Merge branch 'main' into refactor/check_kind

Author: seisman

.github/workflows/check-links.yml

@@ -40,7 +40,7 @@ jobs:
 
     - name: Link Checker
       id: lychee
-      uses: lycheeverse/[email protected].0
+      uses: lycheeverse/[email protected].1
       with:
         fail: false  # Don't fail action on broken links
         output: /tmp/lychee-out.md
@@ -63,9 +63,11 @@ jobs:
           --exclude "^https://test.pypi.org/simple/"
           --exclude "^https://www.adobe.com/jp/print/postscript/pdfs/PLRM.pdf"
           --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"
           --exclude "^https://www.researchgate.net/"
           --exclude "^https://zenodo.org/badge/DOI/"
+          --exclude "^https://stackoverflow.com/a/69170441"
           --verbose
           "repository/*.md"
           "repository/**/*.py"

.github/workflows/ci_tests.yaml

@@ -151,7 +151,7 @@ jobs:
           GH_TOKEN: ${{ github.token }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v6.0.1
+        uses: astral-sh/setup-uv@v6.1.0
         with:
           activate-environment: true
           python-version: ${{ matrix.python-version }}
@@ -183,7 +183,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/[email protected].2
+        uses: codecov/[email protected].3
         if: success() || failure()
         with:
           use_oidc: true

pygmt/datasets/load_remote_dataset.py

@@ -7,10 +7,7 @@
 from typing import Any, Literal, NamedTuple
 
 import xarray as xr
-from pygmt.clib import Session
 from pygmt.exceptions import GMTInvalidInput
-from pygmt.helpers import build_arg_list, kwargs_to_strings
-from pygmt.src import which
 
 with contextlib.suppress(ImportError):
     # rioxarray is needed to register the rio accessor
@@ -502,7 +499,6 @@ class GMTRemoteDataset(NamedTuple):
 }
 
 
-@kwargs_to_strings(region="sequence")
 def _load_remote_dataset(
     name: str,
     prefix: str,
@@ -581,22 +577,9 @@ def _load_remote_dataset(
         raise GMTInvalidInput(msg)
 
     fname = f"@{prefix}_{resolution}_{reg}"
-    kwdict = {"R": region, "T": {"grid": "g", "image": "i"}[dataset.kind]}
-    with Session() as lib:
-        with lib.virtualfile_out(kind=dataset.kind) as voutgrd:
-            lib.call_module(
-                module="read",
-                args=[fname, voutgrd, *build_arg_list(kwdict)],
-            )
-            grid = lib.virtualfile_to_raster(
-                kind=dataset.kind, outgrid=None, vfname=voutgrd
-            )
-
-    # Full path to the grid if not tiled grids.
-    source = which(fname, download="a") if not resinfo.tiled else None
-    # Manually add source to xarray.DataArray encoding to make the GMT accessors work.
-    if source:
-        grid.encoding["source"] = source
+    grid = xr.load_dataarray(
+        fname, engine="gmt", raster_kind=dataset.kind, region=region
+    )
 
     # Add some metadata to the grid
     grid.attrs["description"] = dataset.description

pygmt/figure.py

@@ -4,6 +4,7 @@
 
 import base64
 import os
+import warnings
 from pathlib import Path
 from tempfile import TemporaryDirectory
 from typing import Literal, overload
@@ -119,12 +120,19 @@ def _activate_figure(self) -> None:
         with Session() as lib:
             lib.call_module(module="figure", args=[self._name, fmt])
 
+    # TODO(PyGMT>=v0.18.0):  Remove the _preprocess method.
     def _preprocess(self, **kwargs):
         """
         Call the ``figure`` module before each plotting command to ensure we're plotting
         to this particular figure.
         """
         self._activate_figure()
+        warnings.warn(
+            "The Figure._preprocess() method is deprecated since v0.16.0 and will be "
+            "removed in v0.18.0. Use Figure._activate_figure() instead.",
+            FutureWarning,
+            stacklevel=2,
+        )
         return kwargs
 
     @property

pygmt/helpers/caching.py

@@ -13,53 +13,76 @@ def cache_data() -> None:
     datasets = [
         # List of GMT remote datasets.
         "@earth_age_01d_g",
-        "@earth_day_01d",
-        "@earth_dist_01d",
-        "@earth_edefl_01d",
+        "@earth_age_30m_g",
+        "@earth_day_01d_p",
+        "@earth_dist_01d_g",
+        "@earth_dist_30m_g",
+        "@earth_edefl_01d_g",
+        "@earth_edefl_30m_g",
         "@earth_faa_01d_g",
+        "@earth_faa_30m_g",
         "@earth_faaerror_01d_g",
         "@earth_gebco_01d_g",
         "@earth_gebcosi_01d_g",
         "@earth_gebcosi_15m_p",
         "@earth_geoid_01d_g",
+        "@earth_geoid_30m_g",
         "@earth_mag_01d_g",
+        "@earth_mag_30m_g",
         "@earth_mag4km_01d_g",
+        "@earth_mag4km_20m_g",
         "@earth_mask_01d_g",
         "@earth_mdt_01d_g",
+        "@earth_mdt_30m_g",
         "@earth_mdt_07m_g",
         "@earth_mss_01d_g",
-        "@earth_ndefl_01d",
-        "@earth_night_01d",
+        "@earth_mss_30m_g",
+        "@earth_ndefl_01d_g",
+        "@earth_night_01d_p",
         "@earth_relief_01d_g",
         "@earth_relief_01d_p",
+        "@earth_relief_05m_g",
+        "@earth_relief_05m_p",
         "@earth_relief_10m_g",
         "@earth_relief_10m_p",
         "@earth_relief_30m_g",
         "@earth_relief_30m_p",
-        "@earth_relief_05m_g",
-        "@earth_relief_05m_p",
         "@earth_synbath_01d_g",
         "@earth_vgg_01d_g",
+        "@earth_vgg_30m_g",
         "@earth_wdmam_01d_g",
+        "@earth_wdmam_20m_g",
         "@mars_relief_01d_g",
+        "@mars_relief_30m_g",
         "@mercury_relief_01d_g",
+        "@mercury_relief_30m_g",
         "@moon_relief_01d_g",
+        "@moon_relief_30m_g",
         "@pluto_relief_01d_g",
+        "@pluto_relief_30m_g",
         "@venus_relief_01d_g",
+        "@venus_relief_30m_g",
         # List of tiled remote datasets.
         # Names like @N35E135.earth_relief_03s_g.nc are for internal use only.
         # The naming scheme may change. DO NOT USE IT IN YOUR SCRIPTS.
         "@N00W030.earth_age_01m_g.nc",
         "@N30E060.earth_age_01m_g.nc",
         "@N30E090.earth_age_01m_g.nc",
+        "@S90E000.earth_age_05m_g.nc",
         "@N00W030.earth_dist_01m_g.nc",
+        "@S90E000.earth_dist_05m_g.nc",
         "@N00W030.earth_edefl_01m_p.nc",
+        "@S90E000.earth_edefl_05m_g.nc",
         "@N00W030.earth_faa_01m_p.nc",
+        "@S90E000.earth_faa_05m_g.nc",
         "@N00W030.earth_faaerror_01m_p.nc",
         "@N00W030.earth_geoid_01m_g.nc",
+        "@S90E000.earth_geoid_05m_g.nc",
         "@S30W060.earth_mag_02m_p.nc",
+        "@S90E000.earth_mag_05m_g.nc",
         "@S30W120.earth_mag4km_02m_p.nc",
         "@N30E090.earth_mss_01m_g.nc",
+        "@S90E000.earth_mss_05m_g.nc",
         "@N30E090.earth_ndefl_01m_p.nc",
         "@N00W090.earth_relief_03m_p.nc",
         "@N00E135.earth_relief_30s_g.nc",
@@ -70,12 +93,18 @@ def cache_data() -> None:
         "@N37W120.earth_relief_03s_g.nc",
         "@S15W105.earth_synbath_30s_p.nc",
         "@N00W030.earth_vgg_01m_p.nc",
+        "@S90E000.earth_vgg_05m_g.nc",
         "@S90E000.earth_wdmam_03m_g.nc",
         "@N00W030.mars_relief_01m_g.nc",
+        "@S90E000.mars_relief_05m_g.nc",
         "@N00W030.mercury_relief_01m_g.nc",
+        "@S90E000.mercury_relief_05m_g.nc",
         "@N00W030.moon_relief_01m_g.nc",
+        "@S90E000.moon_relief_05m_g.nc",
         "@N00W030.pluto_relief_01m_g.nc",
+        "@S90E000.pluto_relief_05m_g.nc",
         "@N00W030.venus_relief_01m_g.nc",
+        "@S90E000.venus_relief_05m_g.nc",
         # List of cache files.
         "@EGM96_to_36.txt",
         "@MaunaLoa_CO2.txt",

pygmt/helpers/testing.py

@@ -9,7 +9,6 @@
 
 import xarray as xr
 from pygmt.exceptions import GMTImageComparisonFailure
-from pygmt.src import which
 
 
 def check_figures_equal(*, extensions=("png",), tol=0.0, result_dir="result_images"):
@@ -144,17 +143,18 @@ def wrapper(*args, ext="png", request=None, **kwargs):
     return decorator
 
 
-def load_static_earth_relief():
+def load_static_earth_relief() -> xr.DataArray:
     """
-    Load the static_earth_relief file for internal testing.
+    Load the static_earth_relief.nc file for internal testing.
 
     Returns
     -------
-    data : xarray.DataArray
+    data
         A grid of Earth relief for internal tests.
     """
-    fname = which("@static_earth_relief.nc", download="c")
-    return xr.load_dataarray(fname, engine="gmt", raster_kind="grid")
+    return xr.load_dataarray(
+        "@static_earth_relief.nc", engine="gmt", raster_kind="grid"
+    )
 
 
 def skip_if_no(package):

pygmt/src/basemap.py

@@ -36,7 +36,7 @@ def basemap(self, **kwargs):
     At least one of the parameters ``frame``, ``map_scale``, ``rose``, or
     ``compass`` must be specified if not in subplot mode.
 
-    Full option list at :gmt-docs:`basemap.html`
+    Full GMT docs at :gmt-docs:`basemap.html`.
 
     {aliases}
 
@@ -82,6 +82,6 @@ def basemap(self, **kwargs):
     {perspective}
     {transparency}
     """
-    kwargs = self._preprocess(**kwargs)
+    self._activate_figure()
     with Session() as lib:
         lib.call_module(module="basemap", args=build_arg_list(kwargs))

pygmt/src/binstats.py

@@ -39,7 +39,7 @@ def binstats(
     presented as is or may be normalized by the circle area to
     perhaps give density estimates.
 
-    Full option list at :gmt-docs:`gmtbinstats.html`
+    Full GMT docs at :gmt-docs:`gmtbinstats.html`.
 
     {aliases}
 

pygmt/src/blockm.py

@@ -108,7 +108,7 @@ def blockmean(
 
     Must provide either ``data`` or ``x``, ``y``, and ``z``.
 
-    Full option list at :gmt-docs:`blockmean.html`
+    Full GMT docs at :gmt-docs:`blockmean.html`.
 
     {aliases}
 
@@ -212,7 +212,7 @@ def blockmedian(
 
     Must provide either ``data`` or ``x``, ``y``, and ``z``.
 
-    Full option list at :gmt-docs:`blockmedian.html`
+    Full GMT docs at :gmt-docs:`blockmedian.html`.
 
     {aliases}
 
@@ -310,7 +310,7 @@ def blockmode(
 
     Must provide either ``data`` or ``x``, ``y``, and ``z``.
 
-    Full option list at :gmt-docs:`blockmode.html`
+    Full GMT docs at :gmt-docs:`blockmode.html`.
 
     {aliases}
 

pygmt/src/coast.py

@@ -55,7 +55,7 @@ def coast(self, **kwargs):
 
     A map projection must be supplied.
 
-    Full option list at :gmt-docs:`coast.html`
+    Full GMT docs at :gmt-docs:`coast.html`.
 
     {aliases}
 
@@ -193,7 +193,7 @@ def coast(self, **kwargs):
     >>> # Show the plot
     >>> fig.show()
     """
-    kwargs = self._preprocess(**kwargs)
+    self._activate_figure()
     if not args_in_kwargs(args=["C", "G", "S", "I", "N", "E", "Q", "W"], kwargs=kwargs):
         msg = (
             "At least one of the following parameters must be specified: "