Maintainers Guide

This page contains instructions for project maintainers about how our setup works, making releases, creating packages, etc.

If you want to make a contribution to the project, see the Contributing Guide instead.

Onboarding Access Checklist

Branches

  • main: Always tested and ready to become a new version. Don’t push directly to this branch. Make a new branch and submit a pull request instead.

  • gh-pages: Holds the HTML documentation and is served by GitHub. Pages for the main branch are in the dev folder. Pages for each release are in their own folders. Automatically updated by GitHub Actions so you shouldn’t have to make commits here.

Managing GitHub issues

A few guidelines for managing GitHub issues:

  • Assign labels and the expected milestone to issues as appropriate.

  • When people request to work on an open issue, either assign the issue to that person and post a comment about the assignment or explain why you are not assigning the issue to them and, if possible, recommend other issues for them to work on.

  • People with write access should self-assign issues and/or comment on the issues that they will address.

  • For upstream bugs, close the issue after an upstream release fixes the bug. If possible, post a comment when an upstream PR is merged that fixes the problem, and consider adding a regression test for serious bugs.

Reviewing and merging pull requests

A few guidelines for reviewing:

  • Always be polite and give constructive feedback.

  • Welcome new users and thank them for their time, even if we don’t plan on merging the PR.

  • Don’t be harsh with code style or performance. If the code is bad, either (1) merge the pull request and open a new one fixing the code and pinging the original submitter (2) comment on the PR detailing how the code could be improved. Both ways are focused on showing the contributor how to write good code, not shaming them.

Pull requests should be squash merged. This means that all commits will be collapsed into one. The main advantages of this are:

  • Eliminates experimental commits or commits to undo previous changes.

  • Makes sure every commit on the main branch passes the tests and has a defined purpose.

  • The maintainer writes the final commit message, so we can make sure it’s good and descriptive.

Continuous Integration

We use GitHub Actions continuous integration (CI) services to build and test the project on Linux, macOS and Windows. They rely on the environment.yml file to install required dependencies using conda and the Makefile to run the tests and checks.

There are 11 configuration files located in .github/workflows:

  1. style_checks.yaml (Code lint and style checks)

    This is run on every commit to the main and Pull Request branches. It is also scheduled to run daily on the main branch.

  2. ci_tests.yaml (Tests on Linux/macOS/Windows)

    This is run on every commit to the main and Pull Request branches. It is also scheduled to run daily on the main branch. In draft Pull Requests, only two jobs on Linux are triggered to save on Continuous Integration resources:

    • Minimum NEP29 Python/NumPy versions

    • Latest Python/NumPy versions + optional packages (e.g. GeoPandas)

    This workflow is also responsible for uploading test coverage reports stored in .coverage.xml to https://app.codecov.io/gh/GenericMappingTools/pygmt via the Codecov GitHub Action. More codecov related configurations are stored in .github/codecov.yml.

  3. ci_docs.yml (Build documentation on Linux/macOS/Windows)

    This is run on every commit to the main and Pull Request branches. In draft Pull Requests, only the job on Linux is triggered to save on Continuous Integration resources.

    On the main branch, the workflow also handles the documentation deployment:

    • Updating the development documentation by pushing the built HTML pages from the main branch onto the dev folder of the gh-pages branch.

    • Updating the latest documentation link to the new release.

  4. ci_tests_dev.yaml (GMT Dev Tests on Linux/macOS/Windows).

    This is triggered when a PR is marked as “ready for review”, or using the slash command /test-gmt-dev. It is also scheduled to run daily on the main branch.

  5. cache_data.yaml (Caches GMT remote data files needed for GitHub Actions CI)

    This is scheduled to run every Sunday at 12:00 (UTC). If new remote files are needed urgently, maintainers can manually uncomment the ‘pull_request:’ line in that cache_data.yaml file to refresh the cache.

  6. publish-to-pypi.yml (Publish wheels to PyPI and TestPyPI)

    This workflow is run to publish wheels to PyPI and TestPyPI (for testing only). Archives will be pushed to TestPyPI on every commit to the main branch and tagged releases, and to PyPI for tagged releases only.

  7. release-drafter.yml (Drafts the next release notes)

    This workflow is run to update the next releases notes as pull requests are merged into the main branch.

  8. check-links.yml (Check links in the repository and website)

    This workflow is run weekly to check all external links in plaintext and HTML files. It will create an issue if broken links are found.

  9. format-command.yml (Format the codes using slash command)

    This workflow is triggered in a PR if the slash command /format is used.

  10. dvc-diff.yml (Report changes to test images on dvc remote)

    This workflow is triggered in a PR when any *.png.dvc files have been added, modified, or deleted. A GitHub comment will be published that contains a summary table of the images that have changed along with a visual report.

  11. release-baseline-images.yml (Upload the ZIP archive of baseline images as a release asset)

    This workflow is run to upload the ZIP archive of baseline images as a release asset when a release is published.

Continuous Documentation

We use the Vercel for GitHub App to preview changes made to our documentation website every time we make a commit in a pull request. The service has a configuration file vercel.json, with a list of options to change the default behaviour at https://vercel.com/docs/configuration. The actual script package.json is used by Vercel to install the necessary packages, build the documentation, copy the files to a ‘public’ folder and deploy that to the web, see https://vercel.com/docs/build-step.

Dependencies Policy

PyGMT has adopted NEP29 alongside the rest of the Scientific Python ecosystem, and therefore supports:

  • All minor versions of Python released 42 months prior to the project, and at minimum the two latest minor versions.

  • All minor versions of NumPy released in the 24 months prior to the project, and at minimum the last three minor versions.

In setup.py, the python_requires variable should be set to the minimum supported version of Python. Minimum Python and NumPy version support should be adjusted upward on every major and minor release, but never on a patch release.

Backwards compatibility and deprecation policy

PyGMT is still undergoing rapid development. All of the API is subject to change until the v1.0.0 release. Versioning in PyGMT is based on the semantic versioning specification (e.g. vMAJOR.MINOR.PATCH). Basic policy for backwards compatibility:

  • Any incompatible changes should go through the deprecation process below.

  • Incompatible changes are only allowed in major and minor releases, not in patch releases.

  • Incompatible changes should be documented in the release notes.

When making incompatible changes, we should follow the process:

  • Discuss whether the incompatible changes are necessary on GitHub.

  • Make the changes in a backwards compatible way, and raise a FutureWarning warning for old usage. At least one test using the old usage should be added.

  • The warning message should clearly explain the changes and include the versions in which the old usage is deprecated and is expected to be removed.

  • The FutureWarning warning should appear for 2-4 minor versions, depending on the impact of the changes. It means the deprecation period usually lasts 3-12 months.

  • Remove the old usage and warning when reaching the declared version.

To rename a function parameter, add the @deprecate_parameter decorator near the top after the @fmt_docstring decorator but before the @use_alias decorator (if those two exists). Here is an example:

@fmt_docstring
@deprecate_parameter("columns", "incols", "v0.4.0", remove_version="v0.6.0")
@use_alias(J="projection", R="region", V="verbose", i="incols")
@kwargs_to_strings(R="sequence", i='sequence_comma')
def plot(self, x=None, y=None, data=None, size=None, direction=None, **kwargs):
    pass

In this case, the old parameter name columns is deprecated since v0.4.0, and will be fully removed in v0.6.0. The new parameter name is incols.

Making a Release

We try to automate the release process as much as possible. GitHub Actions workflow handles publishing new releases to PyPI and updating the documentation. The version number is set automatically using setuptools_scm based information obtained from git. There are a few steps that still must be done manually, though.

Updating the changelog

The Release Drafter GitHub Action will automatically keep a draft changelog at https://github.com/GenericMappingTools/pygmt/releases, adding a new entry every time a Pull Request (with a proper label) is merged into the main branch. This release drafter tool has two configuration files, one for the GitHub Action at .github/workflows/release-drafter.yml, and one for the changelog template at .github/release-drafter.yml. Configuration settings can be found at https://github.com/release-drafter/release-drafter.

The drafted release notes are not perfect, so we will need to tidy it prior to publishing the actual release notes at https://www.pygmt.org/latest/changes.html.

  1. Go to https://github.com/GenericMappingTools/pygmt/releases and click on the ‘Edit’ button next to the current draft release note. Copy the text of the automatically drafted release notes under the ‘Write’ tab to doc/changes.md. Add a section separator --- between the new and old changelog sections.

  2. Update the DOI badge in the changelog. Remember to replace the DOI number inside the badge url.

    [![Digital Object Identifier for PyGMT vX.Y.Z](https://zenodo.org/badge/DOI/10.5281/zenodo.<INSERT-DOI-HERE>.svg)](https://doi.org/10.5281/zenodo.<INSERT-DOI-HERE>)

  3. Open a new Pull Request using the title ‘Changelog entry for vX.Y.Z’ with the updated release notes, so that other people can help to review and collaborate on the changelog curation process described next.

  4. Edit the change list to remove any trivial changes (updates to the README, typo fixes, CI configuration, test updates due to GMT releases, etc).

  5. Sort the items within each section (i.e., New Features, Enhancements, etc.) such that similar items are located near each other (e.g., new wrapped modules, gallery examples, API docs changes) and entries within each group are alphabetical.

  6. Move a few important items from the main sections to the highlights section.

  7. Edit the list of people who contributed to the release, linking to their GitHub account. Sort their names by the number of commits made since the last release (e.g., use git shortlog HEAD...v0.4.0 -sne).

  8. Update README.rst with new information on the new release version, including a vX.Y.Z documentation link, and compatibility with GMT/Python/NumPy versions. Follow NEP 29 for compatibility updates.

  9. Refresh citation information. Specifically, the BibTeX in README.rst and CITATION.cff needs to be updated with any metadata changes. Please follow guidelines in AUTHORSHIP.md for updating the author list in the BibTeX. More information about the CITATION.cff specification can be found at https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md

Check the README syntax

GitHub is a bit forgiving when it comes to the RST syntax in the README but PyPI is not. So slightly broken RST can cause the PyPI page to not render the correct content. Check using the rst2html.py script that comes with docutils:

python setup.py --long-description | rst2html.py --no-raw > index.html

Open index.html and check for any flaws or error messages.

Pushing to PyPI and updating the documentation

After the changelog is updated, making a release can be done by going to https://github.com/GenericMappingTools/pygmt/releases, editing the draft release, and clicking on publish. A git tag will also be created, make sure that this tag is a proper version number (following Semantic Versioning) with a leading v. E.g. v0.2.1.

Once the release/tag is created, this should trigger GitHub Actions to do all the work for us. A new source distribution will be uploaded to PyPI, a new folder with the documentation HTML will be pushed to gh-pages, and the latest link will be updated to point to this new folder.

Archiving on Zenodo

Grab both the source code and baseline images zip files from the GitHub release page and upload them to Zenodo using the previously reserved DOI.

Updating the conda package

When a new version is released on PyPI, conda-forge’s bot automatically creates version updates for the feedstock. In most cases, the maintainers can simply merge that PR.

If changes need to be done manually, you can:

  1. Fork the pygmt feedstock repository if you haven’t already. If you have a fork, update it.

  2. Update the version number and sha256 hash on recipe/meta.yaml. You can get the hash from the PyPI “Download files” section.

  3. Add or remove any new dependencies (most are probably only run dependencies).

  4. Make a new branch, commit, and push the changes to your personal fork.

  5. Create a PR against the original feedstock main.

  6. Once the CI tests pass, merge the PR or ask a maintainer to do so.