Refactor to specify numpy dtypes in a consistent way (#3577)

Author: seisman

examples/gallery/symbols/datetime_inputs.py

@@ -40,7 +40,9 @@
 )
 
 # numpy.datetime64 types
-x = np.array(["2010-06-01", "2011-06-01T12", "2012-01-01T12:34:56"], dtype="datetime64")
+x = np.array(
+    ["2010-06-01", "2011-06-01T12", "2012-01-01T12:34:56"], dtype=np.datetime64
+)
 y = [1, 2, 3]
 fig.plot(x=x, y=y, style="c0.4c", pen="1p", fill="red3")
 

examples/tutorials/advanced/date_time_charts.py

@@ -222,7 +222,9 @@
 # before passing it as an argument. However, ``np.array`` objects use less memory and
 # allow developers to specify data types.
 
-x = np.array(["2010-06-01", "2011-06-01T12", "2012-01-01T12:34:56"], dtype="datetime64")
+x = np.array(
+    ["2010-06-01", "2011-06-01T12", "2012-01-01T12:34:56"], dtype=np.datetime64
+)
 y = [2, 7, 5]
 
 fig = pygmt.Figure()

pygmt/clib/session.py

@@ -910,12 +910,12 @@ def _check_dtype_and_dim(self, array: np.ndarray, ndim: int) -> int:
         Examples
         --------
         >>> import numpy as np
-        >>> data = np.array([1, 2, 3], dtype="float64")
+        >>> data = np.array([1, 2, 3], dtype=np.float64)
         >>> with Session() as lib:
         ...     gmttype = lib._check_dtype_and_dim(data, ndim=1)
         ...     gmttype == lib["GMT_DOUBLE"]
         True
-        >>> data = np.ones((5, 2), dtype="float32")
+        >>> data = np.ones((5, 2), dtype=np.float32)
         >>> with Session() as lib:
         ...     gmttype = lib._check_dtype_and_dim(data, ndim=2)
         ...     gmttype == lib["GMT_FLOAT"]
@@ -1505,7 +1505,7 @@ def virtualfile_from_vectors(
                 strings = np.array(
                     [" ".join(vals) for vals in zip(*string_arrays, strict=True)]
                 )
-            strings = np.asanyarray(a=strings, dtype=str)
+            strings = np.asanyarray(a=strings, dtype=np.str_)
             self.put_strings(
                 dataset, family="GMT_IS_VECTOR|GMT_IS_DUPLICATE", strings=strings
             )

pygmt/datatypes/dataset.py

@@ -168,7 +168,7 @@ def to_strings(self) -> np.ndarray[Any, np.dtype[np.str_]]:
             )
             warnings.warn(msg, category=RuntimeWarning, stacklevel=1)
             textvector = [item if item is not None else b"" for item in textvector]
-        return np.char.decode(textvector) if textvector else np.array([], dtype=str)
+        return np.char.decode(textvector) if textvector else np.array([], dtype=np.str_)
 
     def to_dataframe(
         self,

pygmt/helpers/tempfile.py

@@ -50,7 +50,7 @@ class GMTTempFile:
     ...     np.savetxt(tmpfile.name, (x, y, z), fmt="%.1f")
     ...     lines = tmpfile.read()
     ...     print(lines)
-    ...     nx, ny, nz = tmpfile.loadtxt(unpack=True, dtype=float)
+    ...     nx, ny, nz = tmpfile.loadtxt(unpack=True, dtype=np.float64)
     ...     print(nx, ny, nz)
     0.0 1.0 2.0
     0.0 1.0 2.0
@@ -143,9 +143,7 @@ def tempfile_from_geojson(geojson):
             # 32-bit integer overflow issue. Related issues:
             # https://github.com/geopandas/geopandas/issues/967#issuecomment-842877704
             # https://github.com/GenericMappingTools/pygmt/issues/2497
-
             int32_info = np.iinfo(np.int32)
-
             if Version(gpd.__version__).major < 1:  # GeoPandas v0.x
                 # The default engine 'fiona' supports the 'schema' parameter.
                 if geojson.index.name is None:

pygmt/src/info.py

@@ -98,6 +98,6 @@ def info(data, **kwargs):
                 result = np.loadtxt(result.splitlines())
             except ValueError:
                 # Load non-numerical outputs in str type, e.g. for datetime
-                result = np.loadtxt(result.splitlines(), dtype="str")
+                result = np.loadtxt(result.splitlines(), dtype=np.str_)
 
         return result

pygmt/src/text.py

@@ -228,7 +228,7 @@ def text_(  # noqa: PLR0912
                 if name == "angle":
                     extra_arrays.append(arg)
                 else:
-                    extra_arrays.append(np.asarray(arg, dtype=str))
+                    extra_arrays.append(np.asarray(arg, dtype=np.str_))
 
         # If an array of transparency is given, GMT will read it from the last numerical
         # column per data record.
@@ -237,7 +237,7 @@ def text_(  # noqa: PLR0912
             kwargs["t"] = True
 
         # Append text to the last column. Text must be passed in as str type.
-        text = np.asarray(text, dtype=str)
+        text = np.asarray(text, dtype=np.str_)
         encoding = _check_encoding("".join(text.flatten()))
         if encoding != "ascii":
             text = np.vectorize(non_ascii_to_octal, excluded="encoding")(

pygmt/tests/test_clib_dataarray_to_matrix.py

@@ -76,7 +76,7 @@ def test_dataarray_to_matrix_dims_fails():
     Check that it fails for > 2 dims.
     """
     # Make a 3-D regular grid
-    data = np.ones((10, 12, 11), dtype="float32")
+    data = np.ones((10, 12, 11), dtype=np.float32)
     x = np.arange(11)
     y = np.arange(12)
     z = np.arange(10)
@@ -90,7 +90,7 @@ def test_dataarray_to_matrix_irregular_inc_warning():
     Check that it warns for variable increments, see also
     https://github.com/GenericMappingTools/pygmt/issues/1468.
     """
-    data = np.ones((4, 5), dtype="float64")
+    data = np.ones((4, 5), dtype=np.float64)
     x = np.linspace(0, 1, 5)
     y = np.logspace(2, 3, 4)
     grid = xr.DataArray(data, coords=[("y", y), ("x", x)])
@@ -103,7 +103,7 @@ def test_dataarray_to_matrix_zero_inc_fails():
     """
     Check that dataarray_to_matrix fails for zero increments grid.
     """
-    data = np.ones((5, 5), dtype="float32")
+    data = np.ones((5, 5), dtype=np.float32)
     x = np.linspace(0, 1, 5)
     y = np.zeros_like(x)
     grid = xr.DataArray(data, coords=[("y", y), ("x", x)])

pygmt/tests/test_clib_put_strings.py

@@ -24,7 +24,7 @@ def test_put_strings():
         )
         x = np.array([1, 2, 3, 4, 5], dtype=np.int32)
         y = np.array([6, 7, 8, 9, 10], dtype=np.int32)
-        strings = np.array(["a", "bc", "defg", "hijklmn", "opqrst"], dtype=str)
+        strings = np.array(["a", "bc", "defg", "hijklmn", "opqrst"], dtype=np.str_)
         lib.put_vector(dataset, column=lib["GMT_X"], vector=x)
         lib.put_vector(dataset, column=lib["GMT_Y"], vector=y)
         lib.put_strings(
@@ -60,5 +60,5 @@ def test_put_strings_fails():
             lib.put_strings(
                 dataset=None,
                 family="GMT_IS_VECTOR|GMT_IS_DUPLICATE",
-                strings=np.empty(shape=(3,), dtype=str),
+                strings=np.empty(shape=(3,), dtype=np.str_),
             )

pygmt/tests/test_clib_put_vector.py

@@ -208,11 +208,11 @@ def test_put_vector_invalid_dtype():
     for dtype in [
         np.bool_,
         np.bytes_,
-        np.csingle,
-        np.cdouble,
-        np.clongdouble,
-        np.half,
+        np.float16,
         np.longdouble,
+        np.complex64,
+        np.complex128,
+        np.clongdouble,
         np.object_,
     ]:
         with clib.Session() as lib:
@@ -224,7 +224,7 @@ def test_put_vector_invalid_dtype():
             )
             data = np.array([37, 12, 556], dtype=dtype)
             with pytest.raises(GMTInvalidInput, match="Unsupported numpy data type"):
-                lib.put_vector(dataset, column=1, vector=data)
+                lib.put_vector(dataset, column=0, vector=data)
 
 
 def test_put_vector_wrong_column():
@@ -238,7 +238,7 @@ def test_put_vector_wrong_column():
             mode="GMT_CONTAINER_ONLY",
             dim=[1, 3, 0, 0],  # ncolumns, nrows, dtype, unused
         )
-        data = np.array([37, 12, 556], dtype="float32")
+        data = np.array([37, 12, 556], dtype=np.float32)
         with pytest.raises(GMTCLibError):
             lib.put_vector(dataset, column=1, vector=data)
 
@@ -254,6 +254,6 @@ def test_put_vector_2d_fails():
             mode="GMT_CONTAINER_ONLY",
             dim=[1, 6, 0, 0],  # ncolumns, nrows, dtype, unused
         )
-        data = np.array([[37, 12, 556], [37, 12, 556]], dtype="int32")
+        data = np.array([[37, 12, 556], [37, 12, 556]], dtype=np.int32)
         with pytest.raises(GMTInvalidInput):
             lib.put_vector(dataset, column=0, vector=data)