Adds cli and test to extract a cube from a cubelist (#2044)

* Adds cli and test to extract a cube from a cubelist

* Formatting

* update doc string

improver/cli/cubelist_extract.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+# (C) Crown copyright, Met Office. All rights reserved.
+#
+# This file is part of IMPROVER and is released under a BSD 3-Clause license.
+# See LICENSE in the root of the repository for full licensing details.
+"""Script to extract a cube from a cubelist"""
+
+from improver import cli
+
+
+@cli.clizefy
+@cli.with_output
+def process(cubes: cli.inputcubelist, *, name: str):
+    """Extract a single cube from a cubelist whose name matches
+    the provided name.
+
+    Args:
+        cubes (iris.cube.CubeList):
+            A cubelist containing exactly one cube with the provided name to
+            be extracted.
+        name (str):
+            The name of the cube to be extracted.
+    Returns:
+        iris.cube.Cube:
+            The extracted cube whose name matches the provided name.
+
+    """
+    from improver.utilities.cube_extraction import cubelist_extract
+
+    return cubelist_extract(cubes, name)

improver/utilities/cube_extraction.py

@@ -9,7 +9,7 @@
 
 import numpy as np
 from iris import Constraint
-from iris.cube import Cube
+from iris.cube import Cube, CubeList
 from iris.exceptions import CoordinateNotFoundError
 
 from improver import BasePlugin
@@ -346,6 +346,19 @@ def thin_cube(cube: Cube, thinning_dict: Dict[str, int]) -> Cube:
     return cube[tuple(slices)]
 
 
+def cubelist_extract(cubes: CubeList, name: str):
+    """Extract a cube from a CubeList based on provided name.
+    Args:
+        cubes:
+            A CubeList.
+        name:
+            Name of the cube to be extracted.
+    Returns:
+        A single cube matching the input name.
+    """
+    return cubes.extract_cube(name)
+
+
 class ExtractLevel(BasePlugin):
     """
     Class for extracting a pressure or height surface from data-on-levels.

improver_tests/acceptance/SHA256SUMS

@@ -331,6 +331,8 @@ ae2f673bf29b926cac46c3a578a8e1842cce19881f8fe479cba3f51f0d474951  ./copy-attribu
 d3efbc6014743793fafed512a8017a7b75e4f0ffa7fd202cd4f1b4a1086b2583  ./create-grid-with-halo/basic/kgo.nc
 fee00437131d2367dc317e5b0fff44e65e03371b8f096bf1ac0d4cc7253693c9  ./create-grid-with-halo/basic/source_grid.nc
 bf7e42be7897606682c3ecdaeb27bf3d3b6ab13a9a88b46c88ae6e92801c6245  ./create-grid-with-halo/halo_size/kgo.nc
+55ba8a8ca8b5eee667d37fe8ec4a653caddea27f19ea290397428a487eb13ca0  ./cubelist-extract/input_cubelist.nc
+33c7e0cf46ac62ead74ffde502ee28076a59550474fb3872c3e22083c4bd3cc3  ./cubelist-extract/kgo.nc
 fe00aadb6854f44d765b40bb6608c23f4eb4f10193c96f43f207db0590739dab  ./enforce-consistent-forecasts/double_bound_percentile_kgo.nc
 51f9ff2c8e6cad54d04d6323c654ce25b812bea3ba6b0d85df21c19731c580fc  ./enforce-consistent-forecasts/percentile_forecast.nc
 e210bf956dd3574eda3a64fdc3371ab16f85048ca120a3823e90d751d2325c46  ./enforce-consistent-forecasts/percentile_reference.nc

improver_tests/acceptance/test_cubelist_extract.py

@@ -0,0 +1,26 @@
+# (C) Crown copyright, Met Office. All rights reserved.
+#
+# This file is part of IMPROVER and is released under a BSD 3-Clause license.
+# See LICENSE in the root of the repository for full licensing details.
+"""
+Tests for the cubelist-extract CLI
+"""
+
+import pytest
+
+from . import acceptance as acc
+
+pytestmark = [pytest.mark.acc, acc.skip_if_kgo_missing]
+CLI = acc.cli_name_with_dashes(__file__)
+run_cli = acc.run_cli(CLI)
+
+
+def test_basic(tmp_path):
+    """Test basic extraction"""
+    kgo_dir = acc.kgo_root() / "cubelist-extract"
+    kgo_path = kgo_dir / "kgo.nc"
+    input_path = kgo_dir / "input_cubelist.nc"
+    output_path = tmp_path / "output.nc"
+    args = [input_path, "--name=grid_eastward_wind", "--output", output_path]
+    run_cli(args)
+    acc.compare(output_path, kgo_path)

improver_tests/utilities/cube_extraction/test_cube_extraction.py

@@ -20,6 +20,7 @@
 from improver.utilities.cube_extraction import (
     apply_extraction,
     create_constraint,
+    cubelist_extract,
     extract_subcube,
     parse_constraint_list,
 )
@@ -98,6 +99,20 @@ def set_up_uk_gridded_cube():
     )
 
 
+def test_cubelist_extract():
+    """Test the extraction of a single cube from a cube list."""
+
+    cube1 = set_up_variable_cube(
+        np.empty((3, 3), dtype=np.float32), name="temperature", units="K"
+    )
+    cube2 = set_up_variable_cube(
+        np.empty((3, 3), dtype=np.float32), name="precipitation_rate", units="mm h-1"
+    )
+    cube_list = iris.cube.CubeList([cube1, cube2])
+    result = cubelist_extract(cube_list, "temperature")
+    assert result == cube1
+
+
 class Test_create_constraint(IrisTest):
     """Test the creation of constraints that allow for floating point
     comparisons."""