Merge remote-tracking branch 'upstream/main' into aijams-take-function-invalid-dtype

Author: aijams

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ ci:
     skip: [pyright, mypy]
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.3
+    rev: v0.14.3
     hooks:
     -   id: ruff
         args: [--exit-non-zero-on-fix]
@@ -46,7 +46,7 @@ repos:
     -   id: codespell
         types_or: [python, rst, markdown, cython, c]
 -   repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.17.0
+    rev: v0.18.1
     hooks:
     -   id: cython-lint
     -   id: double-quote-cython-strings
@@ -67,11 +67,11 @@ repos:
     -   id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
 -   repo: https://github.com/PyCQA/isort
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
     -   id: isort
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.20.0
+    rev: v3.21.0
     hooks:
     -   id: pyupgrade
         args: [--py311-plus]
@@ -87,7 +87,7 @@ repos:
         types: [text]  # overwrite types: [rst]
         types_or: [python, rst]
 -   repo: https://github.com/sphinx-contrib/sphinx-lint
-    rev: v1.0.0
+    rev: v1.0.1
     hooks:
     - id: sphinx-lint
       args: ["--enable", "all", "--disable", "line-too-long"]

README.md

@@ -179,7 +179,7 @@ If you are simply looking to start working with the pandas codebase, navigate to
 
 You can also triage issues which may include reproducing bug reports, or asking for vital information such as version numbers or reproduction instructions. If you would like to start triaging issues, one easy way to get started is to [subscribe to pandas on CodeTriage](https://www.codetriage.com/pandas-dev/pandas).
 
-Or maybe through using pandas you have an idea of your own or are looking for something in the documentation and thinking ‘this can be improved’...you can do something about it!
+Or maybe through using pandas you have an idea of your own or are looking for something in the documentation and thinking ‘this can be improved’... you can do something about it!
 
 Feel free to ask questions on the [mailing list](https://groups.google.com/forum/?fromgroups#!forum/pydata) or on [Slack](https://pandas.pydata.org/docs/dev/development/community.html?highlight=slack#community-slack).
 

doc/source/user_guide/groupby.rst

@@ -137,7 +137,7 @@ We could naturally group by either the ``A`` or ``B`` columns, or both:
 
    ``df.groupby('A')`` is just syntactic sugar for ``df.groupby(df['A'])``.
 
-The above GroupBy will split the DataFrame on its index (rows). To split by columns, first do
+DataFrame groupby always operates along axis 0 (rows). To split by columns, first do
 a transpose:
 
 .. ipython::

doc/source/whatsnew/v3.0.0.rst

@@ -156,6 +156,8 @@ All warnings for upcoming changes in pandas will have the base class :class:`pan
 
 Other enhancements
 ^^^^^^^^^^^^^^^^^^
+- :class:`pandas.NamedAgg` now supports passing ``*args`` and ``**kwargs``
+  to calls of ``aggfunc`` (:issue:`58283`)
 - :func:`pandas.merge` propagates the ``attrs`` attribute to the result if all
   inputs have identical ``attrs``, as has so far already been the case for
   :func:`pandas.concat`.
@@ -737,7 +739,9 @@ Other Deprecations
 - Deprecated allowing ``fill_value`` that cannot be held in the original dtype (excepting NA values for integer and bool dtypes) in :meth:`Series.shift` and :meth:`DataFrame.shift` (:issue:`53802`)
 - Deprecated backward-compatibility behavior for :meth:`DataFrame.select_dtypes` matching "str" dtype when ``np.object_`` is specified (:issue:`61916`)
 - Deprecated option "future.no_silent_downcasting", as it is no longer used. In a future version accessing this option will raise (:issue:`59502`)
+- Deprecated silent casting of non-datetime 'other' to datetime in :meth:`Series.combine_first` (:issue:`62931`)
 - Deprecated slicing on a :class:`Series` or :class:`DataFrame` with a :class:`DatetimeIndex` using a ``datetime.date`` object, explicitly cast to :class:`Timestamp` instead (:issue:`35830`)
+- Deprecated support for the Dataframe Interchange Protocol (:issue:`56732`)
 - Deprecated the 'inplace' keyword from :meth:`Resampler.interpolate`, as passing ``True`` raises ``AttributeError`` (:issue:`58690`)
 
 .. ---------------------------------------------------------------------------
@@ -960,6 +964,7 @@ Categorical
 ^^^^^^^^^^^
 - Bug in :class:`Categorical` where constructing from a pandas :class:`Series` or :class:`Index` with ``dtype='object'`` did not preserve the categories' dtype as ``object``; now the ``categories.dtype`` is preserved as ``object`` for these cases, while numpy arrays and Python sequences with ``dtype='object'`` continue to infer the most specific dtype (for example, ``str`` if all elements are strings) (:issue:`61778`)
 - Bug in :func:`Series.apply` where ``nan`` was ignored for :class:`CategoricalDtype` (:issue:`59938`)
+- Bug in :func:`bdate_range` raising ``ValueError`` with frequency ``freq="cbh"`` (:issue:`62849`)
 - Bug in :func:`testing.assert_index_equal` raising ``TypeError`` instead of ``AssertionError`` for incomparable ``CategoricalIndex`` when ``check_categorical=True`` and ``exact=False`` (:issue:`61935`)
 - Bug in :meth:`Categorical.astype` where ``copy=False`` would still trigger a copy of the codes (:issue:`62000`)
 - Bug in :meth:`DataFrame.pivot` and :meth:`DataFrame.set_index` raising an ``ArrowNotImplementedError`` for columns with pyarrow dictionary dtype (:issue:`53051`)
@@ -974,12 +979,15 @@ Datetimelike
 - Bug in :class:`Timestamp` constructor failing to raise when given a ``np.datetime64`` object with non-standard unit (:issue:`25611`)
 - Bug in :func:`date_range` where the last valid timestamp would sometimes not be produced (:issue:`56134`)
 - Bug in :func:`date_range` where using a negative frequency value would not include all points between the start and end values (:issue:`56147`)
+- Bug in :func:`infer_freq` with a :class:`Series` with :class:`ArrowDtype` timestamp dtype incorrectly raising ``TypeError`` (:issue:`58403`)
 - Bug in :func:`to_datetime` where passing an ``lxml.etree._ElementUnicodeResult`` together with ``format`` raised  ``TypeError``. Now subclasses of ``str`` are handled. (:issue:`60933`)
 - Bug in :func:`tseries.api.guess_datetime_format` would fail to infer time format when "%Y" == "%H%M" (:issue:`57452`)
 - Bug in :func:`tseries.frequencies.to_offset` would fail to parse frequency strings starting with "LWOM" (:issue:`59218`)
 - Bug in :meth:`DataFrame.fillna` raising an ``AssertionError`` instead of ``OutOfBoundsDatetime`` when filling a ``datetime64[ns]`` column with an out-of-bounds timestamp. Now correctly raises ``OutOfBoundsDatetime``. (:issue:`61208`)
 - Bug in :meth:`DataFrame.min` and :meth:`DataFrame.max` casting ``datetime64`` and ``timedelta64`` columns to ``float64`` and losing precision (:issue:`60850`)
 - Bug in :meth:`Dataframe.agg` with df with missing values resulting in IndexError (:issue:`58810`)
+- Bug in :meth:`DateOffset.rollback` (and subclass methods) with ``normalize=True`` rolling back one offset too long (:issue:`32616`)
+- Bug in :meth:`DatetimeIndex.asof` with a string key giving incorrect results (:issue:`50946`)
 - Bug in :meth:`DatetimeIndex.is_year_start` and :meth:`DatetimeIndex.is_quarter_start` does not raise on Custom business days frequencies bigger then "1C" (:issue:`58664`)
 - Bug in :meth:`DatetimeIndex.is_year_start` and :meth:`DatetimeIndex.is_quarter_start` returning ``False`` on double-digit frequencies (:issue:`58523`)
 - Bug in :meth:`DatetimeIndex.union` and :meth:`DatetimeIndex.intersection` when ``unit`` was non-nanosecond (:issue:`59036`)
@@ -998,6 +1006,7 @@ Datetimelike
 - Bug in comparison between objects with pyarrow date dtype and ``timestamp[pyarrow]`` or ``np.datetime64`` dtype failing to consider these as non-comparable (:issue:`62157`)
 - Bug in constructing arrays with :class:`ArrowDtype` with ``timestamp`` type incorrectly allowing ``Decimal("NaN")`` (:issue:`61773`)
 - Bug in constructing arrays with a timezone-aware :class:`ArrowDtype` from timezone-naive datetime objects incorrectly treating those as UTC times instead of wall times like :class:`DatetimeTZDtype` (:issue:`61775`)
+- Bug in retaining frequency in :meth:`value_counts` specifically for :meth:`DatetimeIndex` and :meth:`TimedeltaIndex` (:issue:`33830`)
 - Bug in setting scalar values with mismatched resolution into arrays with non-nanosecond ``datetime64``, ``timedelta64`` or :class:`DatetimeTZDtype` incorrectly truncating those scalars (:issue:`56410`)
 
 Timedelta
@@ -1049,6 +1058,7 @@ Interval
 - Bug in :class:`Index`, :class:`Series`, :class:`DataFrame` constructors when given a sequence of :class:`Interval` subclass objects casting them to :class:`Interval` (:issue:`46945`)
 - Bug in :func:`interval_range` where start and end numeric types were always cast to 64 bit (:issue:`57268`)
 - Bug in :meth:`IntervalIndex.get_indexer` and :meth:`IntervalIndex.drop` when one of the sides of the index is non-unique (:issue:`52245`)
+- Construction of :class:`IntervalArray` and :class:`IntervalIndex` from arrays with mismatched signed/unsigned integer dtypes (e.g., ``int64`` and ``uint64``) now raises a :exc:`TypeError` instead of proceeding silently. (:issue:`55715`)
 
 Indexing
 ^^^^^^^^
@@ -1114,6 +1124,7 @@ I/O
 - Bug in :meth:`read_csv` for the ``c`` and ``python`` engines where parsing numbers with large exponents caused overflows. Now, numbers with large positive exponents are parsed as ``inf`` or ``-inf`` depending on the sign of the mantissa, while those with large negative exponents are parsed as ``0.0`` (:issue:`62617`, :issue:`38794`, :issue:`62740`)
 - Bug in :meth:`read_csv` raising ``TypeError`` when ``index_col`` is specified and ``na_values`` is a dict containing the key ``None``. (:issue:`57547`)
 - Bug in :meth:`read_csv` raising ``TypeError`` when ``nrows`` and ``iterator`` are specified without specifying a ``chunksize``. (:issue:`59079`)
+- Bug in :meth:`read_csv` where it did not appropriately skip a line when instructed, causing Empty Data Error (:issue:`62739`)
 - Bug in :meth:`read_csv` where the order of the ``na_values`` makes an inconsistency when ``na_values`` is a list non-string values. (:issue:`59303`)
 - Bug in :meth:`read_csv` with ``c`` and ``python`` engines reading big integers as strings. Now reads them as python integers. (:issue:`51295`)
 - Bug in :meth:`read_csv` with ``engine="c"`` reading large float numbers with preceding integers as strings. Now reads them as floats. (:issue:`51295`)
@@ -1174,16 +1185,20 @@ Groupby/resample/rolling
 - Bug in :meth:`Rolling.apply` for ``method="table"`` where column order was not being respected due to the columns getting sorted by default. (:issue:`59666`)
 - Bug in :meth:`Rolling.apply` where the applied function could be called on fewer than ``min_period`` periods if ``method="table"``. (:issue:`58868`)
 - Bug in :meth:`Series.resample` could raise when the date range ended shortly before a non-existent time. (:issue:`58380`)
+- Bug in :meth:`Series.resample` raising error when resampling non-nanosecond resolutions out of bounds for nanosecond precision (:issue:`57427`)
 
 Reshaping
 ^^^^^^^^^
 - Bug in :func:`concat` with mixed integer and bool dtypes incorrectly casting the bools to integers (:issue:`45101`)
 - Bug in :func:`qcut` where values at the quantile boundaries could be incorrectly assigned (:issue:`59355`)
 - Bug in :meth:`DataFrame.combine_first` not preserving the column order (:issue:`60427`)
+- Bug in :meth:`DataFrame.combine_first` with non-unique columns incorrectly raising (:issue:`29135`)
+- Bug in :meth:`DataFrame.combine` with non-unique columns incorrectly raising (:issue:`51340`)
 - Bug in :meth:`DataFrame.explode` producing incorrect result for :class:`pyarrow.large_list` type (:issue:`61091`)
 - Bug in :meth:`DataFrame.join` inconsistently setting result index name (:issue:`55815`)
 - Bug in :meth:`DataFrame.join` when a :class:`DataFrame` with a :class:`MultiIndex` would raise an ``AssertionError`` when :attr:`MultiIndex.names` contained ``None``. (:issue:`58721`)
 - Bug in :meth:`DataFrame.merge` where merging on a column containing only ``NaN`` values resulted in an out-of-bounds array access (:issue:`59421`)
+- Bug in :meth:`Series.combine_first` incorrectly replacing ``None`` entries with ``NaN`` (:issue:`58977`)
 - Bug in :meth:`DataFrame.unstack` producing incorrect results when ``sort=False`` (:issue:`54987`, :issue:`55516`)
 - Bug in :meth:`DataFrame.unstack` raising an error with indexes containing ``NaN`` with ``sort=False`` (:issue:`61221`)
 - Bug in :meth:`DataFrame.merge` when merging two :class:`DataFrame` on ``intc`` or ``uintc`` types on Windows (:issue:`60091`, :issue:`58713`)
@@ -1264,6 +1279,7 @@ Other
 - Bug in ``divmod`` and ``rdivmod`` with :class:`DataFrame`, :class:`Series`, and :class:`Index` with ``bool`` dtypes failing to raise, which was inconsistent with ``__floordiv__`` behavior (:issue:`46043`)
 - Bug in printing a :class:`DataFrame` with a :class:`DataFrame` stored in :attr:`DataFrame.attrs` raised a ``ValueError`` (:issue:`60455`)
 - Bug in printing a :class:`Series` with a :class:`DataFrame` stored in :attr:`Series.attrs` raised a ``ValueError`` (:issue:`60568`)
+- Bug when calling :py:func:`copy.copy` on a :class:`DataFrame` or :class:`Series` which would return a deep copy instead of a shallow copy (:issue:`62971`)
 - Deprecated the keyword ``check_datetimelike_compat`` in :meth:`testing.assert_frame_equal` and :meth:`testing.assert_series_equal` (:issue:`55638`)
 - Fixed bug in :meth:`Series.replace` and :meth:`DataFrame.replace` when trying to replace :class:`NA` values in a :class:`Float64Dtype` object with ``np.nan``; this now works with ``pd.set_option("mode.nan_is_na", False)`` and is irrelevant otherwise (:issue:`55127`)
 - Fixed bug in :meth:`Series.replace` and :meth:`DataFrame.replace` when trying to replace :class:`np.nan` values in a :class:`Int64Dtype` object with :class:`NA`; this is now a no-op with ``pd.set_option("mode.nan_is_na", False)`` and is irrelevant otherwise (:issue:`51237`)

pandas/_libs/tslibs/offsets.pyx

@@ -692,6 +692,9 @@ cdef class BaseOffset:
             Rolled timestamp if not on offset, otherwise unchanged timestamp.
         """
         dt = Timestamp(dt)
+        if self.normalize and (dt - dt.normalize())._value != 0:
+            # GH#32616
+            dt = dt.normalize()
         if not self.is_on_offset(dt):
             dt = dt - type(self)(1, normalize=self.normalize, **self.kwds)
         return dt
@@ -5685,18 +5688,27 @@ def shift_month(stamp: datetime, months: int, day_opt: object = None) -> datetim
     cdef:
         int year, month, day
         int days_in_month, dy
+        npy_datetimestruct dts
+
+    if isinstance(stamp, _Timestamp):
+        creso = (<_Timestamp>stamp)._creso
+        val = (<_Timestamp>stamp)._value
+        pandas_datetime_to_datetimestruct(val, creso, &dts)
+    else:
+        # Plain datetime/date
+        pydate_to_dtstruct(stamp, &dts)
 
-    dy = (stamp.month + months) // 12
-    month = (stamp.month + months) % 12
+    dy = (dts.month + months) // 12
+    month = (dts.month + months) % 12
 
     if month == 0:
         month = 12
         dy -= 1
-    year = stamp.year + dy
+    year = dts.year + dy
 
     if day_opt is None:
         days_in_month = get_days_in_month(year, month)
-        day = min(stamp.day, days_in_month)
+        day = min(dts.day, days_in_month)
     elif day_opt == "start":
         day = 1
     elif day_opt == "end":

pandas/conftest.py

@@ -135,12 +135,14 @@ def pytest_collection_modifyitems(items, config) -> None:
     # Warnings from doctests that can be ignored; place reason in comment above.
     # Each entry specifies (path, message) - see the ignore_doctest_warning function
     ignored_doctest_warnings = [
+        ("api.interchange.from_dataframe", ".*Interchange Protocol is deprecated"),
         ("is_int64_dtype", "is_int64_dtype is deprecated"),
         ("is_interval_dtype", "is_interval_dtype is deprecated"),
         ("is_period_dtype", "is_period_dtype is deprecated"),
         ("is_datetime64tz_dtype", "is_datetime64tz_dtype is deprecated"),
         ("is_categorical_dtype", "is_categorical_dtype is deprecated"),
         ("is_sparse", "is_sparse is deprecated"),
+        ("DataFrame.__dataframe__", "Interchange Protocol is deprecated"),
         ("DataFrameGroupBy.fillna", "DataFrameGroupBy.fillna is deprecated"),
         ("DataFrameGroupBy.corrwith", "DataFrameGroupBy.corrwith is deprecated"),
         ("NDFrame.replace", "Series.replace without 'value'"),

pandas/core/algorithms.py

@@ -868,8 +868,10 @@ def value_counts_internal(
     dropna: bool = True,
 ) -> Series:
     from pandas import (
+        DatetimeIndex,
         Index,
         Series,
+        TimedeltaIndex,
     )
 
     index_name = getattr(values, "name", None)
@@ -934,6 +936,17 @@ def value_counts_internal(
             # Starting in 3.0, we no longer perform dtype inference on the
             #  Index object we construct here, xref GH#56161
             idx = Index(keys, dtype=keys.dtype, name=index_name)
+
+            if (
+                bins is None
+                and not sort
+                and isinstance(values, (DatetimeIndex, TimedeltaIndex))
+                and idx.equals(values)
+                and values.inferred_freq is not None
+            ):
+                # Preserve freq of original index
+                idx.freq = values.inferred_freq  # type: ignore[attr-defined]
+
             result = Series(counts, index=idx, name=name, copy=False)
 
     if sort:

pandas/core/apply.py

@@ -1745,7 +1745,13 @@ def reconstruct_func(
     >>> reconstruct_func("min")
     (False, 'min', None, None)
     """
-    relabeling = func is None and is_multi_agg_with_relabel(**kwargs)
+    from pandas.core.groupby.generic import NamedAgg
+
+    relabeling = func is None and (
+        is_multi_agg_with_relabel(**kwargs)
+        or any(isinstance(v, NamedAgg) for v in kwargs.values())
+    )
+
     columns: tuple[str, ...] | None = None
     order: npt.NDArray[np.intp] | None = None
 
@@ -1766,9 +1772,22 @@ def reconstruct_func(
         # "Callable[..., Any] | str | list[Callable[..., Any] | str] |
         # MutableMapping[Hashable, Callable[..., Any] | str | list[Callable[..., Any] |
         # str]] | None")
+        converted_kwargs = {}
+        for key, val in kwargs.items():
+            if isinstance(val, NamedAgg):
+                aggfunc = val.aggfunc
+                if val.args or val.kwargs:
+                    aggfunc = lambda x, func=aggfunc, a=val.args, kw=val.kwargs: func(
+                        x, *a, **kw
+                    )
+                converted_kwargs[key] = (val.column, aggfunc)
+            else:
+                converted_kwargs[key] = val
+
         func, columns, order = normalize_keyword_aggregation(  # type: ignore[assignment]
-            kwargs
+            converted_kwargs
         )
+
     assert func is not None
 
     return relabeling, func, columns, order

pandas/core/arrays/arrow/array.py

@@ -829,6 +829,14 @@ def __arrow_array__(self, type=None):
         """Convert myself to a pyarrow ChunkedArray."""
         return self._pa_array
 
+    def __array_ufunc__(self, ufunc: np.ufunc, method: str, *inputs, **kwargs):
+        # Need to wrap np.array results GH#62800
+        result = super().__array_ufunc__(ufunc, method, *inputs, **kwargs)
+        if type(self) is ArrowExtensionArray:
+            # Exclude ArrowStringArray
+            return type(self)._from_sequence(result)
+        return result
+
     def __array__(
         self, dtype: NpDtype | None = None, copy: bool | None = None
     ) -> np.ndarray: