Merge pull request #442 from NeuroML/experimental

Add example testing execute_command_in_dir etc.

Author: pgleeson

examples/test_execute_command.py

@@ -0,0 +1,17 @@
+from pyneuroml import pynml
+
+run_dir = '.'
+
+commands = ['pwd', 'ls -alt testss']
+
+for command in commands:
+
+    print("\n====================\n")
+
+    returncode, output = pynml.execute_command_in_dir(command, run_dir, prefix="Output [%s] > "%command, verbose=True) 
+
+    print('  ----  Return code from execute_command_in_dir: %s; output: \n%s\n--------------------------'%(returncode, output))
+
+    success = pynml.execute_command_in_dir_with_realtime_output(command, run_dir, prefix="Output [%s]: "%command, verbose=False) 
+
+    print('  ----  Success of execute_command_in_dir_with_realtime_output: %s'%success)

pyneuroml/__init__.py

@@ -12,7 +12,7 @@
     __version__ = importlib_metadata.version("pyNeuroML")
 
 
-JNEUROML_VERSION = "0.13.3"
+JNEUROML_VERSION = "0.14.0"
 
 logger = logging.getLogger(__name__)
 logger.propagate = False

pyneuroml/lib/jNeuroML-0.13.3-jar-with-dependencies.jar renamed to pyneuroml/lib/jNeuroML-0.14.0-jar-with-dependencies.jar

@@ -902,7 +902,7 @@ def execute_command_in_dir_with_realtime_output(
         )
         with p.stdout:
             for line in iter(p.stdout.readline, ""):
-                print("# %s" % line.strip())
+                print(" %s %s" % (prefix,line.strip()))
         p.wait()  # wait for the subprocess to exit
 
         print("####################################################################")
@@ -920,7 +920,7 @@ def execute_command_in_dir_with_realtime_output(
 
     if not p.returncode == 0:
         logger.critical(
-            "*** Problem running command (return code: %s): \n       %s"
+            "*** Problem running command (return code: %s): [%s]"
             % (p.returncode, command)
         )
 
@@ -990,10 +990,13 @@ def execute_command_in_dir(
         return return_string.decode("utf-8")
 
     except subprocess.CalledProcessError as e:
-        logger.critical("*** Problem running command: \n       %s" % e)
-        logger.critical(
+        logger.critical("*** Problem running last command: %s" % e)
+
+        print("####################################################################")
+        print(
             "%s%s" % (prefix, e.output.decode().replace("\n", "\n" + prefix))
         )
+        print("####################################################################")
         return (e.returncode, e.output.decode())
     except Exception as e:
         logger.critical("*** Unknown problem running command: %s" % e)

pyneuroml/runners.py

@@ -1,6 +1,6 @@
 [metadata]
 name = pyNeuroML
-version = 1.3.14
+version = 1.3.15
 author = Padraig Gleeson
 author_email = [email protected]
 url = https://github.com/NeuroML/pyNeuroML