How do you configure sharepoint to be GDPR compliant?

That's an interesting question, I am not aware of any specific steps right now to take for GDPR compliance in SharePoint.  Saying that, here is some related information, Office 365 and GDPR -

https://www.microsoft.com/en-us/trustcenter/privacy/gdpr/solutions#office-365

Also from https://blogs.microsoft.com/blog/2017/05/24/accelerate-gdpr-compliance-microsoft-cloud:

"In February of this year, we announced that Microsoft cloud services will comply with GDPR by May 25, 2018, across Office 365, Dynamics 365, Azure, including Azure data services, Enterprise Mobility + Security, and Windows 10. We’ve backed this up with our contractual commitments to customers.

The Microsoft Cloud also has a range of compliance controls, audited by third parties. Through these investments, we will also help you validate that when you are using the Microsoft Cloud, you are using services compliant with the GDPR."

Later in the year, there will be new dashboard that allows you to check your GDPR compliance, similar to Office 365 Secure Score:

Keep an eye of the https://www.microsoft.com/en-us/trustcenter/cloudservices/office365https://www.microsoft.com/en-us/trustcenter/cloudservices/office365(plus Office Blogs) for updates as there is more news, which I imagine there will be lots and the main https://www.microsoft.com/en-us/TrustCenter/Privacy/gdpr/default.aspx is a good resource including readiness assessment.

Also, by the way, there is a semi-related https://github.com/SharePoint/sp-dev-gdpr-activity-hub available that you might want to check out - 

Steve Howlett Just to say I have edited my answer a few times!