achilles

This directory is set up and managed by poetry dependencies management. Please refer to this to ensure you have Poetry installed.

Getting started

Clone and create the virtual environment:

git clone <REPOSITORY-URL>
cd achilles
poetry install

Download source.zip from here and extract the foler source.
Put the folder source into the data_popsim
```
cd achilles\data_popsim
```
Run the scripts inside the generator folder to get the data. You can run each file seperately or the easiest would be running the combine_generate.py to get all the needed data for PopSim. For example:
```
cd achilles\data_popsim\generator
python combine_generate.py -l ../source/ -o ../../../popsim/synthesis/data/
```
By this steps you should have all the files you need to run PopSim in the popsim\synthesis\data. If the folder data does not exist creat one then run step 3.
```
cd popsim\synthesis
mkdir data
```
Run the PopSim. The current configuration is for the complex run (with many control atts) and you should expect a run around 1 hour or more. For simple testing you can change the control_file_name in setting.yaml (line 102) to control_simple.csv.
```
cd popsim\synthesis
python run_popsim.py
```
If everything goes right, you will have all the needed results (especially the synthetic data) in the output folder
```
cd popsim\synthesis\output
```
After that, you can run the validation as well to check the results. There is the Jupyter Notebook validation.ipynb that is based from the source code example. You may have to install the jupyter notebook.
```
cd validation
jupyter notebook validation.ipynb
```

To create the scatter plots, run the below code

cd validation\custom
python utils.py -l ../../popsim/synthesis/ -o ./output/

You can view the plots in the output folder, if the output folder does not exist yet, create one and run step 8.
```
cd validation\custom
mkdir output
```