fix: updating of non-dict config values gives error

snakemake/utils.py

@@ -479,7 +479,7 @@ def min_version(version):
 
 
 def update_config(config, overwrite_config):
-    """Recursively update dictionary config with overwrite_config.
+    """Recursively update dictionary config with overwrite_config in-place.
 
     See
     https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth
@@ -488,18 +488,24 @@ def update_config(config, overwrite_config):
     Args:
       config (dict): dictionary to update
       overwrite_config (dict): dictionary whose items will overwrite those in config
-
     """
-
-    def _update(d, u):
-        for key, value in u.items():
+    def _update_config(config, overwrite_config):
+        """Necessary as recursive calls require a return value,
+        but `update_config()` has no return value.
+        """
+        for key, value in overwrite_config.items():
+            if not isinstance(config, collections.abc.Mapping):
+                # the config cannot be updated as it is no dict
+                # -> just overwrite it with the new value
+                config = {}
             if isinstance(value, collections.abc.Mapping):
-                d[key] = _update(d.get(key, {}), value)
+                sub_config = config.get(key, {})
+                config[key] = _update_config(sub_config, value)
             else:
-                d[key] = value
-        return d
+                config[key] = value
+        return config
 
-    _update(config, overwrite_config)
+    _update_config(config, overwrite_config)
 
 
 def available_cpu_count():

tests/test_config_merging/config_cmdline_01.yaml

@@ -2,3 +2,5 @@ block:
     foo: cfg01_foo
     bar: cfg01_bar
     baz: cfg01_baz
+    foobar:
+        cfg01_key: cfg01_val

tests/test_config_merging/config_snakefile.yaml

@@ -1,3 +1,4 @@
 block:
     bar: snake_bar
     fubar: snake_fubar
+    foobar: null

tests/test_config_merging/expected-results/test.out

@@ -1 +1 @@
-{"block": {"bar": "cfg01_bar", "baz": "cfg01_baz", "bowser": "cmdline_bowser", "foo": "cfg02_foo", "fubar": "snake_fubar", "qux": "cfg02_qux", "toad": "cmdline_toad"}}
+{"block": {"bar": "cfg01_bar", "baz": "cfg01_baz", "bowser": "cmdline_bowser", "foo": "cfg02_foo", "fubar": "snake_fubar", "qux": "cfg02_qux", "toad": "cmdline_toad", "foobar": {cfg01_key: cfg01_val}}}