added axes, zoom and pan control

[cpignedoli]

This pull request introduces a comprehensive set of enhancements to the StructureDataViewer in aiidalab_widgets_base/viewers.py, focusing on improved view controls, axis visualization, and test coverage. The changes add user controls for view scaling, panning, and axes display, as well as robust validation and reset mechanisms. Corresponding tests ensure these features work as intended.

Key improvements and new features:

Viewer controls and UI enhancements:

• Added new controls for view scale, pan (X/Y), reset to default view, and toggling axes display and centering in the viewer's appearance tab. Also included a help section explaining the controls. [1] [2] [3]

Axes visualization:

• Implemented logic to add, remove, and center a coordinate axes triad in the viewer, with options to show/hide and center the axes based on user preference. [1] [2] [3]

View transformation logic:

• Introduced properties and methods to handle view scaling and panning, including validation, trait observation, and JavaScript integration for real-time updates. Added a "reset view" function to restore default orientation, scale, and pan. [1] [2]

Test coverage:

• Added tests to verify default view and axes rendering, toggling axes on/off, view transformation (scale and pan), and centered axes functionality. These tests ensure the new controls and visual features behave as expected.

Minor UI improvements:

• Updated the "Center molecule" button label to "Center atoms" for clarity.

These changes collectively provide a more interactive and user-friendly structure viewer, with fine-grained control over visualization and improved test reliability.

Screen.Recording.2026-05-18.at.16.19.52.mov

[codecov]

Codecov Report

❌ Patch coverage is 95.65217% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.12%. Comparing base (7d6b446) to head (42bcd52).

Files with missing lines	Patch %	Lines
aiidalab_widgets_base/viewers.py	95.65%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #745      +/-   ##
==========================================
+ Coverage   84.77%   85.12%   +0.34%     
==========================================
  Files          18       18              
  Lines        3336     3421      +85     
==========================================
+ Hits         2828     2912      +84     
- Misses        508      509       +1     

Flag	Coverage Δ
python-3.12	85.09% <95.65%> (+0.34%)	⬆️
python-3.9	85.10% <95.65%> (+0.34%)	⬆️

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[danielhollas]

tbh I am not sure I am a fan of this PR, especially the inline JS code which seems like it will be very hard to maintain.

It seems like bigger features like this should be discussed in an issue before implementation.

Also I wonder how does this relate to the work on WEAS widget in #559?

[danielhollas]

To preserve the backwards compatibility, it would be better to not show axes by default (for example in AtmoSpec I don't want them).

[cpignedoli]

Hi @danielhollas, I agree that we should discuss. Let's discuss this at the next meeting, to understand when we will have the weas widget, and how we can quickly switch back to a more intuitive default orientation.

[cpignedoli]

I will fix pan functionality after merging of #742

[cpignedoli]

Closing this in favor of #765.

#765 keeps the scope narrow: optional axes plus a default-view button, without the zoom/pan controls or inline JavaScript that were problematic in this PR. It was restarted from current master and tested with both nglview 3.0.8 and 4.0.1.