tutorial_run_simple_example.md

Run the Simple Example in Codespaces

This tutorial will guide you through the steps to run a simple example of EMOD-Malaria within GitHub Codespaces. Everything will be on the web so you don't need to install anything at this time.

Prerequisites

The followign instructions assume you have Codespaces started on the emopdy-malaria repository. To learn how to do this, please the Starting Codespaces Tutorial

Run EMOD example

1. Execute the following command in the “terminal” window

   cd examples-container
   

   "cd" stands for change directory

   

   Notice that the line after executing the command says what folder you are in. In our case, the folder you are in should be:

   /workspaces/emodpy-malaria/examples-container
   

   Most of the following instructions are going to take place in this terminal window.

2. See what examples there are by executing the following command:

   ls
   

   "ls" stands for list files/directories

   

3. Enter the “simple_example” directory by executing the following command:

   cd simple_example
   

   

4. See what files are in this directory by executing the following command:

   ls
   

   

5. Run the example with the following command:

   python example.py
   

   

   This step “Pulling image docker-production-public…” may take a few minutes, but will only happen once per codespace image.

   

   When the simulation is done, you should see the following:

   

View the results

Now that we have run EMOD, lets look at some data to see what happend in the simulations.

1. In the file browser on the left, click on the ">" next to the examples-container folder and continue navigating to the folder:

   examples-container > simple_example > results
   

2. Select the file name **Simple_Example.png".

   

Understand the results

The next "tutorial" explains what you are seeing in this image.