Merge remote-tracking branch 'origin/master' into gmt-master-gh-actions

Author: weiji14

.github/workflows/ci_tests.yaml

@@ -43,8 +43,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [3.6, 3.7, 3.8]
-        #os: [ubuntu-latest, macOS-latest, windows-latest]
-        os: [ubuntu-latest, macOS-latest]
+        os: [ubuntu-latest, macOS-latest, windows-latest]
     # environmental variables used in coverage
     env:
       OS: ${{ matrix.os }}
@@ -112,9 +111,9 @@ jobs:
         run: make test PYTEST_EXTRA="-r P"
 
       # Build the documentation
-      #- name: Build the documentation
-      #  shell: bash -l {0}
-      #  run: make -C doc clean all
+      - name: Build the documentation
+        shell: bash -l {0}
+        run: make -C doc clean all
 
       # Upload coverage to Codecov
       - name: Upload coverage to Codecov

.stickler.yml

@@ -156,7 +156,7 @@ Guidelines for a good tutorial:
 * Explain the options and features in as much detail as possible. The gallery has
   concise examples while the tutorials are detailed and full of text.
 
-Note that the `Figure.plot` function needs to be called for a plot to be inserted into
+Note that the `Figure.show()` function needs to be called for a plot to be inserted into
 the documentation.
 
 

CONTRIBUTING.md

@@ -24,7 +24,7 @@
 
 fig = pygmt.Figure()
 # Plot the earth relief grid on Cylindrical Stereographic projection, masking land areas
-fig.basemap(region="g", frame=True, projection="Cyl_stere/150/-20/8i")
+fig.basemap(region="d", frame=True, projection="Cyl_stere/8i")
 fig.grdimage(grid=grid, cmap="gray")
 fig.coast(land="#666666")
 # Plot using circles (c) of 0.15cm, the sampled bathymetry points

examples/gallery/grid/track_sampling.py

@@ -298,7 +298,7 @@ def shift_origin(self, xshift=None, yshift=None):
         Shift plot origin in x and/or y directions.
 
         This method shifts plot origin relative to the current origin by
-        (*xshift*,*yshift*) and optionally append the length unit (**c**,
+        (*xshift*, *yshift*) and optionally append the length unit (**c**,
         **i**, or **p**).
 
         Prepend **a** to shift the origin back to the original position after
@@ -308,14 +308,22 @@ def shift_origin(self, xshift=None, yshift=None):
         move the origin relative to its current location.
 
         Detailed usage at
-        :gmt-docs:`GMT_Docs.html#plot-positioning-and-layout-the-x-y-options`
+        :gmt-docs:`cookbook/options.html#plot-positioning-and-layout-the-x-y-options`
 
         Parameters
         ----------
         xshift : str
             Shift plot origin in x direction.
         yshift : str
             Shift plot origin in y direction.
+
+        Notes
+        -----
+        For GMT 6.1.0, this function can't be used as the first plotting
+        function of :meth:`pygmt.Figure`, since it relies the *region* and
+        *projection* settings from previous commands.
+
+        .. TODO: Remove the notes when PyGMT bumps to GMT>=6.1.1.
         """
         self._preprocess()
         args = ["-T"]

pygmt/figure.py

@@ -90,6 +90,7 @@ def surface(x=None, y=None, z=None, data=None, **kwargs):
         if outfile == tmpfile.name:  # if user did not set outfile, return DataArray
             with xr.open_dataarray(outfile) as dataarray:
                 result = dataarray.load()
+                _ = result.gmt  # load GMTDataArray accessor information
         elif outfile != tmpfile.name:  # if user sets an outfile, return None
             result = None
 

pygmt/gridding.py

@@ -47,8 +47,8 @@ def grdcut(grid, **kwargs):
 
     Parameters
     ----------
-    grid : str
-        The name of the input grid file.
+    grid : str or xarray.DataArray
+        The file name of the input grid or the grid loaded as a DataArray.
     outgrid : str or None
         The name of the output netCDF file with extension .nc to store the grid
         in.
@@ -94,12 +94,7 @@ def grdcut(grid, **kwargs):
             if kind == "file":
                 file_context = dummy_context(grid)
             elif kind == "grid":
-                raise NotImplementedError(
-                    "xarray.DataArray is not supported as the input grid yet!"
-                )
-                # file_context = lib.virtualfile_from_grid(grid)
-                # See https://github.com/GenericMappingTools/gmt/pull/3532
-                # for a feature request.
+                file_context = lib.virtualfile_from_grid(grid)
             else:
                 raise GMTInvalidInput("Unrecognized data type: {}".format(type(grid)))
 
@@ -113,6 +108,7 @@ def grdcut(grid, **kwargs):
         if outgrid == tmpfile.name:  # if user did not set outgrid, return DataArray
             with xr.open_dataarray(outgrid) as dataarray:
                 result = dataarray.load()
+                _ = result.gmt  # load GMTDataArray accessor information
         else:
             result = None  # if user sets an outgrid, return None
 

pygmt/gridops.py

@@ -180,7 +180,13 @@ def use_alias(**aliases):
     R = bla J = meh
     >>> my_module(region='bla', projection='meh')
     R = bla J = meh
-
+    >>> my_module(
+    ...    region='bla', projection='meh', J="bla"
+    ... )  # doctest: +NORMALIZE_WHITESPACE
+    Traceback (most recent call last):
+      ...
+    pygmt.exceptions.GMTInvalidInput:
+        Arguments in short-form (J) and long-form (projection) can't coexist
     """
 
     def alias_decorator(module_func):
@@ -194,6 +200,10 @@ def new_module(*args, **kwargs):
             New module that parses and replaces the registered aliases.
             """
             for arg, alias in aliases.items():
+                if alias in kwargs and arg in kwargs:
+                    raise GMTInvalidInput(
+                        f"Arguments in short-form ({arg}) and long-form ({alias}) can't coexist"
+                    )
                 if alias in kwargs:
                     kwargs[arg] = kwargs.pop(alias)
             return module_func(*args, **kwargs)

pygmt/helpers/decorators.py

@@ -12,6 +12,12 @@
 from ..helpers import GMTTempFile
 
 
+@pytest.fixture(scope="module", name="grid")
+def fixture_grid():
+    "Load the grid data from the sample earth_relief file"
+    return load_earth_relief(registration="pixel")
+
+
 def test_grdcut_file_in_file_out():
     "grduct an input grid file, and output to a grid file"
     with GMTTempFile(suffix=".nc") as tmpfile:
@@ -26,6 +32,8 @@ def test_grdcut_file_in_dataarray_out():
     "grdcut an input grid file, and output as DataArray"
     outgrid = grdcut("@earth_relief_01d", region="0/180/0/90")
     assert isinstance(outgrid, xr.DataArray)
+    assert outgrid.gmt.registration == 1  # Pixel registration
+    assert outgrid.gmt.gtype == 1  # Geographic type
     # check information of the output grid
     # the '@earth_relief_01d' is in pixel registration, so the grid range is
     # not exactly 0/180/0/90
@@ -39,23 +47,30 @@ def test_grdcut_file_in_dataarray_out():
     assert outgrid.sizes["lon"] == 180
 
 
-def test_grdcut_dataarray_in_file_out():
-    "grdcut an input DataArray, and output to a grid file"
-    # Not supported yet.
-    # See https://github.com/GenericMappingTools/gmt/pull/3532
-
-
-def test_grdcut_dataarray_in_dataarray_out():
+def test_grdcut_dataarray_in_file_out(grid):
     "grdcut an input DataArray, and output to a grid file"
-    # Not supported yet.
-    # See https://github.com/GenericMappingTools/gmt/pull/3532
+    with GMTTempFile(suffix=".nc") as tmpfile:
+        result = grdcut(grid, outgrid=tmpfile.name, region="0/180/0/90")
+        assert result is None  # grdcut returns None if output to a file
+        result = grdinfo(tmpfile.name, C=True)
+        assert result == "0 180 0 90 -8182 5651.5 1 1 180 90 1 1\n"
 
 
-def test_grdcut_dataarray_in_fail():
-    "Make sure that grdcut fails correctly if DataArray is the input grid"
-    with pytest.raises(NotImplementedError):
-        grid = load_earth_relief()
-        grdcut(grid, region="0/180/0/90")
+def test_grdcut_dataarray_in_dataarray_out(grid):
+    "grdcut an input DataArray, and output as DataArray"
+    outgrid = grdcut(grid, region="0/180/0/90")
+    assert isinstance(outgrid, xr.DataArray)
+    # check information of the output grid
+    # the '@earth_relief_01d' is in pixel registration, so the grid range is
+    # not exactly 0/180/0/90
+    assert outgrid.coords["lat"].data.min() == 0.5
+    assert outgrid.coords["lat"].data.max() == 89.5
+    assert outgrid.coords["lon"].data.min() == 0.5
+    assert outgrid.coords["lon"].data.max() == 179.5
+    assert outgrid.data.min() == -8182.0
+    assert outgrid.data.max() == 5651.5
+    assert outgrid.sizes["lat"] == 90
+    assert outgrid.sizes["lon"] == 180
 
 
 def test_grdcut_fails():

pygmt/tests/test_grdcut.py

@@ -2,6 +2,7 @@
 Tests image.
 """
 import os
+import sys
 
 import pytest
 
@@ -11,6 +12,7 @@
 TEST_IMG = os.path.join(os.path.dirname(__file__), "baseline", "test_logo.png")
 
 
+@pytest.mark.skipif(sys.platform == "win32", reason="crashes on Windows")
 @pytest.mark.mpl_image_compare
 def test_image():
     "Place images on map"

pygmt/tests/test_image.py

@@ -23,6 +23,8 @@ def test_surface_input_file():
     fname = which("@tut_ship.xyz", download="c")
     output = surface(data=fname, spacing="5m", region=[245, 255, 20, 30])
     assert isinstance(output, xr.DataArray)
+    assert output.gmt.registration == 0  # Gridline registration
+    assert output.gmt.gtype == 0  # Cartesian type
     return output