atomica

Atomica

Atomica is a simulation engine for compartmental models. It can be used to simulate disease epidemics, health care cascades, and many other things.

For detailed documentation, visit https://atomica.tools/docs

Installation

Atomica is available for Python 3 only. Because we develop using Python 3.7, it is possible that dictionary order is relevant (although we endeavour to use ordered dictionaries via Sciris in places where order matters). Therefore, we only officially support Python 3.7, as this is the first Python release that guarantees ordering of all dictionaries.

Atomica is distributed via PyPI, and the PyPI version corresponds to master branch of this repository. To install via PyPI, it is only necessary to run

pip install atomica

Installation of numpy, scipy and matplotlib will automatically take place via pip because they are dependencies of Atomica. However, in practice these packages may require system-level setup so it is usually easiest to install them separately beforehand. We recommend using Anaconda, which facilitates getting the binaries and dependencies like QT installed in a platform-agnostic manner. We also recommend working within an Anaconda environment.

You may also wish to install mkl first, before installing numpy etc. to improve performance. So for example:

conda install mkl
conda install numpy scipy matplotlib

Git installation

If you want to install a different branch of Atomica, or plan to make changes to the Atomica source code, you will need to install Atomica via Git rather than via PyPI. This can be performed using

git clone https://github.com/atomicateam/atomica.git
cd atomica
pip install -e .

Running tests

Atomica includes a suite of tests, some of which get automatically run and others that are used manually. The automated test suite can be executed with pytest, and can be run from within an isolated environment using tox. To use the tests, you will need to follow the steps above to perform a 'Git installation' because the tests are not included in the PyPI distribution. After installation, you can run individual test scripts from the tests directory with commands like:

python tests/testworkflow.py

Note that many of the tests open matplotlib figures as part of the test. If the test script is run on a machine without a display available, the error

_tkinter.TclError: couldn't connect to display "localhost:0.0"

will be raised. In that case, simply set the matplotlib backend to agg which allows the calls to succeed with a display present. For example, run

export MPLBACKEND=agg
python tests/testworkflow.py

To run the automated suite, install the test dependencies using

pip install -r requirements.txt

which will install the additional development dependencies. Then, to run the automated suite, from the root directory (the one containing README.md) run:

pytest

To run the tests in an isolated virtual environment, from the root directory, run

tox

If you don't have tox, install it using pip install tox. The default configuration expects Python 3.6 and Python 3.7 to be on your system - to test only against a specific version, pass the python version as an argument to tox e.g.

tox -e py37

to test Python 3.7 only.

Troubleshooting

Installation fails due to missing numpy

If running pip install -e . in a new environment, numpy must be installed prior to scipy. In some cases, installing numpy may fail due to missing compiler options. In that case, you may wish to install numpy via Anaconda (by installing Python through Anaconda, and using conda install numpy scipy matplotlib). In general, our experience has been that it is easier to set up the C binaries for numpy and the QT dependencies for matplotlib via Anaconda rather than doing this via the system, which involves different steps on every platform.

Figure plotting hangs

On some systems, the default matplotlib backend may hang - this is not an issue with atomica. To resolve, try changing the backend by including

import matplotlib
matplotlib.use("Qt5Agg")

at the very start of your script. A different backend may be required for your system. You can make the change persistant by setting the backend in your matplotlibrc file.