Merge remote-tracking branch 'upstream/main' into add-typing-aliases

Author: Dr-Irv

.github/workflows/unit-tests.yml

@@ -313,7 +313,7 @@ jobs:
     #    To freeze this file, uncomment out the ``if: false`` condition, and migrate the jobs
     #    to the corresponding posix/windows-macos/sdist etc. workflows.
     # Feel free to modify this comment as necessary.
-    if: false
+    # if: false
     defaults:
       run:
         shell: bash -eou pipefail {0}
@@ -345,7 +345,7 @@ jobs:
       - name: Set up Python Dev Version
         uses: actions/setup-python@v6
         with:
-          python-version: '3.13-dev'
+          python-version: '3.14-dev'
 
       - name: Build Environment
         run: |
@@ -358,6 +358,8 @@ jobs:
 
       - name: Run Tests
         uses: ./.github/actions/run-tests
+        # TEMP allow this to fail until we fixed all test failures (related to chained assignment warnings)
+        continue-on-error: true
 
   # NOTE: this job must be kept in sync with the Pyodide build job in wheels.yml
   emscripten:

README.md

@@ -11,7 +11,7 @@
 | --- | --- |
 | Testing | [![CI - Test](https://github.com/pandas-dev/pandas/actions/workflows/unit-tests.yml/badge.svg)](https://github.com/pandas-dev/pandas/actions/workflows/unit-tests.yml) [![Coverage](https://codecov.io/github/pandas-dev/pandas/coverage.svg?branch=main)](https://codecov.io/gh/pandas-dev/pandas) |
 | Package | [![PyPI Latest Release](https://img.shields.io/pypi/v/pandas.svg)](https://pypi.org/project/pandas/) [![PyPI Downloads](https://img.shields.io/pypi/dm/pandas.svg?label=PyPI%20downloads)](https://pypi.org/project/pandas/) [![Conda Latest Release](https://anaconda.org/conda-forge/pandas/badges/version.svg)](https://anaconda.org/conda-forge/pandas) [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/pandas.svg?label=Conda%20downloads)](https://anaconda.org/conda-forge/pandas) |
-| Meta | [![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3509134.svg)](https://doi.org/10.5281/zenodo.3509134) [![License - BSD 3-Clause](https://img.shields.io/pypi/l/pandas.svg)](https://github.com/pandas-dev/pandas/blob/main/LICENSE) [![Slack](https://img.shields.io/badge/join_Slack-information-brightgreen.svg?logo=slack)](https://pandas.pydata.org/docs/dev/development/community.html?highlight=slack#community-slack) |
+| Meta | [![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3509134.svg)](https://doi.org/10.5281/zenodo.3509134) [![License - BSD 3-Clause](https://img.shields.io/pypi/l/pandas.svg)](https://github.com/pandas-dev/pandas/blob/main/LICENSE) [![Slack](https://img.shields.io/badge/join_Slack-information-brightgreen.svg?logo=slack)](https://pandas.pydata.org/docs/dev/development/community.html?highlight=slack#community-slack) [![LFX Health Score](https://insights.linuxfoundation.org/api/badge/health-score?project=pandas-dev-pandas)](https://insights.linuxfoundation.org/project/pandas-dev-pandas) |
 
 
 ## What is it?

ci/code_checks.sh

@@ -73,6 +73,7 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
         -i "pandas.Period.freq GL08" \
         -i "pandas.Period.ordinal GL08" \
         -i "pandas.errors.IncompatibleFrequency SA01,SS06,EX01" \
+        -i "pandas.api.extensions.ExtensionArray.value_counts EX01,RT03,SA01" \
         -i "pandas.core.groupby.DataFrameGroupBy.plot PR02" \
         -i "pandas.core.groupby.SeriesGroupBy.plot PR02" \
         -i "pandas.core.resample.Resampler.quantile PR01,PR07" \

doc/source/getting_started/intro_tutorials/01_table_oriented.rst

@@ -65,7 +65,7 @@ the values in each list as columns of the ``DataFrame``.
 A :class:`DataFrame` is a 2-dimensional data structure that can store data of
 different types (including characters, integers, floating point values,
 categorical data and more) in columns. It is similar to a spreadsheet, a
-SQL table or the ``data.frame`` in R.
+SQL table or the ``data.frame`` in `R <https://www.r-project.org/>`__.
 
 -  The table has 3 columns, each of them with a column label. The column
    labels are respectively ``Name``, ``Age`` and ``Sex``.

doc/source/whatsnew/v2.3.3.rst

@@ -22,6 +22,7 @@ become the default string dtype in pandas 3.0. See
 
 Bug fixes
 ^^^^^^^^^
+- Fix bug in :meth:`Series.str.replace` using named capture groups (e.g., ``\g<name>``) with the Arrow-backed dtype would raise an error (:issue:`57636`)
 - Fix regression in ``~Series.str.contains``, ``~Series.str.match`` and ``~Series.str.fullmatch``
   with a compiled regex and custom flags (:issue:`62240`)
 

doc/source/whatsnew/v3.0.0.rst

@@ -650,6 +650,7 @@ Other Deprecations
 - Deprecated ``pd.core.internals.api.maybe_infer_ndim`` (:issue:`40226`)
 - Deprecated allowing constructing or casting to :class:`Categorical` with non-NA values that are not present in specified ``dtype.categories`` (:issue:`40996`)
 - Deprecated allowing non-keyword arguments in :meth:`DataFrame.all`, :meth:`DataFrame.min`, :meth:`DataFrame.max`, :meth:`DataFrame.sum`, :meth:`DataFrame.prod`, :meth:`DataFrame.mean`, :meth:`DataFrame.median`, :meth:`DataFrame.sem`, :meth:`DataFrame.var`, :meth:`DataFrame.std`, :meth:`DataFrame.skew`, :meth:`DataFrame.kurt`, :meth:`Series.all`,  :meth:`Series.min`, :meth:`Series.max`, :meth:`Series.sum`, :meth:`Series.prod`, :meth:`Series.mean`, :meth:`Series.median`, :meth:`Series.sem`, :meth:`Series.var`, :meth:`Series.std`, :meth:`Series.skew`, and :meth:`Series.kurt`. (:issue:`57087`)
+- Deprecated allowing non-keyword arguments in :meth:`DataFrame.groupby` and :meth:`Series.groupby` except ``by`` and ``level``. (:issue:`62102`)
 - Deprecated allowing non-keyword arguments in :meth:`Series.to_markdown` except ``buf``. (:issue:`57280`)
 - Deprecated allowing non-keyword arguments in :meth:`Series.to_string` except ``buf``. (:issue:`57280`)
 - Deprecated behavior of :meth:`.DataFrameGroupBy.groups` and :meth:`.SeriesGroupBy.groups`, in a future version ``groups`` by one element list will return tuple instead of scalar. (:issue:`58858`)
@@ -903,6 +904,7 @@ Datetimelike
 - Bug in :meth:`DatetimeIndex.union` and :meth:`DatetimeIndex.intersection` when ``unit`` was non-nanosecond (:issue:`59036`)
 - Bug in :meth:`Index.union` with a ``pyarrow`` timestamp dtype incorrectly returning ``object`` dtype (:issue:`58421`)
 - Bug in :meth:`Series.dt.microsecond` producing incorrect results for pyarrow backed :class:`Series`. (:issue:`59154`)
+- Bug in :meth:`Timestamp.normalize` and :meth:`DatetimeArray.normalize` returning incorrect results instead of raising on integer overflow for very small (distant past) values (:issue:`60583`)
 - Bug in :meth:`Timestamp.replace` failing to update ``unit`` attribute when replacement introduces non-zero ``nanosecond`` or ``microsecond`` (:issue:`57749`)
 - Bug in :meth:`to_datetime` not respecting dayfirst if an uncommon date string was passed. (:issue:`58859`)
 - Bug in :meth:`to_datetime` on float array with missing values throwing ``FloatingPointError`` (:issue:`58419`)
@@ -1082,6 +1084,7 @@ Reshaping
 - 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:`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`)
 - Bug in :meth:`DataFrame.pivot_table` incorrectly subaggregating results when called without an ``index`` argument (:issue:`58722`)
 - Bug in :meth:`DataFrame.pivot_table` incorrectly ignoring the ``values`` argument when also supplied to the ``index`` or ``columns`` parameters (:issue:`57876`, :issue:`61292`)
@@ -1157,6 +1160,7 @@ Other
 - 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`)
 - Deprecated the keyword ``check_datetimelike_compat`` in :meth:`testing.assert_frame_equal` and :meth:`testing.assert_series_equal` (:issue:`55638`)
+- Fixed bug in the :meth:`Series.rank` with object dtype and extremely small float values (:issue:`62036`)
 - Fixed bug where the :class:`DataFrame` constructor misclassified array-like objects with a ``.name`` attribute as :class:`Series` or :class:`Index` (:issue:`61443`)
 - Fixed regression in :meth:`DataFrame.from_records` not initializing subclasses properly (:issue:`57008`)
 -

environment.yml

@@ -91,6 +91,9 @@ dependencies:
   - sphinx
   - sphinx-design
   - sphinx-copybutton
+
+  # static typing
+  - scipy-stubs
   - types-python-dateutil
   - types-PyMySQL
   - types-pytz

pandas/_libs/algos.pyx

@@ -1,7 +1,6 @@
 cimport cython
 from cython cimport Py_ssize_t
 from libc.math cimport (
-    fabs,
     sqrt,
 )
 from libc.stdlib cimport (
@@ -72,13 +71,6 @@ tiebreakers = {
 }
 
 
-cdef bint are_diff(object left, object right):
-    try:
-        return fabs(left - right) > FP_ERR
-    except TypeError:
-        return left != right
-
-
 class Infinity:
     """
     Provide a positive Infinity comparison method for ranking.
@@ -1135,12 +1127,8 @@ cdef void rank_sorted_1d(
             dups += 1
             sum_ranks += i - grp_start + 1
 
-            if numeric_object_t is object:
-                next_val_diff = at_end or are_diff(masked_vals[sort_indexer[i]],
-                                                   masked_vals[sort_indexer[i+1]])
-            else:
-                next_val_diff = at_end or (masked_vals[sort_indexer[i]]
-                                           != masked_vals[sort_indexer[i+1]])
+            next_val_diff = at_end or (masked_vals[sort_indexer[i]]
+                                       != masked_vals[sort_indexer[i+1]])
 
             # We'll need this check later anyway to determine group size, so just
             # compute it here since shortcircuiting won't help

pandas/_libs/sparse.pyi

@@ -1,9 +1,11 @@
-from collections.abc import Sequence
 from typing import Self
 
 import numpy as np
 
-from pandas._typing import npt
+from pandas._typing import (
+    TakeIndexer,
+    npt,
+)
 
 class SparseIndex:
     length: int
@@ -26,7 +28,7 @@ class SparseIndex:
 class IntIndex(SparseIndex):
     indices: npt.NDArray[np.int32]
     def __init__(
-        self, length: int, indices: Sequence[int], check_integrity: bool = ...
+        self, length: int, indices: TakeIndexer, check_integrity: bool = ...
     ) -> None: ...
 
 class BlockIndex(SparseIndex):

pandas/_libs/tslibs/timestamps.pyx

@@ -1339,7 +1339,12 @@ cdef class _Timestamp(ABCTimestamp):
             int64_t ppd = periods_per_day(self._creso)
             _Timestamp ts
 
-        normalized = normalize_i8_stamp(local_val, ppd)
+        try:
+            normalized = normalize_i8_stamp(local_val, ppd)
+        except OverflowError as err:
+            raise ValueError(
+                "Cannot normalize Timestamp without integer overflow"
+            ) from err
         ts = type(self)._from_value_and_reso(normalized, reso=self._creso, tz=None)
         return ts.tz_localize(self.tzinfo)
 
@@ -3547,7 +3552,7 @@ Timestamp.daysinmonth = Timestamp.days_in_month
 
 
 @cython.cdivision(False)
-cdef int64_t normalize_i8_stamp(int64_t local_val, int64_t ppd) noexcept nogil:
+cdef int64_t normalize_i8_stamp(int64_t local_val, int64_t ppd):
     """
     Round the localized nanosecond timestamp down to the previous midnight.
 
@@ -3561,4 +3566,6 @@ cdef int64_t normalize_i8_stamp(int64_t local_val, int64_t ppd) noexcept nogil:
     -------
     int64_t
     """
-    return local_val - (local_val % ppd)
+    with cython.overflowcheck(True):
+        # GH#60583
+        return local_val - (local_val % ppd)