Merge branch 'main' into fix-rolling-std-custom-weights

Author: ihsansecer

.github/workflows/code-checks.yml

@@ -33,7 +33,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -109,7 +109,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -143,7 +143,7 @@ jobs:
         run: docker image prune -f
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -164,7 +164,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/codeql.yml

@@ -27,7 +27,7 @@ jobs:
           - python
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: github/codeql-action/init@v2
         with:
           languages: ${{ matrix.language }}

.github/workflows/comment-commands.yml

@@ -51,7 +51,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/docbuild-and-upload.yml

@@ -36,7 +36,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 

.github/workflows/package-checks.yml

@@ -34,7 +34,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -62,7 +62,7 @@ jobs:
       cancel-in-progress: true
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/unit-tests.yml

@@ -136,7 +136,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
@@ -194,7 +194,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -330,7 +330,7 @@ jobs:
       PYTEST_TARGET: pandas
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/wheels.yml

@@ -48,7 +48,7 @@ jobs:
       sdist_file: ${{ steps.save-path.outputs.sdist_name }}
     steps:
       - name: Checkout pandas
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -103,7 +103,7 @@ jobs:
       IS_SCHEDULE_DISPATCH: ${{ github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' }}
     steps:
       - name: Checkout pandas
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

ci/deps/actions-310.yaml

@@ -46,6 +46,7 @@ dependencies:
   - pymysql>=1.0.2
   - pyreadstat>=1.1.5
   - pytables>=3.7.0
+  - python-calamine>=0.1.6
   - pyxlsb>=1.0.9
   - s3fs>=2022.05.0
   - scipy>=1.8.1

ci/deps/actions-311-downstream_compat.yaml

@@ -47,6 +47,7 @@ dependencies:
   - pymysql>=1.0.2
   - pyreadstat>=1.1.5
   - pytables>=3.7.0
+  - python-calamine>=0.1.6
   - pyxlsb>=1.0.9
   - s3fs>=2022.05.0
   - scipy>=1.8.1

ci/deps/actions-311.yaml

@@ -46,6 +46,7 @@ dependencies:
   - pymysql>=1.0.2
   - pyreadstat>=1.1.5
   # - pytables>=3.7.0, 3.8.0 is first version that supports 3.11
+  - python-calamine>=0.1.6
   - pyxlsb>=1.0.9
   - s3fs>=2022.05.0
   - scipy>=1.8.1

ci/deps/actions-39-minimum_versions.yaml

@@ -48,6 +48,7 @@ dependencies:
   - pymysql=1.0.2
   - pyreadstat=1.1.5
   - pytables=3.7.0
+  - python-calamine=0.1.6
   - pyxlsb=1.0.9
   - s3fs=2022.05.0
   - scipy=1.8.1

ci/deps/actions-39.yaml

@@ -46,6 +46,7 @@ dependencies:
   - pymysql>=1.0.2
   - pyreadstat>=1.1.5
   - pytables>=3.7.0
+  - python-calamine>=0.1.6
   - pyxlsb>=1.0.9
   - s3fs>=2022.05.0
   - scipy>=1.8.1

ci/deps/circle-310-arm64.yaml

@@ -47,6 +47,7 @@ dependencies:
   - pymysql>=1.0.2
   # - pyreadstat>=1.1.5 not available on ARM
   - pytables>=3.7.0
+  - python-calamine>=0.1.6
   - pyxlsb>=1.0.9
   - s3fs>=2022.05.0
   - scipy>=1.8.1

doc/source/getting_started/install.rst

@@ -281,6 +281,7 @@ xlrd                      2.0.1              excel           Reading Excel
 xlsxwriter                3.0.3              excel           Writing Excel
 openpyxl                  3.0.10             excel           Reading / writing for xlsx files
 pyxlsb                    1.0.9              excel           Reading for xlsb files
+python-calamine           0.1.6              excel           Reading for xls/xlsx/xlsb/ods files
 ========================= ================== =============== =============================================================
 
 HTML

doc/source/user_guide/io.rst

@@ -3453,7 +3453,8 @@ Excel files
 The :func:`~pandas.read_excel` method can read Excel 2007+ (``.xlsx``) files
 using the ``openpyxl`` Python module. Excel 2003 (``.xls``) files
 can be read using ``xlrd``. Binary Excel (``.xlsb``)
-files can be read using ``pyxlsb``.
+files can be read using ``pyxlsb``. All formats can be read
+using :ref:`calamine<io.calamine>` engine.
 The :meth:`~DataFrame.to_excel` instance method is used for
 saving a ``DataFrame`` to Excel.  Generally the semantics are
 similar to working with :ref:`csv<io.read_csv_table>` data.
@@ -3494,6 +3495,9 @@ using internally.
 
 * For the engine odf, pandas is using :func:`odf.opendocument.load` to read in (``.ods``) files.
 
+* For the engine calamine, pandas is using :func:`python_calamine.load_workbook`
+  to read in (``.xlsx``), (``.xlsm``), (``.xls``), (``.xlsb``), (``.ods``) files.
+
 .. code-block:: python
 
    # Returns a DataFrame
@@ -3935,7 +3939,8 @@ The :func:`~pandas.read_excel` method can also read binary Excel files
 using the ``pyxlsb`` module. The semantics and features for reading
 binary Excel files mostly match what can be done for `Excel files`_ using
 ``engine='pyxlsb'``. ``pyxlsb`` does not recognize datetime types
-in files and will return floats instead.
+in files and will return floats instead (you can use :ref:`calamine<io.calamine>`
+if you need recognize datetime types).
 
 .. code-block:: python
 
@@ -3947,6 +3952,20 @@ in files and will return floats instead.
    Currently pandas only supports *reading* binary Excel files. Writing
    is not implemented.
 
+.. _io.calamine:
+
+Calamine (Excel and ODS files)
+------------------------------
+
+The :func:`~pandas.read_excel` method can read Excel file (``.xlsx``, ``.xlsm``, ``.xls``, ``.xlsb``)
+and OpenDocument spreadsheets (``.ods``) using the ``python-calamine`` module.
+This module is a binding for Rust library `calamine <https://crates.io/crates/calamine>`__
+and is faster than other engines in most cases. The optional dependency 'python-calamine' needs to be installed.
+
+.. code-block:: python
+
+   # Returns a DataFrame
+   pd.read_excel("path_to_file.xlsb", engine="calamine")
 
 .. _io.clipboard:
 

doc/source/whatsnew/v0.10.0.rst

@@ -180,19 +180,36 @@ labeled the aggregated group with the end of the interval: the next day).
   DataFrame constructor with no columns specified. The v0.9.0 behavior (names
   ``X0``, ``X1``, ...) can be reproduced by specifying ``prefix='X'``:
 
-.. ipython:: python
-   :okexcept:
-
-    import io
-
-    data = """
-    a,b,c
-    1,Yes,2
-    3,No,4
-    """
-    print(data)
-    pd.read_csv(io.StringIO(data), header=None)
-    pd.read_csv(io.StringIO(data), header=None, prefix="X")
+.. code-block:: ipython
+
+    In [6]: import io
+
+    In [7]: data = """
+      ...: a,b,c
+      ...: 1,Yes,2
+      ...: 3,No,4
+      ...: """
+      ...:
+
+    In [8]: print(data)
+
+        a,b,c
+        1,Yes,2
+        3,No,4
+
+    In [9]: pd.read_csv(io.StringIO(data), header=None)
+    Out[9]:
+           0    1  2
+    0      a    b  c
+    1      1  Yes  2
+    2      3   No  4
+
+    In [10]: pd.read_csv(io.StringIO(data), header=None, prefix="X")
+    Out[10]:
+            X0   X1 X2
+    0       a    b  c
+    1       1  Yes  2
+    2       3   No  4
 
 - Values like ``'Yes'`` and ``'No'`` are not interpreted as boolean by default,
   though this can be controlled by new ``true_values`` and ``false_values``

doc/source/whatsnew/v2.1.1.rst

@@ -35,6 +35,7 @@ Bug fixes
 ~~~~~~~~~
 - Fixed bug for :class:`ArrowDtype` raising ``NotImplementedError`` for fixed-size list (:issue:`55000`)
 - Fixed bug in :meth:`DataFrame.stack` with ``future_stack=True`` and columns a non-:class:`MultiIndex` consisting of tuples (:issue:`54948`)
+- Fixed bug in :meth:`Series.dt.tz` with :class:`ArrowDtype` where a string was returned instead of a ``tzinfo`` object (:issue:`55003`)
 - Fixed bug in :meth:`Series.pct_change` and :meth:`DataFrame.pct_change` showing unnecessary ``FutureWarning`` (:issue:`54981`)
 
 .. ---------------------------------------------------------------------------

doc/source/whatsnew/v2.2.0.rst

@@ -14,10 +14,27 @@ including other versions of pandas.
 Enhancements
 ~~~~~~~~~~~~
 
-.. _whatsnew_220.enhancements.enhancement1:
+.. _whatsnew_220.enhancements.calamine:
 
-enhancement1
-^^^^^^^^^^^^
+Calamine engine for :func:`read_excel`
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``calamine`` engine was added to :func:`read_excel`.
+It uses ``python-calamine``, which provides Python bindings for the Rust library `calamine <https://crates.io/crates/calamine>`__.
+This engine supports Excel files (``.xlsx``, ``.xlsm``, ``.xls``, ``.xlsb``) and OpenDocument spreadsheets (``.ods``) (:issue:`50395`).
+
+There are two advantages of this engine:
+
+1. Calamine is often faster than other engines, some benchmarks show results up to 5x faster than 'openpyxl', 20x - 'odf', 4x - 'pyxlsb', and 1.5x - 'xlrd'.
+   But, 'openpyxl' and 'pyxlsb' are faster in reading a few rows from large files because of lazy iteration over rows.
+2. Calamine supports the recognition of datetime in ``.xlsb`` files, unlike 'pyxlsb' which is the only other engine in pandas that can read ``.xlsb`` files.
+
+.. code-block:: python
+
+   pd.read_excel("path_to_file.xlsb", engine="calamine")
+
+
+For more, see :ref:`io.calamine` in the user guide on IO tools.
 
 .. _whatsnew_220.enhancements.enhancement2:
 
@@ -28,7 +45,7 @@ enhancement2
 
 Other enhancements
 ^^^^^^^^^^^^^^^^^^
--
+- DataFrame.apply now allows the usage of numba (via ``engine="numba"``) to JIT compile the passed function, allowing for potential speedups (:issue:`54666`)
 -
 
 .. ---------------------------------------------------------------------------
@@ -158,9 +175,13 @@ Deprecations
 
 Performance improvements
 ~~~~~~~~~~~~~~~~~~~~~~~~
+- Performance improvement in :func:`concat` with ``axis=1`` and objects with unaligned indexes (:issue:`55084`)
 - Performance improvement in :func:`to_dict` on converting DataFrame to dictionary (:issue:`50990`)
+- Performance improvement in :meth:`DataFrame.groupby` when aggregating pyarrow timestamp and duration dtypes (:issue:`55031`)
 - Performance improvement in :meth:`DataFrame.sort_index` and :meth:`Series.sort_index` when indexed by a :class:`MultiIndex` (:issue:`54835`)
+- Performance improvement in :meth:`Index.difference` (:issue:`55108`)
 - Performance improvement when indexing with more than 4 keys (:issue:`54550`)
+-
 
 .. ---------------------------------------------------------------------------
 .. _whatsnew_220.bug_fixes:
@@ -169,6 +190,7 @@ Bug fixes
 ~~~~~~~~~
 - Bug in :class:`AbstractHolidayCalendar` where timezone data was not propagated when computing holiday observances (:issue:`54580`)
 - Bug in :class:`pandas.core.window.Rolling` where duplicate datetimelike indexes are treated as consecutive rather than equal with ``closed='left'`` and ``closed='neither'`` (:issue:`20712`)
+- Bug in :meth:`DataFrame.apply` where passing ``raw=True`` ignored ``args`` passed to the applied function (:issue:`55009`)
 
 Categorical
 ^^^^^^^^^^^
@@ -229,6 +251,7 @@ I/O
 ^^^
 - Bug in :func:`read_csv` where ``on_bad_lines="warn"`` would write to ``stderr`` instead of raise a Python warning. This now yields a :class:`.errors.ParserWarning` (:issue:`54296`)
 - Bug in :func:`read_excel`, with ``engine="xlrd"`` (``xls`` files) erroring when file contains NaNs/Infs (:issue:`54564`)
+- Bug in :func:`to_excel`, with ``OdsWriter`` (``ods`` files) writing boolean/string value (:issue:`54994`)
 
 Period
 ^^^^^^
@@ -247,8 +270,8 @@ Groupby/resample/rolling
 
 Reshaping
 ^^^^^^^^^
+- Bug in :func:`concat` ignoring ``sort`` parameter when passed :class:`DatetimeIndex` indexes (:issue:`54769`)
 - Bug in :func:`merge` returning columns in incorrect order when left and/or right is empty (:issue:`51929`)
--
 
 Sparse
 ^^^^^^

environment.yml

@@ -47,6 +47,7 @@ dependencies:
   - pymysql>=1.0.2
   - pyreadstat>=1.1.5
   - pytables>=3.7.0
+  - python-calamine>=0.1.6
   - pyxlsb>=1.0.9
   - s3fs>=2022.05.0
   - scipy>=1.8.1
@@ -105,7 +106,7 @@ dependencies:
   - ipykernel
 
   # web
-  - jinja2  # in optional dependencies, but documented here as needed
+  # - jinja2  # already listed in optional dependencies, but documented here for reference
   - markdown
   - feedparser
   - pyyaml