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Model builder, latent infection process components and tutorials - #650

Merged

dylanhmorris merged 106 commits into

mainfrom

mem_hier_latent_processes

Feb 6, 2026

Merged

Model builder, latent infection process components and tutorials#650
dylanhmorris merged 106 commits into
mainfrom
mem_hier_latent_processes

Commits on Sep 15, 2025
- Merge branch 'main' of https://github.com/CDCgov/PyRenew
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Commits on Sep 18, 2025
- update
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Commits on Sep 22, 2025
- Merge branch 'main' of github-bf06:CDCgov/PyRenew
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Commits on Oct 5, 2025
- Merge branch 'main' of github-bf06:CDCgov/PyRenew
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Commits on Oct 8, 2025
- Merge branch 'main' of github-bf06:CDCgov/PyRenew
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Commits on Nov 17, 2025
- Merge branch 'main' of github-bf06:CDCgov/PyRenew
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Commits on Nov 24, 2025
- Merge branch 'main' of github-bf06:CDCgov/PyRenew
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Commits on Dec 4, 2025
- Merge branch 'main' of github-bf06:CDCgov/PyRenew
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Commits on Dec 22, 2025
- Merge branch 'main' of github-bf06:CDCgov/PyRenew
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- added generic observation processes and unit tests
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Commits on Dec 23, 2025
- adding tutorials
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- improve test coverage
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- improve unit test coverage
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Commits on Dec 26, 2025
Commits on Dec 29, 2025
Commits on Jan 2, 2026
Commits on Jan 7, 2026
- Update docs/tutorials/observation_processes_measurements.qmd
  
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- Update docs/tutorials/observation_processes_measurements.qmd
  
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- Update docs/tutorials/observation_processes_measurements.qmd
  
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- Update docs/tutorials/observation_processes_measurements.qmd
  
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- Update docs/tutorials/observation_processes_measurements.qmd
  
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- Update docs/tutorials/observation_processes_measurements.qmd
  
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- Update pyrenew/observation/noise.py
  
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- Update pyrenew/observation/noise.py
  
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- Merge branch 'mem_generic_observations' of github-bf06:CDCgov/PyRenew into mem_generic_observations
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- change expected to predicted
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- standardize on param name obs for sample method
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- standardize sample - all methods must have arg obs
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- in order to use np TruncatedDistribution, change use of Gamma to TruncatedNormal
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- Remove the provided helper classes for sampling priors (i.e. pyrenew/randomvariable/hierarchical.py), per reviewer comments
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- updated observation process measurements per reviewer comments
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- more unit tests
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Commits on Jan 8, 2026
- use plotnine for plots in observation_processes tutorial
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- [pre-commit.ci] auto fixes from pre-commit.com hooks
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Commits on Jan 9, 2026
Commits on Jan 13, 2026
- change plate management strategy
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Commits on Jan 14, 2026
- adding hierarchical latent infections, model builder, and unit tests
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- tutorial - latent hierarchical infections
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Commits on Jan 15, 2026
- Fix numpydoc validation and typo errors
  
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- label all code blocks
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- site builds with mkdocs
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- Update docs/tutorials/observation_processes_counts.qmd
  
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- Update docs/tutorials/observation_processes_measurements.qmd
  
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- Merge branch 'mem_generic_observations' of github-bf06:CDCgov/PyRenew into mem_generic_observations
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- user-specified signal name
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- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- lint fix
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- Merge branch 'mem_generic_observations' of github-bf06:CDCgov/PyRenew into mem_generic_observations
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- merge
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- user-specified signal names
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- more unit tests
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- more unit tests; lint fix
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- dataset data loaders have some tests; don't hold to codecov requirements
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- cleanup dataset loaders
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Commits on Jan 16, 2026
- collapse code blocks in tutorials
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Commits on Jan 27, 2026
- code cleanup
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Commits on Jan 29, 2026
- merge fix
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- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- simplify this PR
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- Merge branch 'mem_hier_latent_processes' of github-bf06:CDCgov/PyRenew into mem_hier_latent_processes
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- lint fix
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- simplify this PR - ignore ParitionedInfections
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Commits on Jan 30, 2026
- code cleanup
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- refactoring per issue #662 - option 2
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Commits on Feb 1, 2026
- changes per coderabbit review
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Commits on Feb 2, 2026
- Merge branch 'main' of github-bf06:CDCgov/PyRenew into mem_hier_latent_processes
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- changes per code review
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Commits on Feb 4, 2026
Commits on Feb 5, 2026
- Update pyrenew/observation/noise.py
  
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- temporal processes always use 2D arrays for timepoints
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- Merge branch 'mem_hier_latent_processes' of github-bf06:CDCgov/PyRenew into mem_hier_latent_processes
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- API changes per code review - latent infections doesn't track obs/unobs subpops
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- no default n_initialization_points for low-level classes
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- wordsmithing
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- changes per code review
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Commits on Feb 6, 2026
- Update pyrenew/observation/noise.py
  
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- Update pyrenew/observation/noise.py
  
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- Update pyrenew/model/pyrenew_builder.py
  
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- Update pyrenew/model/pyrenew_builder.py
  
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- Merge branch 'mem_hier_latent_processes' of github-bf06:CDCgov/PyRenew into mem_hier_latent_processes
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- Code review changes: rename processes, reuse RandomWalk/PMF validation, remove fit(), remove sample() return
  
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- changes per code review
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- changes to tutorials per code review
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- [pre-commit.ci] auto fixes from pre-commit.com hooks
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