Contributors Guide

This is a community driven project and everyone is welcome to contribute.

The project is hosted at the PyGMT GitHub repository.

The 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.

Ways to Contribute

Ways to Contribute Documentation and/or Code

  • 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 gallery example of how to do something.

  • Improve the API documentation.

  • Contribute code! This can be code that you already have and it doesn’t need to be perfect! We will help you clean things up, test it, etc.

Ways to Contribute Feedback

  • Provide feedback about how we can improve the project or about your particular use case. Open an issue with feature requests or bug fixes, or post general comments/questions on the forum.

  • Help triage issues, or give a “thumbs up” on issues that others reported which are relevant to you.

Ways to Contribute to Community Building

  • Participate and answer questions on the PyGMT forum Q&A.

  • Participate in discussions at the quarterly PyGMT Community Meetings, which are announced on the forum governance page.

  • Cite PyGMT when using the project.

  • Spread the word about PyGMT or star the project!

Providing Feedback

Reporting a Bug

  • Find the Issues tab on the top of the GitHub repository and click New Issue.

  • Click on Get started next to Bug report.

  • Please try to fill out the template with as much detail as you can.

  • After submitting your bug report, try to answer any follow up questions about the bug as best as you can.

Reporting Upstream Bugs

If you are aware that a bug is caused by an upstream GMT issue rather than a PyGMT-specific issue, you can optionally take the following steps to help resolve the problem:

  • Add the line pygmt.config(GMT_VERBOSE='d') after your import statements, which will report the equivalent GMT commands as one of the debug messages.

  • Either append all messages from running your script to your GitHub issue, or filter the messages to include only the GMT-equivalent commands using a command such as:

    python <test>.py 2>&1 | awk -F': ' '$2=="GMT_Call_Command string" {print "gmt", $3}'
    

    where <test> is the name of your test script.

  • If the bug is produced when passing an in-memory data object (e.g., a pandas.DataFrame or xarray.DataArray) to a PyGMT function, try writing the data to a file (e.g., a NetCDF or ASCII txt file) and passing the data file to the PyGMT function instead. In the GitHub issue, please share the results for both cases along with your code.

Submitting a Feature Request

  • Find the Issues tab on the top of the GitHub repository and click New Issue.

  • Click on Get started next to Feature request.

  • Please try to fill out the template with as much detail as you can.

  • After submitting your feature request, try to answer any follow up questions as best as you can.

Submitting General Comments/Questions

There are several pages on the Community Forum where you can submit general comments and/or questions:

  • For questions about using PyGMT, select New Topic from the PyGMT Q&A Page.

  • For general comments, select New Topic from the Lounge Page.

  • To share your work, select New Topic from the Showcase Page.

General Guidelines

Resources for New Contributors

Please take a look at these resources to learn about Git and pull requests (don’t hesitate to ask questions):

Getting Help

Discussion often happens on GitHub issues and pull requests. In addition, there is a Discourse forum for the project where you can ask questions.

Pull Request Workflow

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 chance 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 Making a Pull Request (PR):

  • What should be included in a PR

    • Have a quick look at the titles of all the existing issues first. If there is already an issue that matches your PR, leave a comment there to let us know what you plan to do. Otherwise, open an issue describing what you want to do.

    • Each pull request should consist of a small and logical collection of changes; larger changes should be broken down into smaller parts and integrated separately.

    • Bug fixes should be submitted in separate PRs.

  • How to write and submit a PR

    • Use underscores for all Python (*.py) files as per PEP8, not hyphens. Directory names should also use underscores instead of hyphens.

    • 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 (e.g.: .gitignore, IDE project files, etc).

    • Write descriptive commit messages. Chris Beams has written a guide on how to write good commit messages.

  • PR review

    • 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.

General Process for Pull Request 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, improvements or alternative implementation details.

To increase the chances of getting your pull request accepted quickly, try to:

  • Submit a friendly PR

    • Write a good and detailed description of what the PR does.

    • Write some documentation for your code (docstrings) and leave comments explaining the reason behind non-obvious things.

    • Write tests for the code you wrote/modified if needed. Please refer to Testing your code or Testing plots.

    • Include an example of new features in the gallery or tutorials. Please refer to Gallery plots or Tutorials.

  • Have a good coding style

    • Use readable code, as it is better than clever code (even with comments).

    • Follow the PEP8 style guide for code and the NumPy style guide for docstrings. Please refer to Code style.

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.

Setting up your Environment

These steps for setting up your environment are necessary for editing the documentation locally and contributing code. A local PyGMT development environment is not needed for editing the documentation on GitHub.

We highly recommend using Anaconda and the conda package manager to install and manage your Python packages. It will make your life a lot easier!

The repository includes a conda environment file environment.yml with the specification for all development requirements to build and test the project. In particular, these are some of the key development dependencies you will need to install to build the documentation and run the unit tests locally:

  • git (for cloning the repo and tracking changes in code)

  • dvc (for downloading baseline images used in tests)

  • pytest-mpl (for checking that generated plots match the baseline)

  • sphinx-gallery (for building the gallery example page)

See the environment.yml file for the full list of dependencies and the environment name (pygmt). Once you have forked and cloned the repository to your local machine, you can use this file to create an isolated environment on which you can work. Run the following on the base of the repository to create a new conda environment from the environment.yml file:

conda env create --file environment.yml

Before building and testing the project, you have to activate the environment (you’ll need to do this every time you start a new terminal):

conda activate pygmt

We 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  # on Linux/macOS
pip install --no-deps -e .  # on Windows

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).

Contributing Documentation

PyGMT Documentation Overview

There are four main components to PyGMT’s documentation:

  • Gallery examples, with source code in Python *.py files under the examples/gallery/ folder.

  • Tutorial examples, with source code in Python *.py files under the examples/tutorials/ folder.

  • API documentation, with source code in the docstrings in Python *.py files under the pygmt/src/ and pygmt/datasets/ folders.

  • Getting started/developer documentation, with source text in ReST *.rst and markdown *.md files under the doc/ folder.

The documentation is written primarily in reStructuredText and built by Sphinx. Please refer to reStructuredText Cheatsheet if you are new to reStructuredText. When contributing documentation, be sure to follow the general guidelines in the pull request workflow section.

There are two primary ways to edit the PyGMT documentation:

Editing the Documentation on GitHub

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 (even better) submitting a fix.

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

  1. On each documentation page, there should be an “Improve This Page” link at the very top.

  2. Click on that link to open the respective source file (usually an .rst file in the doc/ folder or a .py file in the examples/ folder) on GitHub for editing online (you’ll need a GitHub account).

  3. Make your desired changes.

  4. When you’re done, scroll to the bottom of the page.

  5. 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.

  6. Choose “Create a new branch for this commit and start a pull request” and click on the “Propose changes” button to open a pull request.

  7. The pull request will run the GMT automated tests and make a preview deployment. You can see how your change looks in the PyGMT documentation by clicking the “Details” button of the “docs/readthedocs.org:pygmt-dev” status check, after the building has finished (usually 10-15 minutes after the pull request was created).

  8. We’ll review your pull request, recommend changes if necessary, and then merge them in if everything is OK.

  9. Done!

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

Editing the Documentation Locally

For more extensive changes, you can edit the documentation in your cloned repository and build the documentation to preview changes before submitting a pull request. First, follow the setting up your environment instructions. After making your changes, you can build the HTML files from sources using:

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. Follow the pull request workflow to submit your changes for review.

Adding example code

Many of the PyGMT functions have example code in their documentation. To contribute an example, add an “Example” header and put the example code below it. Have all lines begin with >>>. To keep this example code from being run during testing, add the code __doctest_skip__ = [function name] to the top of the module.

Inline code example

Below the import statements at the top of the file

__doctest_skip__ = ["module_name"]

At the end of the function’s docstring

Example
-------
>>> import pygmt
>>> # Comment describing what is happening
>>> Code example

Contributing Tutorials

The tutorials (the User Guide in the docs) are also built by sphinx-gallery from the .py files in the examples/tutorials folder of the repository. To add a new tutorial:

  • Create a .py file in the examples/tutorials/advanced folder.

  • Write the tutorial in “notebook” style with code mixed with paragraphs explaining what is being done. See the other tutorials for the format.

  • Choose the most representative figure as the thumbnail figure by adding a comment line # sphinx_gallery_thumbnail_number = <fig_number> to any place (usually at the top) in the tutorial. The fig_number starts from 1.

Guidelines for a good tutorial:

  • Each tutorial should focus on a particular set of tasks that a user might want to accomplish: plotting grids, interpolation, configuring the frame, projections, etc.

  • The tutorial code should be as simple as possible. Avoid using advanced/complex Python features or abbreviations.

  • Explain the options and features in as much detail as possible. The gallery has concise examples while the tutorials are detailed and full of text.

  • SI units should be used in the example code for tutorial plots.

Note that the pygmt.Figure.show method needs to be called for a plot to be inserted into the documentation.

Editing the API Documentation

The API documentation is built from the docstrings in the Python *.py files under the pygmt/src/ and pygmt/datasets/ folders. 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.

Standards for Example Code

When editing documentation, use the following standards to demonstrate the example code:

  1. Python arguments, such as import statements, Boolean expressions, and function arguments should be wrapped as code by using `` on both sides of the code. Examples: ``import pygmt`` results in import pygmt, ``True`` results in True, ``style=”v”`` results in style="v".

  2. Literal GMT arguments should be bold by wrapping the arguments with ** (two asterisks) on both sides. The argument description should be in italicized with * (single asterisk) on both sides. Examples: **+l**\ *label* results in +llabel, **05m** results in 05m.

  3. Optional arguments are wrapped with [ ] (square brackets).

  4. Arguments that are mutually exclusive are separated with a | (bar) to denote “or”.

  5. Default arguments for parameters and configuration settings are wrapped with [ ] (square brackets) with the prefix “Default is”. Example: [Default is p].

Cross-referencing with Sphinx

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

You can reference functions, classes, modules, and methods from anywhere (including docstrings) using:

  • :func:`package.module.function`

  • :class:`package.module.class`

  • :meth:`package.module.method`

  • :mod:`package.module`

An example would be to use :meth:`pygmt.Figure.grdview` to link to https://www.pygmt.org/latest/api/generated/pygmt.Figure.grdview.html. PyGMT documentation that is not a class, method, or module can be linked with :doc:`Any Link Text </path/to/the/file>`. For example, :doc:`Install instructions </install>` links to https://www.pygmt.org/latest/install.html.

Linking to the GMT documentation and GMT configuration parameters can be done using:

  • :gmt-docs:`page_name.html`

  • :gmt-term:`GMT_PARAMETER`

An example would be using :gmt-docs:`makecpt.html` to link to https://docs.generic-mapping-tools.org/latest/makecpt.html. For GMT configuration parameters, an example is :gmt-term:`COLOR_FOREGROUND` to link to https://docs.generic-mapping-tools.org/latest/gmt.conf#term-COLOR_FOREGROUND.

Sphinx will create a link to the automatically generated page for that function/class/module/method.

Contributing Code

PyGMT Code Overview

The source code for PyGMT is located in the pygmt/ directory. When contributing code, be sure to follow the general guidelines in the pull request workflow section.

Code Style

We use some tools to format the code so we don’t have to think about it:

Black and blackdoc 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

For consistency, we also use UNIX-style line endings (\n) and file permission 644 (-rw-r--r--) throughout the whole project. 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. Even better, you can just write /format in the first line of any comment in a pull request to lint the code automatically.

When wrapping a new alias, use an underscore to separate words bridged by vowels (aeiou), such as no_skip and z_only. Do not use an underscore to separate words bridged only by consonants, such as distcalc, and crossprofile. This convention is not applied by the code checking tools, but the PyGMT maintainers will comment on any pull requests as needed.

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

make check   # Runs black, blackdoc, docformatter, flakeheaven and isort (in check mode)
make lint    # Runs pylint, which is a bit slower

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.

When writing tests, don’t test everything that the GMT function already tests, such as the every unique combination arguments. An exception to this would be the most popular methods, such as pygmt.Figure.plot and pygmt.Figure.basemap. The highest priority for tests should be the Python-specific code, such as numpy, pandas, and xarray objects and the virtualfile mechanism.

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.

Pull the baseline images, run the tests, and calculate test coverage using:

dvc status  # should report any files 'not_in_cache'
dvc pull  # pull down files from DVC remote cache (fetch + checkout)
make test

The coverage report will let you know which lines of code are touched by the tests. If all the tests pass, you can view the coverage reports by opening htmlcov/index.html in your browser. 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.

You can also run tests in just one test script using:

pytest pygmt/tests/NAME_OF_TEST_FILE.py

or run tests which contain names that match a specific keyword expression:

pytest -k KEYWORD pygmt/tests

Testing Plots

Writing an image-based test is only slightly more difficult than a simple test. The main consideration is that you must specify the “baseline” or reference image, and compare it with a “generated” or test image. This is handled using the decorator functions @pytest.mark.mpl_image_compare and @check_figures_equal whose usage are further described below.

Using mpl_image_compare

This is the preferred way to test plots whenever possible.

This method uses the pytest-mpl plug-in to test plot generating code. Every time the tests are run, pytest-mpl compares the generated plots with known correct ones stored in pygmt/tests/baseline. If your test created a pygmt.Figure object, you can test it by adding a decorator and returning the pygmt.Figure object:

@pytest.mark.mpl_image_compare
def test_my_plotting_case():
    "Test that my plotting method works"
    fig = Figure()
    fig.basemap(region=[0, 360, -90, 90], projection="W15c", frame=True)
    return fig

Your test function must return the pygmt.Figure object and you can only test one figure per function.

Before you can run your test, you’ll need to generate a baseline (a correct version) of your plot. Run the following from the repository root:

pytest --mpl-generate-path=baseline pygmt/tests/NAME_OF_TEST_FILE.py

This will create a baseline folder with all the plots generated in your test file. Visually inspect the one corresponding to your test function. If it’s correct, copy it (and only it) to pygmt/tests/baseline. When you run make test the next time, your test should be executed and passing.

Don’t forget to commit the baseline image as well! The images should be pushed up into a remote repository using dvc (instead of git) as will be explained in the next section.

Using Data Version Control (dvc) to Manage Test Images

As the baseline images are quite large blob files that can change often (e.g. with new GMT versions), it is not ideal to store them in git (which is meant for tracking plain text files). Instead, we will use dvc which is like git but for data. What dvc does is to store the hash (md5sum) of a file. For example, given an image file like test_logo.png, dvc will generate a test_logo.png.dvc plain text file containing the hash of the image. This test_logo.png.dvc file can be stored as usual on GitHub, while the test_logo.png file can be stored separately on our dvc remote at https://dagshub.com/GenericMappingTools/pygmt.

To pull or sync files from the dvc remote to your local repository, use the commands below. Note how dvc commands are very similar to git.

dvc status  # should report any files 'not_in_cache'
dvc pull  # pull down files from DVC remote cache (fetch + checkout)

Once the sync/download is complete, you should notice two things. There will be images stored in the pygmt/tests/baseline folder (e.g. test_logo.png) and these images are technically reflinks/symlinks/copies of the files under the .dvc/cache folder. You can now run the image comparison test suite as per usual.

pytest pygmt/tests/test_logo.py  # run only one test
make test  # run the entire test suite

To push or sync changes from your local repository up to the dvc remote at DAGsHub, you will first need to set up authentication using the commands below. This only needs to be done once, i.e. the first time you contribute a test image to the PyGMT project.

dvc remote modify upstream --local auth basic
dvc remote modify upstream --local user "$DAGSHUB_USER"
dvc remote modify upstream --local password "$DAGSHUB_PASS"

The configuration will be stored inside your .dvc/config.local file. Note that the $DAGSHUB_PASS token can be generated at https://dagshub.com/user/settings/tokens after creating a DAGsHub account (can be linked to your GitHub account). Once you have an account set up, please ask one of the PyGMT maintainers to add you as a collaborator at https://dagshub.com/GenericMappingTools/pygmt/settings/collaboration before proceeding with the next steps.

The entire workflow for generating or modifying baseline test images can be summarized as follows:

# Sync with both git and dvc remotes
git pull
dvc pull

# Generate new baseline images
pytest --mpl-generate-path=baseline pygmt/tests/test_logo.py
mv baseline/*.png pygmt/tests/baseline/

# Generate hash for baseline image and stage the *.dvc file in git
dvc status  # check which files need to be added to dvc
dvc add pygmt/tests/baseline/test_logo.png
git add pygmt/tests/baseline/test_logo.png.dvc

# Commit changes and push to both the git and dvc remotes
git commit -m "Add test_logo.png into DVC"
dvc status --remote upstream  # Report which files will be pushed to the dvc remote
dvc push  # Run before git push to enable automated testing with the new images
git push

Using check_figures_equal

This approach draws the same figure using two different methods (the reference method and the tested method), and checks that both of them are the same. It takes two pygmt.Figure objects (‘fig_ref’ and ‘fig_test’), generates a png image, and checks for the Root Mean Square (RMS) error between the two. Here’s an example:

@check_figures_equal()
def test_my_plotting_case():
  "Test that my plotting method works"
  fig_ref, fig_test = Figure(), Figure()
  fig_ref.grdimage("@earth_relief_01d_g", projection="W120/15c", cmap="geo")
  fig_test.grdimage(grid, projection="W120/15c", cmap="geo")
  return fig_ref, fig_test