fix: practical improvements

Author: johanneskoester

README.md

@@ -18,6 +18,7 @@ class ExecutorSettings:
     myparam: int=field(default=None, metadata={"help": "Some help text"})
 
 
+# Required:
 # Specify common settings shared by various executors.
 common_settings = CommonSettings(
     # define whether your executor plugin executes locally
@@ -36,32 +37,33 @@ class Executor(RemoteExecutor)
         self,
         workflow: WorkflowExecutorInterface,
         dag: DAGExecutorInterface,
-        stats: StatsExecutorInterface,
         logger: LoggerExecutorInterface,
-        executor_settings: Optional[ExecutorSettings], # if no ExecutorSettings are defined above, this will receive None
+
     ):
-    super().__init__(
-        workflow,
-        dag,
-        stats,
-        logger,
-        executor_settings,
-        # configure behavior of RemoteExecutor below
-        max_status_checks_per_second=1, # how many status checks should be performed per second
-        disable_default_remote_provider_args=False, # whether arguments for setting the remote provider shall not be passed to jobs
-        disable_default_resources_args=False, # whether arguments for setting default resources shall not be passed to jobs
-        disable_envvar_declarations=False, # whether environment variables shall not be passed to jobs
-    )
-    # access executor specific settings 
-    self.executor_settings
-    # access workflow
-    self.workflow
+        super().__init__(
+            workflow,
+            dag,
+            logger,
+            executor_settings,
+            # configure behavior of RemoteExecutor below
+            pass_default_remote_provider_args=True,  # whether arguments for setting the remote provider shall  be passed to jobs
+            pass_default_resources_args=True,  # whether arguments for setting default resources shall be passed to jobs
+            pass_envvar_declarations_to_cmd=True,  # whether environment variables shall be passed to jobs
+        )
+        # access executor specific settings 
+        self.executor_settings
+        # access workflow
+        self.workflow
+
+        # IMPORTANT: in your plugin, only access methods and properties of Snakemake objects (like Workflow, Persistence, etc.)
+        # that are defined in the interfaces found in THIS package. Other parts of those objects
+        # are NOT guaranteed to remain the same across new releases.
 
-    # IMPORTANT: in your plugin, only access methods and properties of Snakemake objects (like Workflow, Persistence, etc.)
-    # that are defined in the interfaces found in THIS package. Other parts of those objects
-    # are NOT guaranteed to remain the same across new releases.
+        # To ensure that the used interfaces are not changing, you should depend on this package as
+        # >=a.b.c,<d with d=a+1 (i.e. pin the dependency on this package to be at least the version at time of development
+        # and less than the next major version which would introduce breaking changes).
 
-    # To ensure that the used interfaces are not changing, you should depend on this package as
-    # >=a.b.c,<d with d=a+1 (i.e. pin the dependency on this package to be at least the version at time of development
-    # and less than the next major version which would introduce breaking changes).
+    async def _wait_for_jobs(self):
+        # implement here a loop that checks which jobs are already finished
+        
 ```

snakemake_interface_executor_plugins/executors/remote.py

@@ -42,7 +42,7 @@ def __init__(
         logger: LoggerExecutorInterface,
         pass_default_remote_provider_args: bool = True,
         pass_default_resources_args: bool = True,
-        pass_envvar_declarations_to_cmd: bool = False,
+        pass_envvar_declarations_to_cmd: bool = True,
     ):
         super().__init__(
             workflow,

snakemake_interface_executor_plugins/registry/__init__.py

@@ -57,10 +57,16 @@ def _collect_plugins(self):
             ):
                 continue
             module = importlib.import_module(moduleinfo.name)
-            self._register_plugin(moduleinfo.name, module)
+            self.register_plugin(moduleinfo.name, module)
+
+    def register_plugin(self, name: str, plugin: types.ModuleType):
+        """Validate and register a plugin.
+
+        Does nothing if the plugin is already registered.
+        """
+        if name in self.plugins:
+            return
 
-    def _register_plugin(self, name: str, plugin: types.ModuleType):
-        """Validate and register a plugin"""
         self._validate_plugin(name, plugin)
 
         # Derive the shortened name for future access
@@ -69,7 +75,7 @@ def _register_plugin(self, name: str, plugin: types.ModuleType):
         self.plugins[plugin_name] = Plugin(
             plugin_name,
             plugin.Executor,
-            common_settings=getattr(plugin, "common_settings", None),
+            common_settings=plugin.common_settings,
             _executor_settings_cls=getattr(plugin, "ExecutorSettings", None),
         )
 

snakemake_interface_executor_plugins/registry/plugin.py

@@ -59,9 +59,7 @@ def register_cli_args(self, argparser):
 
     def has_executor_settings(self):
         """Determine if a plugin defines custom executor settings"""
-        return self._executor_settings_cls is not None and not isinstance(
-            self._executor_settings_cls, ExecutorSettingsBase
-        )
+        return self._executor_settings_cls is not None
 
     def get_executor_settings(self, args) -> ExecutorSettingsBase:
         """Return an instance of self.executor_settings with values from args.

tests/tests.py

@@ -32,4 +32,5 @@ def test_registry_get_executor_settings(registry):
     args = parser.parse_args([])
     plugin = registry.plugins["flux"]
     settings = plugin.get_executor_settings(args)
+    print(settings, plugin._executor_settings_cls)
     assert isinstance(settings, plugin._executor_settings_cls)