chore: fix isort config and remove isort: skip_file (#2196)

* chore: pass config to isort as it doesn't always detect it

* chore: mark package "test" as local, not stdlib

* chore: remove "isort: skip_file"

* chore: fix app in test_load_security_information

* chore: fix app in test_notification

* chore: fix app in test_index_report

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
     rev: 5.12.0
     hooks:
     -   id: isort
-        args: ["--profile", "black", "--filter-files"]
+        args: ["--settings-path", "pyproject.toml"]
 -   repo: local
     hooks:
     -   id: config-files-check

data/secscan_model/__init__.py

@@ -1,9 +1,5 @@
 import logging
-import os
-from collections import namedtuple
 
-from data.database import Manifest
-from data.registry_model.datatypes import Manifest as ManifestDataType
 from data.secscan_model.datatypes import (
     ScanLookupStatus,
     SecurityInformationLookupResult,

data/secscan_model/test/test_secscan_interface.py

@@ -1,9 +1,7 @@
-from test.fixtures import *
-
 import pytest
 from mock import Mock, patch
 
-from app import app, instance_keys, storage
+from app import instance_keys, storage
 from data.database import IndexerVersion, IndexStatus, ManifestSecurityStatus
 from data.registry_model import registry_model
 from data.secscan_model import secscan_model
@@ -14,6 +12,9 @@ from data.secscan_model.datatypes import (
 from data.secscan_model.secscan_v4_model import IndexReportState
 from data.secscan_model.secscan_v4_model import ScanToken as V4ScanToken
 from data.secscan_model.secscan_v4_model import V4SecurityScanner
+from test.fixtures import *
+
+from app import app  # isort: skip
 
 
 @pytest.mark.parametrize(

endpoints/api/test/test_security.py

@@ -1,16 +1,11 @@
-# isort reordering imports breaks these tests, so tell it to skip
-# isort: skip_file
-from typing import List, Optional, Dict, Tuple, Any, Type
-from mock import patch
+from typing import Any, Dict, List, Optional, Tuple, Type
 
 import pytest
 from flask_principal import AnonymousIdentity
+from mock import patch
 
 import features
 from endpoints.api import api
-from endpoints.api.test.shared import conduct_api_call
-from endpoints.test.shared import client_with_identity, toggle_feature
-
 from endpoints.api.appspecifictokens import *
 from endpoints.api.billing import *
 from endpoints.api.build import *
@@ -18,7 +13,9 @@ from endpoints.api.discovery import *
 from endpoints.api.globalmessages import *  # type: ignore[no-redef]
 from endpoints.api.logs import *  # type: ignore[no-redef]
 from endpoints.api.manifest import *  # type: ignore[no-redef]
-from endpoints.api.organization import *  # type: ignore[no-redef]
+from endpoints.api.mirror import *  # type: ignore[no-redef]
+from endpoints.api.namespacequota import *
+from endpoints.api.organization import *  # type: ignore[assignment,no-redef]
 from endpoints.api.permission import *  # type: ignore[no-redef]
 from endpoints.api.prototype import *
 from endpoints.api.repoemail import *  # type: ignore[no-redef]
@@ -34,13 +31,16 @@ from endpoints.api.suconfig import *  # type: ignore[no-redef]
 from endpoints.api.superuser import *  # type: ignore
 from endpoints.api.tag import *  # type: ignore[no-redef]
 from endpoints.api.team import *
+from endpoints.api.test.shared import conduct_api_call
 from endpoints.api.trigger import *
-from endpoints.api.user import *  # type: ignore[no-redef]
-from endpoints.api.mirror import *  # type: ignore[no-redef]
-from endpoints.api.namespacequota import *
+from endpoints.api.user import *  # type: ignore[assignment,no-redef]
+from endpoints.test.shared import client_with_identity, toggle_feature
 
-from endpoints.api.repository import Repository
+# Next imports should be after all the endpoints.api imports.
+# Repository should be the API resource, not the data model.
+from endpoints.api.repository import Repository  # isort: skip
 
+# app should be the pytest fixture, not the Flask app.
 from test.fixtures import *  # type: ignore[assignment] # isort: skip
 
 ORG_PARAMS = {"orgname": "buynlarge"}

initdb.py

@@ -1,9 +1,3 @@
-# isort: skip_file
-from typing import Dict, Any
-import logging
-import json
-import hashlib
-import random
 import argparse
 import calendar
 import hashlib

pyproject.toml

@@ -3,6 +3,7 @@ line-length = 100
 target-version = ['py39']
 
 [tool.isort]
+known_local_folder = "auth,avatars,buildman,buildtrigger,data,digest,endpoints,features,health,image,notifications,oauth,proxy,storage,test,tools,util,workers,_init,active_migration,app,config,external_libraries,initdb,path_converters,release"
 profile = "black"
 
 [tool.pylint.messages_control]

util/secscan/v4/test/test_secscan.py

@@ -1,18 +1,20 @@
 import unittest
-from test.fixtures import *
 
 import pytest
 from mock import patch
 
-from app import app, instance_keys, storage
+from app import instance_keys, storage
 from config import build_requests_session
 from data.database import ManifestSecurityStatus
 from data.registry_model import registry_model
 from data.secscan_model import secscan_model
+from test.fixtures import *
 from util.secscan.blob import BlobURLRetriever
 from util.secscan.v4.api import APIRequestFailure, ClairSecurityScannerAPI
 from util.secscan.v4.fake import fake_security_scanner
 
+from app import app  # isort: skip
+
 
 def manifest_for(namespace, repository, tagname):
     repository_ref = registry_model.lookup_repository(namespace, repository)

workers/test/test_securityscanningnotificationworker.py

@@ -1,25 +1,21 @@
 import json
 import os
-from test.fixtures import *
 from urllib.parse import urlparse
 
 import pytest
 
-from app import (
-    app,
-    instance_keys,
-    notification_queue,
-    secscan_notification_queue,
-    storage,
-)
+from app import instance_keys, notification_queue, secscan_notification_queue, storage
 from data import database, model
 from data.registry_model import registry_model
 from data.secscan_model import secscan_model
+from test.fixtures import *
 from util.secscan.v4.fake import fake_security_scanner
 from workers.securityscanningnotificationworker import (
     SecurityScanningNotificationWorker,
 )
 
+from app import app  # isort: skip
+
 
 @pytest.mark.skipif(
     os.environ.get("TEST_DATABASE_URI", "").find("mysql") >= 0, reason="Flaky on MySQL"