CI: unpin numpy for CI / Checks github action

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   # required
-  - numpy>=1.16.5, <1.20 # gh-39513
+  - numpy>=1.16.5
   - python=3
   - python-dateutil>=2.7.3
   - pytz

pandas/compat/numpy/__init__.py

@@ -43,7 +43,9 @@ def np_datetime64_compat(s, *args, **kwargs):
     warning, when need to pass '2015-01-01 09:00:00'
     """
     s = tz_replacer(s)
-    return np.datetime64(s, *args, **kwargs)
+    # error: No overload variant of "datetime64" matches argument types "Any",
+    # "Tuple[Any, ...]", "Dict[str, Any]"
+    return np.datetime64(s, *args, **kwargs)  # type: ignore[call-overload]
 
 
 def np_array_datetime64_compat(arr, *args, **kwargs):

pandas/core/aggregation.py

@@ -181,7 +181,9 @@ def normalize_keyword_aggregation(kwargs: dict) -> Tuple[dict, List[str], List[i
 
     # get the new index of columns by comparison
     col_idx_order = Index(uniquified_aggspec).get_indexer(uniquified_order)
-    return aggspec, columns, col_idx_order
+    # error: Incompatible return value type (got "Tuple[defaultdict[Any, Any],
+    # Any, ndarray]", expected "Tuple[Dict[Any, Any], List[str], List[int]]")
+    return aggspec, columns, col_idx_order  # type: ignore[return-value]
 
 
 def _make_unique_kwarg_list(

pandas/core/algorithms.py

@@ -157,7 +157,10 @@ def _ensure_data(values: ArrayLike) -> Tuple[np.ndarray, DtypeObj]:
             with catch_warnings():
                 simplefilter("ignore", np.ComplexWarning)
                 values = ensure_float64(values)
-            return values, np.dtype("float64")
+            # error: Incompatible return value type (got "Tuple[ExtensionArray,
+            # dtype[floating[_64Bit]]]", expected "Tuple[ndarray, Union[dtype[Any],
+            # ExtensionDtype]]")
+            return values, np.dtype("float64")  # type: ignore[return-value]
 
     except (TypeError, ValueError, OverflowError):
         # if we are trying to coerce to a dtype
@@ -173,7 +176,9 @@ def _ensure_data(values: ArrayLike) -> Tuple[np.ndarray, DtypeObj]:
         elif is_timedelta64_dtype(values.dtype):
             from pandas import TimedeltaIndex
 
-            values = TimedeltaIndex(values)._data
+            # error: Incompatible types in assignment (expression has type
+            # "TimedeltaArray", variable has type "ndarray")
+            values = TimedeltaIndex(values)._data  # type: ignore[assignment]
         else:
             # Datetime
             if values.ndim > 1 and is_datetime64_ns_dtype(values.dtype):
@@ -182,27 +187,45 @@ def _ensure_data(values: ArrayLike) -> Tuple[np.ndarray, DtypeObj]:
                 # TODO(EA2D): special case not needed with 2D EAs
                 asi8 = values.view("i8")
                 dtype = values.dtype
-                return asi8, dtype
+                # error: Incompatible return value type (got "Tuple[Any,
+                # Union[dtype, ExtensionDtype, None]]", expected
+                # "Tuple[ndarray, Union[dtype, ExtensionDtype]]")
+                return asi8, dtype  # type: ignore[return-value]
 
             from pandas import DatetimeIndex
 
-            values = DatetimeIndex(values)._data
+            # Incompatible types in assignment (expression has type "DatetimeArray",
+            # variable has type "ndarray")
+            values = DatetimeIndex(values)._data  # type: ignore[assignment]
         dtype = values.dtype
-        return values.asi8, dtype
+        # error: Item "ndarray" of "Union[PeriodArray, Any, ndarray]" has no attribute
+        # "asi8"
+        return values.asi8, dtype  # type: ignore[union-attr]
 
     elif is_categorical_dtype(values.dtype):
-        values = cast("Categorical", values)
-        values = values.codes
+        # error: Incompatible types in assignment (expression has type "Categorical",
+        # variable has type "ndarray")
+        values = cast("Categorical", values)  # type: ignore[assignment]
+        # error: Incompatible types in assignment (expression has type "ndarray",
+        # variable has type "ExtensionArray")
+        # error: Item "ndarray" of "Union[Any, ndarray]" has no attribute "codes"
+        values = values.codes  # type: ignore[assignment,union-attr]
         dtype = pandas_dtype("category")
 
         # we are actually coercing to int64
         # until our algos support int* directly (not all do)
         values = ensure_int64(values)
 
-        return values, dtype
+        # error: Incompatible return value type (got "Tuple[ExtensionArray,
+        # Union[dtype[Any], ExtensionDtype]]", expected "Tuple[ndarray,
+        # Union[dtype[Any], ExtensionDtype]]")
+        return values, dtype  # type: ignore[return-value]
 
     # we have failed, return object
-    values = np.asarray(values, dtype=object)
+
+    # error: Incompatible types in assignment (expression has type "ndarray", variable
+    # has type "ExtensionArray")
+    values = np.asarray(values, dtype=object)  # type: ignore[assignment]
     return ensure_object(values), np.dtype("object")
 
 
@@ -227,24 +250,40 @@ def _reconstruct_data(
         return values
 
     if is_extension_array_dtype(dtype):
-        cls = dtype.construct_array_type()
+        # error: Item "dtype[Any]" of "Union[dtype[Any], ExtensionDtype]" has no
+        # attribute "construct_array_type"
+        cls = dtype.construct_array_type()  # type: ignore[union-attr]
         if isinstance(values, cls) and values.dtype == dtype:
             return values
 
         values = cls._from_sequence(values)
     elif is_bool_dtype(dtype):
-        values = values.astype(dtype, copy=False)
+        # error: Argument 1 to "astype" of "_ArrayOrScalarCommon" has
+        # incompatible type "Union[dtype, ExtensionDtype]"; expected
+        # "Union[dtype, None, type, _SupportsDtype, str, Tuple[Any, int],
+        # Tuple[Any, Union[int, Sequence[int]]], List[Any], _DtypeDict,
+        # Tuple[Any, Any]]"
+        values = values.astype(dtype, copy=False)  # type: ignore[arg-type]
 
         # we only support object dtypes bool Index
         if isinstance(original, ABCIndex):
             values = values.astype(object, copy=False)
     elif dtype is not None:
         if is_datetime64_dtype(dtype):
-            dtype = "datetime64[ns]"
+            # error: Incompatible types in assignment (expression has type
+            # "str", variable has type "Union[dtype, ExtensionDtype]")
+            dtype = "datetime64[ns]"  # type: ignore[assignment]
         elif is_timedelta64_dtype(dtype):
-            dtype = "timedelta64[ns]"
+            # error: Incompatible types in assignment (expression has type
+            # "str", variable has type "Union[dtype, ExtensionDtype]")
+            dtype = "timedelta64[ns]"  # type: ignore[assignment]
 
-        values = values.astype(dtype, copy=False)
+        # error: Argument 1 to "astype" of "_ArrayOrScalarCommon" has
+        # incompatible type "Union[dtype, ExtensionDtype]"; expected
+        # "Union[dtype, None, type, _SupportsDtype, str, Tuple[Any, int],
+        # Tuple[Any, Union[int, Sequence[int]]], List[Any], _DtypeDict,
+        # Tuple[Any, Any]]"
+        values = values.astype(dtype, copy=False)  # type: ignore[arg-type]
 
     return values
 
@@ -296,14 +335,18 @@ def _get_values_for_rank(values: ArrayLike):
     if is_categorical_dtype(values):
         values = cast("Categorical", values)._values_for_rank()
 
-    values, _ = _ensure_data(values)
+    # error: Incompatible types in assignment (expression has type "ndarray", variable
+    # has type "ExtensionArray")
+    values, _ = _ensure_data(values)  # type: ignore[assignment]
     return values
 
 
 def get_data_algo(values: ArrayLike):
     values = _get_values_for_rank(values)
 
-    ndtype = _check_object_for_strings(values)
+    # error: Argument 1 to "_check_object_for_strings" has incompatible type
+    # "ExtensionArray"; expected "ndarray"
+    ndtype = _check_object_for_strings(values)  # type: ignore[arg-type]
     htable = _hashtables.get(ndtype, _hashtables["object"])
 
     return htable, values
@@ -460,17 +503,46 @@ def isin(comps: AnyArrayLike, values: AnyArrayLike) -> np.ndarray:
         )
 
     if not isinstance(values, (ABCIndex, ABCSeries, ABCExtensionArray, np.ndarray)):
-        values = _ensure_arraylike(list(values))
+        # error: Incompatible types in assignment (expression has type "ExtensionArray",
+        # variable has type "Index")
+        # error: Incompatible types in assignment (expression has type "ExtensionArray",
+        # variable has type "Series")
+        # error: Incompatible types in assignment (expression has type "ExtensionArray",
+        # variable has type "ndarray")
+        values = _ensure_arraylike(list(values))  # type: ignore[assignment]
     elif isinstance(values, ABCMultiIndex):
         # Avoid raising in extract_array
-        values = np.array(values)
-    else:
-        values = extract_array(values, extract_numpy=True)
 
-    comps = _ensure_arraylike(comps)
-    comps = extract_array(comps, extract_numpy=True)
+        # error: Incompatible types in assignment (expression has type "ndarray",
+        # variable has type "ExtensionArray")
+        # error: Incompatible types in assignment (expression has type "ndarray",
+        # variable has type "Index")
+        # error: Incompatible types in assignment (expression has type "ndarray",
+        # variable has type "Series")
+        values = np.array(values)  # type: ignore[assignment]
+    else:
+        # error: Incompatible types in assignment (expression has type "Union[Any,
+        # ExtensionArray]", variable has type "Index")
+        # error: Incompatible types in assignment (expression has type "Union[Any,
+        # ExtensionArray]", variable has type "Series")
+        values = extract_array(values, extract_numpy=True)  # type: ignore[assignment]
+
+    # error: Incompatible types in assignment (expression has type "ExtensionArray",
+    # variable has type "Index")
+    # error: Incompatible types in assignment (expression has type "ExtensionArray",
+    # variable has type "Series")
+    # error: Incompatible types in assignment (expression has type "ExtensionArray",
+    # variable has type "ndarray")
+    comps = _ensure_arraylike(comps)  # type: ignore[assignment]
+    # error: Incompatible types in assignment (expression has type "Union[Any,
+    # ExtensionArray]", variable has type "Index")
+    # error: Incompatible types in assignment (expression has type "Union[Any,
+    # ExtensionArray]", variable has type "Series")
+    comps = extract_array(comps, extract_numpy=True)  # type: ignore[assignment]
     if is_extension_array_dtype(comps.dtype):
-        return comps.isin(values)
+        # error: Incompatible return value type (got "Series", expected "ndarray")
+        # error: Item "ndarray" of "Union[Any, ndarray]" has no attribute "isin"
+        return comps.isin(values)  # type: ignore[return-value,union-attr]
 
     elif needs_i8_conversion(comps.dtype):
         # Dispatch to DatetimeLikeArrayMixin.isin
@@ -501,7 +573,19 @@ def f(c, v):
             f = np.in1d
 
     else:
-        common = np.find_common_type([values.dtype, comps.dtype], [])
+        # error: List item 0 has incompatible type "Union[Any, dtype[Any],
+        # ExtensionDtype]"; expected "Union[dtype[Any], None, type, _SupportsDType, str,
+        # Tuple[Any, Union[int, Sequence[int]]], List[Any], _DTypeDict, Tuple[Any,
+        # Any]]"
+        # error: List item 1 has incompatible type "Union[Any, ExtensionDtype]";
+        # expected "Union[dtype[Any], None, type, _SupportsDType, str, Tuple[Any,
+        # Union[int, Sequence[int]]], List[Any], _DTypeDict, Tuple[Any, Any]]"
+        # error: List item 1 has incompatible type "Union[dtype[Any], ExtensionDtype]";
+        # expected "Union[dtype[Any], None, type, _SupportsDType, str, Tuple[Any,
+        # Union[int, Sequence[int]]], List[Any], _DTypeDict, Tuple[Any, Any]]"
+        common = np.find_common_type(
+            [values.dtype, comps.dtype], []  # type: ignore[list-item]
+        )
         values = values.astype(common, copy=False)
         comps = comps.astype(common, copy=False)
         name = common.name
@@ -916,7 +1000,9 @@ def duplicated(values: ArrayLike, keep: Union[str, bool] = "first") -> np.ndarra
     -------
     duplicated : ndarray
     """
-    values, _ = _ensure_data(values)
+    # error: Incompatible types in assignment (expression has type "ndarray", variable
+    # has type "ExtensionArray")
+    values, _ = _ensure_data(values)  # type: ignore[assignment]
     ndtype = values.dtype.name
     f = getattr(htable, f"duplicated_{ndtype}")
     return f(values, keep=keep)
@@ -1188,7 +1274,9 @@ def _get_score(at):
     else:
         q = np.asarray(q, np.float64)
         result = [_get_score(x) for x in q]
-        result = np.array(result, dtype=np.float64)
+        # error: Incompatible types in assignment (expression has type
+        # "ndarray", variable has type "List[Any]")
+        result = np.array(result, dtype=np.float64)  # type: ignore[assignment]
         return result
 
 
@@ -1776,7 +1864,11 @@ def safe_sort(
     if not isinstance(values, (np.ndarray, ABCExtensionArray)):
         # don't convert to string types
         dtype, _ = infer_dtype_from_array(values)
-        values = np.asarray(values, dtype=dtype)
+        # error: Argument "dtype" to "asarray" has incompatible type "Union[dtype[Any],
+        # ExtensionDtype]"; expected "Union[dtype[Any], None, type, _SupportsDType, str,
+        # Union[Tuple[Any, int], Tuple[Any, Union[int, Sequence[int]]], List[Any],
+        # _DTypeDict, Tuple[Any, Any]]]"
+        values = np.asarray(values, dtype=dtype)  # type: ignore[arg-type]
 
     sorter = None
 

pandas/core/apply.py

@@ -1016,7 +1016,11 @@ def apply_standard(self) -> FrameOrSeriesUnion:
 
         with np.errstate(all="ignore"):
             if isinstance(f, np.ufunc):
-                return f(obj)
+                # error: Argument 1 to "__call__" of "ufunc" has incompatible type
+                # "Series"; expected "Union[Union[int, float, complex, str, bytes,
+                # generic], Sequence[Union[int, float, complex, str, bytes, generic]],
+                # Sequence[Sequence[Any]], _SupportsArray]"
+                return f(obj)  # type: ignore[arg-type]
 
             # row-wise access
             if is_extension_array_dtype(obj.dtype) and hasattr(obj._values, "map"):

pandas/core/array_algos/putmask.py

@@ -120,7 +120,11 @@ def putmask_smart(values: np.ndarray, mask: np.ndarray, new) -> np.ndarray:
         return _putmask_preserve(values, new, mask)
 
     dtype = find_common_type([values.dtype, new.dtype])
-    values = values.astype(dtype)
+    # error: Argument 1 to "astype" of "_ArrayOrScalarCommon" has incompatible type
+    # "Union[dtype[Any], ExtensionDtype]"; expected "Union[dtype[Any], None, type,
+    # _SupportsDType, str, Union[Tuple[Any, int], Tuple[Any, Union[int, Sequence[int]]],
+    # List[Any], _DTypeDict, Tuple[Any, Any]]]"
+    values = values.astype(dtype)  # type: ignore[arg-type]
 
     return _putmask_preserve(values, new, mask)
 
@@ -187,10 +191,16 @@ def extract_bool_array(mask: ArrayLike) -> np.ndarray:
         # We could have BooleanArray, Sparse[bool], ...
         #  Except for BooleanArray, this is equivalent to just
         #  np.asarray(mask, dtype=bool)
-        mask = mask.to_numpy(dtype=bool, na_value=False)
 
-    mask = np.asarray(mask, dtype=bool)
-    return mask
+        # error: Incompatible types in assignment (expression has type "ndarray",
+        # variable has type "ExtensionArray")
+        mask = mask.to_numpy(dtype=bool, na_value=False)  # type: ignore[assignment]
+
+    # error: Incompatible types in assignment (expression has type "ndarray", variable
+    # has type "ExtensionArray")
+    mask = np.asarray(mask, dtype=bool)  # type: ignore[assignment]
+    # error: Incompatible return value type (got "ExtensionArray", expected "ndarray")
+    return mask  # type: ignore[return-value]
 
 
 def setitem_datetimelike_compat(values: np.ndarray, num_set: int, other):

pandas/core/array_algos/quantile.py

@@ -143,10 +143,17 @@ def quantile_ea_compat(
     mask = np.asarray(values.isna())
     mask = np.atleast_2d(mask)
 
-    values, fill_value = values._values_for_factorize()
-    values = np.atleast_2d(values)
-
-    result = quantile_with_mask(values, mask, fill_value, qs, interpolation, axis)
+    # error: Incompatible types in assignment (expression has type "ndarray", variable
+    # has type "ExtensionArray")
+    values, fill_value = values._values_for_factorize()  # type: ignore[assignment]
+    # error: No overload variant of "atleast_2d" matches argument type "ExtensionArray"
+    values = np.atleast_2d(values)  # type: ignore[call-overload]
+
+    # error: Argument 1 to "quantile_with_mask" has incompatible type "ExtensionArray";
+    # expected "ndarray"
+    result = quantile_with_mask(
+        values, mask, fill_value, qs, interpolation, axis  # type: ignore[arg-type]
+    )
 
     if not is_sparse(orig.dtype):
         # shape[0] should be 1 as long as EAs are 1D
@@ -160,4 +167,5 @@ def quantile_ea_compat(
             assert result.shape == (1, len(qs)), result.shape
             result = type(orig)._from_factorized(result[0], orig)
 
-    return result
+    # error: Incompatible return value type (got "ndarray", expected "ExtensionArray")
+    return result  # type: ignore[return-value]

pandas/core/array_algos/replace.py

@@ -95,7 +95,9 @@ def _check_comparison_types(
 
     if is_numeric_v_string_like(a, b):
         # GH#29553 avoid deprecation warnings from numpy
-        return np.zeros(a.shape, dtype=bool)
+        # error: Incompatible return value type (got "ndarray", expected
+        # "Union[ExtensionArray, bool]")
+        return np.zeros(a.shape, dtype=bool)  # type: ignore[return-value]
 
     elif is_datetimelike_v_numeric(a, b):
         # GH#29553 avoid deprecation warnings from numpy
@@ -152,6 +154,8 @@ def re_replacer(s):
     f = np.vectorize(re_replacer, otypes=[values.dtype])
 
     if mask is None:
-        values[:] = f(values)
+        # error: Invalid index type "slice" for "ExtensionArray"; expected type
+        # "Union[int, ndarray]"
+        values[:] = f(values)  # type: ignore[index]
     else:
         values[mask] = f(values[mask])