Merge branch 'main' into pep621

Author: seisman

.github/workflows/cache_data.yaml

@@ -19,7 +19,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -39,7 +39,7 @@ jobs:
       - name: Install dependencies
         run: |
           mamba install gmt=6.3.0 numpy pandas xarray netCDF4 packaging \
-                        build matplotlib
+                        build
 
       # Install the package that we want to test
       - name: Install the package
@@ -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

@@ -15,12 +15,12 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         ref: gh-pages
         path: documentation
@@ -42,7 +42,8 @@ jobs:
           --exclude "^https://docs.generic-mapping-tools.org/latest/%s$"
           --exclude "^https://docs.generic-mapping-tools.org/latest/%3Cmodule-name%3E.html$"
           --exclude "^https://www.generic-mapping-tools.org/remote-datasets/%s$"
-          --exclude "https://hackmd.io/@pygmt"
+          --exclude "^https://hackmd.io/@pygmt"
+          --exclude "^https://doi.org"
           --verbose
           "repository/**/*.rst"
           "repository/**/*.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/[email protected].0
+        uses: actions/[email protected].1
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -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@v2.19.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -107,7 +107,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         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/[email protected].0
+        uses: actions/[email protected].1
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -105,7 +105,7 @@ 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@v2.19.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -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@v3.1.0
         with:
           file: ./coverage.xml # optional
           env_vars: OS,PYTHON,NUMPY

.github/workflows/ci_tests_dev.yaml

@@ -45,7 +45,7 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         if: github.event_name != 'repository_dispatch'
         with:
           # fecth all history so that setuptools-scm works
@@ -62,7 +62,7 @@ jobs:
 
       # Checkout the pull request branch
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
         if: github.event_name == 'repository_dispatch'
         with:
           token: ${{ steps.generate-token.outputs.token }}
@@ -71,6 +71,15 @@ jobs:
           # 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: ${{ github.event.client_payload.github.payload.comment.id }}
+          body: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
+
       # Install Mambaforge with conda-forge dependencies
       - name: Setup Mambaforge
         uses: conda-incubator/[email protected]
@@ -97,6 +106,19 @@ jobs:
 
       # 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@v2.19.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -155,17 +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@v2
-        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

.github/workflows/dvc-diff.yml

@@ -13,7 +13,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         # fetch all history so that dvc diff works
         fetch-depth: 0

.github/workflows/format-command.yml

@@ -14,14 +14,14 @@ jobs:
           private_key: ${{ secrets.APP_PRIVATE_KEY }}
 
       # Checkout the pull request branch
-      - uses: actions/[email protected].0
+      - uses: actions/[email protected].1
         with:
           token: ${{ steps.generate-token.outputs.token }}
           repository: ${{ github.event.client_payload.pull_request.head.repo.full_name }}
           ref: ${{ github.event.client_payload.pull_request.head.ref }}
 
       # Setup Python environment
-      - uses: actions/setup-python@v3.0.0
+      - uses: actions/setup-python@v3.1.2
 
       # Install formatting tools
       - name: Install formatting tools

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

@@ -23,13 +23,13 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         # fetch all history so that setuptools-scm works
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/setup-python@v3.0.0
+      uses: actions/setup-python@v3.1.2
       with:
         python-version: '3.10'
 

.github/workflows/release-baseline-images.yml

@@ -16,7 +16,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
 
     - name: Setup data version control (DVC)
       uses: iterative/[email protected]
@@ -34,7 +34,7 @@ jobs:
         shasum -a 256 baseline-images.zip
 
     - name: Upload baseline image as a release asset
-      uses: shogo82148/[email protected].0
+      uses: shogo82148/[email protected].2
       with:
         upload_url: ${{ github.event.release.upload_url }}
         asset_path: baseline-images.zip

.github/workflows/style_checks.yaml

@@ -16,11 +16,11 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].0
+        uses: actions/[email protected].1
 
       # Setup Miniconda
       - name: Set up Python
-        uses: actions/setup-python@v3.0.0
+        uses: actions/setup-python@v3.1.2
         with:
           python-version: '3.10'