Handled type hinting errors revealed by MyPy

Author: tieneupin

src/murfey/client/analyser.py

@@ -398,7 +398,9 @@ def _xml_file(self, data_file: Path) -> Path:
         base_dir, mid_dir = find_longest_data_directory(data_file, data_directories)
         if not base_dir:
             return data_file.with_suffix(".xml")
-        return base_dir / self._environment.visit / mid_dir / file_name
+        # Add the visit directory to the file path and return it
+        # The file is moved from a location where the visit name is not part of its path
+        return base_dir / self._environment.visit / (mid_dir or "") / file_name
 
     def enqueue(self, rsyncer: RSyncerUpdate):
         if not self._stopping and rsyncer.outcome == TransferResult.SUCCESS:

src/murfey/client/contexts/spa.py

@@ -3,7 +3,7 @@
 import logging
 from itertools import count
 from pathlib import Path
-from typing import Any, Dict, List, Optional, OrderedDict, Tuple
+from typing import Any, Optional, OrderedDict
 
 import xmltodict
 
@@ -50,10 +50,10 @@ def _file_transferred_to(
 
 
 def _grid_square_metadata_file(
-    f: Path, data_directories: List[Path], visit: str, grid_square: int
+    f: Path, data_directories: list[Path], visit: str, grid_square: int
 ) -> Path:
     base_dir, mid_dir = find_longest_data_directory(f, data_directories)
-    if not base_dir:
+    if not base_dir or not mid_dir:
         raise ValueError(f"Could not determine grid square metadata path for {f}")
     metadata_file = (
         base_dir
@@ -113,7 +113,7 @@ def __init__(self, acquisition_software: str, basepath: Path, token: str):
         super().__init__("SPA", acquisition_software, token)
         self._basepath = basepath
         self._processing_job_stash: dict = {}
-        self._foil_holes: Dict[int, List[int]] = {}
+        self._foil_holes: dict[int, list[int]] = {}
 
     def gather_metadata(
         self, metadata_file: Path, environment: MurfeyInstanceEnvironment | None = None
@@ -287,7 +287,7 @@ def _position_analysis(
             and self._foil_holes.get(grid_square) is None
         ):
             self._foil_holes[grid_square] = []
-            gs_pix_position: Tuple[
+            gs_pix_position: tuple[
                 Optional[int],
                 Optional[int],
                 Optional[float],
@@ -586,7 +586,7 @@ def _register_processing_job(
         self,
         tag: str,
         environment: MurfeyInstanceEnvironment,
-        parameters: Dict[str, Any] | None = None,
+        parameters: dict[str, Any] | None = None,
     ):
         return
 

src/murfey/client/destinations.py

@@ -14,7 +14,7 @@
 
 
 def find_longest_data_directory(
-    match_path: Path, data_directories: list[str | Path]
+    match_path: Path, data_directories: list[str] | list[Path]
 ) -> tuple[Path | None, Path | None]:
     """
     Determine the longest path in the data_directories list

tests/client/test_destinations.py

@@ -41,15 +41,16 @@ def test_find_longest_data_directory(
 ):
     # Unpack test params
     match_path, use_path, (expected_base_dir, expected_mid_dir) = test_params
-    data_directories: list[str | Path] = [
-        Path(dd) if use_path else dd
-        for dd in (
-            "X:",
-            "X:/DATA",
-            "X:/DoseFractions",
-            "X:/DoseFractions/DATA",
-        )
+
+    # Construct data directories using strings or Paths as needed
+    data_directories: list[str] | list[Path] = [
+        "X:",
+        "X:/DATA",
+        "X:/DoseFractions",
+        "X:/DoseFractions/DATA",
     ]
+    if use_path:
+        data_directories = [Path(dd) for dd in data_directories]
     # Patch Pathlib's 'absolute()' function, since we are simulating Windows on Linux
     mocker.patch("murfey.client.destinations.Path.absolute", lambda self: self)