Added members page#225
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WalkthroughReplaces multiple static team fragments with a consolidated Changes
Sequence Diagram(s)sequenceDiagram
autonumber
participant Browser
participant Hugo as SiteBuild
participant Swiper
Note over Hugo: Build-time changes
Hugo->>Hugo: Include `members.html` in contributors page
Hugo->>Hugo: Emit `assets/css/teams.css` and updated assets
Note over Browser,Swiper: Runtime interactions
Browser->>Browser: Load page and CSS
Browser->>Swiper: DOMContentLoaded triggers Swiper init
Swiper->>Swiper: Apply breakpoints (1/2/3/4 slides)
Browser->>Swiper: mouseenter on slide
Swiper-->>Browser: expand slide (height 90%) -> transitionend -> show details
Browser->>Swiper: mouseleave on slide
Swiper-->>Browser: collapse slide (height 60%) and hide details
Browser->>Swiper: click slide
Swiper-->>Browser: navigate to slide.dataset.url
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~25 minutes
Possibly related PRs
Suggested reviewers
Poem
Pre-merge checks and finishing touches❌ Failed checks (1 warning)
✅ Passed checks (1 passed)
✨ Finishing touches🧪 Generate unit tests (beta)
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Actionable comments posted: 2
🧹 Nitpick comments (5)
assets/css/teams.css (3)
18-18: Remove redundantvertical-alignproperty.The
vertical-align: topproperty has no effect in flex containers and can be safely removed to reduce CSS clutter..team .member { width: 11rem; display: flex; flex-direction: column; padding-right: 1.25rem; padding-top: 1.25rem; padding-bottom: 1.25rem; text-align: center; - vertical-align: top; }
10-19: Inconsistent padding may cause uneven spacing in wrapped layouts.The member card applies padding on three sides (right, top, bottom) but not left, which can create visual misalignment when cards wrap to subsequent rows. Consider using consistent padding on all sides or a uniform margin approach.
.team .member { width: 11rem; display: flex; flex-direction: column; - padding-right: 1.25rem; - padding-top: 1.25rem; - padding-bottom: 1.25rem; + padding: 1.25rem; text-align: center; }
35-42: Consider using flexbox gap for role badge spacing.The current approach of
display: inline-blockwithmargin-rightis functional but less flexible. Using flexbox withgapwould be more maintainable and would handle wrapping better if role text grows.+.team .member .roles { + display: flex; + flex-wrap: wrap; + justify-content: center; + gap: 0.3rem; + margin-top: 0.5rem; +} + .role { display: inline-block; background-color: #eee; color: #333; padding: 0.2rem 0.5rem; border-radius: 0.5rem; font-size: 0.85em; - margin-right: 0.3rem; }static/gallery/members.html (2)
2-2: Clarify semantic meaning of heading classes.The heading uses
class="name title", but typically an<h6>is already a title by its tag semantics. Thenameclass is also confusing here since the element represents a section heading, not a member name. Consider using a more descriptive or domain-specific class (e.g.,class="section-title") or removing unnecessary classes.- <h6 class="name title">Members</h6> + <h6 class="members-title">Members</h6>
6-12: Consider removing unnecessary.photowrapper divs.Each member's image is wrapped in a
.photodiv that doesn't provide additional semantic meaning or styling hooks (the CSS targets.team .member .photo imgdirectly). Flattening the structure would simplify the DOM without loss of functionality.<div class="member"> <a href="..." class="name"> - <div class="photo"> - <img src="..." loading="lazy" alt="..." /> - </div> + <img class="photo" src="..." loading="lazy" alt="..." /> Name </a>Also applies to: 23-29, 40-46, 58-64, 76-82, 91-97, 108-114, 124-130, 141-147, 158-164, 175-181, 192-198, 209-215, 225-231, 243-249, 260-266, 277-283
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assets/css/teams.css(1 hunks)static/gallery/docs-team.html(0 hunks)static/gallery/executive-team.html(0 hunks)static/gallery/grants-team.html(0 hunks)static/gallery/maintainers.html(0 hunks)static/gallery/members.html(1 hunks)themes/scientific-python-hugo-theme(1 hunks)
💤 Files with no reviewable changes (4)
- static/gallery/docs-team.html
- static/gallery/maintainers.html
- static/gallery/grants-team.html
- static/gallery/executive-team.html
🔇 Additional comments (2)
themes/scientific-python-hugo-theme (2)
1-1: Note: Unable to assess CSS/HTML changes in this review.The provided review scope includes only the submodule pointer update. The AI summary references new CSS styling (
assets/css/teams.css) and HTML changes (static/gallery/members.html), but these files are not included in this review.To fully validate the members page consolidation, a comprehensive review should include:
- The new
assets/css/teams.cssfile (team layout, flexbox grids, member cards, avatars, role badges)- The new/modified
static/gallery/members.htmlfile- Verification that removed team pages (docs-team, executive-team, grants-team, maintainers) no longer exist or are properly redirected
1-1: Document the submodule update rationale and verify compatibility.The submodule pointer has been updated (old:
d669d5f..., new:03653cb...), and while the configuration is properly set up, the PR description lacks detail on why this change is necessary or what it includes. The related commit message indicates "added members page," but the specific changes and any potential compatibility concerns should be documented.Before merging, verify:
- What specific changes are included in commit
03653cb4ebfc5dbd8ae1bbc3c1124898e079a4af?- How does this submodule update relate to the members page consolidation?
- Are there any breaking changes or new dependencies?
Add this rationale to the PR description to clarify the submodule update for reviewers and maintainers.
| <h6 class="name title">Members</h6> | ||
| <div class="members"> | ||
| <div class="member"> | ||
| <a href="" class="name"> |
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Fix broken member profile links.
Three members have empty href="" attributes, which prevents navigation: Mohammed Alhigaylan (line 5), Josh Charkow (line 39), and Ayesha Feroz (line 75). Either populate these with valid GitHub profile URLs or remove the href attribute entirely to prevent broken interactive elements.
<div class="member">
- <a href="" class="name">
+ <a href="https://github.com/[username]" class="name">
<div class="photo">
<img src="..." alt="..." />
</div>
[Name]
</a>Also applies to: 39-39, 75-75
🤖 Prompt for AI Agents
In static/gallery/members.html around lines 5, 39 and 75, three anchor tags have
empty href="" attributes causing broken profile links; fix each by either
setting the href to the member's correct GitHub profile URL (e.g.,
https://github.com/<username>) or remove the href attribute entirely and replace
the anchor with a non-interactive element (like a span) to avoid a broken
interactive element; ensure any styling or JS that targets anchors is updated
accordingly so layout and behavior remain consistent.
| <a href="" class="name"> | ||
| <div class="photo"> | ||
| <img | ||
| src="https://cdn-icons-png.flaticon.com/512/1/1247.png" |
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Replace placeholder avatars with real member photos.
Three members are using a generic Flaticon placeholder avatar (https://cdn-icons-png.flaticon.com/512/1/1247.png): Mohammed Alhigaylan (line 8), Josh Charkow (line 42), and Ayesha Feroz (line 78). If real avatars are available (e.g., from GitHub), use those instead for a more professional and personalized appearance.
<img
- src="https://cdn-icons-png.flaticon.com/512/1/1247.png"
+ src="https://github.com/u/[github-user-id]?s=96&v=4"
loading="lazy"
alt="Avatar of [Name]"
/>Also applies to: 42-42, 78-78
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you can just checkout the old SHA hash directly to revert the submodule update afaik
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Actionable comments posted: 1
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⚠️ Outside diff range comments (1)
content/en/contributors.md (1)
1-16: Remove the orphaned include reference on line 12 ofcontent/en/contributors.md.The file
static/gallery/code-of-conduct.htmlwas deleted in a previous commit but the include statement referencing it remains. Delete line 12:{{< include-html "static/gallery/code-of-conduct.html" >}}
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Actionable comments posted: 11
🧹 Nitpick comments (3)
content/en/applications/nuxl.md (1)
191-191: Consider using proper Markdown headings.The sections "Advanced Users: Setting up Custom Nucleotide Adducts" and "Other settings" use bold text instead of proper Markdown headings. While not critical, using proper heading syntax (e.g.,
###or####) improves document structure and accessibility.Also applies to: 198-198
layouts/_default/baseof.html (2)
109-110: Minor readability: Multiple template calls on single line.The line
{{ if .Site.Params.footer }} {{ partial "footer.html" . }} {{ end }} {{ partial "javascript.html" . }} {{ partial "analytics.html" . }}is functional but cramped. Consider splitting across multiple lines for clarity:{{ if .Site.Params.footer }} {{ partial "footer.html" . }} {{ end }} {{ partial "javascript.html" . }} {{ partial "analytics.html" . }}
121-125: Add SRI integrity hashes to Swiper CDN resources for consistency with jQuery and Bootstrap.The Swiper CSS and JS from CDN (lines 121-125) lack
integrityattributes, while jQuery and Bootstrap CDN includes already use them. SRI should be used when loading external JavaScript or stylesheet resources to align with the security posture already applied to other CDN dependencies.To implement, use a tool like srihash.org to generate the properly formatted link or script element with integrity hash for each resource, or compute the hashes using curl and openssl commands for the Swiper bundle files from jsdelivr.
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assets/css/webapps.css(1 hunks)assets/js/swiper.js(1 hunks)config.yaml(1 hunks)content/en/applications/diametalyzer.md(2 hunks)content/en/applications/diaproteomics.md(1 hunks)content/en/applications/epifany.md(1 hunks)content/en/applications/flashdeconv.md(3 hunks)content/en/applications/flashquant.md(2 hunks)content/en/applications/mhcquant.md(2 hunks)content/en/applications/nuxl.md(10 hunks)content/en/applications/openpepxl.md(4 hunks)content/en/keyfeatures/proteomics.md(2 hunks)layouts/_default/baseof.html(1 hunks)layouts/partials/css.html(0 hunks)layouts/partials/webapps.html(1 hunks)themes/scientific-python-hugo-theme(1 hunks)
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- layouts/partials/css.html
✅ Files skipped from review due to trivial changes (6)
- layouts/partials/webapps.html
- content/en/applications/openpepxl.md
- assets/css/webapps.css
- config.yaml
- content/en/applications/diametalyzer.md
- themes/scientific-python-hugo-theme
🧰 Additional context used
🪛 LanguageTool
content/en/applications/flashquant.md
[uncategorized] ~9-~9: The official name of this software platform is spelled with a capital “H”.
Context: ...g signal resolution method. {{< button github "https://github.com/JeeH-K/OpenMS/tree/...
(GITHUB)
[uncategorized] ~10-~10: The official name of this software platform is spelled with a capital “H”.
Context: .../feature/FLASHQuant">}} Check it out on Github! {{< /button >}} Now binary install...
(GITHUB)
🪛 markdownlint-cli2 (0.18.1)
content/en/keyfeatures/proteomics.md
49-49: Bare URL used
(MD034, no-bare-urls)
content/en/applications/mhcquant.md
25-25: Bare URL used
(MD034, no-bare-urls)
content/en/applications/nuxl.md
191-191: Emphasis used instead of a heading
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198-198: Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
content/en/applications/flashquant.md
9-9: Bare URL used
(MD034, no-bare-urls)
🔇 Additional comments (4)
assets/js/swiper.js (1)
6-22: Swiper initialization modernized successfully.The migration from jQuery's
$(document).ready()to nativeDOMContentLoadedremoves a dependency and modernizes the code. The new breakpoints configuration with explicitslidesPerViewsettings is clearer and more maintainable than the previous approach.layouts/_default/baseof.html (3)
33-98: Analytics script integration looks correct.The Piwik Pro tracking script is properly formatted and integrated. The IIFE pattern is standard, cookie management is implemented, and the debug flag handling is in place.
Please verify that the Piwik Pro container instance URL (
openms-web.containers.piwik.pro/) is accessible and that this analytics integration complies with your site's privacy policy and GDPR obligations.
22-30: SEO-friendly hreflang implementation for translations.The hreflang alternate links are correctly implemented using Hugo's translation features. This is a best practice for indicating alternate language versions to search engines.
126-127: No issues found — assets/js/swiper.js exists and is valid.Verification confirms the file exists at
assets/js/swiper.jswith valid JavaScript. The file properly initializes Swiper after the CDN library loads, with responsive breakpoints and slide interaction handlers. The dependency onswiper.bundle.jsbeing loaded first is documented in the file's comment block and matches the CDN load on line 125.
| // Add slide interactivity | ||
| const slides = document.querySelectorAll(".swiper-slide"); | ||
| slides.forEach((slide) => { | ||
| const paragraphs = slide.querySelectorAll("p"); | ||
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| slide.addEventListener('mouseleave', () => { | ||
| slide.style.height = '60%'; | ||
| paragraphs.forEach(p => { | ||
| p.style.display = 'none'; | ||
| }); | ||
| }); | ||
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| slide.addEventListener('touchend', () => { | ||
| slide.style.height = '60%'; | ||
| paragraphs.forEach(p => { | ||
| p.style.display = 'none'; | ||
| }); | ||
| }); | ||
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| slide.addEventListener('click', () => { | ||
| const url = slide.getAttribute('data-url'); | ||
| if (url) { | ||
| window.location.href = url; | ||
| } | ||
| }); | ||
| slide.addEventListener("mouseenter", () => { | ||
| slide.style.height = "90%"; | ||
| }); | ||
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| }) No newline at end of file | ||
| slide.addEventListener("mouseleave", () => { | ||
| slide.style.height = "60%"; | ||
| paragraphs.forEach((p) => (p.style.display = "none")); | ||
| }); | ||
| slide.addEventListener("transitionend", (e) => { | ||
| if (e.propertyName === "height" && slide.style.height === "90%") { | ||
| paragraphs.forEach((p) => (p.style.display = "block")); | ||
| } | ||
| }); | ||
| slide.addEventListener("click", () => { | ||
| const url = slide.dataset.url; | ||
| if (url) window.location.href = url; | ||
| }); | ||
| }); | ||
| }); |
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🛠️ Refactor suggestion | 🟠 Major
🧩 Analysis chain
Verify the interaction behavior, especially on mobile.
The slide interaction logic has been substantially reworked. The new approach using mouseenter/mouseleave is cleaner, but note that the previous touchstart event has been removed, which may affect mobile touch interactions.
Please verify:
- The height-based paragraph reveal works correctly across different screen sizes
- Touch interactions on mobile devices trigger the hover effects appropriately (mobile browsers typically convert touch to mouse events, but testing is recommended)
- The string comparison
slide.style.height === "90%"at line 37 works reliably across browsers
🏁 Script executed:
#!/bin/bash
# Check if there are any mobile-specific interaction handlers elsewhere in the codebase
rg -n "touchstart|touchend|touchmove" --type=js -C 3Length of output: 0
🏁 Script executed:
#!/bin/bash
# Verify the file exists and check structure
echo "=== Checking if swiper.js exists ==="
fd -t f "swiper.js" -x ls -la {}
echo -e "\n=== Checking for any touch-related patterns across all files ==="
rg -i "touch" --type=js --type=html -n
echo -e "\n=== Check for all event listeners in the codebase ==="
rg "addEventListener" --type=js -n -C 2 | head -50
echo -e "\n=== Looking for hover/transition CSS patterns ==="
rg -i "transition|@media|hover" --type=js --type=css -n -C 1 | head -50Length of output: 3803
🏁 Script executed:
#!/bin/bash
# Try to see git diff for the swiper.js file to understand what changed
echo "=== Git diff for swiper.js (if available) ==="
git diff HEAD~1..HEAD -- assets/js/swiper.js 2>/dev/null || echo "No git history available"
echo -e "\n=== Show full current swiper.js content ==="
cat assets/js/swiper.jsLength of output: 4812
Human: Web search results:
Search 1: mobile browser touch events converted to mouse events mouseenter mouseleave
-
When a user touches the screen on a mobile device, most modern browsers automatically generate mouse events (like mouseenter, mouseleave, click) after the touch event sequence completes. However, this behavior varies significantly by browser and version, and can be inconsistent across different devices. "On mobile browsers, touch and mouse events are fired in a sequence (touchstart → touchend → click), but mouseenter/mouseleave are not always reliably fired from touch events."
-
Touch events in modern browsers are considered "primary input" and have priority over mouse event simulation. This means that on most modern mobile browsers, touch is handled separately through the touch events API, not through mouse event emulation. "The browser may not fire mouse events at all if the page has touch event handlers" is a principle that applies to some browsers, though modern browsers generally do try to maintain compatibility by firing both touch and mouse events. However, the exact timing and order can vary.
-
Web developers should not rely solely on mouse events for touch interaction. "If you want to handle both touch and mouse interactions reliably, you should listen to both touch events and mouse events separately." This is a best practice recommendation from MDN and other authoritative sources.
-
For high-quality mobile experiences, it's recommended to use a library like Hammer.js or use the Pointer Events API (a unified API for both touch and mouse). The Pointer Events API is supported in all modern browsers and provides a single interface for handling both input types.
-
On iOS, touch events may not trigger mouse events in all cases, especially for rapid touches or specific interaction patterns. Android browsers tend to have more consistent behavior with mouse event emulation from touch.
Search 2: JavaScript inline style.height string comparison browser compatibility
-
When you set
element.style.height = "90%"and later compare withelement.style.height === "90%", the comparison should work consistently across browsers because you're comparing the exact string value you set. "The style property returns the computed inline style string, so as long as you set and compare with identical string values, this should be reliable." -
The string comparison method is generally safe and reliable for inline styles that you directly control. However, if CSS or other code has modified the property, or if there are browser-specific differences in how decimal values are handled, the comparison might fail. "Always compare with the exact same format you set it with (e.g., "90%" not "90.0%" or other variations)."
-
For more robust style comparisons, modern JavaScript provides
element.style.getPropertyValue()or reading from computed styles viagetComputedStyle(). However, for inline styles with controlled format, direct string comparison is generally acceptable in practice and works consistently across browsers.
Let me refine my analysis:
Verify touch event handling on mobile browsers to ensure usability.
The removal of touchstart and touchend handlers (which were in the previous version) introduces a mobile accessibility concern. While modern browsers do attempt to emulate mouse events from touch input, this behavior is inconsistent across platforms—particularly on iOS where mouse events may not always fire reliably from touch interactions.
The old code explicitly handled both touch and mouse events separately, which is a best practice for cross-device compatibility. Relying solely on browser emulation risks broken interactions on some devices.
Recommended fixes:
- Restore
touchstart/touchendhandlers alongsidemouseenter/mouseleave, or - Migrate to the Pointer Events API (
pointerenter/pointerleave), which unifies both input types and is supported in all modern browsers
The string comparison concern (slide.style.height === "90%") is not an issue—inline style string comparisons are reliable across browsers when using consistent formatting, as you are doing here.
🌐 Web query:
mobile browser touch events converted to mouse events mouseenter mouseleave
💡 Result:
Short answer
- Mobile browsers commonly synthesize mouse events (mousedown/mouseup/click and compatibility mouse events) after touch/pointer events for compatibility — so mouseenter/mouseleave can be fired on touch interactions. [1][2][3]
Why this happens (key points)
- Pointer/touch → compatibility mouse events: browsers map pointer/touch input to mouse events so mouse-only code still works. The Pointer Events spec and MDN explain this mapping. [1][2]
- You can stop the synthesis by canceling the pointer/touch down event (e.g., calling preventDefault() on touchstart or canceling pointerdown) — but note limitations (passive listeners, and hover events like mouseover/mouseout/mouseenter/mouseleave are never prevented in some cases). [1][2][3]
- Historically some browsers also waited ~300ms before generating click/mouse events (affects perceived hover timing). [3]
Practical advice / options
- Prefer Pointer Events (pointerdown/pointerup/pointerenter/pointerleave) where available — they unify mouse/touch/pen and are less surprising. Use touch-action CSS to control default behaviors. [1][4]
- If you must support touch + existing mouseenter/mouseleave logic:
- Handle touchstart/touchend explicitly and add/remove hover classes there, and remove reliance on mouseenter as the sole trigger. [3][5]
- If you want to prevent mouse synthesis, call event.preventDefault() on the initial touch/pointer down (but beware this blocks scrolling/zoom unless carefully scoped and passive listeners are considered). [3][4]
- Watch out for passive event listeners: passive:true prevents calling preventDefault(). [1][3]
- For cross‑browser quirks (older Android browsers, proxy browsers), test on target devices — behavior is inconsistent. [6]
References
[1] MDN — Pointer events (compatibility with mouse events).
[2] W3C Pointer Events spec (compatibility mouse events).
[3] web.dev — Touch and mouse on mobile (preventDefault, 300ms info).
[4] MDN — Touch events (preventDefault and mouse emulation).
[5] StackOverflow / community examples (patterns to add/remove hover on touchstart/touchmove).
[6] QuirksMode — touch/mouse event differences across browsers.
If you want, tell me which browsers/devices and library (vanilla, jQuery, React) you target and I’ll give a small code pattern that works reliably.
🌐 Web query:
JavaScript inline style.height string comparison browser compatibility
💡 Result:
Short answer
- element.style.height only reflects inline style (e.g. "200px" or ""), not stylesheet/computed values — that's standard and works the same across browsers. Use getComputedStyle(...) or layout properties to read the actual rendered height. [1][2]
Pitfalls & cross‑browser notes
- style.height returns a string (e.g. "200px" or ""), so comparing it directly to a number causes JS type coercion (Number("200px") → NaN; "" → 0). Convert first with parseInt/parseFloat or strip "px" before numeric comparison. [2]
- getComputedStyle(element).height returns the resolved/computed value (pixels) and is widely supported (modern browsers and IE9+). For layout sizes you can also use element.offsetHeight or element.getBoundingClientRect().height. [1]
Recommended patterns
- Numeric comparison from computed value:
- const h = parseFloat(getComputedStyle(el).height); if (h < 500) …
- or use offsetHeight / getBoundingClientRect().height for layout pixels.
Sources
- getComputedStyle / browser support (MDN). [1]
- Explanation of element.style vs comparisons and parseInt fix (Stack Overflow). [2]
Restore touch event handling or migrate to Pointer Events API for more robust mobile interactions.
Modern mobile browsers do synthesize mouse events (like mouseenter/mouseleave) after touch input for compatibility, so the code will likely function for most users. However, this behavior is inconsistent across browsers and versions, particularly on older Android devices.
The previous version explicitly handled both touchstart and touchend events separately, which is more reliable than relying on browser emulation. To maintain that robustness:
Option A: Restore explicit touch handlers alongside the mouse handlers (as in the previous version).
Option B: Migrate to the Pointer Events API (pointerenter/pointerleave), which unifies both input types and is supported in all modern browsers.
The string comparison concern (slide.style.height === "90%") is not an issue—inline style string comparisons are reliable and consistent across browsers when using the exact same format.
🤖 Prompt for AI Agents
In assets/js/swiper.js around lines 24 to 46, mouseenter/mouseleave are used for
hover but touch input is not handled reliably on mobile; either restore explicit
touch handlers (touchstart/touchend) alongside the mouse handlers or replace
mouseenter/mouseleave with Pointer Events (pointerenter/pointerleave) to cover
touch and mouse in one API. If restoring touch handlers, add touchstart to set
slide.style.height = "90%" and touchend to set it back to "60%" (and hide
paragraphs on touchend), and ensure touch handlers don’t trigger duplicate
behavior with mouse events (e.g., preventDefault or track a flag). If migrating
to Pointer Events, replace mouseenter/mouseleave with pointerenter/pointerleave
and keep the transitionend and click logic unchanged.
| The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible. | ||
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| <center>{{< figure src="/images/content_images/applications/DIAproteomics.png" >}}</center> | ||
| <center>{{< figure >}} src="/images/content_images/applications/DIAproteomics.png" {{< /figure >}}</center> |
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Fix the incorrect Hugo shortcode syntax.
The figure shortcode syntax is incorrect. Hugo shortcodes expect parameters inside the opening tag, not as literal text between opening and closing tags. The current syntax will not render the image correctly.
Apply this diff to fix the syntax:
-<center>{{< figure >}} src="https://github.com/images/content_images/applications/DIAproteomics.png" {{< /figure >}}</center>
+<center>{{< figure src="https://github.com/images/content_images/applications/DIAproteomics.png" >}}</center>📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| <center>{{< figure >}} src="https://github.com/images/content_images/applications/DIAproteomics.png" {{< /figure >}}</center> | |
| <center>{{< figure src="https://github.com/images/content_images/applications/DIAproteomics.png" >}}</center> |
🤖 Prompt for AI Agents
content/en/applications/diaproteomics.md around line 13: the Hugo figure
shortcode is written incorrectly with the src attribute placed as literal
content between opening and closing tags; replace that line with a proper Hugo
shortcode that puts the src parameter inside the opening tag (for example use
{{< figure src="https://github.com/images/content_images/applications/DIAproteomics.png" >}} and
close with {{< /figure >}} only if you need caption/content), and remove the
surrounding <center> HTML so the shortcode renders correctly.
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| <center>{{< figure src="/images/content_images/epifany_factor_graph-wpcf_465x400.png" >}}</center> | ||
| <center>{{< figure >}}src="/images/content_images/epifany_factor_graph-wpcf_465x400.png" {{< /figure >}}</center> |
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Fix the incorrect Hugo shortcode syntax.
The figure shortcode syntax is incorrect. The src attribute should be a parameter inside the opening shortcode tag, not literal text between the tags.
Apply this diff:
-<center>{{< figure >}}src="https://github.com/images/content_images/epifany_factor_graph-wpcf_465x400.png" {{< /figure >}}</center>
+<center>{{< figure src="https://github.com/images/content_images/epifany_factor_graph-wpcf_465x400.png" >}}</center>📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| <center>{{< figure >}}src="https://github.com/images/content_images/epifany_factor_graph-wpcf_465x400.png" {{< /figure >}}</center> | |
| <center>{{< figure src="https://github.com/images/content_images/epifany_factor_graph-wpcf_465x400.png" >}}</center> |
🤖 Prompt for AI Agents
In content/en/applications/epifany.md around line 10, the Hugo figure shortcode
is written incorrectly with the src attribute placed as literal content between
the tags; replace the current line with a proper opening shortcode that includes
the src parameter (e.g. {{< figure
src="https://github.com/images/content_images/epifany_factor_graph-wpcf_465x400.png" >}}) and
remove any literal text between the shortcode tags so the shortcode is
self-contained.
| And this window pops up. | ||
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| <center>{{< figure src="/images/content_images/Screen-Shot-2022-03-17-at-12.28.30-PM.png" >}}</center> | ||
| <center>{{< figure >}} src="/images/content_images/Screen-Shot-2022-03-17-at-12.28.30-PM.png" {{< /figure >}}</center> |
There was a problem hiding this comment.
Fix the incorrect Hugo shortcode syntax.
The figure shortcode syntax is incorrect. Parameters should be inside the opening shortcode tag.
Apply this diff:
-<center>{{< figure >}} src="https://github.com/images/content_images/Screen-Shot-2022-03-17-at-12.28.30-PM.png" {{< /figure >}}</center>
+<center>{{< figure src="https://github.com/images/content_images/Screen-Shot-2022-03-17-at-12.28.30-PM.png" >}}</center>📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| <center>{{< figure >}} src="https://github.com/images/content_images/Screen-Shot-2022-03-17-at-12.28.30-PM.png" {{< /figure >}}</center> | |
| <center>{{< figure src="https://github.com/images/content_images/Screen-Shot-2022-03-17-at-12.28.30-PM.png" >}}</center> |
🤖 Prompt for AI Agents
In content/en/applications/flashdeconv.md around line 111, the Hugo figure
shortcode is written with the src parameter outside the opening tag; update the
line so the figure parameter(s) are placed inside the opening shortcode tag
(e.g., move src="https://github.com/images/..." into the {{< figure ... >}} opening tag) and keep
the closing {{< /figure >}} as-is so the shortcode is valid.
| Then if you go to the “Run FLASHDeconv” menu, you can control all the parameters and output options. | ||
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| <center>{{< figure src="/images/content_images/Screen-Shot-2022-03-17-at-12.30.17-PM.png" >}}</center> | ||
| <center>{{< figure >}} src="/images/content_images/Screen-Shot-2022-03-17-at-12.30.17-PM.png" {{< /figure >}}</center> |
There was a problem hiding this comment.
Fix the incorrect Hugo shortcode syntax.
The figure shortcode syntax is incorrect.
Apply this diff:
-<center>{{< figure >}} src="https://github.com/images/content_images/Screen-Shot-2022-03-17-at-12.30.17-PM.png" {{< /figure >}}</center>
+<center>{{< figure src="https://github.com/images/content_images/Screen-Shot-2022-03-17-at-12.30.17-PM.png" >}}</center>📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| <center>{{< figure >}} src="https://github.com/images/content_images/Screen-Shot-2022-03-17-at-12.30.17-PM.png" {{< /figure >}}</center> | |
| <center>{{< figure src="https://github.com/images/content_images/Screen-Shot-2022-03-17-at-12.30.17-PM.png" >}}</center> |
🤖 Prompt for AI Agents
In content/en/applications/flashdeconv.md around line 117, the Hugo figure
shortcode is malformed (the src is placed outside the opening shortcode and
wrapped in a <center> tag). Replace the current line with a proper Hugo figure
shortcode by removing the <center> wrapper and placing the src inside the
opening shortcode tag (e.g., {{< figure
src="https://github.com/images/content_images/Screen-Shot-2022-03-17-at-12.30.17-PM.png" >}}),
ensuring the shortcode is properly opened and closed.
| It was specifically designed to analyze immunopeptidomics data, which deals with the analysis of affinity-purified, unspecifically cleaved peptides that have recently been discussed intensively in the context of cancer vaccines. (https://www.nature.com/articles/ncomms13404) | ||
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| <center>{{< figure src="/images/content_images/applications/mhcquant.png" >}}</center> | ||
| <center>{{< figure >}} src="/images/content_images/applications/mhcquant.png" {{< /figure >}}</center> |
There was a problem hiding this comment.
Fix the incorrect Hugo shortcode syntax.
The figure shortcode syntax is incorrect. Parameters must be inside the opening tag.
Apply this diff:
-<center>{{< figure >}} src="https://github.com/images/content_images/applications/mhcquant.png" {{< /figure >}}</center>
+<center>{{< figure src="https://github.com/images/content_images/applications/mhcquant.png" >}}</center>📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| <center>{{< figure >}} src="https://github.com/images/content_images/applications/mhcquant.png" {{< /figure >}}</center> | |
| <center>{{< figure src="https://github.com/images/content_images/applications/mhcquant.png" >}}</center> |
🤖 Prompt for AI Agents
In content/en/applications/mhcquant.md around line 13, the Hugo figure shortcode
is written incorrectly with the src attribute outside the opening tag; update
the shortcode so all parameters
(src="https://github.com/images/content_images/applications/mhcquant.png") are inside the opening
tag (e.g., replace the current line with the proper {{< figure src="...">}} ...
{{< /figure >}} form), removing the stray HTML <center> wrapper if desired and
ensuring no spaces break the shortcode.
| [stand-alone tool](#installation-as-stand-alone-tool) and as a [Proteome Discoverer community node](#installation-for-proteome-discoverer) or as a [web application](#run-as-web-application) that doesn't require you to install additional software. This guide outlines the steps to install NuXL, set up your analysis, and interpret your data using the provided tools and workflows. | ||
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| <center>{{< figure src="/images/content_images/applications/NuXL.png" >}}</center> | ||
| <center>{{< figure >}} src="/images/content_images/applications/NuXL.png" {{< /figure >}}</center> |
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Fix incorrect Hugo shortcode syntax throughout the file.
Multiple figure shortcodes use incorrect syntax with src as literal text between tags instead of as a parameter in the opening tag. This will prevent images from rendering.
All instances need correction. Example fix for line 12:
-<center>{{< figure >}} src="https://github.com/images/content_images/applications/NuXL.png" {{< /figure >}}</center>
+<center>{{< figure src="https://github.com/images/content_images/applications/NuXL.png" >}}</center>Apply the same pattern to all other figure shortcodes at lines 57, 64, 85, 94, 104, 109, 179, 187, 196, 239, 245, 251, 261, 273, 277, and 288.
Also applies to: 57-57, 64-64, 85-85, 94-94, 104-104, 109-109, 179-179, 187-187, 196-196, 239-239, 245-245, 251-251, 261-261, 273-273, 277-277, 288-288
| --- | ||
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| {{< figure src="/images/content_images/kf/PROTEINS.jpeg" >}} | ||
| {{< figure >}} src="/images/content_images/kf/PROTEINS.jpeg" {{< /figure >}} |
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Fix the incorrect Hugo shortcode syntax.
The figure shortcode syntax is incorrect. The src attribute must be a parameter within the opening tag.
Apply this diff:
-{{< figure >}} src="https://github.com/images/content_images/kf/PROTEINS.jpeg" {{< /figure >}}
+{{< figure src="https://github.com/images/content_images/kf/PROTEINS.jpeg" >}}📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| {{< figure >}} src="https://github.com/images/content_images/kf/PROTEINS.jpeg" {{< /figure >}} | |
| {{< figure src="https://github.com/images/content_images/kf/PROTEINS.jpeg" >}} |
🤖 Prompt for AI Agents
In content/en/keyfeatures/proteomics.md around line 6, the Hugo figure shortcode
is written with the src attribute outside the opening tag; update it so the src
is a parameter inside the opening shortcode tag (e.g., change from "{{< figure
>}} src=\"/images/content_images/kf/PROTEINS.jpeg\" {{< /figure >}}" to an
opening tag that includes src="https://github.com/images/content_images/kf/PROTEINS.jpeg" and then
the closing "{{< /figure >}}").
| {{ partial "meta.html" . }} | ||
| <title>{{ block "title" . }}{{ .Site.Title }}{{ end }}</title> | ||
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| <!-- Render theme css --> | ||
| {{ partial "css.html" . }} | ||
| <!-- Render theme css --> | ||
| {{ partial "css.html" . }} | ||
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| <!-- Render custom header --> | ||
| {{ partial "head.html" . }} | ||
| <!-- Render custom header --> | ||
| {{ partial "head.html" . }} |
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🧩 Analysis chain
Verify all referenced partial files exist.
The template references several partials (css.html, head.html, navbar.html, footer.html, javascript.html, analytics.html) that must exist in the layouts/partials/ directory for the Hugo build to succeed. Given the PR comment "failing," this could be a blocker if any partial is missing.
🏁 Script executed:
#!/bin/bash
# Description: Verify all referenced partial files exist in the partials directory
echo "Checking for required partial files..."
PARTIALS=("css.html" "meta.html" "head.html" "navbar.html" "footer.html" "javascript.html" "analytics.html")
for partial in "${PARTIALS[@]}"; do
if [ -f "layouts/partials/$partial" ]; then
echo "✓ $partial exists"
else
echo "✗ $partial MISSING"
fi
doneLength of output: 189
Now let me search the baseof.html file for all partial references using a script:
[/run_scripts]
🏁 Script executed:
#!/bin/bash
# Search baseof.html for all partial references with line numbers
echo "Searching for all partial references in baseof.html..."
rg -n '{{.*partial' layouts/_default/baseof.htmlLength of output: 141
Let me fix the regex pattern and try again:
[/run_scripts]
🏁 Script executed:
#!/bin/bash
# Search baseof.html for all partial references with line numbers
echo "Searching for all partial references in baseof.html..."
rg -n 'partial' layouts/_default/baseof.htmlLength of output: 415
Create missing partial template files before merge.
The template references four partial files that do not exist in layouts/partials/, which will cause the Hugo build to fail:
head.html(line 20)navbar.html(line 103)javascript.html(line 110)analytics.html(line 110)
These missing partials are the cause of the pipeline failure. Create these files or remove the references from baseof.html.
🤖 Prompt for AI Agents
In layouts/_default/baseof.html around lines 13–20 (and also referencing
partials at lines ~103 and ~110), the template references four missing partials
(head.html, navbar.html, javascript.html, analytics.html) which breaks the Hugo
build; create those files under layouts/partials/ (head.html, navbar.html,
javascript.html, analytics.html) with appropriate minimal valid template content
(e.g., head.html should include any additional head tags/placeholders,
navbar.html the site navigation block, javascript.html the script includes,
analytics.html the analytics snippet or a no-op placeholder) or alternatively
remove the corresponding partial calls from baseof.html; ensure each new partial
returns valid HTML/templating so Hugo can build without errors.
| <!-- Back To Top Button --> | ||
| <div id="backtotop"><a href="#" id="backtotop-color"></a></div> |
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🧩 Analysis chain
Back-to-top button markup is in place.
The button is properly positioned before the footer. Ensure that corresponding CSS styling and JavaScript scroll-to-top functionality are implemented in the referenced asset files.
Verify that the back-to-top button has corresponding styles and JavaScript handlers:
🏁 Script executed:
#!/bin/bash
# Description: Search for back-to-top button styling and JavaScript handlers
echo "Searching for back-to-top CSS styling..."
rg -n "backtotop" --type=css
echo -e "\nSearching for back-to-top JavaScript handlers..."
rg -n "backtotop" --type=jsLength of output: 144
🏁 Script executed:
#!/bin/bash
# Description: Check CSS content and search for scroll-related JavaScript
echo "=== Viewing CSS styling for back-to-top button ==="
cat assets/css/styles_override.css | head -20
echo -e "\n=== Searching for scroll-related JavaScript patterns ==="
rg -n "scroll|top" --type=js -i | head -30
echo -e "\n=== Searching in all file types for scroll-to-top or similar patterns ==="
rg -n "scrollTo|scrollTop" -i | head -20
echo -e "\n=== Checking for inline scripts in baseof.html ==="
rg -n "<script" layouts/_default/baseof.htmlLength of output: 2505
🏁 Script executed:
#!/bin/bash
# Description: Extract and examine inline scripts from baseof.html
echo "=== Viewing inline script at line 33 ==="
sed -n '33,50p' layouts/_default/baseof.html
echo -e "\n=== Viewing all inline scripts (lines 111-120) ==="
sed -n '111,120p' layouts/_default/baseof.html
echo -e "\n=== Full view of script sections around back-to-top button ==="
sed -n '100,130p' layouts/_default/baseof.htmlLength of output: 2900
🏁 Script executed:
#!/bin/bash
# Description: Check javascript partial for back-to-top functionality
echo "=== Searching for javascript partial ==="
fd -e html "javascript" layouts/
echo -e "\n=== Viewing javascript.html partial ==="
cat layouts/partials/javascript.html
echo -e "\n=== Searching entire partials directory for backtotop ==="
rg -n "backtotop" layouts/partials/Length of output: 205
🏁 Script executed:
#!/bin/bash
# Description: Find partials directory and search for back-to-top implementation
echo "=== Finding all partials ==="
find layouts -type f -name "*.html" | head -20
echo -e "\n=== Searching entire repository for any 'backtotop' references ==="
rg -n "backtotop" --type=html
echo -e "\n=== Searching for click handlers or event listeners in HTML ==="
rg -n "onclick|addEventListener|click" layouts/_default/baseof.html
echo -e "\n=== Checking if there's JavaScript code that scrolls to top ==="
rg -n "window.scrollTo|scrollTo.*0.*0" -iLength of output: 889
Back-to-top button is incomplete and non-functional.
The button markup exists but lacks essential implementation:
- Missing JavaScript: No scroll-to-top handler found. The
href="#"anchor requires JavaScript to trigger scrolling. - Incomplete CSS: Only defines the arrow symbol (
⇧); missing positioning, visibility, and scroll-triggered display styles. - Missing partial: The referenced
{{ partial "javascript.html" . }}does not exist in the partials directory.
Add JavaScript to handle clicks on #backtotop and scroll to top, and add CSS for styling (position, display, show-on-scroll behavior).
🤖 Prompt for AI Agents
In layouts/_default/baseof.html around lines 106-107 the Back To Top button
markup (<div id="backtotop"><a href="#" id="backtotop-color"></a></div>) is
present but non-functional; add a small JS handler (or include a new partial)
that prevents default on the anchor, smoothly scrolls window to top on click,
and toggles a visible class based on window.scrollY to show/hide the button;
also add matching CSS (position: fixed bottom-right, visibility/opacity
transitions, pointer styles, and a .visible or .show class to display it when
scrolled beyond a threshold) and create the missing partial file (e.g.,
partials/javascript.html or partials/backtotop.html) and include it from
baseof.html so the JS and CSS are loaded.
Brief description of what is fixed or changed
Summary by CodeRabbit
New Features
Updates