Avoid black sphere in structure viewer

[superstar54]

Fix #633 .
In the case of a structure with only one atom, the structure viewer shows a black sphere. As shown below:

This could be because of the overlap between the atoms and the control of the viewer. This PR implements a quick solution by shifting the center of the control in z direction by 1. Now the viewer shows:

[superstar54]

The failed test is related to the query of the Crystallography Open Database, thus it is not related to this PR.

[danielhollas]

Just wondering, is this a bug that should be reported upstream? I.e. is this an nglview problem?

[superstar54]

Just wondering, is this a bug that should be reported upstream? I.e. is this an nglview problem?

I am not sure if it is a bug or not. The problem is that we call the center method after drawing the atoms and bonds. If we use the default setting, the nglview shows the correct atoms, but the view is not centered.
Anyway, I opened an issue and waited for other's options.

[codecov]

Codecov Report

Attention: Patch coverage is 25.00000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 83.43%. Comparing base (152c2bb) to head (3ee8fcb).
Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
aiidalab_widgets_base/viewers.py	25.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #637      +/-   ##
==========================================
- Coverage   83.50%   83.43%   -0.07%     
==========================================
  Files          17       17              
  Lines        3546     3550       +4     
==========================================
+ Hits         2961     2962       +1     
- Misses        585      588       +3     

Flag	Coverage Δ
python-3.11	83.43% <25.00%> (-0.07%)	⬇️
python-3.9	83.47% <25.00%> (-0.07%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[danielhollas]

Not a particularly pretty workaround, but if it works let's ship it :-)