Merge branch 'main' into pyarrow/string

Author: weiji14

.github/workflows/type_checks.yml

@@ -50,8 +50,8 @@ jobs:
           # 4. other packages that are used somewhere in PyGMT
           python -m pip install \
             numpy pandas xarray netcdf4 packaging \
-            contextily geopandas ipython rioxarray \
-            mypy pandas-stubs \
+            contextily geopandas ipython pyarrow rioxarray \
+            mypy pandas-stubs pyarrow-stubs \
             matplotlib pytest
           python -m pip list
 

environment.yml

@@ -16,6 +16,7 @@ dependencies:
     - contextily
     - geopandas
     - ipython
+    - pyarrow
     - rioxarray
     # Development dependencies (general)
     - dvc

examples/tutorials/basics/lines.py

@@ -2,7 +2,7 @@
 Plotting lines
 ==============
 
-Plotting lines is handled by :meth:`pygmt.Figure.plot`.
+Plotting lines is handled by the :meth:`pygmt.Figure.plot` method.
 """
 
 # %%
@@ -12,123 +12,93 @@
 # Plot lines
 # ----------
 #
-# Create a Cartesian figure using ``projection`` parameter and set the axis
-# scales using ``region`` (in this case, each axis is 0-10). Pass a list of
-# ``x`` and ``y`` values to be plotted as a line.
+# Create a Cartesian figure using the :meth:`pygmt.Figure.basemap` method. Pass lists
+# containing two values to the ``x`` and ``y`` parameters of the
+# :meth:`pygmt.Figure.plot` method. By default, a 0.25-points thick, black, solid
+# line is drawn between these two data points.
 
 fig = pygmt.Figure()
-fig.plot(
-    region=[0, 10, 0, 10],
-    projection="X15c/10c",
-    frame="a",
-    x=[1, 8],
-    y=[5, 9],
-    pen="1p,black",
-)
+fig.basemap(region=[0, 10, 0, 10], projection="X15c/10c", frame=True)
+
+fig.plot(x=[1, 5], y=[5, 9])
+
 fig.show()
 
 # %%
-# Additional line segments can be added by including additional values for
-# ``x`` and ``y``.
+# Additional line segments can be added by including more data points in the lists
+# passed to ``x`` and ``y``.
 
 fig = pygmt.Figure()
-fig.plot(
-    region=[0, 10, 0, 10],
-    projection="X15c/10c",
-    frame="a",
-    x=[1, 6, 9],
-    y=[5, 7, 4],
-    pen="1p,black",
-)
+fig.basemap(region=[0, 10, 0, 10], projection="X15c/10c", frame=True)
+
+fig.plot(x=[1, 5, 8], y=[5, 9, 4])
+
 fig.show()
 
 # %%
-# To plot multiple lines, :meth:`pygmt.Figure.plot` needs to be used for each
-# additional line. Parameters such as ``region``, ``projection``, and ``frame``
-# do not need to be repeated in subsequent uses.
+# To plot multiple lines, :meth:`pygmt.Figure.plot` needs to be used for each line
+# separately.
 
 fig = pygmt.Figure()
-fig.plot(
-    region=[0, 10, 0, 10],
-    projection="X15c/10c",
-    frame="a",
-    x=[1, 6, 9],
-    y=[5, 7, 4],
-    pen="2p,blue",
-)
-fig.plot(x=[2, 4, 10], y=[3, 8, 9], pen="2p,red")
+fig.basemap(region=[0, 10, 0, 10], projection="X15c/10c", frame=True)
+
+fig.plot(x=[1, 5, 8], y=[5, 9, 4])
+fig.plot(x=[2, 4, 9], y=[3, 7, 5])
+
 fig.show()
 
 
 # %%
 # Change line attributes
 # ----------------------
 #
-# The line attributes can be set by the ``pen`` parameter. ``pen`` takes a
-# string argument with the optional values *width*,\ *color*,\ *style*.
-#
-# In the example below, the pen width is set to ``5p``, and with ``black`` as
-# the default color and ``solid`` as the default style.
+# The line attributes can be set by the ``pen`` parameter which takes a string
+# argument with the optional values *width*,\ *color*,\ *style*.
 
 fig = pygmt.Figure()
-fig.plot(
-    region=[0, 10, 0, 10],
-    projection="X15c/10c",
-    frame="a",
-    x=[1, 8],
-    y=[3, 9],
-    pen="5p",
-)
+fig.basemap(region=[0, 10, 0, 10], projection="X15c/10c", frame=True)
+
+# Set the pen width to "5p" (5 points), and use the default color "black" and the
+# default style "solid"
+fig.plot(x=[1, 8], y=[3, 9], pen="5p")
+
 fig.show()
 
 # %%
 # The line color can be set and is added after the line width to the ``pen``
-# parameter. In the example below, the line color is set to ``red``.
+# parameter.
 
 fig = pygmt.Figure()
-fig.plot(
-    region=[0, 10, 0, 10],
-    projection="X15c/10c",
-    frame="a",
-    x=[1, 8],
-    y=[3, 9],
-    pen="5p,red",
-)
+fig.basemap(region=[0, 10, 0, 10], projection="X15c/10c", frame=True)
+
+# Set the line color to "red", use the default style "solid"
+fig.plot(x=[1, 8], y=[3, 9], pen="5p,red")
+
 fig.show()
 
 # %%
 # The line style can be set and is added after the line width or color to the
-# ``pen`` parameter.  In the example below, the line style is set to
-# ``..-`` (*dot dot dash*), and the default color ``black`` is used.
+# ``pen`` parameter.
 
 fig = pygmt.Figure()
-fig.plot(
-    region=[0, 10, 0, 10],
-    projection="X15c/10c",
-    frame="a",
-    x=[1, 8],
-    y=[3, 9],
-    pen="5p,..-",
-)
+fig.basemap(region=[0, 10, 0, 10], projection="X15c/10c", frame=True)
+
+# Set the line style to "..-" (dot dot dash), use the default color "black"
+fig.plot(x=[1, 8], y=[3, 9], pen="5p,..-")
+
 fig.show()
 
 # %%
-# The line width, color, and style can all be set in the same ``pen``
-# parameter. In the example below, the line width is set to ``7p``, the color
-# is set to ``green``, and the line style is ``-.-`` (*dash dot dash*).
-#
-# For a gallery showing other ``pen`` settings, see
+# The line width, color, and style can all be set in the same ``pen`` parameter.
+# For a gallery example showing other ``pen`` settings, see
 # :doc:`/gallery/lines/linestyles`.
 
 fig = pygmt.Figure()
-fig.plot(
-    region=[0, 10, 0, 10],
-    projection="X15c/10c",
-    frame="a",
-    x=[1, 8],
-    y=[3, 9],
-    pen="7p,green,-.-",
-)
+fig.basemap(region=[0, 10, 0, 10], projection="X15c/10c", frame=True)
+
+# Draw a 7-points thick, green line with style "-.-" (dash dot dash)
+fig.plot(x=[1, 8], y=[3, 9], pen="7p,green,-.-")
+
 fig.show()
 
-# sphinx_gallery_thumbnail_number = 3
+# sphinx_gallery_thumbnail_number = 6

pygmt/figure.py

@@ -17,7 +17,7 @@
 
 import numpy as np
 from pygmt.clib import Session
-from pygmt.exceptions import GMTError, GMTInvalidInput
+from pygmt.exceptions import GMTInvalidInput
 from pygmt.helpers import launch_external_viewer, unique_name
 
 
@@ -135,7 +135,7 @@ def region(self) -> np.ndarray:
             wesn = lib.extract_region()
         return wesn
 
-    def savefig(  # noqa: PLR0912
+    def savefig(
         self,
         fname: str | PurePath,
         transparent: bool = False,
@@ -177,7 +177,8 @@ def savefig(  # noqa: PLR0912
             The desired figure file name, including the extension. See the list of
             supported formats and their extensions above.
         transparent
-            Use a transparent background for the figure. Only valid for PNG format.
+            Use a transparent background for the figure. Only valid for PNG format and
+            the PNG file asscoiated with KML format.
         crop
             Crop the figure canvas (page) to the plot area.
         anti_alias
@@ -203,9 +204,9 @@ def savefig(  # noqa: PLR0912
             "bmp": "b",
             "eps": "e",
             "jpg": "j",
-            "kml": "g",
+            "kml": "G" if transparent is True else "g",
             "pdf": "f",
-            "png": "g",
+            "png": "G" if transparent is True else "g",
             "ppm": "m",
             "tif": "t",
             "tiff": None,  # GeoTIFF doesn't need the -T option
@@ -226,14 +227,12 @@ def savefig(  # noqa: PLR0912
                 msg = "Extension '.ps' is not supported. Use '.eps' or '.pdf' instead."
                 raise GMTInvalidInput(msg)
             case ext if ext not in fmts:
-                raise GMTInvalidInput(f"Unknown extension '.{ext}'.")
-
-        fmt = fmts[ext]
-        if transparent:
-            if fmt != "g":
-                msg = f"Transparency unavailable for '{ext}', only for png."
+                msg = f"Unknown extension '.{ext}'."
                 raise GMTInvalidInput(msg)
-            fmt = fmt.upper()
+
+        if transparent and ext not in {"kml", "png"}:
+            msg = f"Transparency unavailable for '{ext}', only for png and kml."
+            raise GMTInvalidInput(msg)
         if anti_alias:
             kwargs["Qt"] = 2
             kwargs["Qg"] = 2
@@ -244,18 +243,17 @@ def savefig(  # noqa: PLR0912
                 raise GMTInvalidInput(msg)
             kwargs["W"] = True
 
-        # pytest-mpl v0.17.0 added the "metadata" parameter to Figure.savefig, which
-        # is not recognized. So remove it before calling Figure.psconvert.
+        # pytest-mpl v0.17.0 added the "metadata" parameter to Figure.savefig, which is
+        # not recognized. So remove it before calling Figure.psconvert.
         kwargs.pop("metadata", None)
-        self.psconvert(prefix=prefix, fmt=fmt, crop=crop, **kwargs)
+        self.psconvert(prefix=prefix, fmt=fmts[ext], crop=crop, **kwargs)
 
-        # Remove the .pgw world file if exists.
-        # Not necessary after GMT 6.5.0.
+        # Remove the .pgw world file if exists. Not necessary after GMT 6.5.0.
         # See upstream fix https://github.com/GenericMappingTools/gmt/pull/7865
         if ext == "tiff":
             fname.with_suffix(".pgw").unlink(missing_ok=True)
 
-        # Rename if file extension doesn't match the input file suffix
+        # Rename if file extension doesn't match the input file suffix.
         if ext != suffix[1:]:
             fname.with_suffix("." + ext).rename(fname)
 
@@ -331,11 +329,12 @@ def show(
         match method:
             case "notebook":
                 if not _HAS_IPYTHON:
-                    raise GMTError(
+                    msg = (
                         "Notebook display is selected, but IPython is not available. "
                         "Make sure you have IPython installed, "
                         "or run the script in a Jupyter notebook."
                     )
+                    raise ImportError(msg)
                 png = self._preview(
                     fmt="png", dpi=dpi, anti_alias=True, as_bytes=True, **kwargs
                 )
@@ -344,14 +343,15 @@ def show(
                 pdf = self._preview(
                     fmt="pdf", dpi=dpi, anti_alias=False, as_bytes=False, **kwargs
                 )
-                launch_external_viewer(pdf, waiting=waiting)  # type: ignore[arg-type]
+                launch_external_viewer(pdf, waiting=waiting)
             case "none":
                 pass  # Do nothing
             case _:
-                raise GMTInvalidInput(
-                    f"Invalid display method '{method}'. Valid values are 'external', "
-                    "'notebook', 'none' or None."
+                msg = (
+                    f"Invalid display method '{method}'. "
+                    "Valid values are 'external', 'notebook', 'none' or None."
                 )
+                raise GMTInvalidInput(msg)
 
     def _preview(self, fmt: str, dpi: int, as_bytes: bool = False, **kwargs):
         """
@@ -400,7 +400,7 @@ def _repr_html_(self):
         html = '<img src="data:image/png;base64,{image}" width="{width}px">'
         return html.format(image=base64_png.decode("utf-8"), width=500)
 
-    from pygmt.src import (  # type: ignore [misc]
+    from pygmt.src import (  # type: ignore[misc]
         basemap,
         coast,
         colorbar,

pygmt/tests/test_clib_put_vector.py

@@ -172,10 +172,12 @@ def test_put_vector_string_dtype():
 
 def test_put_vector_timedelta64_dtype():
     """
-    Passing timedelta64 type vectors with various time units (year, month,
-    week, day, hour, minute, second, millisecond, microsecond) to a dataset.
+    Passing timedelta64 type vectors with various date/time units to a dataset.
+
+    Valid date/time units can be found at
+    https://numpy.org/devdocs/reference/arrays.datetime.html#datetime-units.
     """
-    for unit in ["Y", "M", "W", "D", "h", "m", "s", "ms", "μs"]:
+    for unit in ["Y", "M", "W", "D", "h", "m", "s", "ms", "us", "ns", "ps", "fs", "as"]:
         with clib.Session() as lib, GMTTempFile() as tmp_file:
             dataset = lib.create_data(
                 family="GMT_IS_DATASET|GMT_VIA_VECTOR",

pygmt/tests/test_figure.py

@@ -12,7 +12,7 @@
 import numpy.testing as npt
 import pytest
 from pygmt import Figure, set_display
-from pygmt.exceptions import GMTError, GMTInvalidInput
+from pygmt.exceptions import GMTInvalidInput
 from pygmt.figure import SHOW_CONFIG, _get_default_display_method
 from pygmt.helpers import GMTTempFile
 
@@ -196,12 +196,21 @@ def test_figure_savefig_transparent():
         fname = f"{prefix}.{fmt}"
         with pytest.raises(GMTInvalidInput):
             fig.savefig(fname, transparent=True)
-    # png should not raise an error
+
+    # PNG should support transparency and should not raise an error.
     fname = Path(f"{prefix}.png")
     fig.savefig(fname, transparent=True)
     assert fname.exists()
     fname.unlink()
 
+    # The companion PNG file with KML format should also support transparency.
+    fname = Path(f"{prefix}.kml")
+    fig.savefig(fname, transparent=True)
+    assert fname.exists()
+    fname.unlink()
+    assert fname.with_suffix(".png").exists()
+    fname.with_suffix(".png").unlink()
+
 
 def test_figure_savefig_filename_with_spaces():
     """
@@ -321,7 +330,7 @@ def test_figure_show_notebook_error_without_ipython():
     """
     fig = Figure()
     fig.basemap(region=[0, 1, 2, 3], frame=True)
-    with pytest.raises(GMTError):
+    with pytest.raises(ImportError):
         fig.show(method="notebook")
 
 
@@ -361,7 +370,7 @@ def test_set_display(self):
                 assert mock_viewer.call_count == 0
                 assert mock_display.call_count == 1
         else:
-            with pytest.raises(GMTError):
+            with pytest.raises(ImportError):
                 fig.show()
 
         # Test the "external" display method