update tests

.travis.yml

@@ -76,9 +76,6 @@ script:
   #- travis_wait 60 coverage run -m pytest tests/
   - rm -rf tests/testout
   - coverage run -m pytest tests/
-  #copy config file
-  - cp tests/test_files/pyrpipe_conf.yaml .
-  - coverage run -m pytest tests/
   - coverage report --show-missing -i
 after_success:
   - coveralls

pyrpipe/pyrpipe_engine.py

@@ -134,7 +134,7 @@ def get_shell_output(cmd,verbose=None,shell=False):
             stderr=''
         return(result.returncode,stdout,stderr)
     except:
-        return(-1,"","Command failed to execute")
+        return(-1,"Command failed to execute","Command failed to execute")
 
 @dryable
 def get_return_status(cmd):

pyrpipe/runnable.py

@@ -450,10 +450,16 @@ def get_valid_parameters(self,subcommand):
             Returns the list of valid options for the subcommand.
 
         """
-        if subcommand:
-            return self._valid_args[subcommand]
-        return self._valid_args
-        pass
+
+        if isinstance(self._valid_args, list): return self._valid_args
+        #if dict
+        if isinstance(self._valid_args, dict):
+            if subcommand:
+                return self._valid_args[subcommand]
+            #default
+            return self._valid_args[0]
+        #no valid format provided
+        return None
 
     def run(self,*args, subcommand=None, target=None, requires=None, objectid=None, verbose=None,logs=None,**kwargs):
         """
@@ -564,7 +570,8 @@ def run(self,*args, subcommand=None, target=None, requires=None, objectid=None,
             #add to command
             cmd.extend(subcommand)
 
-
+        #get valid args
+        #self.get_valid_parameters(subcommand)
         #parse and add parameters
         if self._args_style=='LINUX':
             cmd.extend(pu.parse_unix_args(self._valid_args,kwargs))      

tests/test_conf.py

@@ -24,7 +24,8 @@
 
 #create configuration
 f=open('pyrpipe_conf.yaml','w')
-f.write('dry: true')
+f.write('dry: true\n')
+f.write('threads: true\n')
 f.close()