makefile(streamlit the same, stlite added, bug for display fixed, out… by EddW1219 · Pull Request #21 · EpiForeSITE/epiworldPythonStreamlit

EddW1219 · 2026-03-25T07:27:22Z

Added AGENTS.md, and Makefile(by using either make dev(streamlit) or make stlite(stlite) version), fixed the bug for display error in stlite, bug remains( output as 0s).

…put as 0 as TD), and AGENTS.md added

Copilot

Pull request overview

This PR adds stlite build scaffolding and contributor guidance while adjusting parameter loading/rendering to better support stlite (including handling nested YAML parameters: blocks and attempting to prevent blank widget values from overwriting defaults).

Changes:

Add stlite build generation via scripts/build_index.py and a new Makefile workflow.
Normalize YAML parameter defaults and add helpers for leaf-parameter defaults/coercion (stlite-specific).
Add AGENTS.md contributor/agent conventions and refactor parameter UI rendering/reset behavior.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
`utils/parameter_ui.py`	Refactors parameter reset/render logic and changes widget keying + sidebar rendering.
`utils/parameter_loader.py`	Adds typing, supports nested `parameters:` YAML layouts, and introduces `get_leaf_defaults`.
`scripts/build_index.py`	New helper to generate `build/index.html` for stlite and mount project files.
`app.py`	Adds stlite detection + parameter normalization/coercion; updates parameter source handling and UI flows.
`Makefile`	New targets for dev/stlite build/serve and quality checks.
`AGENTS.md`	New contributor/agent conventions and documented function contracts.

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Copilot · 2026-03-25T07:33:07Z

app.py

+
+def running_in_stlite() -> bool:
+    """Return True when the app is running inside stlite/Pyodide."""
+    return os.path.abspath(__file__).startswith("/home/pyodide/")


running_in_stlite is defined twice in this module (once near the top and again here). This will trigger a Ruff F811 redefinition error and can confuse readers/tools. Remove the duplicate definition and keep a single implementation.

Suggested change

def running_in_stlite() -> bool:

"""Return True when the app is running inside stlite/Pyodide."""

return os.path.abspath(__file__).startswith("/home/pyodide/")

@EddW1219 while this is a good point, this is a fairly finicky check. Pyodide recommends:

if sys.platform == "emscripten" or "pyodide" in sys.modules: # stuff

Copilot · 2026-03-25T07:33:08Z

utils/parameter_ui.py

+            st.sidebar.markdown(
+                (
+                    f"<div style='margin-left:{indent_level * 1.5}em; "
+                    f"font-weight:600;'>{clean_label}</div>"
+                ),
+                unsafe_allow_html=True,
+            )


clean_label is interpolated directly into HTML while unsafe_allow_html=True. Since parameter labels originate from YAML / uploaded Excel files, this enables HTML/script injection in the sidebar. Escape the label (e.g., html.escape) before inserting it into the <div>, or avoid unsafe_allow_html entirely by using Streamlit primitives for indentation/grouping.

While this is running in a sandboxed browser, this is still good practice and should likely be fixed. I'd search for HTML interpolation events across the code and fix them, if the source is directly modifiable by the user.

Copilot · 2026-03-25T07:33:08Z

Makefile

+	--js $(STLITE_JS) \
+	--title "EpiCON Cost Calculator"
+	@echo "Copying static assets into $(BUILD_DIR)/"
+	@for dir in utils config styles models smelected examples; do \


Typo in the asset-copy loop: smelected is likely meant to be selected. As written, any selected/ directory won't be copied into the build output.

Suggested change

@for dir in utils config styles models smelected examples; do \

@for dir in utils config styles models selected examples; do \

Copilot · 2026-03-25T07:33:08Z

Makefile

+typecheck: ## Run mypy type checker
+	$(UV) run mypy utils
+
+.PHONY: test
+test: ## Run pytest
+	$(UV) run pytest


The typecheck and test targets invoke mypy and pytest, but those tools are not declared in pyproject.toml/uv.lock (only ruff is in the dev group). Either add mypy and pytest to the appropriate dependency group(s), or adjust/remove these targets; otherwise make check will fail in a fresh environment.

Suggested change

typecheck: ## Run mypy type checker

$(UV) run mypy utils

.PHONY: test

test: ## Run pytest

$(UV) run pytest

typecheck: ## (Disabled) mypy type checker; mypy is not configured as a dependency

@echo "typecheck: mypy is not configured in pyproject.toml/uv.lock; skipping type checking."

.PHONY: test

test: ## (Disabled) pytest; pytest is not configured as a dependency

@echo "test: pytest is not configured in pyproject.toml/uv.lock; skipping tests."

@EddW1219 I would reject this, since there's tests in another PR that will get merged in.

Copilot · 2026-03-25T07:33:08Z

AGENTS.md

+- `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, params, label_overrides) -> None`


The function contract listed for render_parameters_with_indent doesn't match the actual implementation/call sites (it takes model_id, not label_overrides). Update this signature in the contract list to avoid misleading contributors/agents.

Suggested change

- `render_parameters_with_indent(param_dict, params, label_overrides) -> None`

- `render_parameters_with_indent(param_dict, params, model_id) -> None`

Copilot · 2026-03-25T07:33:08Z

app.py

        render_parameters_with_indent(
            editable_defaults,
            params,
-            model_id=uploaded_excel_model.name
+            model_id=model_key
        )


In the Excel-driven flow the parameter widget keys are built from model_id (see render_parameters_with_indent), but the reset callback uses uploaded_excel_model.name while the renderer is called with model_id=model_key ("EXCEL_DRIVEN"). This means the Reset button won't update the actual widgets, and widget state may also leak between different uploaded Excel files because the keys stay constant. Use the same identifier for both rendering and resetting (and ideally one that changes with the uploaded Excel filename) so session_state keys line up.

gvegayon · 2026-03-25T16:07:37Z

Thank you, @EddW1219! @olivia-banks, can you take a look at this PR?

olivia-banks

👍!

olivia-banks · 2026-03-25T16:30:30Z

utils/parameter_ui.py

+            st.sidebar.markdown(
+                (
+                    f"<div style='margin-left:{indent_level * 1.5}em; "
+                    f"font-weight:600;'>{clean_label}</div>"
+                ),
+                unsafe_allow_html=True,
+            )


While this is running in a sandboxed browser, this is still good practice and should likely be fixed. I'd search for HTML interpolation events across the code and fix them, if the source is directly modifiable by the user.

olivia-banks · 2026-03-25T16:32:13Z

app.py

+
+def running_in_stlite() -> bool:
+    """Return True when the app is running inside stlite/Pyodide."""
+    return os.path.abspath(__file__).startswith("/home/pyodide/")


@EddW1219 while this is a good point, this is a fairly finicky check. Pyodide recommends:

if sys.platform == "emscripten" or "pyodide" in sys.modules: # stuff

olivia-banks · 2026-03-25T16:32:54Z

Makefile

+typecheck: ## Run mypy type checker
+	$(UV) run mypy utils
+
+.PHONY: test
+test: ## Run pytest
+	$(UV) run pytest


@EddW1219 I would reject this, since there's tests in another PR that will get merged in.

olivia-banks · 2026-03-25T16:33:35Z

scripts/build_index.py

+"""
+
+
+def main() -> None:


Nit: omit the -> None.

olivia-banks · 2026-03-25T16:36:13Z

Makefile

@@ -0,0 +1,82 @@
+UV := uv


Ideally this should be a ?= assignment, to allow for changing from env vars.

olivia-banks · 2026-03-25T16:37:45Z

Makefile

+	done
+	@echo "Build artefacts written to $(BUILD_DIR)/"
+
+$(BUILD_DIR):


I would personally move this up into the INDEX_HTML rule to avoid using the sequencing operator (line 36).

olivia-banks · 2026-03-26T23:34:34Z

Linking to #13.

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

881988e

…put as 0 as TD), and AGENTS.md added

Copilot AI review requested due to automatic review settings March 25, 2026 07:27

Copilot started reviewing on behalf of EddW1219 March 25, 2026 07:27 View session

Copilot AI reviewed Mar 25, 2026

View reviewed changes

gvegayon requested a review from olivia-banks March 25, 2026 16:07

olivia-banks requested changes Mar 25, 2026

View reviewed changes

olivia-banks mentioned this pull request Mar 25, 2026

Address #15; Lay Validation Foundation; Light Cleanup Work #17

Open

10 tasks

	@for dir in utils config styles models smelected examples; do \
	@for dir in utils config styles models selected examples; do \

	- `render_parameters_with_indent(param_dict, params, label_overrides) -> None`
	- `render_parameters_with_indent(param_dict, params, model_id) -> None`

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gvegayon commented Mar 25, 2026

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