Fixed pre-commit | Added one unit test

NiChart_DLMUSE/SegmentImage.py

@@ -2,8 +2,6 @@
 import os
 import shutil
 from typing import Any
-import DLMUSE 
-import DLICV
 
 
 def run_dlicv(

NiChart_DLMUSE/__init__.py

@@ -1 +1 @@
-from .dlmuse_pipeline import run_pipeline, run_dlicv, run_dlmuse
+from .dlmuse_pipeline import run_dlicv, run_dlmuse, run_pipeline

NiChart_DLMUSE/dlmuse_pipeline.py

@@ -1,5 +1,6 @@
 import logging
 import os
+from typing import Any
 
 import pkg_resources  # type: ignore
 
@@ -39,10 +40,10 @@ def run_pipeline(
     in_data: str,
     out_dir: str,
     device: str,
-    dlmuse_extra_args: str = '',
-    dlicv_extra_args: str = '',
+    dlmuse_extra_args: str = "",
+    dlicv_extra_args: str = "",
     sub_fldr: int = 1,
-    progress_bar = None,
+    progress_bar: Any = None,
 ) -> None:
     """
     NiChart pipeline

NiChart_DLMUSE/utils.py

@@ -65,7 +65,9 @@ def remove_common_suffix(list_files: list) -> list:
 
     bnames = list_files
     if len(list_files) == 1:
-        if list_files[0].endswith('_T1'): # If there is a single image with suffix _T1, remove it
+        if list_files[0].endswith(
+            "_T1"
+        ):  # If there is a single image with suffix _T1, remove it
             bnames = [x[0:-3] for x in bnames]
         return bnames
 
@@ -347,7 +349,7 @@ def remove_subfolders(in_dir: str) -> None:
 
 def merge_output_data(in_dir: str) -> None:
     """
-    Takes all the results from the temp_working_fir and moves them into
+    Takes all the results from the temp_working_dir and moves them into
     the output folder
 
     :param in_dir: the input directory

tests/test_utils.py

@@ -9,6 +9,7 @@
     remove_common_suffix,
     remove_subfolders,
     split_data,
+    get_bids_prefix
 )
 
 
@@ -58,8 +59,19 @@ def testing_make_img_list() -> None:
 
 
 def testing_get_bids_prefix() -> None:
-    pass
-
+    temp_file = "test-1234"
+    assert get_bids_prefix(temp_file) == "test"
+    temp_file = "test-1"
+    assert get_bids_prefix(temp_file) == "test"
+    temp_file = "test"
+    assert get_bids_prefix(temp_file) == "test"
+
+    temp_folder = "test_1234"
+    assert get_bids_prefix(temp_folder, True) == "test"
+    temp_folder = "test_1"
+    assert get_bids_prefix(temp_folder, True) == "test"
+    temp_folder = "test"
+    assert get_bids_prefix(temp_folder, True) == "test"
 
 def testing_collect_T1() -> None:
     os.system("mkdir test_collect_T1")