simplify further

src/depiction/tools/cli/correct_baseline.py

@@ -2,13 +2,12 @@
 
 import shutil
 from pathlib import Path
-from typing import Annotated, Literal
+from typing import Literal
 
 import cyclopts
 import yaml
 from loguru import logger
 from pydantic import BaseModel
-from typer import Argument, Option
 
 from depiction.parallel_ops import ParallelConfig
 from depiction.persistence import ImzmlReadFile, ImzmlWriteFile
@@ -26,23 +25,24 @@ class BaselineCorrectionConfig(BaseModel):
 
 @app.command
 def run_config(
-    input_imzml: Annotated[Path, Argument()],
-    output_imzml: Annotated[Path, Argument()],
-    config: Annotated[Path, Argument()],
+    config: Path,
+    input_imzml: Path,
+    output_imzml: Path,
 ) -> None:
     parsed = BaselineCorrectionConfig.validate(yaml.safe_load(config.read_text()))
     correct_baseline(config=parsed, input_imzml=input_imzml, output_imzml=output_imzml)
 
 
 @app.default
 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",
-):
+    input_imzml: Path,
+    output_imzml: Path,
+    *,
+    n_jobs: int | None = None,
+    baseline_variant: BaselineVariants = BaselineVariants.TopHat,
+    window_size: int | float = 5000,
+    window_unit: Literal["ppm", "index"] = "ppm",
+) -> None:
     config = BaselineCorrectionConfig.validate(
         dict(n_jobs=n_jobs, baseline_variant=baseline_variant, window_size=window_size, window_unit=window_unit)
     )
@@ -61,7 +61,7 @@ def correct_baseline(config: BaselineCorrectionConfig, input_imzml: Path, output
             # TODO define some sane default for None and -1 n_jobs e.g. use all available up to a limit (None) or use all (1-r)
             n_jobs = 10
         else:
-            n_jobs = config.n_jobs
+            n_jobs = config.n_jobsf
         parallel_config = ParallelConfig(n_jobs=n_jobs)
         input_file = ImzmlReadFile(input_imzml)
         output_file = ImzmlWriteFile(output_imzml, imzml_mode=input_file.imzml_mode)