I am writing an open source software which will be published as a public Github repository (code+binaries) and the accompanying documentation will be available on ReadTheDocs.com platform.

  I am also planning to write a software paper based on the software and some sections of the paper (~25%) must describe the software.

It's standard practice to run papers through a plagiarism checker. I am concerned that the result may flag the parts from the documentation as plagiarism because they will be similar.

Is there any way to prevent this or should I simply not publish the online documentation until a few months after acceptance of the paper.

I am writing an open source software which will be published as a public Github repository (code+binaries) and the accompanying documentation will be available on ReadTheDocs.com platform. I am also planning to write a software paper based on the software and some sections of the paper (~25%) must describe the software.

It's standard practice for journals to run papers through a plagiarism checker. I am concerned that the result may flag the parts from the documentation as plagiarism because they will be similar.

Is there any way to make sure the similarity between parts of the documentation and the manuscript won't cause the paper to be rejected on grounds of (self-)plagiarism?

Edit: This question asks something similar about an Arxiv preprint. My question asks about technical documentation similar to this unrelated project, whereas Arxiv is an accepted medium for publishing preprints. Therefore, I don't see how this can be a duplicate.