Getting Started

We’re about to walk through building several sets of components for simulations. vivarium supports interactive use, so we could do all of that in a single script or in an interactive environment like a jupyter notebook. This makes sharing code or working collaboratively very difficult, however.

Instead, we’ll first walk through some tips and tools that will help us keep things organized and make collaboration easy. It will also enable us to run simulations from the command line. This is vital for any serious simulation work.

Organizing our work

Instead of storing our work in one or several python files, we’ll store it in a python package. A python package is a bundle of structured python code that a user can install. This is the key to making python’s import statement work.

To start off, pick a place for your work on your computer. I’ll pretend we’re working in ~/code/.

Note

~/ is general shorthand for the user’s home directory. It would be something like C:\Users\<YourUserName>\ on Windows, /home/<YourUserName>/ on Linux, or /Users/<YourUserName>/ on Mac.

In this directory, make a subdirectory called vivarium_examples. This will be our package directory. We then want to generate the following directory structure

~/code/vivarium_examples/
    src/
        vivarium_examples/
            __init__.py
    setup.py

The __init__.py file can be blank. It’s the file that tells python that vivarium_examples is a package. We need to fill out the setup.py file though.

File: ~/code/vivarium_examples/setup.py

 from setuptools import setup, find_packages


 if __name__ == "__main__":

    setup(
        name='vivarium_examples',
        version='1.0',
        description="Examples of simulations built with vivarium",
        author=''  # YOUR NAME HERE,

        package_dir={'': 'src'},
        packages=find_packages(where='src'),
        include_package_data=True,

        install_requires=['vivarium'],
 )

This is the file that lets us install your package and import it from anywhere. We’ll use it shortly.

Version control

Making an environment

The next thing we’ll do is set up a programming environment. This is like a clean room for your code and all the code it depends on. It helps

Installing your library

Next steps