move correct_baseline code

src/depiction/tools/cli/cli.py

@@ -1,10 +1,10 @@
 from cyclopts import App
 
 from depiction.tools.calibrate.__main__ import app as calibrate
-from depiction.tools.cli.cli_correct_baseline import app as correct_baseline
 from depiction.tools.cli.cli_filter_peaks import app as filter_peaks
 from depiction.tools.cli.cli_generate_ion_images import app as generate_ion_images
 from depiction.tools.cli.cli_pick_peaks import app as pick_peaks
+from depiction.tools.correct_baseline.__main__ import app as correct_baseline
 
 app = App()
 app.command(calibrate, name="calibrate")

src/depiction/tools/cli/cli_correct_baseline.py → src/depiction/tools/correct_baseline/__main__.py

@@ -8,7 +8,8 @@
 from loguru import logger
 
 from depiction.persistence import ImzmlReadFile
-from depiction.tools.correct_baseline import BaselineVariants, BaselineCorrectionConfig, correct_baseline
+from depiction.tools.correct_baseline.correct_baseline import correct_baseline
+from depiction.tools.correct_baseline.config import BaselineVariants, BaselineCorrectionConfig
 
 app = cyclopts.App()
 

src/depiction/tools/correct_baseline/config.py

@@ -0,0 +1,18 @@
+from __future__ import annotations
+
+import enum
+from typing import Literal
+
+from pydantic import BaseModel, PositiveInt, PositiveFloat
+
+
+class BaselineVariants(str, enum.Enum):
+    TopHat = "TopHat"
+    LocMedians = "LocMedians"
+
+
+class BaselineCorrectionConfig(BaseModel, use_enum_values=True, validate_default=True):
+    n_jobs: PositiveInt | None = None
+    baseline_variant: BaselineVariants = BaselineVariants.TopHat
+    window_size: PositiveInt | PositiveFloat = 5000.0
+    window_unit: Literal["ppm", "index"] = "ppm"

src/depiction/tools/correct_baseline.py → src/depiction/tools/correct_baseline/correct_baseline.py

@@ -1,35 +1,22 @@
 from __future__ import annotations
 
-import enum
 from pathlib import Path
 from typing import TYPE_CHECKING, Literal
 
 import numpy as np
-from pydantic import BaseModel, PositiveInt, PositiveFloat
 
 from depiction.parallel_ops.parallel_config import ParallelConfig
 from depiction.parallel_ops.write_spectra_parallel import WriteSpectraParallel
 from depiction.persistence import ImzmlWriteFile, ImzmlWriter, ImzmlReader, ImzmlReadFile
 from depiction.spectrum.baseline.local_medians_baseline import LocalMediansBaseline
 from depiction.spectrum.baseline.tophat_baseline import TophatBaseline
+from depiction.tools.correct_baseline.config import BaselineVariants, BaselineCorrectionConfig
 
 if TYPE_CHECKING:
     from numpy.typing import NDArray
     from depiction.spectrum.baseline.baseline import Baseline
 
 
-class BaselineVariants(str, enum.Enum):
-    TopHat = "TopHat"
-    LocMedians = "LocMedians"
-
-
-class BaselineCorrectionConfig(BaseModel, use_enum_values=True, validate_default=True):
-    n_jobs: PositiveInt | None = None
-    baseline_variant: BaselineVariants = BaselineVariants.TopHat
-    window_size: PositiveInt | PositiveFloat = 5000.0
-    window_unit: Literal["ppm", "index"] = "ppm"
-
-
 class CorrectBaseline:
     """Implements baseline correction for imzml files."""
 

src/depiction_targeted_preproc/pipeline_config/model.py

@@ -8,7 +8,7 @@
 from pydantic import BaseModel, ConfigDict
 
 from depiction.tools.calibrate.config import CalibrationConfig
-from depiction.tools.correct_baseline import BaselineCorrectionConfig
+from depiction.tools.correct_baseline.config import BaselineCorrectionConfig
 from depiction.tools.filter_peaks import FilterPeaksConfig
 from depiction.tools.pick_peaks import PickPeaksConfig
 

src/depiction_targeted_preproc/workflow/rules/rules_proc.smk

@@ -17,7 +17,7 @@ rule proc_correct_baseline_run:
     output:
         imzml=temp(multiext("{sample}/corrected.original", ".imzML", ".ibd")),
     shell:
-        "python -m depiction.tools.cli.cli_correct_baseline run-config"
+        "python -m depiction.tools.correct_baseline run-config"
         " --config {input.config}"
         " --input-imzml {input.imzml[0]} --output-imzml {output.imzml[0]}"
 

tests/unit/tools/cli/test_correct_baseline.py → tests/unit/tools/correct_baseline/test_correct_baseline.py

@@ -3,16 +3,18 @@
 import pytest
 from pytest_mock import MockerFixture
 
-from depiction.tools.cli.cli_correct_baseline import run
-from depiction.tools.correct_baseline import BaselineVariants
+from depiction.tools.correct_baseline.__main__ import run
+from depiction.tools.correct_baseline.config import BaselineVariants
 
 
 def test_run_when_other_variant(mocker: MockerFixture) -> None:
     mock_imzml_mode = mocker.MagicMock(name="mock_imzml_mode", spec=[])
-    construct_imzml_read_file = mocker.patch("depiction.tools.correct_baseline.ImzmlReadFile")
+    construct_imzml_read_file = mocker.patch("depiction.tools.correct_baseline.correct_baseline.ImzmlReadFile")
     construct_imzml_read_file.return_value.imzml_mode = mock_imzml_mode
-    construct_imzml_write_file = mocker.patch("depiction.tools.correct_baseline.ImzmlWriteFile")
-    construct_correct_baseline = mocker.patch("depiction.tools.correct_baseline.CorrectBaseline.from_variant")
+    construct_imzml_write_file = mocker.patch("depiction.tools.correct_baseline.correct_baseline.ImzmlWriteFile")
+    construct_correct_baseline = mocker.patch(
+        "depiction.tools.correct_baseline.correct_baseline.CorrectBaseline.from_variant"
+    )
     mock_input_imzml = Path("/dev/null/hello.imzML")
     mock_output_imzml = mocker.MagicMock(name="mock_output_imzml")