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Start richer logging #96

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Start richer logging #96

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ageorgou
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@ageorgou ageorgou commented Nov 1, 2022

Addresses #33.

So far:

  • Adds a description of how the new feature will work, to be included as a tutorial
  • Refactors the existing logging to:
    • allow multiple sub-loggers (as we did in tests and demographics)
    • keep the functionality of "writing" of the population variables of interest as a separate class

Still needed:

  • actually parsing the configuration and determining what should be written at each step!
  • writing of the population at each step
  • moving the tutorial to the docs directory (dependent on Improve Sphinx documentation #91) and adding it in the table of contents so it's part of the generated documentation

All the interaction with Python's logging should now happen only
through the HIVpyLogger. Exceptions are currently the logging in
the tests, and the demographics module - these will be tackled
separately.
Also distinguish between loggers (which control what gets logged
generally) and the new PopulationWriter (which will control how
the population gets recorded for monitoring purposes during the
simulation).
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@pineapple-cat pineapple-cat left a comment

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Tutorial looks good and examples are clear, I'll finish up with moving the updated Sphinx docs and then when everything is merged I'll put the tutorial in the right directory.

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