Recording the serial interval

[mghosh00]

Summary

I have added the ability to record serial intervals of all infection events (which can be used to generate a distribution of serial intervals). The output of this is in a file named serial_intervals.csv.

Checklist

• All new functions have docstrings in the correct style

• I've verified the complete docs build locally without errors

• I've maintained 100% coverage (please mention any 'no cover' annotations explicitly)

• I've unit-tested all new methods directly

• Breaking change (fix or feature that would cause existing functionality to change)

• I have read the CONTRIBUTING document.

• My code follows the code style of this project.

• I have updated the wiki with new parameters/model functionality

Closing issues

Closes #262

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (1cc1fb9) to head (d0564cd).
Report is 14 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##              main      #267    +/-   ##
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  Coverage   100.00%   100.00%            
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  Files          110       110            
  Lines         3876      3978   +102     
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+ Hits          3876      3978   +102     

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[KCGallagher]

@mghosh00 just following up on this so the repo is up to date for publication - how much of this is actually intended to go onto main? For example I see the (untested) triple sweep work here, which I assume was just a simple debugging test and so will not actually be merged into the main repo. If this is the case, it could be more appropriate to close the PR, and perhaps delete the branch if we do not now need this code.

[mghosh00]

Closes #273

[KCGallagher]

Overall great! Thank you for excellent testing of this code too, as I know we wanted to get this feature added quickly. A few additional files you might want to get rid off, and one code change, but on this basis I am happy to pre-approve.

For future code, I'd perhaps reconsider your commenting style - in general we try to aim for self-documenting code, where the variables names are sufficiently self explanatory that you don't need an additional comment to say what each line does because the code explains itself. Comments are then used sparingly to document unusual structures or use cases. I am happy to discuss this in more detail, but you don't need to make those modifications to this (unless you want to).

For an example, take L490 of pyEpiabm/pyEpiabm/routine/simulation.py:

     # The below is a list of dictionaries for each time step
        list_of_dicts = df.to_dict(orient='records')
        for dict_row in list_of_dicts:
            # Write each time step in dictionary form
            self.serial_interval_writer.write(dict_row)

The variable names in this are already pretty meaningful, so the comments add very little additional detail that is not in the code. You could take the comments out (and perhaps just change one of the variable names to make it clear that each row corresponds to a timestep).