Rename latent process classes and update tests and documentation

[cdc-mitzimorris]

This PR implements the first set of name changes in issue #778:

class SharedInfections -> PopulationInfections
class HierarchicalInfections -> SubpopulationInfections
constructor arg initial_log_rt_rv -> log_rt_time_0_rv.

The tests and documentation have been updated accordingly.

[Copilot]

Pull request overview

Renames latent infection process classes and constructor arguments to better match epidemiological terminology, updating tests and tutorials to reflect the new public-facing API.

Changes:

• Renamed SharedInfections → PopulationInfections and HierarchicalInfections → SubpopulationInfections, including updated exports.
• Renamed constructor arg initial_log_rt_rv → log_rt_time_0_rv and propagated through model builder, tests, and integration coverage.
• Updated documentation/tutorials and navigation to reference the new class/argument names.

Reviewed changes

Copilot reviewed 18 out of 18 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
test/test_subpopulation_infections.py	Updates unit tests to use SubpopulationInfections + renamed constructor arg and trace-site prefixes.
test/test_pyrenew_builder.py	Updates builder tests to configure SubpopulationInfections and new arg name.
test/test_population_infections.py	Migrates unit tests from SharedInfections to PopulationInfections and updates deterministic-site expectations.
test/test_interface_coverage.py	Updates interface coverage to instantiate SubpopulationInfections and use renamed arg.
test/integration/test_population_infections_he.py	Updates integration test to new deterministic variable names for PopulationInfections.
test/integration/conftest.py	Updates integration model builder wiring to PopulationInfections + new arg/process param names.
test/conftest.py	Replaces latent fixtures with subpopulation_infections and adds population_infections fixture.
pyrenew/model/pyrenew_builder.py	Updates docstring example for latent class naming.
pyrenew/model/multisignal_model.py	Updates docstring example for latent class naming.
pyrenew/latent/subpopulation_infections.py	Renames class and constructor arg; updates sampling to use log_rt_time_0_rv.
pyrenew/latent/population_infections.py	Renames class and constructor arg; renames process parameter and deterministic-site names.
pyrenew/latent/base.py	Updates base-class docs to reference new class names.
pyrenew/latent/init.py	Updates public exports to PopulationInfections and SubpopulationInfections.
docs/tutorials/latent_subpopulation_infections.qmd	Renames tutorial content and examples to SubpopulationInfections / PopulationInfections + new arg name.
docs/tutorials/latent_infections.qmd	Updates single-population latent tutorial to PopulationInfections and new arg/process parameter names.
docs/tutorials/building_multisignal_models.qmd	Updates builder tutorial examples and narrative to SubpopulationInfections + log_rt_time_0_rv.
docs/tutorials/.pages	Updates tutorials nav entry to latent_subpopulation_infections.md.
docs/index.md	Updates docs landing page links to new tutorial names.

Comments suppressed due to low confidence (5)

pyrenew/latent/population_infections.py:3

• Module docstring has a typo: "Populaton-level" should be "Population-level".
  pyrenew/latent/population_infections.py:30
• The class docstring math markup has an extra space ("$\ mathcal{R}(t)$"), which may render incorrectly in generated docs. Consider changing it to "$\mathcal{R}(t)$".
  docs/tutorials/latent_subpopulation_infections.qmd:116
• This tutorial text still references the old initial-condition name initial_log_rt. It should be updated to log_rt_time_0 to match the renamed constructor argument (log_rt_time_0_rv).
  docs/tutorials/latent_subpopulation_infections.qmd:183
• This print statement labels the value as "Log Rt" but prints exp(log_rt_time_0), which is Rt (not log Rt). Update the label or the printed value so they match.
  pyrenew/latent/subpopulation_infections.py:30
• After renaming the class to SubpopulationInfections, several docstrings in this module still use the old phrasing "hierarchical infections" (e.g., init/validate/sample docstrings). Updating these strings will keep the generated API docs consistent with the new public name.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.44%. Comparing base (0078fbd) to head (f0de42f).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #781   +/-   ##
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  Coverage   98.44%   98.44%           
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  Files          51       51           
  Lines        1675     1675           
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  Hits         1649     1649           
  Misses         26       26           

Flag	Coverage Δ
unittests	98.44% <100.00%> (ø)

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[github-actions]

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[damonbayer]

The latex explanation below still uses the old name $e^{\text{initial\_log\_rt}}$. Perhaps search the codebase for any latex versions of the olde names.

[cdc-mitzimorris]

good catch. thanks!

[damonbayer]

Please review the latex portions of the tutorials / docs for any names that should have been changed. Otherwise, this looks good!