sort imports

Author: mr-c

cwltool/builder.py

@@ -9,7 +9,7 @@
 
 from cwl_utils import expression
 from cwl_utils.file_formats import check_format
-from cwl_utils.types import CWLObjectType, CWLOutputType, CWLDirectoryType, CWLFileType
+from cwl_utils.types import CWLDirectoryType, CWLFileType, CWLObjectType, CWLOutputType
 from mypy_extensions import mypyc_attr
 from rdflib import Graph
 from ruamel.yaml.comments import CommentedMap

cwltool/command_line_tool.py

@@ -25,10 +25,10 @@
 from typing import TYPE_CHECKING, Any, Optional, TextIO, Union, cast
 
 from cwl_utils.types import (
-    CWLObjectType,
-    CWLOutputType,
     CWLDirectoryType,
     CWLFileType,
+    CWLObjectType,
+    CWLOutputType,
     is_directory,
     is_file,
     is_file_or_directory,

cwltool/cwlprov/provenance_profile.py

@@ -6,13 +6,26 @@
 from collections.abc import MutableMapping, MutableSequence, Sequence
 from io import BytesIO
 from pathlib import PurePath, PurePosixPath
-from typing import Any, TYPE_CHECKING, TypedDict, cast
-
-from cwl_utils.types import CWLDirectoryType, CWLFileType, CWLObjectType, is_directory, is_file
+from typing import TYPE_CHECKING, Any, TypedDict, cast
+
+from cwl_utils.types import (
+    CWLDirectoryType,
+    CWLFileType,
+    CWLObjectType,
+    is_directory,
+    is_file,
+)
 from prov.identifier import Identifier, QualifiedName
 from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity
 from schema_salad.sourceline import SourceLine
 
+from ..errors import WorkflowException
+from ..job import CommandLineJob, JobBase
+from ..loghandler import _logger
+from ..process import Process, shortname
+from ..stdfsaccess import StdFsAccess
+from ..utils import JobsType, get_listing, posix_path, versionstring
+from ..workflow_job import WorkflowJob
 from .provenance_constants import (
     ACCOUNT_UUID,
     CWLPROV,
@@ -30,13 +43,6 @@
     WFPROV,
 )
 from .writablebagfile import create_job, write_bag_file  # change this later
-from ..errors import WorkflowException
-from ..job import CommandLineJob, JobBase
-from ..loghandler import _logger
-from ..process import Process, shortname
-from ..stdfsaccess import StdFsAccess
-from ..utils import JobsType, get_listing, posix_path, versionstring
-from ..workflow_job import WorkflowJob
 
 if TYPE_CHECKING:
     from .ro import ResearchObject

cwltool/cwlprov/ro.py

@@ -26,12 +26,7 @@
 
 from ..loghandler import _logger
 from ..stdfsaccess import StdFsAccess
-from ..utils import (
-    create_tmp_dir,
-    local_path,
-    posix_path,
-    versionstring,
-)
+from ..utils import create_tmp_dir, local_path, posix_path, versionstring
 from . import Aggregate, Annotation, AuthoredBy, _valid_orcid, _whoami, checksum_copy
 from .provenance_constants import (
     ACCOUNT_UUID,

cwltool/docker.py

@@ -14,7 +14,7 @@
 from typing import Optional, cast
 
 import requests
-from cwl_utils.types import CWLObjectType, CWLDirectoryType, CWLFileType
+from cwl_utils.types import CWLDirectoryType, CWLFileType, CWLObjectType
 
 from .builder import Builder
 from .context import RuntimeContext

cwltool/job.py

@@ -21,7 +21,7 @@
 from typing import IO, TYPE_CHECKING, Optional, TextIO, Union, cast
 
 import psutil
-from cwl_utils.types import CWLObjectType, CWLOutputType, CWLDirectoryType, CWLFileType
+from cwl_utils.types import CWLDirectoryType, CWLFileType, CWLObjectType, CWLOutputType
 from prov.model import PROV
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dump, json_dumps

cwltool/main.py

@@ -23,7 +23,13 @@
 import coloredlogs
 import requests
 import ruamel.yaml
-from cwl_utils.types import CWLDirectoryType, CWLFileType, CWLObjectType, CWLOutputType, is_file
+from cwl_utils.types import (
+    CWLDirectoryType,
+    CWLFileType,
+    CWLObjectType,
+    CWLOutputType,
+    is_file,
+)
 from rich_argparse import RichHelpFormatter
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from ruamel.yaml.main import YAML

cwltool/process.py

@@ -28,10 +28,10 @@
 
 from cwl_utils import expression
 from cwl_utils.types import (
-    CWLObjectType,
-    CWLOutputType,
     CWLDirectoryType,
     CWLFileType,
+    CWLObjectType,
+    CWLOutputType,
     is_directory,
     is_file,
     is_file_or_directory,

cwltool/singularity.py

@@ -13,7 +13,7 @@
 from subprocess import check_call, check_output  # nosec
 from typing import cast
 
-from cwl_utils.types import CWLObjectType, CWLDirectoryType, CWLFileType
+from cwl_utils.types import CWLDirectoryType, CWLFileType, CWLObjectType
 from packaging.version import Version
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dumps

cwltool/workflow.py

@@ -22,12 +22,7 @@
 from .load_tool import load_tool
 from .loghandler import _logger
 from .process import Process, get_overrides, shortname
-from .utils import (
-    JobsGeneratorType,
-    OutputCallbackType,
-    StepType,
-    aslist,
-)
+from .utils import JobsGeneratorType, OutputCallbackType, StepType, aslist
 from .workflow_job import WorkflowJob