Deprecated nonkeyword arguments for set_codes function

doc/source/whatsnew/v1.3.0.rst

@@ -677,6 +677,7 @@ Deprecations
 - Deprecated setting :attr:`Categorical._codes`, create a new :class:`Categorical` with the desired codes instead (:issue:`40606`)
 - Deprecated behavior of :meth:`DatetimeIndex.union` with mixed timezones; in a future version both will be cast to UTC instead of object dtype (:issue:`39328`)
 - Deprecated using ``usecols`` with out of bounds indices for ``read_csv`` with ``engine="c"`` (:issue:`25623`)
+- Deprecated passing arguments as positional (except for ``"codes"``) in :meth:`MultiIndex.codes` (:issue:`41485`)
 - Deprecated special treatment of lists with first element a Categorical in the :class:`DataFrame` constructor; pass as ``pd.DataFrame({col: categorical, ...})`` instead (:issue:`38845`)
 - Deprecated passing arguments as positional (except for ``"method"``) in :meth:`DataFrame.interpolate` and :meth:`Series.interpolate` (:issue:`41485`)
 - Deprecated passing arguments (apart from ``value``) as positional in :meth:`DataFrame.fillna` and :meth:`Series.fillna` (:issue:`41485`)

pandas/core/indexes/multi.py

@@ -41,6 +41,7 @@
 from pandas.util._decorators import (
     Appender,
     cache_readonly,
+    deprecate_nonkeyword_arguments,
     doc,
 )
 
@@ -994,6 +995,7 @@ def _set_codes(
 
         self._reset_cache()
 
+    @deprecate_nonkeyword_arguments(version=None, allowed_args=["self", "codes"])
     def set_codes(self, codes, level=None, inplace=None, verify_integrity: bool = True):
         """
         Set new codes on MultiIndex. Defaults to returning new index.
@@ -1061,7 +1063,7 @@ def set_codes(self, codes, level=None, inplace=None, verify_integrity: bool = Tr
             warnings.warn(
                 "inplace is deprecated and will be removed in a future version.",
                 FutureWarning,
-                stacklevel=2,
+                stacklevel=3,
             )
         else:
             inplace = False

pandas/tests/indexes/multi/test_get_set.py

@@ -405,3 +405,32 @@ def test_set_levels_inplace_deprecated(idx, inplace):
 
     with tm.assert_produces_warning(FutureWarning):
         idx.set_levels(levels=new_level, level=1, inplace=inplace)
+
+
+def test_set_codes_pos_args_depreciation():
+    # https://github.com/pandas-dev/pandas/issues/41485
+    idx = MultiIndex.from_tuples(
+        [
+            (1, "one"),
+            (1, "two"),
+            (2, "one"),
+            (2, "two"),
+        ],
+        names=["foo", "bar"]
+    )
+    msg = (
+        r"In a future version of pandas all arguments of MultiIndex.set_codes except"
+        r"for the argument 'codes' will be keyword-only"
+    )
+    with tm.assert_produces_warning(FutureWarning, match=msg):
+        result = idx.set_codes([[1, 0, 1, 0], [0, 0, 1, 1]])
+    expected = MultiIndex.from_tuples(
+        [
+            (2, "one"), 
+            (1, "one"), 
+            (2, "two"), 
+            (1, "two"),
+        ],
+        names=["foo", "bar"]
+    )
+    tm.assert_index_equal(result, expected)