cleanups

Author: mr-c

cwltool/executors.py

@@ -144,9 +144,11 @@ def run_jobs(self,
                         else:
                             runtimeContext.prov_obj = job.prov_obj
                         assert runtimeContext.prov_obj
-                        process_run_id, reference_locations = runtimeContext.prov_obj._evaluate(
-                            process, job, job_order_object,
-                            runtimeContext.make_fs_access, runtimeContext)
+                        process_run_id, reference_locations = \
+                                runtimeContext.prov_obj.evaluate(
+                                        process, job, job_order_object,
+                                        runtimeContext.make_fs_access,
+                                        runtimeContext)
                         runtimeContext = runtimeContext.copy()
                         runtimeContext.process_run_id = process_run_id
                         runtimeContext.reference_locations = \

cwltool/provenance.py

@@ -422,13 +422,13 @@ def host_provenance(document):
             self.workflow_run_uri, None, self.engine_uuid, datetime.datetime.now())
         return (self.workflow_run_uri, self.document)
 
-    def _evaluate(self,
-                  process,                 # type: Process
-                  job,                 # type: Any
-                  job_order_object,  # type: Dict[Text, Text]
-                  make_fs_access,    # type: Callable[[Text], StdFsAccess]
-                  runtimeContext     # type: RuntimeContext
-                 ):  # type: (...) -> Tuple[Optional[str], Dict[Text, Text]]
+    def evaluate(self,
+                 process,           # type: Process
+                 job,               # type: Any
+                 job_order_object,  # type: Dict[Text, Text]
+                 make_fs_access,    # type: Callable[[Text], StdFsAccess]
+                 runtimeContext     # type: RuntimeContext
+                ):  # type: (...) -> Tuple[Optional[str], Dict[Text, Text]]
         '''
         evaluate the nature of r and
         initialize the activity start

cwltool/utils.py

@@ -6,6 +6,7 @@
 import platform
 import shutil
 import stat
+import pkg_resources
 from functools import partial  # pylint: disable=unused-import
 from typing import (IO, Any, AnyStr, Callable,  # pylint: disable=unused-import
                     Dict, Iterable, List, Optional, Text, Tuple, TypeVar,
@@ -22,7 +23,6 @@
     import subprocess32 as subprocess  # type: ignore # pylint: disable=import-error,unused-import
 else:
     import subprocess  # type: ignore # pylint: disable=unused-import
-import pkg_resources
 
 windows_default_container_id = "frolvlad/alpine-bash"
 
@@ -40,8 +40,7 @@ def versionstring():
     pkg = pkg_resources.require("cwltool")
     if pkg:
         return u"%s %s" % (sys.argv[0], pkg[0].version)
-    else:
-        return u"%s %s" % (sys.argv[0], "unknown version")
+    return u"%s %s" % (sys.argv[0], "unknown version")
 
 def aslist(l):  # type: (Any) -> List[Any]
     if isinstance(l, list):

cwltool/workflow.py

@@ -478,8 +478,8 @@ def job(self,
 
         if not self.did_callback:
             self.do_output_callback(output_callback)  # could have called earlier on line 336;
-            #depends which one comes first. All steps are completed 
-            #or all outputs have beend produced.
+            #depends which one comes first. All steps are completed
+            #or all outputs have been produced.
 
 class Workflow(Process):
     def __init__(self,
@@ -506,7 +506,7 @@ def __init__(self,
         for index, step in enumerate(self.tool.get("steps", [])):
             try:
                 self.steps.append(WorkflowStep(step, index, loadingContext,
-                                  loadingContext.prov_obj))
+                                               loadingContext.prov_obj))
             except validate.ValidationException as vexc:
                 if _logger.isEnabledFor(logging.DEBUG):
                     _logger.exception("Validation failed at")