Bugfix - dictionary modified instead of copied

There was a bug where a value was been added to a dictionary
unnecessarily, however this was only causing a problem as it was
updating the original dictionary. This commit removes both these issues
by removing the offending line of code, and by copying the resulting
dictionary when working on the values contained within.

Additionally this means that this now works on artemis completing #7

src/experi/pbs.py

@@ -14,6 +14,7 @@
 """
 
 from typing import Any, List, Union, Mapping
+from copy import deepcopy
 from collections import ChainMap, OrderedDict
 import logging
 
@@ -125,7 +126,8 @@ def pbs_header(**kwargs):
 
     # Parse arbitrary options
     for key, val in kwargs.items():
-        header_string += '#PBS -{} {}\n'.format(key, val)
+        logger.warning('Arbitrary key passed: %s', key)
+        # header_string += '#PBS -{} {}\n'.format(key, val)
 
     return header_string
 
@@ -139,6 +141,7 @@ def create_pbs_file(command_group: List[str],
     default options.
 
     """
+    pbs_options = deepcopy(pbs_options)
     try:
         setup_string = parse_setup(pbs_options['setup'])
         del pbs_options['setup']
@@ -153,7 +156,6 @@ def create_pbs_file(command_group: List[str],
         header_string += '#PBS -J 0-{}\n'.format(num_jobs-1)
     else:
         header_string += 'PBS_ARRAY_INDEX=0\n'
-    pbs_options['command_list'] = commands2bash_array(command_group)
     return header_string + PBS_TEMPLATE.format(
         command_list=commands2bash_array(command_group),
         setup=setup_string,