create copy_to method

src/depiction/persistence/imzml_read_file.py

@@ -1,3 +1,4 @@
+import shutil
 from collections import defaultdict
 from collections.abc import Generator
 from contextlib import contextmanager
@@ -185,6 +186,11 @@ def pixel_size(self) -> PixelSize | None:
         # TODO actual check of the unit
         return PixelSize(size_x=pixel_size_x, size_y=pixel_size_y, unit="micrometer")
 
+    def copy_to(self, path: Path) -> None:
+        """Copies the file of this instance to the given path. Needs to end with .imzML."""
+        shutil.copy(self.imzml_file, path)
+        shutil.copy(self.ibd_file, path.with_suffix(".ibd"))
+
     @cached_property
     def _cached_properties(self) -> dict[str, Any]:
         with self.reader() as reader:

src/depiction/tools/pick_peaks.py

@@ -1,7 +1,5 @@
 from __future__ import annotations
 
-import shutil
-from pathlib import Path
 from typing import Literal, Any
 
 from loguru import logger
@@ -145,14 +143,8 @@ def pick_peaks(
     if config.peak_picker is None or (
         not config.force_peak_picker and input_file.imzml_mode == ImzmlModeEnum.PROCESSED
     ):
-        copy_without_picking(input_imzml_path=input_file.imzml_file, output_imzml_path=output_file.imzml_file)
+        logger.info("Peak picking is deactivated")
+        input_file.copy_to(output_file.imzml_file)
     else:
         pick_peaks = PickPeaks(peak_picker=peak_picker, parallel_config=parallel_config)
         pick_peaks.evaluate_file(read_file=input_file, write_file=output_file)
-
-
-def copy_without_picking(input_imzml_path: Path, output_imzml_path: Path) -> None:
-    # TODO this is duplicated in several places and should be unified, in fact it could be a method of ImzmlReadFile
-    logger.info("Peak picking is deactivated")
-    shutil.copy(input_imzml_path, output_imzml_path)
-    shutil.copy(input_imzml_path.with_suffix(".ibd"), output_imzml_path.with_suffix(".ibd"))

tests/unit/persistence/test_imzml_read_file.py

@@ -265,6 +265,17 @@ def test_print_summary(mocker: MockerFixture, mock_read_file: ImzmlReadFile) ->
     mock_print.assert_called_once_with(mock_summary.return_value, file=None)
 
 
+def test_copy_to(mocker: MockerFixture, mock_read_file: ImzmlReadFile) -> None:
+    mock_output_file = mocker.MagicMock(name="mock_output_file")
+    mock_copy = mocker.patch("shutil.copy")
+    mock_read_file.copy_to(mock_output_file)
+    assert mock_copy.mock_calls == [
+        mocker.call(mock_read_file.imzml_file, mock_output_file),
+        mocker.call(mock_read_file.ibd_file, mock_output_file.with_suffix.return_value),
+    ]
+    mock_output_file.with_suffix.assert_called_once_with(".ibd")
+
+
 def test_cached_properties(mocker: MockerFixture, mock_read_file: ImzmlReadFile) -> None:
     mock_reader = MagicMock(name="mock_reader")
     mocker.patch.object(ImzmlReadFile, "reader").return_value.__enter__.return_value = mock_reader