makefile(streamlit the same, stlite added, bug for display fixed, out…

.gitignore

@@ -1,3 +1,25 @@
 .venv/
 __pycache__/
 *.py[cod]
+# Build artifacts
+build/
+.coverage
+*.bak
+__pycache__/
+.pytest_cache/
+.mypy_cache/
+*.pyc
+*.pyo
+.venv/
+.env
+# Build artifacts
+build/
+.coverage
+*.bak
+__pycache__/
+.pytest_cache/
+.mypy_cache/
+*.pyc
+*.pyo
+.venv/
+.env

AGENTS.md

@@ -0,0 +1,221 @@
+# AGENTS.md — EpiCON Cost Calculator
+
+This file describes the conventions, roles, and constraints for contributors working in this
+repository. All agents — whether running in GitHub Actions or invoked interactively — should
+read and follow this document before making changes.
+
+---
+
+## Project overview
+
+**EpiCON** is a browser-based epidemiological cost calculator built with **Streamlit** and
+distributed as a static **stlite** build for browser execution.
+
+The current app supports two model flows:
+
+1. **Python + YAML models**
+   - A Python module in `models/` implements model logic.
+   - A paired YAML file provides default parameters.
+   - `app.py` loads the Python module, loads YAML defaults, renders parameter inputs,
+     runs the model, and renders sections.
+
+2. **Excel-driven models**
+   - An uploaded `.xlsx` file is parsed by `utils/excel_model_runner.py`.
+   - Parameters and computed outputs are rendered from workbook contents.
+
+Current high-level flow:
+
+`discover_models() → load_model_from_file() / load_model_params() → render_parameters_with_indent() → run_model() → build_sections() → render_sections()`
+
+Persistence helpers:
+- `store_model_state()`
+- `save_current_model()`
+
+---
+
+## Repository layout
+
+```text
+epiworldPythonStreamlit/
+├── app.py
+├── models/                 # Python model modules + paired YAML parameter files
+├── utils/
+│   ├── model_loader.py
+│   ├── parameter_loader.py
+│   ├── parameter_ui.py
+│   ├── excel_model_runner.py
+│   └── section_renderer.py
+├── config/
+├── styles/
+├── scripts/                # stlite build helpers
+├── build/                  # generated static output
+├── docs/
+├── pyproject.toml
+├── Makefile
+├── AGENTS.md
+└── README.md
+```
+
+---
+
+## Coding conventions
+
+All agent-generated code must follow these standards.
+
+### Style
+- Follow **PEP 8** for all Python code.
+- Use **type hints** on every function signature.
+- Write **docstrings** for every public function and class.
+- Maximum line length: **100 characters**.
+
+### Testing
+- Tests use **pytest** only.
+- Add or update pytest coverage for every changed public function whenever a `tests/` target
+  exists for that module.
+- Prefer pure-Python tests compatible with the stlite/Pyodide target.
+- Avoid test dependencies that require native binaries.
+- Aim for at least **80% line coverage** on new code where CI coverage is enforced.
+
+### Dependencies
+- Add dependencies via `pyproject.toml` only, managed by `uv`.
+- Runtime dependencies must be **pure-Python** or available as **Pyodide wheels**.
+- Dev-only dependencies are exempt from the Pyodide runtime constraint.
+
+### Security
+- Equations and figure code in YAML files are untrusted input.
+- Validate them with the CPython `ast` module before evaluation.
+- Never use `eval()` or `exec()` on unvalidated user-supplied strings.
+- Do not log or print parameter values that could contain PII.
+
+### Git workflow
+- **No direct pushes to `main`.**
+- Use branch names like:
+  - `feat/<short-description>`
+  - `fix/<short-description>`
+  - `chore/<short-description>`
+- Use **Conventional Commits** for commit messages.
+- Each PR should address a single concern.
+
+---
+
+## Function contracts (current)
+
+Agents must not change a function signature or return type without updating all callers and
+tests.
+
+### App / utility layer
+- `discover_models(path: str) -> dict[str, str]`
+- `load_model_from_file(filepath: str) -> object`
+- `load_model_params(model_file_path: str, uploaded_excel=None) -> dict`
+- `flatten_dict(d, level=0)`
+- `render_parameters_with_indent(param_dict: dict, params: dict, model_id: str) -> None`
+- `reset_parameters_to_defaults(param_dict: dict, params: dict, model_id: str) -> None`
+- `render_sections(sections: list[dict]) -> None`
+
+### Python model modules
+Each Python model module in `models/` must expose:
+- `model_title: str`
+- `model_description: str`
+- `run_model(params: dict, label_overrides: dict | None = None) -> list[dict]`
+- `build_sections(results: list[dict], label_overrides: dict | None = None) -> list[dict]`
+
+---
+
+## Agent roles
+
+### Interactive development agents
+**Scope:** Code generation, refactoring, documentation, tests, YAML schema work, and code
+review suggestions.
+
+**Constraints:**
+- Always read `AGENTS.md` and relevant source files before proposing changes.
+- Do not modify `pyproject.toml` dependencies without explaining Pyodide compatibility.
+- Use AST validation for equation evaluation.
+- Prefer Streamlit-native rendering over heavier plotting dependencies.
+- For browser-only persistence, use browser storage patterns rather than server-side files.
+- Propose tests alongside implementation changes.
+
+### GitHub Actions — CI agent
+**Trigger:** Every push and every PR targeting `main`.
+
+**Expected steps:**
+1. Check out the repository.
+2. Install dependencies with `uv`.
+3. Run `ruff`.
+4. Run `mypy`.
+5. Run `pytest` with coverage.
+6. Fail if configured coverage thresholds are not met.
+
+**Constraints:**
+- Must run in the project’s supported development environment.
+- Do not upload artifacts unless explicitly configured.
+
+### GitHub Actions — agent environment
+**Purpose:** Set up credentials, tools, and optional external service tokens.
+
+**Constraints:**
+- Secrets must be stored in GitHub Actions Secrets.
+- Fail loudly if required secrets are missing.
+
+---
+
+## YAML model schema
+
+The app currently supports both of these YAML layouts.
+
+### 1. Flat key/value defaults
+```yaml
+Cost of measles hospitalization: 31168
+Proportion of cases hospitalized: 0.2
+```
+
+### 2. Nested parameter dictionary
+```yaml
+parameters:
+  Cost of measles hospitalization: 31168
+  Proportion of cases hospitalized: 0.2
+```
+
+Agents must preserve compatibility with both layouts unless the app is explicitly migrated.
+
+### Reference schema for future structured models
+```yaml
+model:
+  metadata:
+  parameters:
+  equations:
+  table:
+  figures:
+  current_parameters:
+```
+
+If generating new structured YAML, keep it compatible with current loaders or update the
+loaders and tests together.
+
+---
+
+## Out-of-scope for agents
+
+The following are off-limits without explicit human approval in PR review:
+
+- Changing branch protection rules.
+- Adding `eval()` or `exec()` on user-supplied strings.
+- Introducing runtime dependencies that require native binaries.
+- Modifying the public function signatures listed above.
+- Writing outside the repository working directory.
+- Disabling or skipping CI checks.
+
+---
+
+## Getting started
+
+```bash
+uv sync
+make dev
+make setup
+make serve
+make check
+```
+
+For architecture questions, refer to the development plan, inline source comments, and current
+utility/model implementations.

Makefile

@@ -0,0 +1,84 @@
+UV ?= uv
+
+STLITE_VER ?= 0.86.0
+PORT ?= 8000
+
+STLITE_CSS := https://cdn.jsdelivr.net/npm/@stlite/browser@$(strip $(STLITE_VER))/build/stlite.css
+STLITE_JS := https://cdn.jsdelivr.net/npm/@stlite/browser@$(strip $(STLITE_VER))/build/stlite.js
+APP_PY := app.py
+BUILD_DIR := build
+INDEX_HTML := $(BUILD_DIR)/index.html
+
+STLITE_INPUTS := $(APP_PY) pyproject.toml scripts/build_index.py \
+	$(shell find models utils config styles selected examples -type f 2>/dev/null)
+
+ASSET_DIRS := utils config styles models selected examples
+
+.DEFAULT_GOAL := help
+
+.PHONY: help
+help:
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | \
+	awk 'BEGIN {FS = ":.*?## "}; {printf "  \033[36m%-20s\033[0m %s\n", $$1, $$2}'
+
+.PHONY: setup
+setup: install build-html ## Install dependencies and build the stlite app
+	@echo ""
+	@echo "EpiCON is ready."
+	@echo "  Dev server (normal Streamlit): make dev"
+	@echo "  Serve stlite build locally:    make serve"
+
+.PHONY: install
+install: ## Install Python dependencies with uv
+	$(UV) sync
+
+.PHONY: build-html
+build-html: $(INDEX_HTML) ## Generate build/index.html (stlite WASM entry point)
+
+$(INDEX_HTML): $(STLITE_INPUTS) | $(BUILD_DIR)
+	@echo "Generating $(INDEX_HTML) (stlite v$(STLITE_VER))"
+	$(UV) run python scripts/build_index.py \
+	--app $(APP_PY) \
+	--out $(INDEX_HTML) \
+	--css $(STLITE_CSS) \
+	--js $(STLITE_JS) \
+	--title "EpiCON Cost Calculator"
+	@echo "Copying static assets into $(BUILD_DIR)/"
+	@for dir in $(ASSET_DIRS); do \
+	    if [ -d "$$dir" ]; then cp -r "$$dir" "$(BUILD_DIR)/"; fi; \
+	done
+	@echo "Build artefacts written to $(BUILD_DIR)/"
+
+$(BUILD_DIR):
+	mkdir -p $@
+
+.PHONY: dev
+dev: ## Run normal Streamlit locally
+	$(UV) run streamlit run $(APP_PY)
+
+.PHONY: serve
+serve: build-html ## Serve the stlite static build
+	@echo "Serving stlite build at http://localhost:$(PORT) (Ctrl-C to stop)"
+	$(UV) run python -m http.server $(PORT) --directory $(BUILD_DIR)
+
+.PHONY: stlite
+stlite: setup serve ## Install, build, and serve the stlite app
+
+.PHONY: lint
+lint: ## Run ruff linter
+	$(UV) run ruff check .
+
+.PHONY: typecheck
+typecheck: ## Run mypy type checker
+	$(UV) run mypy utils
+
+.PHONY: test
+test: ## Run pytest
+	$(UV) run pytest
+
+.PHONY: check
+check: lint typecheck test ## Run all quality checks
+
+.PHONY: clean
+clean: ## Remove build artefacts
+	rm -rf $(BUILD_DIR) .mypy_cache .ruff_cache .pytest_cache __pycache__