Merge branch 'main' into ci/enable-docs-windows

Author: seisman

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -20,7 +20,7 @@ assignees: ''
 
 **Before release**:
 
-- [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/) to see if we need to bump the minimum supported versions of GMT, Python and core package dependencies (NumPy, pandas, Xarray)
+- [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/) to see if we need to bump the minimum supported versions of GMT, Python and core package dependencies (NumPy, pandas, xarray)
 - [ ] Review the ["PyGMT Team" page](https://www.pygmt.org/dev/team.html)
 - [ ] README looks good on TestPyPI. Visit [TestPyPI](https://test.pypi.org/project/pygmt/#history), click the latest pre-release, and check the homepage.
 - [ ] Review new parameter names added/changed for clarity and consistency across the API

.github/dependabot.yml

@@ -16,3 +16,13 @@ updates:
       - "skip-changelog"
     cooldown:
       default-days: 7
+
+  - package-ecosystem: "pre-commit"
+    directory: "/"
+    schedule:
+      interval: "quarterly"
+    labels:
+      - "maintenance"
+      - "skip-changelog"
+    cooldown:
+      default-days: 7

.github/release-drafter.yml

@@ -22,13 +22,14 @@ exclude-labels:
   - 'skip-changelog'
 exclude-contributors:
   - 'actions-bot'
+  - 'Copilot'
+  - 'copilot-swe-agent[bot]'
   - 'dependabot'
   - 'dependabot[bot]'
-  - 'pre-commit-ci'
-  - 'pre-commit-ci[bot]'
 category-template: '### $TITLE'
 change-template: '* $TITLE ([#$NUMBER]($URL))'
 sort-by: 'title'
+sort-direction: 'ascending'
 replacers:
   - search: '/@(\w+)?/g'
     replace: '[@$1](https://github.com/$1)'

.github/workflows/benchmarks.yml

@@ -36,7 +36,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v6.0.1
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -48,7 +48,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
+        uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476 # v3.0.0
         with:
           environment-name: pygmt
           cache-environment: true
@@ -84,7 +84,7 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@4deb3275dd364fb96fb074c953133d29ec96f80f # v4.10.6
+        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

@@ -27,26 +27,30 @@ on:
 
 permissions: {}
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   gmt_cache:
     name: Cache GMT artifacts
-    runs-on: macos-latest
+    runs-on: ubuntu-slim
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v6.0.1
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
           persist-credentials: false
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
+        uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476 # v3.0.0
         with:
           environment-name: pygmt
           create-args: >-
@@ -74,7 +78,7 @@ jobs:
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
-        uses: actions/upload-artifact@v6.0.0
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: gmt-cache
           include-hidden-files: true

.github/workflows/cache_dvc.yaml

@@ -28,14 +28,15 @@ permissions: {}
 jobs:
   dvc_cache:
     name: Cache DVC baseline images
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
+    environment: pr-tests
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v6.0.1
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -52,7 +53,7 @@ jobs:
           dvc pull --no-run-cache --verbose && ls -lhR pygmt/tests/baseline/
 
       - name: Upload DVC cache as artifacts to GitHub
-        uses: actions/upload-artifact@v6.0.0
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: dvc-cache
           include-hidden-files: true

.github/workflows/check-links.yml

@@ -21,26 +21,26 @@ permissions:
 jobs:
   check_links:
     name: Check Links
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     if: github.repository == 'GenericMappingTools/pygmt'
 
     steps:
     - name: Checkout the repository
-      uses: actions/checkout@v6.0.1
+      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
       with:
         path: repository
         persist-credentials: false
 
     - name: Checkout the documentation
-      uses: actions/checkout@v6.0.1
+      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
       with:
         ref: gh-pages
         path: documentation
         persist-credentials: false
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@a8c4c7cb88f0c7386610c35eb25108e448569cb0 # v2.7.0
+      uses: lycheeverse/lychee-action@8646ba30535128ac92d33dfc9133794bfdd9b411 # v2.8.0
       with:
         fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md
@@ -70,7 +70,6 @@ jobs:
           --exclude "^https://www.researchgate.net/"
           --exclude "^https://zenodo.org/badge/DOI/"
           --exclude "^https://stackoverflow.com/a/69170441"
-          --verbose
           "repository/*.md"
           "repository/**/*.py"
           "documentation/dev/**/*.html"

.github/workflows/ci_docs.yml

@@ -71,7 +71,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v6.0.1
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -83,7 +83,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
+        uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476 # v3.0.0
         with:
           environment-name: pygmt
           cache-environment: true
@@ -92,7 +92,7 @@ jobs:
           create-args: >-
             python=3.14
             gmt=6.6.0
-            ghostscript=10.06.0
+            ghostscript=10.07.1
             numpy
             pandas
             xarray
@@ -115,7 +115,7 @@ jobs:
             sphinx_rtd_theme
             cairosvg
             sphinxcontrib-svg2pdfconverter
-            tectonic
+            tectonic=0.15
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -149,7 +149,7 @@ jobs:
           cd ../..
 
       - name: Upload PDF as artifact for previewing on pull requests
-        uses: actions/upload-artifact@v6.0.0
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         if: github.event_name == 'pull_request' && matrix.os == 'ubuntu-latest'
         with:
           name: artifact-pygmt-docs-pdf
@@ -167,7 +167,7 @@ jobs:
           REF_NAME: ${{ github.ref_name }}
 
       - name: Checkout the gh-pages branch
-        uses: actions/checkout@v6.0.1
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

.github/workflows/ci_doctests.yaml

@@ -37,15 +37,15 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v6.0.1
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
           persist-credentials: false
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
+        uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476 # v3.0.0
         with:
           environment-name: pygmt
           create-args: >-

.github/workflows/ci_tests.yaml

@@ -51,6 +51,9 @@ jobs:
   test:
     name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
+    environment:
+      name: pr-tests
+      deployment: false
     permissions:
       id-token: write  # This is required for requesting OIDC token for codecov
     strategy:
@@ -72,9 +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'
@@ -104,7 +107,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v6.0.1
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -116,7 +119,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
+        uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476 # v3.0.0
         with:
           environment-name: pygmt
           cache-environment: true
@@ -125,7 +128,7 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}${{ matrix.optional-packages }}
             gmt=6.6.0
-            ghostscript=10.06.0
+            ghostscript=10.07.1
             numpy=${{ matrix.numpy-version }}
             pandas${{ matrix.pandas-version }}
             xarray${{ matrix.xarray-version }}
@@ -151,7 +154,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@eac588ad8def6316056a12d4907a9d4d84ff7a3b # v7.3.0
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
         with:
           activate-environment: true
           python-version: ${{ matrix.python-version }}
@@ -190,15 +193,15 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v6.0.0
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         if: failure()
         with:
           name: artifact-${{ matrix.os }}-${{ matrix.python-version }}
           path: tmp-test-dir-with-unique-name
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@671740ac38dd9b0130fbe1cec585b89eea48d3de # v5.5.2
+        uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0
         if: success() || failure()
         with:
           use_oidc: true