Changed default behaviour to restart=False, warnings regarding overwr…

…iting still exist.

src/somd2/config/_config.py

@@ -96,7 +96,7 @@ def __init__(
         max_gpus=None,
         run_parallel=True,
         output_directory="output",
-        restart=True,
+        restart=False,
         write_config=True,
         log_level="info",
         log_file=None,

tests/runner/test_config.py

@@ -13,7 +13,7 @@ def test_dynamics_options():
 
         # Instantiate a runner using the default config.
         # (All default options, other than platform="cpu".)
-        runner = Runner(mols, Config(platform="cpu"))
+        runner = Runner(mols, Config(platform="cpu", output_directory=tmpdir))
 
         # Initalise a fake simulation.
         runner._initialise_simulation(runner._system.clone(), 0.0)

tests/runner/test_restart.py

@@ -140,10 +140,13 @@ def test_restart():
 
         config_diffoutputdirectory = config_new.copy()
         config_diffoutputdirectory["runtime"] = "36fs"
-        config_diffoutputdirectory["output_directory"] = "test"
+        with tempfile.TemporaryDirectory() as tmpdir2:
+            config_diffoutputdirectory["output_directory"] = tmpdir2
 
-        with pytest.raises(IndexError):
-            runner_outputdirectory = Runner(mols, Config(**config_diffoutputdirectory))
+            with pytest.raises(IndexError):
+                runner_outputdirectory = Runner(
+                    mols, Config(**config_diffoutputdirectory)
+                )
 
         config_diffperturbableconstraint = config_new.copy()
         config_diffperturbableconstraint["runtime"] = "36fs"
@@ -174,8 +177,3 @@ def test_restart():
 
         with pytest.raises(ValueError):
             runner_swapendstates = Runner(mols, Config(**config_diffswapendstates))
-
-
-if __name__ == "__main__":
-    test_restart()
-    print("test_restart.py: All tests passed.")