Merge branch 'main' into refactor/meca-convention

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -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:
   - [ ] 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/workflows/benchmarks.yml

@@ -45,7 +45,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.3
+        uses: mamba-org/setup-micromamba@v2.0.4
         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/setup-micromamba@v2.0.3
+        uses: mamba-org/setup-micromamba@v2.0.4
         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@v4.5.0
+        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/setup-micromamba@v2.0.3
+        uses: mamba-org/setup-micromamba@v2.0.4
         with:
           environment-name: pygmt
           condarc: |
@@ -163,9 +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/setup-micromamba@v2.0.3
+        uses: mamba-org/setup-micromamba@v2.0.4
         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/setup-micromamba@v2.0.3
+        uses: mamba-org/setup-micromamba@v2.0.4
         with:
           environment-name: pygmt
           condarc: |
@@ -154,7 +154,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5.1.0
+        uses: astral-sh/setup-uv@v5.2.1
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -177,15 +177,15 @@ jobs:
 
       # Upload diff images on test failure
       - name: Upload diff images if any test fails
-        uses: actions/upload-artifact@v4.5.0
+        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/codecov-action@v5.1.2
+        uses: codecov/codecov-action@v5.3.1
         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/setup-micromamba@v2.0.3
+        uses: mamba-org/setup-micromamba@v2.0.4
         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@v4.5.0
+        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

@@ -34,7 +34,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macos-13, windows-2019]
+        os: [ubuntu-22.04, macos-13, windows-2019]
         gmt_version: ['6.4']
     timeout-minutes: 30
     defaults:
@@ -51,7 +51,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v2.0.3
+        uses: mamba-org/setup-micromamba@v2.0.4
         with:
           environment-name: pygmt
           condarc: |

.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/checkout@v4.2.2
       with:
         # fetch all history so that setuptools-scm works
         fetch-depth: 0
+        persist-credentials: false
 
     - name: Set up Python
       uses: actions/setup-python@v5.3.0
@@ -74,11 +71,54 @@ jobs:
         echo "Generated files:"
         ls -lh dist/
 
-    - name: Publish to Test PyPI
-      uses: pypa/gh-action-pypi-publish@v1.12.3
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4.6.0
+      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/download-artifact@v4.1.8
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@v1.12.4
       with:
         repository-url: https://test.pypi.org/legacy/
 
-    - name: Publish to PyPI
-      if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@v1.12.3
+  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/download-artifact@v4.1.8
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@v1.12.4

.github/workflows/release-drafter.yml

@@ -18,7 +18,7 @@ jobs:
 
     steps:
       # Drafts your next Release notes as Pull Requests are merged into "main"
-      - uses: release-drafter/release-drafter@v6.0.0
+      - uses: release-drafter/release-drafter@v6.1.0
         with:
           # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
           config-name: release-drafter.yml

CITATION.cff

@@ -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: 2024-12-31
-doi: 10.5281/zenodo.14535921
+date-released: 2025-02-01
+doi: 10.5281/zenodo.14742338
 license: BSD-3-Clause
 repository-code: https://github.com/GenericMappingTools/pygmt
 type: software
-version: 0.14.0
+version: 0.14.1

README.md

@@ -137,7 +137,7 @@ Feel free to cite our work in your research using the following BibTeX:
 
 ```
 @software{
-  pygmt_2024_14535921,
+  pygmt_2025_14742338,
   author       = {Tian, Dongdong and
                   Uieda, Leonardo and
                   Leong, Wei Ji and
@@ -157,12 +157,12 @@ Feel free to cite our work in your research using the following BibTeX:
                   Quinn, Jamie and
                   Wessel, Paul},
   title        = {{PyGMT: A Python interface for the Generic Mapping Tools}},
-  month        = dec,
-  year         = 2024,
+  month        = feb,
+  year         = 2025,
   publisher    = {Zenodo},
-  version      = {0.14.0},
-  doi          = {10.5281/zenodo.14535921},
-  url          = {https://doi.org/10.5281/zenodo.14535921}
+  version      = {0.14.1},
+  doi          = {10.5281/zenodo.14742338},
+  url          = {https://doi.org/10.5281/zenodo.14742338}
 }
 ```
 

doc/Makefile

@@ -1,14 +1,12 @@
 # Makefile for Sphinx documentation
 
 # You can set these variables from the command line.
-SPHINXOPTS    = -j auto
-SPHINXBUILD   = sphinx-build
+SPHINXOPTS    ?= -j auto
+SPHINXBUILD   ?= sphinx-build
 SPHINXAUTOGEN = sphinx-autogen
+SOURCEDIR     = .
 BUILDDIR      = _build
 
-# Internal variables.
-ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees  $(SPHINXOPTS) .
-
 .PHONY: help all api html server clean
 
 help:
@@ -28,20 +26,20 @@ api:
 	@echo
 	$(SPHINXAUTOGEN) -i -t _templates -o api/generated api/*.rst
 
-html: api
+html latex: api
 	@echo
-	@echo "Building HTML files."
+	@echo "Building "$@" files."
 	@echo
 	# Set PYGMT_USE_EXTERNAL_DISPLAY to "false" to disable external display
-	PYGMT_USE_EXTERNAL_DISPLAY="false" $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	PYGMT_USE_EXTERNAL_DISPLAY="false" $(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS)
 	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+	@echo "Build finished. The files are in $(BUILDDIR)/$@."
 
 html-noplot: api
 	@echo
 	@echo "Building HTML files without example plots."
 	@echo
-	$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) -D plot_gallery=0
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 

doc/_static/version_switch.js

@@ -12,6 +12,7 @@
   var all_versions = {
     'latest': 'latest',
     'dev': 'dev',
+    'v0.14.1': 'v0.14.1',
     'v0.14.0': 'v0.14.0',
     'v0.13.0': 'v0.13.0',
     'v0.12.0': 'v0.12.0',