Merge branch 'main' into paragraph/wysiwyg

Author: seisman

.github/release-drafter.yml

@@ -22,6 +22,8 @@ exclude-labels:
   - 'skip-changelog'
 exclude-contributors:
   - 'actions-bot'
+  - 'Copilot'
+  - 'copilot-swe-agent[bot]'
   - 'dependabot'
   - 'dependabot[bot]'
 category-template: '### $TITLE'

.github/workflows/benchmarks.yml

@@ -84,7 +84,7 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@d872884a306dd4853acf0f584f4b706cf0cc72a2 # v4.13.0
+        uses: CodSpeedHQ/action@3194d9a39c4d46684cb44bf7207fc56626aad8fd # v4.15.1
         with:
           mode: "instrumentation"
           # 'bash -el -c' is needed to use the custom shell.

.github/workflows/cache_data.yaml

@@ -27,10 +27,14 @@ on:
 
 permissions: {}
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   gmt_cache:
     name: Cache GMT artifacts
-    runs-on: macos-slim
+    runs-on: ubuntu-slim
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/ci_docs.yml

@@ -93,7 +93,7 @@ jobs:
           create-args: >-
             python=3.14
             gmt=6.6.0
-            ghostscript=10.07.0
+            ghostscript=10.07.1
             numpy
             pandas
             xarray
@@ -116,7 +116,7 @@ jobs:
             sphinx_rtd_theme
             cairosvg
             sphinxcontrib-svg2pdfconverter
-            tectonic
+            tectonic=0.15
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub

.github/workflows/ci_tests.yaml

@@ -75,9 +75,9 @@ jobs:
         include:
           # Python 3.12 + core packages (minimum supported versions) + optional packages (minimum supported versions if any)
           - python-version: '3.12'
-            numpy-version: '2.0'
-            pandas-version: '=2.2'
-            xarray-version: '=2024.5'
+            numpy-version: '2.1'
+            pandas-version: '=2.3'
+            xarray-version: '=2024.7'
             optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray netCDF4 sphinx-gallery'
           # Python 3.14 + core packages (latest versions) + optional packages
           - python-version: '3.14'
@@ -128,7 +128,7 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}${{ matrix.optional-packages }}
             gmt=6.6.0
-            ghostscript=10.07.0
+            ghostscript=10.07.1
             numpy=${{ matrix.numpy-version }}
             pandas${{ matrix.pandas-version }}
             xarray${{ matrix.xarray-version }}
@@ -154,7 +154,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57 # v8.0.0
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
         with:
           activate-environment: true
           python-version: ${{ matrix.python-version }}

.github/workflows/ci_tests_dev.yaml

@@ -74,7 +74,7 @@ jobs:
             ninja
             curl
             fftw
-            ghostscript=10.07.0
+            ghostscript=10.07.1
             glib
             hdf5
             libblas

.github/workflows/ci_tests_legacy.yaml

@@ -61,9 +61,9 @@ jobs:
             python=3.12
             gmt=${{ matrix.gmt_version }}
             ghostscript
-            numpy=2.0
-            pandas=2.2
-            xarray=2024.5
+            numpy=2.1
+            pandas=2.3
+            xarray=2024.7
             packaging=24.2
             contextily=1.5
             geopandas=1.0

.github/workflows/dvc-diff.yml

@@ -37,6 +37,8 @@ jobs:
 
     - name: Setup continuous machine learning (CML)
       uses: iterative/setup-cml@1b5ab8766e715e8f1aab96bbb1f4f2e3e1e8af45 # v3
+      with:
+        vega: false
 
     # Produce the markdown diff report, which should look like:
     # ## Summary of changed images
@@ -59,6 +61,7 @@ jobs:
     - name: Generate the image diff report
       env:
         REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        PR_BASE_REF: ${{ github.event.pull_request.base.ref }}
         PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
         DAGSHUB_TOKEN: ${{ secrets.DAGSHUB_TOKEN }}
       run: |
@@ -70,7 +73,7 @@ jobs:
 
         # Pull image data from cloud storage
         dvc pull --remote upstream
-        dvc diff --md main HEAD >> report.md
+        dvc diff --md "${PR_BASE_REF}" HEAD >> report.md
 
         # Get just the filename of the added and modified image from the report
         awk 'NF==5 && NR>=7 && $2=="added" {print $4}' report.md > added_files.txt
@@ -79,8 +82,8 @@ jobs:
         # Backup new images in the baseline-new directory
         mkdir pygmt/tests/baseline-new
         cp pygmt/tests/baseline/*.png pygmt/tests/baseline-new/
-        # Pull images in the main branch from cloud storage
-        git checkout main
+        # Pull images in the PR base branch from cloud storage
+        git checkout "${PR_BASE_REF}"
         dvc pull --remote upstream --force
 
         # Append each image to the markdown report

.github/workflows/format-command.yml

@@ -18,10 +18,10 @@ jobs:
     runs-on: ubuntu-slim
     steps:
       # Generate token from GenericMappingTools bot
-      - uses: actions/create-github-app-token@f8d387b68d61c58ab83c6c016672934102569859 # v3.0.0
+      - uses: actions/create-github-app-token@bcd2ba49218906704ab6c1aa796996da409d3eb1 # v3.2.0
         id: generate-token
         with:
-          app-id: ${{ secrets.APP_ID }}
+          client-id: ${{ vars.CLIENT_ID }}
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
 
       # Checkout the pull request branch

.github/workflows/release-drafter.yml

@@ -20,6 +20,6 @@ jobs:
     if: github.repository == 'GenericMappingTools/pygmt'
 
     steps:
-      - uses: release-drafter/release-drafter@5de93583980a40bd78603b6dfdcda5b4df377b32 # v7.2.0
+      - uses: release-drafter/release-drafter@563bf132657a13ded0b01fcb723c5a58cdd824e2 # v7.2.1
         with:
           config-name: release-drafter.yml