Merged main

Author: ritwizsinha

.github/workflows/unit-tests.yml

@@ -346,6 +346,51 @@ jobs:
       - name: Run Tests
         uses: ./.github/actions/run-tests
 
+  python-freethreading:
+    defaults:
+      run:
+        shell: bash -eou pipefail {0}
+    runs-on: ubuntu-22.04
+
+    timeout-minutes: 90
+
+    concurrency:
+      # https://github.community/t/concurrecy-not-work-for-push/183068/7
+      group: ${{ github.event_name == 'push' && github.run_number || github.ref }}-${{ matrix.os }}-python-freethreading-dev
+      cancel-in-progress: true
+
+    env:
+      PYTEST_WORKERS: "auto"
+      PANDAS_CI: 1
+      PATTERN: "not slow and not network and not clipboard and not single_cpu"
+      PYTEST_TARGET: pandas
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python Free-threading Version
+        uses: deadsnakes/[email protected]
+        with:
+          python-version: 3.13-dev
+          nogil: true
+
+      - name: Build Environment
+        run: |
+          python --version
+          python -m pip install --upgrade pip setuptools wheel meson[ninja]==1.2.1 meson-python==0.13.1
+          python -m pip install --pre --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy cython
+          python -m pip install versioneer[toml]
+          python -m pip install python-dateutil pytz tzdata hypothesis>=6.46.1 pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-cov
+          python -m pip install -ve . --no-build-isolation --no-index --no-deps --config-settings=setup-args="--werror"
+          python -m pip list
+
+      - name: Run Tests
+        uses: ./.github/actions/run-tests
+        env:
+          PYTHON_GIL: 0
+
   emscripten:
     # Note: the Python version, Emscripten toolchain version are determined
     # by the Pyodide version. The appropriate versions can be found in the

.pre-commit-config.yaml

@@ -67,6 +67,7 @@ repos:
     -   id: fix-encoding-pragma
         args: [--remove]
     -   id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
 -   repo: https://github.com/PyCQA/isort
     rev: 5.13.2
     hooks:

asv_bench/benchmarks/tslibs/timedelta.py

@@ -20,7 +20,7 @@ def time_from_int(self):
         Timedelta(123456789)
 
     def time_from_unit(self):
-        Timedelta(1, unit="d")
+        Timedelta(1, unit="D")
 
     def time_from_components(self):
         Timedelta(

ci/code_checks.sh

@@ -162,7 +162,7 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
         -i "pandas.Series.ne SA01" \
         -i "pandas.Series.pad PR01,SA01" \
         -i "pandas.Series.plot PR02" \
-        -i "pandas.Series.pop RT03,SA01" \
+        -i "pandas.Series.pop SA01" \
         -i "pandas.Series.prod RT03" \
         -i "pandas.Series.product RT03" \
         -i "pandas.Series.reorder_levels RT03,SA01" \

doc/source/whatsnew/v3.0.0.rst

@@ -230,6 +230,7 @@ Other API changes
 - 3rd party ``py.path`` objects are no longer explicitly supported in IO methods. Use :py:class:`pathlib.Path` objects instead (:issue:`57091`)
 - :func:`read_table`'s ``parse_dates`` argument defaults to ``None`` to improve consistency with :func:`read_csv` (:issue:`57476`)
 - Made ``dtype`` a required argument in :meth:`ExtensionArray._from_sequence_of_strings` (:issue:`56519`)
+- Passing a :class:`Series` input to :func:`json_normalize` will now retain the :class:`Series` :class:`Index`, previously output had a new :class:`RangeIndex` (:issue:`51452`)
 - Updated :meth:`DataFrame.to_excel` so that the output spreadsheet has no styling. Custom styling can still be done using :meth:`Styler.to_excel` (:issue:`54154`)
 - pickle and HDF (``.h5``) files created with Python 2 are no longer explicitly supported (:issue:`57387`)
 - pickled objects from pandas version less than ``1.0.0`` are no longer supported (:issue:`57155`)
@@ -381,6 +382,8 @@ Other Removals
 - Enforced deprecation of strings ``T``, ``L``, ``U``, and ``N`` denoting frequencies in :class:`Minute`, :class:`Milli`, :class:`Micro`, :class:`Nano` (:issue:`57627`)
 - Enforced deprecation of strings ``T``, ``L``, ``U``, and ``N`` denoting units in :class:`Timedelta` (:issue:`57627`)
 - Enforced deprecation of the behavior of :func:`concat` when ``len(keys) != len(objs)`` would truncate to the shorter of the two. Now this raises a ``ValueError`` (:issue:`43485`)
+- Enforced deprecation of the behavior of :meth:`DataFrame.replace` and :meth:`Series.replace` with :class:`CategoricalDtype` that would introduce new categories. (:issue:`58270`)
+- Enforced deprecation of the behavior of :meth:`Series.argsort` in the presence of NA values (:issue:`58232`)
 - Enforced deprecation of values "pad", "ffill", "bfill", and "backfill" for :meth:`Series.interpolate` and :meth:`DataFrame.interpolate` (:issue:`57869`)
 - Enforced deprecation removing :meth:`Categorical.to_list`, use ``obj.tolist()`` instead (:issue:`51254`)
 - Enforced silent-downcasting deprecation for :ref:`all relevant methods <whatsnew_220.silent_downcasting>` (:issue:`54710`)
@@ -545,6 +548,7 @@ MultiIndex
 ^^^^^^^^^^
 - :func:`DataFrame.loc` with ``axis=0``  and :class:`MultiIndex` when setting a value adds extra columns (:issue:`58116`)
 - :meth:`DataFrame.melt` would not accept multiple names in ``var_name`` when the columns were a :class:`MultiIndex` (:issue:`58033`)
+- :meth:`MultiIndex.insert` would not insert NA value correctly at unified location of index -1 (:issue:`59003`)
 -
 
 I/O
@@ -555,8 +559,10 @@ I/O
 - Bug in :meth:`DataFrame.to_stata` when writing :class:`DataFrame` and ``byteorder=`big```. (:issue:`58969`)
 - Bug in :meth:`DataFrame.to_string` that raised ``StopIteration`` with nested DataFrames. (:issue:`16098`)
 - Bug in :meth:`HDFStore.get` was failing to save data of dtype datetime64[s] correctly (:issue:`59004`)
+- Bug in :meth:`read_csv` causing segmentation fault when ``encoding_errors`` is not a string. (:issue:`59059`)
 - 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_excel` raising ``ValueError`` when passing array of boolean values when ``dtype="boolean"``. (:issue:`58159`)
 - Bug in :meth:`read_html` would return an incorrect result when parsing a table with a space character in a ``<td>`` tag. (:issue:`12345`)
 - Bug in :meth:`read_stata` raising ``KeyError`` when input file is stored in big-endian format and contains strL data. (:issue:`58638`)
 
@@ -590,11 +596,12 @@ Reshaping
 ^^^^^^^^^
 - Bug in :meth:`DataFrame.join` inconsistently setting result index name (:issue:`55815`)
 - Bug in :meth:`DataFrame.unstack` producing incorrect results when ``sort=False`` (:issue:`54987`, :issue:`55516`)
+- Bug in :meth:`DataFrame.unstack` producing incorrect results when manipulating empty :class:`DataFrame` with an :class:`ExtentionDtype` (:issue:`59123`)
 
 Sparse
 ^^^^^^
 - Bug in :class:`SparseDtype` for equal comparison with na fill value. (:issue:`54770`)
--
+- Bug in :meth:`DataFrame.sparse.from_spmatrix` which hard coded an invalid ``fill_value`` for certain subtypes. (:issue:`59063`)
 
 ExtensionArray
 ^^^^^^^^^^^^^^

pandas/_libs/src/datetime/pd_datetime.c

@@ -245,7 +245,12 @@ static int pandas_datetime_exec(PyObject *Py_UNUSED(module)) {
 }
 
 static PyModuleDef_Slot pandas_datetime_slots[] = {
-    {Py_mod_exec, pandas_datetime_exec}, {0, NULL}};
+    {Py_mod_exec, pandas_datetime_exec},
+#if PY_VERSION_HEX >= 0x030D0000
+    {Py_mod_gil, Py_MOD_GIL_NOT_USED},
+#endif
+    {0, NULL},
+};
 
 static struct PyModuleDef pandas_datetimemodule = {
     PyModuleDef_HEAD_INIT,

pandas/_libs/src/parser/pd_parser.c

@@ -161,7 +161,12 @@ static int pandas_parser_exec(PyObject *Py_UNUSED(module)) {
 }
 
 static PyModuleDef_Slot pandas_parser_slots[] = {
-    {Py_mod_exec, pandas_parser_exec}, {0, NULL}};
+    {Py_mod_exec, pandas_parser_exec},
+#if PY_VERSION_HEX >= 0x030D0000
+    {Py_mod_gil, Py_MOD_GIL_NOT_USED},
+#endif
+    {0, NULL},
+};
 
 static struct PyModuleDef pandas_parsermodule = {
     PyModuleDef_HEAD_INIT,

pandas/_libs/tslibs/dtypes.pyx

@@ -453,10 +453,6 @@ class Resolution(Enum):
         """
         cdef:
             str abbrev
-        if freq in {"T", "t", "L", "l", "U", "u", "N", "n"}:
-            raise ValueError(
-                f"Frequency \'{freq}\' is no longer supported."
-            )
         try:
             if freq in c_DEPR_ABBREVS:
                 abbrev = c_DEPR_ABBREVS[freq]

pandas/_libs/tslibs/timedeltas.pyi

@@ -39,8 +39,6 @@ UnitChoices: TypeAlias = Literal[
     "minute",
     "min",
     "minutes",
-    "T",
-    "t",
     "s",
     "seconds",
     "sec",
@@ -50,21 +48,17 @@ UnitChoices: TypeAlias = Literal[
     "millisecond",
     "milli",
     "millis",
-    "L",
-    "l",
     "us",
     "microseconds",
     "microsecond",
     "µs",
     "micro",
     "micros",
-    "u",
     "ns",
     "nanoseconds",
     "nano",
     "nanos",
     "nanosecond",
-    "n",
 ]
 _S = TypeVar("_S", bound=timedelta)
 

pandas/_libs/tslibs/timedeltas.pyx

@@ -1818,11 +1818,6 @@ class Timedelta(_Timedelta):
         * 'microseconds', 'microsecond', 'micros', 'micro', or 'us'
         * 'nanoseconds', 'nanosecond', 'nanos', 'nano', or 'ns'.
 
-        .. deprecated:: 2.2.0
-
-            Values `H`, `T`, `S`, `L`, `U`, and `N` are deprecated in favour
-            of the values `h`, `min`, `s`, `ms`, `us`, and `ns`.
-
         .. deprecated:: 3.0.0
 
             Allowing the values `w`, `d`, `MIN`, `MS`, `US` and `NS` to denote units