Python BIOGEME - A Docker on Windows tutorial

The goals of this repository are twofold:

Create an updated version of a python biogeme docker image, and to maintain that image updated
Create a tutorial for windows users to be able to use Biogeme without the manual steps and overheads of a full virtual box

The docker image

It is a basic linux image of Python 3.6, to which we install only BIOGEME, enabling Python Biogeme

All the steps below assume that you have created your Biogeme image by cloning or downloading this repository to your local machine and running the following command on the root of the folder

Also, this should work on ANY operating system that supports Docker, although there are no many reasons to use Docker for BIOGEME estimation if you are on Linux or MacOS.

docker build -t biogeme .

Running a generic BIOGEME script

After the biogeme image has been created, it is ready to be used on any command interface of your liking.

Let's assume that you have a PythonBiogeme file called estimate.py and a dataset called dataset.dat and that they are both on the same D:/biogeme/

In order to run PythonBiogeme using docker, you just need to run the following command on your command prompt:

docker run -v D:/BIOGEME://tmp/mr -w //tmp/mr biogeme pythonbiogeme estimate dataset.dat

Note that the folder separator is always LINUX one / and not \, regardless of the operating system you are working on.

However, if you are not working on Windows, you will need a single / after the :, which makes

docker run -v D:/BIOGEME:/tmp/mr -w /tmp/mr biogeme pythonbiogeme estimate dataset.dat

A workable example

In order to create a meaningful example of how one could use Biogeme on Docker, I decided to use the examples provided in the Biogeme webpage.

The scenario we are working with is the following: We want to run all the models that exist there and save them in individual folders, with all the estimation/run outputs.

In order to do that, the user would clone/download this repository and run the "estimate_all_examples.py" file This piece of code moves all estimation scripts into subfolder named after the estimation scripts themselves and creates a batch file that can be run to run all biogeme examples in a sequence without interruptions.

A more complete overview

For a better overview of what motivated the creation of this repo, you can go to my blog. There you will find a link to some references and to a video tutorial where I go over the entire process.

Credits