Add model editor app for building YAML model files by Copilot · Pull Request #42 · EpiForeSITE/epicc

Copilot · 2026-04-17T21:36:11Z

Locate all emoji in source files
Remove emoji from src/epicc/editor/__main__.py UI strings
All 107 tests pass

…tion Create a separate Streamlit app for building and editing YAML model files: - src/epicc/editor/ package with helpers.py (pure logic) and __main__.py (UI) - editor.py entry point at repository root - Makefile 'editor' target - 29 tests covering helpers, validation, and round-trip serialization Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/a4e6dd31-6c9a-4ef2-9059-59a5f3af997d Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com>

Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/a4e6dd31-6c9a-4ef2-9059-59a5f3af997d Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com>

gvegayon

@copilot, I tried the new app, and it is not working as expected. The main issues I saw:

The list of authors failed to properly load the authors of the measles model:

The buttons to add or remove anything are not working. I tried adding/removing authors, parameters, scenarios, etc., and none worked.

- Use on_click callbacks for all add/remove buttons so state changes happen before the next render cycle (fixes buttons appearing to do nothing) - Track uploaded file identity to prevent re-processing on every rerun - Use st.rerun() after file upload to force fresh widget creation - Embed a version counter in all dynamic widget keys so structural changes (upload, add, remove) create truly new widgets that honour the value parameter from loaded data (fixes author names not loading) Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/f7916fb3-4db3-4e2d-b88a-1306009dcf25 Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com>

Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/f7916fb3-4db3-4e2d-b88a-1306009dcf25 Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com>

Copilot · 2026-04-17T22:11:12Z

@copilot, I tried the new app, and it is not working as expected. The main issues I saw:

The list of authors failed to properly load the authors of the measles model:...

Fixed both issues in 93c8b1f:

Authors not loading: Streamlit caches widget values by key — even after updating st.session_state["authors"] from the uploaded file, the old widget keys (author_name_0, etc.) retained their empty values. Fixed by embedding a version counter in all dynamic widget keys and calling st.rerun() after upload, so widgets are genuinely new and use the loaded data.

Add/remove buttons not working: The old code used st.button() return values which only update after rendering — too late for the current frame. Fixed by switching all add/remove buttons to on_click callbacks, which execute before the next render cycle.

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I tried to connect to the following addresses, but was blocked by firewall rules:

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- Triggering command: /home/REDACTED/work/epicc/epicc/.venv/bin/streamlit streamlit run editor.py --server.headless true --server.port 8502 (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

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Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Copilot

Pull request overview

Adds a dedicated Streamlit “Model Editor” app for creating/editing EPICC YAML model files, with pure-logic helpers and accompanying tests.

Changes:

Introduce epicc.editor package with YAML↔state parsing, validation, and serialization helpers.
Add a Streamlit UI app (epicc.editor.__main__) plus editor.py entrypoint to run it similarly to app.py.
Add pytest coverage for helper logic and YAML/state round-trips.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
`src/epicc/editor/helpers.py`	Implements editor helper functions (coercion/parsing, YAML→state, state→doc, validation, YAML serialization).
`src/epicc/editor/__main__.py`	Streamlit UI for editing model metadata, parameters, equations, scenarios, report blocks, and figures; supports upload/validate/download/preview.
`src/epicc/editor/__init__.py`	Declares the new `epicc.editor` package.
`editor.py`	Entry point to run the editor app via `streamlit run editor.py`.
`Makefile`	Adds `make editor` target for launching the editor.
`tests/epicc/test_editor.py`	Adds tests for helper functions and YAML/state/document round-trips.

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Changed '\n'.join(p.get('references', [])) to '\n'.join(p.get('references') or []) to prevent TypeError when references is null or invalid type.

…y swallowing them Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/180e9200-681b-41c4-bc4b-545f4c14acc6 Co-authored-by: olivia-banks <53623746+olivia-banks@users.noreply.github.com>

…or; show structured field errors in editor UI Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/a5e3de79-3ec7-4a80-8bcc-72bd03c603b5 Co-authored-by: olivia-banks <53623746+olivia-banks@users.noreply.github.com>

…_word variable for readability Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/a5e3de79-3ec7-4a80-8bcc-72bd03c603b5 Co-authored-by: olivia-banks <53623746+olivia-banks@users.noreply.github.com>

Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/760e0c5a-25bc-4a30-8aa6-82a77e634550 Co-authored-by: olivia-banks <53623746+olivia-banks@users.noreply.github.com>

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 7 out of 7 changed files in this pull request and generated 5 comments.

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+        file_id = f"{uploaded.name}:{uploaded.size}"
+        if st.session_state.get("_uploaded_file_id") != file_id:


+        param: dict[str, Any] = {
+            "type": p["type"],
+            "label": p["label"],
+            "default": coerce_numeric(str(p["default"])),


+        if p["type"] == "enum" and p.get("options"):
+            options = parse_key_value_lines(p["options"])
+            param["options"] = {str(k): str(v) for k, v in options.items()}


+    """Parse ``key: value`` lines into a dict, coercing numeric values."""
+    result: dict[str, Any] = {}
+    for line in text.strip().splitlines():
+        if ":" not in line:
+            continue
+        key, _, val = line.partition(":")
+        val = val.strip()
+        try:
+            result[key.strip()] = int(val)
+        except ValueError:
+            try:
+                result[key.strip()] = float(val)
+            except ValueError:
+                result[key.strip()] = val


+    # Authors
+    authors_raw = data.get("authors", [])
+    state["authors"] = [
+        {"name": a.get("name", ""), "email": a.get("email", "")} for a in authors_raw
+    ] or [{"name": "", "email": ""}]


olivia-banks · 2026-05-05T19:49:33Z

@gvegayon I'm looking through the code in earnest now, and it's really not all that great. Copilot didn't really seem to read the rest of the code and emitted something that sort of exists along a tangent (e.g., the code for creating models with graphs hardcodes a bunch of information even though this is readily exposed by the block Pydantic models).

I think I'm going to use some of this code as a base but then write the rest myself. Closing for now unless you think we should pursue this route.

Initial plan

1ffd196

Copilot AI assigned Copilot and gvegayon Apr 17, 2026

Copilot started work on behalf of gvegayon April 17, 2026 21:36 View session

Copilot AI linked an issue Apr 17, 2026 that may be closed by this pull request

Create a separate app for building model files #41

Open

Copilot AI and others added 2 commits April 17, 2026 21:45

Address code review feedback: simplify redundant conditionals

15aff80

Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/a4e6dd31-6c9a-4ef2-9059-59a5f3af997d Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Add a separate app for building model files~~ Add model editor app for building YAML model files Apr 17, 2026

Copilot finished work on behalf of gvegayon April 17, 2026 21:47

Copilot AI requested a review from gvegayon April 17, 2026 21:47

gvegayon requested changes Apr 17, 2026

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Copilot started work on behalf of gvegayon April 17, 2026 21:55 View session

Copilot AI and others added 2 commits April 17, 2026 22:09

Only bump widget version when removal actually occurs

7be4c7f

Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/f7916fb3-4db3-4e2d-b88a-1306009dcf25 Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com>

Copilot finished work on behalf of gvegayon April 17, 2026 22:11

Copilot AI requested a review from gvegayon April 17, 2026 22:11

gvegayon marked this pull request as ready for review April 17, 2026 22:14

Copilot AI review requested due to automatic review settings April 17, 2026 22:14

Copilot started reviewing on behalf of gvegayon April 17, 2026 22:14 View session

Copilot AI reviewed Apr 17, 2026

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Comment thread src/epicc/editor/helpers.py Outdated

Comment thread src/epicc/editor/helpers.py

Comment thread src/epicc/editor/helpers.py

Comment thread src/epicc/editor/__main__.py

gvegayon mentioned this pull request Apr 20, 2026

Make scenario parameters dynamic in the model #40

Merged

9 tasks

EddW1219 added 3 commits April 21, 2026 12:03

Fix Issue #2: Type-safe references handling

00361c2

Fix Issue #2: Type-safe references handling

b5ec710

Fix Issue #2: Type-safe references handling

1bd8693

Changed '\n'.join(p.get('references', [])) to '\n'.join(p.get('references') or []) to prevent TypeError when references is null or invalid type.

Copilot started work on behalf of olivia-banks April 21, 2026 18:35 View session

Copilot AI requested a review from olivia-banks April 21, 2026 18:36

Copilot started work on behalf of olivia-banks April 21, 2026 18:36 View session

Copilot started work on behalf of olivia-banks April 21, 2026 18:38 View session

Show YAML serialization errors via st.dialog modal instead of silentl…

087d275

…y swallowing them Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/180e9200-681b-41c4-bc4b-545f4c14acc6 Co-authored-by: olivia-banks <53623746+olivia-banks@users.noreply.github.com>

Copilot finished work on behalf of olivia-banks April 21, 2026 18:43

Copilot started work on behalf of olivia-banks April 21, 2026 18:44 View session

Copilot AI and others added 2 commits April 21, 2026 18:48

Address review: success banner only on successful load; extract issue…

74d5a9e

…_word variable for readability Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/a5e3de79-3ec7-4a80-8bcc-72bd03c603b5 Co-authored-by: olivia-banks <53623746+olivia-banks@users.noreply.github.com>

Copilot finished work on behalf of olivia-banks April 21, 2026 18:51

Copilot started work on behalf of olivia-banks April 21, 2026 18:51 View session

Remove emoji from editor UI strings

65d0e37

Agent-Logs-Url: https://github.com/EpiForeSITE/epicc/sessions/760e0c5a-25bc-4a30-8aa6-82a77e634550 Co-authored-by: olivia-banks <53623746+olivia-banks@users.noreply.github.com>

Copilot finished work on behalf of olivia-banks April 21, 2026 18:54

Update src/epicc/editor/helpers.py

694ec89

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

olivia-banks requested a review from Copilot May 5, 2026 19:39

Copilot started reviewing on behalf of olivia-banks May 5, 2026 19:40 View session

Copilot AI reviewed May 5, 2026

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olivia-banks closed this May 5, 2026

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Add model editor app for building YAML model files#42

Add model editor app for building YAML model files#42
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Copilot AI commented Apr 17, 2026 •

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Copilot AI commented Apr 17, 2026 •

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olivia-banks commented May 5, 2026 •

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		file_id = f"{uploaded.name}:{uploaded.size}"
		if st.session_state.get("_uploaded_file_id") != file_id:

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Copilot AI commented Apr 17, 2026 •

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