swap setpgrp to setsid

for some reason, setsid does NOT hang when using
containerized seqtk, while setpgrp does.
in the future, when dropping python2 support,
should probably switch to the start_new_session
option instead

docs/changelog.md

@@ -1,15 +1,18 @@
 # Changelog
 
-## [0.12.0] -- unreleased
+## [0.12.0] -- 2019-08-02
+
 ### Added
 - Use profile to determine total elapsed time
 - `logging` functions directly on `PipelineManager`
 - Re-export `add_logging_options` from `logmuse`, for direct use by a pipeline author.
 - `logger_via_cli` that defaults to the `strict=False` behavior of the same-named function from `logmuse`
+- Use logging for pypiper-generated output.
+
 ### Fixed
 - Fix childless processes memory monitoring issue
 - Fix problems with runtime reading from pipeline profile TSV formatted according to two styles
-
+- Fix problems running containerized executables that would sometimes hang
 
 ## [0.11.3] -- 2019-06-17
 ### Fixed

pypiper/manager.py

@@ -930,10 +930,10 @@ def make_hash(o):
         for i in range(len(param_list)):
             running_processes.append(i)
             if i == 0:
-                processes.append(psutil.Popen(preexec_fn=os.setpgrp, **param_list[i]))
+                processes.append(psutil.Popen(preexec_fn=os.setsid, **param_list[i]))
             else:
                 param_list[i]["stdin"] = processes[i - 1].stdout
-                processes.append(psutil.Popen(preexec_fn=os.setpgrp, **param_list[i]))
+                processes.append(psutil.Popen(preexec_fn=os.setsid, **param_list[i]))
             self.running_procs[processes[-1].pid] = {
                 "proc_name": get_proc_name(param_list[i]["args"]),
                 "start_time": start_time,
@@ -991,9 +991,11 @@ def proc_wrapup(i):
         sleeptime = .0001
 
         while running_processes:
+            self.debug("running")
             for i in running_processes:
                 local_maxmems[i] = max(local_maxmems[i], (get_mem_child_sum(processes[i])))
                 self.peak_memory = max(self.peak_memory, local_maxmems[i])
+                self.debug(processes[i])
                 if not self._attend_process(processes[i], sleeptime):
                     proc_wrapup_text[i] = proc_wrapup(i)