feat!: pass common settings to SpawedJobArgsFactory; shell command arg quoting fixes (#58)

Author: johanneskoester

snakemake_interface_executor_plugins/cli.py

@@ -1,19 +1,19 @@
 from abc import ABC, abstractmethod
 from typing import Mapping
 
+from snakemake_interface_executor_plugins.settings import CommonSettings
+
 
 class SpawnedJobArgsFactoryExecutorInterface(ABC):
     @abstractmethod
     def general_args(
         self,
-        pass_default_storage_provider_args: bool = True,
-        pass_default_resources_args: bool = False,
-        pass_group_args: bool = False,
+        executor_common_settings: CommonSettings,
     ) -> str:
         ...
 
     @abstractmethod
-    def precommand(self) -> str:
+    def precommand(self, executor_common_settings: CommonSettings) -> str:
         ...
 
     @abstractmethod

snakemake_interface_executor_plugins/executors/real.py

@@ -131,7 +131,10 @@ def get_envvar_declarations(self):
             defs = " ".join(
                 f"{var}={repr(value)}" for var, value in self.envvars().items()
             )
-            return f"export {defs} &&"
+            if defs:
+                return f"export {defs} &&"
+            else:
+                return ""
         else:
             return ""
 
@@ -149,12 +152,10 @@ def format_job_exec(self, job: JobExecutorInterface) -> str:
         if suffix:
             suffix = f"&& {suffix}"
         general_args = self.workflow.spawned_job_args_factory.general_args(
-            pass_default_storage_provider_args=self.common_settings.pass_default_storage_provider_args,
-            pass_default_resources_args=self.common_settings.pass_default_resources_args,
-            pass_group_args=self.common_settings.pass_group_args,
+            executor_common_settings=self.common_settings
         )
         precommand = self.workflow.spawned_job_args_factory.precommand(
-            auto_deploy_default_storage_provider=self.common_settings.auto_deploy_default_storage_provider
+            executor_common_settings=self.common_settings
         )
         if precommand:
             precommand += " &&"

snakemake_interface_executor_plugins/settings.py

@@ -48,6 +48,11 @@ class CommonSettings:
         Number of seconds to wait before starting to check the status of spawned jobs.
     pass_group_args : bool
         Whether to pass group arguments to spawned jobs.
+    spawned_jobs_assume_shared_fs: bool
+        Whether spawned jobs in the executor should always assume a shared FS regardless
+        of the user provided settings. This should be True if the executor spawns
+        another non-local executor that runs jobs on the same node.
+        For example, it is used in snakemake-executor-plugin-slurm-jobstep.
     """
 
     non_local_exec: bool
@@ -62,6 +67,7 @@ class CommonSettings:
     auto_deploy_default_storage_provider: bool = True
     init_seconds_before_status_checks: int = 0
     pass_group_args: bool = False
+    spawned_jobs_assume_shared_fs: bool = False
 
     @property
     def local_exec(self):

snakemake_interface_executor_plugins/utils.py

@@ -6,6 +6,7 @@
 import asyncio
 from collections import UserDict
 from pathlib import Path
+import shlex
 import threading
 from typing import Any, List
 from urllib.parse import urlparse
@@ -45,7 +46,9 @@ def format_cli_value(value: Any) -> str:
     if isinstance(value, SettingsEnumBase):
         return value.item_to_choice()
     elif isinstance(value, Path):
-        return str(value)
+        return shlex.quote(str(value))
+    elif isinstance(value, str):
+        return shlex.quote(value)
     else:
         return repr(value)