isort everything

.isort.cfg

@@ -0,0 +1,2 @@
+[settings]
+profile = black

Makefile

@@ -35,6 +35,10 @@ deps: $(DEPS) ## install the dependencies
 lint: ## run linter script
 	parsl/tests/lint-inits.sh
 
+.PHONY: isort
+isort: ## run isort on all files
+	isort --check .
+
 .PHONY: flake8
 flake8:  ## run flake
 	flake8 parsl/
@@ -93,7 +97,7 @@ perf_test:
 	parsl-perf --time 5 --config parsl/tests/configs/local_threads.py
 
 .PHONY: test ## run all tests with all config types
-test: clean_coverage lint flake8 mypy local_thread_test htex_local_test htex_local_alternate_test wqex_local_test vineex_local_test radical_local_test config_local_test perf_test ## run all tests
+test: clean_coverage isort lint flake8 mypy local_thread_test htex_local_test htex_local_alternate_test wqex_local_test vineex_local_test radical_local_test config_local_test perf_test ## run all tests
 
 .PHONY: tag
 tag: ## create a tag in git. to run, do a 'make VERSION="version string" tag

docs/conf.py

@@ -19,9 +19,12 @@
 #
 import os
 import sys
+
 import requests
+
 sys.path.insert(0, os.path.abspath('../'))
 import parsl
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.

docs/teaching_scripts/test_apps.py

@@ -3,8 +3,8 @@
 
 import numpy as np
 
-from parsl import python_app, HighThroughputExecutor, Config
 import parsl
+from parsl import Config, HighThroughputExecutor, python_app
 
 parsl.load(Config(executors=[HighThroughputExecutor(label='htex_spawn', max_workers_per_node=1, address='127.0.0.1')]))
 

docs/userguide/examples/config.py

@@ -1,5 +1,5 @@
-from parsl.config import Config
 from parsl.channels import LocalChannel
+from parsl.config import Config
 from parsl.executors import HighThroughputExecutor
 from parsl.providers import LocalProvider
 

docs/userguide/examples/library.py

@@ -1,5 +1,6 @@
 from parsl import python_app
 
+
 @python_app
 def increment(x):
     return x + 1

docs/userguide/examples/run_increment.py

@@ -1,7 +1,8 @@
-import parsl
 from config import htex_config
 from library import increment
 
+import parsl
+
 parsl.load(htex_config)
 
 for i in range(5):

parsl/__init__.py

@@ -15,24 +15,23 @@
 
 """
 import logging
+import multiprocessing as _multiprocessing
 import os
 import platform
 
-from parsl.version import VERSION
 from parsl.app.app import bash_app, join_app, python_app
 from parsl.config import Config
-from parsl.executors import ThreadPoolExecutor
-from parsl.executors import HighThroughputExecutor
-from parsl.executors import WorkQueueExecutor
-from parsl.log_utils import set_stream_logger
-from parsl.log_utils import set_file_logger
-from parsl.monitoring import MonitoringHub
-
 from parsl.data_provider.files import File
-
 from parsl.dataflow.dflow import DataFlowKernel, DataFlowKernelLoader
+from parsl.executors import (
+    HighThroughputExecutor,
+    ThreadPoolExecutor,
+    WorkQueueExecutor,
+)
+from parsl.log_utils import set_file_logger, set_stream_logger
+from parsl.monitoring import MonitoringHub
+from parsl.version import VERSION
 
-import multiprocessing as _multiprocessing
 if platform.system() == 'Darwin':
     _multiprocessing.set_start_method('fork', force=True)
 

parsl/addresses.py

@@ -8,17 +8,19 @@
 
 import logging
 import platform
-import requests
 import socket
+
+import requests
+
 try:
     import fcntl
 except ImportError:
     fcntl = None  # type: ignore[assignment]
 import struct
-import typeguard
-import psutil
+from typing import Callable, List, Set
 
-from typing import Set, List, Callable
+import psutil
+import typeguard
 
 logger = logging.getLogger(__name__)
 

parsl/app/app.py

@@ -3,19 +3,16 @@
 The App class encapsulates a generic leaf task that can be executed asynchronously.
 """
 import logging
-import typeguard
 from abc import ABCMeta, abstractmethod
 from inspect import signature
-from typing import List, Optional, Sequence, Union
+from typing import Any, Callable, Dict, List, Optional, Sequence, Union
+
+import typeguard
 from typing_extensions import Literal
 
 from parsl.dataflow.dflow import DataFlowKernel
-
-from typing import Any, Callable, Dict
-
 from parsl.dataflow.futures import AppFuture
 
-
 logger = logging.getLogger(__name__)
 
 

parsl/app/bash.py

@@ -1,10 +1,9 @@
-from functools import update_wrapper
-from functools import partial
-from inspect import signature, Parameter
 import logging
+from functools import partial, update_wrapper
+from inspect import Parameter, signature
 
-from parsl.app.errors import wrap_error
 from parsl.app.app import AppBase
+from parsl.app.errors import wrap_error
 from parsl.data_provider.files import File
 from parsl.dataflow.dflow import DataFlowKernelLoader
 
@@ -17,6 +16,7 @@ def remote_side_bash_executor(func, *args, **kwargs):
     """
     import os
     import subprocess
+
     import parsl.app.errors as pe
     from parsl.utils import get_std_fname_mode
 

parsl/app/errors.py

@@ -1,10 +1,11 @@
 """Exceptions raised by Apps."""
+import logging
 from functools import wraps
-from typing import Callable, List, Optional, TypeVar, Union
-from typing_extensions import ParamSpec
 from types import TracebackType
-import logging
+from typing import Callable, List, Optional, TypeVar, Union
+
 from tblib import Traceback
+from typing_extensions import ParamSpec
 
 from parsl.data_provider.files import File
 from parsl.errors import ParslError
@@ -134,6 +135,7 @@ def wrap_error(func: Callable[P, R]) -> Callable[P, Union[R, RemoteExceptionWrap
     @wraps(func)
     def wrapper(*args: P.args, **kwargs: P.kwargs) -> Union[R, RemoteExceptionWrapper]:
         import sys
+
         from parsl.app.errors import RemoteExceptionWrapper
         try:
             return func(*args, **kwargs)

parsl/app/futures.py

@@ -1,12 +1,12 @@
 """This module implements DataFutures.
 """
 import logging
-import typeguard
 from concurrent.futures import Future
+from typing import Optional
 
-from parsl.data_provider.files import File
+import typeguard
 
-from typing import Optional
+from parsl.data_provider.files import File
 
 logger = logging.getLogger(__name__)
 

parsl/app/python.py

@@ -2,6 +2,7 @@
 import threading
 
 import tblib.pickling_support
+
 tblib.pickling_support.install()
 
 from functools import wraps
@@ -11,14 +12,14 @@
 from parsl.dataflow.dflow import DataFlowKernelLoader
 from parsl.utils import AutoCancelTimer
 
-
 logger = logging.getLogger(__name__)
 
 
 def timeout(f, seconds: float):
     @wraps(f)
     def wrapper(*args, **kwargs):
         import ctypes
+
         import parsl.app.errors
 
         def inject_exception(thread):

parsl/benchmark/perf.py

@@ -1,7 +1,8 @@
 import argparse
+import concurrent.futures
 import importlib
 import time
-import concurrent.futures
+
 import parsl
 
 min_iterations = 2

parsl/channels/__init__.py

@@ -1,7 +1,7 @@
 from parsl.channels.base import Channel
-from parsl.channels.ssh.ssh import SSHChannel
 from parsl.channels.local.local import LocalChannel
-from parsl.channels.ssh_il.ssh_il import SSHInteractiveLoginChannel
 from parsl.channels.oauth_ssh.oauth_ssh import OAuthSSHChannel
+from parsl.channels.ssh.ssh import SSHChannel
+from parsl.channels.ssh_il.ssh_il import SSHInteractiveLoginChannel
 
 __all__ = ['Channel', 'SSHChannel', 'LocalChannel', 'SSHInteractiveLoginChannel', 'OAuthSSHChannel']

parsl/channels/base.py

@@ -1,5 +1,4 @@
 from abc import ABCMeta, abstractmethod, abstractproperty
-
 from typing import Dict, Tuple
 
 

parsl/channels/errors.py

@@ -1,8 +1,9 @@
 ''' Exceptions raise by Apps.
 '''
-from parsl.errors import ParslError
 from typing import Optional
 
+from parsl.errors import ParslError
+
 
 class ChannelError(ParslError):
     """ Base class for all exceptions

parsl/channels/oauth_ssh/oauth_ssh.py

@@ -1,13 +1,14 @@
 import logging
-import paramiko
 import socket
 
-from parsl.errors import OptionalModuleMissing
+import paramiko
+
 from parsl.channels.ssh.ssh import SSHChannel
+from parsl.errors import OptionalModuleMissing
 
 try:
-    from oauth_ssh.ssh_service import SSHService
     from oauth_ssh.oauth_ssh_token import find_access_token
+    from oauth_ssh.ssh_service import SSHService
     _oauth_ssh_enabled = True
 except (ImportError, NameError):
     _oauth_ssh_enabled = False

parsl/channels/ssh/ssh.py

@@ -3,8 +3,16 @@
 import os
 
 import paramiko
+
 from parsl.channels.base import Channel
-from parsl.channels.errors import BadHostKeyException, AuthException, SSHException, BadScriptPath, BadPermsScriptPath, FileCopyException
+from parsl.channels.errors import (
+    AuthException,
+    BadHostKeyException,
+    BadPermsScriptPath,
+    BadScriptPath,
+    FileCopyException,
+    SSHException,
+)
 from parsl.utils import RepresentationMixin
 
 logger = logging.getLogger(__name__)

parsl/channels/ssh_il/ssh_il.py

@@ -2,6 +2,7 @@
 import logging
 
 import paramiko
+
 from parsl.channels.ssh.ssh import SSHChannel
 
 logger = logging.getLogger(__name__)

parsl/concurrent/__init__.py

@@ -1,8 +1,8 @@
 """Interfaces modeled after Python's `concurrent library <https://docs.python.org/3/library/concurrent.html>`_"""
-from typing import Callable, Dict, Optional, Iterator, Iterable
+import time
 from concurrent.futures import Executor
+from typing import Callable, Dict, Iterable, Iterator, Optional
 from warnings import warn
-import time
 
 from parsl import Config, DataFlowKernel
 from parsl.app.python import PythonApp

parsl/config.py

@@ -1,17 +1,17 @@
 import logging
-import typeguard
-
 from typing import Callable, Iterable, Optional, Sequence, Union
+
+import typeguard
 from typing_extensions import Literal
 
-from parsl.utils import RepresentationMixin
 from parsl.dataflow.dependency_resolvers import DependencyResolver
+from parsl.dataflow.taskrecord import TaskRecord
+from parsl.errors import ConfigurationError
 from parsl.executors.base import ParslExecutor
 from parsl.executors.threads import ThreadPoolExecutor
-from parsl.errors import ConfigurationError
-from parsl.dataflow.taskrecord import TaskRecord
 from parsl.monitoring import MonitoringHub
 from parsl.usage_tracking.api import UsageInformation
+from parsl.utils import RepresentationMixin
 
 logger = logging.getLogger(__name__)
 

parsl/configs/ASPIRE1.py

@@ -1,9 +1,9 @@
-from parsl.providers import PBSProProvider
-from parsl.launchers import MpiRunLauncher
+from parsl.addresses import address_by_interface
 from parsl.config import Config
 from parsl.executors import HighThroughputExecutor
-from parsl.addresses import address_by_interface
+from parsl.launchers import MpiRunLauncher
 from parsl.monitoring.monitoring import MonitoringHub
+from parsl.providers import PBSProProvider
 
 config = Config(
         executors=[

parsl/configs/Azure.py

@@ -1,14 +1,13 @@
 """Config for Azure"""
-from parsl.config import Config
+import getpass
 
-from parsl.providers import AzureProvider
-from parsl.executors import HighThroughputExecutor
-from parsl.data_provider.http import HTTPInTaskStaging
+from parsl.addresses import address_by_query
+from parsl.config import Config
 from parsl.data_provider.ftp import FTPInTaskStaging
+from parsl.data_provider.http import HTTPInTaskStaging
 from parsl.data_provider.rsync import RSyncStaging
-from parsl.addresses import address_by_query
-
-import getpass
+from parsl.executors import HighThroughputExecutor
+from parsl.providers import AzureProvider
 
 vm_reference = {
     # All fields below are required

parsl/configs/ad_hoc.py

@@ -1,8 +1,9 @@
-from parsl.providers import AdHocProvider
+from typing import Any, Dict
+
 from parsl.channels import SSHChannel
-from parsl.executors import HighThroughputExecutor
 from parsl.config import Config
-from typing import Any, Dict
+from parsl.executors import HighThroughputExecutor
+from parsl.providers import AdHocProvider
 
 user_opts: Dict[str, Dict[str, Any]]
 user_opts = {'adhoc':