fix: remove raise that limits using --config with dicts

snakemake/__init__.py

@@ -958,8 +958,6 @@ def unparse_config(config):
         raise ValueError("config is not a dict")
     items = []
     for key, value in config.items():
-        if isinstance(value, dict):
-            raise ValueError("config may only be a flat dict")
         encoded = "'{}'".format(value) if isinstance(value, str) else value
         items.append("{}={}".format(key, encoded))
     return items

tests/testapi.py

@@ -57,3 +57,22 @@ async def main():
         async_run(main())
     else:
         asyncio.run(main())
+
+
+def test_dicts_in_config():
+    with tempfile.TemporaryDirectory() as tmpdir:
+        path = os.path.join(tmpdir, "Snakefile")
+        with open(path, "w") as f:
+            print(
+                dedent(
+                    """
+                rule:
+                    output: 'result.txt'
+                    run:
+                        with open(output[0], 'w') as f:
+                            print("hello, this option " + config["this_option"] + "; this test dictionary " + config["test"]["this_dict"], file=f)
+                """
+                ),
+                file=f,
+            )
+        snakemake(path, workdir=tmpdir, config={"this_option": "does_not_break", "test": {'this_dict':'shoult_not_either'}})