cleanups

Author: mr-c

cwltool/errors.py

@@ -8,10 +8,8 @@
 
 # flake8: noqa: F401
 
-from cwl_utils.errors import WorkflowException as WorkflowException
-
-
 from cwl_utils.errors import GraphTargetMissingException as GraphTargetMissingException
+from cwl_utils.errors import WorkflowException as WorkflowException
 
 
 class UnsupportedRequirement(WorkflowException):

cwltool/job.py

@@ -461,7 +461,11 @@ def stderr_stdout_log_path(
                 with runtimeContext.workflow_eval_lock:
                     self.output_callback(outputs, processStatus)
 
-            if runtimeContext.rm_tmpdir and self.stagedir is not None and os.path.exists(self.stagedir):
+            if (
+                runtimeContext.rm_tmpdir
+                and self.stagedir is not None
+                and os.path.exists(self.stagedir)
+            ):
                 _logger.debug(
                     "[job %s] Removing input staging directory %s",
                     self.name,
@@ -889,7 +893,6 @@ def docker_monitor(
         kill_switch: threading.Event,
     ) -> None:
         """Record memory usage of the running Docker container. Terminate if kill_switch is activated."""
-
         ks_tm: "Optional[Timer]" = None
         cid: Optional[str] = None
 

cwltool/update.py

@@ -11,12 +11,11 @@
     cast,
 )
 
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import Loader
 from schema_salad.sourceline import SourceLine
 
-from ruamel.yaml.comments import CommentedMap, CommentedSeq
-
 from .loghandler import _logger
 from .utils import CWLObjectType, CWLOutputType, aslist, visit_class, visit_field
 

tests/test_path_checks.py

@@ -7,14 +7,14 @@
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.sourceline import cmap
 
+from cwltool.builder import content_limit_respected_read
 from cwltool.command_line_tool import CommandLineTool
 from cwltool.context import LoadingContext, RuntimeContext
+from cwltool.errors import WorkflowException
 from cwltool.main import main
 from cwltool.stdfsaccess import StdFsAccess
 from cwltool.update import INTERNAL_VERSION
-from cwltool.utils import CWLObjectType, CONTENT_LIMIT, bytes2str_in_dicts
-from cwltool.builder import content_limit_respected_read
-from cwltool.errors import WorkflowException
+from cwltool.utils import CONTENT_LIMIT, CWLObjectType, bytes2str_in_dicts
 
 from .util import needs_docker