Merge branch 'main' into code-pygmt-logo

Author: yvonnefroehlich

.github/workflows/benchmarks.yml

@@ -84,8 +84,9 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@76578c2a7ddd928664caa737f0e962e3085d4e7c # v3.8.1
+        uses: CodSpeedHQ/action@6eeb021fd0f305388292348b775d96d95253adf4 # v4.0.0
         with:
+          mode: "instrumentation"
           # 'bash -el -c' is needed to use the custom shell.
           # See https://github.com/CodSpeedHQ/action/issues/65.
           run: bash -el -c "python -c \"import pygmt; pygmt.show_versions()\"; PYGMT_USE_EXTERNAL_DISPLAY=false python -m pytest -r P --pyargs pygmt --codspeed --override-ini addopts='--verbose'"

.github/workflows/check-links.yml

@@ -40,7 +40,7 @@ jobs:
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@5c4ee84814c983aa7164eaee476f014e53ff3963 # v2.5.0
+      uses: lycheeverse/lychee-action@885c65f3dc543b57c898c8099f4e08c8afd178a2 # v2.6.1
       with:
         fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md

.github/workflows/ci_tests.yaml

@@ -73,8 +73,8 @@ jobs:
           # Python 3.11 + core packages (minimum supported versions) + optional packages (minimum supported versions if any)
           - python-version: '3.11'
             numpy-version: '1.26'
-            pandas-version: '=2.1'
-            xarray-version: '=2023.07'
+            pandas-version: '=2.2'
+            xarray-version: '=2023.10'
             optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray netCDF4 sphinx-gallery'
           # Python 3.13 + core packages (latest versions) + optional packages
           - python-version: '3.13'
@@ -151,7 +151,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@557e51de59eb14aaaba2ed9621916900a91d50c6 # v6.6.1
+        uses: astral-sh/setup-uv@b75a909f75acd358c2196fb9a5f1299a9a8868a4 # v6.7.0
         with:
           activate-environment: true
           python-version: ${{ matrix.python-version }}
@@ -163,7 +163,11 @@ jobs:
 
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
-        run: uv run dvc pull --no-run-cache --verbose && ls -lhR pygmt/tests/baseline/
+        run: |
+          uv run dvc remote modify upstream url https://${DAGSHUB_TOKEN}@dagshub.com/GenericMappingTools/pygmt.dvc --local
+          uv run dvc pull --no-run-cache --verbose && ls -lhR pygmt/tests/baseline/
+        env:
+          DAGSHUB_TOKEN: ${{ secrets.DAGSHUB_TOKEN }}
 
       # Install the package that we want to test
       - name: Install the package
@@ -183,7 +187,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@fdcc8476540edceab3de004e990f80d881c6cc00 # v5.5.0
+        uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5.5.1
         if: success() || failure()
         with:
           use_oidc: true

.github/workflows/ci_tests_dev.yaml

@@ -38,7 +38,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-24.04, ubuntu-24.04-arm, macos-15, windows-2025]
+        os: [ubuntu-24.04, ubuntu-24.04-arm, macos-26, windows-2025]
         gmt_git_ref: [master]
     timeout-minutes: 30
     defaults:
@@ -161,7 +161,11 @@ jobs:
 
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
-        run: dvc pull --no-run-cache --verbose && ls -lhR pygmt/tests/baseline/
+        run: |
+          dvc remote modify upstream url https://${DAGSHUB_TOKEN}@dagshub.com/GenericMappingTools/pygmt.dvc --local
+          dvc pull --no-run-cache --verbose && ls -lhR pygmt/tests/baseline/
+        env:
+          DAGSHUB_TOKEN: ${{ secrets.DAGSHUB_TOKEN }}
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub

.github/workflows/ci_tests_legacy.yaml

@@ -62,8 +62,8 @@ jobs:
             gmt=${{ matrix.gmt_version }}
             ghostscript<10
             numpy=1.26
-            pandas
-            xarray
+            pandas=2.2
+            xarray=2023.10
             packaging=24.2
             contextily=1.5
             geopandas=1.0

.github/workflows/dvc-diff.yml

@@ -14,7 +14,9 @@ on:
     paths:
       - 'pygmt/tests/baseline/*.png.dvc'
 
-permissions: {}
+permissions:
+  contents: read
+  pull-requests: write
 
 jobs:
   dvc-diff:
@@ -55,12 +57,16 @@ jobs:
     # Report last updated at commit abcdef
     - name: Generate the image diff report
       env:
-        repo_token: ${{ github.token }}
+        REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
+        DAGSHUB_TOKEN: ${{ secrets.DAGSHUB_TOKEN }}
       run: |
         echo -e "## Summary of changed images\n" > report.md
         echo -e "This is an auto-generated report of images that have changed on the DVC remote\n" >> report.md
 
+        # Configure DVC to use the DAGsHub remote via a token
+        dvc remote modify upstream url https://${DAGSHUB_TOKEN}@dagshub.com/GenericMappingTools/pygmt.dvc --local
+
         # Pull image data from cloud storage
         dvc pull --remote upstream
         dvc diff --md main HEAD >> report.md

.github/workflows/format-command.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Generate token from GenericMappingTools bot
-      - uses: actions/create-github-app-token@v2.1.1
+      - uses: actions/create-github-app-token@v2.1.4
         id: generate-token
         with:
           app-id: ${{ secrets.APP_ID }}
@@ -31,14 +31,14 @@ jobs:
           persist-credentials: false
 
       # Setup Python environment
-      - uses: actions/setup-python@v5.6.0
+      - uses: actions/setup-python@v6.0.0
         with:
           python-version: '3.13'
 
       # Install formatting tools
       - name: Install formatting tools
         run: |
-          python -m pip install ruff pre-commit
+          python -m pip install ruff prek
           python -m pip list
 
       # Run "make format" and commit the change to the PR branch

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

@@ -50,7 +50,7 @@ jobs:
         persist-credentials: false
 
     - name: Set up Python
-      uses: actions/setup-python@v5.6.0
+      uses: actions/setup-python@v6.0.0
       with:
         python-version: '3.13'
 
@@ -99,7 +99,7 @@ jobs:
         path: dist/
 
     - name: Publish distribution 📦 to TestPyPI
-      uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4
+      uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0
       with:
         repository-url: https://test.pypi.org/legacy/
 
@@ -123,4 +123,4 @@ jobs:
         path: dist/
 
     - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4
+      uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0

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

@@ -31,7 +31,11 @@ jobs:
       uses: iterative/setup-dvc@175771be1dc3d119268e00a896b52a4b77decb5e # v1.2.0
 
     - name: Pull baseline image data from dvc remote
-      run: dvc pull && ls -lhR pygmt/tests/baseline/
+      run: |
+        dvc remote modify upstream url https://${DAGSHUB_TOKEN}@dagshub.com/GenericMappingTools/pygmt.dvc --local
+        dvc pull && ls -lhR pygmt/tests/baseline/
+      env:
+        DAGSHUB_TOKEN: ${{ secrets.DAGSHUB_TOKEN }}
 
     - name: Create the baseline image asset in zip format
       run: |

.github/workflows/style_checks.yaml

@@ -32,19 +32,19 @@ jobs:
 
       # Setup Python
       - name: Set up Python
-        uses: actions/setup-python@v5.6.0
+        uses: actions/setup-python@v6.0.0
         with:
           python-version: '3.13'
 
       - name: Install packages
         run: |
-          python -m pip install ruff pre-commit
+          python -m pip install ruff prek
           python -m pip list
 
-      - name: Formatting check (ruff + pre-commit)
+      - name: Formatting check (ruff + prek)
         run: |
            make check
-           pre-commit run --all-files
+           prek run --all-files
 
       - name: Ensure example scripts have at least one code block separator
         run: |