Merge branch 'main' into python-3.13

Author: weiji14

.github/workflows/benchmarks.yml

@@ -25,7 +25,7 @@ concurrency:
 
 jobs:
   benchmarks:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     if: github.repository == 'GenericMappingTools/pygmt' && (github.event_name != 'pull_request' || contains(github.event.pull_request.labels.*.name, 'run/benchmark'))
     defaults:
       run:
@@ -34,7 +34,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -88,7 +88,7 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v3.0.1
+        uses: CodSpeedHQ/action@v3.1.0
         with:
           # 'bash -el -c' is needed to use the custom shell.
           # See https://github.com/CodSpeedHQ/action/issues/65.

.github/workflows/cache_data.yaml

@@ -36,7 +36,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -76,7 +76,7 @@ jobs:
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
-        uses: actions/[email protected].0
+        uses: actions/[email protected].3
         with:
           name: gmt-cache
           include-hidden-files: true

.github/workflows/check-links.yml

@@ -23,12 +23,12 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/[email protected].1
+      uses: actions/[email protected].2
       with:
         path: repository
 
     - name: Checkout the documentation
-      uses: actions/[email protected].1
+      uses: actions/[email protected].2
       with:
         ref: gh-pages
         path: documentation

.github/workflows/ci_docs.yml

@@ -69,7 +69,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -104,6 +104,7 @@ jobs:
             contextily
             geopandas<1.0
             ipython
+            pyarrow
             rioxarray
             make
             pip
@@ -115,7 +116,7 @@ jobs:
             sphinx-copybutton
             sphinx-design
             sphinx-gallery
-            sphinx_rtd_theme
+            sphinx_rtd_theme<3.0
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -139,7 +140,7 @@ jobs:
         run: make -C doc clean all
 
       - name: Checkout the gh-pages branch
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

.github/workflows/ci_doctests.yaml

@@ -35,7 +35,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

.github/workflows/ci_tests.yaml

@@ -85,9 +85,9 @@ jobs:
           - os: 'ubuntu-latest'
             python-version: '3.11'  # Can't be 3.10 or 3.13.
             numpy-version: '1.24'
-            pandas-version: ''
+            pandas-version: '=2.1'
             xarray-version: ''
-            optional-packages: ' geopandas<1'
+            optional-packages: ' geopandas<1 pyarrow'
 
     timeout-minutes: 30
     defaults:
@@ -103,7 +103,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -171,7 +171,7 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/[email protected].0
+        uses: actions/[email protected].3
         if: failure()
         with:
           name: artifact-${{ runner.os }}-${{ matrix.python-version }}

.github/workflows/ci_tests_dev.yaml

@@ -46,7 +46,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -87,9 +87,17 @@ jobs:
             pcre
             zlib
 
+      # Install the GSHHG and DCW datasets on Linux/macOS to avoid corrupted files
+      # during GMT auto-downloading. Currently, we can't install them on Windows CI,
+      # because the Windows CI fails to compile "gshhg_version.c" due to unknown reasons
+      # (likely missing DLLs).
+      - name: Install GMT GSHHG and DCW datasets (Linux/macOS)
+        run: micromamba install dcw-gmt gshhg-gmt
+        if: runner.os != 'Windows'
+
       # Checkout current GMT repository
       - name: Checkout the GMT source from ${{ matrix.gmt_git_ref }} branch
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           repository: 'GenericMappingTools/gmt'
           ref: ${{ matrix.gmt_git_ref }}
@@ -180,7 +188,7 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/[email protected].0
+        uses: actions/[email protected].3
         if: ${{ failure() }}
         with:
           name: artifact-GMT-${{ matrix.gmt_git_ref }}-${{ runner.os }}

.github/workflows/ci_tests_legacy.yaml

@@ -44,7 +44,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0

.github/workflows/dvc-diff.yml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/[email protected].1
+      uses: actions/[email protected].2
       with:
         # fetch all history so that dvc diff works
         fetch-depth: 0

.github/workflows/format-command.yml

@@ -18,14 +18,14 @@ jobs:
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
 
       # Checkout the pull request branch
-      - uses: actions/[email protected].1
+      - uses: actions/[email protected].2
         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@v5.2.0
+      - uses: actions/setup-python@v5.3.0
         with:
           python-version: '3.13'