Renaming The Infections Seeding Initialization

[AFg6K7h4fhy2]

This PR clarifies naming for $I_{v:0}$, i.e. the seeded infections, by framing the variable for infections seeding in terms of "initialization" versus "seeding", which, in most instances, is perceived by users as the value for pseudo-random number generation reproducibility.

[codecov]

Codecov Report

Attention: Patch coverage is 88.88889% with 2 lines in your changes missing coverage. Please review.

Project coverage is 92.69%. Comparing base (6f3a5a8) to head (877e00a).

Files	Patch %	Lines
model/src/pyrenew/latent/infections.py	75.00%	1 Missing ⚠️
model/src/pyrenew/latent/infectionswithfeedback.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #261   +/-   ##
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  Coverage   92.69%   92.69%           
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  Files          40       40           
  Lines         904      904           
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  Hits          838      838           
  Misses         66       66           

Flag	Coverage Δ
unittests	92.69% <88.88%> (ø)

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[damonbayer]

Thanks @AFg6K7h4fhy2! I think we should perform more renaming throughout. For instance, InfectionSeedingProcess should be InfectionInitializationProcess. In general, you should search the whole repo for seed and make sure it is only used in the context of RNG seeds. @dylanhmorris do you agree?

[AFg6K7h4fhy2]

Thanks @AFg6K7h4fhy2! I think we should perform more renaming throughout. For instance, InfectionSeedingProcess should be InfectionInitializationProcess. In general, you should search the whole repo for seed and make sure it is only used in the context of RNG seeds. @dylanhmorris do you agree?

I agree. I held off because I didn't want to decide unilaterally. Beyond InfectionSeedingProcess, I am thinking any other place where we have "Infection" and "Seeding" not in reference to pseudo-random number usage are place worth using "Initialization" or "Initial".

[dylanhmorris]

Thanks @AFg6K7h4fhy2! I think we should perform more renaming throughout. For instance, InfectionSeedingProcess should be InfectionInitializationProcess. In general, you should search the whole repo for seed and make sure it is only used in the context of RNG seeds. @dylanhmorris do you agree?

I do. @AFg6K7h4fhy2, I think you can assume initialization is the agreed-upon substitute for seeding throughout.

[AFg6K7h4fhy2]

I do. @AFg6K7h4fhy2, I think you can assume initialization is the agreed-upon substitute for seeding throughout.

Sounds good, I will edit this after I get through #241

[AFg6K7h4fhy2]

@damonbayer Mind taking a look here while I resolve the conflicts?

I changed InfectionSeedingMethod, InfectionSeedingProcess, and post_seed_infections to InfectionInitializationMethod, InfectionInitializationProcess, and post_initialized_infections, respectively.

[damonbayer]

Thanks @AFg6K7h4fhy2! I prefer post_initialization_infections over post_initialized_infections.

The documentation, for example docs/source/msei_reference/latent.rst, also needs to be changed.

[AFg6K7h4fhy2]

Thanks @AFg6K7h4fhy2! I prefer post_initialization_infections over post_initialized_infections.

The documentation, for example docs/source/msei_reference/latent.rst, also needs to be changed.

Will do on post_initialized_infections → post_initialization_infections. Good catch on the ./docs/ changes. I think I was one level off when doing Command-Shift-F.

[damonbayer]

I think we also want to rename the InfectionInitializationMethods (e.g., SeedInfectionsExponentialGrowth -> InitializeInfectionsExponentialGrowth).

[AFg6K7h4fhy2]

I think we also want to rename the InfectionInitializationMethods (e.g., SeedInfectionsExponentialGrowth -> InitializeInfectionsExponentialGrowth).

I was thinking that since they were subclasses the connection with seeding infections shouldn't be completely removed, but I see the point. Will change.

[damonbayer]

Looks good. Thanks @AFg6K7h4fhy2!