Merge branch 'main' into uv/resolution-lowest

Author: weiji14

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -11,6 +11,7 @@ assignees: ''
 **Scheduled Date**: 20YY/MM/DD
 **Pull request due date**: 20YY/MM/DD
 **DOI**: `10.5281/zenodo.XXXXXXX`
+**Announcement draft**: https://hackmd.io/@pygmt/xxxxxxxx
 
 **Priority PRs/issues to complete prior to release**
 
@@ -39,11 +40,15 @@ assignees: ''
   - [ ] Edit the draft release notes with the finalized changelog
   - [ ] Set the tag version and release title to vX.Y.Z
   - [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too
+- [ ] Verify that [all workflows triggered by the release](https://github.com/GenericMappingTools/pygmt/actions?query=event%3Arelease) pass
+  - [ ] The latest version is correct on [PyPI](https://pypi.org/project/pygmt/)
+  - [ ] The latest version is correct on https://www.pygmt.org/latest/
+  - [ ] The [release page](https://github.com/GenericMappingTools/pygmt/releases) has five assets, including `baseline-images.zip`, `pygmt-docs.zip` and `pygmt-docs.pdf`
 - [ ] Download pygmt-X.Y.Z.zip (rename to pygmt-vX.Y.Z.zip) and baseline-images.zip from the release page, and upload the two zip files to https://zenodo.org/deposit, ensure that they are filed under the correct reserved DOI
 
 **After release**:
 
-- [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) [Done automatically by conda-forge's bot. Remember to pin GMT, Python and SPEC0 versions]
+- [ ] Update conda-forge [pygmt-feedstock](https://github.com/conda-forge/pygmt-feedstock) (Done automatically by conda-forge's bot. If you don't want to wait, open a new issue in the `conda-forge/pygmt-feedstock` repository with the title `@conda-forge-admin, please update version`. This will trigger the bot immediately. Remember to pin GMT, Python and SPEC0 versions)
 - [ ] 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)

.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/upload-artifact@v4.6.1
+        uses: actions/upload-artifact@v4.6.2
         with:
           name: gmt-cache
           include-hidden-files: true

.github/workflows/check-links.yml

@@ -15,7 +15,8 @@ on:
   schedule:
     - cron: '0 12 * * 0'
 
-permissions: {}
+permissions:
+  issues: write
 
 jobs:
   check_links:
@@ -49,11 +50,14 @@ jobs:
           --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/%7Brepository%7D"
           --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/download/%7B%7Bpath%7D%7D/pygmt-docs.pdf"
+          --exclude "^https://github.com/GenericMappingTools/pygmt/releases/download/%7B%7Bpath%7D%7D/pygmt-docs.zip"
           --exclude "^https://github.com/GenericMappingTools/pygmt/releases/tag/%7B%7Bpath%7D%7D"
           --exclude "^https://hackmd.io/@pygmt"
           --exclude "^https://test.pypi.org/simple/"
@@ -63,8 +67,7 @@ jobs:
           --exclude "^https://www.researchgate.net/"
           --exclude "^https://zenodo.org/badge/DOI/"
           --verbose
-          "repository/**/*.rst"
-          "repository/**/*.md"
+          "repository/*.md"
           "repository/**/*.py"
           "documentation/dev/**/*.html"
 
@@ -73,7 +76,7 @@ jobs:
       run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
 
     - name: Create Issue From File
-      if: env.lychee_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

@@ -2,15 +2,14 @@
 #
 # This workflow builds the documentation on Linux/macOS/Windows.
 #
-# It is run on every commit to the main and pull request branches, and also
-# when a new release is published.
-# In draft pull requests, only the job on Linux is triggered to save on
-# Continuous Integration resources.
+# It is run on every commit to the main and pull request branches, and also when a new
+# release is published. In draft pull requests, only the job on Linux is triggered to
+# save on Continuous Integration resources.
 #
 # On the main branch, the workflow also handles the documentation deployment:
 #
-# * Updating the development documentation by pushing the built HTML pages
-#   from the main branch onto the dev folder of the gh-pages branch.
+# * Updating the development documentation by pushing the built HTML pages from the main
+#   branch onto the dev folder of the gh-pages branch.
 # * Updating the latest documentation link to the new release.
 #
 name: Docs
@@ -43,7 +42,8 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
 
-permissions: {}
+permissions:
+  contents: write
 
 jobs:
   docs:
@@ -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/upload-artifact@v4.6.1
+        uses: actions/upload-artifact@v4.6.2
         if: github.event_name == 'pull_request' && matrix.os == 'ubuntu-latest'
         with:
           name: artifact-pygmt-docs-pdf
@@ -176,7 +176,7 @@ jobs:
           path: deploy
           # Download the entire history
           fetch-depth: 0
-          persist-credentials: false
+          persist-credentials: true
         if: (github.event_name == 'release' || github.event_name == 'push') && (matrix.os == 'ubuntu-latest')
 
       - name: Push the built HTML to gh-pages

.github/workflows/ci_tests.yaml

@@ -49,7 +49,7 @@ concurrency:
 
 jobs:
   test:
-    name: ${{ matrix.os }} - Python ${{ matrix.python-version }} / NumPy ${{ matrix.numpy-version }}
+    name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     permissions:
       id-token: write  # This is required for requesting OIDC token for codecov
@@ -73,7 +73,7 @@ jobs:
           # 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'
+            pandas-version: '=2.1'
             xarray-version: '=2023.04'
             optional-packages: ' contextily geopandas<1 ipython pyarrow-core rioxarray sphinx-gallery'
           # Python 3.13 + core packages (latest versions) + optional packages
@@ -152,7 +152,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5.3.1
+        uses: astral-sh/setup-uv@v5.4.1
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -175,7 +175,7 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v4.6.1
+        uses: actions/upload-artifact@v4.6.2
         if: failure()
         with:
           name: artifact-${{ matrix.os }}-${{ matrix.python-version }}

.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/upload-artifact@v4.6.1
+        uses: actions/upload-artifact@v4.6.2
         if: ${{ failure() }}
         with:
           name: artifact-${{ matrix.os }}-GMT-${{ matrix.gmt_git_ref }}

.github/workflows/format-command.yml

@@ -8,14 +8,15 @@ on:
   repository_dispatch:
     types: [format-command]
 
-permissions: {}
+permissions:
+  contents: write
 
 jobs:
   format:
     runs-on: ubuntu-latest
     steps:
       # Generate token from GenericMappingTools bot
-      - uses: actions/create-github-app-token@v1.11.6
+      - uses: actions/create-github-app-token@v1.12.0
         id: generate-token
         with:
           app-id: ${{ secrets.APP_ID }}
@@ -30,7 +31,7 @@ jobs:
           persist-credentials: false
 
       # Setup Python environment
-      - uses: actions/setup-python@v5.4.0
+      - uses: actions/setup-python@v5.5.0
         with:
           python-version: '3.13'
 

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

@@ -50,7 +50,7 @@ jobs:
         persist-credentials: false
 
     - name: Set up Python
-      uses: actions/setup-python@v5.4.0
+      uses: actions/setup-python@v5.5.0
       with:
         python-version: '3.13'
 
@@ -74,7 +74,7 @@ jobs:
         ls -lh dist/
 
     - name: Store the distribution packages
-      uses: actions/upload-artifact@v4.6.1
+      uses: actions/upload-artifact@v4.6.2
       with:
         name: python-package-distributions
         path: dist/
@@ -93,7 +93,7 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v4.2.0
+      uses: actions/download-artifact@v4.2.1
       with:
         name: python-package-distributions
         path: dist/
@@ -117,7 +117,7 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v4.2.0
+      uses: actions/download-artifact@v4.2.1
       with:
         name: python-package-distributions
         path: dist/

.github/workflows/release-drafter.yml

@@ -1,8 +1,7 @@
 # Draft the next release notes
 #
-# This workflow is run to update the next release notes as pull requests are
-# merged into the main branch. The configuration file is located at
-# `.github/release-drafter.yml`.
+# This workflow is run to update the next release notes as pull requests are merged into
+# the main branch. The configuration file is located at `.github/release-drafter.yml`.
 #
 name: Release Drafter
 
@@ -11,10 +10,14 @@ on:
     branches:
       - main
 
-permissions: {}
+permissions:
+  contents: read
 
 jobs:
   update_release_draft:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
     runs-on: ubuntu-latest
     if: github.repository == 'GenericMappingTools/pygmt'
 

.github/workflows/slash-command-dispatch.yml

@@ -10,7 +10,8 @@ on:
     # Add "edited" type for test purposes. Where possible, avoid using to prevent processing unnecessary events.
     # types: [created, edited]
 
-permissions: {}
+permissions:
+  issues: write
 
 jobs:
   slashCommandDispatch:

.github/workflows/style_checks.yaml

@@ -32,7 +32,7 @@ jobs:
 
       # Setup Python
       - name: Set up Python
-        uses: actions/setup-python@v5.4.0
+        uses: actions/setup-python@v5.5.0
         with:
           python-version: '3.13'
 

.github/workflows/type_checks.yml

@@ -41,7 +41,7 @@ jobs:
 
       # Setup Python
       - name: Set up Python
-        uses: actions/setup-python@v5.4.0
+        uses: actions/setup-python@v5.5.0
         with:
           python-version: '3.13'
 

.mailmap

@@ -0,0 +1,19 @@
+Dongdong Tian <seisman.info@gmail.com>
+Dongdong Tian <seisman.info@gmail.com> <seisman@users.noreply.github.com>
+Jiayuan Yao <coreman.seism@gmail.com>
+Jiayuan Yao <coreman.seism@gmail.com> <core-man@users.noreply.github.com>
+Jing-Hui Tong <86273921+JingHuiTong@users.noreply.github.com>
+Jing-Hui Tong <86273921+JingHuiTong@users.noreply.github.com> <r0922422020@g.ntu.edu.tw>
+Max Jones <14077947+maxrjones@users.noreply.github.com>
+Max Jones <14077947+maxrjones@users.noreply.github.com> <meghanj@alum.mit.edu>
+Max Jones <14077947+maxrjones@users.noreply.github.com> <meghanj@hawaii.edu>
+Max Jones <14077947+maxrjones@users.noreply.github.com> <meghanrjones@users.noreply.github.com>
+Michael Grund <michael_grund@gmx.de> <23025878+michaelgrund@users.noreply.github.com>
+Michael Grund <michael_grund@gmx.de> <michael.grund@kit.edu>
+Michael Grund <michael_grund@gmx.de> <michaelgrund@users.noreply.github.com>
+Wei Ji Leong <23487320+weiji14@users.noreply.github.com>
+Wei Ji Leong <23487320+weiji14@users.noreply.github.com> <weiji.leong@vuw.ac.nz>
+Wei Ji Leong <23487320+weiji14@users.noreply.github.com> <weiji14@users.noreply.github.com>
+Will Schlitzer <schlitzer90@gmail.com> <willschlitzer@users.noreply.github.com>
+Yvonne Fröhlich <94163266+yvonnefroehlich@users.noreply.github.com> <yvonne.froehlich@kit.edu>
+Yvonne Fröhlich <94163266+yvonnefroehlich@users.noreply.github.com> <yfroe@gpiseis16.gpi.kit.edu>

.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