Merging version bumps from last Bioc release and updating GHA - #148

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lmweber merged 5 commits into
drighelli:develfrom
lmweber:devel
Mar 18, 2024
Merged

Merging version bumps from last Bioc release and updating GHA#148
lmweber merged 5 commits into
drighelli:develfrom
lmweber:devel

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@lmweber

@lmweberlmweber commented Mar 14, 2024

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Hi, this PR merges the version bumps from the last Bioc release cycle and updates the GitHub Actions workflow to the latest Bioc versions. Once this is merged into GitHub devel branch we can re-synchronize GitHub / origin and Bioc / upstream.

@lmweber

lmweber commented Mar 14, 2024

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Looks like the GitHub Actions checks error is due to the package files exceeding 5 MB, which gets flagged by BiocCheck. I believe this is only an error for initial submission, not updates, so should be ok.

@lmweber

lmweber commented Mar 14, 2024

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In fact looking at my commit above to update the GitHub Actions workflow (5fcc22c), we had previously commented out BiocCheck, presumably for this same reason. I'll re-comment it out again to avoid this error.

@lmweberlmweber mentioned this pull request Mar 15, 2024
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@drighelli

drighelli commented Mar 18, 2024

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is this solved now? It seems so to me!

Thanks!

@lmweber

lmweber commented Mar 18, 2024

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Great, thanks for approving. I'll merge this and push the version bumps to upstream / Bioc.

@lmweber
lmweber merged commit 9c1845f into drighelli:develMar 18, 2024
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 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" + '

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Merging version bumps from last Bioc release and updating GHA - #148
Merged
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
Mar 18, 2024
Merged
Merging version bumps from last Bioc release and updating GHA#148
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
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@lmweber
@lmweberlmweber
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Mar 14, 2024

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Hi, this PR merges the version bumps from the last Bioc release cycle and updates the GitHub Actions workflow to the latest Bioc versions. Once this is merged into GitHub devel branch we can re-synchronize GitHub / origin and Bioc / upstream.
@lmweber
lmweber
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Mar 14, 2024

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Looks like the GitHub Actions checks error is due to the package files exceeding 5 MB, which gets flagged by BiocCheck. I believe this is only an error for initial submission, not updates, so should be ok.
@lmweber
lmweber
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Mar 14, 2024

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In fact looking at my commit above to update the GitHub Actions workflow (5fcc22c), we had previously commented out BiocCheck, presumably for this same reason. I'll re-comment it out again to avoid this error.
@lmweberlmweber
mentioned this pull request
Mar 15, 2024
 Open

@drighelli
drighelli
commented
Mar 18, 2024

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is this solved now? It seems so to me!
Thanks!
@lmweber
lmweber
commented
Mar 18, 2024

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Great, thanks for approving. I'll merge this and push the version bumps to upstream / Bioc.
@lmweber
lmweber
merged commit 9c1845f
into
drighelli:develMar 18, 2024
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@lmweber@drighelli@jwokaty

, '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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Merging version bumps from last Bioc release and updating GHA - #148
Merged
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
Mar 18, 2024
Merged
Merging version bumps from last Bioc release and updating GHA#148
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
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@lmweber
@lmweberlmweber
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Mar 14, 2024

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Hi, this PR merges the version bumps from the last Bioc release cycle and updates the GitHub Actions workflow to the latest Bioc versions. Once this is merged into GitHub devel branch we can re-synchronize GitHub / origin and Bioc / upstream.
@lmweber
lmweber
commented
Mar 14, 2024

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CollaboratorAuthor
Looks like the GitHub Actions checks error is due to the package files exceeding 5 MB, which gets flagged by BiocCheck. I believe this is only an error for initial submission, not updates, so should be ok.
@lmweber
lmweber
commented
Mar 14, 2024

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In fact looking at my commit above to update the GitHub Actions workflow (5fcc22c), we had previously commented out BiocCheck, presumably for this same reason. I'll re-comment it out again to avoid this error.
@lmweberlmweber
mentioned this pull request
Mar 15, 2024
 Open

@drighelli
drighelli
commented
Mar 18, 2024

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Owner
is this solved now? It seems so to me!
Thanks!
@lmweber
lmweber
commented
Mar 18, 2024

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Great, thanks for approving. I'll merge this and push the version bumps to upstream / Bioc.
@lmweber
lmweber
merged commit 9c1845f
into
drighelli:develMar 18, 2024
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@lmweber@drighelli@jwokaty

, '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
Merging version bumps from last Bioc release and updating GHA - #148
Merged
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
Mar 18, 2024
Merged
Merging version bumps from last Bioc release and updating GHA#148
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
Conversation
@lmweber
@lmweberlmweber
commented
Mar 14, 2024

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Hi, this PR merges the version bumps from the last Bioc release cycle and updates the GitHub Actions workflow to the latest Bioc versions. Once this is merged into GitHub devel branch we can re-synchronize GitHub / origin and Bioc / upstream.
@lmweber
lmweber
commented
Mar 14, 2024

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CollaboratorAuthor
Looks like the GitHub Actions checks error is due to the package files exceeding 5 MB, which gets flagged by BiocCheck. I believe this is only an error for initial submission, not updates, so should be ok.
@lmweber
lmweber
commented
Mar 14, 2024

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In fact looking at my commit above to update the GitHub Actions workflow (5fcc22c), we had previously commented out BiocCheck, presumably for this same reason. I'll re-comment it out again to avoid this error.
@lmweberlmweber
mentioned this pull request
Mar 15, 2024
 Open

@drighelli
drighelli
commented
Mar 18, 2024

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is this solved now? It seems so to me!
Thanks!
@lmweber
lmweber
commented
Mar 18, 2024

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Great, thanks for approving. I'll merge this and push the version bumps to upstream / Bioc.
@lmweber
lmweber
merged commit 9c1845f
into
drighelli:develMar 18, 2024
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3 participants

@lmweber@drighelli@jwokaty

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

Skip to content
Merging version bumps from last Bioc release and updating GHA - #148
Merged
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
Mar 18, 2024
Merged
Merging version bumps from last Bioc release and updating GHA#148
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
Conversation
@lmweber
@lmweberlmweber
commented
Mar 14, 2024

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Hi, this PR merges the version bumps from the last Bioc release cycle and updates the GitHub Actions workflow to the latest Bioc versions. Once this is merged into GitHub devel branch we can re-synchronize GitHub / origin and Bioc / upstream.
@lmweber
lmweber
commented
Mar 14, 2024

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CollaboratorAuthor
Looks like the GitHub Actions checks error is due to the package files exceeding 5 MB, which gets flagged by BiocCheck. I believe this is only an error for initial submission, not updates, so should be ok.
@lmweber
lmweber
commented
Mar 14, 2024

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CollaboratorAuthor
In fact looking at my commit above to update the GitHub Actions workflow (5fcc22c), we had previously commented out BiocCheck, presumably for this same reason. I'll re-comment it out again to avoid this error.
@lmweberlmweber
mentioned this pull request
Mar 15, 2024
 Open

@drighelli
drighelli
commented
Mar 18, 2024

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Owner
is this solved now? It seems so to me!
Thanks!
@lmweber
lmweber
commented
Mar 18, 2024

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CollaboratorAuthor
Great, thanks for approving. I'll merge this and push the version bumps to upstream / Bioc.
@lmweber
lmweber
merged commit 9c1845f
into
drighelli:develMar 18, 2024
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3 participants

@lmweber@drighelli@jwokaty

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Merging version bumps from last Bioc release and updating GHA - #148
Merged
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
Mar 18, 2024
Merged
Merging version bumps from last Bioc release and updating GHA#148
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
Conversation
@lmweber
@lmweberlmweber
commented
Mar 14, 2024

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Hi, this PR merges the version bumps from the last Bioc release cycle and updates the GitHub Actions workflow to the latest Bioc versions. Once this is merged into GitHub devel branch we can re-synchronize GitHub / origin and Bioc / upstream.
@lmweber
lmweber
commented
Mar 14, 2024

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CollaboratorAuthor
Looks like the GitHub Actions checks error is due to the package files exceeding 5 MB, which gets flagged by BiocCheck. I believe this is only an error for initial submission, not updates, so should be ok.
@lmweber
lmweber
commented
Mar 14, 2024

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CollaboratorAuthor
In fact looking at my commit above to update the GitHub Actions workflow (5fcc22c), we had previously commented out BiocCheck, presumably for this same reason. I'll re-comment it out again to avoid this error.
@lmweberlmweber
mentioned this pull request
Mar 15, 2024
 Open

@drighelli
drighelli
commented
Mar 18, 2024

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Owner
is this solved now? It seems so to me!
Thanks!
@lmweber
lmweber
commented
Mar 18, 2024

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CollaboratorAuthor
Great, thanks for approving. I'll merge this and push the version bumps to upstream / Bioc.
@lmweber
lmweber
merged commit 9c1845f
into
drighelli:develMar 18, 2024
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3 participants

@lmweber@drighelli@jwokaty

, '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
Merging version bumps from last Bioc release and updating GHA - #148
Merged
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
Mar 18, 2024
Merged
Merging version bumps from last Bioc release and updating GHA#148
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
Conversation
@lmweber
@lmweberlmweber
commented
Mar 14, 2024

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Hi, this PR merges the version bumps from the last Bioc release cycle and updates the GitHub Actions workflow to the latest Bioc versions. Once this is merged into GitHub devel branch we can re-synchronize GitHub / origin and Bioc / upstream.
@lmweber
lmweber
commented
Mar 14, 2024

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CollaboratorAuthor
Looks like the GitHub Actions checks error is due to the package files exceeding 5 MB, which gets flagged by BiocCheck. I believe this is only an error for initial submission, not updates, so should be ok.
@lmweber
lmweber
commented
Mar 14, 2024

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CollaboratorAuthor
In fact looking at my commit above to update the GitHub Actions workflow (5fcc22c), we had previously commented out BiocCheck, presumably for this same reason. I'll re-comment it out again to avoid this error.
@lmweberlmweber
mentioned this pull request
Mar 15, 2024
 Open

@drighelli
drighelli
commented
Mar 18, 2024

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Owner
is this solved now? It seems so to me!
Thanks!
@lmweber
lmweber
commented
Mar 18, 2024

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CollaboratorAuthor
Great, thanks for approving. I'll merge this and push the version bumps to upstream / Bioc.
@lmweber
lmweber
merged commit 9c1845f
into
drighelli:develMar 18, 2024
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3 participants

@lmweber@drighelli@jwokaty

, '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); }
})();
})();

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Merging version bumps from last Bioc release and updating GHA - #148
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lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
Mar 18, 2024
Merged
Merging version bumps from last Bioc release and updating GHA#148
lmweber merged 5 commits into
drighelli:develfrom 
lmweber:devel
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@lmweber
@lmweberlmweber
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Mar 14, 2024

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Hi, this PR merges the version bumps from the last Bioc release cycle and updates the GitHub Actions workflow to the latest Bioc versions. Once this is merged into GitHub devel branch we can re-synchronize GitHub / origin and Bioc / upstream.
@lmweber
lmweber
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Mar 14, 2024

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Looks like the GitHub Actions checks error is due to the package files exceeding 5 MB, which gets flagged by BiocCheck. I believe this is only an error for initial submission, not updates, so should be ok.
@lmweber
lmweber
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Mar 14, 2024

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In fact looking at my commit above to update the GitHub Actions workflow (5fcc22c), we had previously commented out BiocCheck, presumably for this same reason. I'll re-comment it out again to avoid this error.
@lmweberlmweber
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Mar 15, 2024
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@drighelli
drighelli
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Mar 18, 2024

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is this solved now? It seems so to me!
Thanks!
@lmweber
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Mar 18, 2024

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Great, thanks for approving. I'll merge this and push the version bumps to upstream / Bioc.
@lmweber
lmweber
merged commit 9c1845f
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drighelli:develMar 18, 2024
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@lmweber@drighelli@jwokaty