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Introduce `ObservationChainLayout` and `ObservationLayout` types for observation metadata, and update `observation_layout` to return them. Export the new types and add tests for constructor validation and derived cumulative names.
Build model UWDs without predeclared outer ports and let `oapply_typed` derive the boundary from junctions. Update shared construction helpers to add internal junctions only, simplify stage setup, and adjust tests to assert empty outer boundaries for the generated diagrams.
Extracted model-specific junction selection into `_strain_junction` methods for `NoCrossImmunity` and `CompleteCrossImmunity`, and updated `generate_transition_names` to use this dispatch-based logic. This removes inline branching, keeps strain resolution clearer, and preserves explicit failure behavior via `only(...)` when junction assumptions are violated. The doc example comments were also corrected to reflect 3 boxes per strain (6 names for 2 strains) instead of 4.
Improve `create_model` documentation by clarifying the UWD intermediate role and tightening wording around typed Petri-net construction. In `vectorfield_flat`, simplify and rename accumulator helpers (`_zeroed_accumulator`, `_writeback_accumulator!`), make zeroing behavior explicit when accumulating directly into `du`, and trim overly specific performance commentary while keeping core implementation notes.
Refines `ObservationTarget.jl` comments to better explain pullback-based model composition versus pushout-based observation attachment, and rewrites the optimization rationale with clearer performance context. Also clarifies prevalence sampling behavior by noting detection is non-removing.
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Unresolved name-collision, input-validation, typing, and observation-chain issues can produce failures or incorrect models.
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What changed in this PR
Introduces AlgebraicEpiMech, a Julia package for constructing, composing, observing, and simulating typed epidemiological Petri-net models.
Changes:
- Adds compartmental, multistrain, immune-history, and stratification abstractions.
- Adds model construction, observation attachment/layout, and flattened vector fields.
- Adds comprehensive tests and Julia CI.
| File | Description |
|---|---|
.github/workflows/test.yaml |
Adds multi-version Julia CI. |
.gitignore |
Ignores manifests and macOS metadata. |
AlgebraicEpiMech/Project.toml |
Defines package dependencies and compatibility. |
AlgebraicEpiMech/src/AlgebraicEpiMech.jl |
Defines module exports and includes. |
AlgebraicEpiMech/src/CompartmentalModel.jl |
Defines compartmental model types. |
AlgebraicEpiMech/src/ImmuneHistory.jl |
Implements immune-history classes. |
AlgebraicEpiMech/src/MultiStrainModel.jl |
Defines multistrain models. |
AlgebraicEpiMech/src/ObservationLayout.jl |
Extracts observation-chain metadata. |
AlgebraicEpiMech/src/ObservationTarget.jl |
Attaches event and compartment observations. |
AlgebraicEpiMech/src/Stratification.jl |
Defines contact stratifications. |
AlgebraicEpiMech/src/construction_helpers.jl |
Adds shared UWD construction helpers. |
AlgebraicEpiMech/src/create_model.jl |
Provides unified model construction. |
AlgebraicEpiMech/src/create_model_uwd.jl |
Builds model-specific UWDs. |
AlgebraicEpiMech/src/docstrings.jl |
Configures documentation templates. |
AlgebraicEpiMech/src/generate_transition_names.jl |
Generates model transition names. |
AlgebraicEpiMech/src/mechanisms.jl |
Defines epidemiological UWD mechanisms. |
AlgebraicEpiMech/src/typing.jl |
Defines epidemiological type systems. |
AlgebraicEpiMech/src/vectorfield_flat.jl |
Implements flattened-name vector fields. |
AlgebraicEpiMech/test/Aqua.jl |
Adds Aqua quality checks. |
AlgebraicEpiMech/test/Project.toml |
Defines test dependencies. |
AlgebraicEpiMech/test/runtests.jl |
Runs package test items. |
AlgebraicEpiMech/test/test_age_stratification.jl |
Tests legacy age stratification. |
AlgebraicEpiMech/test/test_compartmental_models.jl |
Tests compartmental constructors. |
AlgebraicEpiMech/test/test_construction_helpers.jl |
Tests construction helpers. |
AlgebraicEpiMech/test/test_contact_stratification.jl |
Tests stratification types. |
AlgebraicEpiMech/test/test_create_age_stratification.jl |
Tests age-model generation. |
AlgebraicEpiMech/test/test_create_basic_model.jl |
Tests basic model generation. |
AlgebraicEpiMech/test/test_create_contact_stratification.jl |
Tests contact-model generation. |
AlgebraicEpiMech/test/test_create_model_uwd.jl |
Tests UWD construction. |
AlgebraicEpiMech/test/test_create_multistrain_model.jl |
Tests multistrain generation. |
AlgebraicEpiMech/test/test_epi_schema.jl |
Tests typing schemas. |
AlgebraicEpiMech/test/test_immune_history.jl |
Tests immune-history behavior. |
AlgebraicEpiMech/test/test_mechanisms.jl |
Tests mechanism primitives. |
AlgebraicEpiMech/test/test_observation_chain.jl |
Tests observation layouts. |
AlgebraicEpiMech/test/test_observation_rewriting.jl |
Tests observation attachment. |
AlgebraicEpiMech/test/test_stratification.jl |
Tests stratification composition. |
AlgebraicEpiMech/test/test_transition_naming.jl |
Tests transition naming. |
AlgebraicEpiMech/test/test_vectorfield_flat.jl |
Tests flattened vector fields. |
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Add constructor and helper checks for positive stage counts, unique strain names, and flattened symbol collisions before building models or vector fields. Observation attachment now treats repeated applications as idempotent only when the existing chain shape matches, and throws a clear error when the same prefix/target is reused incompatibly. The multistrain APIs and docs were also tightened to reflect the required typing and the removal of observation reflexives from composition.
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Summary
This PR introduces the core package that gives:
AlgebraicPetri, in particular usingoapply_typedto generate typed petri nets. This allows categorical pullback composition across other typed petri netsPackage details
Core type system and model abstractions:
AlgebraicEpiMechmodule, defining the abstract base typeEpiMechModeland exporting a comprehensive set of model types and utility functions. The module includes submodules for epidemiological typing, mechanisms, compartmental models, multistrain models, immune history, stratification, model construction, vectorfield utilities, and observation attachment. (AlgebraicEpiMech/src/AlgebraicEpiMech.jl)SI,SEI,SIR,SEIR,SIS,SEIS,SEIRS), each with relevant fields and constructors, enabling clean dispatch and extensibility for various epidemiological dynamics. (AlgebraicEpiMech/src/CompartmentalModel.jl)NoCrossImmunity,CompleteCrossImmunity), supporting different cross-immunity assumptions and flexible strain naming. (AlgebraicEpiMech/src/MultiStrainModel.jl)ImmuneHistoryModeandImmuneHistorytypes, supporting both full and latest-infection immune tracking, with internal utilities for immune class computation and naming. (AlgebraicEpiMech/src/ImmuneHistory.jl)Observation metadata:
ObservationChainLayoutandObservationLayouttypes, along with theobservation_layoutfunction, to provide deterministic metadata for observation chains in augmented Petri nets. This centralizes observation-state naming and ordering for downstream analysis. (AlgebraicEpiMech/src/ObservationLayout.jl)Project and CI setup:
Project.tomlfor theAlgebraicEpiMechpackage, specifying dependencies, authorship, and Julia compatibility for versions 1.11–1.13. (AlgebraicEpiMech/Project.toml)test.yaml) to run tests on Julia versions 1.11, 1.12, and 1.13, ensuring CI coverage for the supported Julia versions. (.github/workflows/test.yaml)