Merge branch 'main' into pass-arg-list-to-module

Author: seisman

examples/gallery/embellishments/colorbar.py

@@ -6,7 +6,7 @@
 The colormap is set via the ``cmap`` parameter. A full list of available
 color palette tables can be found at :gmt-docs:`reference/cpts.html`.
 Use the ``frame`` parameter to add labels to the **x** and **y** axes
-of the colorbar by appending **+l** followed by the desired text. To Add
+of the colorbar by appending **+l** followed by the desired text. To add
 and adjust the annotations (**a**) and ticks (**f**) append the letter
 followed by the desired interval. The placement of the colorbar is set
 via the ``position`` parameter. There are the following options:

pygmt/clib/conversion.py

@@ -2,7 +2,9 @@
 Functions to convert data types into ctypes friendly formats.
 """
 
+import ctypes as ctp
 import warnings
+from collections.abc import Sequence
 
 import numpy as np
 from pygmt.exceptions import GMTInvalidInput
@@ -243,41 +245,81 @@ def as_c_contiguous(array):
     return array
 
 
-def kwargs_to_ctypes_array(argument, kwargs, dtype):
+def sequence_to_ctypes_array(sequence: Sequence, ctype, size: int) -> ctp.Array | None:
     """
-    Convert an iterable argument from kwargs into a ctypes array variable.
+    Convert a sequence of numbers into a ctypes array variable.
 
-    If the argument is not present in kwargs, returns ``None``.
+    If the sequence is ``None``, returns ``None``. Otherwise, returns a ctypes array.
+    The function only works for sequences of numbers. For converting a sequence of
+    strings, use ``strings_to_ctypes_array`` instead.
 
     Parameters
     ----------
-    argument : str
-        The name of the argument.
-    kwargs : dict
-        Dictionary of keyword arguments.
-    dtype : ctypes type
-        The ctypes array type (e.g., ``ctypes.c_double*4``)
+    sequence
+        The sequence to convert. If ``None``, returns ``None``. Otherwise, it must be a
+        sequence (e.g., list, tuple, numpy array).
+    ctype
+        The ctypes type of the array (e.g., ``ctypes.c_int``).
+    size
+        The size of the array. If the sequence is smaller than the size, the remaining
+        elements will be filled with zeros. If the sequence is larger than the size, an
+        exception will be raised.
 
     Returns
     -------
-    ctypes_value : ctypes array or None
+    ctypes_array
+        The ctypes array variable.
 
     Examples
     --------
-
-    >>> import ctypes as ct
-    >>> value = kwargs_to_ctypes_array("bla", {"bla": [10, 10]}, ct.c_long * 2)
-    >>> type(value)
-    <class 'pygmt.clib.conversion.c_long_Array_2'>
-    >>> should_be_none = kwargs_to_ctypes_array(
-    ...     "swallow", {"bla": 1, "foo": [20, 30]}, ct.c_int * 2
-    ... )
-    >>> print(should_be_none)
+    >>> import ctypes as ctp
+    >>> ctypes_array = sequence_to_ctypes_array([1, 2, 3], ctp.c_long, 3)
+    >>> type(ctypes_array)
+    <class 'pygmt.clib.conversion.c_long_Array_3'>
+    >>> ctypes_array[:]
+    [1, 2, 3]
+    >>> ctypes_array = sequence_to_ctypes_array([1, 2], ctp.c_long, 5)
+    >>> type(ctypes_array)
+    <class 'pygmt.clib.conversion.c_long_Array_5'>
+    >>> ctypes_array[:]
+    [1, 2, 0, 0, 0]
+    >>> ctypes_array = sequence_to_ctypes_array(None, ctp.c_long, 5)
+    >>> print(ctypes_array)
     None
+    >>> ctypes_array = sequence_to_ctypes_array([1, 2, 3, 4, 5, 6], ctp.c_long, 5)
+    Traceback (most recent call last):
+    ...
+    IndexError: invalid index
+    """
+    if sequence is None:
+        return None
+    return (ctype * size)(*sequence)
+
+
+def strings_to_ctypes_array(strings: Sequence[str]) -> ctp.Array:
+    """
+    Convert a sequence (e.g., a list) of strings into a ctypes array.
+
+    Parameters
+    ----------
+    strings
+        A sequence of strings.
+
+    Returns
+    -------
+    ctypes_array
+        A ctypes array of strings.
+
+    Examples
+    --------
+    >>> strings = ["first", "second", "third"]
+    >>> ctypes_array = strings_to_ctypes_array(strings)
+    >>> type(ctypes_array)
+    <class 'pygmt.clib.conversion.c_char_p_Array_3'>
+    >>> [s.decode() for s in ctypes_array]
+    ['first', 'second', 'third']
     """
-    if argument in kwargs:
-        return dtype(*kwargs[argument])
-    return None
+    return (ctp.c_char_p * len(strings))(*[s.encode() for s in strings])
 
 
 def array_to_datetime(array):

pygmt/clib/session.py

@@ -19,7 +19,8 @@
     array_to_datetime,
     as_c_contiguous,
     dataarray_to_matrix,
-    kwargs_to_ctypes_array,
+    sequence_to_ctypes_array,
+    strings_to_ctypes_array,
     vectors_to_arrays,
 )
 from pygmt.clib.loading import load_libgmt
@@ -656,7 +657,17 @@ def call_module(self, module: str, args: list[str]):
                 f"Module '{module}' failed with status code {status}:\n{self._error_message}"
             )
 
-    def create_data(self, family, geometry, mode, **kwargs):
+    def create_data(
+        self,
+        family,
+        geometry,
+        mode,
+        dim=None,
+        ranges=None,
+        inc=None,
+        registration="GMT_GRID_NODE_REG",
+        pad=None,
+    ):
         """
         Create an empty GMT data container.
 
@@ -720,15 +731,13 @@ def create_data(self, family, geometry, mode, **kwargs):
             valid_modifiers=["GMT_GRID_IS_CARTESIAN", "GMT_GRID_IS_GEO"],
         )
         geometry_int = self._parse_constant(geometry, valid=GEOMETRIES)
-        registration_int = self._parse_constant(
-            kwargs.get("registration", "GMT_GRID_NODE_REG"), valid=REGISTRATIONS
-        )
+        registration_int = self._parse_constant(registration, valid=REGISTRATIONS)
 
         # Convert dim, ranges, and inc to ctypes arrays if given (will be None
         # if not given to represent NULL pointers)
-        dim = kwargs_to_ctypes_array("dim", kwargs, ctp.c_uint64 * 4)
-        ranges = kwargs_to_ctypes_array("ranges", kwargs, ctp.c_double * 4)
-        inc = kwargs_to_ctypes_array("inc", kwargs, ctp.c_double * 2)
+        dim = sequence_to_ctypes_array(dim, ctp.c_uint64, 4)
+        ranges = sequence_to_ctypes_array(ranges, ctp.c_double, 4)
+        inc = sequence_to_ctypes_array(inc, ctp.c_double, 2)
 
         # Use a NULL pointer (None) for existing data to indicate that the
         # container should be created empty. Fill it in later using put_vector
@@ -742,7 +751,7 @@ def create_data(self, family, geometry, mode, **kwargs):
             ranges,
             inc,
             registration_int,
-            self._parse_pad(family, kwargs),
+            self._parse_pad(family, pad),
             None,
         )
 
@@ -751,15 +760,14 @@ def create_data(self, family, geometry, mode, **kwargs):
 
         return data_ptr
 
-    def _parse_pad(self, family, kwargs):
+    def _parse_pad(self, family, pad):
         """
         Parse and return an appropriate value for pad if none is given.
 
         Pad is a bit tricky because, for matrix types, pad control the matrix ordering
         (row or column major). Using the default pad will set it to column major and
         mess things up with the numpy arrays.
         """
-        pad = kwargs.get("pad", None)
         if pad is None:
             pad = 0 if "MATRIX" in family else self["GMT_PAD_DEFAULT"]
         return pad
@@ -918,13 +926,9 @@ def put_vector(self, dataset, column, vector):
 
         gmt_type = self._check_dtype_and_dim(vector, ndim=1)
         if gmt_type in (self["GMT_TEXT"], self["GMT_DATETIME"]):
-            vector_pointer = (ctp.c_char_p * len(vector))()
             if gmt_type == self["GMT_DATETIME"]:
-                vector_pointer[:] = np.char.encode(
-                    np.datetime_as_string(array_to_datetime(vector))
-                )
-            else:
-                vector_pointer[:] = np.char.encode(vector)
+                vector = np.datetime_as_string(array_to_datetime(vector))
+            vector_pointer = strings_to_ctypes_array(vector)
         else:
             vector_pointer = vector.ctypes.data_as(ctp.c_void_p)
         status = c_put_vector(
@@ -981,13 +985,12 @@ def put_strings(self, dataset, family, strings):
             restype=ctp.c_int,
         )
 
-        strings_pointer = (ctp.c_char_p * len(strings))()
-        strings_pointer[:] = np.char.encode(strings)
-
         family_int = self._parse_constant(
             family, valid=FAMILIES, valid_modifiers=METHODS
         )
 
+        strings_pointer = strings_to_ctypes_array(strings)
+
         status = c_put_strings(
             self.session_pointer, family_int, dataset, strings_pointer
         )
@@ -1108,7 +1111,7 @@ def write_data(self, family, geometry, mode, wesn, output, data):
             self["GMT_IS_FILE"],
             geometry_int,
             self[mode],
-            (ctp.c_double * 6)(*wesn),
+            sequence_to_ctypes_array(wesn, ctp.c_double, 6),
             output.encode(),
             data,
         )

pygmt/tests/test_blockm.py

@@ -82,6 +82,7 @@ def test_blockmean_input_filename():
             data="@tut_ship.xyz",
             spacing="5m",
             region=[245, 255, 20, 30],
+            output_type="file",
             outfile=tmpfile.name,
         )
         assert output is None  # check that output is None since outfile is set

pygmt/tests/test_blockmedian.py

@@ -79,6 +79,7 @@ def test_blockmedian_input_filename():
             data="@tut_ship.xyz",
             spacing="5m",
             region=[245, 255, 20, 30],
+            output_type="file",
             outfile=tmpfile.name,
         )
         assert output is None  # check that output is None since outfile is set

pygmt/tests/test_grdtrack.py

@@ -70,7 +70,9 @@ def test_grdtrack_input_csvfile_and_dataarray(dataarray, expected_array):
     Run grdtrack by passing in a csvfile and xarray.DataArray as inputs.
     """
     with GMTTempFile() as tmpfile:
-        output = grdtrack(points=POINTS_DATA, grid=dataarray, outfile=tmpfile.name)
+        output = grdtrack(
+            points=POINTS_DATA, grid=dataarray, output_type="file", outfile=tmpfile.name
+        )
         assert output is None  # check that output is None since outfile is set
         assert Path(tmpfile.name).stat().st_size > 0  # check that outfile exists
         output = np.loadtxt(tmpfile.name)

pygmt/tests/test_project.py

@@ -62,6 +62,7 @@ def test_project_output_filename(dataframe):
             center=[0, -1],
             azimuth=45,
             flat_earth=True,
+            output_type="file",
             outfile=tmpfile.name,
         )
         assert output is None  # check that output is None since outfile is set

pygmt/tests/test_select.py

@@ -56,6 +56,7 @@ def test_select_input_filename():
             data="@tut_ship.xyz",
             region=[250, 251, 26, 27],
             z_subregion=["-/-630", "-120/0+a"],
+            output_type="file",
             outfile=tmpfile.name,
         )
         assert output is None  # check that output is None since outfile is set