feat: add support for env_var specification in ExecutorSettings

Author: johanneskoester

README.md

@@ -15,7 +15,16 @@ from snakemake_interface_executor_plugins import ExecutorSettingsBase, CommonSet
 # Omit this class if you don't need any.
 @dataclass
 class ExecutorSettings:
-    myparam: int=field(default=None, metadata={"help": "Some help text"})
+    myparam: int=field(
+        default=None,
+        metadata={
+            "help": "Some help text", 
+            # optionally request that argument is also available for specification
+            # via an environment variable. The variable will be named automatically as
+            # SNAKEMAKE_<executor-name>_<param-name>, all upper case.
+            "env_var": True
+        }
+    )
 
 
 # Required:
@@ -36,13 +45,11 @@ class Executor(RemoteExecutor)
     def __init__(
         self,
         workflow: WorkflowExecutorInterface,
-        dag: DAGExecutorInterface,
         logger: LoggerExecutorInterface,
 
     ):
         super().__init__(
             workflow,
-            dag,
             logger,
             executor_settings,
             # configure behavior of RemoteExecutor below

pyproject.toml

@@ -8,7 +8,7 @@ readme = "README.md"
 version = "1.2.0"
 
 [tool.poetry.dependencies]
-argparse-dataclass = "^2.0.0"
+argparse-dataclass = {git = "https://github.com/johanneskoester/argparse_dataclass.git"}
 python = "^3.9"
 throttler = "^1.2.2"
 snakemake-interface-common = "^1.3.1"

snakemake_interface_executor_plugins/registry/plugin.py

@@ -3,7 +3,7 @@
 __email__ = "johannes.koester@uni-due.de"
 __license__ = "MIT"
 
-from argparse_dataclass import _add_dataclass_options, fields
+from argparse_dataclass import field_to_argument_args, field_to_argument_kwargs, fields
 from dataclasses import dataclass
 from typing import Optional, Type
 import copy
@@ -53,9 +53,15 @@ def register_cli_args(self, argparser):
             field.name = prefixed_name
             dc.__dataclass_fields__[field.name] = field
 
-        # When we get here, we have a namespaced dataclass.
-        # If there is overlap in snakemake args, it should error
-        _add_dataclass_options(dc, argparser)
+        settings = argparser.add_argument_group(f"{self.name} executor settings")
+
+        for field in fields(dc):
+            args = field_to_argument_args(field)
+            kwargs = field_to_argument_kwargs(field)
+            
+            if field.metadata.get("env_var"):
+                kwargs["env_var"] = f"SNAKEMAKE_{prefixed_name.upper()}"
+            settings.add_argument(*args, **kwargs)
 
     def has_executor_settings(self):
         """Determine if a plugin defines custom executor settings"""