1101 Extend integrator classes and reimplement SDE models.

[reneSchm]

Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

• Extend IntegratorCore and OdeIntegrator to accept a fixed number of DerivFunctions (rather than only one).
• Add classes SimulationBase and FlowSimulationBase to avoid code duplication between different Simulations.
• Add class StochasticModel which is a Compartmental- or FlowModel with additional get_noise function.
• Add class StochasticSimulation, which makes use of a second DerivFunction to evaluate get_noise.
• Add class EulerMaruyamaIntegratorCore, implementing a (step of a) Euler-Maruyama scheme.

If need be, add additional information and what the reviewer should look out for in particular:

• Check the naming of new classes, in particular the new Order template parameter, the get_noise function and the XdeIntegrator (maybe "DeIntegrator" or just "Integrator"?).
• Are there Simulation classes that should be rebuild on the new *base classes now?
• Should the rescaler used by Euler-Maruyama be modular?

Merge Request - Guideline Checklist

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Checks by code author

• Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
• New code adheres to coding guidelines
• No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• Tests are added for new functionality and a local test run was successful (with and without OpenMP)
• Appropriate documentation for new functionality has been added (Doxygen in the code and Markdown files if necessary)
• Proper attention to licenses, especially no new third-party software with conflicting license has been added
• (For ABM development) Checked benchmark results and ran and posted a local test above from before and after development to ensure performance is monitored.

Checks by code reviewer(s)

• Corresponding issue(s) is/are linked and addressed
• Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
• Appropriate unit tests have been added, CI passes, code coverage and performance is acceptable (did not decrease)
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• On merge, add 2-5 lines with the changes (main added features, changed items, or corrected bugs) to the merge-commit-message. This can be taken from the briefly-list-the-changes above (best case) or the separate commit messages (worst case).

Closes #1009
Closes #1101
Closes #1165
Closes #1218

[codecov]

Codecov Report

Attention: Patch coverage is 96.96970% with 5 lines in your changes missing coverage. Please review.

Project coverage is 97.35%. Comparing base (3a0d789) to head (57cbe8c).
Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
cpp/memilio/compartments/compartmental_model.h	0.00%	2 Missing ⚠️
cpp/memilio/compartments/stochastic_model.h	75.00%	2 Missing ⚠️
cpp/memilio/compartments/stochastic_simulation.h	94.44%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1296      +/-   ##
==========================================
+ Coverage   97.27%   97.35%   +0.08%     
==========================================
  Files         171      174       +3     
  Lines       15117    15015     -102     
==========================================
- Hits        14705    14618      -87     
+ Misses        412      397      -15     

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[reneSchm]

@nijawa Could you double check that this PR solves the NaN issues (mathematically) correctly?

[HenrZu]

code is great :) Some comments. Some functions are short in/missing documentation. Also consider the readthedocs doc. However, it would make sense to update this in the branch there.