Add examples and more tests

[sivonxay]

• Fix issue when initializing a nanoparticle from dict, when the nanoparticle has previously had its hosts pruned to only 'Y'.

[codecov]

Codecov Report

Merging #46 (46b0bd6) into main (5521c45) will increase coverage by 4.71%.
The diff coverage is 59.52%.

@@            Coverage Diff             @@
##             main      #46      +/-   ##
==========================================
+ Coverage   80.45%   85.16%   +4.71%     
==========================================
  Files          43       43              
  Lines        3479     3499      +20     
==========================================
+ Hits         2799     2980     +181     
+ Misses        680      519     -161     

Files	Coverage Δ
.../NanoParticleTools/differential_kinetics/runner.py	100.00% <ø> (ø)
...rc/NanoParticleTools/differential_kinetics/util.py	100.00% <ø> (ø)
src/NanoParticleTools/inputs/nanoparticle.py	91.25% <83.33%> (-0.47%)	⬇️
.../NanoParticleTools/analysis/simulation_replayer.py	96.51% <72.22%> (+82.83%)	⬆️
src/NanoParticleTools/flows/jobs.py	16.83% <16.66%> (+0.50%)	⬆️

... and 2 files with indirect coverage changes

[sivonxay]

Since we are introducing tests for previously untested files, we can ignore the failed check