Merge branch 'main' into virtualfile_from_data/meca

Author: weiji14

.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@v3.0.0
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -51,8 +51,6 @@ jobs:
       - name: Download remote data
         run: |
           python -c "from pygmt.helpers.testing import download_test_data; download_test_data()"
-        env:
-          GMT_DATA_SERVER: https://oceania.generic-mapping-tools.org/
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub

.github/workflows/check-links.yml

@@ -15,18 +15,18 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/checkout@v2.4.0
+      uses: actions/checkout@v3.0.0
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/checkout@v2.4.0
+      uses: actions/checkout@v3.0.0
       with:
         ref: gh-pages
         path: documentation
 
     - name: Link Checker
-      uses: lycheeverse/lychee-action@v1.2.0
+      uses: lycheeverse/lychee-action@v1.3.2
       with:
         # 429: Too many requests
         args: >

.github/workflows/ci_docs.yml

@@ -13,7 +13,6 @@ on:
       - '*.json'
       - 'LICENSE.txt'
       - '.gitignore'
-      - '.pylintrc'
   release:
     types:
       - published
@@ -50,7 +49,7 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.4.0
+        uses: actions/checkout@v3.0.0
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -81,7 +80,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.16.0
+        uses: dawidd6/action-download-artifact@v2.17.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -108,7 +107,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/checkout@v2.4.0
+        uses: actions/checkout@v3.0.0
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

.github/workflows/ci_tests.yaml

@@ -15,7 +15,6 @@ on:
       - 'README.rst'
       - 'LICENSE.txt'
       - '.gitignore'
-      - '.pylintrc'
   release:
     types:
       - published
@@ -44,14 +43,14 @@ jobs:
           # - os: ubuntu-latest
           #   python-version: 3.7
           #   isDraft: true
-        # Pair Python 3.8 with NumPy 1.19 and Python 3.9 with NumPy 1.21
-        # Only install optional packages on Python 3.9/NumPy 1.21
+        # 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
         include:
           - python-version: '3.8'
             numpy-version: '1.19'
             optional-packages: ''
           - python-version: '3.9'
-            numpy-version: '1.21'
+            numpy-version: '1.22'
             optional-packages: 'geopandas ipython'
     timeout-minutes: 30
     defaults:
@@ -73,7 +72,7 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.4.0
+        uses: actions/checkout@v3.0.0
         with:
           # fecth all history so that setuptools-scm works
           fetch-depth: 0
@@ -106,7 +105,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.16.0
+        uses: dawidd6/action-download-artifact@v2.17.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -125,7 +124,7 @@ jobs:
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
         run: |
-          dvc pull
+          dvc pull --verbose
           ls -lhR pygmt/tests/baseline/
 
       # Install the package that we want to test

.github/workflows/ci_tests_dev.yaml

@@ -15,7 +15,6 @@ on:
       - 'README.rst'
       - 'LICENSE.txt'
       - '.gitignore'
-      - '.pylintrc'
   repository_dispatch:
     types: [test-gmt-dev-command]
   # Schedule daily tests
@@ -46,7 +45,7 @@ jobs:
 
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v2.4.0
+        uses: actions/checkout@v3.0.0
         if: github.event_name != 'repository_dispatch'
         with:
           # fecth all history so that setuptools-scm works
@@ -63,7 +62,7 @@ jobs:
 
       # Checkout the pull request branch
       - name: Checkout
-        uses: actions/checkout@v2.4.0
+        uses: actions/checkout@v3.0.0
         if: github.event_name == 'repository_dispatch'
         with:
           token: ${{ steps.generate-token.outputs.token }}
@@ -96,6 +95,12 @@ jobs:
                         dvc ipython 'pytest>=6.0' pytest-cov \
                         pytest-mpl sphinx-gallery tomli
 
+      # Pull baseline image data from dvc remote (DAGsHub)
+      - name: Pull baseline image data from dvc remote
+        run: |
+          dvc pull
+          ls -lhR pygmt/tests/baseline/
+
       # Build and install latest GMT from GitHub
       - name: Install GMT ${{ matrix.gmt_git_ref }} branch (Linux/macOS)
         run: curl https://raw.githubusercontent.com/GenericMappingTools/gmt/master/ci/build-gmt.sh | bash
@@ -110,7 +115,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.16.0
+        uses: dawidd6/action-download-artifact@v2.17.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success
@@ -126,11 +131,6 @@ jobs:
           touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt
           ls -lhR ~/.gmt
 
-      # Pull baseline image data from dvc remote (DAGsHub)
-      - name: Pull baseline image data from dvc remote
-        run: |
-          dvc pull
-          ls -lhR pygmt/tests/baseline/
 
       # Install the package that we want to test
       - name: Install the package

.github/workflows/dvc-diff.yml

@@ -13,7 +13,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v2.4.0
+      uses: actions/checkout@v3.0.0
       with:
         # fetch all history so that dvc diff works
         fetch-depth: 0
@@ -22,7 +22,7 @@ jobs:
       uses: iterative/setup-dvc@v1.0.3
 
     - name: Setup continuous machine learning (CML)
-      uses: iterative/setup-cml@v1.1.0
+      uses: iterative/setup-cml@v1.1.3
 
     - name: Pull image data from cloud storage
       run: dvc pull --remote upstream

.github/workflows/format-command.yml

@@ -14,14 +14,14 @@ jobs:
           private_key: ${{ secrets.APP_PRIVATE_KEY }}
 
       # Checkout the pull request branch
-      - uses: actions/checkout@v2.4.0
+      - uses: actions/checkout@v3.0.0
         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 }}
 
       # Setup Python environment
-      - uses: actions/setup-python@v2.3.1
+      - uses: actions/setup-python@v2.3.2
 
       # Install formatting tools
       - name: Install formatting tools

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

@@ -23,13 +23,13 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v2.4.0
+      uses: actions/checkout@v3.0.0
       with:
         # fetch all history so that setuptools-scm works
         fetch-depth: 0
 
     - name: Set up Python
-      uses: actions/setup-python@v2.3.1
+      uses: actions/setup-python@v2.3.2
       with:
         python-version: '3.10'
 
@@ -53,13 +53,13 @@ jobs:
         ls -lh dist/
 
     - name: Publish to Test PyPI
-      uses: pypa/gh-action-pypi-publish@v1.4.2
+      uses: pypa/gh-action-pypi-publish@v1.5.0
       with:
         password: ${{ secrets.TEST_PYPI_API_TOKEN }}
         repository_url: https://test.pypi.org/legacy/
 
     - name: Publish to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@v1.4.2
+      uses: pypa/gh-action-pypi-publish@v1.5.0
       with:
         password: ${{ secrets.PYPI_API_TOKEN }}

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

@@ -16,7 +16,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v2.4.0
+      uses: actions/checkout@v3.0.0
 
     - name: Setup data version control (DVC)
       uses: iterative/setup-dvc@v1.0.3
@@ -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@v1.4.0
+      uses: shogo82148/actions-upload-release-asset@v1.5.0
       with:
         upload_url: ${{ github.event.release.upload_url }}
         asset_path: baseline-images.zip

.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@v5.15.0
+      - uses: release-drafter/release-drafter@v5.18.1
         with:
           # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
           config-name: release-drafter.yml