Merge branch 'main' into feature/scatter

Author: seisman

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -1,6 +1,6 @@
 ---
 name: PyGMT release checklist
-about: Checklist for a new PyGMT release.
+about: Checklist for a new PyGMT release. [For project maintainers only!]
 title: Release PyGMT vX.Y.Z
 labels: maintenance
 assignees: ''
@@ -19,17 +19,15 @@ 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.
 - [ ] 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
+  - [ ] Deprecated workarounds/codes/tests are removed. Run `grep "# TODO" **/*.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)
-- [ ] 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
+- [ ] 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)
 - [ ] Run `make codespell` to check common misspellings. If there are any, either fix them or add them to `ignore-words-list` in `pyproject.toml`
@@ -41,18 +39,16 @@ 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
-- [ ] 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
+- [ ] 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 Python and SPEC0 versions]
+- [ ] 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]
 - [ ] 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, add new version 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 the release page 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/ISSUE_TEMPLATE/5-bump_gmt_checklist.md

@@ -1,6 +1,6 @@
 ---
 name: Bump GMT version checklist
-about: Checklist for bumping the minimum required GMT version.
+about: Checklist for bumping the minimum required GMT version. [For project maintainers only!]
 title: Bump to GMT X.Y.Z
 labels: maintenance
 assignees: ''

.github/PULL_REQUEST_TEMPLATE.md

@@ -20,7 +20,6 @@ Fixes #
 - [ ] 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.
-- [ ] Use underscores (not hyphens) in names of Python files and directories.
 
 **Slash Commands**
 

.github/workflows/benchmarks.yml

@@ -45,14 +45,9 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].3
+        uses: mamba-org/[email protected].4
         with:
           environment-name: pygmt
-          condarc: |
-            channels:
-              - conda-forge
-              - nodefaults
-          cache-downloads: false
           cache-environment: true
           # environment cache is persistent for one week.
           cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
@@ -87,7 +82,7 @@ jobs:
 
       # Run the benchmark tests
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v3.2.0
+        uses: CodSpeedHQ/action@v3.4.0
         with:
           # 'bash -el -c' is needed to use the custom shell.
           # See https://github.com/CodSpeedHQ/action/issues/65.

.github/workflows/cache_data.yaml

@@ -43,13 +43,9 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].3
+        uses: mamba-org/[email protected].4
         with:
           environment-name: pygmt
-          condarc: |
-            channels:
-              - conda-forge
-              - nodefaults
           create-args: >-
             python=3.13
             gmt=6.5.0
@@ -76,7 +72,7 @@ jobs:
 
       # Upload the downloaded files as artifacts to GitHub
       - name: Upload artifacts to GitHub
-        uses: actions/upload-artifact@v4.4.3
+        uses: actions/upload-artifact@v4.6.1
         with:
           name: gmt-cache
           include-hidden-files: true

.github/workflows/check-links.yml

@@ -35,7 +35,7 @@ jobs:
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/lychee-action@v2.1.0
+      uses: lycheeverse/lychee-action@v2.3.0
       with:
         fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md

.github/workflows/ci_docs.yml

@@ -80,14 +80,9 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].3
+        uses: mamba-org/[email protected].4
         with:
           environment-name: pygmt
-          condarc: |
-            channels:
-              - conda-forge
-              - nodefaults
-          cache-downloads: false
           cache-environment: true
           # environment cache is persistent for one week.
           cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
@@ -108,6 +103,7 @@ jobs:
             make
             pip
             python-build
+            geodatasets
             myst-nb
             panel
             sphinx>=6.2
@@ -116,6 +112,9 @@ jobs:
             sphinx-design
             sphinx-gallery
             sphinx_rtd_theme<3.0
+            cairosvg
+            sphinxcontrib-svg2pdfconverter
+            tectonic
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
@@ -134,9 +133,36 @@ jobs:
           python -m build --sdist
           python -m pip install dist/*
 
-      # Build the documentation
-      - name: Build the documentation
-        run: make -C doc clean all
+      - name: Build the HTML documentation
+        run: make -C doc clean html
+
+      - name: Build the PDF documentation
+        run:  make -C doc pdf
+
+      - name: Create the HTML ZIP archive and rename the PDF file
+        run: |
+          cd doc/_build/
+          cp -r html/ pygmt-docs/
+          zip -r pygmt-docs.zip pygmt-docs/
+          mv latex/pygmt.pdf pygmt-docs.pdf
+          cd ../..
+
+      - name: Upload PDF as artifact for previewing on pull requests
+        uses: actions/[email protected]
+        if: github.event_name == 'pull_request' && matrix.os == 'ubuntu-latest'
+        with:
+          name: artifact-pygmt-docs-pdf
+          path: doc/_build/pygmt-docs.pdf
+
+      - name: Copy the HTML ZIP archive and PDF to the html folder for dev version
+        run: cp -v doc/_build/pygmt-docs.zip doc/_build/pygmt-docs.pdf doc/_build/html/
+        if: github.event_name == 'push' && matrix.os == 'ubuntu-latest'
+
+      - name: Upload the HTML ZIP archive and PDF as release assets
+        run: gh release upload ${{ github.ref_name }} doc/_build/pygmt-docs.zip doc/_build/pygmt-docs.pdf
+        if: github.event_name == 'release' && matrix.os == 'ubuntu-latest'
+        env:
+          GH_TOKEN: ${{ github.token }}
 
       - name: Checkout the gh-pages branch
         uses: actions/[email protected]
@@ -162,9 +188,14 @@ jobs:
           # to get the right commit hash.
           message="Deploy $version from $(git rev-parse --short HEAD)"
           cd deploy
-          # Need to have this file so that GitHub doesn't try to run Jekyll
+          # Create some files in the root directory.
+          # .nojekyll: Need to have this file so that GitHub doesn't try to run Jekyll
           touch .nojekyll
-          # Delete all the files and replace with our new  set
+          # CNAME: Set the custom domain name
+          echo "www.pygmt.org" > CNAME
+          # index.html: Redirect to the latest version
+          echo '<meta http-equiv="Refresh" content="0;url=latest/"/>' > index.html
+          # Delete all the files and replace with our new set
           echo -e "\nRemoving old files from previous builds of ${version}:"
           rm -rvf ${version}
           echo -e "\nCopying HTML files to ${version}:"

.github/workflows/ci_doctests.yaml

@@ -42,13 +42,9 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].3
+        uses: mamba-org/[email protected].4
         with:
           environment-name: pygmt
-          condarc: |
-            channels:
-              - conda-forge
-              - nodefaults
           create-args: >-
             python=3.13
             gmt=6.5.0

.github/workflows/ci_tests.yaml

@@ -57,12 +57,14 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ['3.11', '3.13']
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, ubuntu-24.04-arm, macos-latest, windows-latest]
         # Is it a draft Pull Request (true or false)?
         isDraft:
           - ${{ github.event.pull_request.draft }}
-        # Only run three jobs on Ubuntu for draft PRs
+        # Only run jobs on Ubuntu for draft PRs
         exclude:
+          - os: ubuntu-24.04-arm
+            isDraft: true
           - os: macos-latest
             isDraft: true
           - os: windows-latest
@@ -113,14 +115,9 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].3
+        uses: mamba-org/[email protected].4
         with:
           environment-name: pygmt
-          condarc: |
-            channels:
-              - conda-forge
-              - nodefaults
-          cache-downloads: false
           cache-environment: true
           # environment cache is persistent for one week.
           cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
@@ -154,20 +151,18 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/[email protected]
+        uses: astral-sh/[email protected]
+        with:
+          python-version: ${{ matrix.python-version }}
 
       - name: Install dvc
         run: |
-          uv venv
-          source .venv/bin/activate
           uv pip install dvc
           uv pip list
 
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote
-        run: |
-          source .venv/bin/activate
-          uv run dvc pull --no-run-cache --verbose && ls -lhR pygmt/tests/baseline/
+        run: uv run dvc pull --no-run-cache --verbose && ls -lhR pygmt/tests/baseline/
 
       # Install the package that we want to test
       - name: Install the package
@@ -179,15 +174,15 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v4.4.3
+        uses: actions/upload-artifact@v4.6.1
         if: failure()
         with:
-          name: artifact-${{ runner.os }}-${{ matrix.python-version }}
+          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@v5.1.1
+        uses: codecov/codecov-action@v5.3.1
         if: success() || failure()
         with:
           use_oidc: true

.github/workflows/ci_tests_dev.yaml

@@ -36,7 +36,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-24.04, macos-15, windows-2022]
+        os: [ubuntu-24.04, ubuntu-24.04-arm, macos-15, windows-2025]
         gmt_git_ref: [master]
     timeout-minutes: 30
     defaults:
@@ -57,14 +57,9 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].3
+        uses: mamba-org/[email protected].4
         with:
           environment-name: pygmt
-          condarc: |
-            channels:
-              - conda-forge
-              - nodefaults
-          cache-downloads: false
           cache-environment: true
           # environment cache is persistent for one week.
           cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
@@ -187,8 +182,8 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v4.4.3
+        uses: actions/upload-artifact@v4.6.1
         if: ${{ failure() }}
         with:
-          name: artifact-GMT-${{ matrix.gmt_git_ref }}-${{ runner.os }}
+          name: artifact-${{ matrix.os }}-GMT-${{ matrix.gmt_git_ref }}
           path: tmp-test-dir-with-unique-name

.github/workflows/ci_tests_legacy.yaml

@@ -34,7 +34,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macos-13, windows-2019]
+        os: [ubuntu-22.04, ubuntu-22.04-arm, macos-13, windows-2019]
         gmt_version: ['6.4']
     timeout-minutes: 30
     defaults:
@@ -51,13 +51,9 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].3
+        uses: mamba-org/[email protected].4
         with:
           environment-name: pygmt
-          condarc: |
-            channels:
-              - conda-forge
-              - nodefaults
           create-args: >-
             python=3.11
             gmt=${{ matrix.gmt_version }}

.github/workflows/format-command.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Generate token from GenericMappingTools bot
-      - uses: actions/[email protected].0
+      - uses: actions/[email protected].6
         id: generate-token
         with:
           app-id: ${{ secrets.APP_ID }}
@@ -25,7 +25,7 @@ jobs:
           ref: ${{ github.event.client_payload.pull_request.head.ref }}
 
       # Setup Python environment
-      - uses: actions/setup-python@v5.3.0
+      - uses: actions/setup-python@v5.4.0
         with:
           python-version: '3.13'