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Contributing Guidelines

🎉 First off, thank you for considering contributing to our project! 🎉

These are some of the many ways to contribute:

  • 🐛 Submitting bug reports and feature requests
  • 📝 Writing tutorials or examples
  • 🔍 Fixing typos and improving to the documentation
  • 💡 Writing code for everyone to use

If you get stuck at any point you can create an issue on GitHub (look for the Issues tab in the repository) or contact us at one of the other channels mentioned below.

For more information on contributing to open source projects, GitHub's own guide is a great starting point if you are new to version control. Also, checkout the Zen of Scientific Software Maintenance for some guiding principles on how to create high quality scientific software contributions.

This document is inspired by the Fatiando a Terra contributing guide.

Ground Rules

Our goal is to maintain a diverse community that's pleasant for everyone. Please be considerate and respectful of others. Everyone must abide by our Code of Conduct and we encourage all to read it carefully.

Contents

What Can I Do?

  • Tackle any issue that you wish! Some issues are labeled as "good first issues" to indicate that they are beginner friendly, meaning that they don't require extensive knowledge of the project.
  • Make a tutorial or example of how to do something.
  • Provide feedback about how we can improve the project or about your particular use case.
  • Contribute code you already have. It doesn't need to be perfect! We will help you clean things up, test it, etc.

How Can I Talk to You?

Discussion usually happens in the issues and pull requests. If you have a question, please feel free to open an issue on GitHub or leave comment on an existing one if it's related to the same topic.

Getting credit for contributions

We appreciate the effort that goes into making a contribution to our open-source projects. To say "thank you" and provide an extra incentive, we have established some criteria for giving credit to contributors in different ways: from having your name in the changelog, to authorship on academic publications. Please read the CompGeoLab Authorship Guidelines for more information.

Reporting a Bug

Find the Issues tab on the top of the GitHub repository and click New Issue. Please try to provide as much detail as you can. Remember: the more information we have, the easier it will be for us to solve your problem.

Editing the Documentation

If you're browsing the documentation and notice a typo or something that could be improved, please consider letting us know by creating an issue or submitting a fix (even better 🌟).

You can submit fixes to the documentation pages completely online without having to download and install anything:

  • On each documentation page, there should be a "Suggest edit" link at the very top (click on the GitHub logo).
  • Click on that link to open the respective source file (usually an .rst file in the doc folder) on GitHub for editing online (you'll need a GitHub account).
  • Make your desired changes.
  • When you're done, scroll to the bottom of the page.
  • Fill out the two fields under "Commit changes": the first is a short title describing your fixes; the second is a more detailed description of the changes. Try to be as detailed as possible and describe why you changed something.
  • Click on the "Commit changes" button to open a pull request (see below).
  • We'll review your changes and then merge them in if everything is OK.
  • Done 🎉🍺

Alternatively, you can make the changes offline to the files in the doc folder or the example scripts. See Contributing Code for instructions.

Contributing Code

Is this your first contribution? Please take a look at these resources to learn about git and pull requests (don't hesitate to ask questions):

If you're new to working with git, GitHub, and the Unix Shell, we recommend starting with the Software Carpentry lessons, which are available in English and Spanish:

General guidelines

We follow the git pull request workflow to make changes to our codebase. Every change made goes through a pull request, even our own, so that our continuous integration services have a change to check that the code is up to standards and passes all our tests. This way, the main branch is always stable.

General guidelines for pull requests (PRs):

  • Open an issue first describing what you want to do. If there is already an issue that matches your PR, leave a comment there instead to let us know what you plan to do.
  • Each pull request should consist of a small and logical collection of changes.
  • Larger changes should be broken down into smaller components and integrated separately.
  • Bug fixes should be submitted in separate PRs.
  • Describe what your PR changes and why this is a good thing. Be as specific as you can. The PR description is how we keep track of the changes made to the project over time.
  • Do not commit changes to files that are irrelevant to your feature or bugfix (eg: .gitignore, IDE project files, etc).
  • Write descriptive commit messages. Chris Beams has written a guide on how to write good commit messages.
  • Be willing to accept criticism and work on improving your code; we don't want to break other users' code, so care must be taken not to introduce bugs.
  • Be aware that the pull request review process is not immediate, and is generally proportional to the size of the pull request.

Setting up your environment

We highly recommend using the Mambaforge Python distribution
and the mamba package manager (or conda if you prefer) to install and manage your Python packages. It will make your life a lot easier!

Most of our repositories include a conda environment file environment.yml with the specification for all development requirements to build and test the project. Once you have forked and cloned the repository to your local machine, you use this file to create an isolated environment on which you can work. Run the following on the base of the repository:

mamba env create

Note: Environment creation only needs to be done once.

Before building and testing the project, you have to activate the environment (see the environment.yml file for the environment name):

mamba activate ENVIRONMENT_NAME

Note: You'll need to activate the environment every time you start a new terminal.

Most repositories will also have a Makefile that provides commands for installing, running the tests and coverage analysis, running linters, etc. If you don't want to use make, open the Makefile and copy the commands you want to run.

To install the current source code into your testing environment, run:

make install

This installs your project in editable mode, meaning that changes made to the source code will be available when you import the package (even if you're on a different directory).

Code style

We use Black to format the code so we don't have to think about it. Black loosely follows the PEP8 guide but with a few differences. Regardless, you won't have to worry about formatting the code yourself. Before committing, run it to automatically format your code:

make format

Don't worry if you forget to do it. Our continuous integration systems will warn us and you can make a new commit with the formatted code.

We also use flake8 to check the quality of the code and quickly catch common errors. The Makefile contains rules for running the check:

make check   # Runs flake8, isort, and black (in check mode)

Docstrings

All docstrings should follow the numpy style guide. All functions/classes/methods should have docstrings with a full description of all arguments and return values.

While the maximum line length for code is automatically set by Black, docstrings must be formatted manually. To play nicely with Jupyter and IPython, keep docstrings limited to 79 characters per line.

Testing your code

Automated testing helps ensure that our code is as free of bugs as it can be. It also lets us know immediately if a change we make breaks any other part of the code.

All of our test code and data are stored in the tests subpackage. We use the pytest framework to run the test suite.

Please write tests for your code so that we can be sure that it won't break any of the existing functionality. Tests also help us be confident that we won't break your code in the future.

If you're new to testing, see existing test files for examples of things to do. Don't let the tests keep you from submitting your contribution! If you're not sure how to do this or are having trouble, submit your pull request anyway. We will help you create the tests and sort out any kind of problem during code review.

Run the tests and calculate test coverage using:

make test

The coverage report will let you know which lines of code are touched by the tests. Strive to get 100% coverage for the lines you changed. It's OK if you can't or don't know how to test something. Leave a comment in the PR and we'll help you out.

Documentation

The documentation sources are in the doc folder. We use sphinx to build the web pages from these sources. To build the HTML files:

cd doc
make all

This will build the HTML files in doc/_build/html. Open doc/_build/html/index.html in your browser to view the pages.

The API reference is manually assembled in doc/api/index.rst. The autodoc sphinx extension will automatically create pages for each function/class/module listed there.

You can reference classes, functions, and modules from anywhere (including docstrings) using :func:`package.module.function`, :class:`package.module.class`, or :mod:`package.module`. Sphinx will create a link to the automatically generated page for that function/class/module.

Code Review

After you've submitted a pull request, you should expect to hear at least a comment within a couple of days. We may suggest some changes or improvements or alternatives.

Some things that will increase the chance that your pull request is accepted quickly:

  • Write a good and detailed description of what the PR does.
  • Write tests for the code you wrote/modified.
  • Readable code is better than clever code (even with comments).
  • Write documentation for your code (docstrings) and leave comments explaining the reason behind non-obvious things.
  • Include an example of new features in the gallery or tutorials.
  • Follow the numpy guide for documentation.
  • Run the automatic code formatter and style checks.

Pull requests will automatically have tests run by GitHub Actions. This includes running both the unit tests as well as code linters. Github will show the status of these checks on the pull request. Try to get them all passing (green). If you have any trouble, leave a comment in the PR or get in touch.