Merge pull request #158 from MetOffice/general-cleanup

General cleanup

pyproject.toml

@@ -12,9 +12,10 @@ classifiers = [
 ]
 dependencies = [
     "numpy",
-    "scitools-iris",
+    "scitools-iris >= 3.6",
     "ruamel.yaml >= 0.17",
     "importlib_resources >= 3.0.0 ; python_version < '3.9'",
+    "pygraphviz >= 1.11"
 ]
 
 [project.urls]

src/CSET/operators/constraints.py

@@ -30,7 +30,7 @@ def generate_stash_constraint(stash: str, **kwargs) -> iris.AttributeConstraint:
     Arguments
     ---------
     stash: str
-        stash code to build iris constraint, currently using "m01s03i236"
+        stash code to build iris constraint, such as "m01s03i236"
 
     Returns
     -------

src/CSET/operators/filters.py

@@ -18,33 +18,35 @@
 
 import iris
 import iris.cube
+from typing import Union
 
 
 def filter_cubes(
-    cubelist: iris.cube.CubeList, constraint: iris.Constraint, **kwargs
+    cube: Union[iris.cube.Cube, iris.cube.CubeList],
+    constraint: iris.Constraint,
+    **kwargs,
 ) -> iris.cube.Cube:
     """
     Filters a cubelist down to a single cube based on a constraint.
 
     Arguments
     ---------
-    cubelist: iris.cube.CubeList
-        Cubes to iterate over
+    cube: iris.cube.Cube | iris.cube.CubeList
+        Cube(s) to iterate over
     constraint: iris.Constraint
         Constraint to extract
 
     Returns
     -------
-    cube: iris.cube.Cube
-        Single variable
+    iris.cube.Cube
 
     Raises
     ------
     ValueError
         If the constraint doesn't produce a single cube.
     """
 
-    filtered_cubes = cubelist.extract(constraint)
+    filtered_cubes = cube.extract(constraint)
 
     # Check filtered cubes is a CubeList containing one cube.
     if len(filtered_cubes) == 1:

src/CSET/recipes/__init__.py

@@ -37,7 +37,7 @@ def _unpack_recipes_from_dir(input_dir: Path, output_dir: Path):
         output_dir.mkdir(parents=True, exist_ok=True)
         if file.is_file() and file.suffix == ".yaml":
             if output_dir.joinpath(file.name).exists():
-                logging.warn(
+                logging.warning(
                     "%s already exists in target directory, skipping.", file.name
                 )
             else:

tests/test_cli.py

@@ -25,15 +25,20 @@
 
 
 def test_command_line_help():
+    """Check that help commands work."""
+
     subprocess.run(["cset", "--help"], check=True)
     # test verbose options. This is really just to up the coverage number.
     subprocess.run(["cset", "-v"], check=True)
     subprocess.run(["cset", "-vv"], check=True)
+    subprocess.run(["cset", "--version"], check=True)
     # Gain coverage of __main__.py
     subprocess.run(["python3", "-m", "CSET", "-h"], check=True)
 
 
 def test_recipe_execution():
+    """Test running CSET recipe from the command line."""
+
     subprocess.run(
         [
             "cset",
@@ -48,6 +53,7 @@ def test_recipe_execution():
 
 def test_environ_var_recipe():
     """Test recipe coming from environment variable."""
+
     os.environ[
         "CSET_RECIPE"
     ] = """
@@ -82,8 +88,28 @@ def test_graph_creation():
     output_file.unlink()
 
 
+def test_graph_creation_env_var():
+    """
+    Generates a graph with the command line interface from an environment
+    variable.
+    """
+
+    os.environ[
+        "CSET_RECIPE"
+    ] = """
+        steps:
+          - operator: misc.noop
+        """
+    # Run with output path specified
+    output_file = Path(tempfile.gettempdir(), f"{uuid4()}.svg")
+    subprocess.run(("cset", "graph", "-o", str(output_file)), check=True)
+    assert output_file.exists()
+    output_file.unlink()
+
+
 def test_graph_details():
     """Generate a graph with details with details."""
+
     output_file = Path(tempfile.gettempdir(), f"{uuid4()}.svg")
     subprocess.run(
         (
@@ -102,13 +128,15 @@ def test_graph_details():
 
 def test_cookbook_cwd():
     """Unpacking the recipes into the current working directory."""
+
     subprocess.run(["cset", "cookbook"], check=True)
     assert Path.cwd().joinpath("recipes/extract_instant_air_temp.yaml").exists()
     shutil.rmtree(Path.cwd().joinpath("recipes"))
 
 
 def test_cookbook_path():
     """Unpacking the recipes into a specified directory."""
+
     with tempfile.TemporaryDirectory() as tmpdir:
         subprocess.run(["cset", "cookbook", tmpdir], check=True)
         assert Path(tmpdir, "extract_instant_air_temp.yaml").exists()