Fix precedence of commandline options and yaml options

commandline options should take precedence over options specied in yaml
file, but default values should be used if options are not set in yaml
file. Fixes #180

src/ephemeris/shed_tools.py

@@ -602,16 +602,19 @@ def main():
         tool_list = dict()
 
     # Get some of the other installation arguments
-    kwargs = dict(
-        default_install_tool_dependencies=tool_list.get("install_tool_dependencies") or getattr(args,
-                                                                                                "install_tool_dependencies",
-                                                                                                False),
-        default_install_repository_dependencies=tool_list.get("install_repository_dependencies") or getattr(args,
-                                                                                                            "install_repository_dependencies",
-                                                                                                            False),
-        default_install_resolver_dependencies=tool_list.get("install_resolver_dependencies") or getattr(args,
-                                                                                                        "install_resolver_dependencies",
-                                                                                                        False))
+    # Command line arguments should take precedence over arguments in the tool list,
+    # but only if the command line argument has actually been used.
+    kwargs = {}
+    for arg in ['install_tool_dependencies', 'install_repository_dependencies', 'install_resolver_dependencies']:
+        if not getattr(args, f"{arg}_set", False):
+            # commandline argument not set, use tool_list argument
+            arg_val = tool_list.get(arg)
+            if arg_val is None:
+                # Not specified in yaml file, use command line default, even if not set
+                arg_val = getattr(args, arg, False)
+        else:
+            arg_val = getattr(args, arg)
+        kwargs[f"default_{arg}"] = arg_val
 
     # Start installing/updating and store the results in install_results.
     # Or do testing if the action is `test`

src/ephemeris/shed_tools_args.py

@@ -5,6 +5,23 @@
 from .common_parser import get_common_args
 
 
+class StoredTrue(argparse.Action):
+
+    _value = True
+
+    def __init__(self, option_strings, dest, nargs=0, **kwargs):
+        super().__init__(option_strings, dest, nargs=nargs, **kwargs)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest + '_set', True)
+        setattr(namespace, self.dest, self._value)
+
+
+class StoredFalse(StoredTrue):
+
+    _value = False
+
+
 def parser():
     """construct the parser object"""
     common_arguments = get_common_args(log_file=True)
@@ -106,32 +123,32 @@ def parser():
     for command_parser in [update_command_parser, install_command_parser]:
         command_parser.add_argument(
             "--skip_install_tool_dependencies",
-            action="store_false",
+            action=StoredFalse,
             dest="install_tool_dependencies",
             default=False,  # Override True default for this function
             help=argparse.SUPPRESS)  # Deprecated function. Leave for backwards compatibility.
         command_parser.add_argument(
             "--install_tool_dependencies",
-            action="store_true",
+            action=StoredTrue,
             dest="install_tool_dependencies",
             help="Turn on installation of tool dependencies using classic toolshed packages. "
                  "Can be overwritten on a per-tool basis in the tools file.")
         command_parser.add_argument(
             "--install_resolver_dependencies",
-            action="store_true",
+            action=StoredTrue,
             dest="install_resolver_dependencies",
             default=True,  # Override False default for this function
             help=argparse.SUPPRESS)  # Deprecated function. Leave for backwards compatibility.
         command_parser.add_argument(
             "--skip_install_resolver_dependencies",
-            action="store_false",
+            action=StoredFalse,
             dest="install_resolver_dependencies",
             help="Skip installing tool dependencies through resolver (e.g. conda). "
                  "Will be ignored on galaxy releases older than 16.07. "
                  "Can be overwritten on a per-tool basis in the tools file")
         command_parser.add_argument(
             "--skip_install_repository_dependencies",
-            action="store_false",
+            action=StoredFalse,
             dest="install_repository_dependencies",
             help="Skip installing the repository dependencies."
         )