Merge branch 'main' into update-baseline-images-for-gmt-dev

GenericMappingTools · Apr 14, 2022 · b089189 · b089189
2 parents 6cff4fb + 13ab551
commit b089189
Showing 112 changed files with 2,417 additions and 626 deletions.
diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md
@@ -21,8 +21,12 @@ assignees: ''
 - [ ] 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.cff` and BibTeX at 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-gmt-and-pythonnumpy-versions
+    - [ ] Update authorship list
+    - [ ] Update DOI (and url for BibTeX)
+    - [ ] Update version
+    - [ ] Update date released
+  - [ ] Add the documentation link https://github.com/GenericMappingTools/pygmt#compatibility-with-gmtpythonnumpy-versions
+  - [ ] Add compatibility information https://github.com/GenericMappingTools/pygmt#compatibility-with-gmtpythonnumpy-versions
   - [ ] Copy draft changelog from Release Drafter and edit it to look nice ([see maintainers guide for details](https://www.pygmt.org/dev/maintenance.html#updating-the-changelog))
 
 **Release**:
@@ -33,11 +37,10 @@ assignees: ''
 - [ ] Manually upload the pygmt-vX.Y.Z.zip and baseline-images.zip files 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]
+- [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) [Done automatically by conda-forge's bot, but remember to pin NEP29 versions]
 - [ ] Bump PyGMT version on https://github.com/GenericMappingTools/try-gmt (after conda-forge update)
 - [ ] Announce the release on:
   - [ ] GMT [forum](https://forum.generic-mapping-tools.org/c/news/) (do this announcement first! draft on https://hackmd.io/@pygmt. requires moderator status)
-  - [ ] [Major/Minor releases only] GMT [website](https://github.com/GenericMappingTools/website) (News)
   - [ ] [ResearchGate](https://www.researchgate.net/project/PyGMT-A-Python-interface-for-the-Generic-Mapping-Tools) (after forum announcement)
   - [ ] [Twitter](https://twitter.com/gmt_dev) (after forum announcement)
 ---

diff --git a/.github/workflows/cache_data.yaml b/.github/workflows/cache_data.yaml
@@ -38,13 +38,13 @@ jobs:
       # Install GMT and other required dependencies from conda-forge
       - name: Install dependencies
         run: |
-          mamba install gmt=6.3.0 \
-                        numpy pandas xarray netCDF4 packaging matplotlib
+          mamba install gmt=6.3.0 numpy pandas xarray netCDF4 packaging \
+                        build
 
       # Install the package that we want to test
       - name: Install the package
         run: |
-          python setup.py sdist --formats=zip
+          python -m build --sdist
           pip install dist/*
 
       # Download remote files
@@ -54,7 +54,7 @@ jobs:
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: gmt-cache
           path: |

diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml
@@ -26,7 +26,7 @@ jobs:
         path: documentation
 
     - name: Link Checker
-      uses: lycheeverse/lychee-action@v1.3.2
+      uses: lycheeverse/lychee-action@v1.4.1
       with:
         # 429: Too many requests
         args: >
@@ -41,7 +41,9 @@ jobs:
           --exclude "^file://"
           --exclude "^https://docs.generic-mapping-tools.org/latest/%s$"
           --exclude "^https://docs.generic-mapping-tools.org/latest/%3Cmodule-name%3E.html$"
-          --exclude "https://hackmd.io/@pygmt"
+          --exclude "^https://www.generic-mapping-tools.org/remote-datasets/%s$"
+          --exclude "^https://hackmd.io/@pygmt"
+          --exclude "^https://doi.org"
           --verbose
           "repository/**/*.rst"
           "repository/**/*.md"
@@ -55,7 +57,7 @@ jobs:
       run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
 
     - name: Create Issue From File
-      uses: peter-evans/create-issue-from-file@v3
+      uses: peter-evans/create-issue-from-file@v4
       with:
         title: Link Checker Report on ${{ steps.date.outputs.date }}
         content-filepath: ./lychee/out.md
diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml
@@ -24,12 +24,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
         os: [ubuntu-latest, macOS-latest, windows-latest]
         # Is it a draft Pull Request (true or false)?
         isDraft:
           - ${{ github.event.pull_request.draft }}
-        # Only run one job (Ubuntu + Python 3.9) for draft PRs
+        # Only run one job (Ubuntu + Python 3.10) for draft PRs
         exclude:
           - os: macOS-latest
             isDraft: true
@@ -71,7 +71,7 @@ jobs:
       - name: Install dependencies
         run: |
           mamba install gmt=6.3.0 numpy pandas xarray netCDF4 packaging \
-                        ipython make myst-parser geopandas \
+                        build ipython make myst-parser geopandas \
                         sphinx sphinx-copybutton sphinx-gallery sphinx_rtd_theme
 
       # Show installed pkg information for postmortem diagnostic
@@ -99,7 +99,7 @@ jobs:
       # Install the package that we want to test
       - name: Install the package
         run: |
-          python setup.py sdist --formats=zip
+          python -m build --sdist
           pip install dist/*
 
       # Build the documentation

diff --git a/.github/workflows/ci_tests.yaml b/.github/workflows/ci_tests.yaml
@@ -29,12 +29,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9']
+        python-version: ['3.8', '3.10']
         os: [ubuntu-latest, macOS-latest, windows-latest]
         # Is it a draft Pull Request (true or false)?
         isDraft:
           - ${{ github.event.pull_request.draft }}
-        # Only run one job (Ubuntu + Python 3.9) for draft PRs
+        # Only run one job (Ubuntu + Python 3.10) for draft PRs
         exclude:
           - os: macOS-latest
             isDraft: true
@@ -43,13 +43,13 @@ jobs:
           # - os: ubuntu-latest
           #   python-version: 3.7
           #   isDraft: true
-        # Pair Python 3.8 with NumPy 1.19 and Python 3.9 with NumPy 1.22
-        # Only install optional packages on Python 3.9/NumPy 1.22
+        # Pair Python 3.8 with NumPy 1.19 and Python 3.10 with NumPy 1.22
+        # Only install optional packages on Python 3.10/NumPy 1.22
         include:
           - python-version: '3.8'
             numpy-version: '1.19'
             optional-packages: ''
-          - python-version: '3.9'
+          - python-version: '3.10'
             numpy-version: '1.22'
             optional-packages: 'geopandas ipython'
     timeout-minutes: 30
@@ -96,8 +96,8 @@ jobs:
           mamba install gmt=6.3.0 numpy=${{ matrix.numpy-version }} \
                         pandas xarray netCDF4 packaging \
                         ${{ matrix.optional-packages }} \
-                        dvc make pytest>=6.0 \
-                        pytest-cov pytest-mpl sphinx-gallery tomli
+                        build dvc make pytest>=6.0 \
+                        pytest-cov pytest-doctestplus pytest-mpl sphinx-gallery tomli
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages
@@ -130,7 +130,7 @@ jobs:
       # Install the package that we want to test
       - name: Install the package
         run: |
-          python setup.py sdist --formats=zip
+          python -m build --sdist
           pip install dist/*
 
       # Run the tests
@@ -139,15 +139,15 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         if: ${{ failure() }}
         with:
           name: artifact-${{ runner.os }}-${{ matrix.python-version }}
           path: tmp-test-dir-with-unique-name
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2.1.0
+        uses: codecov/codecov-action@v3.0.0
         with:
           file: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY

diff --git a/.github/workflows/ci_tests_dev.yaml b/.github/workflows/ci_tests_dev.yaml
@@ -67,10 +67,18 @@ jobs:
         with:
           token: ${{ steps.generate-token.outputs.token }}
           repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
-          ref: ${{ github.event.pull_request.head.sha }}
+          ref: ${{ github.event.client_payload.pull_request.head.ref }}
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
 
+      - name: Show job URL
+        uses: peter-evans/[email protected]
+        if: github.event_name == 'repository_dispatch' && (matrix.os == 'ubuntu-latest')
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+          comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
+
       # Install Mambaforge with conda-forge dependencies
       - name: Setup Mambaforge
         uses: conda-incubator/[email protected]
@@ -92,14 +100,18 @@ jobs:
                         geopandas ghostscript libnetcdf hdf5 zlib curl pcre make
           pip install --pre --prefer-binary \
                         numpy pandas xarray netCDF4 packaging \
-                        dvc ipython 'pytest>=6.0' pytest-cov \
-                        pytest-mpl sphinx-gallery tomli
+                        build dvc ipython 'pytest>=6.0' pytest-cov \
+                        pytest-doctestplus pytest-mpl sphinx-gallery tomli
 
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
         run: |
+          ORIGINAL_BRANCH=$(git branch --show-current)
+          # Pull down GMT 6.4 baseline images from the gmt-6.4 branch
+          git checkout gmt-6.4
           dvc pull
           ls -lhR pygmt/tests/baseline/
+          git checkout ${ORIGINAL_BRANCH}
 
       # Build and install latest GMT from GitHub
       - name: Install GMT ${{ matrix.gmt_git_ref }} branch (Linux/macOS)
@@ -131,11 +143,10 @@ jobs:
           touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
           ls -lhR ~/.gmt
 
-
       # Install the package that we want to test
       - name: Install the package
         run: |
-          python setup.py sdist --formats=zip
+          python -m build --sdist
           pip install dist/*
 
       - name: Add GMT's bin to PATH (Linux/macOS)
@@ -156,17 +167,8 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         if: ${{ failure() }}
         with:
           name: artifact-GMT-${{ matrix.gmt_git_ref }}-${{ runner.os }}
           path: tmp-test-dir-with-unique-name
-
-      - name: Add reaction
-        uses: peter-evans/create-or-update-comment@v1
-        if: github.event_name == 'repository_dispatch'
-        with:
-          token: ${{ steps.generate-token.outputs.token }}
-          repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
-          comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
-          reaction-type: hooray
diff --git a/.github/workflows/dvc-diff.yml b/.github/workflows/dvc-diff.yml
@@ -95,7 +95,7 @@ jobs:
         echo ::set-output name=report::$report
 
     - name: Find comment with image diff report
-      uses: peter-evans/find-comment@v1.3.0
+      uses: peter-evans/find-comment@v2.0.0
       id: fc
       with:
         issue-number: ${{ github.event.pull_request.number }}
@@ -104,14 +104,14 @@ jobs:
 
     - name: Create comment with image diff report
       if: steps.fc.outputs.comment-id == ''
-      uses: peter-evans/create-or-update-comment@v1.4.4
+      uses: peter-evans/create-or-update-comment@v2
       with:
         issue-number: ${{ github.event.pull_request.number }}
         body: ${{ steps.image-diff.outputs.report }}
 
     - name: Update comment with new image diff report
       if: steps.fc.outputs.comment-id != ''
-      uses: peter-evans/create-or-update-comment@v1.4.4
+      uses: peter-evans/create-or-update-comment@v2
       with:
         comment-id: ${{ steps.fc.outputs.comment-id }}
         body: ${{ steps.image-diff.outputs.report }}

diff --git a/.github/workflows/format-command.yml b/.github/workflows/format-command.yml
@@ -18,10 +18,10 @@ jobs:
         with:
           token: ${{ steps.generate-token.outputs.token }}
           repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
-          ref: ${{ github.event.pull_request.head.sha }}
+          ref: ${{ github.event.client_payload.pull_request.head.ref }}
 
       # Setup Python environment
-      - uses: actions/setup-python@v2.3.2
+      - uses: actions/setup-python@v3.1.0
 
       # Install formatting tools
       - name: Install formatting tools
@@ -43,7 +43,7 @@ jobs:
           fi
 
       - name: Add reaction
-        uses: peter-evans/create-or-update-comment@v1
+        uses: peter-evans/create-or-update-comment@v2
         with:
           token: ${{ steps.generate-token.outputs.token }}
           repository: ${{ github.event.client_payload.github.payload.repository.full_name }}

diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -29,12 +29,12 @@ jobs:
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/setup-python@v2.3.2
+      uses: actions/setup-python@v3.1.0
       with:
         python-version: '3.10'
 
     - name: Install dependencies
-      run: python -m pip install setuptools wheel
+      run: python -m pip install build
 
     # This step is only necessary for testing purposes and for TestPyPI
     - name: Fix up version string for TestPyPI
@@ -43,7 +43,7 @@ jobs:
         # Change setuptools-scm local_scheme to "no-local-version" so the
         # local part of the version isn't included, making the version string
         # compatible with PyPI.
-        sed --in-place "s/node-and-date/no-local-version/g" setup.py
+        sed --in-place "s/node-and-date/no-local-version/g" pyproject.toml
 
     - name: Build source and wheel distributions
       run: |

diff --git a/.github/workflows/release-baseline-images.yml b/.github/workflows/release-baseline-images.yml
@@ -34,7 +34,7 @@ jobs:
         shasum -a 256 baseline-images.zip
 
     - name: Upload baseline image as a release asset
-      uses: shogo82148/actions-upload-release-asset@v1.5.0
+      uses: shogo82148/actions-upload-release-asset@v1.6.2
       with:
         upload_url: ${{ github.event.release.upload_url }}
         asset_path: baseline-images.zip
diff --git a/.github/workflows/release-drafter.yml b/.github/workflows/release-drafter.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Drafts your next Release notes as Pull Requests are merged into "main"
-      - uses: release-drafter/release-drafter@v5.18.1
+      - uses: release-drafter/release-drafter@v5.19.0
         with:
           # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
           config-name: release-drafter.yml

diff --git a/.github/workflows/slash-command-dispatch.yml b/.github/workflows/slash-command-dispatch.yml
@@ -17,7 +17,7 @@ jobs:
           private_key: ${{ secrets.APP_PRIVATE_KEY }}
 
       - name: Slash Command Dispatch
-        uses: peter-evans/slash-command-dispatch@v2
+        uses: peter-evans/slash-command-dispatch@v3
         with:
           token: ${{ steps.generate-token.outputs.token }}
           commands: |

diff --git a/.github/workflows/style_checks.yaml b/.github/workflows/style_checks.yaml
@@ -20,7 +20,7 @@ jobs:
 
       # Setup Miniconda
       - name: Set up Python
-        uses: actions/setup-python@v2.3.2
+        uses: actions/setup-python@v3.1.0
         with:
           python-version: '3.10'
 

diff --git a/AUTHORS.md b/AUTHORS.md
@@ -9,16 +9,16 @@ The following people have contributed code and/or documentation to the project
 (alphabetical by name) and are considered to be "PyGMT Developers":
 
 * [Abhishek Anant](https://twitter.com/itsabhianant) | [0000-0002-5751-2010](https://orcid.org/0000-0002-5751-2010) | Unaffiliated
-* [Dongdong Tian](https://seisman.info/) | [0000-0001-7967-1197](https://orcid.org/0000-0001-7967-1197) | China University of Geosciences
-* [Jamie Quinn](http://jamiejquinn.com) | [0000-0002-0268-7032](https://orcid.org/0000-0002-0268-7032) | University College London
-* [Jiayuan Yao](https://github.com/core-man) | [0000-0001-7036-4238](https://orcid.org/0000-0001-7036-4238) | Nanyang Technological University
-* [Kathryn Materna](https://github.com/kmaterna) | [0000-0002-6687-980X](https://orcid.org/0000-0002-6687-980X) | US Geological Survey
-* [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
-* [Meghan Jones](https://github.com/meghanrjones) | [0000-0003-0180-8928](https://orcid.org/0000-0003-0180-8928) | University of Hawai'i at Mānoa
-* [Michael Grund](https://github.com/michaelgrund) | [0000-0001-8759-2018](https://orcid.org/0000-0001-8759-2018) | Innoplexia GmbH
-* [Tyler Newton](http://www.tnewton.com/) | [0000-0002-1560-6553](https://orcid.org/0000-0002-1560-6553) | University of Oregon
-* [Wei Ji Leong](https://github.com/weiji14) | [0000-0003-2354-1988](https://orcid.org/0000-0003-2354-1988) | The Ohio State University
+* [Dongdong Tian](https://seisman.info/) | [0000-0001-7967-1197](https://orcid.org/0000-0001-7967-1197) | China University of Geosciences, China
+* [Jamie Quinn](http://jamiejquinn.com) | [0000-0002-0268-7032](https://orcid.org/0000-0002-0268-7032) | University College London, United Kingdom
+* [Jiayuan Yao](https://github.com/core-man) | [0000-0001-7036-4238](https://orcid.org/0000-0001-7036-4238) | Nanyang Technological University, Singapore
+* [Kathryn Materna](https://github.com/kmaterna) | [0000-0002-6687-980X](https://orcid.org/0000-0002-6687-980X) | US Geological Survey, USA
+* [Leonardo Uieda](http://www.leouieda.com/) | [0000-0001-6123-9515](https://orcid.org/0000-0001-6123-9515) | University of Liverpool, United Kingdom
+* [Liam Toney](https://liam.earth/) | [0000-0003-0167-9433](https://orcid.org/0000-0003-0167-9433) | University of Alaska Fairbanks, USA
+* [Malte Ziebarth](https://github.com/mjziebarth) | [0000-0002-5190-4478](https://orcid.org/0000-0002-5190-4478) | GFZ German Research Centre for Geosciences, Germany
+* [Meghan Jones](https://github.com/meghanrjones) | [0000-0003-0180-8928](https://orcid.org/0000-0003-0180-8928) | University of Hawai'i at Mānoa, USA
+* [Michael Grund](https://github.com/michaelgrund) | [0000-0001-8759-2018](https://orcid.org/0000-0001-8759-2018) | Innoplexia GmbH, Germany
+* [Tyler Newton](http://www.tnewton.com/) | [0000-0002-1560-6553](https://orcid.org/0000-0002-1560-6553) | University of Oregon, USA
+* [Wei Ji Leong](https://github.com/weiji14) | [0000-0003-2354-1988](https://orcid.org/0000-0003-2354-1988) | The Ohio State University, USA
 * [William Schlitzer](https://github.com/willschlitzer) | [0000-0002-5843-2282](https://orcid.org/0000-0002-5843-2282) | Unaffiliated
-* [Yohai Magen](https://github.com/yohaimagen) | [0000-0002-4892-4013](https://orcid.org/0000-0002-4892-4013) | Tel Aviv University
+* [Yohai Magen](https://github.com/yohaimagen) | [0000-0002-4892-4013](https://orcid.org/0000-0002-4892-4013) | Tel Aviv University, Israel