Fixed some more flake8 errors

Author: pavelvazquez

src/omnipy/__init__.py

@@ -4,15 +4,17 @@
 import sys
 from typing import Optional
 
+from omnipy.hub.runtime import Runtime
+
 ROOT_DIR = os.path.dirname(os.path.abspath(__file__))
 
-# TODO: The check disabling runtime for tests also trigger for tests that are run outside of Omnipy, breaking
-#       tests on the user side. Find a better way to disable the global runtime object for Omnipy tests
+# TODO: The check disabling runtime for tests also trigger for tests that are run outside of Omnipy,
+#  breaking tests on the user side.
+#  Find a better way to disable the global runtime object for Omnipy tests
 
 
 def _get_runtime() -> Optional['Runtime']:
     if 'pytest' not in sys.modules:
-        from omnipy.hub.runtime import Runtime
         return Runtime()
     else:
         return None

src/omnipy/config/job.py

@@ -1,10 +1,11 @@
 from dataclasses import dataclass, field
-from datetime import datetime
+# from datetime import datetime
 from pathlib import Path
-from typing import Optional
 
 from omnipy.api.enums import ConfigPersistOutputsOptions, ConfigRestoreOutputsOptions
 
+# from typing import Optional
+
 
 def _get_persist_data_dir_path() -> str:
     return str(Path.cwd().joinpath(Path('data')))

src/omnipy/modules/fairtracks/create_filter.py

@@ -7,7 +7,7 @@
 import requests
 
 #########################################################
-### user parameters
+# user parameters
 #######################################################
 download_all_projects = False
 download_all_cases = False
@@ -17,7 +17,7 @@
 # NB very few annotations per case, get all
 
 #######################################################
-###endpoints definition
+# endpoints definition
 ########################################################
 projects_endpt = 'https://api.gdc.cancer.gov/projects'
 cases_endpt = 'https://api.gdc.cancer.gov/cases'
@@ -73,7 +73,7 @@
 projects_list = (response.json()['data']['hits'])
 
 ##########################################################################
-#Step3: filtered query on 'cases' (filter on project_id) to get cases ID for each TCGA project
+# Step3: filtered query on 'cases' (filter on project_id) to get cases ID for each TCGA project
 #      the IDs for all the files are also available form this endpoint
 ########################################################################
 
@@ -102,7 +102,7 @@
     proj['cases'] = cases
 
 ##########################################################################
-#step4: filtered query on 'annotations' (filter on case_id) to get cases ID for each TCGA project
+# step4: filtered query on 'annotations' (filter on case_id) to get cases ID for each TCGA project
 #      the IDs for all the files are also available form this endpoint
 ########################################################################
 

src/omnipy/modules/fairtracks/get_from_filter.py

@@ -13,7 +13,7 @@
 
     with open(endpt_str + '_filter.json', 'r') as infile:
         filters = json.load(infile)
-        params = {  #'fields': fields,
+        params = {  # 'fields': fields,
             'filters': json.dumps(filters),
         }
     response = requests.get(endpt, params=params)

src/omnipy/modules/general/models.py

@@ -5,4 +5,4 @@
 
 class NotIteratorExceptStrings(Model[object]):
     def _parse_data(cls, data: object) -> object:
-        assert isinstance(data, str) or not isinstance(data, Iterable)
+        assert isinstance(data, str) or not isinstance(data, Iterable)

src/omnipy/modules/raw/serializers.py

@@ -1,11 +1,11 @@
 from typing import Any, Dict, IO, Type
 
-from typing_inspect import get_generic_bases, get_generic_type, get_origin, get_parameters
-
 from omnipy.data.dataset import Dataset
 from omnipy.data.model import Model
 from omnipy.data.serializer import TarFileSerializer
 
+# from typing_inspect import get_generic_bases, get_generic_type, get_origin, get_parameters
+
 
 class RawDatasetToTarFileSerializer(TarFileSerializer):
     """"""