Fix example_end_to_end_run.py so it can be run with poetry run (#257)

- Fix permissions to make it executable
- Add hash-bang
- Automatically make output/

I also added testing the example to CI.

.github/workflows/test-example.yaml

@@ -0,0 +1,28 @@
+name: Run example
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  example:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Set up python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - name: Install global dependencies
+      run: |
+        pip install poetry
+
+    - name: Run Example
+      run: |
+        poetry install
+        poetry run examples/example_end_to_end_run.py

README.md

@@ -31,7 +31,7 @@ Subject to change, current transmission dynamics follow this basic model
 
 ## Quick Start
 
-As a first pass at running model ODEs and inference of parameters, take a look at `example_end_to_end_run.py` to see the process of running our model. You will probably need to `poetry install` to get started as well.
+As a first pass at running model ODEs and inference of parameters, take a look at `example_end_to_end_run.py` to see the process of running our model. You will probably need to `poetry install` to get started as well, and then run it with `poetry run examples/example_end_to_end_run.py`.
 
 Within `example_end_to_end_run.py` there is an optional `--infer` flag added from the terminal. This will kick off an example inference on synthetic data generated by the model itself and will produce different output.
 

examples/example_end_to_end_run.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 """
 A basic local covid example meant to show off the flow of running the mechanistic model
 
@@ -10,6 +11,7 @@
 """
 
 import argparse
+import os
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -37,6 +39,10 @@
     args = parser.parse_args()
     infer = args.infer
 
+    # Make the output directory.
+    if not os.path.exists("output"):
+        os.mkdir("output")
+
     # step 1: define your paths
     config_path = "config/"
     # global_config include definitions such as age bin bounds and strain definitions