.. image:: https://travis-ci.org/ihmeuw/dismod_mr.svg?branch=master
:target: https://travis-ci.org/ihmeuw/dismod_mr
:alt: Latest Version
This project is the descriptive epidemiological meta-regression tool,
DisMod-MR, which grew out of the Global Burden of Disease (GBD) Study
2010. DisMod-MR has been developed for the Institute of Health
Metrics and Evaluation at the University of Washington from 2008-2013.
.. contents::
Examples
--------
`A motivating example: descriptive epidemiological meta-regression of Parkinson's Disease <http://nbviewer.ipython.org/github/ihmeuw/dismod_mr/blob/master/examples/pd_sim_data.ipynb>`_
`All examples <http://nbviewer.ipython.org/github/ihmeuw/dismod_mr/tree/master/examples/>`_
Installation
------------
Dismod MR requires PyMC2 which does not play nicely with normal Python
installation tools. Fortunately, ``conda`` has solved this issue for us.
So first you'll need to setup a conda environment
(after `installing conda, if necessary <https://docs.conda.io/projects/conda/en/latest/user-guide/install/>`_)
and install ``pymc`` version ``2.3.8``. Then you can install ``dismod_mr`` using ``pip``.
.. code-block:: sh
conda create --name=dismod_mr python=3.6 pymc==2.3.8
conda activate dismod_mr
pip install dismod_mr
If you get an error stating
.. code-block:: sh
ERROR: Complete output from command python setup.py egg_info:
ERROR: Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-d9fbq7v3/pymc/setup.py", line 8, in <module>
from numpy.distutils.misc_util import Configuration
ModuleNotFoundError: No module named 'numpy'
----------------------------------------
ERROR: Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-d9fbq7v3/pymc/
or something similar, you do not have ``pymc`` properly installed.
Installing from source
++++++++++++++++++++++
If you want to install ``dismod_mr`` locally in an editable mode, the
instructions are very similar. We'll clone the repository and install it
from a local directory instead of using ``pip`` to grab it from the Python
package index.
.. code-block:: sh
conda create --name=dismod_mr python=3.6 pymc==2.3.8
conda activate dismod_mr
git clone git@github.com:ihmeuw/dismod_mr.git
cd dismod_mr
pip install -e .
To test this, you can use ``pytest``, which you must first install.
.. code-block:: sh
pip install pytest
pytest
If you have things setup right, this will still generate many
warnings, but there should be no tests that produce failures or
errors.
Coding Practices
----------------
* Write tests before code
* Write equations before tests
* Test quantitatively with simulation data
* Test qualitatively with real data
* Automate tests
* Use a package instead of DIY
* Test the package
* Optimize code later
* Optimize code for readability before speed
* `.py` files should be short, less than 500 lines
* Functions should be short, less than 25 lines
