Merge pull request #739 from ghisvail/bug/workflow-fixes

FIX: Add environment argument to TaskBase._run_task() and Workflow subclass

pydra/engine/core.py

@@ -380,7 +380,7 @@ def can_resume(self):
         return self._can_resume
 
     @abc.abstractmethod
-    def _run_task(self):
+    def _run_task(self, environment=None):
         pass
 
     @property
@@ -1329,7 +1329,7 @@ async def _run(self, submitter=None, rerun=False, **kwargs):
         self._check_for_hash_changes()
         return result
 
-    async def _run_task(self, submitter, rerun=False):
+    async def _run_task(self, submitter, rerun=False, environment=None):
         if not submitter:
             raise Exception("Submitter should already be set.")
         for nd in self.graph.nodes:

pydra/engine/submitter.py

@@ -90,7 +90,6 @@ async def submit_from_call(self, runnable, rerun, environment):
             # 2
             if runnable.state is None:
                 # run_el should always return a coroutine
-                print("in SUBM", environment)
                 await self.worker.run_el(runnable, rerun=rerun, environment=environment)
             # 3
             else: