Fix LightningCLI not saving correctly seed_everything for run=True

src/lightning/pytorch/CHANGELOG.md

@@ -165,6 +165,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 - Fixed FSDP re-applying activation checkpointing when the user had manually applied it already ([#18006](https://github.com/Lightning-AI/lightning/pull/18006))
 
+
+- `LightningCLI` not saving correctly `seed_everything` when `run=True` and `seed_everything=True` ([#18056](https://github.com/Lightning-AI/lightning/pull/18056))
+
+
 ## [2.0.3] - 2023-06-07
 
 ### Changed

src/lightning/pytorch/cli.py

@@ -691,7 +691,10 @@ def _set_seed(self) -> None:
             config_seed = seed_everything(workers=True)
         else:
             config_seed = seed_everything(config_seed, workers=True)
-        self.config["seed_everything"] = config_seed
+        if self.subcommand:
+            self.config[self.subcommand]["seed_everything"] = config_seed
+        else:
+            self.config["seed_everything"] = config_seed
 
 
 def _class_path_from_class(class_type: Type) -> str:

tests/tests_pytorch/test_cli.py

@@ -318,6 +318,16 @@ def test_lightning_cli_save_config_only_once(cleandir):
     cli.trainer.test(cli.model)  # Should not fail because config already saved
 
 
+def test_lightning_cli_save_config_seed_everything(cleandir):
+    config_path = Path("config.yaml")
+    cli_args = ["fit", "--seed_everything=true", "--trainer.logger=false", "--trainer.max_epochs=1"]
+    with mock.patch("sys.argv", ["any.py"] + cli_args):
+        cli = LightningCLI(BoringModel)
+    config = yaml.safe_load(config_path.read_text())
+    assert isinstance(config["seed_everything"], int)
+    assert config["seed_everything"] == cli.config.fit.seed_everything
+
+
 def test_save_to_log_dir_false_error():
     with pytest.raises(ValueError):
         SaveConfigCallback(