Skip to content

Latest commit

 

History

History
219 lines (160 loc) · 10.1 KB

CONTRIBUTING.md

File metadata and controls

219 lines (160 loc) · 10.1 KB
Raw

Contributing to MRtrix3

There are many ways in which to contribute to the ongoing improvement of MRtrix3:

Bug reporting

  1. Please search on both the MRtrix3 community forum and the GitHub issue list to see if anybody else has lodged a similar observation.

  2. How confident are you that the behaviour you have observed is in fact a genuine bug, and not a misunderstanding?

    • Confident: Please open a new GitHub issue; select the "bug report" issue template to get started.

    • Not so confident: That's fine! Consider instead creating a new topic on the MRtrix3 community forum; others can then comment on your observation and determine the appropriate level of escalation.

Requesting a new feature

Please search the GitHub issue list to see if anybody else has made a comparable request:

  • If a corresponding issue already exists, please add a comment to that issue to escalate the request. Additionally, describe any aspect of that feature not yet described in the existing issue.

  • If no such listing exists, then you are welcome to create a new issue outlining the request. Be sure to select the "feature request" option to get started with writing the Issue.

Asking questions

General questions regarding MRtrix3 installation, usage, or any other aspect that is not specific to the MRtrix3 code, should be directed to the community forum. Also consider perusing the online documentation for the software, in case your issue has already been described there.

Making direct contributions

Thanks for your interest in making direct contributions to MRtrix3! We are excited to expand the breadth of researchers involved in improving and expanding this software, and to ensure that all who make such contributions receive appropriate acknowledgement through Git.

The instructions below give an overview of how to go about generating a proposed change to MRtrix3. The MRtrix3 developers are however more than willing to be engaged in the process for those without experience in Git or GitHub.

  1. You will need to create a fork of the MRtrix3 repository into your GitHub account, where unlike the main MRtrix3 repository, you will have full write access to make the requisite changes.

  2. Create a Git branch that is named appropriately according to the modifications that are being made. The existing code branch on which this new derived branch should be based depends on the nature of the proposed change (described later below).

  3. Generate one or more Git commits that apply your proposed changes to the repository:

    • Individual commits should ideally have a clear singular purpose, and not incorporate multiple unrelated changes. If your proposed changes involve multiple disparate components, consider breaking those changes up into individual commits.

      Conversely, if multiple code changes are logically grouped with / linked to one another, these should ideally be integrated into a single commit.

    • Commits should contain an appropriate message that adequately describes the change encapsulated within.

      If the change demands a longer description, then the commit message should be broken into a synopsis (less than 80 characters) and message body, separated by two newline characters (as this enables GitHub to parse them appropriately).

      This can be achieved at the command-line as follows:

      $ git commit -m $'Commit synopsis\n\nHere is a much longer and wordier description of my proposed changes that doesn\'t fit into 80 characters.\nI can even spread the message body across multiple lines.'

      (Note also the escape character "\" necessary for including an apostrophe in the message text)

    • Where relevant, commit messages can also contain references to GitHub issues or pull requests (type the "#" character followed by the issue / PR number), and/or other individual commits (copy and paste the first 8-10 characters of the commit hash).

    • If multiple persons have contributed to the proposed changes, it is possible to modify individual Git commits to have multiple authors, to ensure that all contributors receive appropriate acknowledgement.

    As a general rule: Git commits and commit messages should be constructed in such a way that, at some time in the future, when one is navigating through the contribution history, the evolution of the code is as clear as possible.

  4. Identify the appropriate classification of the change that you propose to make, and read the relevant instructions there:

    • "Fixing a bug": If the current code behaviour is egregiously incorrect.

    • "Adding or altering features": If:

      • The current code behaviour is considered incorrect or non-ideal, but is nevertheless functional;

      • The proposed change would alter the output data generated by a command;

      • The proposed change improves the performance of a particular command or process, but does not change its output.

    • "Documentation": If you wish to make changes to the MRtrix3 documentation.

  5. Check that your modified code does not prevent MRtrix3 from passing existing tests (all files are in the MRtrix3 root directory):

    1. If adding or modifying C++ code, make sure that script "check_syntax" executes successfully.

    2. If adding or modifying Python code, make sure that script "run_pylint" executes successfully.

    3. If there is a chance of your modifications altering the observable behaviour of one or more existing commands, make sure that script "run_tests" executes successfully.

  6. For code contributions, if possible, a unit test or reproducibility test should be added. This not only demonstrates the behaviour of the proposed code, but will also preclude future regression of the behaviour of that code. For tests that require the addition of raw data to the test_data repository, please coordinate with one of the MRtrix3 developers.

  7. Once completed, a Pull Request should be generated that merges the corresponding branch in your forked version of the MRtrix3 repository into the appropriate target branch of the main MRtrix3 repository itself:

    • If your intended changes are complete, and you consider them ready to be reviewed by an MRtrix3 team member and merged imminently, then create a standard Pull Request.

    • If your changes are ongoing, and you are seeking feedback from the MRtrix3 developers before completing them, then create a draft Pull Request.

Fixing a bug

  1. If there does not already exist a GitHub Issue describing the bug, consider reporting the bug as a standalone Issue prior to progressing further; that way developers can confirm the issue, and possibly provide guidance if you intend to resolve the issue yourself. Later, the Pull Request incorporating the necessary changes should then reference the listed Issue (simply add somewhere in the description section the "#" character followed by the issue number).

  2. Bug fixes are merged directly to master; as such, modifications to the code should be made in a branch that is derived from master, and the corresponding Pull Request should select master as the target branch for code merging.

  3. A unit test or reproducibility test should ideally be added: such a test should fail when executed using the current master code, but pass when executed with the proposed changes.

Adding or altering features

  1. New features, as well as any code changes that alter the output data produced by a command, are merged to the dev branch, which contains all resolved changes since the most recent tag update. As such, any proposed changes that fall under this classification should be made in a branch that is based off of the dev branch, and the corresponding Pull Request should select dev as the target branch for code merging.

Coding conventions

While we do not have strict enforced coding conventions in MRtrix3, the accepted conventions should be self-evident from the code itself.

A few explicit notes on such:

  1. For both C++ and Python, indentation is achieved using two space characters.

  2. Newline characters are Unix-style ("LF" / '\n'); any changes that introduce Windows-style newline characters ("CR LF" / "\r\n") will need to be edited accordingly.

  3. In Python, variable / class / module names are enforced through pylint. Script "run_pylint" in the MRtrix3 root directory will test any code modifications against these expectations.

  4. If the operation of your code is not trivially self-apparent, please endeavour to comment appropriately.

  5. Do not leave excess newline characters at the end of a file.

Documentation

For proposed documentation changes, please communicate with the MRtrix3 developers by creating a new GitHub issue. The appropriate course of action will depend on the component of the documentation intended to be changed as well as the nature of the change. In addition, the location of much of the MRtrix3 documentation will be changing imminently (Pull Request #1622), and so any proposed documentation content changes would need to be coordinated with such.