Merge branch 'main' into remove/array-to-datetime

Author: seisman

.github/workflows/ci_docs.yml

@@ -117,6 +117,9 @@ 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
@@ -135,9 +138,11 @@ 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: Checkout the gh-pages branch
         uses: actions/[email protected]

.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
@@ -154,7 +156,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/[email protected].1
+        uses: astral-sh/[email protected].2
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/ci_tests_dev.yaml

@@ -36,7 +36,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-24.04, macos-15, windows-2025]
+        os: [ubuntu-24.04, ubuntu-24.04-arm, macos-15, windows-2025]
         gmt_git_ref: [master]
     timeout-minutes: 30
     defaults:

.github/workflows/ci_tests_legacy.yaml

@@ -34,7 +34,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, macos-13, windows-2019]
+        os: [ubuntu-22.04, ubuntu-22.04-arm, macos-13, windows-2019]
         gmt_version: ['6.4']
     timeout-minutes: 30
     defaults:

.github/workflows/format-command.yml

@@ -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'
 

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

@@ -48,7 +48,7 @@ jobs:
         persist-credentials: false
 
     - name: Set up Python
-      uses: actions/setup-python@v5.3.0
+      uses: actions/setup-python@v5.4.0
       with:
         python-version: '3.13'
 

.github/workflows/style_checks.yaml

@@ -28,7 +28,7 @@ jobs:
 
       # Setup Python
       - name: Set up Python
-        uses: actions/setup-python@v5.3.0
+        uses: actions/setup-python@v5.4.0
         with:
           python-version: '3.13'
 

.github/workflows/type_checks.yml

@@ -37,7 +37,7 @@ jobs:
 
       # Setup Python
       - name: Set up Python
-        uses: actions/setup-python@v5.3.0
+        uses: actions/setup-python@v5.4.0
         with:
           python-version: '3.13'
 

ci/requirements/docs.yml

@@ -32,3 +32,6 @@ dependencies:
     - sphinx-design
     - sphinx-gallery
     - sphinx_rtd_theme<3.0
+    # Dev dependencies (building PDF documentation)
+    # 'sphinxcontrib-svg2pdfconverter' is required since it's added to `extensions`.
+    - sphinxcontrib-svg2pdfconverter

doc/Makefile

@@ -15,6 +15,7 @@ help:
 	@echo "  api          generate rst source files of API documentation"
 	@echo "  html         build the HTML files from the existing rst sources"
 	@echo "  html-noplot  build the HTML files without running any examples"
+	@echo "  pdf          build the PDF documentation"
 	@echo "  server       make a local HTTP server for previewing the built documentation"
 	@echo "  clean        clean up built and generated files"
 
@@ -43,6 +44,14 @@ html-noplot: api
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
+pdf: latex
+	@echo
+	@echo "Building PDF via Tectonic."
+	@echo
+	tectonic -X compile $(BUILDDIR)/latex/pygmt.tex
+	@echo
+	@echo "PDF build finished. The PDF file is in $(BUILDDIR)/latex/pygmt.pdf."
+
 server:
 	@echo
 	@echo "Running a server on port 8009."

doc/conf.py

@@ -28,16 +28,17 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "sphinx.ext.coverage",
-    "sphinx.ext.mathjax",
     "sphinx.ext.doctest",
-    "sphinx.ext.viewcode",
     "sphinx.ext.extlinks",
     "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
     "sphinx_autodoc_typehints",
     "sphinx_copybutton",
     "sphinx_design",
     "sphinx_gallery.gen_gallery",
+    "sphinxcontrib.cairosvgconverter",
 ]
 
 # Suppress warnings
@@ -55,7 +56,7 @@
 myst_enable_extensions = [
     "attrs_inline",  # Allow inline attributes after images
     "colon_fence",  # Allow code fences using colons
-    "substitution",  # Allow substituitions
+    "substitution",  # Allow substitutions
 ]
 # These enable substitutions using {{ key }} in the Markdown files
 myst_substitutions = {
@@ -248,3 +249,6 @@
     "github_version": "main",
     "commit": commit_link,
 }
+
+# Configurations for LaTeX
+latex_engine = "xelatex"

environment.yml

@@ -44,6 +44,10 @@ dependencies:
     - sphinx-design
     - sphinx-gallery>=0.17.0
     - sphinx_rtd_theme<3.0
+    # Dev dependencies (building PDF documentation)
+    - cairosvg
+    - sphinxcontrib-svg2pdfconverter
+    - tectonic
     # Dev dependencies (type hints)
     - mypy
     - pandas-stubs

pygmt/tests/test_contour.py

@@ -2,6 +2,7 @@
 Test Figure.contour.
 """
 
+import platform
 from pathlib import Path
 
 import numpy as np
@@ -30,6 +31,7 @@ def fixture_region():
 
 
 @pytest.mark.mpl_image_compare
+@pytest.mark.xfail(platform.machine() == "aarch64", reason="Fails on Linux ARM64")
 def test_contour_vec(region):
     """
     Plot an x-centered gaussian kernel with different y scale.
@@ -130,6 +132,7 @@ def test_contour_multiple_levels(region):
 
 
 @pytest.mark.mpl_image_compare(filename="test_contour_vec.png")
+@pytest.mark.xfail(platform.machine() == "aarch64", reason="Fails on Linux ARM64")
 def test_contour_incols_transposed_data(region):
     """
     Make sure that transposing the data matrix still produces a correct result with

pygmt/tests/test_x2sys_cross.py

@@ -3,6 +3,7 @@
 """
 
 import copy
+import platform
 import sys
 from pathlib import Path
 from tempfile import TemporaryDirectory
@@ -270,7 +271,7 @@ def test_x2sys_cross_region_interpolation_numpoints():
         )
 
         assert isinstance(output, pd.DataFrame)
-        if sys.platform == "darwin":
+        if platform.machine() in {"aarch64", "arm64"}:
             assert output.shape == (3894, 12)
             # Check crossover errors (z_X) and mean value of observables (z_M)
             npt.assert_allclose(output.z_X.mean(), -138.23215, rtol=1e-4)
@@ -298,7 +299,7 @@ def test_x2sys_cross_trackvalues():
         output = x2sys_cross(tracks=["@tut_ship.xyz"], tag=tag, trackvalues=True)
 
         assert isinstance(output, pd.DataFrame)
-        if sys.platform == "darwin":
+        if platform.machine() in {"aarch64", "arm64"}:
             assert output.shape == (14374, 12)
             # Check mean of track 1 values (z_1) and track 2 values (z_2)
             npt.assert_allclose(output.z_1.mean(), -2422.973372, rtol=1e-4)