fix PATH error flagged by ruff

eye2bids/_base.py

@@ -68,7 +68,9 @@ def write(
     ) -> None:
         """Write to json."""
         content = {key: value for key, value in self.items() if self[key] is not None}
-        with open(output_dir / self.output_filename(recording=recording), "w") as outfile:
+        with (output_dir / self.output_filename(recording=recording)).open(
+            "w"
+        ) as outfile:
             json.dump(content, outfile, indent=4)
 
 
@@ -110,7 +112,7 @@ def write(
                 self[key] = value
 
         content = {key: value for key, value in self.items() if self[key] is not None}
-        with open(output_dir / self.output_filename(), "w") as outfile:
+        with (output_dir / self.output_filename()).open("w") as outfile:
             json.dump(content, outfile, indent=4)
 
 
@@ -196,5 +198,7 @@ def write(
                 self[key] = value
 
         content = {key: value for key, value in self.items() if self[key] is not None}
-        with open(output_dir / self.output_filename(recording=recording), "w") as outfile:
+        with (output_dir / self.output_filename(recording=recording)).open(
+            "w"
+        ) as outfile:
             json.dump(content, outfile, indent=4)

eye2bids/edf2bids.py

@@ -312,7 +312,7 @@ def _extract_StopTime(events: list[str]) -> int:
 
 
 def _load_asc_file(events_asc_file: str | Path) -> list[str]:
-    with open(events_asc_file) as f:
+    with Path(events_asc_file).open() as f:
         return f.readlines()
 
 
@@ -424,7 +424,7 @@ def generate_physio_json(
     if metadata_file is None:
         metadata = {}
     else:
-        with open(metadata_file) as f:
+        with Path(metadata_file).open() as f:
             metadata = yaml.load(f, Loader=SafeLoader)
 
     events = _load_asc_file(events_asc_file)
@@ -543,7 +543,7 @@ def edf2bids(
     if metadata_file is None:
         metadata = {}
     else:
-        with open(metadata_file) as f:
+        with metadata_file.open() as f:
             metadata = yaml.load(f, Loader=SafeLoader)
 
     events_json = BaseEventsJson(metadata)

pyproject.toml

@@ -133,7 +133,6 @@ skip-magic-trailing-comma = false
 dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 fixable = ["ALL"]
 ignore = [
-    "PTH123",
     "PD901",
     "N802",
     "D205",

tests/test_edf2bids.py

@@ -69,7 +69,7 @@ def _check_output_content(output_dir, input_file, eye=1):
         ).with_suffix(".json")
 
         df = pd.read_csv(tsv_file, sep="\t", header=None)
-        with open(json_file) as f:
+        with json_file.open() as f:
             metadata = json.load(f)
         assert len(df.columns) == len(metadata["Columns"])
 
@@ -141,12 +141,12 @@ def test_edf_end_to_end(eyelink_test_data_dir):
     _check_output_exists(output_dir, input_file)
 
     expected_events_sidecar = output_dir / f"{input_file.stem}_events.json"
-    with open(expected_events_sidecar) as f:
+    with expected_events_sidecar.open() as f:
         events = json.load(f)
     assert events["StimulusPresentation"]["ScreenResolution"] == [1919, 1079]
 
     expected_data_sidecar = output_dir / f"{input_file.stem}_recording-eye1_physio.json"
-    with open(expected_data_sidecar) as f:
+    with expected_data_sidecar.open() as f:
         eyetrack = json.load(f)
     assert eyetrack["SamplingFrequency"] == 500
     assert eyetrack["RecordedEye"] == "Right"
@@ -189,14 +189,14 @@ def test_edf_end_to_end_2eyes(eyelink_test_data_dir):
     _check_output_content(output_dir, input_file)
 
     expected_events_sidecar_eye1 = output_dir / f"{input_file.stem}_events.json"
-    with open(expected_events_sidecar_eye1) as f:
+    with expected_events_sidecar_eye1.open() as f:
         events = json.load(f)
     assert events["StimulusPresentation"]["ScreenResolution"] == [1919, 1079]
 
     expected_data_sidecar_eye1 = (
         output_dir / f"{input_file.stem}_recording-eye1_physio.json"
     )
-    with open(expected_data_sidecar_eye1) as f:
+    with expected_data_sidecar_eye1.open() as f:
         eyetrack = json.load(f)
     assert eyetrack["SamplingFrequency"] == 1000
     assert eyetrack["AverageCalibrationError"] == [[0.29]]
@@ -208,7 +208,7 @@ def test_edf_end_to_end_2eyes(eyelink_test_data_dir):
     expected_data_sidecar_eye2 = (
         output_dir / f"{input_file.stem}_recording-eye2_physio.json"
     )
-    with open(expected_data_sidecar_eye2) as f:
+    with expected_data_sidecar_eye2.open() as f:
         eyetrack = json.load(f)
     assert eyetrack["AverageCalibrationError"] == [[0.35]]
     assert eyetrack["RecordedEye"] == "Right"

tools/download_test_data.py

@@ -25,7 +25,7 @@
 
 # Download the zip file
 r = requests.get(download_url, stream=True)
-with open(output_file, "wb") as f:
+with output_file.open("wb") as f:
     for chunk in r.iter_content(chunk_size=1024):
         if chunk:
             f.write(chunk)