pygmt.grdvolume: Refactor to store output in virtual files instead of temporary files (#3102)

Author: seisman

pygmt/src/grdvolume.py

@@ -2,10 +2,12 @@
 grdvolume - Calculate grid volume and area constrained by a contour.
 """
 
+from typing import Literal
+
+import numpy as np
 import pandas as pd
 from pygmt.clib import Session
 from pygmt.helpers import (
-    GMTTempFile,
     build_arg_string,
     fmt_docstring,
     kwargs_to_strings,
@@ -24,7 +26,12 @@
     V="verbose",
 )
 @kwargs_to_strings(C="sequence", R="sequence")
-def grdvolume(grid, output_type="pandas", outfile=None, **kwargs):
+def grdvolume(
+    grid,
+    output_type: Literal["pandas", "numpy", "file"] = "pandas",
+    outfile: str | None = None,
+    **kwargs,
+) -> pd.DataFrame | np.ndarray | None:
     r"""
     Determine the volume between the surface of a grid and a plane.
 
@@ -41,15 +48,8 @@ def grdvolume(grid, output_type="pandas", outfile=None, **kwargs):
     Parameters
     ----------
     {grid}
-    output_type : str
-        Determine the format the output data will be returned in [Default is
-        ``pandas``]:
-
-            - ``numpy`` - :class:`numpy.ndarray`
-            - ``pandas``-  :class:`pandas.DataFrame`
-            - ``file`` - ASCII file (requires ``outfile``)
-    outfile : str
-        The file name for the output ASCII file.
+    {output_type}
+    {outfile}
     contour : str, float, or list
         *cval*\|\ *low/high/delta*\|\ **r**\ *low/high*\|\ **r**\ *cval*.
         Find area, volume and mean height (volume/area) inside and above the
@@ -69,14 +69,13 @@ def grdvolume(grid, output_type="pandas", outfile=None, **kwargs):
 
     Returns
     -------
-    ret : pandas.DataFrame or numpy.ndarray or None
+    ret
         Return type depends on ``outfile`` and ``output_type``:
 
-        - None if ``outfile`` is set (output will be stored in file set by
+        - ``None`` if ``outfile`` is set (output will be stored in file set by
           ``outfile``)
-        - :class:`pandas.DataFrame` or :class:`numpy.ndarray` if ``outfile``
-          is not set (depends on ``output_type`` [Default is
-          :class:`pandas.DataFrame`])
+        - :class:`pandas.DataFrame` or :class:`numpy.ndarray` if ``outfile`` is not set
+          (depends on ``output_type``)
 
     Example
     -------
@@ -103,22 +102,13 @@ def grdvolume(grid, output_type="pandas", outfile=None, **kwargs):
     """
     output_type = validate_output_table_type(output_type, outfile=outfile)
 
-    with GMTTempFile() as tmpfile:
-        with Session() as lib:
-            with lib.virtualfile_in(check_kind="raster", data=grid) as vingrd:
-                if outfile is None:
-                    outfile = tmpfile.name
-                lib.call_module(
-                    module="grdvolume",
-                    args=build_arg_string(kwargs, infile=vingrd, outfile=outfile),
-                )
-
-        # Read temporary csv output to a pandas table
-        if outfile == tmpfile.name:  # if user did not set outfile, return pd.DataFrame
-            result = pd.read_csv(tmpfile.name, sep="\t", header=None, comment=">")
-        elif outfile != tmpfile.name:  # return None if outfile set, output in outfile
-            result = None
-
-        if output_type == "numpy":
-            result = result.to_numpy()
-    return result
+    with Session() as lib:
+        with (
+            lib.virtualfile_in(check_kind="raster", data=grid) as vingrd,
+            lib.virtualfile_out(kind="dataset", fname=outfile) as vouttbl,
+        ):
+            lib.call_module(
+                module="grdvolume",
+                args=build_arg_string(kwargs, infile=vingrd, outfile=vouttbl),
+            )
+            return lib.virtualfile_to_dataset(output_type=output_type, vfname=vouttbl)

pygmt/tests/test_grdvolume.py

@@ -2,15 +2,11 @@
 Test pygmt.grdvolume.
 """
 
-from pathlib import Path
-
 import numpy as np
 import numpy.testing as npt
 import pandas as pd
 import pytest
 from pygmt import grdvolume
-from pygmt.exceptions import GMTInvalidInput
-from pygmt.helpers import GMTTempFile
 from pygmt.helpers.testing import load_static_earth_relief
 
 
@@ -22,14 +18,6 @@ def fixture_grid():
     return load_static_earth_relief()
 
 
-@pytest.fixture(scope="module", name="region")
-def fixture_region():
-    """
-    Set the data region for the tests.
-    """
-    return [-53, -50, -22, -20]
-
-
 @pytest.fixture(scope="module", name="data")
 def fixture_data():
     """
@@ -47,57 +35,15 @@ def fixture_data():
     return data
 
 
-def test_grdvolume_format(grid, region):
-    """
-    Test that correct formats are returned.
-    """
-    grdvolume_default = grdvolume(grid=grid, region=region)
-    assert isinstance(grdvolume_default, pd.DataFrame)
-    grdvolume_array = grdvolume(grid=grid, output_type="numpy", region=region)
-    assert isinstance(grdvolume_array, np.ndarray)
-    grdvolume_df = grdvolume(grid=grid, output_type="pandas", region=region)
-    assert isinstance(grdvolume_df, pd.DataFrame)
-
-
-def test_grdvolume_invalid_format(grid):
-    """
-    Test that grdvolume fails with incorrect output_type argument.
-    """
-    with pytest.raises(GMTInvalidInput):
-        grdvolume(grid=grid, output_type=1)
-
-
-def test_grdvolume_no_outfile(grid):
-    """
-    Test that grdvolume fails when output_type set to 'file' but no outfile is
-    specified.
-    """
-    with pytest.raises(GMTInvalidInput):
-        grdvolume(grid=grid, output_type="file")
-
-
 @pytest.mark.benchmark
-def test_grdvolume_no_outgrid(grid, data, region):
+def test_grdvolume(grid, data):
     """
-    Test the expected output of grdvolume with no output file set.
+    Test the basic functionality of grdvolume.
     """
     test_output = grdvolume(
-        grid=grid, contour=[200, 400, 50], output_type="numpy", region=region
+        grid=grid,
+        contour=[200, 400, 50],
+        region=[-53, -50, -22, -20],
     )
+    assert isinstance(test_output, pd.DataFrame)
     npt.assert_allclose(test_output, data)
-
-
-def test_grdvolume_outgrid(grid, region):
-    """
-    Test the expected output of grdvolume with an output file set.
-    """
-    with GMTTempFile(suffix=".csv") as tmpfile:
-        result = grdvolume(
-            grid=grid,
-            contour=[200, 400, 50],
-            output_type="file",
-            outfile=tmpfile.name,
-            region=region,
-        )
-        assert result is None  # return value is None
-        assert Path(tmpfile.name).stat().st_size > 0  # check that outfile exists