COVID19 Setup

Setup a COVID19 simulation for the JHU pipeline.

Requirements

We assume you have Python 3.6 or greater and docker.

Next, you'll need to make some changes to the config.yml.template. First create a copy named config.yml.

cp config.yml.template config.yml

Then you'll need at least to edit where you see things between << >>.

After you have this setup, then you can run the following commands:

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

# Create the makefile
python3 render.py makefile -c config.yml -o Makefile

# Get the necessary shapefiles
python3 render.py shapefile -c config.yml --use-cache

# Build the docker file
cd docker
docker build -t covid .
cd ..

# Make the output directory
mkdir output

# Run the model
docker run --rm \
  -v "$(pwd)/config.yml:/home/app/covidsp/config.yml" \
  -v "$(pwd)/output:/home/app/covidsp/final_model_output" \
  -v "$(pwd)/data:/home/app/covidsp/data" \
  -v "$(pwd)/Makefile:/home/app/covidsp/Makefile" \
  covid

After everything is finished, you should find a file whose name looks like output.*.tar.gz in your output folder. This contains all the simulated output from the above command.

The easiest thing to do with this is to open up hospitalization_plots.ipynb in a jupyter (Python) notebook and hit Restart and Run All, which will generate several plots.

In future runs, you can just execute the last line after switching up the config.yml.

TODO

Figure out why our input rebuild script doesn't produce the same output as their input rebuild script.