fix typos and pep8

Dockerfile

@@ -30,7 +30,7 @@ ENV FSLTCLSH="${FSLDIR}/bin/fsltclsh"
 ENV FSLWISH="${FSLDIR}/bin/fslwish"
 ENV FSLGECUDAQ="cuda.q"
 
-# Install dc fro FSL bet and wget for fetching data
+# Update and install some utils
 RUN apt-get -y update && apt-get -y install dc wget npm unzip
 
 # Fetch data

dcm2bids/sidecar.py

@@ -462,7 +462,7 @@ def searchDcmTagEntity(self, sidecar, desc):
             # If dir found in custom_entities and concatenated_matches.keys we keep it
             if "custom_entities" in desc.keys():
                 entities = set(concatenated_matches.keys()).intersection(set(descWithTask["custom_entities"]))
-                
+
                 # custom_entities not a key for extractor or auto_extract_entities
                 complete_entities = [ent for ent in descWithTask["custom_entities"] if '-' in ent]
                 entities = entities.union(set(complete_entities))
@@ -478,7 +478,7 @@ def searchDcmTagEntity(self, sidecar, desc):
                     if left_auto_entities:
                         self.logger.warning(f"{left_auto_entities} have not been found for datatype '{descWithTask['datatype']}' "
                                             f"and suffix '{descWithTask['suffix']}'.")
-                    
+
                     entities = list(entities) + list(auto_entities)
                     entities = list(set(entities))
                     descWithTask["custom_entities"] = entities

dcm2bids/utils/utils.py

@@ -5,7 +5,7 @@
 import logging
 import os
 from pathlib import Path
-from subprocess import check_output, Popen, PIPE
+from subprocess import Popen, PIPE
 
 
 class DEFAULT(object):
@@ -74,7 +74,7 @@ class DEFAULT(object):
                      "fmap_TB1SRGE": ["echo", "inv"],
                      "perf_physio": ["task"],
                      "perf_stim": ["task"]}
-    
+
     compKeys = ["AcquisitionTime", "SeriesNumber", "SidecarFilename"]
     search_methodChoices = ["fnmatch", "re"]
     search_method = "fnmatch"
@@ -148,9 +148,10 @@ def run_shell_command(commandLine, log=True):
 
     pipes = Popen(commandLine, stdout=PIPE, stderr=PIPE)
     std_out, std_err = pipes.communicate()
- 
+
     return std_out
 
+
 def convert_dir(dir):
     """ Convert Direction
     Args:
@@ -163,15 +164,15 @@ def convert_dir(dir):
 
 
 def combine_dict_extractors(d1, d2):
-    """ combine dict 
+    """ combine dict
     Args:
         d1 (dic): dictionary
         d2 (dic): dictionary
-    
+
     Returns:
         dict: dictionary with combined information
               if d1 d2 use the same keys, return dict will return a list of items.
-    """    
+    """
     return {
             k: [d[k][0] for d in (d1, d2) if k in d]
             for k in set(d1.keys()) | set(d2.keys())