Merge branch 'main' into doc/alias-list

Author: seisman

.github/workflows/ci_tests.yaml

@@ -183,7 +183,7 @@ jobs:
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v5.4.2
+        uses: codecov/codecov-action@v5.4.3
         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,
@@ -581,23 +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
-    source: str | list = which(fname, verbose="q")
-    if resinfo.tiled:
-        source = sorted(source)[0]  # get first grid for tiled grids
-    # Manually add source to xarray.DataArray encoding to make the GMT accessors work.
-    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/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: "

pygmt/src/colorbar.py

@@ -42,7 +42,7 @@ def colorbar(self, **kwargs):
     linear scale, all be equal size, or by providing a file with individual
     tile widths.
 
-    Full option list at :gmt-docs:`colorbar.html`
+    Full GMT docs at :gmt-docs:`colorbar.html`.
 
     {aliases}
 
@@ -144,6 +144,6 @@ def colorbar(self, **kwargs):
     >>> # Show the plot
     >>> fig.show()
     """
-    kwargs = self._preprocess(**kwargs)
+    self._activate_figure()
     with Session() as lib:
         lib.call_module(module="colorbar", args=build_arg_list(kwargs))

pygmt/src/contour.py

@@ -49,7 +49,7 @@ def contour(
 
     Must provide either ``data`` or ``x``, ``y``, and ``z``.
 
-    Full option list at :gmt-docs:`contour.html`
+    Full GMT docs at :gmt-docs:`contour.html`.
 
     {aliases}
 
@@ -133,7 +133,7 @@ def contour(
     {perspective}
     {transparency}
     """
-    kwargs = self._preprocess(**kwargs)
+    self._activate_figure()
 
     # Specify levels for contours or annotations.
     # One level is converted to a string with a trailing comma to separate it from

pygmt/src/dimfilter.py

@@ -43,7 +43,7 @@ def dimfilter(
     Thus, an additional filtering (e.g., Gaussian via :func:`pygmt.grdfilter`)
     of the DiM-filtered data is generally recommended.
 
-    Full option list at :gmt-docs:`dimfilter.html`
+    Full GMT docs at :gmt-docs:`dimfilter.html`.
 
     {aliases}
 

pygmt/src/filter1d.py

@@ -40,7 +40,7 @@ def filter1d(
     Read a table and output as a :class:`numpy.ndarray`,
     :class:`pandas.DataFrame`, or ASCII file.
 
-    Full option list at :gmt-docs:`filter1d.html`
+    Full GMT docs at :gmt-docs:`filter1d.html`.
 
     {aliases}
 

pygmt/src/grd2cpt.py

@@ -75,7 +75,7 @@ def grd2cpt(grid: PathLike | xr.DataArray, **kwargs):
     :gmt-docs:`gmt.conf <gmt.conf>` file or the ``color_model`` parameter
     will be used.
 
-    Full option list at :gmt-docs:`grd2cpt.html`
+    Full GMT docs at :gmt-docs:`grd2cpt.html`.
 
     {aliases}
 

pygmt/src/grd2xyz.py

@@ -48,7 +48,7 @@ def grd2xyz(
     Read a grid and output xyz-triplets as a :class:`numpy.ndarray`,
     :class:`pandas.DataFrame`, or ASCII file.
 
-    Full option list at :gmt-docs:`grd2xyz.html`
+    Full GMT docs at :gmt-docs:`grd2xyz.html`.
 
     {aliases}
 

pygmt/src/grdclip.py

@@ -135,7 +135,7 @@ def grdclip(
     values is required, or for reclassification of data values. The values can be any
     number or NaN (Not a Number).
 
-    Full option list at :gmt-docs:`grdclip.html`
+    Full GMT docs at :gmt-docs:`grdclip.html`.
 
     {aliases}
        - G = outgrid

pygmt/src/grdcontour.py

@@ -44,7 +44,7 @@ def grdcontour(self, grid: PathLike | xr.DataArray, **kwargs):
 
     Takes a grid file name or an :class:`xarray.DataArray` object as input.
 
-    Full option list at :gmt-docs:`grdcontour.html`
+    Full GMT docs at :gmt-docs:`grdcontour.html`.
 
     {aliases}
 
@@ -138,7 +138,7 @@ def grdcontour(self, grid: PathLike | xr.DataArray, **kwargs):
     >>> # Show the plot
     >>> fig.show()
     """
-    kwargs = self._preprocess(**kwargs)
+    self._activate_figure()
 
     # Specify levels for the annotation and levels parameters.
     # One level is converted to a string with a trailing comma to separate it from

pygmt/src/grdcut.py

@@ -48,7 +48,7 @@ def grdcut(
     to determine the corresponding rectangular ``region`` that will give a grid
     that fully covers the oblique domain.
 
-    Full option list at :gmt-docs:`grdcut.html`
+    Full GMT docs at :gmt-docs:`grdcut.html`.
 
     {aliases}
 

pygmt/src/grdfill.py

@@ -131,7 +131,7 @@ def grdfill(
     replace the hole values. If no holes are found the original unchanged grid is
     returned.
 
-    Full option list at :gmt-docs:`grdfill.html`.
+    Full GMT docs at :gmt-docs:`grdfill.html`.
 
     .. rubric:: Aliases:
     .. hlist::

pygmt/src/grdfilter.py

@@ -38,7 +38,7 @@ def grdfilter(
     half-width of the input edges. If the filter is low-pass, then the output
     may be less frequently sampled than the input.
 
-    Full option list at :gmt-docs:`grdfilter.html`
+    Full GMT docs at :gmt-docs:`grdfilter.html`.
 
     {aliases}
 

pygmt/src/grdgradient.py

@@ -40,7 +40,7 @@ def grdgradient(
     Can accept ``azimuth``, ``direction``, and ``radiance`` input to create
     the resulting gradient.
 
-    Full option list at :gmt-docs:`grdgradient.html`
+    Full GMT docs at :gmt-docs:`grdgradient.html`.
 
     {aliases}