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Contributing to pydicom

This is the guide for contributing code, documentation and tests to pydicom, as well as information on filing issues. Please read it carefully to help make the code review process go as smoothly as possible and maximize the likelihood of your contribution being merged.

How to contribute

The preferred workflow for contributing to pydicom is to fork the main repository on GitHub, clone, and develop on a branch. Steps:

  1. Fork the project repository by clicking on the 'Fork' button near the top right of the page. This creates a copy of the code under your GitHub user account. For more details on how to fork a repository see this guide.

  2. Clone your fork of the pydicom repo from your GitHub account to your local disk:

    $ git clone https://github.com/YourUsername/pydicom
$ cd pydicom/

  3. Install pre-commit:

    $ pip install pre-commit
$ pre-commit install

  4. Create a feature branch to hold your development changes:

    $ git checkout -b my-feature

    Always use a feature branch. It's good practice to never work on the main branch!

  5. Develop the feature on your feature branch. Add changed files using git add and then git commit files:

    $ git add modified_files
$ git commit

  6. Add a meaningful commit message. Pull requests are "squash-merged", e.g. squashed into one commit with all commit messages combined. The commit messages can be edited during the merge, but it helps if they are clearly and briefly showing what has been done in the commit. Check out the seven commonly accepted rules for commit messages. Here are some examples, taken from actual commits:

    Add support for new VRs OV, SV, UV

-  closes #1016

    Add warning when saving compressed without encapsulation  

    Add optional handler argument to Dataset.decompress()

- also add it to Dataset.convert_pixel_data()
- add separate error handling for given handle
- see #537

    When you run git commit the pre-commit checks will automatically run, if it finds any errors then they should be fixed before calling git commit again.

  7. To record your changes in Git, push the changes to your GitHub account with:

    $ git push -u origin my-feature

  8. Follow these instructions to create a pull request from your fork. This will send an email to the committers.

(If any of the above seems like magic to you, please look up the Git documentation on the web, or ask a friend or another contributor for help.)

Pull Request Checklist

We recommend that your contribution complies with the following rules before you submit a pull request:

  • Follow the style used in the rest of the code. That mostly means to follow PEP-8 guidelines for the code, and the NumPy style for documentation.

  • If your pull request addresses an issue, please use the pull request title to describe the issue and mention the issue number in the pull request description. This will make sure a link back to the original issue is created. Use "closes #issue-number" or "fixes #issue-number" to let GitHub automatically close the related issue on commit. Use any other keyword (i.e. works on, related) to avoid GitHub to close the referenced issue.

  • All public methods should have informative docstrings with sample usage presented as doctests when appropriate.

  • Please prefix the title of your pull request with [MRG] (Ready for Merge), if the contribution is complete and ready for a detailed review. Some of the core developers will review your code, make suggestions for changes, and approve it as soon as it is ready for merge. Pull requests are usually merged after two approvals by core developers, or other developers asked to review the code. An incomplete contribution -- where you expect to do more work before receiving a full review -- should be prefixed with [WIP] (to indicate a work in progress) and changed to [MRG] when it matures. WIPs may be useful to: indicate you are working on something to avoid duplicated work, request broad review of functionality or API, or seek collaborators. WIPs often benefit from the inclusion of a task list in the PR description.

  • When adding additional functionality, check if it makes sense to add one or more example scripts in the examples/ folder. Have a look at other examples for reference. Examples should demonstrate why the new functionality is useful in practice and, if possible, compare it to other methods available in pydicom.

  • Documentation and high-coverage tests are necessary for enhancements to be accepted. Bug-fixes shall be provided with regression tests that fail before the fix. For new features, the correct behavior shall be verified by feature tests. A good practice to write sufficient tests is test-driven development.

You can also check for common programming errors and style issues with the following tools:

  • The test coverage should be at least as good as the current coverage and any new lines of code must be covered:
$ pip install pytest pytest-cov
$ cd pydicom/
$ pytest --cov=pydicom tests/

  • The type hints, code syntax, spelling and formatting should be checked:

    $ pre-commit run

Alternatively you can run these checks manually without pre-commit:

  • Check the type hints
$ pip install mypy
$ cd pydicom/
$ mypy
  • Check the code style and syntax
$ pip install ruff
$ cd pydicom/
$ ruff check .

  • Consistent code formatting

    $ pip install black
$ cd pydicom/
$ black src/pydicom/
$ black tests/

Filing issues

We use GitHub issues to track all bugs and feature requests; feel free to open an issue if you have found a bug or wish to see a feature implemented.

It is recommended to check that your issue complies with the following rules before submitting:

  • Verify that your issue is not being currently addressed by other issues or pull requests.

  • Please ensure all code snippets and error messages are formatted in appropriate code blocks. See Creating and highlighting code blocks.

  • Please include your operating system type and version number, as well as your Python and pydicom versions.

    Please use the pydicom_env_info module to gather this information :

    $ python -m pydicom.env_info

  • Please include a reproducible code snippet or link to a gist. If an exception is raised, please provide the complete traceback. (use %xmode in ipython to use the non beautified version of the trackeback)

Documentation

We are glad to accept any sort of documentation: function docstrings, reStructuredText documents, tutorials, etc. reStructuredText documents live in the source code repository under the doc/ directory.

You can edit the documentation using any text editor and then generate the HTML output by typing make html from the doc/ directory. Alternatively, make can be used to quickly generate the documentation without the example gallery. The resulting HTML files will be placed in _build/html/ and are viewable in a web browser. See the README file in the doc/ directory for more information.

Install the dependencies needed for building the documentation::

```bash
$ cd pydicom/
$ pip install -e .[docs]
```

To build the documentation itself::

```bash
$ cd pydicom/doc/
$ make clean && make html
```

When you are writing documentation that references DICOM, it is often helpful to reference the related part of the DICOM standard. Try to make the explanations intuitive and understandable also for users not fluent in DICOM.