Did you read the README.md ?
They tell you exactly how to install (so what to download).
Making a long story short: https://github.com/d3/d3/releases/tag/v4.3.0 (current release) and you find the link to d3.zip and there inside you can't really miss the file.
To deploy D3 on your OBIEE 12c you have 2 options:
A) load the library directly from d3js.org (as the install part of the README.md cover) but you will need to configure CSP in your instanceconfig.xml
B) add it to a folder deployed on your OBIEE 12c weblogic (so same domain => no CSP), historically this folder has always been analyticsRes used for custom styles and skins. The doc cover how to deploy this folder: Customizing the Oracle BI Web User Interface (Approach 2)