Merge branch 'development' into development

README.md

@@ -11,6 +11,8 @@ pyNeuroML
 [![GitHub Org's stars](https://img.shields.io/github/stars/NeuroML?style=social)](https://github.com/NeuroML)
 [![Twitter Follow](https://img.shields.io/twitter/follow/NeuroML?style=social)](https://twitter.com/NeuroML)
 [![Gitter](https://badges.gitter.im/NeuroML/community.svg)](https://gitter.im/NeuroML/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
+[![DOI](https://zenodo.org/badge/27832592.svg)](https://zenodo.org/doi/10.5281/zenodo.5744044)
+
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
 [![All Contributors](https://img.shields.io/badge/all_contributors-17-orange.svg?style=flat-square)](#contributors-)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->

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: