Merge branch 'main' into feature/clip

Author: seisman

.github/workflows/cache_data.yaml

@@ -75,7 +75,7 @@ jobs:
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         with:
           name: gmt-cache
           include-hidden-files: true

.github/workflows/check-links.yml

@@ -1,7 +1,7 @@
 # Check links in the repository and documentation
 #
-# This workflow runs the lychee tool to check all external links in plaintext
-# and HTML files. It will create an issue if broken links are found.
+# This workflow runs the lychee tool to check all external links in plaintext and HTML
+# files. It will create an issue if broken links are found.
 #
 # It is scheduled to run weekly at 12 noon every Sunday.
 #
@@ -40,7 +40,7 @@ jobs:
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v2.3.0
+      uses: lycheeverse/lychee-action@v2.4.0
       with:
         fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md
@@ -76,7 +76,7 @@ jobs:
       run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
 
     - name: Create Issue From File
-      if: ${{ steps.lychee.outputs.exit_code }} != 0
+      if: steps.lychee.outputs.exit_code != 0
       run: |
         cd repository/
         title="Link Checker Report on ${CURRENT_DATE}"

.github/workflows/ci_docs.yml

@@ -114,7 +114,7 @@ jobs:
             sphinx-copybutton
             sphinx-design
             sphinx-gallery
-            sphinx_rtd_theme<3.0
+            sphinx_rtd_theme
             cairosvg
             sphinxcontrib-svg2pdfconverter
             tectonic
@@ -151,7 +151,7 @@ jobs:
           cd ../..
 
       - name: Upload PDF as artifact for previewing on pull requests
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         if: github.event_name == 'pull_request' && matrix.os == 'ubuntu-latest'
         with:
           name: artifact-pygmt-docs-pdf

.github/workflows/ci_tests.yaml

@@ -72,16 +72,16 @@ jobs:
         include:
           # Python 3.11 + core packages (minimum supported versions) + optional packages (minimum supported versions if any)
           - python-version: '3.11'
-            numpy-version: '1.25'
-            pandas-version: '=2.0'
-            xarray-version: '=2023.04'
-            optional-packages: ' contextily geopandas<1 ipython pyarrow-core rioxarray sphinx-gallery'
+            numpy-version: '1.26'
+            pandas-version: '=2.1'
+            xarray-version: '=2023.07'
+            optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray sphinx-gallery'
           # Python 3.13 + core packages (latest versions) + optional packages
           - python-version: '3.13'
             numpy-version: '2.2'
             pandas-version: ''
             xarray-version: ''
-            optional-packages: ' contextily geopandas>=1.0 ipython pyarrow-core rioxarray sphinx-gallery'
+            optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray sphinx-gallery'
           # Python 3.12 + core packages (Linux only)
           - os: 'ubuntu-latest'
             python-version: '3.12'
@@ -152,7 +152,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/[email protected].1
+        uses: astral-sh/[email protected].2
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -175,15 +175,15 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         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/[email protected].0
+        uses: codecov/[email protected].2
         if: success() || failure()
         with:
           use_oidc: true

.github/workflows/ci_tests_dev.yaml

@@ -186,7 +186,7 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/[email protected].1
+        uses: actions/[email protected].2
         if: ${{ failure() }}
         with:
           name: artifact-${{ matrix.os }}-GMT-${{ matrix.gmt_git_ref }}

.github/workflows/ci_tests_legacy.yaml

@@ -36,7 +36,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, ubuntu-22.04-arm, macos-13, windows-2019]
+        os: [ubuntu-22.04, ubuntu-22.04-arm, macos-13, windows-2022]
         gmt_version: ['6.4']
     timeout-minutes: 30
     defaults:
@@ -61,15 +61,15 @@ jobs:
             python=3.11
             gmt=${{ matrix.gmt_version }}
             ghostscript<10
-            numpy<2
+            numpy=1.26
             pandas
             xarray
             netCDF4
             packaging
-            contextily
-            geopandas
+            contextily=1.5
+            geopandas=1.0
             ipython
-            pyarrow-core
+            pyarrow-core=16
             rioxarray
             sphinx-gallery
             make

.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@v1.12.0
+      - uses: actions/create-github-app-token@v2.0.2
         id: generate-token
         with:
           app-id: ${{ secrets.APP_ID }}

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

@@ -74,7 +74,7 @@ jobs:
         ls -lh dist/
 
     - name: Store the distribution packages
-      uses: actions/[email protected].1
+      uses: actions/[email protected].2
       with:
         name: python-package-distributions
         path: dist/
@@ -93,7 +93,7 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         name: python-package-distributions
         path: dist/
@@ -117,7 +117,7 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/[email protected].0
+      uses: actions/[email protected].1
       with:
         name: python-package-distributions
         path: dist/

.mailmap

@@ -0,0 +1,19 @@
+Dongdong Tian <[email protected]>
+Dongdong Tian <[email protected]> <[email protected]>
+Jiayuan Yao <[email protected]>
+Jiayuan Yao <[email protected]> <[email protected]>
+Jing-Hui Tong <[email protected]>
+Jing-Hui Tong <[email protected]> <[email protected]>
+Max Jones <[email protected]>
+Max Jones <[email protected]> <[email protected]>
+Max Jones <[email protected]> <[email protected]>
+Max Jones <[email protected]> <[email protected]>
+Michael Grund <[email protected]> <[email protected]>
+Michael Grund <[email protected]> <[email protected]>
+Michael Grund <[email protected]> <[email protected]>
+Wei Ji Leong <[email protected]>
+Wei Ji Leong <[email protected]> <[email protected]>
+Wei Ji Leong <[email protected]> <[email protected]>
+Will Schlitzer <[email protected]> <[email protected]>
+Yvonne Fröhlich <[email protected]> <[email protected]>
+Yvonne Fröhlich <[email protected]> <[email protected]>

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
     - id: chmod
       args: ['644']
 - repo: https://github.com/woodruffw/zizmor-pre-commit
-  rev: v1.5.1
+  rev: v1.5.2
   hooks:
   - id: zizmor