Merge branch 'main' into add-tut-symbols

.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

@@ -45,7 +45,7 @@ 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: |

.github/workflows/cache_data.yaml

@@ -43,7 +43,7 @@ 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: |
@@ -76,7 +76,7 @@ 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@v4.6.0
         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@v2.2.0
       with:
         fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md

.github/workflows/ci_docs.yml

@@ -80,7 +80,7 @@ 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: |
@@ -108,6 +108,7 @@ jobs:
             make
             pip
             python-build
+            geodatasets
             myst-nb
             panel
             sphinx>=6.2
@@ -162,9 +163,14 @@ 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

@@ -42,7 +42,7 @@ 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: |

.github/workflows/ci_tests.yaml

@@ -113,7 +113,7 @@ 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: |
@@ -154,20 +154,18 @@ 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 +177,15 @@ 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@v4.6.0
         if: failure()
         with:
           name: artifact-${{ runner.os }}-${{ matrix.python-version }}
           path: tmp-test-dir-with-unique-name
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/[email protected].1
+        uses: codecov/[email protected].2
         if: success() || failure()
         with:
           use_oidc: true

.github/workflows/ci_tests_dev.yaml

@@ -57,7 +57,7 @@ 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: |
@@ -187,7 +187,7 @@ 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@v4.6.0
         if: ${{ failure() }}
         with:
           name: artifact-GMT-${{ matrix.gmt_git_ref }}-${{ runner.os }}

.github/workflows/ci_tests_legacy.yaml

@@ -51,7 +51,7 @@ 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: |

.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].1
         id: generate-token
         with:
           app-id: ${{ secrets.APP_ID }}

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

@@ -35,20 +35,17 @@ on:
   #    - main
 
 jobs:
-  publish-pypi:
-    name: Publish to PyPI
+  build:
+    name: Build distribution 📦
     runs-on: ubuntu-latest
-    permissions:
-      # This permission is mandatory for OIDC publishing
-      id-token: write
-    if: github.repository == 'GenericMappingTools/pygmt'
 
     steps:
     - name: Checkout
       uses: actions/[email protected]
       with:
         # fetch all history so that setuptools-scm works
         fetch-depth: 0
+        persist-credentials: false
 
     - name: Set up Python
       uses: actions/[email protected]
@@ -74,11 +71,54 @@ jobs:
         echo "Generated files:"
         ls -lh dist/
 
-    - name: Publish to Test PyPI
+    - name: Store the distribution packages
+      uses: actions/[email protected]
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    if: github.repository == 'GenericMappingTools/pygmt'
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/project/pygmt
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted OIDC publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/[email protected]
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish distribution 📦 to TestPyPI
       uses: pypa/[email protected]
       with:
         repository-url: https://test.pypi.org/legacy/
 
-    - name: Publish to PyPI
-      if: startsWith(github.ref, 'refs/tags')
+  publish-pypi:
+    name: Publish Python 🐍 distribution 📦 to PyPI
+    if: github.repository == 'GenericMappingTools/pygmt' && startsWith(github.ref, 'refs/tags/')
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/pygmt/
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted OIDC publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/[email protected]
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish distribution 📦 to PyPI
       uses: pypa/[email protected]

.github/workflows/style_checks.yaml

@@ -52,3 +52,15 @@ jobs:
             rm output.txt
             exit $nfiles
           fi
+
+      - name: Ensure hyphens are not used in names of directories and Python files
+        run: |
+          git ls-files '*.py' | grep '-' > output.txt || true
+          git ls-tree -rd --name-only HEAD | grep '-' >> output.txt || true
+          nfiles=$(wc --lines output.txt | awk '{print $1}')
+          if [[ $nfiles > 0 ]]; then
+            echo "Following directories/files use hyphens in file names:"
+            cat output.txt
+            rm output.txt
+            exit $nfiles
+          fi

CITATION.cff

@@ -40,14 +40,14 @@ authors:
   family-names: Yao
   affiliation: Nanyang Technological University, Singapore
   orcid: https://orcid.org/0000-0001-7036-4238
+- given-names: Jing-Hui
+  family-names: Tong
+  affiliation: National Taiwan Normal University, Taiwan
+  orcid: https://orcid.org/0009-0002-7195-3071
 - given-names: Yohai
   family-names: Magen
   affiliation: Tel Aviv University, Israel
   orcid: https://orcid.org/0000-0002-4892-4013
-- given-names: Tong
-  family-names: Jing-Hui
-  affiliation: National Taiwan Normal University, Taiwan
-  orcid: https://orcid.org/0009-0002-7195-3071
 - given-names: Kathryn
   family-names: Materna
   affiliation: US Geological Survey, USA
@@ -76,9 +76,9 @@ authors:
   family-names: Wessel
   affiliation: University of Hawaiʻi at Mānoa, USA
   orcid: https://orcid.org/0000-0001-5708-7336
-date-released: 2024-09-05
-doi: 10.5281/zenodo.13679420
+date-released: 2024-12-31
+doi: 10.5281/zenodo.14535921
 license: BSD-3-Clause
 repository-code: https://github.com/GenericMappingTools/pygmt
 type: software
-version: 0.13.0
+version: 0.14.0

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2017-2024 The PyGMT Developers
+Copyright (c) 2017-2025 The PyGMT Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,