Merge branch 'master' into put-vector-text

Author: seisman

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -1,24 +1,35 @@
 ---
 name: PyGMT release checklist
 about: Checklist for a new PyGMT release.
-title: Release PyGMT x.x.x
+title: Release PyGMT vX.Y.Z
 labels: maintenance
 assignees: ''
 
 ---
 
-**Release**: [v0.x.x](https://github.com/GenericMappingTools/pygmt/milestones/0.x.x)
+**Release**: [v0.x.x](https://github.com/GenericMappingTools/pygmt/milestones/?)
 **Scheduled Date**: YYYY/MM/DD
+**Pull request due date**: YYYY/MM/DD
+
+**Priority PRs/issues to complete prior to release**
+- [ ] Wrap X ()
+- [ ] Wrap Y ()
 
 **Before release**:
 - [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
-- [ ] Update Changelog
-- [ ] Add a new entry in `doc/_static/version_switch.js` for documentation switcher
-- [ ] Update citation information https://github.com/GenericMappingTools/pygmt#citing-pygmt
+- [ ] Finish up 'Changelog entry for v0.x.x' Pull Request:
+  - [ ] Add a new entry in `doc/_static/version_switch.js` for documentation switcher
+  - [ ] Update citation information https://github.com/GenericMappingTools/pygmt#citing-pygmt
+  - [ ] Add the documentation link https://github.com/GenericMappingTools/pygmt#documentation-for-other-versions
+  - [ ] Add compatibility information https://github.com/GenericMappingTools/pygmt#compatibility-with-python-and-gmt-versions
+  - [ ] Copy draft changelog from Release Drafter and edit it to look nice
 
 **Release**:
-- [ ] Go to [GitHub Release](https://github.com/GenericMappingTools/pygmt/releases) and make a release, this will automatically create a tag too
-- [ ] Manually upload the pygmt-vX.Y.Z.zip file to https://zenodo.org/deposit, make sure you file it under the correct reserved DOI
+- [ ] At the [PyGMT release page on GitHub](https://github.com/GenericMappingTools/pygmt/releases):
+  - [ ] Edit the draft release notes with the finalized changelog
+  - [ ] Set the tag version and release title to vX.Y.Z
+  - [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too
+- [ ] Manually upload the pygmt-vX.Y.Z.zip file to https://zenodo.org/deposit, ensure that it is filed under the correct reserved DOI
 
 **After release**:
 - [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) [Usually done automatically by conda-forge's bot]

.github/release-drafter.yml

@@ -1,5 +1,10 @@
-name-template: 'v$NEXT_PATCH_VERSION'
-tag-template: 'v$NEXT_PATCH_VERSION'
+name-template: 'v$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+version-resolver:
+  minor:
+    labels:
+      - 'feature'
+  default: patch
 categories:
   - title: 'New Features'
     label: 'feature'

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

@@ -47,7 +47,7 @@ jobs:
 
     - name: Build source and wheel distributions
       run: |
-        python setup.py sdist bdist_wheel
+        make package
         echo ""
         echo "Generated files:"
         ls -lh dist/

AUTHORS.md

@@ -9,6 +9,7 @@ The following people have contributed code and/or documentation to the project
 (alphabetical by name) and are considered to be "PyGMT Developers":
 
 * [Dongdong Tian](https://seisman.info/) | [0000-0001-7967-1197](https://orcid.org/0000-0001-7967-1197) | Michigan State University
+* [Jiayuan Yao](https://github.com/core-man) | [0000-0001-7036-4238](https://orcid.org/0000-0001-7036-4238) | Nanyang Technological University
 * [Leonardo Uieda](http://www.leouieda.com/) | [0000-0001-6123-9515](https://orcid.org/0000-0001-6123-9515) | University of Liverpool
 * [Liam Toney](https://liam.earth/) | [0000-0003-0167-9433](https://orcid.org/0000-0003-0167-9433) | University of Alaska Fairbanks
 * [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

@@ -6,6 +6,13 @@ making releases, creating packages, etc.
 If you want to make a contribution to the project, see the
 [Contributing Guide](CONTRIBUTING.md) instead.
 
+## Onboarding Access Checklist
+
+- [ ] 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)
+- [ ] Added as moderator on [GMT forum](https://forum.generic-mapping-tools.org) (to see mod-only discussions)
+- [ ] Added as member on the [PyGMT devs Slack channel](https://pygmtdevs.slack.com) (for casual conversations)
+- [ ] Added as maintainer on [PyPI](https://pypi.org/project/pygmt/) and [Test PyPI](https://test.pypi.org/project/pygmt) [optional]
+- [ ] Added as member on [HackMD](https://hackmd.io/@pygmt) [optional]
 
 ## Branches
 
@@ -47,43 +54,58 @@ conda and the `Makefile` to run the tests and checks.
 
 ### GitHub Actions
 
-There are 5 configuration files located in `.github/workflows`:
+There are 8 configuration files located in `.github/workflows`:
 
 1. `style_checks.yaml` (Code lint and style checks)
 
-This is ran on every commit to the *master* and Pull Request branches.
-It is also scheduled to run daily on the *master* branch.
+   This is run on every commit to the *master* and Pull Request branches.
+   It is also scheduled to run daily on the *master* branch.
 
 2. `ci_tests.yaml` (Tests on Linux/macOS/Windows)
 
-This is ran on every commit to the *master* and Pull Request branches.
-It is also scheduled to run daily on the *master* branch.
-In draft Pull Requests, only one job (Ubuntu + Python latest)
-is triggered to save on Continuous Integration resources.
+   This is run on every commit to the *master* and Pull Request branches.
+   It is also scheduled to run daily on the *master* branch.
+   In draft Pull Requests, only one job (Ubuntu + Python latest)
+   is triggered to save on Continuous Integration resources.
 
-On the *master* branch, the workflow also handles the documentation deployment:
+   On the *master* branch, the workflow also handles the documentation
+   deployment:
 
-* Updating the development documentation by pushing the built HTML pages from the
-  *master* branch onto the `dev` folder of the *gh-pages* branch.
-* Updated the `latest` documentation link to the new release.
+   * Updating the development documentation by pushing the built HTML pages
+     from the *master* branch onto the `dev` folder of the *gh-pages* branch.
+   * Updating the `latest` documentation link to the new release.
 
 3. `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 *master* branch.
+   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
+   *master* branch.
 
 4. `cache_data.yaml` (Caches GMT remote data files needed for GitHub Actions CI)
 
-This is scheduled to run every Sunday at 12 noon.
-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.
+   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.
 
 5. `publish-to-pypi.yml` (Publish wheels to PyPI and TestPyPI)
 
-This workflow is ran to publish wheels to PyPI and TestPyPI (for testing only).
-Archives will be pushed to TestPyPI on every commit to the *master* branch and
-tagged releases, and to PyPI for tagged releases only.
+   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 *master* branch
+   and tagged releases, and to PyPI for tagged releases only.
+
+6. `release-drafter.yml` (Drafts the next release notes)
+
+    This workflow is run to update the next releases notes as pull requests are
+    merged into master.
+
+7. `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.
 
+8. `format-command.yml` (Format the codes using slash command)
+
+   This workflow is triggered in a PR if the slash command `/format` is used.
 
 ## Continuous Documentation
 
@@ -116,31 +138,28 @@ 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. Generate a list of commits between the last release tag and now:
+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.
 
-    ```bash
-    git log HEAD...v0.1.2 --pretty="* %s" > changes.txt
     ```
-
-2. Edit the changes list to remove any trivial changes (updates to the README, typo
-   fixes, CI configuration, etc).
-3. Replace the PR number in the commit titles with a link to the GitHub PR page.
-   Use ``sed -i.bak -E 's$\(#([0-9]*)\)$(`#\1 <https://github.com/GenericMappingTools/pygmt/pull/\1>`__)$g' changes.rst``
-   to make the change automatically.
-4. Copy the remaining changes to `doc/changes.rst` under a new section for the
-   intended release.
-5. Add a list of people who contributed to the release (use
-   `` git shortlog HEAD...v0.1.2 -sne ``).
-6. Include the DOI badge in the changelog. Remember to replace your DOI 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>)
     ```
-    .. image:: https://zenodo.org/badge/DOI/<INSERT-DOI-HERE>.svg
-        :alt: Digital Object Identifier for the Zenodo archive
-        :target: https://doi.org/<INSERT-DOI-HERE>
-    ```
-
-7. Add a link to the new release version documentation in `README.rst`.
-8. Open a new PR with the updated changelog.
+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, etc).
+5. 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...v0.1.2 -sne ``).
+6. Update `README.rst` with new information on the new release version, namely
+   the BibTeX citation, a vX.Y.Z documentation link, and compatibility with
+   Python and GMT versions.
 
 ### Check the README syntax
 

Makefile

@@ -15,6 +15,7 @@ help:
 	@echo "Commands:"
 	@echo ""
 	@echo "  install   install in editable mode"
+	@echo "  package   build source and wheel distributions"
 	@echo "  test      run the test suite (including doctests) and report coverage"
 	@echo "  format    run black, blackdoc, docformatter and isort to automatically format the code"
 	@echo "  check     run code style and quality checks (black, blackdoc, docformatter, flake8 and isort)"
@@ -26,6 +27,9 @@ help:
 install:
 	pip install --no-deps -e .
 
+package:
+	python setup.py sdist bdist_wheel
+
 test:
 	# Run a tmp folder to make sure the tests are run on the installed version
 	mkdir -p $(TESTDIR)
@@ -57,10 +61,11 @@ clean:
 	find . -name "*.pyc" -exec rm -v {} +
 	find . -name "*~" -exec rm -v {} +
 	find . -type d -name  "__pycache__" -exec rm -rv {} +
-	rm -rvf build dist MANIFEST .coverage .cache .pytest_cache htmlcov coverage.xml
+	rm -rvf build dist .eggs MANIFEST .coverage .cache .pytest_cache htmlcov coverage.xml
 	rm -rvf $(TESTDIR)
 	rm -rvf baseline
 	rm -rvf result_images
+	rm -rvf results
 
 distclean: clean
 	rm -rvf *.egg-info

README.rst

@@ -12,10 +12,10 @@ PyGMT
     :target: https://pypi.python.org/pypi/pygmt
 .. image:: https://github.com/GenericMappingTools/pygmt/workflows/Tests/badge.svg
     :alt: GitHub Actions Tests status
-    :target: https://github.com/GenericMappingTools/pygmt/actions?query=workflow%3ATests
+    :target: https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests.yaml
 .. image:: https://github.com/GenericMappingTools/pygmt/workflows/GMT%20Dev%20Tests/badge.svg
     :alt: GitHub Actions GMT Dev Tests status
-    :target: https://github.com/GenericMappingTools/pygmt/actions?query=workflow%3A%22GMT+Latest+Tests%22
+    :target: https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests_dev.yaml
 .. image:: https://img.shields.io/codecov/c/github/GenericMappingTools/pygmt/master.svg?style=flat-square
     :alt: Test coverage status
     :target: https://codecov.io/gh/GenericMappingTools/pygmt
@@ -86,8 +86,8 @@ Project goals
 * Build a Pythonic API for GMT.
 * Interface with the GMT C API directly using ctypes (no system calls).
 * Support for rich display in the Jupyter notebook.
-* Integration with the `PyData <https://pydata.org/>`__ ecosystem: 
-  ``numpy.ndarray`` or ``pandas.DataFrame`` for data tables and 
+* Integration with the `PyData <https://pydata.org/>`__ ecosystem:
+  ``numpy.ndarray`` or ``pandas.DataFrame`` for data tables and
   ``xarray.DataArray`` for grids.
 
 

pygmt/clib/loading.py

@@ -116,7 +116,10 @@ def clib_full_names(env=None):
         )
         assert libfullpath.exists()
         yield str(libfullpath)
-    except (FileNotFoundError, AssertionError):  # command not found
+    except (FileNotFoundError, AssertionError, sp.CalledProcessError):
+        # the 'gmt' executable  is not found
+        # the gmt library is not found
+        # the 'gmt' executable is broken
         pass
 
     # 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

@@ -1,70 +1,13 @@
 """
-Test basic functionality for loading datasets.
+Test basic functionality for loading Earth relief datasets.
 """
 import numpy as np
 import numpy.testing as npt
 import pytest
-from pygmt.datasets import (
-    load_earth_relief,
-    load_japan_quakes,
-    load_ocean_ridge_points,
-    load_sample_bathymetry,
-    load_usgs_quakes,
-)
+from pygmt.datasets import load_earth_relief
 from pygmt.exceptions import GMTInvalidInput
 
 
-def test_japan_quakes():
-    """
-    Check that the dataset loads without errors.
-    """
-    data = load_japan_quakes()
-    assert data.shape == (115, 7)
-    summary = data.describe()
-    assert summary.loc["min", "year"] == 1987
-    assert summary.loc["max", "year"] == 1988
-    assert summary.loc["min", "month"] == 1
-    assert summary.loc["max", "month"] == 12
-    assert summary.loc["min", "day"] == 1
-    assert summary.loc["max", "day"] == 31
-
-
-def test_ocean_ridge_points():
-    """
-    Check that the @ridge.txt dataset loads without errors.
-    """
-    data = load_ocean_ridge_points()
-    assert data.shape == (4146, 2)
-    summary = data.describe()
-    assert summary.loc["min", "longitude"] == -179.9401
-    assert summary.loc["max", "longitude"] == 179.935
-    assert summary.loc["min", "latitude"] == -65.6182
-    assert summary.loc["max", "latitude"] == 86.8
-
-
-def test_sample_bathymetry():
-    """
-    Check that the @tut_ship.xyz dataset loads without errors.
-    """
-    data = load_sample_bathymetry()
-    assert data.shape == (82970, 3)
-    summary = data.describe()
-    assert summary.loc["min", "longitude"] == 245.0
-    assert summary.loc["max", "longitude"] == 254.705
-    assert summary.loc["min", "latitude"] == 20.0
-    assert summary.loc["max", "latitude"] == 29.99131
-    assert summary.loc["min", "bathymetry"] == -7708.0
-    assert summary.loc["max", "bathymetry"] == -9.0
-
-
-def test_usgs_quakes():
-    """
-    Check that the dataset loads without errors.
-    """
-    data = load_usgs_quakes()
-    assert data.shape == (1197, 22)
-
-
 def test_earth_relief_fails():
     """
     Make sure earth relief fails for invalid resolutions.