update tests

.travis.yml

@@ -76,6 +76,9 @@ 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

@@ -91,12 +91,12 @@ def parse_cmd(cmd):
     return cmd
 
 @dryable
-def get_shell_output(cmd,verbose=None):
+def get_shell_output(cmd,verbose=None,shell=False):
     """Function to run a shell command and return returncode, stdout and stderr
     Currently (pyrpipe v 0.0.4) this function is called in 
     get_return_status(), get_program_version()
     
-    pyrpipe v0.0.5 onwards the get_shell_output function uses shell=True
+    pyrpipe v0.0.5 onwards the get_shell_output function allows shell=True
     
     
     Parameters
@@ -114,12 +114,15 @@ def get_shell_output(cmd,verbose=None):
     #not logging these commands
     cmd=parse_cmd(cmd)
     log_message=cmd
+    #command_name=cmd.split()[0]
+
+
     starttime_str=time.strftime("%y-%m-%d %H:%M:%S", time.localtime(time.time()))
     if verbose:
         pu.print_notification("Start:"+starttime_str)
         pu.print_blue("$ "+log_message)
     try:
-        result = subprocess.Popen(cmd,stdout=subprocess.PIPE,stderr=subprocess.STDOUT,shell=True)
+        result = subprocess.Popen(cmd,stdout=subprocess.PIPE,stderr=subprocess.STDOUT,shell=shell)
         stdout,stderr = result.communicate()
         if stdout:
             stdout=stdout.decode("utf-8")

tests/test_files/pyrpipe_conf.yaml

@@ -0,0 +1,3 @@
+dry: True
+threads: 1
+force: True