Merge remote-tracking branch 'upstream/main' into fix-docstring

Author: fbourgey

.circleci/config.yml

@@ -92,7 +92,13 @@ jobs:
           no_output_timeout: 30m # Sometimes the tests won't generate any output, make sure the job doesn't get killed by that
           command: |
             pip3 install cibuildwheel==2.20.0
-            cibuildwheel --output-dir wheelhouse
+            if [[ $CIBW_BUILD == cp313t* ]]; then
+              # TODO: temporarily run 3.13 free threaded builds without build isolation
+              # since we need pre-release cython
+              CIBW_BUILD_FRONTEND="pip; args: --no-build-isolation" cibuildwheel --output-dir wheelhouse
+            else
+              cibuildwheel --output-dir wheelhouse
+            fi
 
           environment:
             CIBW_BUILD: << parameters.cibw-build >>
@@ -141,6 +147,10 @@ workflows:
               cibw-build: ["cp310-manylinux_aarch64",
                            "cp311-manylinux_aarch64",
                            "cp312-manylinux_aarch64",
+                           "cp313-manylinux_aarch64",
+                           "cp313t-manylinux_aarch64",
                            "cp310-musllinux_aarch64",
                            "cp311-musllinux_aarch64",
-                           "cp312-musllinux_aarch64",]
+                           "cp312-musllinux_aarch64",
+                           "cp313-musllinux_aarch64",
+                           "cp313t-musllinux_aarch64"]

.github/actions/setup-conda/action.yml

@@ -9,6 +9,8 @@ runs:
     - name: Install ${{ inputs.environment-file }}
       uses: mamba-org/setup-micromamba@v1
       with:
+        # Pinning to avoid 2.0 failures
+        micromamba-version: '1.5.10-0'
         environment-file: ${{ inputs.environment-file }}
         environment-name: test
         condarc-file: ci/.condarc

.github/workflows/wheels.yml

@@ -102,9 +102,7 @@ jobs:
         python: [["cp310", "3.10"], ["cp311", "3.11"], ["cp312", "3.12"], ["cp313", "3.13"], ["cp313t", "3.13"]]
         include:
         # TODO: Remove this plus installing build deps in cibw_before_build.sh
-        # and test deps in cibw_before_test.sh after pandas can be built with a released NumPy/Cython
-        - python: ["cp313", "3.13"]
-          cibw_build_frontend: 'pip; args: --no-build-isolation'
+        # after pandas can be built with a released NumPy/Cython
         - python: ["cp313t", "3.13"]
           cibw_build_frontend: 'pip; args: --no-build-isolation'
         # Build Pyodide wheels and upload them to Anaconda.org
@@ -187,11 +185,9 @@ jobs:
       - name: Test Windows Wheels
         if: ${{ matrix.buildplat[1] == 'win_amd64' }}
         shell: pwsh
-        # TODO: Remove NumPy nightly install when there's a 3.13 wheel on PyPI
         run: |
           $TST_CMD = @"
           python -m pip install hypothesis>=6.84.0 pytest>=7.3.2 pytest-xdist>=3.4.0;
-          ${{ matrix.python[1] == '3.13' && 'python -m pip install -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy;' }}
           python -m pip install `$(Get-Item pandas\wheelhouse\*.whl);
           python -c `'import pandas as pd; pd.test(extra_args=[`\"--no-strict-data-files`\", `\"-m not clipboard and not single_cpu and not slow and not network and not db`\"])`';
           "@

MANIFEST.in

@@ -65,4 +65,3 @@ graft pandas/_libs/include
 
 # Include cibw script in sdist since it's needed for building wheels
 include scripts/cibw_before_build.sh
-include scripts/cibw_before_test.sh

ci/code_checks.sh

@@ -73,7 +73,6 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
         -i "pandas.Period.freq GL08" \
         -i "pandas.Period.ordinal GL08" \
         -i "pandas.RangeIndex.from_range PR01,SA01" \
-        -i "pandas.RangeIndex.step SA01" \
         -i "pandas.Series.cat.add_categories PR01,PR02" \
         -i "pandas.Series.cat.as_ordered PR01" \
         -i "pandas.Series.cat.as_unordered PR01" \
@@ -97,10 +96,7 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
         -i "pandas.Series.dt.tz_localize PR01,PR02" \
         -i "pandas.Series.dt.unit GL08" \
         -i "pandas.Series.pad PR01,SA01" \
-        -i "pandas.Series.sparse.fill_value SA01" \
         -i "pandas.Series.sparse.from_coo PR07,SA01" \
-        -i "pandas.Series.sparse.npoints SA01" \
-        -i "pandas.Series.sparse.sp_values SA01" \
         -i "pandas.Timedelta.max PR02" \
         -i "pandas.Timedelta.min PR02" \
         -i "pandas.Timedelta.resolution PR02" \
@@ -111,48 +107,31 @@ 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_dict_like PR07,SA01" \
-        -i "pandas.api.types.is_file_like PR07,SA01" \
         -i "pandas.api.types.is_float PR01,SA01" \
-        -i "pandas.api.types.is_float_dtype SA01" \
-        -i "pandas.api.types.is_hashable PR01,RT03,SA01" \
-        -i "pandas.api.types.is_int64_dtype SA01" \
         -i "pandas.api.types.is_integer PR01,SA01" \
-        -i "pandas.api.types.is_interval_dtype SA01" \
         -i "pandas.api.types.is_iterator PR07,SA01" \
-        -i "pandas.api.types.is_list_like SA01" \
-        -i "pandas.api.types.is_named_tuple PR07,SA01" \
-        -i "pandas.api.types.is_object_dtype SA01" \
-        -i "pandas.api.types.is_re 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" \
-        -i "pandas.arrays.BooleanArray SA01" \
         -i "pandas.arrays.DatetimeArray SA01" \
         -i "pandas.arrays.IntegerArray SA01" \
         -i "pandas.arrays.IntervalArray.left SA01" \
         -i "pandas.arrays.IntervalArray.length SA01" \
-        -i "pandas.arrays.IntervalArray.mid SA01" \
         -i "pandas.arrays.IntervalArray.right SA01" \
         -i "pandas.arrays.NumpyExtensionArray SA01" \
         -i "pandas.arrays.SparseArray PR07,SA01" \
         -i "pandas.arrays.TimedeltaArray PR07,SA01" \
         -i "pandas.core.groupby.DataFrameGroupBy.__iter__ RT03,SA01" \
-        -i "pandas.core.groupby.DataFrameGroupBy.agg RT03" \
-        -i "pandas.core.groupby.DataFrameGroupBy.aggregate RT03" \
         -i "pandas.core.groupby.DataFrameGroupBy.boxplot PR07,RT03,SA01" \
         -i "pandas.core.groupby.DataFrameGroupBy.get_group RT03,SA01" \
         -i "pandas.core.groupby.DataFrameGroupBy.groups SA01" \
-        -i "pandas.core.groupby.DataFrameGroupBy.hist RT03" \
         -i "pandas.core.groupby.DataFrameGroupBy.indices SA01" \
         -i "pandas.core.groupby.DataFrameGroupBy.nth PR02" \
         -i "pandas.core.groupby.DataFrameGroupBy.nunique SA01" \
         -i "pandas.core.groupby.DataFrameGroupBy.ohlc SA01" \
         -i "pandas.core.groupby.DataFrameGroupBy.plot PR02" \
         -i "pandas.core.groupby.DataFrameGroupBy.sem SA01" \
         -i "pandas.core.groupby.SeriesGroupBy.__iter__ RT03,SA01" \
-        -i "pandas.core.groupby.SeriesGroupBy.agg RT03" \
-        -i "pandas.core.groupby.SeriesGroupBy.aggregate RT03" \
         -i "pandas.core.groupby.SeriesGroupBy.get_group RT03,SA01" \
         -i "pandas.core.groupby.SeriesGroupBy.groups SA01" \
         -i "pandas.core.groupby.SeriesGroupBy.indices SA01" \
@@ -163,7 +142,6 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
         -i "pandas.core.groupby.SeriesGroupBy.plot PR02" \
         -i "pandas.core.groupby.SeriesGroupBy.sem SA01" \
         -i "pandas.core.resample.Resampler.__iter__ RT03,SA01" \
-        -i "pandas.core.resample.Resampler.ffill RT03" \
         -i "pandas.core.resample.Resampler.get_group RT03,SA01" \
         -i "pandas.core.resample.Resampler.groups SA01" \
         -i "pandas.core.resample.Resampler.indices SA01" \
@@ -178,15 +156,13 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
         -i "pandas.core.resample.Resampler.sum SA01" \
         -i "pandas.core.resample.Resampler.transform PR01,RT03,SA01" \
         -i "pandas.core.resample.Resampler.var SA01" \
-        -i "pandas.date_range RT03" \
         -i "pandas.errors.AttributeConflictWarning SA01" \
         -i "pandas.errors.CSSWarning SA01" \
         -i "pandas.errors.CategoricalConversionWarning SA01" \
         -i "pandas.errors.ChainedAssignmentError SA01" \
         -i "pandas.errors.ClosedFileError SA01" \
         -i "pandas.errors.DataError SA01" \
         -i "pandas.errors.DuplicateLabelError SA01" \
-        -i "pandas.errors.EmptyDataError SA01" \
         -i "pandas.errors.IntCastingNaNError SA01" \
         -i "pandas.errors.InvalidIndexError SA01" \
         -i "pandas.errors.InvalidVersion SA01" \
@@ -368,7 +344,6 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
         -i "pandas.tseries.offsets.SemiMonthBegin.n GL08" \
         -i "pandas.tseries.offsets.SemiMonthBegin.normalize GL08" \
         -i "pandas.tseries.offsets.SemiMonthBegin.rule_code GL08" \
-        -i "pandas.tseries.offsets.SemiMonthEnd SA01" \
         -i "pandas.tseries.offsets.SemiMonthEnd.day_of_month GL08" \
         -i "pandas.tseries.offsets.SemiMonthEnd.is_on_offset GL08" \
         -i "pandas.tseries.offsets.SemiMonthEnd.n GL08" \
@@ -382,7 +357,6 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
         -i "pandas.tseries.offsets.Week.n GL08" \
         -i "pandas.tseries.offsets.Week.normalize GL08" \
         -i "pandas.tseries.offsets.Week.weekday GL08" \
-        -i "pandas.tseries.offsets.WeekOfMonth SA01" \
         -i "pandas.tseries.offsets.WeekOfMonth.is_on_offset GL08" \
         -i "pandas.tseries.offsets.WeekOfMonth.n GL08" \
         -i "pandas.tseries.offsets.WeekOfMonth.normalize GL08" \

doc/source/conf.py

@@ -254,7 +254,9 @@
         "json_url": "https://pandas.pydata.org/versions.json",
         "version_match": switcher_version,
     },
-    "show_version_warning_banner": True,
+    # This shows a warning for patch releases since the
+    # patch version doesn't compare as equal (e.g. 2.2.1 != 2.2.0 but it should be)
+    "show_version_warning_banner": False,
     "icon_links": [
         {
             "name": "Mastodon",

doc/source/development/contributing.rst

@@ -305,15 +305,15 @@ It is important to periodically update your local ``main`` branch with updates f
 branch and update your development environment to reflect any changes to the various packages that
 are used during development.
 
-If using :ref:`mamba <contributing.mamba>`, run:
+If using :ref:`conda <contributing.conda>`, run:
 
 .. code-block:: shell
 
     git checkout main
     git fetch upstream
     git merge upstream/main
-    mamba activate pandas-dev
-    mamba env update -f environment.yml --prune
+    conda activate pandas-dev
+    conda env update -f environment.yml --prune
 
 If using :ref:`pip <contributing.pip>` , do:
 

doc/source/development/contributing_codebase.rst

@@ -244,7 +244,7 @@ in your python environment.
 
 .. warning::
 
-    * Please be aware that the above commands will use the current python environment. If your python packages are older/newer than those installed by the pandas CI, the above commands might fail. This is often the case when the ``mypy`` or ``numpy`` versions do not match. Please see :ref:`how to setup the python environment <contributing.mamba>` or select a `recently succeeded workflow <https://github.com/pandas-dev/pandas/actions/workflows/code-checks.yml?query=branch%3Amain+is%3Asuccess>`_, select the "Docstring validation, typing, and other manual pre-commit hooks" job, then click on "Set up Conda" and "Environment info" to see which versions the pandas CI installs.
+    * Please be aware that the above commands will use the current python environment. If your python packages are older/newer than those installed by the pandas CI, the above commands might fail. This is often the case when the ``mypy`` or ``numpy`` versions do not match. Please see :ref:`how to setup the python environment <contributing.conda>` or select a `recently succeeded workflow <https://github.com/pandas-dev/pandas/actions/workflows/code-checks.yml?query=branch%3Amain+is%3Asuccess>`_, select the "Docstring validation, typing, and other manual pre-commit hooks" job, then click on "Set up Conda" and "Environment info" to see which versions the pandas CI installs.
 
 .. _contributing.ci:
 

doc/source/development/contributing_environment.rst

@@ -43,17 +43,17 @@ and consult the ``Linux`` instructions below.
 
 **macOS**
 
-To use the :ref:`mamba <contributing.mamba>`-based compilers, you will need to install the
+To use the :ref:`conda <contributing.conda>`-based compilers, you will need to install the
 Developer Tools using ``xcode-select --install``.
 
 If you prefer to use a different compiler, general information can be found here:
 https://devguide.python.org/setup/#macos
 
 **Linux**
 
-For Linux-based :ref:`mamba <contributing.mamba>` installations, you won't have to install any
-additional components outside of the mamba environment. The instructions
-below are only needed if your setup isn't based on mamba environments.
+For Linux-based :ref:`conda <contributing.conda>` installations, you won't have to install any
+additional components outside of the conda environment. The instructions
+below are only needed if your setup isn't based on conda environments.
 
 Some Linux distributions will come with a pre-installed C compiler. To find out
 which compilers (and versions) are installed on your system::
@@ -82,19 +82,18 @@ Before we begin, please:
 * Make sure that you have :any:`cloned the repository <contributing.forking>`
 * ``cd`` to the pandas source directory you just created with the clone command
 
-.. _contributing.mamba:
+.. _contributing.conda:
 
-Option 1: using mamba (recommended)
+Option 1: using conda (recommended)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-* Install miniforge to get `mamba <https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html>`_
-* Make sure your mamba is up to date (``mamba update mamba``)
-* Create and activate the ``pandas-dev`` mamba environment using the following commands:
+* Install miniforge to get `conda <https://github.com/conda-forge/miniforge?tab=readme-ov-file#download>`_
+* Create and activate the ``pandas-dev`` conda environment using the following commands:
 
-.. code-block:: none
+.. code-block:: bash
 
-   mamba env create --file environment.yml
-   mamba activate pandas-dev
+   conda env create --file environment.yml
+   conda activate pandas-dev
 
 .. _contributing.pip:
 

doc/source/development/maintaining.rst

@@ -344,7 +344,7 @@ in the next places:
 - Git repo with a `new tag <https://github.com/pandas-dev/pandas/tags>`_
 - Source distribution in a `GitHub release <https://github.com/pandas-dev/pandas/releases>`_
 - Pip packages in the `PyPI <https://pypi.org/project/pandas/>`_
-- Conda/Mamba packages in `conda-forge <https://anaconda.org/conda-forge/pandas>`_
+- Conda packages in `conda-forge <https://anaconda.org/conda-forge/pandas>`_
 
 The process for releasing a new version of pandas is detailed next section.