error while loading. Please reload this page. scverse /spatialdataPublic Notifications You must be signed in to change notification settings Fork 93 Star 387 Code Issues263 Pull requests17 Discussions Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights Io/hot fix#138 New issue Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Sign up for GitHub By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails. Already on GitHub? Sign in to your account Merged LucaMarconato merged 23 commits into main from io/hot_fixMar 2, 2023 Conversation 74 Commits 23 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged Io/hot fix #138 Show file tree Hide file tree Changes from all commits Commits Show all changes 23 commits Select commit Hold shift + click to select a range 5953adb wip (all tests passes) LucaMarconato Feb 14, 2023e34d602 Merge branch 'old_legacy_code' into io/hot_fix LucaMarconato Feb 14, 2023ff8ea87 merged with most recent pr LucaMarconato Feb 14, 202347d240f adedd TODO for improving performance LucaMarconato Feb 14, 2023572a4c6 added safety assert before calling rmtree LucaMarconato Feb 14, 2023ed3a37f fixed a performance detail that I had left as a TODO LucaMarconato Feb 15, 20231e6a08f removed shutil usage from .write() LucaMarconato Feb 16, 20236200757 removed _called_from_write parameter LucaMarconato Feb 16, 20239c55ec8 removed all the other shutil usages LucaMarconato Feb 16, 2023e52d1df [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 16, 20238dc1a94 added docstrings for landmark-based align funcs; slighly modified them LucaMarconato Feb 16, 2023c3ea935 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Feb 16, 2023a04987d better tests for landmark-based alignment LucaMarconato Feb 16, 2023823b871 using Path instead of str LucaMarconato Feb 16, 2023e097dbf AnnData.concatenate -> ad.concat LucaMarconato Feb 16, 20235aa93a9 Apply suggestions from code review LucaMarconato Feb 22, 2023d5ed060 Merge branch 'main' into io/hot_fix LucaMarconato Feb 22, 2023fd6cddb removed tmpdir based atomic update/save LucaMarconato Feb 27, 20235ad85cc Merge branch 'main' into io/hot_fix giovp Mar 2, 2023f2e5ef3 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Mar 2, 2023584ad9d Apply suggestions from code review LucaMarconato Mar 2, 202316c4801 added os.path.realpath(); implemented giovp suggestions after review LucaMarconato Mar 2, 2023a775f67 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Mar 2, 2023 File filter Filter by extension Filter by extension .py (5) All 1 file type selected Viewed files Clear filters Conversations Failed to load comments. Loading Uh oh! There was an error while loading. Please reload this page. Jump to Jump to file Failed to load files. Loading Uh oh! There was an error while loading. Please reload this page. Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace spatialdata/_core/_spatialdata.py _spatialdata.py spatialdata/_io/read.py read.py spatialdata/utils.py utils.py tests/_io/test_readwrite.py test_readwrite.py tests/test_utils.py test_utils.py There are no files selected for viewing Loading Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 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Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , '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 contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert Uh oh! There was an error while loading. Please reload this page. scverse /spatialdataPublic Notifications You must be signed in to change notification settings Fork 93 Star 387 Code Issues263 Pull requests17 Discussions Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights Io/hot fix#138 New issue Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Sign up for GitHub By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails. Already on GitHub? Sign in to your account Merged LucaMarconato merged 23 commits into main from io/hot_fixMar 2, 2023 Conversation 74 Commits 23 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged Io/hot fix #138 Show file tree Hide file tree Changes from all commits Commits Show all changes 23 commits Select commit Hold shift + click to select a range 5953adb wip (all tests passes) LucaMarconato Feb 14, 2023e34d602 Merge branch 'old_legacy_code' into io/hot_fix LucaMarconato Feb 14, 2023ff8ea87 merged with most recent pr LucaMarconato Feb 14, 202347d240f adedd TODO for improving performance LucaMarconato Feb 14, 2023572a4c6 added safety assert before calling rmtree LucaMarconato Feb 14, 2023ed3a37f fixed a performance detail that I had left as a TODO LucaMarconato Feb 15, 20231e6a08f removed shutil usage from .write() LucaMarconato Feb 16, 20236200757 removed _called_from_write parameter LucaMarconato Feb 16, 20239c55ec8 removed all the other shutil usages LucaMarconato Feb 16, 2023e52d1df [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 16, 20238dc1a94 added docstrings for landmark-based align funcs; slighly modified them LucaMarconato Feb 16, 2023c3ea935 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Feb 16, 2023a04987d better tests for landmark-based alignment LucaMarconato Feb 16, 2023823b871 using Path instead of str LucaMarconato Feb 16, 2023e097dbf AnnData.concatenate -> ad.concat LucaMarconato Feb 16, 20235aa93a9 Apply suggestions from code review LucaMarconato Feb 22, 2023d5ed060 Merge branch 'main' into io/hot_fix LucaMarconato Feb 22, 2023fd6cddb removed tmpdir based atomic update/save LucaMarconato Feb 27, 20235ad85cc Merge branch 'main' into io/hot_fix giovp Mar 2, 2023f2e5ef3 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Mar 2, 2023584ad9d Apply suggestions from code review LucaMarconato Mar 2, 202316c4801 added os.path.realpath(); implemented giovp suggestions after review LucaMarconato Mar 2, 2023a775f67 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Mar 2, 2023 File filter Filter by extension Filter by extension .py (5) All 1 file type selected Viewed files Clear filters Conversations Failed to load comments. Loading Uh oh! There was an error while loading. Please reload this page. Jump to Jump to file Failed to load files. Loading Uh oh! There was an error while loading. Please reload this page. Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace spatialdata/_core/_spatialdata.py _spatialdata.py spatialdata/_io/read.py read.py spatialdata/utils.py utils.py tests/_io/test_readwrite.py test_readwrite.py tests/test_utils.py test_utils.py There are no files selected for viewing Loading Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later. Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , '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 contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert Uh oh! There was an error while loading. Please reload this page. scverse /spatialdataPublic Notifications You must be signed in to change notification settings Fork 93 Star 387 Code Issues263 Pull requests17 Discussions Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights Io/hot fix#138 New issue Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Sign up for GitHub By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails. Already on GitHub? Sign in to your account Merged LucaMarconato merged 23 commits into main from io/hot_fixMar 2, 2023 Conversation 74 Commits 23 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged Io/hot fix #138 Show file tree Hide file tree Changes from all commits Commits Show all changes 23 commits Select commit Hold shift + click to select a range 5953adb wip (all tests passes) LucaMarconato Feb 14, 2023e34d602 Merge branch 'old_legacy_code' into io/hot_fix LucaMarconato Feb 14, 2023ff8ea87 merged with most recent pr LucaMarconato Feb 14, 202347d240f adedd TODO for improving performance LucaMarconato Feb 14, 2023572a4c6 added safety assert before calling rmtree LucaMarconato Feb 14, 2023ed3a37f fixed a performance detail that I had left as a TODO LucaMarconato Feb 15, 20231e6a08f removed shutil usage from .write() LucaMarconato Feb 16, 20236200757 removed _called_from_write parameter LucaMarconato Feb 16, 20239c55ec8 removed all the other shutil usages LucaMarconato Feb 16, 2023e52d1df [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 16, 20238dc1a94 added docstrings for landmark-based align funcs; slighly modified them LucaMarconato Feb 16, 2023c3ea935 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Feb 16, 2023a04987d better tests for landmark-based alignment LucaMarconato Feb 16, 2023823b871 using Path instead of str LucaMarconato Feb 16, 2023e097dbf AnnData.concatenate -> ad.concat LucaMarconato Feb 16, 20235aa93a9 Apply suggestions from code review LucaMarconato Feb 22, 2023d5ed060 Merge branch 'main' into io/hot_fix LucaMarconato Feb 22, 2023fd6cddb removed tmpdir based atomic update/save LucaMarconato Feb 27, 20235ad85cc Merge branch 'main' into io/hot_fix giovp Mar 2, 2023f2e5ef3 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Mar 2, 2023584ad9d Apply suggestions from code review LucaMarconato Mar 2, 202316c4801 added os.path.realpath(); implemented giovp suggestions after review LucaMarconato Mar 2, 2023a775f67 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Mar 2, 2023 File filter Filter by extension Filter by extension .py (5) All 1 file type selected Viewed files Clear filters Conversations Failed to load comments. Loading Uh oh! There was an error while loading. Please reload this page. Jump to Jump to file Failed to load files. Loading Uh oh! There was an error while loading. Please reload this page. Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace spatialdata/_core/_spatialdata.py _spatialdata.py spatialdata/_io/read.py read.py spatialdata/utils.py utils.py tests/_io/test_readwrite.py test_readwrite.py tests/test_utils.py test_utils.py There are no files selected for viewing Loading Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later. Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , '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 contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert Uh oh! There was an error while loading. Please reload this page. scverse /spatialdataPublic Notifications You must be signed in to change notification settings Fork 93 Star 387 Code Issues263 Pull requests17 Discussions Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Discussions Actions Projects Security and quality Insights Io/hot fix#138 New issue Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Sign up for GitHub By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails. Already on GitHub? Sign in to your account Merged LucaMarconato merged 23 commits into main from io/hot_fixMar 2, 2023 Conversation 74 Commits 23 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged Io/hot fix #138 Show file tree Hide file tree Changes from all commits Commits Show all changes 23 commits Select commit Hold shift + click to select a range 5953adb wip (all tests passes) LucaMarconato Feb 14, 2023e34d602 Merge branch 'old_legacy_code' into io/hot_fix LucaMarconato Feb 14, 2023ff8ea87 merged with most recent pr LucaMarconato Feb 14, 202347d240f adedd TODO for improving performance LucaMarconato Feb 14, 2023572a4c6 added safety assert before calling rmtree LucaMarconato Feb 14, 2023ed3a37f fixed a performance detail that I had left as a TODO LucaMarconato Feb 15, 20231e6a08f removed shutil usage from .write() LucaMarconato Feb 16, 20236200757 removed _called_from_write parameter LucaMarconato Feb 16, 20239c55ec8 removed all the other shutil usages LucaMarconato Feb 16, 2023e52d1df [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 16, 20238dc1a94 added docstrings for landmark-based align funcs; slighly modified them LucaMarconato Feb 16, 2023c3ea935 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Feb 16, 2023a04987d better tests for landmark-based alignment LucaMarconato Feb 16, 2023823b871 using Path instead of str LucaMarconato Feb 16, 2023e097dbf AnnData.concatenate -> ad.concat LucaMarconato Feb 16, 20235aa93a9 Apply suggestions from code review LucaMarconato Feb 22, 2023d5ed060 Merge branch 'main' into io/hot_fix LucaMarconato Feb 22, 2023fd6cddb removed tmpdir based atomic update/save LucaMarconato Feb 27, 20235ad85cc Merge branch 'main' into io/hot_fix giovp Mar 2, 2023f2e5ef3 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Mar 2, 2023584ad9d Apply suggestions from code review LucaMarconato Mar 2, 202316c4801 added os.path.realpath(); implemented giovp suggestions after review LucaMarconato Mar 2, 2023a775f67 Merge branch 'io/hot_fix' of https://github.com/scverse/spatialdata i… LucaMarconato Mar 2, 2023 File filter Filter by extension Filter by extension .py (5) All 1 file type selected Viewed files Clear filters Conversations Failed to load comments. Loading Uh oh! There was an error while loading. Please reload this page. Jump to Jump to file Failed to load files. Loading Uh oh! There was an error while loading. Please reload this page. Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace spatialdata/_core/_spatialdata.py _spatialdata.py spatialdata/_io/read.py read.py spatialdata/utils.py utils.py tests/_io/test_readwrite.py test_readwrite.py tests/test_utils.py test_utils.py There are no files selected for viewing Loading Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later. Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time.