Metadata-Version: 2.1
Name: june
Version: 1.0.5
Summary: A framework for high resolution Agent Based Modelling.
Home-page: https://github.com/idas-durham/june
Author: IDAS-Durham
Author-email: arnauq@protonmail.com
License: GPLv3 license
Platform: UNKNOWN
Description-Content-Type: text/markdown
Requires-Dist: alabaster (==0.7.12)
Requires-Dist: attrs (==19.3.0)
Requires-Dist: autoconf (==0.6.1)
Requires-Dist: autofit (==0.65.0)
Requires-Dist: Babel (==2.8.0)
Requires-Dist: bleach (==3.1.5)
Requires-Dist: certifi (==2020.6.20)
Requires-Dist: chardet (==3.0.4)
Requires-Dist: corner (==2.1.0)
Requires-Dist: cycler (==0.10.0)
Requires-Dist: decorator (==4.4.2)
Requires-Dist: defusedxml (==0.6.0)
Requires-Dist: dill (==0.3.2)
Requires-Dist: docutils (==0.16)
Requires-Dist: dynesty (==1.0.1)
Requires-Dist: emcee (==3.0.2)
Requires-Dist: entrypoints (==0.3)
Requires-Dist: future (==0.18.2)
Requires-Dist: h5py (==2.10.0)
Requires-Dist: idna (==2.10)
Requires-Dist: imagesize (==1.2.0)
Requires-Dist: importlib-metadata (==1.7.0)
Requires-Dist: ipython-genutils (==0.2.0)
Requires-Dist: Jinja2 (==2.11.2)
Requires-Dist: joblib (==0.16.0)
Requires-Dist: jsonschema (==3.2.0)
Requires-Dist: jupyter-core (==4.6.3)
Requires-Dist: kiwisolver (==1.2.0)
Requires-Dist: llvmlite (==0.33.0)
Requires-Dist: MarkupSafe (==1.1.1)
Requires-Dist: matplotlib (==3.3.0)
Requires-Dist: mistune (==0.8.4)
Requires-Dist: mypy-extensions (==0.4.3)
Requires-Dist: nbconvert (==5.6.1)
Requires-Dist: nbformat (==5.0.7)
Requires-Dist: nbsphinx (==0.7.1)
Requires-Dist: nbsphinx-link (==1.3.0)
Requires-Dist: numba (==0.50.1)
Requires-Dist: numpy (==1.19.1)
Requires-Dist: numpydoc (==1.1.0)
Requires-Dist: packaging (==20.4)
Requires-Dist: pandas (==1.1.0)
Requires-Dist: pandocfilters (==1.4.2)
Requires-Dist: Pillow (==7.2.0)
Requires-Dist: Pygments (==2.6.1)
Requires-Dist: pyparsing (==2.4.7)
Requires-Dist: pyprojroot (==0.2.0)
Requires-Dist: pyrsistent (==0.16.0)
Requires-Dist: pyswarms (==1.1.0)
Requires-Dist: pytest (>=5.4.2)
Requires-Dist: pytest-cov (>=2.8.1)
Requires-Dist: python-dateutil (==2.8.1)
Requires-Dist: pytz (==2020.1)
Requires-Dist: PyYAML (==5.3.1)
Requires-Dist: recordclass (==0.13.2)
Requires-Dist: requests (==2.24.0)
Requires-Dist: scikit-learn (==0.23.1)
Requires-Dist: scipy (==1.5.2)
Requires-Dist: seaborn (==0.10.1)
Requires-Dist: setuptools-scm (==4.1.2)
Requires-Dist: six (==1.15.0)
Requires-Dist: snowballstemmer (==2.0.0)
Requires-Dist: Sphinx (==3.1.2)
Requires-Dist: sphinxcontrib-applehelp (==1.0.2)
Requires-Dist: sphinxcontrib-devhelp (==1.0.2)
Requires-Dist: sphinxcontrib-htmlhelp (==1.0.3)
Requires-Dist: sphinxcontrib-jsmath (==1.0.1)
Requires-Dist: sphinxcontrib-qthelp (==1.0.3)
Requires-Dist: sphinxcontrib-serializinghtml (==1.1.4)
Requires-Dist: testpath (==0.4.4)
Requires-Dist: threadpoolctl (==2.1.0)
Requires-Dist: tqdm (==4.48.0)
Requires-Dist: traitlets (==4.3.3)
Requires-Dist: typing-extensions (==3.7.4.2)
Requires-Dist: typing-inspect (==0.6.0)
Requires-Dist: urllib3 (==1.25.10)
Requires-Dist: webencodings (==0.5.1)
Requires-Dist: zipp (==3.1.0)
Requires-Dist: mpi4py (==3.0.3)
Requires-Dist: tables (==3.6.1)

![Python package](https://github.com/IDAS-Durham/JUNE/workflows/Python%20package/badge.svg?branch=master)
[![codecov](https://codecov.io/gh/idas-durham/june/branch/master/graph/badge.svg?token=6TKUHtWxJZ)](https://codecov.io/gh/idas-durham/june)

# JUNE: open-source individual-based epidemiology simulation

This is the offical repository of JUNE, named after [June Almeida](https://en.wikipedia.org/wiki/June_Almeida), who was the female Scottish virologist that first identified the coronavirus group of viruses. checkout the [release paper](https://www.medrxiv.org/content/10.1101/2020.12.15.20248246v1) for a physical description of the model.


# Setup

The easiest way to get JUNE up and running is to install the latest stable version,

```
pip install june
```

and download the data by running the command

```
get_june_data.sh
```

if the above command fails, then manually clone the repo and use the script ```scripts/get_june_data.sh```.


Disclaimer: All the data is constructed by mixing different datasets from the Office for National Statistics (ONS), thus it may contain modifications. Please refere to the original source (cited in the [release paper](https://www.medrxiv.org/content/10.1101/2020.12.15.20248246v1)) for the raw dataset.

This will require a working installation of Openmpi or Intelmpi to compile ``mpi4py``. 

If you want to get the most up-to-date version of the code, then you can clone this repository, and install it using

```
pip install -e .
```

This should automatically install any requirements as well. You can then get the data using the same command as the pip version.

# How to use the code

Have a look at ``Notebooks/quickstart.ipynb`` for a gentle introduction to how JUNE works. You can also checkout some scripts in ``example_scripts``.

The ``docs`` directory contains the source files and HTML outputs to
display all information auto-generated from the `june` codebase docstrings,
including auto-generated class and module diagrams.

# Tests

Run the tests with

```
cd test_june
pytest
```


