feat: add data structures for particle info

[redeboer]

Closes #40

This PR is part of the ongoing effort to make the codebase of the expertsystem more readible.

• Cleans up and improves the existing Spin class
• Introduces a ParticleDatabase (dict of Particle object) that is to replace the particle.DATABASE global
• Since switching to ParticleDatabase requires refactoring almost the entire codebase, all old functionality has been moved to a namespace particle.deprecated, which will be gradually removed in follow-up PRs.
• Run mypy over tests as well (but do not enforce type hints in the definitions there)
• Compute finer test coverage with branch coverage.

(This PR has been rebased on #41)

[ghost]

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[codecov]

Codecov Report

Merging #42 into master will decrease coverage by 10.40%.
The diff coverage is 91.66%.

@@             Coverage Diff             @@
##           master      #42       +/-   ##
===========================================
- Coverage   85.34%   74.94%   -10.41%     
===========================================
  Files          16       20        +4     
  Lines        2395     3105      +710     
===========================================
+ Hits         2044     2327      +283     
- Misses        351      778      +427     

Impacted Files	Coverage Δ
expertsystem/state/conservationrules.py	84.83% <76.92%> (+0.23%)	⬆️
expertsystem/state/particle.py	75.46% <87.09%> (-0.76%)	⬇️
expertsystem/particle.py	94.26% <94.26%> (ø)
expertsystem/__init__.py	50.00% <100.00%> (+2.94%)	⬆️
expertsystem/amplitude/canonicaldecay.py	96.96% <100.00%> (ø)
expertsystem/amplitude/helicitydecay.py	94.63% <100.00%> (-0.02%)	⬇️
expertsystem/state/propagation.py	83.11% <100.00%> (ø)
expertsystem/ui/default_settings.py	100.00% <100.00%> (ø)
expertsystem/ui/system_control.py	92.08% <100.00%> (-0.02%)	⬇️
expertsystem/solvers/constraint/version.py	100.00% <0.00%> (ø)
... and 4 more

[spflueger]

Looks quite good already. I made some small specific comments.
On a larger scale:

• Can it be avoided having this deprecated version? I assume the amount of changes when replacing it are too big?
• The ParticleDatabase code seems quite large and not DRY. I have to look at it more closely later. But it seems like the loading can be shortend. So just have a single load_from_dict method. The individual parsers for xml yml etc would just have to provide a to dict function. I personally would also just go with a single format as default (yml) and others would have to be implemented by the user himself if she/he prefers another format.

[redeboer]

The DeepCode error is incorrect, because pyyaml and xmltodict don't work with binary mode. It seems the only way to ignore this issue is to put deepcode comments into the code. I don't like that, so I suggests giving up the deepcode checks -- it's too inflexible and and we already have sufficient checks through Codacy.

[redeboer]

#42 (comment)
All serialisation functionality has been removed so that the classes in this are purely data objects. The construction of these data objects will be further addressed in #44.

[redeboer]

Note that we may also want to add some tools that allow you to create a new particle instance based on another particle instance as template in Python code (so that you can for instance create duplicates of fake particles such as an e+i- collision at different energies or hypothetical particles). But as that functionality is not yet needed, I did not spend time on creating an interface for this yet.

--> #6

[redeboer]

This PR will be split up into small PRs that address specific issues