manually lint code

clinica/engine/prov_model.py

@@ -1,13 +1,12 @@
+from abc import ABC, abstractmethod
+from typing import List, Union
 from xml.dom.minidom import Element
-from attr import define, field
+
 import attr
 import cattr
-from typing import Union, List
-from abc import ABC, abstractmethod
-
+from attr import define, field
 from matplotlib.style import context
 
-
 #  Define PROV abstract concepts
 
 

clinica/engine/prov_utils.py

@@ -1,5 +1,5 @@
-from typing import Optional, List
 from pathlib import Path
+from typing import List, Optional
 
 from .prov_model import *
 
@@ -12,8 +12,8 @@ def get_files_list(self, pipeline_fullname: str, dict_field="input_to") -> List[
 
     return list of 'Path's to the files used in the pipeline
     """
-    from clinica.utils.inputs import clinica_file_reader
     import clinica.utils.input_files as cif
+    from clinica.utils.inputs import clinica_file_reader
 
     dict_field_options = ["input_to", "output_from"]
     if dict_field not in dict_field_options:

clinica/engine/provenance.py

@@ -1,6 +1,5 @@
 import functools
 from os import read
-
 from pathlib import Path
 from typing import List
 
@@ -56,7 +55,7 @@ def get_history_record(paths_files: List[Path]) -> ProvRecord:
         a ProvRecord for the associated files in path_files
     """
 
-    from .prov_utils import read_prov_jsonld, get_path_prov
+    from .prov_utils import get_path_prov, read_prov_jsonld
 
     prov_record = ProvRecord({}, [])
 
@@ -127,13 +126,14 @@ def extend_prov(prov_main: dict, prov_new: dict) -> dict:
 
 
 def get_agent() -> ProvAgent:
-    import clinica
+    from clinica import __name__, __version__
+
     from .prov_utils import generate_agent_id
 
     new_agent = ProvAgent(uid=generate_agent_id())
 
-    new_agent.attributes["version"] = clinica.__version__
-    new_agent.attributes["label"] = clinica.__name__
+    new_agent.attributes["version"] = __version__
+    new_agent.attributes["label"] = __name__
 
     return new_agent
 
@@ -144,13 +144,14 @@ def get_activity(self, agent: Identifier, entities: List[ProvEntity]) -> ProvAct
         ProvActivity from related entities and associated agent
     """
     import sys
+
     from .prov_utils import generate_activity_id
 
     new_activity = ProvActivity(uid=generate_activity_id(self.fullname))
 
     new_activity.attributes["parameters"] = self.parameters
     new_activity.attributes["label"] = self.fullname
-    new_activity.attributes["command"] = (sys.argv[1:],)
+    new_activity.attributes["command"] = sys.argv[1:]
     new_activity.attributes["used"] = [str(x.uid) for x in entities]
     new_activity.attributes["wasAssociatedWith"] = str(agent.uid)
 

clinica/pipelines/engine.py

@@ -7,6 +7,7 @@
 
 import click
 from nipype.pipeline.engine import Workflow
+
 import clinica.engine.provenance as prov