Introduce Pydantic Models for Builtin Models

[olivia-banks]

Introduce Pydantic models for builtin models, and hook this up to the UI. Fixed some reactivity issues, and enabled better diagnostics when a YAML file doesn't look right.

For example, here's what happens when we try to upload Measles parameters to the Tuberculosis model.

As with #24, this is based on #17, and the files to look at are:

modified:   src/epicc/__main__.py
modified:   src/epicc/model/base.py
modified:   src/epicc/models/measles_outbreak.py
modified:   src/epicc/models/tb_isolation.py
modified:   src/epicc/utils/parameter_loader.py

[Copilot]

Pull request overview

This PR migrates the app from ad-hoc Python/YAML handling to a structured, typed approach: built-in simulation models now declare Pydantic parameter schemas, parameter files are loaded via a unified format layer (YAML/XLSX), and the Streamlit UI is rewired to validate and surface better diagnostics when uploads don’t match a model’s schema.

Changes:

• Introduces a BaseSimulationModel contract plus Pydantic parameter models for the built-in TB Isolation and Measles Outbreak simulations (including default YAML parameter files).
• Adds a generic “formats” layer (BaseFormat, YAMLFormat, XLSXFormat) with template generation utilities and new unit tests.
• Replaces the legacy top-level app.py + utils/ loaders with a packaged Streamlit entrypoint (src/epicc/__main__.py) and src/epicc/utils/* helpers.

Reviewed changes

Copilot reviewed 35 out of 43 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
utils/section_renderer.py	Removed legacy non-packaged section renderer (moved under src/epicc/utils).
utils/parameter_ui.py	Removed legacy non-packaged sidebar parameter UI (moved under src/epicc/utils).
utils/parameter_loader.py	Removed legacy YAML/XLSX parameter loader (replaced by epicc.formats + typed loading).
utils/model_loader.py	Removed legacy dynamic module discovery/loader (replaced by explicit built-in registry).
src/epicc/web/sidebar.css	Adds sidebar styling used by the packaged Streamlit app.
src/epicc/utils/section_renderer.py	New packaged section rendering with safer defaults (get() for missing keys).
src/epicc/utils/parameter_ui.py	Packaged sidebar parameter widgets + reset logic.
src/epicc/utils/parameter_loader.py	Loads/validates uploaded params via format layer + Pydantic, then flattens for UI.
src/epicc/utils/model_loader.py	Defines built-in model registry returned to the UI.
src/epicc/utils/excel_model_runner.py	Refactors formatting and reuses shared flatten_dict.
src/epicc/models/tb_isolation.yaml	Adds default TB Isolation parameter YAML.
src/epicc/models/tb_isolation.py	Adds TB Isolation built-in model + Pydantic parameter schema + YAML defaults loader.
src/epicc/models/measles_outbreak.yaml	Adds default Measles Outbreak parameter YAML.
src/epicc/models/measles_outbreak.py	Adds Measles Outbreak built-in model + Pydantic parameter schema + YAML defaults loader.
src/epicc/model/schema.py	Adds a typed schema for declarative YAML-defined models (Model, Parameter, Equation, etc.).
src/epicc/model/base.py	Introduces BaseSimulationModel abstract interface for Python models.
src/epicc/model/init.py	Adds load_model() for YAML-defined models using the formats layer.
src/epicc/formats/base.py	Adds BaseFormat abstraction for YAML/XLSX IO + template writing.
src/epicc/formats/yaml.py	Adds YAML format reader/writer.
src/epicc/formats/xlsx.py	Adds XLSX format reader/writer + template writer.
src/epicc/formats/template.py	Adds Pydantic-based template generation utilities.
src/epicc/formats/init.py	Adds format registry, validation helpers, and read_from_format().
src/epicc/config/schema.py	Adds typed config schema (Config, DefaultsConfig, etc.).
src/epicc/config/default.yaml	Adds packaged default configuration YAML.
src/epicc/config/init.py	Adds packaged config loader and exports CONFIG.
src/epicc/main.py	New packaged Streamlit entrypoint wired to built-in models + typed validation errors.
tests/epicc/test_model_loader.py	Adds tests for epicc.model.load_model().
tests/epicc/test_formats.py	Adds tests for format selection and typed read helper.
tests/epicc/test_formats_yaml.py	Adds YAML format read/write tests.
tests/epicc/test_formats_xlsx.py	Adds XLSX format read/write tests.
tests/epicc/test_formats_template.py	Adds integration tests for template generation.
sample/TB Isolation.xlsx	Adds sample TB Isolation workbook.
sample/Measles Outbreak.xlsx	Adds sample Measles Outbreak workbook.
sample/~$TB Isolation.xlsx	Adds an Excel lock/temp file (should not be committed).
pyproject.toml	Adds Pydantic + ruamel.yaml deps, pytest dev dep, and pytest pythonpath config.
models/tb_isolation.py	Removes legacy TB Isolation model module (superseded by packaged model).
models/measles_outbreak.py	Removes legacy Measles model module (superseded by packaged model).
config/paths.yaml	Removes legacy app configuration file (superseded by packaged config).
config/global_defaults.yaml	Removes legacy defaults file (superseded by packaged config).
config/app.yaml	Removes legacy app config (superseded by packaged config).
app.py	Removes legacy top-level Streamlit app entrypoint (replaced by src/epicc/__main__.py).
.gitignore	Expands ignored editor/build artifacts.

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[olivia-banks]

Blocked by #17.

[Copilot]

Pull request overview

Copilot reviewed 8 out of 11 changed files in this pull request and generated 3 comments.

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[Copilot]

MeaslesOutbreakModel.run() narrows the params argument type to MeaslesOutbreakParams, but BaseSimulationModel.run() now declares params: BaseModel. This override is not type-compatible (LSP) and will likely fail strict type-checking. Consider making BaseSimulationModel generic over a ParamsT: BaseModel (so run() and parameter_model() share the same type), or keep the override signature accepting BaseModel and cast/validate internally.

[Copilot]

TBIsolationModel.run() narrows the params argument type to TBIsolationParams, but BaseSimulationModel.run() declares params: BaseModel. This override is not type-compatible and can break the repository's strict type-checking. Consider making BaseSimulationModel generic over a ParamsT: BaseModel (and returning type[ParamsT] from parameter_model()), or keep run() accepting BaseModel and downcast after validation.

Suggested change

	params: TBIsolationParams,
	label_overrides: dict[str, str] | None = None,
	) -> dict[str, Any]:
	params: BaseModel,
	label_overrides: dict[str, str] | None = None,
	) -> dict[str, Any]:
	if isinstance(params, TBIsolationParams):
	params = params
	else:
	params = TBIsolationParams.model_validate(params.model_dump())

[Copilot]

st.set_page_config(...) was removed, and there are no other calls in the codebase. This changes the app's title/layout behavior (e.g., losing layout="wide" and the configured page title) and can’t be added later once Streamlit has emitted elements. If this removal wasn’t intentional, reintroduce st.set_page_config at the top of __main__.py (before _load_styles() or any other st.* calls).

Suggested change

	st.set_page_config(page_title=CONFIG.app.title)