Merge branch 'main' into wrap/gmtselect

weiji14 · web-flow · commit 8ffb2d0102ff · 2021-08-24T19:54:11.000+12:00
diff --git a/doc/api/index.rst b/doc/api/index.rst
@@ -93,8 +93,8 @@ Operations on grids:
     grdcut
     grdfill
     grdfilter
-    grdlandmask
     grdgradient
+    grdlandmask
     grdsample
     grdtrack
     xyz2grd
diff --git a/pygmt/datasets/earth_relief.py b/pygmt/datasets/earth_relief.py
@@ -66,8 +66,8 @@ def load_earth_relief(resolution="01d", region=None, registration=None, use_srtm
     Notes
     -----
     The :class:`xarray.DataArray` grid doesn't support slice operation, for
-    Earth relief data with resolutions higher than "05m", which are stored as
-    smaller tiles.
+    Earth relief data with resolutions of 5 arc-minutes or higher, which are
+    stored as smaller tiles.
 
     Examples
     --------
diff --git a/pygmt/helpers/tempfile.py b/pygmt/helpers/tempfile.py
@@ -84,7 +84,7 @@ def read(self, keep_tabs=False):
         content : str
             Content of the temporary file as a Unicode string.
         """
-        with open(self.name) as tmpfile:
+        with open(self.name, mode="r", encoding="utf8") as tmpfile:
             content = tmpfile.read()
             if not keep_tabs:
                 content = content.replace("\t", " ")
diff --git a/pygmt/sphinx_gallery.py b/pygmt/sphinx_gallery.py
@@ -24,7 +24,7 @@ def __call__(self, block, block_vars, gallery_conf):
         Called by sphinx-gallery to save the figures generated after running
         code.
         """
-        image_names = list()
+        image_names = []
         image_path_iterator = block_vars["image_path_iterator"]
         figures = SHOWED_FIGURES
         while figures:
diff --git a/pygmt/src/contour.py b/pygmt/src/contour.py
@@ -27,11 +27,17 @@
     N="no_clip",
     R="region",
     S="skip",
+    U="timestamp",
     V="verbose",
     W="pen",
     X="xshift",
     Y="yshift",
+    b="binary",
     c="panel",
+    d="nodata",
+    e="find",
+    f="coltypes",
+    h="header",
     i="incols",
     l="label",
     p="perspective",
@@ -81,7 +87,10 @@ def contour(self, x=None, y=None, z=None, data=None, **kwargs):
     E : str
         Network information.
     label_placement : str
-        Placement of labels.
+        [**d**\|\ **f**\|\ **n**\|\ **l**\|\ **L**\|\ **x**\|\ **X**]\ *args*.
+        Control the placement of labels along the quoted lines. It supports
+        five controlling algorithms. See :gmt-docs:`contour.html#g` for
+        details.
     I : bool
         Color the triangles using CPT.
     triangular_mesh_pen : str
@@ -103,9 +112,15 @@ def contour(self, x=None, y=None, z=None, data=None, **kwargs):
         to be of the format [*annotcontlabel*][/*contlabel*]. If either
         label contains a slash (/) character then use ``|`` as the
         separator for the two labels instead.
+    {U}
     {V}
     {XY}
+    {b}
     {c}
+    {d}
+    {e}
+    {f}
+    {h}
     {i}
     {p}
     {t}
diff --git a/pygmt/src/grdcontour.py b/pygmt/src/grdcontour.py
@@ -77,9 +77,9 @@ def grdcontour(self, grid, **kwargs):
     label_placement : str
         [**d**\|\ **f**\|\ **n**\|\ **l**\|\ **L**\|\ **x**\|\ **X**]\
         *args*.
-        The required parameter controls the placement of labels along the
-        quoted lines. It supports five controlling algorithms. See
-        :gmt-docs:`grdcontour.html#g` for details.
+        Control the placement of labels along the quoted lines. It supports
+        five controlling algorithms. See :gmt-docs:`grdcontour.html#g` for
+        details.
     {U}
     {V}
     {W}
diff --git a/pygmt/src/grdlandmask.py b/pygmt/src/grdlandmask.py
@@ -16,13 +16,17 @@
 
 @fmt_docstring
 @use_alias(
+    A="area_thresh",
+    D="resolution",
+    E="bordervalues",
     G="outgrid",
     I="spacing",
+    N="maskvalues",
     R="region",
     V="verbose",
     r="registration",
 )
-@kwargs_to_strings(R="sequence")
+@kwargs_to_strings(R="sequence", N="sequence", E="sequence")
 def grdlandmask(**kwargs):
     r"""
     Create a grid file with set values for land and water.
@@ -45,6 +49,38 @@ def grdlandmask(**kwargs):
         in.
     {I}
     {R}
+    {A}
+    resolution : str
+        *res*\[\ **+f**\]. Selects the resolution of the data set to use
+        ((**f**)ull, (**h**)igh, (**i**)ntermediate, (**l**)ow, or
+        (**c**)rude). The resolution drops off by ~80% between data sets.
+        [Default is **l**]. Append **+f** to automatically select a lower
+        resolution should the one requested not be available
+        [abort if not found]. Alternatively, choose (**a**)uto to automatically
+        select the best resolution given the chosen region. Note that because
+        the coastlines differ in details a node in a mask file using one
+        resolution is not guaranteed to remain inside [or outside] when a
+        different resolution is selected.
+    bordervalues : bool or str or float or list
+        Nodes that fall exactly on a polygon boundary should be
+        considered to be outside the polygon [Default considers them to be
+        inside]. Alternatively, append either a list of four values
+        [*cborder*, *lborder*, *iborder*, *pborder*] or just the single value
+        *bordervalue* (for the case when they should all be the same value).
+        This turns on the line-tracking mode. Now, after setting the mask
+        values specified via ``maskvalues`` we trace the lines and change the
+        node values for all cells traversed by a line to the corresponding
+        border value. Here, *cborder* is used for cells traversed by the
+        coastline, *lborder* for cells traversed by a lake outline, *iborder*
+        for islands-in-lakes outlines, and *pborder* for
+        ponds-in-islands-in-lakes outlines [Default is no line tracing].
+    maskvalues : str or list
+        [*wet*, *dry*] or [*ocean*, *land*, *lake*, *island*, *pond*].
+        Sets the values that will be assigned to nodes. Values can
+        be any number, including the textstring NaN
+        [Default is [0, 1, 0, 1, 0] (i.e., [0, 1])]. Also select
+        ``bordervalues`` to let nodes exactly on feature boundaries be
+        considered outside [Default is inside].
     {V}
     {r}
 
diff --git a/pygmt/src/grdview.py b/pygmt/src/grdview.py
@@ -34,6 +34,7 @@
     Y="yshift",
     c="panel",
     f="coltypes",
+    n="interpolation",
     p="perspective",
     t="transparency",
 )
@@ -116,6 +117,7 @@ def grdview(self, grid, **kwargs):
     {XY}
     {c}
     {f}
+    {n}
     {p}
     {t}
     """
diff --git a/pygmt/src/histogram.py b/pygmt/src/histogram.py
@@ -27,10 +27,16 @@
     X="xshift",
     Y="yshift",
     Z="histtype",
+    b="binary",
     c="panel",
+    d="nodata",
+    e="find",
+    g="gap",
+    h="header",
     l="label",
     p="perspective",
     t="transparency",
+    w="wrap",
 )
 @kwargs_to_strings(R="sequence", T="sequence", c="sequence_comma", p="sequence")
 def histogram(self, table, **kwargs):
@@ -119,9 +125,15 @@ def histogram(self, table, **kwargs):
     {XY}
     {U}
     {V}
+    {b}
+    {d}
+    {e}
+    {g}
+    {h}
     {l}
     {p}
     {t}
+    {w}
     """
     kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
     with Session() as lib:
diff --git a/pygmt/src/image.py b/pygmt/src/image.py
@@ -12,6 +12,7 @@
     D="position",
     F="box",
     M="monochrome",
+    U="timestamp",
     V="verbose",
     X="xshift",
     Y="yshift",
@@ -54,6 +55,7 @@ def image(self, imagefile, **kwargs):
     monochrome : bool
         Convert color image to monochrome grayshades using the (television)
         YIQ-transformation.
+    {U}
     {V}
     {XY}
     {c}
diff --git a/pygmt/src/legend.py b/pygmt/src/legend.py
@@ -19,6 +19,7 @@
     J="projection",
     D="position",
     F="box",
+    U="timestamp",
     V="verbose",
     X="xshift",
     Y="yshift",
@@ -64,6 +65,7 @@ def legend(self, spec=None, position="JTR+jTR+o0.2c", box="+gwhite+p1p", **kwarg
         using :gmt-term:`MAP_FRAME_PEN`. By default, uses
         **+g**\ white\ **+p**\ 1p which draws a box around the legend using a
         1p black pen and adds a white background.
+    {U}
     {V}
     {XY}
     {c}
diff --git a/pygmt/src/plot.py b/pygmt/src/plot.py
@@ -207,6 +207,12 @@ def plot(self, x=None, y=None, data=None, size=None, direction=None, **kwargs):
     extra_arrays = []
     if "S" in kwargs and kwargs["S"][0] in "vV" and direction is not None:
         extra_arrays.extend(direction)
+    elif (
+        "S" not in kwargs
+        and kind == "geojson"
+        and data.geom_type.isin(["Point", "MultiPoint"]).all()
+    ):  # checking if the geometry of a geoDataFrame is Point or MultiPoint
+        kwargs["S"] = "s0.2c"
     if "G" in kwargs and not isinstance(kwargs["G"], str):
         if kind != "vectors":
             raise GMTInvalidInput(
diff --git a/pygmt/src/plot3d.py b/pygmt/src/plot3d.py
@@ -177,6 +177,12 @@ def plot3d(
     extra_arrays = []
     if "S" in kwargs and kwargs["S"][0] in "vV" and direction is not None:
         extra_arrays.extend(direction)
+    elif (
+        "S" not in kwargs
+        and kind == "geojson"
+        and data.geom_type.isin(["Point", "MultiPoint"]).all()
+    ):  # checking if the geometry of a geoDataFrame is Point or MultiPoint
+        kwargs["S"] = "u0.2c"
     if "G" in kwargs and not isinstance(kwargs["G"], str):
         if kind != "vectors":
             raise GMTInvalidInput(
diff --git a/pygmt/src/rose.py b/pygmt/src/rose.py
@@ -36,10 +36,16 @@
     X="xshift",
     Y="yshift",
     Z="scale",
+    b="binary",
+    d="nodata",
+    e="find",
+    g="gap",
+    h="header",
     i="incols",
     c="panel",
     p="perspective",
     t="transparency",
+    w="wrap",
 )
 @kwargs_to_strings(R="sequence", c="sequence_comma", i="sequence_comma", p="sequence")
 def rose(self, length=None, azimuth=None, data=None, **kwargs):
@@ -186,10 +192,16 @@ def rose(self, length=None, azimuth=None, data=None, **kwargs):
     {U}
     {V}
     {XY}
+    {b}
     {c}
+    {d}
+    {e}
+    {g}
+    {h}
     {i}
     {p}
     {t}
+    {w}
     """
 
     kwargs = self._preprocess(**kwargs)  # pylint: disable=protected-access
diff --git a/pygmt/src/text.py b/pygmt/src/text.py
@@ -24,14 +24,20 @@
     D="offset",
     G="fill",
     N="no_clip",
+    U="timestamp",
     V="verbose",
     W="pen",
     X="xshift",
     Y="yshift",
+    a="aspatial",
     c="panel",
+    e="find",
     f="coltypes",
+    h="header",
+    i="incols",
     p="perspective",
     t="transparency",
+    w="wrap",
 )
 @kwargs_to_strings(
     R="sequence",
@@ -141,14 +147,20 @@ def text_(
         style = solid].
     no_clip : bool
         Do NOT clip text at map boundaries [Default is will clip].
+    {U}
     {V}
     {XY}
+    {a}
     {c}
+    {e}
     {f}
+    {h}
+    {i}
     {p}
     {t}
         *transparency* can also be a 1d array to set varying transparency
         for texts, but this option is only valid if using x/y/text.
+    {w}
     """
 
     # pylint: disable=too-many-locals
diff --git a/pygmt/tests/baseline/test_geopandas_plot3d_default_cube.png.dvc b/pygmt/tests/baseline/test_geopandas_plot3d_default_cube.png.dvc
@@ -0,0 +1,4 @@
+outs:
+- md5: 48e8bd30372aa5ab9004c1fd53db7ab6
+  size: 12132
+  path: test_geopandas_plot3d_default_cube.png
diff --git a/pygmt/tests/baseline/test_geopandas_plot3d_non_default_circle.png.dvc b/pygmt/tests/baseline/test_geopandas_plot3d_non_default_circle.png.dvc
@@ -0,0 +1,4 @@
+outs:
+- md5: 54cdcd316554c9db4d71cc2bea2a690a
+  size: 12028
+  path: test_geopandas_plot3d_non_default_circle.png
diff --git a/pygmt/tests/baseline/test_geopandas_plot_default_square.png.dvc b/pygmt/tests/baseline/test_geopandas_plot_default_square.png.dvc
@@ -0,0 +1,4 @@
+outs:
+- md5: 6c395fb503f67d024925a2c86cae7ba8
+  size: 4272
+  path: test_geopandas_plot_default_square.png
diff --git a/pygmt/tests/baseline/test_geopandas_plot_non_default_circle.png.dvc b/pygmt/tests/baseline/test_geopandas_plot_non_default_circle.png.dvc
@@ -0,0 +1,4 @@
+outs:
+- md5: 4a946506f8a48be04792fdabffc6fa07
+  size: 4451
+  path: test_geopandas_plot_non_default_circle.png
diff --git a/pygmt/tests/test_geopandas.py b/pygmt/tests/test_geopandas.py
diff --git a/pygmt/tests/test_helpers.py b/pygmt/tests/test_helpers.py
diff --git a/pygmt/tests/test_legend.py b/pygmt/tests/test_legend.py
diff --git a/pygmt/tests/test_meca.py b/pygmt/tests/test_meca.py
diff --git a/pygmt/tests/test_psconvert.py b/pygmt/tests/test_psconvert.py
diff --git a/pygmt/tests/test_text.py b/pygmt/tests/test_text.py
diff --git a/pygmt/tests/test_x2sys_cross.py b/pygmt/tests/test_x2sys_cross.py
diff --git a/pygmt/tests/test_x2sys_init.py b/pygmt/tests/test_x2sys_init.py
diff --git a/setup.py b/setup.py
