MyPy fixes.

Author: Peter Amstutz

cwltool/context.py

@@ -101,7 +101,7 @@ def __init__(self, kwargs=None):
         self.docker_stagedir = ""       # type: Text
         self.js_console = False         # type: bool
         self.job_script_provider = None  # type: Optional[DependenciesConfiguration]
-        self.select_resources = None    # type: Optional[Callable[[Dict[Text, int]], Dict[Text, int]]]
+        self.select_resources = None    # type: Optional[Callable[[Dict[Text, int], RuntimeContext], Dict[Text, int]]]
         self.eval_timeout = 20          # type: float
         self.postScatterEval = None     # type: Optional[Callable[[Dict[Text, Any]], Dict[Text, Any]]]
         self.on_error = "stop"          # type: Text
@@ -110,7 +110,7 @@ def __init__(self, kwargs=None):
         self.cidfile_dir = None
         self.cidfile_prefix = None
 
-        self.workflow_eval_lock = None  # type: threading.Condition
+        self.workflow_eval_lock = None  # type: Optional[threading.Condition]
 
         super(RuntimeContext, self).__init__(kwargs)
 

cwltool/executors.py

@@ -140,7 +140,7 @@ def __init__(self):  # type: () -> None
         super(MultithreadedJobExecutor, self).__init__()
         self.threads = set()  # type: Set[threading.Thread]
         self.exceptions = []  # type: List[WorkflowException]
-        self.pending_jobs = []
+        self.pending_jobs = []  # type: List[JobBase]
 
         self.max_ram = psutil.virtual_memory().total / 2**20
         self.max_cores = psutil.cpu_count()
@@ -207,9 +207,10 @@ def runner():
                 self.allocated_cores += job.builder.resources["cores"]
             thread.start()
 
-    def wait_for_next_completion(self, runtimeContext):  # type: () -> None
+    def wait_for_next_completion(self, runtimeContext):  # type: (RuntimeContext) -> None
         """ Wait for jobs to finish. """
-        runtimeContext.workflow_eval_lock.wait()
+        if runtimeContext.workflow_eval_lock is not None:
+            runtimeContext.workflow_eval_lock.wait()
         if self.exceptions:
             raise self.exceptions[0]
 
@@ -222,6 +223,9 @@ def run_jobs(self,
 
         jobiter = process.job(job_order_object, self.output_callback, runtimeContext)
 
+        if runtimeContext.workflow_eval_lock is None:
+            raise WorkflowException("runtimeContext.workflow_eval_lock must not be None")
+
         runtimeContext.workflow_eval_lock.acquire()
         for job in jobiter:
             if job is not None:

cwltool/job.py

@@ -324,6 +324,9 @@ def _execute(self,
                                 host_outdir, p.target[len(container_outdir)+1:])
                         os.remove(host_outdir_tgt)
 
+        if runtimeContext.workflow_eval_lock is None:
+            raise WorkflowException("runtimeContext.workflow_eval_lock must not be None")
+
         with runtimeContext.workflow_eval_lock:
             self.output_callback(outputs, processStatus)