Merge branch 'main' into wrap-clip

Author: Max Jones

.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)
 ---

.github/workflows/cache_data.yaml

@@ -19,7 +19,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.4.0
+        uses: actions/checkout@v3.0.2
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -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: |

.github/workflows/check-links.yml

@@ -15,18 +15,18 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/checkout@v2.4.0
+      uses: actions/checkout@v3.0.2
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/checkout@v2.4.0
+      uses: actions/checkout@v3.0.2
       with:
         ref: gh-pages
         path: documentation
 
     - name: Link Checker
-      uses: lycheeverse/lychee-action@v1.3.1
+      uses: lycheeverse/lychee-action@v1.5.0
       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

.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
@@ -49,7 +49,7 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.4.0
+        uses: actions/checkout@v3.0.2
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -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
@@ -80,7 +80,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.17.0
+        uses: dawidd6/action-download-artifact@v2.20.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -99,15 +99,15 @@ 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
       - name: Build the documentation
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/checkout@v2.4.0
+        uses: actions/checkout@v3.0.2
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

.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
@@ -72,7 +72,7 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.4.0
+        uses: actions/checkout@v3.0.2
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -96,16 +96,16 @@ 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
         run: mamba list
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.17.0
+        uses: dawidd6/action-download-artifact@v2.20.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -130,24 +130,30 @@ 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
-      - name: Test with pytest
+      # Run the regular tests
+      - name: Run tests
+        if: github.event.schedule != '0 0 * * 3'
         run: make test PYTEST_EXTRA="-r P"
 
+      # Run full tests including doctests on Wednesday
+      - name: Run full tests
+        if: github.event_name == 'schedule' && github.event.schedule == '0 0 * * 3'
+        run: make fulltest PYTEST_EXTRA="-r P"
+
       # 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@v3.1.0
         with:
           file: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY

.github/workflows/ci_tests_dev.yaml

@@ -17,9 +17,9 @@ on:
       - '.gitignore'
   repository_dispatch:
     types: [test-gmt-dev-command]
-  # Schedule daily tests
+  # Schedule tests on Monday/Wednesday/Friday
   schedule:
-    - cron: '0 0 * * *'
+    - cron: '0 0 * * 1,3,5'
 
 jobs:
   test_gmt_dev:
@@ -45,7 +45,7 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.4.0
+        uses: actions/checkout@v3.0.2
         if: github.event_name != 'repository_dispatch'
         with:
           # fecth all history so that setuptools-scm works
@@ -62,15 +62,24 @@ jobs:
 
       # Checkout the pull request branch
       - name: Checkout
-        uses: actions/checkout@v2.4.0
+        uses: actions/checkout@v3.0.2
         if: github.event_name == 'repository_dispatch'
         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/create-or-update-comment@v2.0.0
+        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: ${{ github.event.client_payload.github.payload.comment.id }}
+          body: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
+
       # Install Mambaforge with conda-forge dependencies
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2.1.1
@@ -92,11 +101,24 @@ jobs:
                         geopandas ghostscript libnetcdf hdf5 zlib curl pcre make
           pip install --pre --prefer-binary \
                         numpy pandas xarray netCDF4 packaging \
-                        dvc ipython 'pytest>=6.0' pytest-cov \
-                        pytest-mpl sphinx-gallery tomli
+                        build dvc ipython 'pytest>=6.0' pytest-cov \
+                        pytest-doctestplus pytest-mpl sphinx-gallery tomli
+
+      # Pull baseline image data from dvc remote (DAGsHub)
+      - name: Pull baseline image data from dvc remote
+        if: github.event_name == 'schedule'
+        run: |
+          ORIGINAL_BRANCH=$(git branch --show-current)
+          # Pull down GMT 6.4 baseline images from the gmt-6.4 branch
+          # https://github.com/GenericMappingTools/pygmt/pull/1883
+          git checkout gmt-6.4
+          dvc pull
+          ls -lhR pygmt/tests/baseline/
+          git checkout ${ORIGINAL_BRANCH}
 
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
+        if: github.event_name != 'schedule'
         run: |
           dvc pull
           ls -lhR pygmt/tests/baseline/
@@ -115,7 +137,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.17.0
+        uses: dawidd6/action-download-artifact@v2.20.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -131,11 +153,10 @@ 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 +177,8 @@ 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