changes p.stdout.read to communicate()

src/watts/fileutils.py

@@ -84,7 +84,7 @@ class tee_stderr(_TeeStream):
     _stream = "stderr"
 
 
-def run(args):
+def run(args, wait=None):
     """Function that mimics subprocess.run but actually writes to sys.stdout and
     sys.stderr (not the same as the underlying file descriptors)
 
@@ -94,15 +94,16 @@ def run(args):
     p = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
                          universal_newlines=True)
 
-    while True:
-        select.select([p.stdout, p.stderr], [], [])
+    select.select([p.stdout, p.stderr], [], [])
 
-        stdout_data = p.stdout.read()
-        stderr_data = p.stderr.read()
-        if stdout_data:
-            sys.stdout.write(stdout_data)
-        if stderr_data:
-            sys.stderr.write(stderr_data)
+    try:
+        stdout_data, stderr_data = p.communicate(timeout=wait)
+    except subprocess.TimeoutExpired:
+        p.kill()
+        stdout_data, stderr_data = p.communicate()
 
-        if p.poll() is not None:
-            break
+    if stdout_data:
+        sys.stdout.write(stdout_data)
+
+    if stderr_data:
+        sys.stderr.write(stderr_data)

src/watts/plugin.py

@@ -223,7 +223,8 @@ def postrun(self, params: Parameters, name: str, **kwargs) -> Results:
         return results_cls(params, name, time, inputs, outputs, **kwargs)
 
     def run(self, mpi_args: Optional[List[str]] = None,
-            extra_args: Optional[List[str]] = None):
+            extra_args: Optional[List[str]] = None, 
+            wait: Optional[int] = 60):
         """Run plugin
 
         Parameters
@@ -234,9 +235,13 @@ def run(self, mpi_args: Optional[List[str]] = None,
         extra_args
             Additional command-line arguments to append after the main command
 
+        wait 
+            The time in seconds that `watts` will wait before terminating the process.
+            Default is 60 seconds.
+
         """
         if mpi_args is None:
             mpi_args = []
         if extra_args is None:
             extra_args = []
-        run_proc(mpi_args + self.execute_command + extra_args)
+        run_proc(mpi_args + self.execute_command + extra_args, wait)