more code style

src/depiction/evaluate_signal_proc.py

@@ -26,7 +26,8 @@ def evaluate(self, mz_values: np.ndarray, int_values: np.ndarray) -> np.ndarray:
             # Don't filter
             return int_values
         else:
-            # the problem with below's implementation was, that e.g. for input of size 1 it would create an output of size 5 (since it choses the bigger size of the two arrays)
+            # the problem with below's implementation was, that e.g. for input of size 1
+            # it would create an output of size 5 (since it choses the bigger size of the two arrays)
             # return scipy.signal.convolve(int_array, gaussian_filter, mode='same')
             values = np.convolve(int_values, gaussian_filter, mode="same")
             values[0] = int_values[0]

src/depiction/persistence/imzml_mode_enum.py

@@ -1,3 +1,4 @@
+from __future__ import annotations
 import enum
 
 
@@ -8,12 +9,12 @@ class ImzmlModeEnum(enum.Enum):
     PROCESSED = enum.auto()
 
     @classmethod
-    def as_pyimzml_str(cls, instance) -> str:
+    def as_pyimzml_str(cls, instance: ImzmlModeEnum) -> str:
         """Returns the string representation of the enum value as used by pyimzml."""
         return instance.name.lower()
 
     @classmethod
-    def from_pyimzml_str(cls, value: str) -> "ImzmlModeEnum":
+    def from_pyimzml_str(cls, value: str) -> ImzmlModeEnum:
         if value == "continuous":
             return cls.CONTINUOUS
         elif value == "processed":

src/depiction/persistence/imzml_read_file.py

@@ -3,7 +3,7 @@
 from contextlib import contextmanager
 from functools import cached_property
 from pathlib import Path
-from typing import Any, Optional
+from typing import Any, Optional, TextIO
 
 import pyimzml.ImzMLParser
 from numpy.typing import NDArray
@@ -164,7 +164,7 @@ def summary(self, checksums: bool = True) -> str:
             f"{mz_range_line}"
         )
 
-    def print_summary(self, checksums: bool = True, file=None) -> None:
+    def print_summary(self, checksums: bool = True, file: TextIO | None = None) -> None:
         print(self.summary(checksums=checksums), file=file)
 
     @cached_property

src/depiction/persistence/imzml_reader.py

@@ -10,6 +10,7 @@
 from depiction.persistence.imzml_mode_enum import ImzmlModeEnum
 
 if TYPE_CHECKING:
+    from types import TracebackType
     from pathlib import Path
     from numpy.typing import NDArray
 
@@ -60,7 +61,7 @@ def __getstate__(self) -> dict[str, Any]:
         }
 
     # TODO
-    def __setstate__(self, state: dict[str, Any]):
+    def __setstate__(self, state: dict[str, Any]) -> None:
         # self._portable_reader = state["portable_reader"]
         self._imzml_path = state["imzml_path"]
         self._ibd_file = None
@@ -100,7 +101,9 @@ def ibd_mmap(self) -> mmap.mmap:
     def __enter__(self) -> ImzmlReader:
         return self
 
-    def __exit__(self, exc_type, exc_val, exc_tb):
+    def __exit__(
+        self, exc_type: type[BaseException] | None, exc_val: BaseException | None, exc_tb: TracebackType | None
+    ) -> None:
         self.close()
 
     def close(self) -> None:

src/depiction/persistence/imzml_write_file.py

@@ -1,9 +1,13 @@
-from contextlib import contextmanager
+from __future__ import annotations
+from contextlib import contextmanager, AbstractContextManager
 from pathlib import Path
+from typing import TYPE_CHECKING
 
-from depiction.persistence.imzml_mode_enum import ImzmlModeEnum
 from depiction.persistence.imzml_writer import ImzmlWriter
 
+if TYPE_CHECKING:
+    from depiction.persistence.imzml_mode_enum import ImzmlModeEnum
+
 
 class ImzmlWriteFile:
     """A handle for a .imzML file that is to be written.
@@ -38,7 +42,7 @@ def imzml_mode(self) -> ImzmlModeEnum:
         return self._imzml_mode
 
     @contextmanager
-    def writer(self):
+    def writer(self) -> AbstractContextManager[ImzmlWriter]:
         """Opens the .imzML file for writing and yields an `ImzmlWriter` instance."""
         if self._write_mode == "x":
             if self.imzml_file.exists():

src/depiction/persistence/imzml_writer.py

@@ -1,8 +1,7 @@
+from __future__ import annotations
 from pathlib import Path
-from typing import Optional, TYPE_CHECKING
-from collections.abc import Sequence
+from typing import TYPE_CHECKING
 
-import numpy as np
 import pyimzml
 import pyimzml.ImzMLWriter
 from tqdm import tqdm
@@ -11,6 +10,8 @@
 from depiction.persistence.imzml_mode_enum import ImzmlModeEnum
 
 if TYPE_CHECKING:
+    from collections.abc import Sequence
+    import numpy as np
     from depiction.persistence.imzml_reader import ImzmlReader
 
 
@@ -19,13 +20,13 @@ def __init__(
         self,
         *,
         wrapped_imzml_writer: pyimzml.ImzMLWriter.ImzMLWriter,
-        imzml_alignment_tracker: Optional[ImzmlAlignmentTracker],
+        imzml_alignment_tracker: ImzmlAlignmentTracker | None,
     ) -> None:
         self._imzml_writer = wrapped_imzml_writer
         self._imzml_alignment_tracker = imzml_alignment_tracker
 
     @classmethod
-    def open(cls, path: str | Path, imzml_mode: ImzmlModeEnum, imzml_alignment_tracking: bool = True):
+    def open(cls, path: str | Path, imzml_mode: ImzmlModeEnum, imzml_alignment_tracking: bool = True) -> ImzmlWriter:
         """Opens an imzML file."""
         imzml_alignment_tracker = ImzmlAlignmentTracker() if imzml_alignment_tracking else None
         return cls(
@@ -37,7 +38,8 @@ def open(cls, path: str | Path, imzml_mode: ImzmlModeEnum, imzml_alignment_track
         )
 
     # TODO this currently has a bug, when closing a reader to which not a single spectrum was added.
-    #      it should be handled gracefully, since there are reasonable cases where this could occur with the use of "with" clauses.
+    #      it should be handled gracefully, since there are reasonable cases,
+    #      where this could occur with the use of "with" clauses.
     def close(self) -> None:
         self._imzml_writer.close()
 
@@ -75,20 +77,19 @@ def add_spectrum(
         if self._imzml_alignment_tracker:
             self._imzml_alignment_tracker.track_mz_array(mz_arr)
 
-        if self.imzml_mode == ImzmlModeEnum.CONTINUOUS and self._imzml_alignment_tracker:
-            if not self.is_aligned:
-                raise ValueError(
-                    "The m/z array of the first spectrum must be identical to the m/z array of all other spectra!"
-                )
+        if self.imzml_mode == ImzmlModeEnum.CONTINUOUS and self._imzml_alignment_tracker and not self.is_aligned:
+            raise ValueError(
+                "The m/z array of the first spectrum must be identical to the m/z array of all other spectra!"
+            )
 
         # Write the spectrum.
         self._imzml_writer.addSpectrum(mz_arr, int_arr, coordinates)
 
     def copy_spectra(
         self,
-        reader: "ImzmlReader",
+        reader: ImzmlReader,
         spectra_indices: Sequence[int],
-        tqdm_position: Optional[int] = None,
+        tqdm_position: int | None = None,
     ) -> None:
         """
         Copies spectra from an existing reader. Not optimized yet.
@@ -97,12 +98,12 @@ def copy_spectra(
         """
         if tqdm_position is not None:
 
-            def progress_fn(x):
+            def progress_fn(x: Sequence[int]) -> tqdm:
                 return tqdm(x, desc=" spectrum", position=tqdm_position)
 
         else:
 
-            def progress_fn(x):
+            def progress_fn(x: Sequence[int]) -> Sequence[int]:
                 return x
 
         for spectrum_index in progress_fn(spectra_indices):

src/depiction/persistence/ram_reader.py

@@ -1,13 +1,20 @@
-from typing import Any, NoReturn
+from __future__ import annotations
+
+from typing import Any, NoReturn, TYPE_CHECKING
 
 import numpy as np
-from numpy._typing import NDArray
 
 from depiction.persistence import ImzmlModeEnum
 
+if TYPE_CHECKING:
+    from types import TracebackType
+    from numpy.typing import NDArray
+
 
 class RamReader:
-    def __init__(self, mz_arr_list, int_arr_list, coordinates) -> None:
+    def __init__(
+        self, mz_arr_list: list[NDArray[float]], int_arr_list: list[NDArray[float]], coordinates: NDArray[int]
+    ) -> None:
         self._mz_arr_list = mz_arr_list
         self._int_arr_list = int_arr_list
         self._coordinates = coordinates
@@ -27,10 +34,12 @@ def ibd_mmap(self) -> NoReturn:
         # TODO a problem, right?
         raise NotImplementedError
 
-    def __enter__(self):
+    def __enter__(self) -> RamReader:
         return self
 
-    def __exit__(self, exc_type, exc_val, exc_tb):
+    def __exit__(
+        self, exc_type: type[BaseException] | None, exc_val: BaseException | None, exc_tb: TracebackType | None
+    ) -> None:
         self.close()
 
     def close(self) -> None:
@@ -55,11 +64,11 @@ def n_spectra(self) -> int:
         return len(self._mz_arr_list)
 
     @property
-    def coordinates(self):
+    def coordinates(self) -> NDArray[int]:
         return self._coordinates
 
     @property
-    def coordinates_2d(self):
+    def coordinates_2d(self) -> NDArray[int]:
         return self._coordinates[:, :2]
 
     def get_spectrum(self, i_spectrum: int) -> tuple[np.ndarray, np.ndarray]:
@@ -76,7 +85,7 @@ def get_spectra(self, i_spectra: list[int]) -> tuple[np.ndarray | list[np.ndarra
     def get_spectrum_mz(self, i_spectrum: int) -> NDArray[float]:
         return self._mz_arr_list[i_spectrum]
 
-    def get_spectrum_int(self, i_spectrum) -> NDArray[float]:
+    def get_spectrum_int(self, i_spectrum: int) -> NDArray[float]:
         return self._int_arr_list[i_spectrum]
 
     def get_spectrum_n_points(self, i_spectrum: int) -> int:

src/depiction/tools/split_imzml.py

@@ -2,7 +2,6 @@
 
 import logging
 import os
-from pathlib import Path
 from typing import Optional
 
 import numpy as np

src/depiction/visualize/plot_mass_spectra_samples.py

@@ -27,7 +27,7 @@ def __init__(self, data_df: pl.DataFrame) -> None:
         self._data_df = data_df
         self._charts = []
 
-    def plot_spectrum(self, spectrum_name: str):
+    def plot_spectrum(self, spectrum_name: str) -> None:
         data = self._data_df.filter(spectrum_name=spectrum_name)
         chart = (
             alt.Chart(data)