move imzml code into a dedicated package

src/depiction/persistence/__init__.py

@@ -1,8 +1,8 @@
-from .imzml_mode_enum import ImzmlModeEnum
-from .imzml_read_file import ImzmlReadFile
-from .imzml_reader import ImzmlReader
-from .imzml_write_file import ImzmlWriteFile
-from .imzml_writer import ImzmlWriter
+from depiction.persistence.imzml.imzml_mode_enum import ImzmlModeEnum
+from depiction.persistence.imzml.imzml_read_file import ImzmlReadFile
+from depiction.persistence.imzml.imzml_reader import ImzmlReader
+from depiction.persistence.imzml.imzml_write_file import ImzmlWriteFile
+from depiction.persistence.imzml.imzml_writer import ImzmlWriter
 from .ram_read_file import RamReadFile
 from .ram_reader import RamReader
 

src/depiction/persistence/imzml_read_file.py → src/depiction/persistence/imzml/imzml_read_file.py

@@ -10,8 +10,8 @@
 from numpy.typing import NDArray
 
 from depiction.persistence.file_checksums import FileChecksums
-from depiction.persistence.imzml_mode_enum import ImzmlModeEnum
-from depiction.persistence.imzml_reader import ImzmlReader
+from depiction.persistence.imzml.imzml_mode_enum import ImzmlModeEnum
+from depiction.persistence.imzml.imzml_reader import ImzmlReader
 from depiction.persistence.pixel_size import PixelSize
 
 

src/depiction/persistence/imzml_reader.py → src/depiction/persistence/imzml/imzml_reader.py

@@ -7,7 +7,7 @@
 import numpy as np
 import pyimzml.ImzMLParser
 
-from depiction.persistence.imzml_mode_enum import ImzmlModeEnum
+from depiction.persistence.imzml.imzml_mode_enum import ImzmlModeEnum
 
 if TYPE_CHECKING:
     from types import TracebackType

src/depiction/persistence/imzml_write_file.py → src/depiction/persistence/imzml/imzml_write_file.py

@@ -3,10 +3,10 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-from depiction.persistence.imzml_writer import ImzmlWriter
+from depiction.persistence.imzml.imzml_writer import ImzmlWriter
 
 if TYPE_CHECKING:
-    from depiction.persistence.imzml_mode_enum import ImzmlModeEnum
+    from depiction.persistence.imzml.imzml_mode_enum import ImzmlModeEnum
 
 
 class ImzmlWriteFile:

src/depiction/persistence/imzml_writer.py → src/depiction/persistence/imzml/imzml_writer.py

@@ -6,13 +6,13 @@
 import pyimzml.ImzMLWriter
 from tqdm import tqdm
 
-from depiction.persistence.imzml_alignment_tracker import ImzmlAlignmentTracker
-from depiction.persistence.imzml_mode_enum import ImzmlModeEnum
+from depiction.persistence.imzml.imzml_alignment_tracker import ImzmlAlignmentTracker
+from depiction.persistence.imzml.imzml_mode_enum import ImzmlModeEnum
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
     import numpy as np
-    from depiction.persistence.imzml_reader import ImzmlReader
+    from depiction.persistence.imzml.imzml_reader import ImzmlReader
 
 
 class ImzmlWriter:

src/depiction_targeted_preproc/workflow/proc/export_raw_metadata.py

@@ -5,7 +5,7 @@
 from loguru import logger
 from pydantic import ValidationError
 
-from depiction.persistence.extract_metadata import ExtractMetadata, Metadata
+from depiction.persistence.imzml.extract_metadata import ExtractMetadata, Metadata
 from depiction.persistence.pixel_size import PixelSize
 
 

src/depiction_targeted_preproc/workflow/vis/images_ome_tiff.py

@@ -4,7 +4,7 @@
 import typer
 import xarray
 
-from depiction.persistence.extract_metadata import Metadata
+from depiction.persistence.imzml.extract_metadata import Metadata
 from depiction.persistence.format_ome_tiff import OmeTiff
 
 

tests/unit/persistence/test_imzml_read_file.py → tests/unit/persistence/imzml/test_imzml_read_file.py

@@ -158,7 +158,7 @@ def test_metadata_checksums_when_both_checksums_available(mocker: MockerFixture,
 
 
 def test_ibd_checksums(mocker: MockerFixture, mock_read_file: ImzmlReadFile) -> None:
-    mock_file_checksums = mocker.patch("depiction.persistence.imzml_read_file.FileChecksums")
+    mock_file_checksums = mocker.patch("depiction.persistence.imzml.imzml_read_file.FileChecksums")
     assert mock_file_checksums.return_value == mock_read_file.ibd_checksums
     mock_file_checksums.assert_called_once_with(file_path=mock_read_file.ibd_file)
 

tests/unit/persistence/test_imzml_reader.py → tests/unit/persistence/imzml/test_imzml_reader.py

@@ -239,7 +239,7 @@ def test_get_spectra_mz_range_when_none(self, mock_get_spectrum_mz) -> None:
         self.assertTupleEqual((0.5, 6), mz_range)
         self.assertListEqual([call(0), call(1), call(2)], mock_get_spectrum_mz.mock_calls)
 
-    @patch("depiction.persistence.imzml_reader.pyimzml.ImzMLParser.ImzMLParser")
+    @patch("depiction.persistence.imzml.imzml_reader.pyimzml.ImzMLParser.ImzMLParser")
     def test_parse_imzml(self, module_imzml_parser) -> None:
         mock_path = MagicMock(name="mock_path", spec=[])
         mock_portable_spectrum_reader = MagicMock(name="mock_portable_spectrum_reader")