Merge branch 'main' into python-3.13

Author: weiji14

.dvcignore

@@ -1,3 +1,2 @@
-# Add patterns of files dvc should ignore, which could improve
-# the performance. Learn more at
-# https://dvc.org/doc/user-guide/dvcignore
+# Add patterns of files dvc should ignore, which could improve the performance.
+# Learn more at https://dvc.org/doc/user-guide/project-structure/dvcignore-files

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -19,7 +19,8 @@ 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)
 - [ ] Check to ensure that:
   - [ ] Deprecations and related tests are removed for this version by running `grep --include="*.py" -r vX.Y.Z` from the base of the repository

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,6 +8,10 @@
 Fixes #
 
 
+<!-- If significant changes to the documentation are made, please insert the link to the documentation page after it has been built. -->
+**Preview**:
+
+
 **Reminders**
 
 - [ ] Run `make format` and `make check` to make sure the code follows the style guide.

.github/release-drafter.yml

@@ -24,6 +24,8 @@ 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

@@ -88,7 +88,7 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/[email protected].0
+        uses: CodSpeedHQ/[email protected].1
         with:
           # 'bash -el -c' is needed to use the custom shell.
           # See https://github.com/CodSpeedHQ/action/issues/65.

.github/workflows/check-links.yml

@@ -35,32 +35,29 @@ jobs:
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v1.10.0
+      uses: lycheeverse/lychee-action@v2.0.2
       with:
+        fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md
         # 429: Too many requests
         args: >
           --accept 429
-          --exclude "^https://doi.org/10.5281/zenodo$"
-          --exclude "^https://zenodo.org/badge/DOI/$"
-          --exclude "^https://zenodo.org/badge/DOI/10.5281/zenodo$"
-          --exclude "^https://github.com/GenericMappingTools/pygmt/pull/[0-9]*$"
-          --exclude "^https://github.com/GenericMappingTools/pygmt/issues/[0-9]*$"
+          --exclude "^https://docs.generic-mapping-tools.org/6.[0-9]?/%s$"
+          --exclude "^https://docs.generic-mapping-tools.org/6.[0-9]?/%3Cmodule-name%3E.html$"
+          --exclude "^https://doi.org"
           --exclude "^https://github.com/GenericMappingTools/gmt/releases/tag/X.Y.Z$"
           --exclude "^https://github.com/GenericMappingTools/pygmt/edit"
           --exclude "^https://github.com/GenericMappingTools/pygmt/issues/new"
+          --exclude "^https://github.com/GenericMappingTools/pygmt/pull/[0-9]*$"
+          --exclude "^https://github.com/GenericMappingTools/pygmt/issues/[0-9]*$"
           --exclude "^https://github.com/GenericMappingTools/pygmt/releases/tag/%7B%7Bpath%7D%7D"
-          --exclude "^https://www.pygmt.org/%7B%7Bpath%7D%7D"
-          --exclude "^git"
-          --exclude "^file://"
-          --exclude "https://www.adobe.com/jp/print/postscript/pdfs/PLRM.pdf"
-          --exclude "^https://docs.generic-mapping-tools.org/6.5/%s$"
-          --exclude "^https://docs.generic-mapping-tools.org/6.5/%3Cmodule-name%3E.html$"
-          --exclude "^https://www.generic-mapping-tools.org/remote-datasets/%s$"
           --exclude "^https://hackmd.io/@pygmt"
-          --exclude "^https://doi.org"
-          --exclude "^https://www.researchgate.net/"
           --exclude "^https://test.pypi.org/simple/"
+          --exclude "^https://www.adobe.com/jp/print/postscript/pdfs/PLRM.pdf"
+          --exclude "^https://www.generic-mapping-tools.org/remote-datasets/%s$"
+          --exclude "^https://www.pygmt.org/%7B%7Bpath%7D%7D"
+          --exclude "^https://www.researchgate.net/"
+          --exclude "^https://zenodo.org/badge/DOI/"
           --verbose
           "repository/**/*.rst"
           "repository/**/*.md"

.github/workflows/ci_tests.yaml

@@ -17,8 +17,8 @@
 # In draft pull request, only two jobs on Linux are triggered to save on
 # Continuous Integration resources:
 #
-# - Minimum supported Python/NumPy/Pandas/Xarray versions following [SPEC 0](https://scientific-python.org/specs/spec-0000/)
-# - Latest Python/NumPy versions + optional packages (e.g. GeoPandas)
+# - Minimum supported Python, NumPy, pandas, Xarray versions following [SPEC 0](https://scientific-python.org/specs/spec-0000/)
+# - Latest Python, NumPy versions + optional packages (e.g. GeoPandas)
 #
 name: Tests
 
@@ -65,8 +65,8 @@ jobs:
             isDraft: true
           - os: windows-latest
             isDraft: true
-        # Pair Python 3.10 with the minimum supported versions of NumPy/Pandas/Xarray
-        # and Python 3.13 with the latest versions of NumPy/Pandas/Xarray
+        # Pair Python 3.10 with the minimum supported versions of NumPy, pandas, Xarray
+        # and Python 3.13 with the latest versions of NumPy, pandas, Xarray
         # Only install optional packages on Python 3.13
         include:
           - python-version: '3.10'
@@ -79,7 +79,7 @@ jobs:
             pandas-version: ''
             xarray-version: ''
             optional-packages: ' contextily geopandas ipython pyarrow rioxarray sphinx-gallery'
-          # The job below is for testing geopandas v0.x on Ubuntu.
+          # The job below is for testing GeoPandas v0.x on Ubuntu.
           # The python-version here can't be the versions in the matrix.python-version
           # defined above. Otherwise, other jobs will be overridden by this one.
           - os: 'ubuntu-latest'

.github/workflows/ci_tests_dev.yaml

@@ -1,7 +1,7 @@
 # Test PyGMT with GMT dev version on Linux/macOS/Windows
 #
 # This workflow runs regular PyGMT tests with the GMT dev version, and also pre-release
-# versions of several dependencies like NumPy, Pandas, Xarray, etc. If any tests fail,
+# versions of several dependencies like NumPy, pandas, Xarray, etc. If any tests fail,
 # it also uploads the diff images as workflow artifacts. The GMT dev version is
 # installed by fetching the latest source codes from the GMT master branch and
 # compiling.

.github/workflows/ci_tests_legacy.yaml

@@ -1,8 +1,8 @@
 # Test PyGMT with GMT legacy versions on Linux/macOS/Windows
 #
-# This workflow runs regular PyGMT tests with GMT legacy versions. Due to the
-# minor baseline image changes between GMT versions, the workflow only runs
-# the tests but doesn't do image comparisons.
+# This workflow runs regular PyGMT tests with GMT legacy versions. Due to the minor
+# baseline image changes between GMT versions, the workflow only runs the tests but
+# doesn't do image comparisons.
 #
 # It is scheduled to run every Tuesday on the main branch.
 #
@@ -34,7 +34,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macos-12, windows-2019]
+        os: [ubuntu-20.04, macos-13, windows-2019]
         gmt_version: ['6.4']
     timeout-minutes: 30
     defaults:
@@ -63,7 +63,7 @@ jobs:
             gmt=${{ matrix.gmt_version }}
             ghostscript<10
             numpy
-            pandas<2
+            pandas
             xarray
             netCDF4
             packaging
@@ -85,9 +85,9 @@ jobs:
         run: |
           # Download cached files to ~/.gmt directory and list them
           gh run download --name gmt-cache --dir ~/.gmt/
-          # Change modification times of the two files, so GMT won't refresh it
-          # The two files are in the `~/.gmt/server` directory for GMT<=6.4, and
-          # in the `~/.gmt` directory for GMT>=6.5.
+          # Change modification times of the two files, so GMT won't refresh it.
+          # The two files are in the `~/.gmt/server` directory for GMT<=6.4, and in the
+          # `~/.gmt` directory for GMT>=6.5.
           mkdir -p ~/.gmt/server/
           mv ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt ~/.gmt/server/
           touch ~/.gmt/server/gmt_data_server.txt ~/.gmt/server/gmt_hash_server.txt

README.md

@@ -194,7 +194,7 @@ PyGMT has adopted [SPEC 0](https://scientific-python.org/specs/spec-0000/) along
 rest of the Scientific Python ecosystem, and therefore:
 
 - Support for Python versions be dropped 3 years after their initial release.
-- Support for core package dependencies (NumPy/Pandas/Xarray) be dropped 2 years after
+- Support for core package dependencies (NumPy, pandas, Xarray) be dropped 2 years after
   their initial release.
 
 Similarly, the PyGMT team has decided to discontinue support for GMT versions 3 years