Merge pull request #16 from molssi-seamm/option-handling

Updated for the new command-line argument handling

packmol_step/packmol.py

@@ -2,8 +2,6 @@
 
 """A step for building fluids with Packmol in a SEAMM flowchart"""
 
-import argparse
-import configargparse
 import logging
 import mendeleev
 import os.path
@@ -20,14 +18,6 @@
 printer = printing.getPrinter('packmol')
 
 
-def upcase(string):
-    """Return an uppercase version of the string.
-
-    Used for the type argument in argparse/
-    """
-    return string.upper()
-
-
 class Packmol(seamm.Node):
 
     def __init__(self, flowchart=None, extension=None):
@@ -38,50 +28,6 @@ def __init__(self, flowchart=None, extension=None):
 
         logger.debug('Handling arguments in Packmol {}'.format(self))
 
-        # Argument/config parsing
-        self.parser = configargparse.ArgParser(
-            auto_env_var_prefix='',
-            default_config_files=[
-                '/etc/seamm/packmol.ini',
-                '/etc/seamm/packmol_step.ini',
-                '/etc/seamm/seamm.ini',
-                '~/.seamm/packmol.ini',
-                '~/.seamm/packmol_step.ini',
-                '~/.seamm/seamm.ini',
-            ]
-        )
-
-        self.parser.add_argument(
-            '--seamm-configfile',
-            is_config_file=True,
-            default=None,
-            help='a configuration file to override others'
-        )
-
-        # Options for this plugin
-        self.parser.add_argument(
-            "--packmol-log-level",
-            default=argparse.SUPPRESS,
-            choices=[
-                'CRITICAL', 'ERROR', 'WARNING', 'INFO', 'DEBUG', 'NOTSET'
-            ],
-            type=upcase,
-            help="the logging level for the Packmol step"
-        )
-
-        # Options for Packmol
-        self.parser.add_argument(
-            '--packmol-path',
-            default='',
-            help='the path to the Packmol executables'
-        )
-
-        self.options, self.unknown = self.parser.parse_known_args()
-
-        # Set the logging level for this module if requested
-        if 'packmol_log_level' in self.options:
-            logger.setLevel(self.options.packmol_log_level)
-
         super().__init__(
             flowchart=flowchart,
             title='Packmol',
@@ -104,6 +50,32 @@ def git_revision(self):
         """
         return packmol_step.__git_revision__
 
+    def create_parser(self):
+        """Setup the command-line / config file parser
+        """
+        parser_name = self.step_type
+        parser = seamm.getParser()
+
+        # Remember if the parser exists ... this type of step may have been
+        # found before
+        parser_exists = parser.exists(parser_name)
+
+        # Create the standard options, e.g. log-level
+        result = super().create_parser(name=parser_name)
+
+        if parser_exists:
+            return result
+
+        # Options for Packmol
+        parser.add_argument(
+            self.step_type,
+            '--packmol-path',
+            default='',
+            help='the path to the Packmol executables'
+        )
+
+        return result
+
     def description_text(self, P=None):
         """Return a short description of this step.
 
@@ -167,13 +139,11 @@ def run(self):
         system = self.get_variable('_system')
 
         # The options from command line, config file ...
-        o = self.options
+        path = self.options['packmol_path']
 
-        packmol_exe = os.path.join(o.packmol_path, 'packmol')
+        packmol_exe = os.path.join(path, 'packmol')
 
-        seamm_util.check_executable(
-            packmol_exe, key='--packmol-path', parser=self.parser
-        )
+        seamm_util.check_executable(packmol_exe)
 
         P = self.parameters.current_values_to_dict(
             context=seamm.flowchart_variables._data