ensure test passes

src/depiction/tools/cli/correct_baseline.py

@@ -18,14 +18,14 @@
 
 
 class BaselineCorrectionConfig(BaseModel):
-    n_jobs: int
+    n_jobs: int | None
     baseline_variant: BaselineVariants = BaselineVariants.TopHat
     window_size: int | float = 5000.0
     window_unit: Literal["ppm", "index"] = "ppm"
 
 
 @app.command
-def config(
+def run_config(
     input_imzml: Annotated[Path, Argument()],
     output_imzml: Annotated[Path, Argument()],
     config: Annotated[Path, Argument()],
@@ -35,19 +35,18 @@ def config(
 
 
 @app.default
-def main_args(
+def run(
     input_imzml: Annotated[Path, Argument()],
     output_imzml: Annotated[Path, Argument()],
     n_jobs: Annotated[int, Option()] = None,
     baseline_variant: Annotated[BaselineVariants, Option()] = BaselineVariants.TopHat,
     window_size: Annotated[int | float, Option()] = 5000,
     window_unit: Annotated[Literal["ppm", "index"], Option()] = "ppm",
 ):
-    parsed = BaselineCorrectionConfig(
-        n_jobs=n_jobs, baseline_type=baseline_variant, window_size=window_size, window_unit=window_unit
+    config = BaselineCorrectionConfig.validate(
+        dict(n_jobs=n_jobs, baseline_variant=baseline_variant, window_size=window_size, window_unit=window_unit)
     )
-    parsed.validate()
-    correct_baseline(config=parsed, input_imzml=input_imzml, output_imzml=output_imzml)
+    correct_baseline(config=config, input_imzml=input_imzml, output_imzml=output_imzml)
 
 
 def correct_baseline(config: BaselineCorrectionConfig, input_imzml: Path, output_imzml: Path) -> None:

tests/unit/tools/cli/test_correct_baseline.py

@@ -2,19 +2,17 @@
 
 import pytest
 
-from depiction.tools.cli.correct_baseline import correct_baseline
+from depiction.tools.cli.correct_baseline import run
 from depiction.tools.correct_baseline import BaselineVariants
 
 
-def test_correct_baseline_when_variant_zero(mocker) -> None:
+def test_run_when_variant_zero(mocker) -> None:
     mock_copyfile = mocker.patch("shutil.copyfile")
     mock_logger = mocker.patch("depiction.tools.cli.correct_baseline.logger")
     mock_input_imzml = Path("/dev/null/hello.imzML")
     mock_output_imzml = mocker.MagicMock(name="mock_output_imzml")
 
-    correct_baseline(
-        input_imzml=mock_input_imzml, output_imzml=mock_output_imzml, baseline_variant=BaselineVariants.Zero
-    )
+    run(input_imzml=mock_input_imzml, output_imzml=mock_output_imzml, baseline_variant=BaselineVariants.Zero)
 
     assert mock_copyfile.mock_calls == [
         mocker.call(mock_input_imzml, mock_output_imzml),
@@ -24,7 +22,7 @@ def test_correct_baseline_when_variant_zero(mocker) -> None:
     mock_logger.info.assert_called_once()
 
 
-def test_correct_baseline_when_other_variant(mocker) -> None:
+def test_run_when_other_variant(mocker) -> None:
     mock_logger = mocker.patch("loguru.logger")
     mock_imzml_mode = mocker.MagicMock(name="mock_imzml_mode", spec=[])
     construct_imzml_read_file = mocker.patch("depiction.tools.cli.correct_baseline.ImzmlReadFile")
@@ -34,9 +32,7 @@ def test_correct_baseline_when_other_variant(mocker) -> None:
     mock_input_imzml = Path("/dev/null/hello.imzML")
     mock_output_imzml = mocker.MagicMock(name="mock_output_imzml")
 
-    correct_baseline(
-        input_imzml=mock_input_imzml, output_imzml=mock_output_imzml, baseline_variant=BaselineVariants.TopHat
-    )
+    run(input_imzml=mock_input_imzml, output_imzml=mock_output_imzml, baseline_variant=BaselineVariants.TopHat)
 
     construct_correct_baseline.assert_called_once_with(
         parallel_config=mocker.ANY, variant=BaselineVariants.TopHat, window_size=5000, window_unit="ppm"