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‎.github/ISSUE_TEMPLATE/release_checklist.md

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---
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name: PyGMT release checklist
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about: Checklist for a new PyGMT release.
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title: Release PyGMT x.x.x
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title: Release PyGMT vX.Y.Z
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labels: maintenance
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assignees: ''
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---
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**Release**: [v0.x.x](https://github.com/GenericMappingTools/pygmt/milestones/0.x.x)
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**Release**: [v0.x.x](https://github.com/GenericMappingTools/pygmt/milestones/?)
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**Scheduled Date**: YYYY/MM/DD
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**Pull request due date**: YYYY/MM/DD
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**Priority PRs/issues to complete prior to release**
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- [ ] Wrap X ()
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- [ ] Wrap Y ()
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**Before release**:
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- [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
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- [ ] Update Changelog
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- [ ] Add a new entry in `doc/_static/version_switch.js` for documentation switcher
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- [ ] Update citation information https://github.com/GenericMappingTools/pygmt#citing-pygmt
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- [ ] Finish up 'Changelog entry for v0.x.x' Pull Request:
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- [ ] Add a new entry in `doc/_static/version_switch.js` for documentation switcher
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- [ ] Update citation information https://github.com/GenericMappingTools/pygmt#citing-pygmt
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- [ ] Add the documentation link https://github.com/GenericMappingTools/pygmt#documentation-for-other-versions
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- [ ] Add compatibility information https://github.com/GenericMappingTools/pygmt#compatibility-with-python-and-gmt-versions
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- [ ] Copy draft changelog from Release Drafter and edit it to look nice
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**Release**:
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- [ ] Go to [GitHub Release](https://github.com/GenericMappingTools/pygmt/releases) and make a release, this will automatically create a tag too
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- [ ] Manually upload the pygmt-vX.Y.Z.zip file to https://zenodo.org/deposit, make sure you file it under the correct reserved DOI
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- [ ] At the [PyGMT release page on GitHub](https://github.com/GenericMappingTools/pygmt/releases):
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- [ ] Edit the draft release notes with the finalized changelog
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- [ ] Set the tag version and release title to vX.Y.Z
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- [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too
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- [ ] Manually upload the pygmt-vX.Y.Z.zip file to https://zenodo.org/deposit, ensure that it is filed under the correct reserved DOI
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**After release**:
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- [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) [Usually done automatically by conda-forge's bot]

‎.github/release-drafter.yml

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name-template: 'v$NEXT_PATCH_VERSION'
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tag-template: 'v$NEXT_PATCH_VERSION'
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name-template: 'v$RESOLVED_VERSION'
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tag-template: 'v$RESOLVED_VERSION'
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version-resolver:
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minor:
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labels:
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- 'feature'
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default: patch
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categories:
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- title: 'New Features'
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label: 'feature'

‎.github/workflows/publish-to-pypi.yml

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- name: Build source and wheel distributions
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run: |
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python setup.py sdist bdist_wheel
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make package
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echo ""
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echo "Generated files:"
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ls -lh dist/

‎AUTHORS.md

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(alphabetical by name) and are considered to be "PyGMT Developers":
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* [Dongdong Tian](https://seisman.info/) | [0000-0001-7967-1197](https://orcid.org/0000-0001-7967-1197) | Michigan State University
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* [Jiayuan Yao](https://github.com/core-man) | [0000-0001-7036-4238](https://orcid.org/0000-0001-7036-4238) | Nanyang Technological University
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* [Leonardo Uieda](http://www.leouieda.com/) | [0000-0001-6123-9515](https://orcid.org/0000-0001-6123-9515) | University of Liverpool
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* [Liam Toney](https://liam.earth/) | [0000-0003-0167-9433](https://orcid.org/0000-0003-0167-9433) | University of Alaska Fairbanks
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* [Malte Ziebarth](https://github.com/mjziebarth) | [0000-0002-5190-4478](https://orcid.org/0000-0002-5190-4478) | GFZ German Research Centre for Geosciences

‎MAINTENANCE.md

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If you want to make a contribution to the project, see the
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[Contributing Guide](CONTRIBUTING.md) instead.
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## Onboarding Access Checklist
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- [ ] Added to [python-maintainers](https://github.com/orgs/GenericMappingTools/teams/python-maintainers) team in the [GenericMappingTools](https://github.com/orgs/GenericMappingTools/teams/) organization on GitHub (gives 'maintain' permissions)
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- [ ] Added as moderator on [GMT forum](https://forum.generic-mapping-tools.org) (to see mod-only discussions)
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- [ ] Added as member on the [PyGMT devs Slack channel](https://pygmtdevs.slack.com) (for casual conversations)
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- [ ] Added as maintainer on [PyPI](https://pypi.org/project/pygmt/) and [Test PyPI](https://test.pypi.org/project/pygmt) [optional]
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- [ ] Added as member on [HackMD](https://hackmd.io/@pygmt) [optional]
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## Branches
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### GitHub Actions
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There are 5 configuration files located in `.github/workflows`:
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There are 8 configuration files located in `.github/workflows`:
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1. `style_checks.yaml` (Code lint and style checks)
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This is ran on every commit to the *master* and Pull Request branches.
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It is also scheduled to run daily on the *master* branch.
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This is run on every commit to the *master* and Pull Request branches.
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It is also scheduled to run daily on the *master* branch.
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2. `ci_tests.yaml` (Tests on Linux/macOS/Windows)
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This is ran on every commit to the *master* and Pull Request branches.
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It is also scheduled to run daily on the *master* branch.
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In draft Pull Requests, only one job (Ubuntu + Python latest)
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is triggered to save on Continuous Integration resources.
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This is run on every commit to the *master* and Pull Request branches.
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It is also scheduled to run daily on the *master* branch.
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In draft Pull Requests, only one job (Ubuntu + Python latest)
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is triggered to save on Continuous Integration resources.
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On the *master* branch, the workflow also handles the documentation deployment:
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On the *master* branch, the workflow also handles the documentation
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deployment:
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* Updating the development documentation by pushing the built HTML pages from the
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*master* branch onto the `dev` folder of the *gh-pages* branch.
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* Updated the `latest` documentation link to the new release.
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* Updating the development documentation by pushing the built HTML pages
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from the *master* branch onto the `dev` folder of the *gh-pages* branch.
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* Updating the `latest` documentation link to the new release.
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3. `ci_tests_dev.yaml` (GMT Dev Tests on Linux/macOS/Windows).
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This is triggered when a PR is marked as "ready for review", or using the slash
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command `/test-gmt-dev`. It is also scheduled to run daily on the *master* branch.
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This is triggered when a PR is marked as "ready for review", or using the
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slash command `/test-gmt-dev`. It is also scheduled to run daily on the
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*master* branch.
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4. `cache_data.yaml` (Caches GMT remote data files needed for GitHub Actions CI)
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This is scheduled to run every Sunday at 12 noon.
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If new remote files are needed urgently, maintainers can manually uncomment
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the 'pull_request:' line in that `cache_data.yaml` file to refresh the cache.
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This is scheduled to run every Sunday at 12:00 (UTC).
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If new remote files are needed urgently, maintainers can manually uncomment
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the 'pull_request:' line in that `cache_data.yaml` file to refresh the cache.
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5. `publish-to-pypi.yml` (Publish wheels to PyPI and TestPyPI)
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This workflow is ran to publish wheels to PyPI and TestPyPI (for testing only).
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Archives will be pushed to TestPyPI on every commit to the *master* branch and
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tagged releases, and to PyPI for tagged releases only.
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This workflow is run to publish wheels to PyPI and TestPyPI (for testing only).
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Archives will be pushed to TestPyPI on every commit to the *master* branch
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and tagged releases, and to PyPI for tagged releases only.
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6. `release-drafter.yml` (Drafts the next release notes)
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This workflow is run to update the next releases notes as pull requests are
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merged into master.
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7. `check-links.yml` (Check links in the repository and website)
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This workflow is run weekly to check all external links in plaintext and
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HTML files. It will create an issue if broken links are found.
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8. `format-command.yml` (Format the codes using slash command)
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This workflow is triggered in a PR if the slash command `/format` is used.
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## Continuous Documentation
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The drafted release notes are not perfect, so we will need to tidy it prior to
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publishing the actual release notes at https://www.pygmt.org/latest/changes.html.
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1. Generate a list of commits between the last release tag and now:
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1. Go to https://github.com/GenericMappingTools/pygmt/releases and click on the
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'Edit' button next to the current draft release note. Copy the text of the
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automatically drafted release notes under the 'Write' tab to
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`doc/changes.md`. Add a section separator `---` between the new and old
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changelog sections.
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2. Update the DOI badge in the changelog. Remember to replace the DOI number
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inside the badge url.
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```bash
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git log HEAD...v0.1.2 --pretty="* %s" > changes.txt
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```
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2. Edit the changes list to remove any trivial changes (updates to the README, typo
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fixes, CI configuration, etc).
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3. Replace the PR number in the commit titles with a link to the GitHub PR page.
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Use ``sed -i.bak -E 's$\(#([0-9]*)\)$(`#\1 <https://github.com/GenericMappingTools/pygmt/pull/\1>`__)$g' changes.rst``
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to make the change automatically.
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4. Copy the remaining changes to `doc/changes.rst` under a new section for the
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intended release.
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5. Add a list of people who contributed to the release (use
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`` git shortlog HEAD...v0.1.2 -sne ``).
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6. Include the DOI badge in the changelog. Remember to replace your DOI inside the badge url.
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[![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>)
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```
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.. image:: https://zenodo.org/badge/DOI/<INSERT-DOI-HERE>.svg
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:alt: Digital Object Identifier for the Zenodo archive
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:target: https://doi.org/<INSERT-DOI-HERE>
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```
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7. Add a link to the new release version documentation in `README.rst`.
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8. Open a new PR with the updated changelog.
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3. Open a new Pull Request using the title 'Changelog entry for vX.Y.Z' with
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the updated release notes, so that other people can help to review and
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collaborate on the changelog curation process described next.
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4. Edit the change list to remove any trivial changes (updates to the README,
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typo fixes, CI configuration, etc).
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5. Edit the list of people who contributed to the release, linking to their
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GitHub account. Sort their names by the number of commits made since the
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last release (e.g. use `` git shortlog HEAD...v0.1.2 -sne ``).
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6. Update `README.rst` with new information on the new release version, namely
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the BibTeX citation, a vX.Y.Z documentation link, and compatibility with
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Python and GMT versions.
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### Check the README syntax
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‎Makefile

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@echo "Commands:"
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@echo ""
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@echo " install install in editable mode"
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@echo " package build source and wheel distributions"
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@echo " test run the test suite (including doctests) and report coverage"
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@echo " format run black, blackdoc, docformatter and isort to automatically format the code"
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@echo " check run code style and quality checks (black, blackdoc, docformatter, flake8 and isort)"
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install:
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pip install --no-deps -e .
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package:
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python setup.py sdist bdist_wheel
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test:
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# Run a tmp folder to make sure the tests are run on the installed version
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mkdir -p $(TESTDIR)
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find . -name "*.pyc" -exec rm -v {} +
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find . -name "*~" -exec rm -v {} +
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find . -type d -name "__pycache__" -exec rm -rv {} +
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rm -rvf build dist MANIFEST .coverage .cache .pytest_cache htmlcov coverage.xml
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rm -rvf build dist .eggs MANIFEST .coverage .cache .pytest_cache htmlcov coverage.xml
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rm -rvf $(TESTDIR)
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rm -rvf baseline
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rm -rvf results
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distclean: clean
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rm -rvf *.egg-info

‎README.rst

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:target: https://pypi.python.org/pypi/pygmt
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.. image:: https://github.com/GenericMappingTools/pygmt/workflows/Tests/badge.svg
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:alt: GitHub Actions Tests status
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:target: https://github.com/GenericMappingTools/pygmt/actions?query=workflow%3ATests
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:target: https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests.yaml
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.. image:: https://github.com/GenericMappingTools/pygmt/workflows/GMT%20Dev%20Tests/badge.svg
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:alt: GitHub Actions GMT Dev Tests status
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:target: https://github.com/GenericMappingTools/pygmt/actions?query=workflow%3A%22GMT+Latest+Tests%22
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:target: https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests_dev.yaml
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.. image:: https://img.shields.io/codecov/c/github/GenericMappingTools/pygmt/master.svg?style=flat-square
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:alt: Test coverage status
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:target: https://codecov.io/gh/GenericMappingTools/pygmt
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* Build a Pythonic API for GMT.
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* Interface with the GMT C API directly using ctypes (no system calls).
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* Support for rich display in the Jupyter notebook.
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* Integration with the `PyData <https://pydata.org/>`__ ecosystem:
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``numpy.ndarray`` or ``pandas.DataFrame`` for data tables and
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* Integration with the `PyData <https://pydata.org/>`__ ecosystem:
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``numpy.ndarray`` or ``pandas.DataFrame`` for data tables and
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``xarray.DataArray`` for grids.
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‎pygmt/clib/loading.py

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)
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assert libfullpath.exists()
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yield str(libfullpath)
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except (FileNotFoundError, AssertionError): # command not found
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except (FileNotFoundError, AssertionError, sp.CalledProcessError):
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# the 'gmt' executable is not found
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# the gmt library is not found
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# the 'gmt' executable is broken
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pass
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# 3. Search for DLLs in PATH by calling find_library() (Windows only)

‎pygmt/tests/test_datasets.py renamed to ‎pygmt/tests/test_datasets_earth_relief.py

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"""
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Test basic functionality for loading datasets.
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Test basic functionality for loading Earth relief datasets.
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"""
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import numpy as np
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import numpy.testing as npt
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import pytest
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from pygmt.datasets import (
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load_earth_relief,
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load_japan_quakes,
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load_ocean_ridge_points,
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load_sample_bathymetry,
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load_usgs_quakes,
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)
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from pygmt.datasets import load_earth_relief
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from pygmt.exceptions import GMTInvalidInput
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def test_japan_quakes():
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"""
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Check that the dataset loads without errors.
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"""
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data = load_japan_quakes()
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assert data.shape == (115, 7)
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summary = data.describe()
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assert summary.loc["min", "year"] == 1987
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assert summary.loc["max", "year"] == 1988
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assert summary.loc["min", "month"] == 1
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assert summary.loc["max", "month"] == 12
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assert summary.loc["min", "day"] == 1
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assert summary.loc["max", "day"] == 31
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def test_ocean_ridge_points():
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"""
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Check that the @ridge.txt dataset loads without errors.
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"""
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data = load_ocean_ridge_points()
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assert data.shape == (4146, 2)
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summary = data.describe()
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assert summary.loc["min", "longitude"] == -179.9401
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assert summary.loc["max", "longitude"] == 179.935
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assert summary.loc["min", "latitude"] == -65.6182
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assert summary.loc["max", "latitude"] == 86.8
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44-
45-
def test_sample_bathymetry():
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"""
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Check that the @tut_ship.xyz dataset loads without errors.
48-
"""
49-
data = load_sample_bathymetry()
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assert data.shape == (82970, 3)
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summary = data.describe()
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assert summary.loc["min", "longitude"] == 245.0
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assert summary.loc["max", "longitude"] == 254.705
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assert summary.loc["min", "latitude"] == 20.0
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assert summary.loc["max", "latitude"] == 29.99131
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assert summary.loc["min", "bathymetry"] == -7708.0
57-
assert summary.loc["max", "bathymetry"] == -9.0
58-
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60-
def test_usgs_quakes():
61-
"""
62-
Check that the dataset loads without errors.
63-
"""
64-
data = load_usgs_quakes()
65-
assert data.shape == (1197, 22)
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6811
def test_earth_relief_fails():
6912
"""
7013
Make sure earth relief fails for invalid resolutions.

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