Session.virtualfile_in: Deprecate parameter 'required_z'. Use 'mincols' instead (will be removed in v0.20.0) (#3369)

Co-authored-by: Wei Ji <[email protected]>

Author: seisman

pygmt/clib/session.py

@@ -1748,16 +1748,18 @@ def virtualfile_from_stringio(
                     seg.header = None
                     seg.text = None
 
+    # TODO(PyGMT>=0.20.0): Remove the deprecated parameter 'required_z'.
     # TODO(PyGMT>=0.20.0): Remove the deprecated parameter 'extra_arrays'.
-    def virtualfile_in(
+    def virtualfile_in(  # noqa: PLR0912
         self,
         check_kind=None,
         data=None,
         x=None,
         y=None,
         z=None,
-        required_z=False,
+        mincols=2,
         required_data=True,
+        required_z=False,
         extra_arrays=None,
     ):
         """
@@ -1778,11 +1780,19 @@ def virtualfile_in(
             data input.
         x/y/z : 1-D arrays or None
             x, y, and z columns as numpy arrays.
-        required_z : bool
-            State whether the 'z' column is required.
+        mincols
+            Number of minimum required columns. Default is 2 (i.e. require x and y
+            columns).
         required_data : bool
             Set to True when 'data' is required, or False when dealing with
             optional virtual files. [Default is True].
+        required_z : bool
+            State whether the 'z' column is required.
+
+            .. deprecated:: v0.16.0
+               The parameter 'required_z' will be removed in v0.20.0. Use parameter
+               'mincols' instead. E.g., ``required_z=True`` is equivalent to
+               ``mincols=3``.
         extra_arrays : list of 1-D arrays
             A list of numpy arrays in addition to x, y, and z. All of these arrays must
             be of the same size as the x/y/z arrays.
@@ -1818,13 +1828,23 @@ def virtualfile_in(
         ...             print(fout.read().strip())
         <vector memory>: N = 3 <7/9> <4/6> <1/3>
         """
+        if required_z is True:
+            warnings.warn(
+                "The parameter 'required_z' is deprecated in v0.16.0 and will be "
+                "removed in v0.20.0. Use parameter 'mincols' instead. E.g., "
+                "``required_z=True`` is equivalent to ``mincols=3``.",
+                category=FutureWarning,
+                stacklevel=1,
+            )
+            mincols = 3
+
         kind = data_kind(data, required=required_data)
         _validate_data_input(
             data=data,
             x=x,
             y=y,
             z=z,
-            required_z=required_z,
+            mincols=mincols,
             required_data=required_data,
             kind=kind,
         )

pygmt/helpers/utils.py

@@ -43,7 +43,7 @@
 
 
 def _validate_data_input(  # noqa: PLR0912
-    data=None, x=None, y=None, z=None, required_z=False, required_data=True, kind=None
+    data=None, x=None, y=None, z=None, mincols=2, required_data=True, kind=None
 ) -> None:
     """
     Check if the combination of data/x/y/z is valid.
@@ -66,29 +66,29 @@ def _validate_data_input(  # noqa: PLR0912
     Traceback (most recent call last):
         ...
     pygmt.exceptions.GMTInvalidInput: Must provide both x and y.
-    >>> _validate_data_input(x=[1, 2, 3], y=[4, 5, 6], required_z=True)
+    >>> _validate_data_input(x=[1, 2, 3], y=[4, 5, 6], mincols=3)
     Traceback (most recent call last):
         ...
     pygmt.exceptions.GMTInvalidInput: Must provide x, y, and z.
     >>> import numpy as np
     >>> import pandas as pd
     >>> import xarray as xr
     >>> data = np.arange(8).reshape((4, 2))
-    >>> _validate_data_input(data=data, required_z=True, kind="matrix")
+    >>> _validate_data_input(data=data, mincols=3, kind="matrix")
     Traceback (most recent call last):
         ...
     pygmt.exceptions.GMTInvalidInput: data must provide x, y, and z columns.
     >>> _validate_data_input(
     ...     data=pd.DataFrame(data, columns=["x", "y"]),
-    ...     required_z=True,
+    ...     mincols=3,
     ...     kind="vectors",
     ... )
     Traceback (most recent call last):
         ...
     pygmt.exceptions.GMTInvalidInput: data must provide x, y, and z columns.
     >>> _validate_data_input(
     ...     data=xr.Dataset(pd.DataFrame(data, columns=["x", "y"])),
-    ...     required_z=True,
+    ...     mincols=3,
     ...     kind="vectors",
     ... )
     Traceback (most recent call last):
@@ -116,6 +116,7 @@ def _validate_data_input(  # noqa: PLR0912
     GMTInvalidInput
         If the data input is not valid.
     """
+    required_z = mincols >= 3
     if data is None:  # data is None
         if x is None and y is None:  # both x and y are None
             if required_data:  # data is not optional

pygmt/src/blockm.py

@@ -56,7 +56,7 @@ def _blockm(
     with Session() as lib:
         with (
             lib.virtualfile_in(
-                check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
+                check_kind="vector", data=data, x=x, y=y, z=z, mincols=3
             ) as vintbl,
             lib.virtualfile_out(kind="dataset", fname=outfile) as vouttbl,
         ):

pygmt/src/contour.py

@@ -148,7 +148,7 @@ def contour(
 
     with Session() as lib:
         with lib.virtualfile_in(
-            check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
+            check_kind="vector", data=data, x=x, y=y, z=z, mincols=3
         ) as vintbl:
             lib.call_module(
                 module="contour", args=build_arg_list(kwargs, infile=vintbl)

pygmt/src/nearneighbor.py

@@ -147,7 +147,7 @@ def nearneighbor(
     with Session() as lib:
         with (
             lib.virtualfile_in(
-                check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
+                check_kind="vector", data=data, x=x, y=y, z=z, mincols=3
             ) as vintbl,
             lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd,
         ):

pygmt/src/plot3d.py

@@ -259,7 +259,5 @@ def plot3d(  # noqa: PLR0912
         kwargs["S"] = "u0.2c"
 
     with Session() as lib:
-        with lib.virtualfile_in(
-            check_kind="vector", data=data, required_z=True
-        ) as vintbl:
+        with lib.virtualfile_in(check_kind="vector", data=data, mincols=3) as vintbl:
             lib.call_module(module="plot3d", args=build_arg_list(kwargs, infile=vintbl))

pygmt/src/project.py

@@ -246,7 +246,7 @@ def project(
                 x=x,
                 y=y,
                 z=z,
-                required_z=False,
+                mincols=2,
                 required_data=False,
             ) as vintbl,
             lib.virtualfile_out(kind="dataset", fname=outfile) as vouttbl,

pygmt/src/surface.py

@@ -161,7 +161,7 @@ def surface(
     with Session() as lib:
         with (
             lib.virtualfile_in(
-                check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
+                check_kind="vector", data=data, x=x, y=y, z=z, mincols=3
             ) as vintbl,
             lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd,
         ):

pygmt/src/triangulate.py

@@ -144,7 +144,7 @@ def regular_grid(
         with Session() as lib:
             with (
                 lib.virtualfile_in(
-                    check_kind="vector", data=data, x=x, y=y, z=z, required_z=False
+                    check_kind="vector", data=data, x=x, y=y, z=z, mincols=2
                 ) as vintbl,
                 lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd,
             ):
@@ -244,7 +244,7 @@ def delaunay_triples(
         with Session() as lib:
             with (
                 lib.virtualfile_in(
-                    check_kind="vector", data=data, x=x, y=y, z=z, required_z=False
+                    check_kind="vector", data=data, x=x, y=y, z=z, mincols=2
                 ) as vintbl,
                 lib.virtualfile_out(kind="dataset", fname=outfile) as vouttbl,
             ):

pygmt/src/wiggle.py

@@ -109,6 +109,6 @@ def wiggle(
 
     with Session() as lib:
         with lib.virtualfile_in(
-            check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
+            check_kind="vector", data=data, x=x, y=y, z=z, mincols=3
         ) as vintbl:
             lib.call_module(module="wiggle", args=build_arg_list(kwargs, infile=vintbl))

pygmt/src/xyz2grd.py

@@ -155,7 +155,7 @@ def xyz2grd(
     with Session() as lib:
         with (
             lib.virtualfile_in(
-                check_kind="vector", data=data, x=x, y=y, z=z, required_z=True
+                check_kind="vector", data=data, x=x, y=y, z=z, mincols=3
             ) as vintbl,
             lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd,
         ):

pygmt/tests/test_clib_virtualfile_in.py

@@ -41,9 +41,7 @@ def test_virtualfile_in_required_z_matrix(array_func, kind):
     )
     data = array_func(dataframe)
     with clib.Session() as lib:
-        with lib.virtualfile_in(
-            data=data, required_z=True, check_kind="vector"
-        ) as vfile:
+        with lib.virtualfile_in(data=data, mincols=3, check_kind="vector") as vfile:
             with GMTTempFile() as outfile:
                 lib.call_module("info", [vfile, f"->{outfile.name}"])
                 output = outfile.read(keep_tabs=True)
@@ -64,10 +62,26 @@ def test_virtualfile_in_required_z_matrix_missing():
     data = np.ones((5, 2))
     with clib.Session() as lib:
         with pytest.raises(GMTInvalidInput):
-            with lib.virtualfile_in(data=data, required_z=True, check_kind="vector"):
+            with lib.virtualfile_in(data=data, mincols=3, check_kind="vector"):
                 pass
 
 
+# TODO(PyGMT>=0.20.0): Remove this test for the deprecated 'required_z' parameter.
+def test_virtualfile_in_required_z_deprecated():
+    """
+    Same as test_virtualfile_in_required_z_matrix_missing but using the deprecated
+    'required_z' parameter.
+    """
+    data = np.ones((5, 2))
+    with clib.Session() as lib:
+        with pytest.raises(GMTInvalidInput):  # noqa: PT012
+            with pytest.warns(FutureWarning):
+                with lib.virtualfile_in(
+                    data=data, required_z=True, check_kind="vector"
+                ):
+                    pass
+
+
 def test_virtualfile_in_fail_non_valid_data(data):
     """
     Should raise an exception if too few or too much data is given.
@@ -91,7 +105,7 @@ def test_virtualfile_in_fail_non_valid_data(data):
         with clib.Session() as lib:
             with pytest.raises(GMTInvalidInput):
                 lib.virtualfile_in(
-                    x=variable[0], y=variable[1], z=variable[2], required_z=True
+                    x=variable[0], y=variable[1], z=variable[2], mincols=3
                 )
 
     # Should also fail if given too much data