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CONTRIBUTING.md

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@@ -4,9 +4,10 @@ Welcome to the Nipype repository! We're excited you're here and want to contribu
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These guidelines are designed to make it as easy as possible to get involved. If you have any questions that aren't discussed below, please let us know by opening an [issue][link_issues]!
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Before you start you'll need to set up a free [GitHub][link_github] account and sign in, here are some [instructions][link_signupinstructions].
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If you are not familiar with version control system and Git,
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you will find introduction and links to tutorials [here](http://www.reproducibleimaging.org/module-reproducible-basics/02-vcs/).
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Before you start you'll need to set up a free [GitHub][link_github] account and sign in. Here are some [instructions][link_signupinstructions].
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If you are not familiar with version control systems such as git,
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[introductions and tutorials](http://www.reproducibleimaging.org/module-reproducible-basics/02-vcs/)
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may be found on [ReproducibleImaging.org](https://www.reproducibleimaging.org/).
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Already know what you're looking for in this guide? Jump to the following sections:
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* [Understanding issue labels](#issue-labels)
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**2. [Fork][link_fork] the [Nipype repository][link_nipype] to your profile.**
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This is now your own unique copy of Nipype repository.
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This is now your own unique copy of the Nipype repository.
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Changes here won't affect anyone else's work, so it's a safe space to explore edits to the code!
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You can clone your Nipype repository in order to create a local copy of the code on your machine.
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In your local Nipype directory, run `pip install -e .[dev]`.
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This will add your version of nipype to your local python environment and
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install dependencies needed for development.
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To install your version of Nipype, and the dependencies needed for development,
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in your Python environment, run `pip install -e ".[dev]"` from your local Nipype
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directory.
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Make sure to [keep your fork up to date][link_updateupstreamwiki] with the original Nipype repository.
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Make sure to keep your fork up to date with the original Nipype repository.
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One way to do this is to [configure a new remote named "upstream"](https://help.github.com/articles/configuring-a-remote-for-a-fork/)
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and to [sync your fork with the upstream repository][link_updateupstreamwiki].
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**3. Make the changes you've discussed.**
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If you're adding a new tool from an existing neuroimaging toolkit (e.g., 3dDeconvolve from AFNI),
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check out the [guide for adding new interfaces to Nipype][link_new_interfaces].
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When you are working on your changes, you should test frequently if you are not breaking the existing code,
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more on testing you will find [the testing section of Nipype documentation](http://nipype.readthedocs.io/en/latest/devel/testing_nipype.html).
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When you are working on your changes, test frequently to ensure you are not breaking the existing code.
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For more on testing, please see [the testing section of Nipype documentation](http://nipype.readthedocs.io/en/latest/devel/testing_nipype.html).
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Before pushing your changes to GitHub run `make check-before-commit`, this will remove trailing spaces, create new auto tests,
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test entire package and build the documentation.
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Before pushing your changes to GitHub, run `make check-before-commit`. This will remove trailing spaces, create new auto tests,
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test the entire package, and build the documentation.
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If you get no errors, you're ready to submit your changes!
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It's a good practice to create [a new branch](https://help.github.com/articles/about-branches/)
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This tells the development team that your pull request is a "work-in-progress", and that you plan to continue working on it.
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Review and discussion on new code can begin well before the work is complete, and the more discussion the better!
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This provides the opportunity to check with the development team the path you've outlined.
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The development team may prefer a different path than you've outlined, so it's better to discuss it and get approval at the early stage of your work.
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One your PR is ready a member of the development team will review your changes to confirm that they can be merged into the main codebase.
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doc/devel/testing_nipype.rst

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Nipype is tested inside Docker containers and users can use nipype images to test local versions.
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First, install the `Docker Engine <https://docs.docker.com/engine/installation/>`_.
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Nipype has one base docker image called nipype/base:latest, that contains several useful tools
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(FreeSurfer, AFNI, FSL, ANTs, etc.), and additional test images
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Nipype has one base docker image called nipype/nipype:base, that contains several useful tools
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(FreeSurfer, AFNI, FSL, ANTs, etc.), and additional test images
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for specific Python versions: py27 for Python 2.7 and py36 for Python 3.6.
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Users can pull the nipype image for Python 3.6 as follows::
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docker pull nipype/base:py36
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docker pull nipype/nipype:py36
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In order to test a local version of nipype you can run test within container as follows::
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Additional comments
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-------------------
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If the project is tested both on your local OS and within a Docker container you might have to remove all
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``__pycache__`` directories before switching between your OS and a container.
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If the project is tested both on your local OS and within a Docker container, you might have to remove all
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``__pycache__`` directories before switching between your OS and a container.

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