Merge branch 'main' into arg_with_space

Author: weiji14

pygmt/src/blockm.py

@@ -85,7 +85,7 @@ def _blockm(block_method, data, x, y, z, outfile, **kwargs):
     r="registration",
     w="wrap",
 )
-@kwargs_to_strings(R="sequence", i="sequence_comma", o="sequence_comma")
+@kwargs_to_strings(I="sequence", R="sequence", i="sequence_comma", o="sequence_comma")
 def blockmean(data=None, x=None, y=None, z=None, outfile=None, **kwargs):
     r"""
     Block average (x,y,z) data tables by mean estimation.
@@ -182,7 +182,7 @@ def blockmean(data=None, x=None, y=None, z=None, outfile=None, **kwargs):
     r="registration",
     w="wrap",
 )
-@kwargs_to_strings(R="sequence", i="sequence_comma", o="sequence_comma")
+@kwargs_to_strings(I="sequence", R="sequence", i="sequence_comma", o="sequence_comma")
 def blockmedian(data=None, x=None, y=None, z=None, outfile=None, **kwargs):
     r"""
     Block average (x,y,z) data tables by median estimation.
@@ -270,7 +270,7 @@ def blockmedian(data=None, x=None, y=None, z=None, outfile=None, **kwargs):
     r="registration",
     w="wrap",
 )
-@kwargs_to_strings(R="sequence", i="sequence_comma", o="sequence_comma")
+@kwargs_to_strings(I="sequence", R="sequence", i="sequence_comma", o="sequence_comma")
 def blockmode(data=None, x=None, y=None, z=None, outfile=None, **kwargs):
     r"""
     Block average (x,y,z) data tables by mode estimation.

pygmt/src/contour.py

@@ -6,15 +6,13 @@
 from pygmt.helpers import (
     build_arg_string,
     check_data_input_order,
-    deprecate_parameter,
     fmt_docstring,
     kwargs_to_strings,
     use_alias,
 )
 
 
 @fmt_docstring
-@deprecate_parameter("columns", "incols", "v0.4.0", remove_version="v0.6.0")
 @check_data_input_order("v0.5.0", remove_version="v0.7.0")
 @use_alias(
     A="annotation",

pygmt/src/grdfilter.py

@@ -26,7 +26,7 @@
     f="coltypes",
     r="registration",
 )
-@kwargs_to_strings(R="sequence")
+@kwargs_to_strings(I="sequence", R="sequence")
 def grdfilter(grid, **kwargs):
     r"""
     Filter a grid in the space (or time) domain.

pygmt/src/grdlandmask.py

@@ -27,7 +27,7 @@
     V="verbose",
     r="registration",
 )
-@kwargs_to_strings(R="sequence", N="sequence", E="sequence")
+@kwargs_to_strings(I="sequence", R="sequence", N="sequence", E="sequence")
 def grdlandmask(**kwargs):
     r"""
     Create a grid file with set values for land and water.

pygmt/src/grdproject.py

@@ -30,7 +30,7 @@
     n="interpolation",
     r="registration",
 )
-@kwargs_to_strings(C="sequence", R="sequence")
+@kwargs_to_strings(C="sequence", D="sequence", R="sequence")
 def grdproject(grid, **kwargs):
     r"""
     Change projection of gridded data between geographical and rectangular.

pygmt/src/nearneighbor.py

@@ -33,7 +33,7 @@
     r="registration",
     w="wrap",
 )
-@kwargs_to_strings(R="sequence", i="sequence_comma")
+@kwargs_to_strings(I="sequence", R="sequence", i="sequence_comma")
 def nearneighbor(data=None, x=None, y=None, z=None, **kwargs):
     r"""
     Grid table data using a "Nearest neighbor" algorithm

pygmt/src/plot.py

@@ -7,7 +7,6 @@
     build_arg_string,
     check_data_input_order,
     data_kind,
-    deprecate_parameter,
     fmt_docstring,
     is_nonstr_iter,
     kwargs_to_strings,
@@ -17,8 +16,6 @@
 
 
 @fmt_docstring
-@deprecate_parameter("sizes", "size", "v0.4.0", remove_version="v0.6.0")
-@deprecate_parameter("columns", "incols", "v0.4.0", remove_version="v0.6.0")
 @check_data_input_order("v0.5.0", remove_version="v0.7.0")
 @use_alias(
     A="straight_line",

pygmt/src/plot3d.py

@@ -7,7 +7,6 @@
     build_arg_string,
     check_data_input_order,
     data_kind,
-    deprecate_parameter,
     fmt_docstring,
     is_nonstr_iter,
     kwargs_to_strings,
@@ -17,8 +16,6 @@
 
 
 @fmt_docstring
-@deprecate_parameter("columns", "incols", "v0.4.0", remove_version="v0.6.0")
-@deprecate_parameter("sizes", "size", "v0.4.0", remove_version="v0.6.0")
 @check_data_input_order("v0.5.0", remove_version="v0.7.0")
 @use_alias(
     A="straight_line",

pygmt/src/rose.py

@@ -6,15 +6,13 @@
 from pygmt.helpers import (
     build_arg_string,
     check_data_input_order,
-    deprecate_parameter,
     fmt_docstring,
     kwargs_to_strings,
     use_alias,
 )
 
 
 @fmt_docstring
-@deprecate_parameter("columns", "incols", "v0.4.0", remove_version="v0.6.0")
 @check_data_input_order("v0.5.0", remove_version="v0.7.0")
 @use_alias(
     A="sector",

pygmt/src/surface.py

@@ -33,7 +33,7 @@
     r="registration",
     w="wrap",
 )
-@kwargs_to_strings(R="sequence")
+@kwargs_to_strings(I="sequence", R="sequence")
 def surface(data=None, x=None, y=None, z=None, **kwargs):
     r"""
     Grids table data using adjustable tension continuous curvature splines.

pygmt/tests/test_contour.py

@@ -76,10 +76,13 @@ def test_contour_from_file(region):
 
 
 @pytest.mark.mpl_image_compare(filename="test_contour_vec.png")
-def test_contour_deprecate_columns_to_incols(region):
+def test_contour_incols_transposed_data(region):
     """
-    Make sure that the old parameter "columns" is supported and it reports an
-    warning.
+    Make sure that transposing the data matrix still produces a correct result
+    with incols reordering the columns.
+
+    This is a regression test for
+    https://github.com/GenericMappingTools/pygmt/issues/1313
 
     Modified from the test_contour_vec() test.
     """
@@ -96,14 +99,12 @@ def test_contour_deprecate_columns_to_incols(region):
     # switch x and y from here onwards to simulate different column order
     data = np.array([y, x, z]).T
 
-    with pytest.warns(expected_warning=FutureWarning) as record:
-        fig.contour(
-            data,
-            projection="X10c",
-            region=region,
-            frame="a",
-            pen=True,
-            columns=[1, 0, 2],
-        )
-        assert len(record) == 1  # check that only one warning was raised
+    fig.contour(
+        data,
+        projection="X10c",
+        region=region,
+        frame="a",
+        pen=True,
+        incols=[1, 0, 2],
+    )
     return fig

pygmt/tests/test_plot.py

@@ -452,53 +452,6 @@ def test_plot_datetime():
     return fig
 
 
-@pytest.mark.mpl_image_compare(filename="test_plot_sizes.png")
-def test_plot_deprecate_sizes_to_size(data, region):
-    """
-    Make sure that the old parameter "sizes" is supported and it reports a
-    warning.
-
-    Modified from the test_plot_sizes() test.
-    """
-    fig = Figure()
-    with pytest.warns(expected_warning=FutureWarning) as record:
-        fig.plot(
-            x=data[:, 0],
-            y=data[:, 1],
-            sizes=0.5 * data[:, 2],
-            region=region,
-            projection="X10c",
-            style="cc",
-            color="blue",
-            frame="af",
-        )
-        assert len(record) == 1  # check that only one warning was raised
-    return fig
-
-
-@pytest.mark.mpl_image_compare(filename="test_plot_from_file.png")
-def test_plot_deprecate_columns_to_incols(region):
-    """
-    Make sure that the old parameter "columns" is supported and it reports a
-    warning.
-
-    Modified from the test_plot_from_file() test.
-    """
-    fig = Figure()
-    with pytest.warns(expected_warning=FutureWarning) as record:
-        fig.plot(
-            data=POINTS_DATA,
-            region=region,
-            projection="X10c",
-            style="d1c",
-            color="yellow",
-            frame=True,
-            columns=[0, 1],
-        )
-        assert len(record) == 1  # check that only one warning was raised
-    return fig
-
-
 @pytest.mark.mpl_image_compare
 def test_plot_ogrgmt_file_multipoint_default_style():
     """

pygmt/tests/test_plot3d.py

@@ -423,58 +423,6 @@ def test_plot3d_scalar_xyz():
     return fig
 
 
-@pytest.mark.mpl_image_compare(filename="test_plot3d_sizes.png")
-def test_plot3d_deprecate_sizes_to_size(data, region):
-    """
-    Make sure that the old parameter "sizes" is supported and it reports an
-    warning.
-
-    Modified from the test_plot3d_sizes() test.
-    """
-    fig = Figure()
-    with pytest.warns(expected_warning=FutureWarning) as record:
-        fig.plot3d(
-            x=data[:, 0],
-            y=data[:, 1],
-            z=data[:, 2],
-            zscale=5,
-            perspective=[225, 30],
-            sizes=0.5 * data[:, 2],
-            region=region,
-            projection="X10c",
-            style="ui",
-            color="blue",
-            frame=["af", "zaf"],
-        )
-        assert len(record) == 1  # check that only one warning was raised
-    return fig
-
-
-@pytest.mark.mpl_image_compare(filename="test_plot3d_matrix.png")
-def test_plot3d_deprecate_columns_to_incols(data, region):
-    """
-    Make sure that the old parameter "columns" is supported and it reports an
-    warning.
-
-    Modified from the test_plot3d_matrix() test.
-    """
-    fig = Figure()
-    with pytest.warns(expected_warning=FutureWarning) as record:
-        fig.plot3d(
-            data,
-            zscale=5,
-            perspective=[225, 30],
-            region=region,
-            projection="M20c",
-            style="c1c",
-            color="#aaaaaa",
-            frame=["a", "za"],
-            columns="0,1,2",
-        )
-        assert len(record) == 1  # check that only one warning was raised
-    return fig
-
-
 @pytest.mark.mpl_image_compare
 def test_plot3d_ogrgmt_file_multipoint_default_style():
     """

pygmt/tests/test_rose.py

@@ -184,37 +184,3 @@ def test_rose_bools(data_fractures_compilation):
         shift=False,
     )
     return fig
-
-
-@pytest.mark.mpl_image_compare(filename="test_rose_bools.png")
-def test_rose_deprecate_columns_to_incols(data_fractures_compilation):
-    """
-    Make sure that the old parameter "columns" is supported and it reports a
-    warning.
-
-    Modified from the test_rose_bools() test.
-    """
-
-    # swap data column order of the sample fractures compilation dataset,
-    # as the use of the 'columns' parameter will reverse this action
-    data = data_fractures_compilation[["azimuth", "length"]]
-
-    fig = Figure()
-    with pytest.warns(expected_warning=FutureWarning) as record:
-        fig.rose(
-            data,
-            region=[0, 1, 0, 360],
-            sector=10,
-            columns=[1, 0],
-            diameter="10c",
-            frame=["x0.2g0.2", "y30g30", "+glightgray"],
-            color="red3",
-            pen="1p",
-            orientation=False,
-            norm=True,
-            vectors=True,
-            no_scale=True,
-            shift=False,
-        )
-        assert len(record) == 1  # check that only one warning was raised
-    return fig