Fix more tests

Author: Peter Amstutz

cwltool/job.py

@@ -523,7 +523,6 @@ def _job_popen(
         if stderr_path is not None:
             stderr = open(stderr_path, "wb")
 
-        print("ZZZ", commands)
         sproc = subprocess.Popen(commands,
                                  shell=False,
                                  close_fds=not onWindows(),

cwltool/pack.py

@@ -178,7 +178,7 @@ def rewrite_id(r, mainuri):
         if isinstance(dcr, CommentedSeq):
             dcr = dcr[0]
             dcr = cast(CommentedMap, dcr)
-        if not isinstance(dcr, dict):
+        if not isinstance(dcr, MutableMapping):
             continue
         for doc in (dcr, metadata):
             if "$schemas" in doc:

cwltool/workflow.py

@@ -602,11 +602,13 @@ def __init__(self,
 
         loadingContext = loadingContext.copy()
 
-        loadingContext.requirements = (getdefault(loadingContext.requirements, []) +
-                                  toolpath_object.get("requirements", []) +
-                                  get_overrides(getdefault(loadingContext.overrides_list, []),
+        loadingContext.requirements = copy.deepcopy(getdefault(loadingContext.requirements, []))
+        loadingContext.requirements.extend(toolpath_object.get("requirements", []))
+        loadingContext.requirements.extend(get_overrides(getdefault(loadingContext.overrides_list, []),
                                                 self.id).get("requirements", []))
-        loadingContext.hints = getdefault(loadingContext.hints, []) + toolpath_object.get("hints", [])
+
+        loadingContext.hints = copy.deepcopy(getdefault(loadingContext.hints, []))
+        loadingContext.hints.extend(toolpath_object.get("hints", []))
 
         try:
             if isinstance(toolpath_object["run"], MutableMapping):