Merge pull request #429 from NeuroML/experimental

Fixes for validating - should be possible to validate xml files as nml too...

Author: sanjayankur31

pyneuroml/pynml.py

@@ -874,13 +874,13 @@ def _evaluate_arguments(args):
 
             exit(0)
         elif args.validate:
-            file_types = ["nml"]
+            file_types = ["nml","xml"]
             pre_args = "-validate"
             exit_on_fail = True
             run_multi = True
 
         elif args.validatev1:
-            file_types = ["nml"]
+            file_types = ["nml","xml"]
             pre_args = "-validatev1"
             exit_on_fail = True
             run_multi = True

pyneuroml/runners.py

@@ -770,14 +770,11 @@ def run_jneuroml(
                     return False
 
         if report_jnml_output:
-            logger.debug(
+            logger.info(
                 "Successfully ran the following command using pyNeuroML v%s: \n    %s"
                 % (__version__, command)
             )
-            logger.debug("Output:\n\n%s" % output)
-
-    #  except KeyboardInterrupt as e:
-    #    raise e
+            logger.info("Output:\n\n%s" % output)
 
     except Exception as e:
         logger.error("*** Execution of jnml has failed! ***")

pyneuroml/utils/__init__.py

@@ -35,12 +35,6 @@
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
 
-try:
-    import libsedml
-except ModuleNotFoundError:
-    logger.warning("Please install optional dependencies to use SED-ML features:")
-    logger.warning("pip install pyneuroml[combine]")
-
 
 MAX_COLOUR = (255, 0, 0)  # type: typing.Tuple[int, int, int]
 MIN_COLOUR = (255, 255, 0)  # type: typing.Tuple[int, int, int]
@@ -721,6 +715,13 @@ def get_model_file_list(
             lems_def_dir = get_model_file_list(inc, filelist, rootdir, lems_def_dir)
 
     elif rootfile.endswith(".sedml"):
+
+        try:
+            import libsedml
+        except ModuleNotFoundError:
+            logger.error("Please install optional dependencies to use SED-ML features:")
+            logger.error("pip install pyneuroml[combine]")
+
         if pathlib.Path(rootfile).is_absolute():
             rootdoc = libsedml.readSedMLFromFile(rootfile)
         else: