Documentation

How to edit the cellfinder documentation

Intro

Documentation for cellfinder is very important because it is aimed at researchers who although are excellent scientists, they may not have much computational experience. In particular:

  • Installation, although simple via PyPI, assumes a lot (functional Python installation, CUDA installation etc.)

  • Although most parts of cellfinder can be run through a single command, there are a lot of steps, and so a lot to understand.

  • cellfinder currently uses a lot of file formats that users may not be familiar with (.xml, .nii etc.).

  • There are a lot of parameters that can be changed, and their impact on the final results is not always obvious.

  • It is not immediately obvious how to use the results of the pipeline to answer the particular biological question.

For these reasons (and others) it is important that every part of cellfinder is documented as well as possible, and all new features must be fully documented.

Editing the documentation

The documentation is built with gitbook and mirrored in a GitHub repository.

There are three ways to edit the documentation:

  • On GitHub: Click on the link on the right hand side of the page you want to edit (Edit on GitHUb), make changes online and submit them as a pull request.

  • Locally: Fork the repository, clone locally, then submit your changes as a pull request.

  • On gitbook: If you find yourself editing the documentation a lot, get in contact and I can give you permissions to edit the documentation directly on gitbook.

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