[BUG] Python3.13 stability

[MBartkowiakSTFC]

Description of the error
As of today, VTK 9.4.0 became available, which includes wheels for Python 3.13.
rdkit for python 3.13 is still missing.

It is possible to install and run MDANSE by removing rdkit from the code. This affects atom selection options and automatic molecule naming.

Describe the expected result
Ideally, MDANSE should run on Python 3.13 same as on 3.9-3.12.

Describe the actual result
Problems observed so far:

1. The MDAnalysis converter crashed with a segmentation fault when converting a Gromacs trajectory from SlimMD (CCPBioSim). This was not reproducible and did not happen at the second attempt.
2. On exiting GUI, an error typically appears in the text console:

Exception ignored in atexit callback <function shutdown at 0x147aa5940>:
Traceback (most recent call last):
  File "/opt/homebrew/Cellar/[email protected]/3.13.0_1/Frameworks/Python.framework/Versions/3.13/lib/python3.13/logging/__init__.py", line 2242, in shutdown
    if getattr(h, 'flushOnClose', True):
RuntimeError: wrapped C/C++ object of type JobEntry has been deleted

Suggested fix
Some initial errors could be caused by files created by the older versions, which might not be fully compatible. This includes the Qt settings, database files, configuration files and instrument database. It has to be investigated if switching between Python versions makes the problems reappear.
Qt object deletion can be investigated and improved.

Additional details
More problems will be found as the testing continues. They should be mentioned here.