Merge branch 'main' into fix-fig-region

Author: Chuan1937

.github/ISSUE_TEMPLATE/3-module_request.md

@@ -27,6 +27,10 @@ labels: ["feature request"]
 - [ ] ~~`-X`/`-Y`~~: Use `Figure.shift_origin` instead.
 - [ ] ~~`--PAR=value`~~: Use `pygmt.config` instead.
 
+## Related GMT configurations
+
+*List any related GMT configurations that may affect the behavior.*
+
 ## Notes on Input Formats
 
 *Add any notes on the input formats, especially the meaning of columns.*

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -20,14 +20,16 @@ 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
 - [ ] Check to ensure that:
   - [ ] Deprecated workarounds/codes/tests are removed. Run `grep -r "# TODO" --include="*.py" .` to find all potential TODOs.
   - [ ] All tests pass in the ["GMT Legacy Tests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests_legacy.yaml)
   - [ ] All tests pass in the ["GMT Dev Tests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_tests_dev.yaml)
   - [ ] All tests pass in the ["Doctests" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_doctests.yaml)
+  - [ ] All links work in the ["Check Links" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/check-links.yml)
 - [ ] Update warnings in `pygmt/_show_versions.py` as well as notes in [Not working transparency](https://www.pygmt.org/dev/install.html#not-working-transparency) regarding GMT-Ghostscript incompatibility
 - [ ] Reserve a DOI on [Zenodo](https://zenodo.org) by clicking on "New Version"
 - [ ] Finish up the "Changelog entry for v0.x.x" Pull Request (Use the previous changelog PR as a reference)
@@ -52,7 +54,7 @@ assignees: ''
 - [ ] Bump PyGMT version on https://github.com/GenericMappingTools/try-gmt (after conda-forge update)
 - [ ] Announce the release on:
   - [ ] GMT [forum](https://forum.generic-mapping-tools.org/c/news/) (do this announcement first! Requires moderator status)
-  - [ ] [ResearchGate](https://www.researchgate.net) (after forum announcement; download the ZIP file of the new release from the release page and add it as research item via the **code** category, be sure to include the corresponding new Zenodo DOI)
+  - [ ] [ResearchGate](https://www.researchgate.net) (after forum announcement; download the ZIP file of the new release from Zenodo and add it as research item via the **code** category, be sure to include the corresponding new Zenodo DOI)
 - [ ] Update release checklist template with any additional bullet points that may have arisen during the release
 
 ---

.github/dependabot.yml

@@ -16,3 +16,11 @@ updates:
       - "skip-changelog"
     cooldown:
       default-days: 7
+
+  - package-ecosystem: "pre-commit"
+    directory: "/"
+    schedule:
+      interval: "quarterly"
+    labels:
+      - "maintenance"
+      - "skip-changelog"

.github/release-drafter.yml

@@ -24,8 +24,6 @@ exclude-contributors:
   - 'actions-bot'
   - 'dependabot'
   - 'dependabot[bot]'
-  - 'pre-commit-ci'
-  - 'pre-commit-ci[bot]'
 category-template: '### $TITLE'
 change-template: '* $TITLE ([#$NUMBER]($URL))'
 sort-by: 'title'

.github/workflows/benchmarks.yml

@@ -84,7 +84,7 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@972e3437949c89e1357ebd1a2dbc852fcbc57245 # v4.5.1
+        uses: CodSpeedHQ/action@281164b0f014a4e7badd2c02cecad9b595b70537 # v4.11.1
         with:
           mode: "instrumentation"
           # 'bash -el -c' is needed to use the custom shell.

.github/workflows/cache_data.yaml

@@ -74,7 +74,7 @@ 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@v7.0.0
         with:
           name: gmt-cache
           include-hidden-files: true

.github/workflows/cache_dvc.yaml

@@ -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@v6.0.0
+        uses: actions/upload-artifact@v7.0.0
         with:
           name: dvc-cache
           include-hidden-files: true

.github/workflows/check-links.yml

@@ -40,7 +40,7 @@ jobs:
 
     - 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

@@ -150,7 +150,7 @@ jobs:
           cd ../..
 
       - name: Upload PDF as artifact for previewing on pull requests
-        uses: actions/upload-artifact@v6.0.0
+        uses: actions/upload-artifact@v7.0.0
         if: github.event_name == 'pull_request' && matrix.os == 'ubuntu-latest'
         with:
           name: artifact-pygmt-docs-pdf

.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:
@@ -151,7 +154,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0
+        uses: astral-sh/setup-uv@eac588ad8def6316056a12d4907a9d4d84ff7a3b # v7.3.0
         with:
           activate-environment: true
           python-version: ${{ matrix.python-version }}
@@ -190,7 +193,7 @@ 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@v7.0.0
         if: failure()
         with:
           name: artifact-${{ matrix.os }}-${{ matrix.python-version }}