Merge branch 'main' into feature/direction_rose

Author: seisman

.github/ISSUE_TEMPLATE/2-feature_request.yaml

@@ -1,4 +1,4 @@
-name: Feature request - General feature
+name: Feature request
 description: Request the addition of a new feature/functionality
 labels: ["feature request"]
 body:

.github/ISSUE_TEMPLATE/3-module_request.md

@@ -0,0 +1,41 @@
+---
+name: Wrapper for a GMT module
+about: Track the progress of wrapping a GMT module. [For project maintainers only!]
+title: "Wrapper: Description of the module"
+labels: ["feature request"]
+
+---
+
+*This issue serves as the central place for discussing and tracking the implementation of the `<wrapper>` method in PyGMT. The issue will be closed when the initial implementation is complete. Progress is tracked at https://github.com/orgs/GenericMappingTools/projects/3.*
+
+## Documentation
+
+- GMT: https://docs.generic-mapping-tools.org/dev/<module>.html
+- 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 Modifiers
+
+☑️: *Implemented*; ⬜: *To be implemented/discussed*; ~~Strikethrough~~: *Won't implement*.
+
+- [ ] `-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.
+
+## Notes on Input Formats
+
+*Add any notes on the input formats, especially the meaning of columns.*
+
+## Linked Pull Requests
+
+- [ ] Initial feature implementation
+- [ ] Add a tutorial or gallery example
+
+## Related Issues and Discussions
+
+*Add links to related wrapper discussions, API design threads, or upstream GMT changes here.*

.github/ISSUE_TEMPLATE/3-module_request.yaml

@@ -24,7 +24,7 @@ assignees: ''
 - [ ] 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.
 - [ ] Check to ensure that:
-  - [ ] Deprecated workarounds/codes/tests are removed. Run `grep "# TODO" **/*.py` to find all potential TODOs.
+  - [ ] 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)

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -7,11 +7,10 @@ assignees: ''
 
 ---
 
-:tada: [GMT X.Y.Z](https://github.com/GenericMappingTools/gmt/releases/tag/X.Y.Z) has been released!
-It is installable from the [conda-forge channel](https://anaconda.org/conda-forge/gmt/files)
-using the following command:
-
-`mamba install -c conda-forge gmt=X.Y.Z`
+:tada: [GMT X.Y.Z](https://github.com/GenericMappingTools/gmt/releases/tag/X.Y.Z) has been released! It is installable from the [conda-forge channel](https://anaconda.org/conda-forge/gmt/files) using the following command:
+```
+mamba install -c conda-forge gmt=X.Y.Z
+```
 
 <!-- Please add specific checklist items for the tests, xfail pytest markers, and deprecated syntax that need to be updated. -->
 
@@ -29,13 +28,19 @@ using the following command:
   - [ ] Update GMT 6.x minor version for `extlinks` urls in `doc/conf.py`
 - [ ] Fix failing tests (1 or more PRs)
 - [ ] Fix failing doctests reported in the ["Doctest" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/ci_doctests.yaml)
-- [ ] Fix [xfail](https://docs.pytest.org/en/stable/skipping.html#xfail-mark-test-functions-as-expected-to-fail) pytest markers on tests that are now xpass
+- [ ] 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 this checklist if necessary
 
 **To-Do for bumping the minimum required GMT version**:
 
 - [ ] Bump the minimum required GMT version (1 PR)
   - [ ] Update `required_gmt_version` in `pygmt/clib/__init__.py`
   - [ ] Remove unsupported GMT version from `.github/workflows/ci_tests_legacy.yaml`
   - [ ] Ensure minimum required version is correct in `doc/minversions.md`
-- [ ] Remove [xfail](https://docs.pytest.org/en/stable/skipping.html#xfail-mark-test-functions-as-expected-to-fail) pytest markers on tests that are now xpass
+- [ ] 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 deprecated syntax in source code and examples based on the [GMT Changelog](https://docs.generic-mapping-tools.org/latest/changes.html)
+- [ ] Update this checklist if necessary

.github/ISSUE_TEMPLATE/5-bump_gmt_checklist.md

@@ -11,15 +11,11 @@ Fixes #
 <!-- If significant changes to the documentation are made, please insert the link to the documentation page after it has been built. -->
 **Preview**:
 
+**Guidelines**
 
-**Reminders**
-
-- [ ] Run `make format` and `make check` to make sure the code follows the style guide.
-- [ ] Add tests for new features or tests that would have caught the bug that you're fixing.
-- [ ] Add new public functions/methods/classes to `doc/api/index.rst`.
-- [ ] Write detailed docstrings for all functions/methods.
-- [ ] If wrapping a new module, open a 'Wrap new GMT module' issue and submit reasonably-sized PRs.
-- [ ] If adding new functionality, add an example to docstrings or tutorials.
+- [General Guidelines for Pull Request](https://www.pygmt.org/dev/contributing.html#general-guidelines-for-making-a-pull-request-pr)
+- [Guidelines for Contributing Documentation](https://www.pygmt.org/dev/contributing.html#contributing-documentation)
+- [Guidelines for Contributing Code](https://www.pygmt.org/dev/contributing.html#contributing-code)
 
 **Slash Commands**
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -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@6b43a0cd438f6ca5ad26f9ed03ed159ed2df7da9 # v4.1.1
+        uses: CodSpeedHQ/action@6a8e2b874c338bf81cc5e8be715ada75908d3871 # v4.3.4
         with:
           mode: "instrumentation"
           # 'bash -el -c' is needed to use the custom shell.

.github/workflows/benchmarks.yml

@@ -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@v4.6.2
+        uses: actions/upload-artifact@v5.0.0
         with:
           name: gmt-cache
           include-hidden-files: true

.github/workflows/cache_data.yaml

@@ -0,0 +1,59 @@
+# Cache baseline images tracked by DVC and upload as artifacts.
+#
+# This workflow downloads dvc cache needed by PyGMT tests and uploads them as workflow
+# artifacts, which can then be accessed by other GitHub Actions workflows.
+#
+# This workflow serves as a workaround for the DagsHub authentication issue that
+# prevents PRs from forks to access the DVC remote.
+# Related issue: https://github.com/GenericMappingTools/pygmt/issues/4147
+#
+# It is scheduled to run every Sunday at 12:00 (UTC) and on the main branch if there are
+# any changes to the baseline images.
+#
+name: Cache DVC
+
+on:
+  push:
+    branches: [ main ]
+    paths:
+      - 'pygmt/tests/baseline/*.png.dvc'
+  # pull_request:  # For testing only.
+  workflow_dispatch:
+  # Schedule runs on 12 noon every Sunday
+  schedule:
+    - cron: '0 12 * * 0'
+
+permissions: {}
+
+jobs:
+  dvc_cache:
+    name: Cache DVC baseline images
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6.0.1
+        with:
+          # fetch all history so that setuptools-scm works
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: Setup data version control (DVC)
+        uses: iterative/setup-dvc@175771be1dc3d119268e00a896b52a4b77decb5e # v1.2.0
+
+      - name: Pull baseline image data from dvc remote
+        env:
+          DAGSHUB_TOKEN: ${{ secrets.DAGSHUB_TOKEN }}
+        run: |
+          dvc remote modify upstream url https://${DAGSHUB_TOKEN}@dagshub.com/GenericMappingTools/pygmt.dvc --local
+          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
+        with:
+          name: dvc-cache
+          include-hidden-files: true
+          path: .dvc/cache/

.github/workflows/cache_dvc.yaml

@@ -26,21 +26,21 @@ 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
         persist-credentials: false
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@885c65f3dc543b57c898c8099f4e08c8afd178a2 # v2.6.1
+      uses: lycheeverse/lychee-action@a8c4c7cb88f0c7386610c35eb25108e448569cb0 # v2.7.0
       with:
         fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md