From b7a1f34645e4b2f4317e269fbfc7c80057417172 Mon Sep 17 00:00:00 2001
From: lauraporta <ucqflpo@ucl.ac.uk>
Date: Tue, 5 Nov 2024 15:29:29 +0000
Subject: [PATCH] Pre-commit hook modifications

---
 calcium_imaging_automation/core/reader.py |  4 +++-
 examples/example_usage.py                 | 16 ++++++++++------
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/calcium_imaging_automation/core/reader.py b/calcium_imaging_automation/core/reader.py
index 400044d..ea77848 100644
--- a/calcium_imaging_automation/core/reader.py
+++ b/calcium_imaging_automation/core/reader.py
@@ -13,7 +13,9 @@ def __init__(
         self.folder_read_pattern = folder_read_pattern
 
         self.datasets_paths = self.get_folders_first_layer(raw_data_folder)
-        self.dataset_names = [dataset_path.name for dataset_path in self.datasets_paths]
+        self.dataset_names = [
+            dataset_path.name for dataset_path in self.datasets_paths
+        ]
 
     def get_folders_first_layer(self, file_path: Path) -> List[Path]:
         return list(file_path.glob(self.folder_read_pattern))
diff --git a/examples/example_usage.py b/examples/example_usage.py
index 4b19a1b..3e638ca 100644
--- a/examples/example_usage.py
+++ b/examples/example_usage.py
@@ -1,6 +1,6 @@
 import argparse
-from pathlib import Path
 import logging
+from pathlib import Path
 
 from calcium_imaging_automation.core.reader import ReadAllPathsInFolder
 from calcium_imaging_automation.core.writer import DatashuttleWrapper
@@ -19,7 +19,7 @@ def main(
         filename=output_path / "logs" / "pipeline.log",
         level=logging.INFO,
         format="%(asctime)s - %(message)s",
-    ) 
+    )
 
     reader = ReadAllPathsInFolder(
         raw_data_path, filetypes_of_interest, folder_read_pattern
@@ -28,22 +28,26 @@ def main(
     logging.info(f"Dataset names: {reader.dataset_names}")
 
     writer = DatashuttleWrapper(output_path)
-    
+
     number_of_tiffs = reader.max_session_number(filetype="tif")
     writer.create_folders(reader.dataset_names, session_number=number_of_tiffs)
 
     # [Placeholder for data processing]
 
     logging.info("Pipeline finished.")
-    
+
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         description="Example usage of the pipeline manager."
     )
 
-    parser.add_argument("raw_data_path", type=Path, help="Path to the raw data.")
-    parser.add_argument("output_path", type=Path, help="Path to the output data.")
+    parser.add_argument(
+        "raw_data_path", type=Path, help="Path to the raw data."
+    )
+    parser.add_argument(
+        "output_path", type=Path, help="Path to the output data."
+    )
     parser.add_argument(
         "--filetypes",
         type=list,