My currently open-source project was made so that I could analyze a specific dataset. However, when in talks with the data holders, they want to keep their data in a Creative Commons Attribution-NonCommercial 4.0 International license. How can I handle this? My code is under GPLv3 and I would like to include the data with the repo.

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Generally, an application and the input to it are two distinct works for copyright and they can be licensed independently of each other.

If your application reads the dataset from a file and doesn't really care what dataset it reads as long as the structure is correct, then the application and dataset are definitely separate, independent works. The simple fact that they happen to be stored in the same repository doesn't change anything here. The one thing you need to do is to make it clear that different parts of the repository are covered under different licenses and which license applies to which part.

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