[Feature request]: Rewrite examples/simple_usa_statelevel/inference_benchmark.ipynb To Use Only Data In flepiMoP

[TimothyWillard]

Label

documentation, gempyor, meta/workflow

Priority Label

low priority

Is your feature request related to a problem? Please describe.

The inference_benchmark.ipynb notebook (in the feature/403/emcee_batch branch) relies on undeclared dependencies and files that reside outside of the flepiMoP repository. This makes the notebook not reproducible and limits it's usefulness as a teaching tool.

Is your feature request related to a new application, scenario round, pathogen? Please describe.

No response

Describe the solution you'd like

The notebook should be rewritten so:

• It uses dependencies that are installed by default (either remove undeclared dependencies or add dependencies to flepiMoP in an optional dependency group), and
• Only uses data contained in the flepiMoP repository.

This would make it a useful tool for teaching by allowing users to run it locally. A complete solution involves creating a new GitHub action workflow that would regenerate the notebook on changes to gempyor or the example this notebook is relevant to.

[jcblemai]

What data does it uses outside ?

[TimothyWillard]

What data does it uses outside ?

flepiMoP/examples/simple_usa_statelevel/inference_benchmark.ipynb

Lines 448 to 462 in eda84e4

	{
	"cell_type": "code",
	"execution_count": 9,
	"metadata": {},
	"outputs": [],
	"source": [
	"results = {}\n",
	"for folder in [\"SMH_R18_noBoo_lowIE_blk1\", \"SMH_R18_allBoo_lowIE_blk1\"]:\n",
	" results[folder] = []\n",
	" for fn in sorted(gempyor.utils.list_filenames(folder=f\"../../../COVID19_USA/result/{folder}\", filters=[\"hosp.parquet\"])):\n",
	" df = gempyor.read_df(fn)\n",
	" df = df.set_index(\"date\")\n",
	" results[folder].append(df)"
	]
	},

Looks maybe something in https://github.com/HopkinsIDD/COVID19_USA, although relies on a hard-coded path and it's unclear what branch. Regardless, not data that is contained within the flepiMoP repository.

[jcblemai]

oh wow, this part should not belong to this notebook, it's some scenario analysis from long ago (I guess because I got inspired from this code to make a comparison plot). Sorry about that.