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CONTRIBUTING.md

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Contributing to pyradiomics

There are many ways to contribute to pyradiomics, with varying levels of effort. Do try to look through the documentation first if something is unclear, and let us know how we can do better.

We encourage a range of Pull Requests, from patches that include passing tests and documentation, all the way down to half-baked ideas that launch discussions.

The PR Process, Circle CI, and Related Gotchas

How to submit a PR ?

If you are new to pyradiomics development and you don't have push access to the pyradiomics repository, here are the steps:

  1. Fork and clone the repository.
  2. Create a branch.
  3. Push the branch to your GitHub fork.
  4. Create a Pull Request.

This corresponds to the Fork & Pull Model mentioned in the GitHub flow guides.

If you have push access to pyradiomics repository, you could simply push your branch into the main repository and create a Pull Request. This corresponds to the Shared Repository Model and will facilitate other developers to checkout your topic without having to configure a remote. It will also simplify the workflow when you are co-developing a branch.

When submitting a PR, make sure to add a Cc: @Radiomics/developers comment to notify pyradiomics developers of your awesome contributions. Based on the comments posted by the reviewers, you may have to revisit your patches.

How to integrate a PR ?

Getting your contributions integrated is relatively straightforward, here is the checklist:

  • All tests pass
  • Consensus is reached. This usually means that at least one reviewer added a LGTM comment and a reasonable amount of time passed without anyone objecting. LGTM is an acronym for Looks Good to Me.

Next, there are two scenarios:

  • You do NOT have push access: A pyradiomics core developer will integrate your PR.
  • You have push access: Simply click on the "Merge pull request" button.

Then, click on the "Delete branch" button that appears afterward.

Automatic testing of pull requests

Every pull request is tested automatically using CircleCI each time you push a commit to it. The Github UI will restrict users from merging pull requests until the CI build has returned with a successful result indicating that all tests have passed and there were no problems detected by the linter.

Sphinx documentation updates

If you contribute a change that will add a new module/function to pyradiomics, the package index used by sphinx for auto-generating documentation needs to be updated. To do that, follow the instructions on this page to set up sphinx on your system

https://github.com/Radiomics/pyradiomics/wiki/Documentation-infrastructure

and update the package index file radiomics-api.rst by issuing the following command from the docs folder (make sure you include the updated file in your PR!)

sphinx-apidoc -f -o . ../radiomics