flake8 and refacto

backend/metagenedb/apps/catalog/admin/__init__.py

 from .gene import GeneAdmin
 from .function import FunctionAdmin, KeggOrthologyAdmin
+
+
+__all__ = ['GeneAdmin', 'FunctionAdmin', 'KeggOrthologyAdmin']

backend/metagenedb/apps/catalog/admin/admin.py

@@ -26,4 +26,3 @@ class FunctionAdmin(admin.ModelAdmin):
 
     list_display = ('function_id', 'name', 'source')
     search_fields = ('function_id',)
-

backend/metagenedb/apps/catalog/migrations/0001_initial.py

@@ -18,13 +18,13 @@ class Migration(migrations.Migration):
                 ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
                 ('function_id', models.CharField(db_index=True, max_length=100)),
                 ('name', models.CharField(max_length=100)),
-                ('source', models.CharField(choices=[('undef', 'Undefined'), ('kegg', 'KEGG'), ('eggnog', 'EggNOG')], default='undef', max_length=10)),
+                ('source', models.CharField(choices=[('undef', 'Undefined'), ('kegg', 'KEGG'), ('eggnog', 'EggNOG')], default='undef', max_length=10)),  # noqa
             ],
         ),
         migrations.CreateModel(
             name='KeggOrthology',
             fields=[
-                ('function_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='catalog.Function')),
+                ('function_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='catalog.Function')),  # noqa
                 ('ec_number', models.CharField(blank=True, default='', max_length=200)),
                 ('long_name', models.CharField(max_length=500)),
             ],

backend/metagenedb/apps/catalog/models/__init__.py

 from .function import Function, KeggOrthology
 from .gene import Gene
+
+
+__all__ = ['Function', 'KeggOrthology', 'Gene']

backend/metagenedb/apps/catalog/models/gene.py

@@ -10,4 +10,3 @@ class Gene(models.Model):
 
     def __str__(self):
         return self.gene_id
-

backend/metagenedb/apps/catalog/serializers.py

@@ -14,4 +14,3 @@ class GeneSerializer(serializers.ModelSerializer):
     class Meta:
         model = Gene
         fields = ('gene_id', 'gene_length', 'functions')
-

backend/metagenedb/apps/catalog/tests.py

-from django.test import TestCase
-
-# Create your tests here.

backend/metagenedb/apps/catalog/views.py

@@ -11,6 +11,7 @@ from .serializers import GeneSerializer
 def index(request):
     return HttpResponse(f"Welcome to the catalog page.")
 
+
 @api_view(['GET'])
 def gene_list(request):
     """
@@ -37,7 +38,7 @@ def gene_list(request):
     return Response({'data': serializer.data, 'count': paginator.count, 'numpages': paginator.num_pages,
                      'nextlink': '/api/genes/?page=' + str(nextPage),
                      'prevlink': '/api/genes/?page=' + str(previousPage)})
-    
+
 
 @api_view(['GET'])
 def gene_detail(request, gene_id):

backend/metagenedb/tests/test_user.py

+from django.contrib.auth.models import User
+from django.test import TestCase
+
+
+class TestDatabase(TestCase):
+    def test_create_user(self):
+        user = User.objects.create_user(
+            username='user',
+            email='user@foo.com',
+            password='pass'
+        )
+        user.save()
+        user_count = User.objects.all().count()
+        self.assertEqual(user_count, 1)

backend/metagenedb/urls.py

@@ -16,7 +16,6 @@ Including another URLconf
 from django.contrib import admin
 from django.urls import include, path
 
-from rest_framework import routers
 
 urlpatterns = [
     path('admin/', admin.site.urls),

backend/requirements_dev.txt

@@ -49,3 +49,4 @@ traitlets==4.3.2
 wcwidth==0.1.7
 webencodings==0.5.1
 widgetsnbextension==3.4.2
+flake8

backend/scripts/import_igc_data.py

@@ -12,7 +12,7 @@ from django.core.exceptions import ValidationError
 os.environ.setdefault("DJANGO_SETTINGS_MODULE", "metagenedb.settings")
 django.setup()
 
-from metagenedb.apps.catalog.models import Gene, Function
+from metagenedb.apps.catalog.models import Gene, Function  # noqa
 
 logging.basicConfig(level=logging.INFO)
 _LOGGER = logging.getLogger(__name__)

backend/scripts/load_kegg_ko.py

@@ -12,7 +12,7 @@ from django.core.exceptions import ValidationError
 os.environ.setdefault("DJANGO_SETTINGS_MODULE", "metagenedb.settings")
 django.setup()
 
-from metagenedb.apps.catalog.models import KeggOrthology
+from metagenedb.apps.catalog.models import KeggOrthology  # noqa
 
 logging.basicConfig(level=logging.INFO)
 _LOGGER = logging.getLogger(__name__)
@@ -62,7 +62,7 @@ def create_kegg_ko(kegg_ko):
 
 
 def run():
-    args = parse_arguments()
+    args = parse_arguments()  # noqa
     all_ko = requests.get("http://rest.kegg.jp/list/ko")
     all_ko.raise_for_status()
     inserted_kegg = 0
@@ -84,6 +84,5 @@ def run():
     # Create unknown entry
 
 
-
 if __name__ == "__main__":
     run()

backend/setup.py

@@ -11,5 +11,4 @@ setup(name="metagenedb",
           'djangorestframework'
       ],
       packages=find_packages(),
-      scripts=['scripts/manage.py'],
-)
+      scripts=['scripts/manage.py'])