refactor: clarify CLI; fix subtle bug

easy_slurm/run/submit.py

@@ -187,32 +187,41 @@ def parse_args(argv=None):
     parser = argparse.ArgumentParser()
 
     for argument in ARGUMENTS:
-        kwargs = {k: v for k, v in argument.items() if k != "args"}
-        parser.add_argument(*argument["args"], **kwargs)
+        parser.add_argument(
+            *argument["args"],
+            **{k: v for k, v in argument.items() if k != "args"},
+        )
 
     args = parser.parse_args(argv)
 
     return args
 
 
-def main(argv=None):
-    args = parse_args(argv)
+def load_job_config(args):
+    # Load from CLI.
+    job_config = {k: v for k, v in vars(args).items() if v is not None}
 
+    # Load from file.
     if args.job:
         with open(args.job) as f:
-            job_config = yaml.safe_load(f)
+            job_config.update(yaml.safe_load(f))
 
+    # Extra config for formatting purposes.
     if args.config:
         with open(args.config) as f:
             job_config["config"] = yaml.safe_load(f)
 
-    job_config = {
-        **{k: v for k, v in vars(args).items() if v is not None},
-        **job_config,
-    }
+    # Discard unexpected keys.
+    for k in job_config:
+        if k not in JOB_CONFIG_KEYS:
+            del job_config[k]
+
+    return job_config
 
-    job_config = {k: v for k, v in job_config.items() if k in JOB_CONFIG_KEYS}
 
+def main(argv=None):
+    args = parse_args(argv)
+    job_config = load_job_config(args)
     submit_job(**job_config)