toil 9.1.1__py3-none-any.whl → 9.2.0__py3-none-any.whl

toil/test/lib/test_ec2.py

@@ -13,15 +13,14 @@
 # limitations under the License.
 import logging
 import os
-
 from unittest import mock
 
 from toil.lib.aws.ami import (
+    ReleaseFeedUnavailableError,
     aws_marketplace_flatcar_ami_search,
     feed_flatcar_ami_release,
     flatcar_release_feed_ami,
     get_flatcar_ami,
-    ReleaseFeedUnavailableError
 )
 from toil.test import ToilTest, needs_aws_ec2, needs_online
 
@@ -33,27 +32,29 @@ logging.basicConfig(level=logging.DEBUG)
 class FlatcarFeedTest(ToilTest):
     """Test accessing the Flatcar AMI release feed, independent of the AWS API"""
 
-    # Note that we need to support getting an empty list back, because
-    # sometimes the Flatcar feeds are just down, and we can't fail CI at those
-    # times.
+    # Note that we need to support getting no AMI back, because sometimes the
+    # Flatcar feeds are just down, and we can't fail CI at those times.
 
     def test_parse_archive_feed(self):
         """Make sure we can get a Flatcar release from the Internet Archive."""
         ami = flatcar_release_feed_ami("us-west-2", "amd64", "archive")
-        self.assertEqual(len(ami), len("ami-02b46c73fed689d1c"))
-        self.assertTrue(ami.startswith("ami-"))
+        if ami is not None:
+            self.assertEqual(len(ami), len("ami-02b46c73fed689d1c"))
+            self.assertTrue(ami.startswith("ami-"))
 
     def test_parse_beta_feed(self):
         """Make sure we can get a Flatcar release from the beta channel."""
         ami = flatcar_release_feed_ami("us-west-2", "amd64", "beta")
-        self.assertEqual(len(ami), len("ami-02b46c73fed689d1c"))
-        self.assertTrue(ami.startswith("ami-"))
+        if ami is not None:
+            self.assertEqual(len(ami), len("ami-02b46c73fed689d1c"))
+            self.assertTrue(ami.startswith("ami-"))
 
     def test_parse_stable_feed(self):
         """Make sure we can get a Flatcar release from the stable channel."""
         ami = flatcar_release_feed_ami("us-west-2", "amd64", "stable")
-        self.assertEqual(len(ami), len("ami-02b46c73fed689d1c"))
-        self.assertTrue(ami.startswith("ami-"))
+        if ami is not None:
+            self.assertEqual(len(ami), len("ami-02b46c73fed689d1c"))
+            self.assertTrue(ami.startswith("ami-"))
 
 
 @needs_aws_ec2

toil/test/lib/test_history.py

@@ -12,15 +12,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from collections.abc import Generator
-from pathlib import Path
 import logging
 import time
-
-from toil.lib.history import HistoryManager
+from collections.abc import Generator
+from pathlib import Path
 
 import pytest
 
+from toil.lib.history import HistoryManager
+
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.DEBUG)
 

toil/test/lib/test_trs.py

@@ -12,20 +12,21 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import io
 import logging
-import pytest
-from typing import IO
 import urllib.request
+from typing import IO
 from urllib.error import URLError
 
+import pytest
+
 from toil.lib.retry import retry
-from toil.lib.trs import find_workflow, fetch_workflow
+from toil.lib.trs import fetch_workflow, find_workflow
 from toil.test import ToilTest, needs_online
 
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.DEBUG)
 
+
 @pytest.mark.integrative
 @needs_online
 class DockstoreLookupTest(ToilTest):
@@ -57,7 +58,9 @@ class DockstoreLookupTest(ToilTest):
         PAGE_URL = "https://dockstore.org/workflows/github.com/dockstore/bcc2020-training/HelloWorld:master?tab=info"
         trs_id, trs_version, language = find_workflow(PAGE_URL)
 
-        self.assertEqual(trs_id, "#workflow/github.com/dockstore/bcc2020-training/HelloWorld")
+        self.assertEqual(
+            trs_id, "#workflow/github.com/dockstore/bcc2020-training/HelloWorld"
+        )
         self.assertEqual(trs_version, "master")
         self.assertEqual(language, "WDL")
 
@@ -65,7 +68,7 @@ class DockstoreLookupTest(ToilTest):
         TRS_ID = "#workflow/github.com/dockstore-testing/md5sum-checker"
         TRS_VERSION = "master"
         trs_id, trs_version, language = find_workflow(f"{TRS_ID}:{TRS_VERSION}")
-        
+
         self.assertEqual(trs_id, TRS_ID)
         self.assertEqual(trs_version, TRS_VERSION)
         self.assertEqual(language, "CWL")
@@ -90,7 +93,7 @@ class DockstoreLookupTest(ToilTest):
         # checker workflow itself.
         WORKFLOW_URL = "https://raw.githubusercontent.com/dockstore-testing/md5sum-checker/master/md5sum/md5sum-workflow.cwl"
         looked_up = fetch_workflow(TRS_ID, TRS_VERSION, LANGUAGE)
-        
+
         data_from_lookup = self.read_result(looked_up).read()
         data_from_source = self.read_result(WORKFLOW_URL).read()
         self.assertEqual(data_from_lookup, data_from_source)
@@ -104,7 +107,7 @@ class DockstoreLookupTest(ToilTest):
         fetch_workflow(TRS_ID, TRS_VERSION, LANGUAGE)
         # This lookup is definitely cached
         looked_up = fetch_workflow(TRS_ID, TRS_VERSION, LANGUAGE)
-        
+
         data_from_lookup = self.read_result(looked_up).read()
         data_from_source = self.read_result(WORKFLOW_URL).read()
         self.assertEqual(data_from_lookup, data_from_source)
@@ -112,7 +115,7 @@ class DockstoreLookupTest(ToilTest):
     def test_lookup_from_trs_with_version(self) -> None:
         TRS_VERSIONED_ID = "#workflow/github.com/dockstore-testing/md5sum-checker:workflowWithHTTPImport"
         trs_id, trs_version, language = find_workflow(TRS_VERSIONED_ID)
-        
+
         parts = TRS_VERSIONED_ID.split(":")
 
         self.assertEqual(trs_id, parts[0])
@@ -130,10 +133,12 @@ class DockstoreLookupTest(ToilTest):
             looked_up = find_workflow(TRS_VERSIONED_ID)
 
     def test_lookup_from_trs_nonexistent_version(self) -> None:
-        TRS_VERSIONED_ID = "#workflow/github.com/dockstore-testing/md5sum-checker:notARealVersion"
+        TRS_VERSIONED_ID = (
+            "#workflow/github.com/dockstore-testing/md5sum-checker:notARealVersion"
+        )
         with self.assertRaises(FileNotFoundError):
             looked_up = find_workflow(TRS_VERSIONED_ID)
-    
+
     def test_get_nonexistent_workflow(self) -> None:
         TRS_ID = "#workflow/github.com/adamnovak/veryfakerepo"
         TRS_VERSION = "notARealVersion"
@@ -156,6 +161,3 @@ class DockstoreLookupTest(ToilTest):
         LANGUAGE = "CWL"
         with self.assertRaises(FileNotFoundError):
             looked_up = fetch_workflow(TRS_ID, TRS_VERSION, LANGUAGE)
-
-
-

toil/test/lib/test_url.py

@@ -11,20 +11,18 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-import getpass
 import logging
 
 from pytest_httpserver import HTTPServer
 
-from toil.lib.misc import get_user_name
 from toil.lib.url import URLAccess
-from toil.test import needs_aws_s3, needs_online
-
+from toil.test import needs_aws_s3
 
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.DEBUG)
 
-class TestURLAccess():
+
+class TestURLAccess:
     """
     Test URLAccess class handling read, list,
     and checking the size/existence of resources at given URL
@@ -54,8 +52,11 @@ class TestURLAccess():
     @needs_aws_s3
     def test_read_from_url(self) -> None:
         import io
+
         output = io.BytesIO()
-        size, executable = URLAccess.read_from_url("s3://toil-datasets/hello.txt", output)
+        size, executable = URLAccess.read_from_url(
+            "s3://toil-datasets/hello.txt", output
+        )
         assert isinstance(size, int)
         assert size > 0
         assert not executable

toil/test/lib/url_plugin_test.py

@@ -11,29 +11,18 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-import logging
-from typing import IO, Optional, Union
-
-from configargparse import ArgParser, ArgumentParser
-
-from toil.batchSystems.abstractBatchSystem import (
-    AbstractBatchSystem,
-    UpdatedBatchJobInfo,
-)
-from toil.batchSystems.cleanup_support import BatchSystemCleanupSupport
-from toil.batchSystems.options import OptionSetter
-from toil.batchSystems.registry import add_batch_system_factory
-from toil.common import Toil, addOptions
-from toil.job import JobDescription
-
 import io
+import logging
+from typing import IO
 from urllib.parse import ParseResult
-from toil.test import ToilTest
-from toil.lib.url import URLAccess
+
 from toil.lib.plugins import register_plugin, remove_plugin
+from toil.lib.url import URLAccess
+from toil.test import ToilTest
 
 logger = logging.getLogger(__name__)
 
+
 class FakeURLPlugin(URLAccess):
     @classmethod
     def _supports_url(cls, url: ParseResult, export: bool = False) -> bool:
@@ -66,7 +55,12 @@ class FakeURLPlugin(URLAccess):
         return io.BytesIO(b"hello world")
 
     @classmethod
-    def _write_to_url(cls, readable: Union[IO[bytes], IO[str]], url: ParseResult, executable: bool = False) -> None:
+    def _write_to_url(
+        cls,
+        readable: IO[bytes] | IO[str],
+        url: ParseResult,
+        executable: bool = False,
+    ) -> None:
         pass
 
 

toil/test/provisioners/aws/awsProvisionerTest.py

@@ -11,7 +11,6 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-import datetime
 import logging
 import os
 import subprocess
@@ -26,17 +25,15 @@ from uuid import uuid4
 import pytest
 
 import toil.lib.aws.session
-
 from toil.lib.aws import zone_to_region
 from toil.provisioners import cluster_factory
-from toil.provisioners.aws.awsProvisioner import AWSProvisioner
 from toil.provisioners.aws import (
     _get_spot_history,
     get_aws_zone_from_spot_market,
     get_best_aws_zone,
 )
+from toil.provisioners.aws.awsProvisioner import AWSProvisioner
 from toil.test import (
-    ToilTest,
     get_data,
     integrative,
     needs_aws_ec2,
@@ -63,6 +60,7 @@ if TYPE_CHECKING:
 
 log = logging.getLogger(__name__)
 
+
 @pytest.fixture
 def aws_zone():
     """
@@ -74,6 +72,7 @@ def aws_zone():
     ), "Could not determine AWS availability zone to test in; is TOIL_AWS_ZONE set?"
     return zone
 
+
 @pytest.fixture
 def aws_region(aws_zone):
     """
@@ -81,6 +80,7 @@ def aws_region(aws_zone):
     """
     return zone_to_region(aws_zone)
 
+
 @pytest.fixture
 def ec2_client(aws_region):
     """
@@ -147,7 +147,9 @@ class TestAWSProvisionerBenchTest:
         Make sure that we can process spot price history to pick a zone.
         """
         zone_options = ["us-west-2a", "af-south-1c"]
-        zone_choice = get_aws_zone_from_spot_market(0.01, "t3.large", ec2_client, zone_options)
+        zone_choice = get_aws_zone_from_spot_market(
+            0.01, "t3.large", ec2_client, zone_options
+        )
         assert zone_choice in zone_options
 
 
@@ -208,7 +210,7 @@ class AbstractAWSAutoscaleTest(AbstractClusterTest):
         instances.sort(key=lambda x: x.get("LaunchTime"))
         leader: "InstanceTypeDef" = instances[0]  # assume leader was launched first
 
-        bdm: Optional[list["InstanceBlockDeviceMappingTypeDef"]] = leader.get(
+        bdm: list["InstanceBlockDeviceMappingTypeDef"] | None = leader.get(
             "BlockDeviceMappings"
         )
         assert bdm is not None
@@ -305,7 +307,7 @@ class AbstractAWSAutoscaleTest(AbstractClusterTest):
         self.cluster.destroyCluster()
         boto3_ec2: "EC2Client" = self.aws.client(region=self.region, service_name="ec2")
         volume_filter: "FilterTypeDef" = {"Name": "volume-id", "Values": [volumeID]}
-        volumes: Optional[list["VolumeTypeDef"]] = None
+        volumes: list["VolumeTypeDef"] | None = None
         for attempt in range(6):
             # https://github.com/BD2KGenomics/toil/issues/1567
             # retry this for up to 1 minute until the volume disappears
@@ -456,7 +458,7 @@ class AWSStaticAutoscaleTest(AWSAutoscaleTest):
 
         worker: "InstanceTypeDef" = next(wait_instances_running(boto3_ec2, [worker]))
 
-        bdm: Optional[list["InstanceBlockDeviceMappingTypeDef"]] = worker.get(
+        bdm: list["InstanceBlockDeviceMappingTypeDef"] | None = worker.get(
             "BlockDeviceMappings"
         )
         assert bdm is not None

toil/test/provisioners/clusterScalerTest.py

@@ -21,7 +21,6 @@ from argparse import Namespace
 from collections import defaultdict
 from queue import Empty, Queue
 from threading import Event, Thread
-from typing import Optional
 from unittest.mock import MagicMock
 
 from toil.batchSystems.abstractBatchSystem import (
@@ -975,9 +974,7 @@ class MockBatchSystemAndProvisioner(AbstractScalableBatchSystem, AbstractProvisi
         pass
 
     # AbstractProvisioner methods
-    def setAutoscaledNodeTypes(
-        self, node_types: list[tuple[set[Shape], Optional[float]]]
-    ):
+    def setAutoscaledNodeTypes(self, node_types: list[tuple[set[Shape], float | None]]):
         self.node_shapes_for_testing = sorted(it for t in node_types for it in t[0])
         super().setAutoscaledNodeTypes(node_types)
 
@@ -1040,7 +1037,7 @@ class MockBatchSystemAndProvisioner(AbstractScalableBatchSystem, AbstractProvisi
         return dict(self.jobBatchSystemIDToIssuedJob).values()
 
     # AbstractScalableBatchSystem functionality
-    def getNodes(self, preemptible: Optional[bool] = False, timeout: int = 600):
+    def getNodes(self, preemptible: bool | None = False, timeout: int = 600):
         nodes = dict()
         for node in self.nodesToWorker:
             if node.preemptible == preemptible:

toil/test/provisioners/clusterTest.py

@@ -15,7 +15,6 @@ import logging
 import os
 import subprocess
 import time
-from typing import Optional
 from uuid import uuid4
 
 from toil.lib.aws import zone_to_region
@@ -30,7 +29,6 @@ from toil.test import (
     needs_fetchable_appliance,
     slow,
 )
-
 from toil.test.cwl.cwlTest import TestCWLv12Conformance
 
 log = logging.getLogger(__name__)
@@ -193,7 +191,7 @@ class AbstractClusterTest(ToilTest):
         subprocess.check_call(cmd)
 
     @retry(errors=[subprocess.CalledProcessError], intervals=[1, 1])
-    def createClusterUtil(self, args: Optional[list[str]] = None) -> None:
+    def createClusterUtil(self, args: list[str] | None = None) -> None:
         args = [] if args is None else args
 
         command = [

toil/test/server/serverTest.py

@@ -25,7 +25,6 @@ from typing import TYPE_CHECKING, Optional
 from urllib.parse import urlparse
 
 try:
-    from flask import Flask
     from flask.testing import FlaskClient
     from werkzeug.test import TestResponse
 except ImportError:
@@ -33,7 +32,14 @@ except ImportError:
     # extra wasn't installed. We'll then skip them all.
     pass
 
-from toil.test import ToilTest, needs_aws_s3, needs_celery_broker, needs_cwl, needs_server, integrative
+from toil.test import (
+    ToilTest,
+    integrative,
+    needs_aws_s3,
+    needs_celery_broker,
+    needs_cwl,
+    needs_server,
+)
 
 logger = logging.getLogger(__name__)
 logging.basicConfig(level=logging.INFO)
@@ -195,10 +201,10 @@ class BucketUsingTest(ToilTest):
         from mypy_boto3_s3 import S3ServiceResource
         from mypy_boto3_s3.service_resource import Bucket
 
-    region: Optional[str]
+    region: str | None
     s3_resource: Optional["S3ServiceResource"]
     bucket: Optional["Bucket"]
-    bucket_name: Optional[str]
+    bucket_name: str | None
 
     @classmethod
     def setUpClass(cls) -> None:
@@ -292,12 +298,14 @@ class TrueDict(dict):
     Used as a workaround to set httpx post request encoding as recommended in
     <https://github.com/encode/httpx/discussions/2399#discussioncomment-3814186>.
     """
+
     def __bool__(self) -> bool:
         """
         Always say the object is truthy.
         """
         return True
 
+
 @needs_server
 class AbstractToilWESServerTest(ToilTest):
     """
@@ -557,6 +565,7 @@ class ToilWESServerBenchTest(AbstractToilWESServerTest):
         self.assertIn("system_state_counts", service_info)
         self.assertIn("tags", service_info)
 
+
 @needs_cwl
 class ToilWESServerWorkflowTest(AbstractToilWESServerTest):
     """

toil/test/sort/restart_sort.py

@@ -65,9 +65,7 @@ def down(job, inputFileStoreID, N, path, downCheckpoints, options, memory=sortMe
     length = os.path.getsize(inputFile)
     if length > N:
         # We will subdivide the file
-        RealtimeLogger.critical(
-            "Splitting file: %s of size: %s" % (inputFileStoreID, length)
-        )
+        RealtimeLogger.critical(f"Splitting file: {inputFileStoreID} of size: {length}")
         # Split the file into two copies
         midPoint = getMidPoint(inputFile, 0, length)
         t1 = job.fileStore.getLocalTempFile()
@@ -109,9 +107,7 @@ def down(job, inputFileStoreID, N, path, downCheckpoints, options, memory=sortMe
         ).rv()
     else:
         # We can sort this bit of the file
-        RealtimeLogger.critical(
-            "Sorting file: %s of size: %s" % (inputFileStoreID, length)
-        )
+        RealtimeLogger.critical(f"Sorting file: {inputFileStoreID} of size: {length}")
         # Sort the copy and write back to the fileStore
         shutil.copyfile(inputFile, inputFile + ".sort")
         sort(inputFile + ".sort")

toil/test/sort/sort.py

@@ -12,8 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""A demonstration of toil. Sorts the lines of a file into ascending order by doing a parallel merge sort.
-"""
+"""A demonstration of toil. Sorts the lines of a file into ascending order by doing a parallel merge sort."""
 import codecs
 import os
 import random
@@ -64,9 +63,7 @@ def down(job, inputFileStoreID, N, path, downCheckpoints, options, memory=sortMe
     length = os.path.getsize(inputFile)
     if length > N:
         # We will subdivide the file
-        RealtimeLogger.critical(
-            "Splitting file: %s of size: %s" % (inputFileStoreID, length)
-        )
+        RealtimeLogger.critical(f"Splitting file: {inputFileStoreID} of size: {length}")
         # Split the file into two copies
         midPoint = getMidPoint(inputFile, 0, length)
         t1 = job.fileStore.getLocalTempFile()
@@ -108,9 +105,7 @@ def down(job, inputFileStoreID, N, path, downCheckpoints, options, memory=sortMe
         ).rv()
     else:
         # We can sort this bit of the file
-        RealtimeLogger.critical(
-            "Sorting file: %s of size: %s" % (inputFileStoreID, length)
-        )
+        RealtimeLogger.critical(f"Sorting file: {inputFileStoreID} of size: {length}")
         # Sort the copy and write back to the fileStore
         shutil.copyfile(inputFile, inputFile + ".sort")
         sort(inputFile + ".sort")

toil/test/src/deferredFunctionTest.py

@@ -11,14 +11,13 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-from argparse import Namespace
-from collections.abc import Callable, Generator, Sequence
 import logging
 import os
-from pathlib import Path
 import signal
 import time
-from typing import Optional
+from argparse import Namespace
+from collections.abc import Callable, Generator, Sequence
+from pathlib import Path
 from uuid import uuid4
 
 import psutil
@@ -262,6 +261,7 @@ def _writeNonLocalFilesLambda(job: Job, files: tuple[Path, Path]) -> None:
     def lmd(x: Path, nlf: Path) -> None:
         x.unlink()
         nlf.unlink()
+
     for nlf in files:
         with nlf.open("wb") as nonLocalFileHandle:
             nonLocalFileHandle.write(os.urandom(1 * 1024 * 1024))
@@ -282,7 +282,7 @@ def _deferredFunctionRunsWithFailuresFn(job: Job, files: tuple[Path, Path]) -> N
         job.defer(_deleteFile, files[1])
 
 
-def _deleteFile(nonLocalFile: Path, nlf: Optional[Path] = None) -> None:
+def _deleteFile(nonLocalFile: Path, nlf: Path | None = None) -> None:
     """
     Delete nonLocalFile and nlf
     :param nonLocalFile:
@@ -350,7 +350,7 @@ def _testNewJobsCanHandleOtherJobDeaths_C(
 
 class _deleteMethods:
     @staticmethod
-    def _deleteFileMethod(nonLocalFile: Path, nlf: Optional[Path] = None) -> None:
+    def _deleteFileMethod(nonLocalFile: Path, nlf: Path | None = None) -> None:
         """
         Delete nonLocalFile and nlf
         """
@@ -360,7 +360,7 @@ class _deleteMethods:
 
     @classmethod
     def _deleteFileClassMethod(
-        cls, nonLocalFile: Path, nlf: Optional[Path] = None
+        cls, nonLocalFile: Path, nlf: Path | None = None
     ) -> None:
         """
         Delete nonLocalFile and nlf

toil/test/src/environmentTest.py

@@ -16,7 +16,6 @@ import os
 import time
 from argparse import Namespace
 from threading import Thread
-from typing import Optional
 
 from toil.common import Toil
 from toil.job import Job
@@ -87,7 +86,7 @@ def check_environment_repeatedly(job):
     check3 = waiter.addFollowOnJobFn(check_environment, "try3")
 
 
-def main(options: Optional[Namespace] = None):
+def main(options: Namespace | None = None):
     """
     Run the actual workflow with the given options.
     """

toil/test/src/fileStoreTest.py

@@ -95,7 +95,9 @@ class hidden:
             options.realTimeLogging = True
             options.workDir = self.work_dir
             options.clean = "always"
-            log_fd, options.logFile = tempfile.mkstemp(dir=self.work_dir, prefix="logFile")
+            log_fd, options.logFile = tempfile.mkstemp(
+                dir=self.work_dir, prefix="logFile"
+            )
             os.close(log_fd)
             return options
 
@@ -375,7 +377,7 @@ class hidden:
             Ensures that files imported to the leader preserve their executable permissions
             when they are read by the fileStore.
             """
-            
+
             for executable in True, False:
                 file_path = self.create_file(content="Hello", executable=executable)
                 initial_permissions = os.stat(file_path).st_mode & stat.S_IXUSR
@@ -537,9 +539,7 @@ class hidden:
                     # The options namespace and the Config object now have the exact same behavior
                     # which means parse_jobstore will be called with argparse rather than with the config object
                     # so remove the prepended file: scheme
-                    jobStoreDev = os.stat(
-                        os.path.dirname(options.jobStore[5:])
-                    ).st_dev
+                    jobStoreDev = os.stat(os.path.dirname(options.jobStore[5:])).st_dev
                 else:
                     jobStoreDev = os.stat(os.path.dirname(options.jobStore)).st_dev
                 if workDirDev == jobStoreDev:

toil/test/src/importExportFileTest.py

@@ -13,11 +13,13 @@
 # limitations under the License.
 
 
-from argparse import Namespace
 import os
-from pathlib import Path
 import stat
 import uuid
+from argparse import Namespace
+from pathlib import Path
+
+import pytest
 
 from toil.common import Toil
 from toil.exceptions import FailedJobsException
@@ -26,9 +28,6 @@ from toil.fileStores.abstractFileStore import AbstractFileStore
 from toil.job import Job
 from toil.test import pslow as slow
 
-import pytest
-from pytest_subtests import SubTests
-
 
 def create_file(tmp_path: Path, content: str, executable: bool = False) -> Path:
     file_path = tmp_path / str(uuid.uuid4())
@@ -109,7 +108,7 @@ class TestImportExportFile:
     def test_import_export_restart_false(self, tmp_path: Path) -> None:
         self._run_import_export_workflow(tmp_path, restart=False)
 
-    def test_basic_import_export(self, tmp_path: Path, subtests: SubTests) -> None:
+    def test_basic_import_export(self, tmp_path: Path, subtests: pytest.Subtests) -> None:
         """
         Ensures that uploaded files preserve their file permissions when they
         are downloaded again. This function checks that an imported executable file