Merge remote-tracking branch 'upstream/main' into string-dtype-tests-quantile

jorisvandenbossche · jorisvandenbossche · commit 5fa24d292088 · 2024-10-31T09:43:50.000+01:00
diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
@@ -86,7 +86,6 @@ jobs:
       TEST_ARGS: ${{ matrix.test_args || '' }}
       PYTEST_WORKERS: 'auto'
       PYTEST_TARGET: ${{ matrix.pytest_target || 'pandas' }}
-      NPY_PROMOTION_STATE: ${{ matrix.env_file == 'actions-311-numpydev.yaml' && 'weak' || 'legacy' }}
       # Clipboard tests
       QT_QPA_PLATFORM: offscreen
       REMOVE_PYARROW: ${{ matrix.name == 'Future infer strings (without pyarrow)' && '1' || '0' }}
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -156,7 +156,7 @@ jobs:
         run: echo "sdist_name=$(cd ./dist && ls -d */)" >> "$GITHUB_ENV"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.21.0
+        uses: pypa/cibuildwheel@v2.21.3
         with:
          package-dir: ./dist/${{ startsWith(matrix.buildplat[1], 'macosx') && env.sdist_name || needs.build_sdist.outputs.sdist_file }}
         env:
diff --git a/ci/code_checks.sh b/ci/code_checks.sh
@@ -85,7 +85,6 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
         -i "pandas.Timestamp.resolution PR02" \
         -i "pandas.Timestamp.tzinfo GL08" \
         -i "pandas.Timestamp.year GL08" \
-        -i "pandas.api.types.is_iterator PR07,SA01" \
         -i "pandas.api.types.is_re_compilable PR07,SA01" \
         -i "pandas.api.types.pandas_dtype PR07,RT03,SA01" \
         -i "pandas.arrays.ArrowExtensionArray PR07,SA01" \
@@ -144,7 +143,6 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
         -i "pandas.io.stata.StataWriter.write_file SA01" \
         -i "pandas.plotting.andrews_curves RT03,SA01" \
         -i "pandas.plotting.scatter_matrix PR07,SA01" \
-        -i "pandas.set_eng_float_format RT03,SA01" \
         -i "pandas.tseries.offsets.BDay PR02,SA01" \
         -i "pandas.tseries.offsets.BQuarterBegin.is_on_offset GL08" \
         -i "pandas.tseries.offsets.BQuarterBegin.n GL08" \
diff --git a/ci/deps/actions-311-pyarrownightly.yaml b/ci/deps/actions-311-pyarrownightly.yaml
@@ -18,7 +18,7 @@ dependencies:
 
   # required dependencies
   - python-dateutil
-  - numpy<2
+  - numpy
   - pip
 
   - pip:
diff --git a/doc/source/user_guide/cookbook.rst b/doc/source/user_guide/cookbook.rst
@@ -35,7 +35,7 @@ These are some neat pandas ``idioms``
    )
    df
 
-if-then...
+If-then...
 **********
 
 An if-then on one column
@@ -176,7 +176,7 @@ One could hard code:
 Selection
 ---------
 
-Dataframes
+DataFrames
 **********
 
 The :ref:`indexing <indexing>` docs.
@@ -1489,7 +1489,7 @@ of the data values:
    )
    df
 
-Constant series
+Constant Series
 ---------------
 
 To assess if a series has a constant value, we can check if ``series.nunique() <= 1``.
diff --git a/doc/source/user_guide/gotchas.rst b/doc/source/user_guide/gotchas.rst
@@ -121,7 +121,7 @@ Below is how to check if any of the values are ``True``:
     if pd.Series([False, True, False]).any():
         print("I am any")
 
-Bitwise boolean
+Bitwise Boolean
 ~~~~~~~~~~~~~~~
 
 Bitwise boolean operators like ``==`` and ``!=`` return a boolean :class:`Series`
diff --git a/doc/source/user_guide/groupby.rst b/doc/source/user_guide/groupby.rst
@@ -618,7 +618,7 @@ this will make an extra copy.
 
 .. _groupby.aggregate.udf:
 
-Aggregation with User-Defined Functions
+Aggregation with user-defined functions
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Users can also provide their own User-Defined Functions (UDFs) for custom aggregations.
@@ -1261,7 +1261,7 @@ with
     df.groupby("A", group_keys=False).apply(lambda x: x, include_groups=False)
 
 
-Numba Accelerated Routines
+Numba accelerated routines
 --------------------------
 
 .. versionadded:: 1.1
@@ -1696,7 +1696,7 @@ introduction <categorical>` and the
 
     dfg.groupby(["A", [0, 0, 0, 1, 1]]).ngroup()
 
-Groupby by indexer to 'resample' data
+GroupBy by indexer to 'resample' data
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Resampling produces new hypothetical samples (resamples) from already existing observed data or from a model that generates data. These new samples are similar to the pre-existing samples.
diff --git a/doc/source/user_guide/integer_na.rst b/doc/source/user_guide/integer_na.rst
@@ -147,7 +147,7 @@ Reduction and groupby operations such as :meth:`~DataFrame.sum` work as well.
    df.sum()
    df.groupby("B").A.sum()
 
-Scalar NA Value
+Scalar NA value
 ---------------
 
 :class:`arrays.IntegerArray` uses :attr:`pandas.NA` as its scalar
diff --git a/doc/source/user_guide/io.rst b/doc/source/user_guide/io.rst
@@ -5996,7 +5996,7 @@ Full documentation can be found `here <https://pandas-gbq.readthedocs.io/en/late
 
 .. _io.stata:
 
-Stata format
+STATA format
 ------------
 
 .. _io.stata_writer:
diff --git a/doc/source/whatsnew/v1.0.2.rst b/doc/source/whatsnew/v1.0.2.rst
@@ -47,7 +47,7 @@ Fixed regressions
 
 .. ---------------------------------------------------------------------------
 
-Indexing with nullable boolean arrays
+Indexing with nullable Boolean arrays
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Previously indexing with a nullable Boolean array containing ``NA`` would raise a ``ValueError``, however this is now permitted with ``NA`` being treated as ``False``. (:issue:`31503`)
diff --git a/doc/source/whatsnew/v3.0.0.rst b/doc/source/whatsnew/v3.0.0.rst
@@ -592,6 +592,7 @@ Performance improvements
 - Performance improvement in :meth:`RangeIndex.take` returning a :class:`RangeIndex` instead of a :class:`Index` when possible. (:issue:`57445`, :issue:`57752`)
 - Performance improvement in :func:`merge` if hash-join can be used (:issue:`57970`)
 - Performance improvement in :meth:`CategoricalDtype.update_dtype` when ``dtype`` is a :class:`CategoricalDtype` with non ``None`` categories and ordered (:issue:`59647`)
+- Performance improvement in :meth:`DataFrame.astype` when converting to extension floating dtypes, e.g. "Float64" (:issue:`60066`)
 - Performance improvement in :meth:`to_hdf` avoid unnecessary reopenings of the HDF5 file to speedup data addition to files with a very large number of groups . (:issue:`58248`)
 - Performance improvement in ``DataFrameGroupBy.__len__`` and ``SeriesGroupBy.__len__`` (:issue:`57595`)
 - Performance improvement in indexing operations for string dtypes (:issue:`56997`)
diff --git a/pandas/_libs/lib.pyx b/pandas/_libs/lib.pyx
@@ -259,15 +259,23 @@ def is_iterator(obj: object) -> bool:
     Check if the object is an iterator.
 
     This is intended for generators, not list-like objects.
+    This method checks whether the passed object is an iterator. It
+    returns `True` if the object is an iterator, and `False` otherwise.
 
     Parameters
     ----------
     obj : The object to check
+        The object to check for iterator type.
 
     Returns
     -------
     is_iter : bool
         Whether `obj` is an iterator.
+        `True` if the object is of iterator type, otherwise `False`.
+
+    See Also
+    --------
+    api.types.is_list_like : Check if the input is list-like.
 
     Examples
     --------
diff --git a/pandas/_libs/tslibs/timedeltas.pyx b/pandas/_libs/tslibs/timedeltas.pyx
@@ -2178,8 +2178,10 @@ class Timedelta(_Timedelta):
         Parameters
         ----------
         freq : str
-            Frequency string indicating the ceiling resolution.
-            It uses the same units as class constructor :class:`~pandas.Timedelta`.
+            Frequency string indicating the ceiling resolution. Must be a fixed
+            frequency like 's' (second) not 'ME' (month end). See
+            :ref:`frequency aliases <timeseries.offset_aliases>` for
+            a list of possible `freq` values.
 
         Returns
         -------
diff --git a/pandas/conftest.py b/pandas/conftest.py
@@ -667,7 +667,8 @@ def _create_mi_with_dt64tz_level():
 
 
 indices_dict = {
-    "string": Index([f"pandas_{i}" for i in range(10)]),
+    "object": Index([f"pandas_{i}" for i in range(10)], dtype=object),
+    "string": Index([f"pandas_{i}" for i in range(10)], dtype="str"),
     "datetime": date_range("2020-01-01", periods=10),
     "datetime-tz": date_range("2020-01-01", periods=10, tz="US/Pacific"),
     "period": period_range("2020-01-01", periods=10, freq="D"),
diff --git a/pandas/core/arrays/numeric.py b/pandas/core/arrays/numeric.py
@@ -174,6 +174,8 @@ def _coerce_to_data_and_mask(
             raise TypeError(f"{values.dtype} cannot be converted to {name}")
 
     elif values.dtype.kind == "b" and checker(dtype):
+        # fastpath
+        mask = np.zeros(len(values), dtype=np.bool_)
         if not copy:
             values = np.asarray(values, dtype=default_dtype)
         else:
@@ -190,6 +192,10 @@ def _coerce_to_data_and_mask(
         if values.dtype.kind in "iu":
             # fastpath
             mask = np.zeros(len(values), dtype=np.bool_)
+        elif values.dtype.kind == "f":
+            # np.isnan is faster than is_numeric_na() for floats
+            # github issue: #60066
+            mask = np.isnan(values)
         else:
             mask = libmissing.is_numeric_na(values)
     else:
diff --git a/pandas/core/frame.py b/pandas/core/frame.py
@@ -718,7 +718,7 @@ def __init__(
                     "is deprecated and will raise in a future version. "
                     "Use public APIs instead.",
                     DeprecationWarning,
-                    stacklevel=1,  # bump to 2 once pyarrow 15.0 is released with fix
+                    stacklevel=2,
                 )
 
             data = data.copy(deep=False)
diff --git a/pandas/core/generic.py b/pandas/core/generic.py
@@ -3339,7 +3339,7 @@ def to_latex(
             The subset of columns to write. Writes all columns by default.
         header : bool or list of str, default True
             Write out the column names. If a list of strings is given,
-            it is assumed to be aliases for the column names.
+            it is assumed to be aliases for the column names. Braces must be escaped.
         index : bool, default True
             Write row names (index).
         na_rep : str, default 'NaN'
diff --git a/pandas/io/formats/format.py b/pandas/io/formats/format.py
@@ -1926,6 +1926,9 @@ def set_eng_float_format(accuracy: int = 3, use_eng_prefix: bool = False) -> Non
     """
     Format float representation in DataFrame with SI notation.
 
+    Sets the floating-point display format for ``DataFrame`` objects using engineering
+    notation (SI units), allowing easier readability of values across wide ranges.
+
     Parameters
     ----------
     accuracy : int, default 3
@@ -1936,6 +1939,13 @@ def set_eng_float_format(accuracy: int = 3, use_eng_prefix: bool = False) -> Non
     Returns
     -------
     None
+        This method does not return a value. it updates the global display format
+        for floats in DataFrames.
+
+    See Also
+    --------
+    set_option : Set the value of the specified option or options.
+    reset_option : Reset one or more options to their default value.
 
     Examples
     --------
diff --git a/pandas/io/stata.py b/pandas/io/stata.py
@@ -569,7 +569,11 @@ def _cast_to_stata_types(data: DataFrame) -> DataFrame:
             if getattr(data[col].dtype, "numpy_dtype", None) is not None:
                 data[col] = data[col].astype(data[col].dtype.numpy_dtype)
             elif is_string_dtype(data[col].dtype):
+                # TODO could avoid converting string dtype to object here,
+                # but handle string dtype in _encode_strings
                 data[col] = data[col].astype("object")
+                # generate_table checks for None values
+                data.loc[data[col].isna(), col] = None
 
         dtype = data[col].dtype
         empty_df = data.shape[0] == 0
@@ -2725,6 +2729,7 @@ def _encode_strings(self) -> None:
                 continue
             column = self.data[col]
             dtype = column.dtype
+            # TODO could also handle string dtype here specifically
             if dtype.type is np.object_:
                 inferred_dtype = infer_dtype(column, skipna=True)
                 if not ((inferred_dtype == "string") or len(column) == 0):
diff --git a/pandas/tests/dtypes/test_dtypes.py b/pandas/tests/dtypes/test_dtypes.py
@@ -1243,3 +1243,12 @@ def test_loc_setitem_empty_labels_no_dtype_conversion():
 
     assert df.a.dtype == "int64"
     tm.assert_frame_equal(df, expected)
+
+
+def test_categorical_nan_no_dtype_conversion():
+    # GH 43996
+
+    df = pd.DataFrame({"a": Categorical([np.nan], [1]), "b": [1]})
+    expected = pd.DataFrame({"a": Categorical([1], [1]), "b": [1]})
+    df.loc[0, "a"] = np.array([1])
+    tm.assert_frame_equal(df, expected)
diff --git a/pandas/tests/indexes/test_any_index.py b/pandas/tests/indexes/test_any_index.py
@@ -40,7 +40,7 @@ def test_map_identity_mapping(index, request):
     # GH#12766
 
     result = index.map(lambda x: x)
-    if index.dtype == object and result.dtype == bool:
+    if index.dtype == object and (result.dtype == bool or result.dtype == "string"):
         assert (index == result).all()
         # TODO: could work that into the 'exact="equiv"'?
         return  # FIXME: doesn't belong in this file anymore!
diff --git a/pandas/tests/indexes/test_old_base.py b/pandas/tests/indexes/test_old_base.py
@@ -256,7 +256,7 @@ def test_ensure_copied_data(self, index):
                 "RangeIndex cannot be initialized from data, "
                 "MultiIndex and CategoricalIndex are tested separately"
             )
-        elif index.dtype == object and index.inferred_type == "boolean":
+        elif index.dtype == object and index.inferred_type in ["boolean", "string"]:
             init_kwargs["dtype"] = index.dtype
 
         index_type = type(index)
diff --git a/pandas/tests/indexes/test_setops.py b/pandas/tests/indexes/test_setops.py
@@ -299,7 +299,13 @@ def test_difference_base(self, sort, index):
                 first.difference([1, 2, 3], sort)
 
     @pytest.mark.filterwarnings(r"ignore:PeriodDtype\[B\] is deprecated:FutureWarning")
-    def test_symmetric_difference(self, index):
+    def test_symmetric_difference(self, index, using_infer_string, request):
+        if (
+            using_infer_string
+            and index.dtype == "object"
+            and index.inferred_type == "string"
+        ):
+            request.applymarker(pytest.mark.xfail(reason="TODO: infer_string"))
         if isinstance(index, CategoricalIndex):
             pytest.skip(f"Not relevant for {type(index).__name__}")
         if len(index) < 2:
diff --git a/pandas/tests/io/test_parquet.py b/pandas/tests/io/test_parquet.py
@@ -17,7 +17,6 @@
     pa_version_under13p0,
     pa_version_under15p0,
     pa_version_under17p0,
-    pa_version_under18p0,
 )
 
 import pandas as pd
@@ -974,21 +973,9 @@ def test_timestamp_nanoseconds(self, pa):
         df = pd.DataFrame({"a": pd.date_range("2017-01-01", freq="1ns", periods=10)})
         check_round_trip(df, pa, write_kwargs={"version": ver})
 
-    def test_timezone_aware_index(self, request, pa, timezone_aware_date_list):
+    def test_timezone_aware_index(self, pa, timezone_aware_date_list):
         pytest.importorskip("pyarrow", "11.0.0")
 
-        if (
-            timezone_aware_date_list.tzinfo != datetime.timezone.utc
-            and pa_version_under18p0
-        ):
-            request.applymarker(
-                pytest.mark.xfail(
-                    reason=(
-                        "pyarrow returns pytz.FixedOffset while pandas "
-                        "constructs datetime.timezone https://github.com/pandas-dev/pandas/issues/37286"
-                    )
-                )
-            )
         idx = 5 * [timezone_aware_date_list]
         df = pd.DataFrame(index=idx, data={"index_as_col": idx})
 
@@ -1005,6 +992,18 @@ def test_timezone_aware_index(self, request, pa, timezone_aware_date_list):
         expected = df[:]
         if pa_version_under11p0:
             expected.index = expected.index.as_unit("ns")
+        if timezone_aware_date_list.tzinfo != datetime.timezone.utc:
+            # pyarrow returns pytz.FixedOffset while pandas constructs datetime.timezone
+            # https://github.com/pandas-dev/pandas/issues/37286
+            try:
+                import pytz
+            except ImportError:
+                pass
+            else:
+                offset = df.index.tz.utcoffset(timezone_aware_date_list)
+                tz = pytz.FixedOffset(offset.total_seconds() / 60)
+                expected.index = expected.index.tz_convert(tz)
+                expected["index_as_col"] = expected["index_as_col"].dt.tz_convert(tz)
         check_round_trip(df, pa, check_dtype=False, expected=expected)
 
     def test_filter_row_groups(self, pa):
diff --git a/pandas/tests/io/test_stata.py b/pandas/tests/io/test_stata.py
diff --git a/pandas/tests/test_algos.py b/pandas/tests/test_algos.py
diff --git a/web/pandas/about/team.md b/web/pandas/about/team.md

-Original file line number
+Diff line change
         run: echo "sdist_name=$(cd ./dist && ls -d */)" >> "$GITHUB_ENV"
       - name: Build wheels
 -        uses: pypa/[email protected].0
 +        uses: pypa/[email protected].3
         with:
          package-dir: ./dist/${{ startsWith(matrix.buildplat[1], 'macosx') && env.sdist_name || needs.build_sdist.outputs.sdist_file }}
         env: