style: Use of isort in pre-commit

.pre-commit-config.yaml

@@ -20,6 +20,26 @@ repos:
     args:
     - --markdown-linebreak-ext=md
 
+# isort (in black-compatibility mode)
+- repo: https://github.com/pycqa/isort
+  rev: 5.12.0
+  hooks:
+  - id: isort
+    args:
+    - --profile
+    - black
+    - --filter-files
+
+# Black (uncompromising) Python code formatter
+- repo: https://github.com/psf/black
+  rev: 23.11.0
+  hooks:
+  - id: black
+    args:
+    - --skip-string-normalization
+    - --target-version
+    - py311
+
 # MyPy
 #- repo: https://github.com/pre-commit/mirrors-mypy
 #  rev: v1.7.1
@@ -32,16 +52,6 @@ repos:
 #    - types-python-dateutil
 #    - types-requests
 
-# Black (uncompromising) Python code formatter
-- repo: https://github.com/psf/black
-  rev: 23.11.0
-  hooks:
-  - id: black
-    args:
-    - --skip-string-normalization
-    - --target-version
-    - py311
-
 # Pylint
 - repo: https://github.com/pycqa/pylint
   rev: v2.17.7

api/remote_ispyb_connector.py

@@ -1,14 +1,15 @@
 import threading
+import time
+import traceback
+
+import pymysql
+import sshtunnel
 from ispyb.connector.mysqlsp.main import ISPyBMySQLSPConnector as Connector
 from ispyb.exception import (
     ISPyBConnectionException,
     ISPyBNoResultException,
     ISPyBRetrieveFailed,
 )
-import sshtunnel
-import time
-import traceback
-import pymysql
 
 
 class SSHConnector(Connector):

api/security.py

@@ -2,20 +2,19 @@
 import logging
 import os
 import time
-
 from pathlib import Path
-
 from wsgiref.util import FileWrapper
-from django.http import Http404
-from django.http import HttpResponse
+
 from django.db.models import Q
+from django.http import Http404, HttpResponse
 from ispyb.connector.mysqlsp.main import ISPyBMySQLSPConnector as Connector
 from ispyb.connector.mysqlsp.main import ISPyBNoResultException
 from rest_framework import viewsets
-from .remote_ispyb_connector import SSHConnector
 
 from viewer.models import Project
 
+from .remote_ispyb_connector import SSHConnector
+
 logger = logging.getLogger(__name__)
 
 USER_LIST_DICT = {}

api/urls.py

@@ -135,9 +135,9 @@
 router.register("job_override", viewer_views.JobOverrideView, basename='job_override')
 
 
-from rest_framework_swagger.renderers import OpenAPIRenderer, SwaggerUIRenderer
-from rest_framework.decorators import api_view, renderer_classes
 from rest_framework import response, schemas
+from rest_framework.decorators import api_view, renderer_classes
+from rest_framework_swagger.renderers import OpenAPIRenderer, SwaggerUIRenderer
 
 
 @api_view()

api/utils.py

@@ -3,12 +3,11 @@
 from django.contrib.auth.models import User
 from django.core.exceptions import ObjectDoesNotExist
 from django.http import HttpResponse
+from frag.utils.network_utils import canon_input
 from rdkit import Chem
 from rdkit.Chem import AllChem, Atom, rdDepictor
 from rdkit.Chem.Draw import rdMolDraw2D
 from rest_framework.authtoken.models import Token
-from frag.utils.network_utils import canon_input
-
 
 ISO_COLOUR_MAP = {
     100: (1, 0, 0),

docs/source/conf.py

@@ -11,12 +11,12 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import inspect
-import sys
 import os
+import sys
 
 import django
-from django.utils.html import strip_tags
 from django.utils.encoding import force_text
+from django.utils.html import strip_tags
 
 sys.path.insert(0, os.path.abspath('../..'))
 os.environ['DJANGO_SETTINGS_MODULE'] = 'fragalysis.settings'

fragalysis/celery.py

@@ -21,6 +21,7 @@ def config_loggers(*args, **kwargs):
     del args, kwargs
 
     from logging.config import dictConfig  # noqa
+
     from django.conf import settings  # noqa
 
     dictConfig(settings.LOGGING)

fragalysis/schema.py

@@ -1,7 +1,8 @@
 import graphene
+import pandda.schema
+
 import hotspots.schema
 import hypothesis.schema
-import pandda.schema
 import scoring.schema
 import viewer.schema
 import xcdb.schema

fragalysis/settings.py

@@ -14,10 +14,10 @@
 from datetime import timedelta
 
 import sentry_sdk
-from sentry_sdk.integrations.django import DjangoIntegration
 from sentry_sdk.integrations.celery import CeleryIntegration
-from sentry_sdk.integrations.redis import RedisIntegration
+from sentry_sdk.integrations.django import DjangoIntegration
 from sentry_sdk.integrations.excepthook import ExcepthookIntegration
+from sentry_sdk.integrations.redis import RedisIntegration
 
 # SECURITY WARNING: don't run with debug turned on in production!
 DEBUG = False

fragalysis/urls.py

@@ -14,13 +14,13 @@
     2. Add a URL to urlpatterns:  url(r'^blog/', include('blog.urls'))
 """
 import mozilla_django_oidc.views
-import fragalysis.views
 from django.conf.urls import include
-from django.urls import path, re_path
 from django.contrib import admin
+from django.urls import path, re_path
 from django.views.generic.base import RedirectView
 from graphene_django.views import GraphQLView
 
+import fragalysis.views
 
 urlpatterns = [
     re_path(r"^$", RedirectView.as_view(url="/viewer/react/landing")),

fragalysis/views.py

@@ -1,9 +1,9 @@
 # Classes/Methods to override default OIDC Views (Keycloak authentication)
 import os
 
-from mozilla_django_oidc.views import OIDCLogoutView
-from django.http import JsonResponse
 from django.conf import settings
+from django.http import JsonResponse
+from mozilla_django_oidc.views import OIDCLogoutView
 
 
 def keycloak_logout(request):

hotspots/migrations/0001_initial.py

@@ -1,7 +1,7 @@
 # Generated by Django 3.2.20 on 2023-08-18 15:06
 
-from django.db import migrations, models
 import django.db.models.deletion
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

hotspots/models.py

@@ -1,6 +1,6 @@
 from django.db import models
 
-from viewer.models import Target, SiteObservation
+from viewer.models import SiteObservation, Target
 
 
 class HotspotMap(models.Model):

hotspots/schema.py

@@ -1,5 +1,6 @@
 import graphene
 from graphene_django.rest_framework.mutation import SerializerMutation
+
 from hotspots.serializers import HotspotMapSerializer
 
 relay = graphene.relay

hypothesis/migrations/0001_initial.py

@@ -1,7 +1,7 @@
 # Generated by Django 3.2.20 on 2023-08-18 15:05
 
-from django.db import migrations, models
 import django.db.models.deletion
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

hypothesis/models.py

@@ -1,7 +1,7 @@
 from django.db import models
 
 from hypothesis.definitions import IntTypes, VectTypes
-from viewer.models import SiteObservation, Target, Compound
+from viewer.models import Compound, SiteObservation, Target
 
 
 class TargetResidue(models.Model):

hypothesis/schema.py

@@ -2,11 +2,11 @@
 from graphene_django.rest_framework.mutation import SerializerMutation
 
 from hypothesis.serializers import (
-    Vector3DSerializer,
-    VectorSerializer,
     InteractionPointSerializer,
     InteractionSerializer,
     TargetResidueSerialzier,
+    Vector3DSerializer,
+    VectorSerializer,
 )
 
 relay = graphene.relay

hypothesis/serializers.py

@@ -1,11 +1,6 @@
 from rest_framework import serializers
 
-from hypothesis.models import (
-    Vector,
-    Interaction,
-    InteractionPoint,
-    TargetResidue,
-)
+from hypothesis.models import Interaction, InteractionPoint, TargetResidue, Vector
 
 
 class Vector3DSerializer(serializers.Serializer):

hypothesis/views.py

@@ -1,13 +1,9 @@
 from rest_framework import viewsets
 
-from hypothesis.models import (
-    Interaction,
-    InteractionPoint,
-    TargetResidue,
-)
+from hypothesis.models import Interaction, InteractionPoint, TargetResidue
 from hypothesis.serializers import (
-    InteractionSerializer,
     InteractionPointSerializer,
+    InteractionSerializer,
     TargetResidueSerialzier,
 )
 

media_serve/urls.py

@@ -1,5 +1,4 @@
-from django.urls import path
-from django.urls import re_path
+from django.urls import path, re_path
 
 from . import views
 

media_serve/views.py

@@ -1,8 +1,8 @@
-from api.security import ISpyBSafeStaticFiles
-from api.security import ISpyBSafeStaticFiles2
-from viewer.models import SiteObservation, Target
 import logging
 
+from api.security import ISpyBSafeStaticFiles, ISpyBSafeStaticFiles2
+from viewer.models import SiteObservation, Target
+
 logger = logging.getLogger(__name__)
 
 # def prot_download(request, file_path):

scoring/managers.py

@@ -1,11 +1,7 @@
 import logging
 
 from django.apps import apps
-
-from django.db.models import QuerySet
-from django.db.models import Manager
-from django.db.models import F
-
+from django.db.models import F, Manager, QuerySet
 
 logger = logging.getLogger(__name__)
 

scoring/migrations/0001_initial.py

@@ -1,8 +1,8 @@
 # Generated by Django 3.2.20 on 2023-08-18 15:06
 
+import django.db.models.deletion
 from django.conf import settings
 from django.db import migrations, models
-import django.db.models.deletion
 
 
 class Migration(migrations.Migration):

scoring/migrations/0003_auto_20231020_1501.py

@@ -1,7 +1,7 @@
 # Generated by Django 3.2.20 on 2023-10-20 15:01
 
-from django.db import migrations, models
 import django.db.models.deletion
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

scoring/models.py

@@ -1,7 +1,7 @@
 from django.contrib.auth.models import User
 from django.db import models
 
-from viewer.models import SiteObservation, Compound, Target, Snapshot
+from viewer.models import Compound, SiteObservation, Snapshot, Target
 
 from .managers import ScoreChoiceDataManager
 

scoring/schema.py

@@ -2,9 +2,9 @@
 from graphene_django.rest_framework.mutation import SerializerMutation
 
 from scoring.serializers import (
-    ViewSceneSerializer,
     CmpdChoiceSerializer,
     ScoreChoiceSerializer,
+    ViewSceneSerializer,
 )
 
 relay = graphene.relay

scoring/serializers.py

@@ -1,12 +1,12 @@
 from rest_framework import serializers
 
 from scoring.models import (
-    ViewScene,
     CmpdChoice,
-    SiteObservationChoice,
     ScoreChoice,
-    SiteObservationGroup,
     SiteObservationAnnotation,
+    SiteObservationChoice,
+    SiteObservationGroup,
+    ViewScene,
 )
 
 

scoring/views.py

@@ -1,23 +1,24 @@
 import json
+
 from django.http import HttpResponse
 from frag.conf.functions import generate_confs_for_vector
 from rest_framework import viewsets
 
 from scoring.models import (
-    ViewScene,
     CmpdChoice,
-    SiteObservationChoice,
-    SiteObservationAnnotation,
     ScoreChoice,
+    SiteObservationAnnotation,
+    SiteObservationChoice,
     SiteObservationGroup,
+    ViewScene,
 )
 from scoring.serializers import (
-    ViewSceneSerializer,
     CmpdChoiceSerializer,
-    SiteObservationChoiceSerializer,
-    SiteObservationAnnotationSerializer,
     ScoreChoiceSerializer,
+    SiteObservationAnnotationSerializer,
+    SiteObservationChoiceSerializer,
     SiteObservationGroupSerializer,
+    ViewSceneSerializer,
 )