fix: various fixes

snakemake_interface_common/plugin_registry/plugin.py

@@ -56,6 +56,9 @@ def get_settings(self, tag: Optional[str] = None) -> SettingsBase:
                 )
             raise WorkflowError(msg)
 
+    def __iter__(self):
+        return iter(self._inner.values())
+
 
 class PluginBase(ABC):
     @property
@@ -166,6 +169,9 @@ def get_name_and_value(field):
             if thefield.metadata.get("required"):
                 required_args.add(name)
 
+            if value is None:
+                continue
+
             def extract_values(value, thefield, name, tag=None):
                 # This will only add instantiated values, and
                 # skip over dataclasses._MISSING_TYPE and similar
@@ -209,12 +215,12 @@ def check_required(kwargs, tag=None):
 
         # convert into the dataclass
         if self.support_tagged_values:
-            tagged_settings = TaggedSettings()
+            tagged_settings = TaggedSettings(self.name)
             for tag, kwargs in kwargs_tagged.items():
                 check_required(kwargs, tag=tag)
                 tagged_settings.register_settings(dc(**kwargs), tag=tag)
             try:
-                check_required(kwargs)
+                check_required(kwargs_all)
                 tagged_settings.register_settings(dc(kwargs_all))
             except WorkflowError:
                 # if untagged settings are not complete, do not register them

snakemake_interface_common/plugin_registry/tests.py

@@ -1,7 +1,11 @@
 from abc import ABC, abstractmethod
 import configargparse
 
-from snakemake_interface_common.plugin_registry.plugin import PluginBase, SettingsBase
+from snakemake_interface_common.plugin_registry.plugin import (
+    PluginBase,
+    SettingsBase,
+    TaggedSettings,
+)
 from snakemake_interface_common.plugin_registry import PluginRegistryBase
 
 
@@ -39,16 +43,20 @@ def test_registry_register_cli_args(self):
         prefix = registry.get_plugin(self.get_test_plugin_name()).cli_prefix
         for action in parser._actions:
             if not action.dest == "help":
-                assert action.dest.startswith(prefix)
+                assert action.dest.startswith(
+                    prefix.replace("-", "_")
+                ), f"{prefix} is not a prefix of {action.dest}"
 
     def test_registry_cli_args_to_settings(self):
         registry = self.get_registry()
 
-        parser = argparse.ArgumentParser()
+        parser = configargparse.ArgumentParser()
         registry.register_cli_args(parser)
         args = parser.parse_args([])
 
         plugin = registry.get_plugin(self.get_test_plugin_name())
         settings = plugin.get_settings(args)
-
-        self.validate_settings(settings, plugin)
+        if not isinstance(settings, TaggedSettings):
+            settings = [settings]
+        for s in settings:
+            self.validate_settings(s, plugin)