Bump mypy from 1.6.1 to 1.7.0

contrib/mypy-stubs/configargparse/__init__.pyi

@@ -1,3 +1,3 @@
 from .configargparse import ArgParser as ArgParser
-from .configargparse import YAMLConfigFileParser as YAMLConfigFileParser
 from .configargparse import ArgumentParser as ArgumentParser
+from .configargparse import YAMLConfigFileParser as YAMLConfigFileParser

contrib/mypy-stubs/configargparse/configargparse.pyi

@@ -1,11 +1,7 @@
 import argparse
-from typing import Sequence, Any, TypeVar, OrderedDict
+from typing import Any, OrderedDict, Sequence, TypeVar
 
-__all__ = [
-    "ArgumentParser",
-    "YAMLConfigFileParser",
-    "ConfigFileParser"
-]
+__all__ = ["ArgumentParser", "YAMLConfigFileParser", "ConfigFileParser"]
 _N = TypeVar("_N")
 
 class ConfigFileParser(object):
@@ -16,17 +12,17 @@ class ConfigFileParser(object):
 class YAMLConfigFileParser(ConfigFileParser):
     def get_syntax_description(self) -> str: ...
     def parse(self, stream: Any) -> OrderedDict[Any, Any]: ...
-    def serialize(self, items: OrderedDict[Any, Any], default_flow_style: bool = ...) -> Any: ...
+    def serialize(
+        self, items: OrderedDict[Any, Any], default_flow_style: bool = ...
+    ) -> Any: ...
 
 class ArgumentParser(argparse.ArgumentParser):
     @property
     def _config_file_parser(self) -> Any: ...
-
     def __init__(self, *args: Any, **kwargs: Any) -> None: ...
     # There may be a better way of type hinting this without a type: ignore, but mypy gets unhappy pretty much no matter what as the signatures for parse_args doesn't match with its superclass in argparse
-    def parse_args(self, args: Sequence[str] | None = None, namespace: Namespace | None = None, config_file_contents: str | None = None, env_vars: Any=None) -> Namespace: ... # type: ignore[override]
-
+    def parse_args(self, args: Sequence[str] | None = None, namespace: Namespace | None = None, config_file_contents: str | None = None, env_vars: Any = None) -> Namespace: ...  # type: ignore[override]
     def get_source_to_settings_dict(self) -> OrderedDict[Any, Any]: ...
 
 Namespace = argparse.Namespace
-ArgParser = ArgumentParser
+ArgParser = ArgumentParser

requirements-dev.txt

@@ -11,7 +11,7 @@ astroid>=2.15,<3
 sphinx-autodoc-typehints>=1.24.0,<2
 sphinxcontrib-autoprogram==0.1.8
 cwltest>=2.2.20211116163652
-mypy==1.6.1
+mypy==1.7.0
 types-requests
 types-setuptools
 types-boto

setup.py

@@ -12,9 +12,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 # import imp
+import os
 import types
 from importlib.machinery import SourceFileLoader
-import os
 from tempfile import NamedTemporaryFile
 
 from setuptools import find_packages, setup

src/toil/__init__.py

@@ -20,6 +20,7 @@
 import time
 from datetime import datetime
 from typing import TYPE_CHECKING, Optional, Tuple
+
 import requests
 from pytz import timezone
 

src/toil/batchSystems/abstractBatchSystem.py

@@ -15,19 +15,19 @@
 import logging
 import os
 import shutil
+import time
 from abc import ABC, abstractmethod
 from argparse import ArgumentParser, _ArgumentGroup
 from contextlib import contextmanager
 from threading import Condition
-import time
 from typing import (Any,
                     ContextManager,
                     Dict,
-                    List,
-                    Set,
                     Iterator,
+                    List,
                     NamedTuple,
                     Optional,
+                    Set,
                     Union,
                     cast)
 
@@ -135,7 +135,6 @@ def set_message_bus(self, message_bus: MessageBus) -> None:
         bus, so that it can send informational messages about the jobs it is
         running to other Toil components.
         """
-        pass
 
     @abstractmethod
     def issueBatchJob(self, jobDesc: JobDescription, job_environment: Optional[Dict[str, str]] = None) -> int:
@@ -264,7 +263,6 @@ def setOptions(cls, setOption: OptionSetter) -> None:
             setOption(option_name, parsing_function=None, check_function=None, default=None, env=None)
             returning nothing, used to update run configuration as a side effect.
         """
-        pass
 
     def getWorkerContexts(self) -> List[ContextManager[Any]]:
         """

src/toil/batchSystems/abstractGridEngineBatchSystem.py

@@ -17,13 +17,13 @@
 from datetime import datetime
 from queue import Empty, Queue
 from threading import Lock, Thread
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 from toil.batchSystems.abstractBatchSystem import (BatchJobExitReason,
                                                    UpdatedBatchJobInfo)
 from toil.batchSystems.cleanup_support import BatchSystemCleanupSupport
 from toil.bus import ExternalBatchIdMessage
-from toil.job import JobDescription, AcceleratorRequirement
+from toil.job import AcceleratorRequirement
 from toil.lib.misc import CalledProcessErrorStderr
 
 logger = logging.getLogger(__name__)

src/toil/batchSystems/awsBatch.py

@@ -34,25 +34,25 @@
 import time
 import uuid
 from argparse import ArgumentParser, _ArgumentGroup
-from typing import Any, Callable, Dict, Iterator, List, Optional, Set, Union
+from typing import Any, Dict, Iterator, List, Optional, Set, Union
 
 from boto.exception import BotoServerError
 
 from toil import applianceSelf
 from toil.batchSystems.abstractBatchSystem import (EXIT_STATUS_UNAVAILABLE_VALUE,
                                                    BatchJobExitReason,
-                                                   UpdatedBatchJobInfo,
-                                                   InsufficientSystemResources)
-from toil.batchSystems.options import OptionSetter
+                                                   InsufficientSystemResources,
+                                                   UpdatedBatchJobInfo)
 from toil.batchSystems.cleanup_support import BatchSystemCleanupSupport
 from toil.batchSystems.contained_executor import pack_job
-from toil.bus import ExternalBatchIdMessage, MessageBus, MessageOutbox
+from toil.batchSystems.options import OptionSetter
+from toil.bus import ExternalBatchIdMessage
 from toil.common import Config, Toil
 from toil.job import JobDescription, Requirer
-from toil.lib.aws import get_current_aws_region, zone_to_region
+from toil.lib.aws import get_current_aws_region
 from toil.lib.aws.session import establish_boto3_session
-from toil.lib.conversions import b_to_mib, mib_to_b
-from toil.lib.misc import slow_down, unix_now_ms, utc_now
+from toil.lib.conversions import b_to_mib
+from toil.lib.misc import slow_down, unix_now_ms
 from toil.lib.retry import retry
 from toil.resource import Resource
 

src/toil/batchSystems/htcondor.py

@@ -24,7 +24,6 @@
 
 from toil.batchSystems.abstractGridEngineBatchSystem import \
     AbstractGridEngineBatchSystem
-
 from toil.job import AcceleratorRequirement
 from toil.lib.retry import retry
 

src/toil/batchSystems/kubernetes.py

@@ -24,22 +24,22 @@
 import logging
 import math
 import os
-from queue import Empty, Queue
 import string
 import sys
 import tempfile
-from threading import Event, Thread, Condition, RLock
 import time
 import uuid
 from argparse import ArgumentParser, _ArgumentGroup
+from queue import Empty, Queue
+from threading import Condition, Event, RLock, Thread
 from typing import (Any,
                     Callable,
                     Dict,
                     Iterator,
                     List,
-                    Set,
                     Literal,
                     Optional,
+                    Set,
                     Tuple,
                     Type,
                     TypeVar,
@@ -104,7 +104,7 @@
 from toil.batchSystems.cleanup_support import BatchSystemCleanupSupport
 from toil.batchSystems.contained_executor import pack_job
 from toil.batchSystems.options import OptionSetter
-from toil.common import Config, Toil, SYS_MAX_SIZE
+from toil.common import SYS_MAX_SIZE, Config, Toil
 from toil.job import JobDescription, Requirer
 from toil.lib.conversions import human2bytes
 from toil.lib.misc import get_user_name, slow_down, utc_now

src/toil/batchSystems/mesos/batchSystem.py

@@ -18,11 +18,9 @@
 import pickle
 import pwd
 import socket
-import sys
 import time
 import traceback
 from argparse import ArgumentParser, _ArgumentGroup
-from contextlib import contextmanager
 from queue import Empty, Queue
 from typing import Dict, Optional, Union
 from urllib.parse import quote_plus

src/toil/batchSystems/options.py

@@ -14,16 +14,16 @@
 import logging
 import sys
 from argparse import ArgumentParser, _ArgumentGroup
-from typing import Any, Callable, List, Optional, TypeVar, Union, cast
+from typing import Any, Callable, List, Optional, TypeVar, Union
 
 if sys.version_info >= (3, 8):
     from typing import Protocol
 else:
     from typing_extensions import Protocol
 
-from toil.batchSystems.registry import (get_batch_system,
-                                        get_batch_systems,
-                                        DEFAULT_BATCH_SYSTEM)
+from toil.batchSystems.registry import (DEFAULT_BATCH_SYSTEM,
+                                        get_batch_system,
+                                        get_batch_systems)
 from toil.lib.threading import cpu_count
 
 logger = logging.getLogger(__name__)
@@ -81,6 +81,7 @@ def set_batchsystem_options(batch_system: Optional[str], set_option: OptionSette
 
 def add_all_batchsystem_options(parser: Union[ArgumentParser, _ArgumentGroup]) -> None:
     from toil.common import SYS_MAX_SIZE
+
     # Do the global cross-batch-system arguments
     parser.add_argument(
         "--batchSystem",

src/toil/batchSystems/parasol.py

@@ -22,7 +22,7 @@
 from queue import Empty, Queue
 from shutil import which
 from threading import Thread
-from typing import Dict, Optional, Union, Type, Any
+from typing import Dict, Optional, Union
 
 from toil.batchSystems.abstractBatchSystem import (BatchSystemSupport,
                                                    UpdatedBatchJobInfo)

src/toil/batchSystems/registry.py

@@ -13,8 +13,8 @@
 # limitations under the License.
 
 import importlib
-import pkgutil
 import logging
+import pkgutil
 import warnings
 from typing import TYPE_CHECKING, Callable, Dict, List, Sequence, Tuple, Type
 

src/toil/batchSystems/singleMachine.py

@@ -22,23 +22,25 @@
 from argparse import ArgumentParser, _ArgumentGroup
 from queue import Empty, Queue
 from threading import Event, Lock, Thread
-from typing import Dict, List, Optional, Set, Sequence, Tuple, Union
+from typing import Dict, List, Optional, Sequence, Set, Tuple, Union
 
 import toil
 from toil import worker as toil_worker
 from toil.batchSystems.abstractBatchSystem import (EXIT_STATUS_UNAVAILABLE_VALUE,
                                                    BatchSystemSupport,
+                                                   InsufficientSystemResources,
                                                    ResourcePool,
                                                    ResourceSet,
-                                                   UpdatedBatchJobInfo,
-                                                   InsufficientSystemResources)
-
-from toil.bus import ExternalBatchIdMessage
+                                                   UpdatedBatchJobInfo)
 from toil.batchSystems.options import OptionSetter
-
+from toil.bus import ExternalBatchIdMessage
 from toil.common import SYS_MAX_SIZE, Config, Toil, make_open_interval_action
-from toil.job import JobDescription, AcceleratorRequirement, accelerator_satisfies, Requirer
-from toil.lib.accelerators import get_individual_local_accelerators, get_restrictive_environment_for_local_accelerators
+from toil.job import (AcceleratorRequirement,
+                      JobDescription,
+                      Requirer,
+                      accelerator_satisfies)
+from toil.lib.accelerators import (get_individual_local_accelerators,
+                                   get_restrictive_environment_for_local_accelerators)
 from toil.lib.threading import cpu_count
 
 logger = logging.getLogger(__name__)

src/toil/batchSystems/slurm.py

@@ -16,13 +16,13 @@
 import os
 from argparse import ArgumentParser, _ArgumentGroup
 from shlex import quote
-from typing import Callable, Dict, List, Optional, TypeVar, Union
+from typing import Dict, List, Optional, TypeVar, Union
 
 from toil.batchSystems.abstractGridEngineBatchSystem import \
     AbstractGridEngineBatchSystem
 from toil.batchSystems.options import OptionSetter
-from toil.lib.misc import CalledProcessErrorStderr, call_command
 from toil.job import Requirer
+from toil.lib.misc import CalledProcessErrorStderr, call_command
 
 logger = logging.getLogger(__name__)
 

src/toil/batchSystems/torque.py

@@ -16,7 +16,6 @@
 import os
 import shlex
 import tempfile
-import time
 from queue import Empty
 from shlex import quote
 from typing import Dict, List, Optional

src/toil/bus.py

@@ -61,15 +61,13 @@
 """
 
 import collections
-from dataclasses import dataclass
-import inspect
+import json
 import logging
-
 import os
 import queue
-import json
 import tempfile
 import threading
+from dataclasses import dataclass
 from typing import (IO,
                     Any,
                     Callable,
@@ -80,7 +78,6 @@
                     Optional,
                     Type,
                     TypeVar,
-                    Union,
                     cast)
 
 from pubsub.core import Publisher