feat(model): SIR model#101
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@copilot fix the pre-commit issue |
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@emptymalei I've opened a new pull request, #102, to work on those changes. Once the pull request is ready, I'll request review from you. |
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Pull request overview
Adds an SIR (Susceptible–Infected–Recovered) epidemiological model to hamilflow, along with documentation, a tutorial, and CI/linting updates to support the new feature (resolves #100).
Changes:
- Introduce
hamilflow.models.sir.SIRwith Pydantic-based system/IC models. - Add SIR documentation pages and a tutorial notebook/script, and wire them into MkDocs navigation.
- Update lint config and bump GitHub Actions versions in workflows.
Reviewed changes
Copilot reviewed 11 out of 24 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
hamilflow/models/sir.py |
Implements the new SIR model and simulation API. |
tests/test_models/test_sir.py |
Adds initial unit tests for SIR initialization and basic simulation outputs. |
docs/tutorials/sir.py |
Adds a tutorial demonstrating SIR usage and plotting. |
docs/references/models/sir.md |
Adds reference doc entry for the SIR module. |
mkdocs.yml |
Adds SIR pages to nav and configures watch paths for docs/dev loop. |
hamilflow/models/utils/typing.py |
Adjusts TypeTime typing definition used by the model call signature. |
pyproject.toml |
Updates Ruff ignores (docstring rules, magic numbers in tests). |
.github/workflows/tests.yaml |
Updates action versions and coverage-comment action pin. |
.github/workflows/publish.yaml |
Updates action versions for publishing pipeline. |
.github/workflows/docs-publish.yaml |
Updates action versions; modifies pre-commit job steps. |
.github/workflows/docs-preview.yaml |
Updates action versions; modifies pre-commit job steps. |
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Resolves: #100