Merge branch 'main' into AliasSystem/params/frame

Author: seisman

.github/ISSUE_TEMPLATE/3-module_request.md

@@ -14,14 +14,16 @@ labels: ["feature request"]
 - GMT.jl: https://www.generic-mapping-tools.org/GMTjl_doc/documentation/modules/<module>
 - PyGMT: https://www.pygmt.org/dev/api/generated/<wrapper>.html
 
-## GMT Option Flags and Modifieres
+## GMT Option Flags and Modifiers
 
 ☑️: *Implemented*; ⬜: *To be implemented/discussed*; ~~Strikethrough~~: *Won't implement*.
 
-- [ ] `-R`: `region` #XXX @XXX
-- [ ] `-J`: `projection` #XXX @XXX
+- [ ] `-B`: `frame`
+- [ ] `-J`: `projection`
+- [ ] `-R`: `region`
 - [ ] ...
 - [ ] ~~`-U`~~: Use `Figure.timestamp` instead.
+- [ ] `-V`: `verbose`
 - [ ] ~~`-X`/`-Y`~~: Use `Figure.shift_origin` instead.
 - [ ] ~~`--PAR=value`~~: Use `pygmt.config` instead.
 
@@ -31,7 +33,7 @@ labels: ["feature request"]
 
 ## Linked Pull Requests
 
-- [ ] Initial feature implementation #XXX @XXX
+- [ ] Initial feature implementation
 - [ ] Add a tutorial or gallery example
 
 ## Related Issues and Discussions

.github/ISSUE_TEMPLATE/5-bump_gmt_checklist.md

@@ -31,6 +31,7 @@ mamba install -c conda-forge gmt=X.Y.Z
 - [ ] Run `grep -r "# TODO(GMT.*)" --include="*.py" .` to find TODO items related to GMT
   - [ ] Remove related workarounds/patches
   - [ ] Fix tests with pytest `xfail`/`skipif` markers that now pass
+- [ ] Update URLs to manually inserted images of the GMT documentation
 - [ ] Update this checklist if necessary
 
 **To-Do for bumping the minimum required GMT version**:

.github/dependabot.yml

@@ -2,7 +2,6 @@
 
 version: 2
 updates:
-
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
@@ -15,3 +14,5 @@ updates:
     labels:
       - "maintenance"
       - "skip-changelog"
+    cooldown:
+      default-days: 7

.github/workflows/benchmarks.yml

@@ -36,7 +36,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v5.0.0
+        uses: actions/checkout@v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -56,7 +56,7 @@ jobs:
           cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
           create-args: >-
             gmt=6.6.0
-            python=3.13
+            python=3.14
             numpy
             pandas
             xarray
@@ -84,7 +84,7 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@6a8e2b874c338bf81cc5e8be715ada75908d3871 # v4.3.4
+        uses: CodSpeedHQ/action@972e3437949c89e1357ebd1a2dbc852fcbc57245 # v4.5.1
         with:
           mode: "instrumentation"
           # 'bash -el -c' is needed to use the custom shell.

.github/workflows/cache_data.yaml

@@ -38,7 +38,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v5.0.0
+        uses: actions/checkout@v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -50,7 +50,7 @@ jobs:
         with:
           environment-name: pygmt
           create-args: >-
-            python=3.13
+            python=3.14
             gmt=6.6.0
             numpy
             pandas
@@ -74,7 +74,7 @@ jobs:
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
-        uses: actions/upload-artifact@v5.0.0
+        uses: actions/upload-artifact@v6.0.0
         with:
           name: gmt-cache
           include-hidden-files: true

.github/workflows/cache_dvc.yaml

@@ -35,7 +35,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v5.0.0
+        uses: actions/checkout@v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -52,7 +52,7 @@ jobs:
           dvc pull --no-run-cache --verbose && ls -lhR pygmt/tests/baseline/
 
       - name: Upload DVC cache as artifacts to GitHub
-        uses: actions/upload-artifact@v5.0.0
+        uses: actions/upload-artifact@v6.0.0
         with:
           name: dvc-cache
           include-hidden-files: true

.github/workflows/check-links.yml

@@ -26,13 +26,13 @@ jobs:
 
     steps:
     - name: Checkout the repository
-      uses: actions/checkout@v5.0.0
+      uses: actions/checkout@v6.0.1
       with:
         path: repository
         persist-credentials: false
 
     - name: Checkout the documentation
-      uses: actions/checkout@v5.0.0
+      uses: actions/checkout@v6.0.1
       with:
         ref: gh-pages
         path: documentation

.github/workflows/ci_docs.yml

@@ -72,7 +72,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v5.0.0
+        uses: actions/checkout@v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -91,7 +91,7 @@ jobs:
           # environment cache is persistent for one week.
           cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
           create-args: >-
-            python=3.13
+            python=3.14
             gmt=6.6.0
             ghostscript=10.06.0
             numpy
@@ -106,7 +106,6 @@ jobs:
             make
             pip
             python-build
-            geodatasets
             myst-nb
             panel
             sphinx>=6.2
@@ -151,7 +150,7 @@ jobs:
           cd ../..
 
       - name: Upload PDF as artifact for previewing on pull requests
-        uses: actions/upload-artifact@v5.0.0
+        uses: actions/upload-artifact@v6.0.0
         if: github.event_name == 'pull_request' && matrix.os == 'ubuntu-latest'
         with:
           name: artifact-pygmt-docs-pdf
@@ -169,7 +168,7 @@ jobs:
           REF_NAME: ${{ github.ref_name }}
 
       - name: Checkout the gh-pages branch
-        uses: actions/checkout@v5.0.0
+        uses: actions/checkout@v6.0.1
         with:
           ref: gh-pages
           # Checkout to this folder instead of the current one

.github/workflows/ci_doctests.yaml

@@ -37,7 +37,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v5.0.0
+        uses: actions/checkout@v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -49,7 +49,7 @@ jobs:
         with:
           environment-name: pygmt
           create-args: >-
-            python=3.13
+            python=3.14
             gmt=6.6.0
             numpy
             pandas

.github/workflows/ci_tests.yaml

@@ -56,7 +56,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.11', '3.13']
+        python-version: ['3.12', '3.14']
         os: [ubuntu-latest, ubuntu-24.04-arm, macos-latest, windows-latest]
         # Is it a draft Pull Request (true or false)?
         isDraft:
@@ -70,21 +70,21 @@ jobs:
           - os: windows-latest
             isDraft: true
         include:
-          # Python 3.11 + core packages (minimum supported versions) + optional packages (minimum supported versions if any)
-          - python-version: '3.11'
+          # 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'
             optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray netCDF4 sphinx-gallery'
-          # Python 3.13 + core packages (latest versions) + optional packages
-          - python-version: '3.13'
-            numpy-version: '2.3'
+          # Python 3.14 + core packages (latest versions) + optional packages
+          - python-version: '3.14'
+            numpy-version: '2.4'
             pandas-version: ''
             xarray-version: ''
             optional-packages: ' contextily geopandas ipython pyarrow-core rioxarray netCDF4 sphinx-gallery'
-          # Python 3.12 + core packages (Linux only)
+          # Python 3.13 + core packages (Linux only)
           - os: 'ubuntu-latest'
-            python-version: '3.12'
+            python-version: '3.13'
             numpy-version: ''
             pandas-version: ''
             xarray-version: ''
@@ -104,7 +104,7 @@ jobs:
     steps:
       # Checkout current git repository
       - name: Checkout
-        uses: actions/checkout@v5.0.0
+        uses: actions/checkout@v6.0.1
         with:
           # fetch all history so that setuptools-scm works
           fetch-depth: 0
@@ -151,7 +151,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@85856786d1ce8acfbcc2f13a5f3fbd6b938f9f41 # v7.1.2
+        uses: astral-sh/setup-uv@681c641aba71e4a1c380be3ab5e12ad51f415867 # v7.1.6
         with:
           activate-environment: true
           python-version: ${{ matrix.python-version }}
@@ -190,15 +190,15 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v5.0.0
+        uses: actions/upload-artifact@v6.0.0
         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@5a1091511ad55cbe89839c7260b706298ca349f7 # v5.5.1
+        uses: codecov/codecov-action@671740ac38dd9b0130fbe1cec585b89eea48d3de # v5.5.2
         if: success() || failure()
         with:
           use_oidc: true