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.

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) and install pymc version 2.3.8. Then you can install dismod_mr using pip.

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

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.

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.

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

Metadata

Release files for dismod-mr 1.1.2.7

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Source distribution (sdist)

Source distribution for dismod-mr 1.1.2.7
File	Size	Uploaded
dismod_mr-1.1.2.7.tar.gz	54.6 kB	Apr 11, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for dismod-mr 1.1.2.7
File	Interpreter	ABI	Platform	Reset
dismod_mr-1.1.2.7-py3-none-any.whl 57.2 kB Apr 11, 2023	Python 3	none	any	Details

Total release size: 111.8 kB

Release files / dismod_mr-1.1.2.7.tar.gz

Download URL	dismod_mr-1.1.2.7.tar.gz
Size	54.6 kB
Tags	Source
SHA-256 checksum How to use checksums	`87523f4c2e9ac1e4ef41ca3671ef3b139423aedba207b8b5a67082c4b77d2ce5`
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Upload date	Apr 11, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.10.10`

Release files / dismod_mr-1.1.2.7-py3-none-any.whl

Download URL	dismod_mr-1.1.2.7-py3-none-any.whl
Size	57.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`304611d3c693143b2464a82e4e9f7491b060015d35c533474c242116cd9f5feb`
BLAKE2b-256 checksum How to use checksums	`ae75a4453b622095b1391481e14a01e146f03a14860f26e28dc4813b16685e32`
Upload date	Apr 11, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.10.10`