Add new parameter 'required_cols' and remove the parameter 'required_z'

Author: seisman

pygmt/clib/session.py

@@ -1605,8 +1605,8 @@ def virtualfile_in(  # noqa: PLR0912
         x=None,
         y=None,
         z=None,
-        required_z=False,
         required_data=True,
+        required_cols: int = 2,
     ):
         """
         Store any data inside a virtual file.
@@ -1626,11 +1626,11 @@ def virtualfile_in(  # noqa: PLR0912
             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.
         required_data : bool
             Set to True when 'data' is required, or False when dealing with
             optional virtual files. [Default is True].
+        required_cols
+            Number of required columns.
 
         Returns
         -------
@@ -1664,8 +1664,8 @@ def virtualfile_in(  # noqa: PLR0912
             x=x,
             y=y,
             z=z,
-            required_z=required_z,
             required_data=required_data,
+            required_cols=required_cols,
             kind=kind,
         )
 
@@ -1775,8 +1775,8 @@ def virtualfile_from_data(
             x=x,
             y=y,
             z=z,
-            required_z=required_z,
             required_data=required_data,
+            required_cols=3 if required_z else 2,
         )
 
     @contextlib.contextmanager

pygmt/helpers/utils.py

@@ -21,7 +21,7 @@
 
 
 def _validate_data_input(
-    data=None, x=None, y=None, z=None, required_z=False, required_data=True, kind=None
+    data=None, x=None, y=None, z=None, required_data=True, required_cols=2, kind=None
 ):
     """
     Check if the combination of data/x/y/z is valid.
@@ -44,34 +44,33 @@ def _validate_data_input(
     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], required_cols=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, required_cols=3, kind="matrix")
     Traceback (most recent call last):
         ...
-    pygmt.exceptions.GMTInvalidInput: data must provide x, y, and z columns.
+    pygmt.exceptions.GMTInvalidInput: data needs 3 columns but 2 column(s) are given.
     >>> _validate_data_input(
     ...     data=pd.DataFrame(data, columns=["x", "y"]),
-    ...     required_z=True,
+    ...     required_cols=3,
     ...     kind="matrix",
     ... )
     Traceback (most recent call last):
         ...
-    pygmt.exceptions.GMTInvalidInput: data must provide x, y, and z columns.
+    pygmt.exceptions.GMTInvalidInput: data needs 3 columns but 2 column(s) are given.
     >>> _validate_data_input(
     ...     data=xr.Dataset(pd.DataFrame(data, columns=["x", "y"])),
-    ...     required_z=True,
-    ...     kind="matrix",
+    ...     required_cols=3,
     ... )
     Traceback (most recent call last):
         ...
-    pygmt.exceptions.GMTInvalidInput: data must provide x, y, and z columns.
+    pygmt.exceptions.GMTInvalidInput: data needs 3 columns but 2 column(s) are given.
     >>> _validate_data_input(data="infile", x=[1, 2, 3])
     Traceback (most recent call last):
         ...
@@ -94,26 +93,38 @@ def _validate_data_input(
     GMTInvalidInput
         If the data input is not valid.
     """
-    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
+    if kind is None:
+        kind = data_kind(data, required=required_data)
+
+    if data is not None and any(v is not None for v in (x, y, z)):
+        raise GMTInvalidInput("Too much data. Use either data or x/y/z.")
+
+    match kind:
+        case "none":
+            if x is None and y is None:  # both x and y are None
                 raise GMTInvalidInput("No input data provided.")
-        elif x is None or y is None:  # either x or y is None
-            raise GMTInvalidInput("Must provide both x and y.")
-        if required_z and z is None:  # both x and y are not None, now check z
-            raise GMTInvalidInput("Must provide x, y, and z.")
-    else:  # data is not None
-        if x is not None or y is not None or z is not None:
-            raise GMTInvalidInput("Too much data. Use either data or x/y/z.")
-        # For 'matrix' kind, check if data has the required z column
-        if kind == "matrix" and required_z:
-            if hasattr(data, "shape"):  # np.ndarray or pd.DataFrame
-                if len(data.shape) == 1 and data.shape[0] < 3:
-                    raise GMTInvalidInput("data must provide x, y, and z columns.")
-                if len(data.shape) > 1 and data.shape[1] < 3:
-                    raise GMTInvalidInput("data must provide x, y, and z columns.")
-            if hasattr(data, "data_vars") and len(data.data_vars) < 3:  # xr.Dataset
-                raise GMTInvalidInput("data must provide x, y, and z columns.")
+            if x is None or y is None:  # either x or y is None
+                raise GMTInvalidInput("Must provide both x and y.")
+            if required_cols >= 3 and z is None:
+                # both x and y are not None, now check z
+                raise GMTInvalidInput("Must provide x, y, and z.")
+        case "matrix":  # 2-D numpy.ndarray
+            if (actual_cols := data.shape[1]) < required_cols:
+                msg = f"data needs {required_cols} columns but {actual_cols} column(s) are given."
+                raise GMTInvalidInput(msg)
+        case "vectors":
+            if hasattr(data, "items") and not hasattr(data, "to_frame"):
+                # Dict, pd.DataFrame, xr.Dataset
+                arrays = [array for _, array in data.items()]
+                if (actual_cols := len(arrays)) < required_cols:
+                    msg = f"data needs {required_cols} columns but {actual_cols} column(s) are given."
+                    raise GMTInvalidInput(msg)
+
+                # Loop over columns to make sure they're not None
+                for idx, array in enumerate(arrays[:required_cols]):
+                    if array is None:
+                        msg = f"data needs {required_cols} columns but the {idx} column is None."
+                        raise GMTInvalidInput(msg)
 
 
 def _check_encoding(

pygmt/src/blockm.py

@@ -55,7 +55,7 @@ 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, required_cols=3
             ) as vintbl,
             lib.virtualfile_out(kind="dataset", fname=outfile) as vouttbl,
         ):

pygmt/src/contour.py

@@ -145,7 +145,7 @@ def contour(self, data=None, x=None, y=None, z=None, **kwargs):
 
     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, required_cols=3
         ) as vintbl:
             lib.call_module(
                 module="contour", args=build_arg_list(kwargs, infile=vintbl)

pygmt/src/nearneighbor.py

@@ -140,7 +140,7 @@ 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, required_cols=3
             ) as vintbl,
             lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd,
         ):

pygmt/src/plot.py

@@ -211,6 +211,7 @@ def plot(  # noqa: PLR0912
     kind = data_kind(data)
     if kind == "none":  # Vectors input
         data = {"x": x, "y": y}
+        x, y = None, None
         # Parameters for vector styles
         if (
             kwargs.get("S") is not None
@@ -255,5 +256,5 @@ def plot(  # noqa: PLR0912
                 pass
 
     with Session() as lib:
-        with lib.virtualfile_in(check_kind="vector", data=data) as vintbl:
+        with lib.virtualfile_in(check_kind="vector", data=data, x=x, y=y) as vintbl:
             lib.call_module(module="plot", args=build_arg_list(kwargs, infile=vintbl))

pygmt/src/plot3d.py

@@ -186,6 +186,7 @@ def plot3d(  # noqa: PLR0912
     kind = data_kind(data)
     if kind == "none":  # Vectors input
         data = {"x": x, "y": y, "z": z}
+        x, y, z = None, None, None
         # Parameters for vector styles
         if (
             kwargs.get("S") is not None
@@ -231,6 +232,6 @@ def plot3d(  # noqa: PLR0912
 
     with Session() as lib:
         with lib.virtualfile_in(
-            check_kind="vector", data=data, required_z=True
+            check_kind="vector", data=data, x=x, y=y, z=z, required_cols=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,
+                required_cols=2,
                 required_data=False,
             ) as vintbl,
             lib.virtualfile_out(kind="dataset", fname=outfile) as vouttbl,

pygmt/src/surface.py

@@ -153,7 +153,7 @@ def surface(data=None, x=None, y=None, z=None, outgrid: str | None = None, **kwa
     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, required_cols=3
             ) as vintbl,
             lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd,
         ):

pygmt/src/triangulate.py

@@ -138,7 +138,7 @@ 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, required_cols=2
                 ) as vintbl,
                 lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd,
             ):
@@ -238,7 +238,7 @@ 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, required_cols=2
                 ) as vintbl,
                 lib.virtualfile_out(kind="dataset", fname=outfile) as vouttbl,
             ):

pygmt/src/wiggle.py

@@ -108,6 +108,6 @@ 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, required_cols=3
         ) as vintbl:
             lib.call_module(module="wiggle", args=build_arg_list(kwargs, infile=vintbl))

pygmt/src/xyz2grd.py

@@ -145,7 +145,7 @@ def xyz2grd(data=None, x=None, y=None, z=None, outgrid: str | None = None, **kwa
     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, required_cols=3
             ) as vintbl,
             lib.virtualfile_out(kind="grid", fname=outgrid) as voutgrd,
         ):

pygmt/tests/test_clib_virtualfiles.py

@@ -141,7 +141,7 @@ 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"
+            data=data, required_cols=3, check_kind="vector"
         ) as vfile:
             with GMTTempFile() as outfile:
                 lib.call_module("info", [vfile, f"->{outfile.name}"])
@@ -163,7 +163,7 @@ 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, required_cols=3, check_kind="vector"):
                 pass
 
 
@@ -190,7 +190,7 @@ 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], required_cols=3
                 )
 
     # Should also fail if given too much data