gbd-mapping 5.1.0

Backward-compatibility shim. The real package is now vivarium-gbd-mapping.

** NOTE: This repository has been archived.**

The gbd_mapping package has been renamed and migrated into the vivarium-suite monorepo.

What changed

• PyPI distribution: gbd_mapping -> vivarium-gbd-mapping

• Import paths: - gbd_mapping -> vivarium.gbd_mapping - gbd_mapping_generator -> vivarium.gbd_mapping_generator

• Source: ihmeuw/gbd_mapping (archived) -> ihmeuw/vivarium-suite (under libs/gbd-mapping/)

• Docs: https://vivarium-gbd-mapping.readthedocs.io/

What this last release (v5.1.0) is

A backward-compatibility shim. It contains no code; installing it pulls in:

• vivarium-gbd-mapping>=6.0.0 - the real implementation under the new import paths. Also provides the build_mapping console script.

• vivarium-compat>=0.5.0 - an import hook that lets import gbd_mapping and import gbd_mapping_generator continue to work, emitting a DeprecationWarning. Update your imports before the hook is removed.

If you depend on a specific pre-rename version (e.g. gbd_mapping==5.0.4), pin to that version - those earlier releases still ship the original modules and continue to install standalone.

To migrate fully to the new package

Mapping of Global Burden of Disease (GBD) entities to their metadata.

There are two packages offered in this distribution. The first, the gbd_mapping_generator is a set of scripts that define templates and data gathering code used to produce the second, the gbd_mapping. The gbd_mapping_generator package will not function without access to the IHME cluster and some of our internally used data access libraries. Mapping updates are managed by an automated toolchain, so this shouldn’t be an issue.

The gbd_mapping is a programmatically accessible (and TAB-complete-able) set of mappings for GBD entities including:

• Causes

• Risks

• Covariates

• Etiologies

• Sequelae

You can install gbd_mapping from PyPI with pip:

> pip install gbd_mapping

or build it from source with

> git clone https://github.com/ihmeuw/gbd_mapping.git

> cd gbd_mapping

> pip install .

Development and Mapping Generation

In order to generate or regenerate the mappings from data, you must have access to the Institute for Health Metrics and Evaluation cluster and internal PyPI server. Contact <[e-mail]> if you need further instructions on that.

Given proper permissions, you can set up this library in development mode with

> git clone https://github.com/ihmeuw/gbd_mapping.git

> cd gbd_mapping

> pip install -e .['dev']

Check out the docs!