Merge branch 'main' into remove-sequence_join-separator

Author: seisman

.github/ISSUE_TEMPLATE/4-release_checklist.md

@@ -28,6 +28,7 @@ assignees: ''
   - [ ] 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)
+  - [ ] All links work in the ["Check Links" workflow](https://github.com/GenericMappingTools/pygmt/actions/workflows/check-links.yml)
 - [ ] 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)
@@ -52,7 +53,7 @@ assignees: ''
 - [ ] 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; 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)
+  - [ ] [ResearchGate](https://www.researchgate.net) (after forum announcement; download the ZIP file of the new release from Zenodo 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/check-links.yml

@@ -63,6 +63,7 @@ jobs:
           --exclude "^https://hackmd.io/@pygmt"
           --exclude "^https://test.pypi.org/simple/"
           --exclude "^https://www.adobe.com/jp/print/postscript/pdfs/PLRM.pdf"
+          --exclude "^https://naciscdn.org/naturalearth"
           --exclude "^https://www.generic-mapping-tools.org/remote-datasets/%s$"
           --exclude "^https://www.gnu.org/software/libc/manual/html_node/TZ-Variable.html"
           --exclude "^https://www.pygmt.org/%7B%7Bpath%7D%7D"

.github/workflows/ci_tests.yaml

@@ -151,7 +151,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@681c641aba71e4a1c380be3ab5e12ad51f415867 # v7.1.6
+        uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0
         with:
           activate-environment: true
           python-version: ${{ matrix.python-version }}

.github/workflows/ci_tests_dev.yaml

@@ -103,44 +103,30 @@ jobs:
 
       # Build GMT from source on Linux/macOS, script is adapted from
       # https://github.com/GenericMappingTools/gmt/blob/6.5.0/ci/build-gmt.sh
-      - name: Build GMT on Linux/macOS
-        run: |
-          cd gmt/
-          mkdir build
-          cd build
-          cmake -G Ninja .. \
-            -DCMAKE_INSTALL_PREFIX=${GMT_INSTALL_DIR} \
-            -DCMAKE_BUILD_TYPE=Release \
-            -DGMT_ENABLE_OPENMP=TRUE \
-            -DGMT_USE_THREADS=TRUE
-          cmake --build .
-          cmake --build . --target install
-          cd ..
-          rm -rf gmt/
-        env:
-          GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir
-        if: runner.os != 'Windows'
-
-      - name: Build GMT on Windows
+      - name: Build GMT from source
         shell: bash
         run: |
           cd gmt/
           mkdir build
           cd build
-          cmd.exe /c "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+            cmd.exe /c "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+            CMAKE_PREFIX_PATH="$MAMBA_ROOT_PREFIX/envs/pygmt/Library"
+          else
+            CMAKE_PREFIX_PATH="$MAMBA_ROOT_PREFIX/envs/pygmt"
+          fi
           cmake -G Ninja .. \
+            -DCMAKE_PREFIX_PATH="$CMAKE_PREFIX_PATH" \
             -DCMAKE_INSTALL_PREFIX="$GMT_INSTALL_DIR" \
             -DCMAKE_BUILD_TYPE=Release \
-            -DCMAKE_PREFIX_PATH="$MAMBA_ROOT_PREFIX/envs/pygmt/Library" \
             -DGMT_ENABLE_OPENMP=TRUE \
             -DGMT_USE_THREADS=TRUE
           cmake --build .
           cmake --build . --target install
           cd ..
-          rm -rf gmt/
+          rm -rf build
         env:
           GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir
-        if: runner.os == 'Windows'
 
       - name: Add GMT's bin to PATH
         run: echo '${{ runner.temp }}/gmt-install-dir/bin' >> $GITHUB_PATH

examples/tutorials/basics/plot.py

@@ -13,7 +13,7 @@
 import io
 
 import pygmt
-from pygmt.params import Position
+from pygmt.params import Box, Position
 
 # %%
 # For example, let's load the sample dataset of tsunami generating earthquakes
@@ -72,7 +72,12 @@
 legend = io.StringIO(
     "\n".join(f"S 0.4 c {0.02 * 2**m:.2f} - 1p 1 Mw {m}" for m in [3, 4, 5])
 )
-fig.legend(spec=legend, position=Position("BR", offset=0.2), line_spacing=2.0, box=True)
+fig.legend(
+    spec=legend,
+    position=Position("BR", offset=0.2),
+    line_spacing=2,
+    box=Box(fill="white", pen="black"),
+)
 fig.show()
 
 # %%
@@ -104,7 +109,12 @@
     pen="black",
 )
 fig.colorbar(frame="xaf+lDepth (km)")
-fig.legend(spec=legend, position=Position("BR", offset=0.2), line_spacing=2.0, box=True)
+fig.legend(
+    spec=legend,
+    position=Position("BR", offset=0.2),
+    line_spacing=2,
+    box=Box(fill="white", pen="black"),
+)
 fig.show()
 
 # sphinx_gallery_thumbnail_number = 3

pygmt/src/binstats.py

@@ -9,6 +9,7 @@
 from pygmt._typing import PathLike, TableLike
 from pygmt.alias import Alias, AliasSystem
 from pygmt.clib import Session
+from pygmt.exceptions import GMTTypeError, GMTValueError
 from pygmt.helpers import build_arg_list, fmt_docstring, use_alias
 
 
@@ -166,6 +167,16 @@ def binstats(
     )
     aliasdict.merge(kwargs)
     if statistic == "quantile":
+        if not isinstance(quantile_value, (int, float)):
+            raise GMTTypeError(
+                quantile_value, reason="quantile_value must be an 'int' or 'float'."
+            )
+        if not (0 <= quantile_value <= 100):
+            raise GMTValueError(
+                quantile_value,
+                description="quantile_value",
+                reason="Must be a value between 0 and 100.",
+            )
         aliasdict["C"] += f"{quantile_value}"
 
     with Session() as lib:

pygmt/src/config.py

@@ -2,6 +2,7 @@
 config - Change GMT default settings globally or locally.
 """
 
+import warnings
 from inspect import Parameter, Signature
 from typing import ClassVar
 
@@ -22,6 +23,12 @@ class config:  # noqa: N801
             ...
 
     Full GMT defaults list at :gmt-docs:`gmt.conf.html`.
+
+    .. note::
+
+        :gmt-term:`PS_CONVERT` is not supported.
+        To configure conversion options, please pass parameters to
+        :meth:`pygmt.Figure.savefig` or :meth:`pygmt.Figure.show` instead.
     """
 
     # Manually set the __signature__ attribute to enable tab autocompletion
@@ -135,7 +142,7 @@ class config:  # noqa: N801
         "PS_CHAR_ENCODING",
         "PS_COLOR_MODEL",
         "PS_COMMENTS",
-        "PS_CONVERT",
+        # "PS_CONVERT",  # Not supported; use parameters of Figure.savefig/show instead
         "PS_IMAGE_COMPRESS",
         "PS_LINE_CAP",
         "PS_LINE_JOIN",
@@ -188,6 +195,16 @@ class config:  # noqa: N801
     )
 
     def __init__(self, **kwargs):
+        if "PS_CONVERT" in kwargs:
+            warnings.warn(
+                message="Parameter 'PS_CONVERT' is not supported. "
+                "To configure conversion options, please pass parameters to "
+                "pygmt.Figure.savefig or pygmt.Figure.show instead.",
+                category=SyntaxWarning,
+                stacklevel=2,
+            )
+            kwargs.pop("PS_CONVERT")
+
         # Save values so that we can revert to their initial values
         self.old_defaults = {}
         with Session() as lib:

pygmt/src/grdfill.py

@@ -78,6 +78,7 @@ def _validate_params(
 @fmt_docstring
 # TODO(PyGMT>=0.19.0): Remove the deprecated 'no_data' parameter.
 # TODO(PyGMT>=0.19.0): Remove the deprecated 'mode' parameter.
+# TODO(PyGMT>=0.20.0): Remove the deprecated '*fill' parameters.
 @deprecate_parameter("no_data", "hole", "v0.15.0", remove_version="v0.19.0")
 @deprecate_parameter(
     "constantfill", "constant_fill", "v0.18.0", remove_version="v0.20.0"

pygmt/src/grdlandmask.py

@@ -16,6 +16,8 @@
 
 
 @fmt_docstring
+# TODO(PyGMT>=0.20.0): Remove the deprecated 'maskvalues' parameter.
+# TODO(PyGMT>=0.20.0): Remove the deprecated 'bordervalues' parameter.
 @deprecate_parameter("maskvalues", "mask_values", "v0.18.0", remove_version="v0.20.0")
 @deprecate_parameter(
     "bordervalues", "border_values", "v0.18.0", remove_version="v0.20.0"

pygmt/src/grdview.py

@@ -17,6 +17,8 @@
 
 
 @fmt_docstring
+# TODO(PyGMT>=0.20.0): Remove the deprecated '*pen' parameters.
+# TODO(PyGMT>=0.20.0): Remove the deprecated 'drapegrid' parameter.
 @deprecate_parameter("contourpen", "contour_pen", "v0.18.0", remove_version="v0.20.0")
 @deprecate_parameter("facadepen", "facade_pen", "v0.18.0", remove_version="v0.20.0")
 @deprecate_parameter("meshpen", "mesh_pen", "v0.18.0", remove_version="v0.20.0")