Group navbar tabs into dropdown menus for improved navigation

[Copilot]

The top navigation bar contained 20+ flat links causing visual clutter and poor discoverability. This groups related links into three logical dropdown menus while preserving all destinations.

Changes

Navigation Structure

• Grouped 12 links into 3 dropdowns:
  • Apps: Pharmmaker, coMD, ESSA, CryoDy, ClustENMD, InSty, WatFinder, Scipion
  • Learn: Tutorials, Workshops
  • Resources: Downloads, Statistics
• Preserved 8 individual links: ProDy, Evol, NMWiz, SignDy, membrANM, MechStiff, PRS, DruGUI
• Search form remains right-aligned

Bootstrap Compatibility

• Replaced Bootstrap 3.3.6 CDN with local Bootstrap 2.x JS to match existing Bootstrap 2.3.1 CSS
• Applied Bootstrap 2 dropdown markup: li.dropdown > a.dropdown-toggle[data-toggle="dropdown"] > ul.dropdown-menu

Interaction & Accessibility

• Dropdowns open via click (Bootstrap JS), hover (CSS), and keyboard focus (focus-within)
• Added aria-haspopup="true", aria-expanded="false", and role="menu" attributes

Example

<li class="dropdown">
  <a class="dropdown-toggle" data-toggle="dropdown" href="#" 
     aria-haspopup="true" aria-expanded="false">
    Apps <b class="caret"></b>
  </a>
  <ul class="dropdown-menu" role="menu">
    <li title="Pharmmaker"><a href="{{ pathto('pharmmaker', 1) }}">Pharmmaker</a></li>
    <!-- ... -->
  </ul>
</li>

Screenshots

Apps dropdown expanded:

Learn dropdown expanded:

Original prompt

Goal
Group the top navigation tabs into logical dropdown categories in the site navbar, using existing Bootstrap (v2.x) styles already present in the repo, without removing or renaming any destinations. Keep the right-aligned search form intact. This improves organization and discoverability of many top-level links.

Context

• Repo: prody/ProDy-website
• The current top navigation is defined in _template/index.html as a flat list of <li> items (Pharmmaker, coMD, ESSA, CryoDy, ClustENMD, InSty, WatFinder, Scipion, Downloads, Tutorials, Workshops, Statistics, plus a right-aligned search form).
• The site ships with Bootswatch United CSS for Bootstrap 2 (_static/css/bootswatch-united.css) and custom CSS (_static/css/prodydocs.css) that already include navbar and dropdown menu styling.
• Page-local nav tabs (e.g., in _template/downloads.html) are unrelated and should not be changed.

Requirements

1. Update _template/index.html to convert the existing flat top nav into three dropdown groups:

   • "Apps": Pharmmaker, coMD, ESSA, CryoDy, ClustENMD, InSty, WatFinder, Scipion
   • "Learn": Tutorials, Workshops
   • "Resources": Downloads, Statistics
     Keep the search form as a right-aligned item (li.pull-right) exactly as-is.

2. Use Bootstrap 2 navbar dropdown markup:

   • li.dropdown > a.dropdown-toggle[data-toggle="dropdown"] with a nested ul.dropdown-menu
   • Preserve existing title attributes and {{ pathto(...) }} Jinja calls for each link.

3. Do not change the destinations, slugs, or search form action/inputs.

4. Accessibility: add role="menu" to dropdown menus and aria-haspopup="true" to toggles. This is optional in Bootstrap 2 but improves semantics.

5. Ensure the dropdowns work with the current JS includes. If Bootstrap dropdown JS is not already included globally, add it in the appropriate base template include used by _template/index.html so that click-to-open works. Do not downgrade or change framework versions; only include the necessary Bootstrap 2 dropdown behavior if missing.

6. (Optional, non-blocking) Add CSS to enable hover-to-open on non-touch devices for better discoverability:
   In _static/css/prodydocs.css, append:

   .navbar .dropdown:hover .dropdown-menu { display: block; }

   This should not break click behavior.

File changes

• _template/index.html: Replace the existing top-level <ul class="nav"> ... </ul> block that contains the nav links with the grouped dropdown structure below. Do not alter surrounding layout or the right-aligned search form.

Proposed replacement for the nav list in _template/index.html:

• Apps
  • Pharmmaker
  • coMD
  • ESSA
  • CryoDy
  • ClustENMD
  • InSty
  • WatFinder
  • Scipion
• Learn
  • Tutorials
  • Workshops
• Resources
  • Downloads
  • Statistics
• Go

(Optional) CSS addition to _static/css/prodydocs.css at the end of the file:

/* Show dropdowns on hover as well as click */
.navbar ...

This pull request was created from Copilot chat.

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