Merge branch 'main' into depr-internals

.github/workflows/code-checks.yml

@@ -124,7 +124,7 @@ jobs:
       run: |
         cd asv_bench
         asv machine --yes
-        asv run --quick --dry-run --durations=30 --python=same
+        asv run --quick --dry-run --durations=30 --python=same --show-stderr
 
   build_docker_dev_environment:
     name: Build Docker Dev Environment

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

@@ -67,7 +67,7 @@ jobs:
       run: cp doc/cheatsheet/Pandas_Cheat_Sheet* web/build/
 
     - name: Upload web
-      run: rsync -az --delete --exclude='pandas-docs' --exclude='docs' web/build/ web@${{ secrets.server_ip }}:/var/www/html
+      run: rsync -az --delete --exclude='pandas-docs' --exclude='docs' --exclude='benchmarks' web/build/ web@${{ secrets.server_ip }}:/var/www/html
       if: github.event_name == 'push' && github.ref == 'refs/heads/main'
 
     - name: Upload dev docs

.github/workflows/package-checks.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        extra: ["test", "performance", "computation", "fss", "aws", "gcp", "excel", "parquet", "feather", "hdf5", "spss", "postgresql", "mysql", "sql-other", "html", "xml", "plot", "output_formatting", "clipboard", "compression", "consortium-standard", "all"]
+        extra: ["test", "performance", "computation", "fss", "aws", "gcp", "excel", "parquet", "feather", "hdf5", "spss", "postgresql", "mysql", "sql-other", "html", "xml", "plot", "output-formatting", "clipboard", "compression", "consortium-standard", "all"]
       fail-fast: false
     name: Install Extras - ${{ matrix.extra }}
     concurrency:

.github/workflows/unit-tests.yml

@@ -230,11 +230,13 @@ jobs:
               git -c user.email="you@example.com" merge --no-commit my_ref_name
           fi
       - name: Build environment and Run Tests
+        # https://github.com/numpy/numpy/issues/24703#issuecomment-1722379388
         run: |
           /opt/python/cp311-cp311/bin/python -m venv ~/virtualenvs/pandas-dev
           . ~/virtualenvs/pandas-dev/bin/activate
           python -m pip install --no-cache-dir -U pip wheel setuptools meson[ninja]==1.2.1 meson-python==0.13.1
-          python -m pip install --no-cache-dir versioneer[toml] cython numpy python-dateutil pytz pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-asyncio>=0.17 hypothesis>=6.46.1
+          python -m pip install numpy --config-settings=setup-args="-Dallow-noblas=true"
+          python -m pip install --no-cache-dir versioneer[toml] "cython<3.0.3" python-dateutil pytz pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-asyncio>=0.17 hypothesis>=6.46.1
           python -m pip install --no-cache-dir --no-build-isolation -e .
           python -m pip list --no-cache-dir
           export PANDAS_CI=1
@@ -272,7 +274,7 @@ jobs:
           /opt/python/cp311-cp311/bin/python -m venv ~/virtualenvs/pandas-dev
           . ~/virtualenvs/pandas-dev/bin/activate
           python -m pip install --no-cache-dir -U pip wheel setuptools meson-python==0.13.1 meson[ninja]==1.2.1
-          python -m pip install --no-cache-dir versioneer[toml] cython numpy python-dateutil pytz pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-asyncio>=0.17 hypothesis>=6.46.1
+          python -m pip install --no-cache-dir versioneer[toml] "cython<3.0.3" numpy python-dateutil pytz pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-asyncio>=0.17 hypothesis>=6.46.1
           python -m pip install --no-cache-dir --no-build-isolation -e .
           python -m pip list --no-cache-dir
 
@@ -345,7 +347,7 @@ jobs:
           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
           python -m pip install versioneer[toml]
-          python -m pip install python-dateutil pytz tzdata cython hypothesis>=6.46.1 pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-cov pytest-asyncio>=0.17
+          python -m pip install python-dateutil pytz tzdata "cython<3.0.3" hypothesis>=6.46.1 pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-cov pytest-asyncio>=0.17
           python -m pip install -ve . --no-build-isolation --no-index
           python -m pip list
 

.github/workflows/wheels.yml

@@ -138,7 +138,7 @@ jobs:
         run: echo "sdist_name=$(cd ./dist && ls -d */)" >> "$GITHUB_ENV"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.15.0
+        uses: pypa/cibuildwheel@v2.16.2
         with:
          package-dir: ./dist/${{ matrix.buildplat[1] == 'macosx_*' && env.sdist_name || needs.build_sdist.outputs.sdist_file }}
         env:

.gitignore

@@ -39,7 +39,7 @@
 .mesonpy-native-file.ini
 MANIFEST
 compile_commands.json
-debug
+.debug
 
 # Python files #
 ################

.pre-commit-config.yaml

@@ -20,11 +20,11 @@ ci:
 repos:
 -   repo: https://github.com/hauntsaninja/black-pre-commit-mirror
     # black compiled with mypyc
-    rev: 23.7.0
+    rev: 23.9.1
     hooks:
       - id: black
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.287
+    rev: v0.0.291
     hooks:
     -   id: ruff
         args: [--exit-non-zero-on-fix]
@@ -84,7 +84,7 @@ repos:
             '--filter=-readability/casting,-runtime/int,-build/include_subdir,-readability/fn_size'
         ]
 -   repo: https://github.com/pylint-dev/pylint
-    rev: v3.0.0a7
+    rev: v3.0.0b0
     hooks:
     -   id: pylint
         stages: [manual]
@@ -107,7 +107,7 @@ repos:
     hooks:
     -   id: isort
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+    rev: v3.13.0
     hooks:
     -   id: pyupgrade
         args: [--py39-plus]

asv_bench/benchmarks/algorithms.py

@@ -1,6 +1,7 @@
 from importlib import import_module
 
 import numpy as np
+import pyarrow as pa
 
 import pandas as pd
 
@@ -72,7 +73,16 @@ class Duplicated:
     params = [
         [True, False],
         ["first", "last", False],
-        ["int", "uint", "float", "string", "datetime64[ns]", "datetime64[ns, tz]"],
+        [
+            "int",
+            "uint",
+            "float",
+            "string",
+            "datetime64[ns]",
+            "datetime64[ns, tz]",
+            "timestamp[ms][pyarrow]",
+            "duration[s][pyarrow]",
+        ],
     ]
     param_names = ["unique", "keep", "dtype"]
 
@@ -87,6 +97,12 @@ def setup(self, unique, keep, dtype):
             "datetime64[ns, tz]": pd.date_range(
                 "2011-01-01", freq="H", periods=N, tz="Asia/Tokyo"
             ),
+            "timestamp[ms][pyarrow]": pd.Index(
+                np.arange(N), dtype=pd.ArrowDtype(pa.timestamp("ms"))
+            ),
+            "duration[s][pyarrow]": pd.Index(
+                np.arange(N), dtype=pd.ArrowDtype(pa.duration("s"))
+            ),
         }[dtype]
         if not unique:
             data = data.repeat(5)

asv_bench/benchmarks/groupby.py

@@ -841,6 +841,23 @@ def time_groupby_sum_multiindex(self):
         self.df.groupby(level=[0, 1]).sum()
 
 
+class SumTimeDelta:
+    # GH 20660
+    def setup(self):
+        N = 10**4
+        self.df = DataFrame(
+            np.random.randint(1000, 100000, (N, 100)),
+            index=np.random.randint(200, size=(N,)),
+        ).astype("timedelta64[ns]")
+        self.df_int = self.df.copy().astype("int64")
+
+    def time_groupby_sum_timedelta(self):
+        self.df.groupby(lambda x: x).sum()
+
+    def time_groupby_sum_int(self):
+        self.df_int.groupby(lambda x: x).sum()
+
+
 class Transform:
     def setup(self):
         n1 = 400

asv_bench/benchmarks/tslibs/period.py

@@ -72,7 +72,7 @@ def time_now(self, freq):
         self.per.now(freq)
 
     def time_asfreq(self, freq):
-        self.per.asfreq("A")
+        self.per.asfreq("Y")
 
     def time_str(self, freq):
         str(self.per)

ci/code_checks.sh

@@ -63,16 +63,6 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
 
     MSG='Partially validate docstrings (EX03)' ;  echo $MSG
     $BASE_DIR/scripts/validate_docstrings.py --format=actions --errors=EX03 --ignore_functions \
-        pandas.Series.loc \
-        pandas.Series.iloc \
-        pandas.Series.pop \
-        pandas.Series.describe \
-        pandas.Series.skew \
-        pandas.Series.var \
-        pandas.Series.last \
-        pandas.Series.tz_convert \
-        pandas.Series.tz_localize \
-        pandas.Series.dt.month_name \
         pandas.Series.dt.day_name \
         pandas.Series.str.len \
         pandas.Series.cat.set_categories \

ci/deps/actions-310.yaml

@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33
+  - cython>=0.29.33, <3.0.3
   - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
@@ -34,7 +34,7 @@ dependencies:
   - gcsfs>=2022.05.0
   - jinja2>=3.1.2
   - lxml>=4.8.0
-  - matplotlib>=3.6.1
+  - matplotlib>=3.6.1, <3.8
   - numba>=0.55.2
   - numexpr>=2.8.0
   - odfpy>=1.4.1

ci/deps/actions-311-downstream_compat.yaml

@@ -7,7 +7,7 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33
+  - cython>=0.29.33, <3.0.3
   - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
@@ -35,7 +35,7 @@ dependencies:
   - gcsfs>=2022.05.0
   - jinja2>=3.1.2
   - lxml>=4.8.0
-  - matplotlib>=3.6.1
+  - matplotlib>=3.6.1, <3.8
   - numba>=0.55.2
   - numexpr>=2.8.0
   - odfpy>=1.4.1

ci/deps/actions-311-numpydev.yaml

@@ -8,7 +8,7 @@ dependencies:
   - versioneer[toml]
   - meson[ninja]=1.2.1
   - meson-python=0.13.1
-  - cython>=0.29.33
+  - cython>=0.29.33, <3.0.3
 
   # test dependencies
   - pytest>=7.3.2

ci/deps/actions-311-pyarrownightly.yaml

@@ -7,7 +7,7 @@ dependencies:
   # build dependencies
   - versioneer[toml]
   - meson[ninja]=1.2.1
-  - cython>=0.29.33
+  - cython>=0.29.33, <3.0.3
   - meson-python=0.13.1
 
   # test dependencies

ci/deps/actions-311.yaml

@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33
+  - cython>=0.29.33, <3.0.3
   - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
@@ -34,7 +34,7 @@ dependencies:
   - gcsfs>=2022.05.0
   - jinja2>=3.1.2
   - lxml>=4.8.0
-  - matplotlib>=3.6.1
+  - matplotlib>=3.6.1, <3.8
   - numba>=0.55.2
   - numexpr>=2.8.0
   - odfpy>=1.4.1

ci/deps/actions-39-minimum_versions.yaml

@@ -8,7 +8,7 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33
+  - cython>=0.29.33, <3.0.3
   - meson[ninja]=1.2.1
   - meson-python=0.13.1
 

ci/deps/actions-39.yaml

@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33
+  - cython>=0.29.33, <3.0.3
   - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
@@ -34,7 +34,7 @@ dependencies:
   - gcsfs>=2022.05.0
   - jinja2>=3.1.2
   - lxml>=4.8.0
-  - matplotlib>=3.6.1
+  - matplotlib>=3.6.1, <3.8
   - numba>=0.55.2
   - numexpr>=2.8.0
   - odfpy>=1.4.1

ci/deps/actions-pypy-39.yaml

@@ -9,7 +9,7 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33
+  - cython>=0.29.33, <3.0.3
   - meson[ninja]=1.2.1
   - meson-python=0.13.1
 

ci/deps/circle-310-arm64.yaml

@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - cython>=0.29.33
+  - cython>=0.29.33, <3.0.3
   - meson[ninja]=1.2.1
   - meson-python=0.13.1
 
@@ -34,7 +34,7 @@ dependencies:
   - gcsfs>=2022.05.0
   - jinja2>=3.1.2
   - lxml>=4.8.0
-  - matplotlib>=3.6.1
+  - matplotlib>=3.6.1, <3.8
   # test_numba_vs_cython segfaults with numba 0.57
   - numba>=0.55.2, <0.57.0
   - numexpr>=2.8.0

doc/make.py

@@ -123,14 +123,14 @@ def _sphinx_build(self, kind: str):
 
         Parameters
         ----------
-        kind : {'html', 'latex'}
+        kind : {'html', 'latex', 'linkcheck'}
 
         Examples
         --------
         >>> DocBuilder(num_jobs=4)._sphinx_build('html')
         """
-        if kind not in ("html", "latex"):
-            raise ValueError(f"kind must be html or latex, not {kind}")
+        if kind not in ("html", "latex", "linkcheck"):
+            raise ValueError(f"kind must be html, latex or linkcheck, not {kind}")
 
         cmd = ["sphinx-build", "-b", kind]
         if self.num_jobs:
@@ -288,6 +288,12 @@ def zip_html(self):
         os.chdir(dirname)
         self._run_os("zip", zip_fname, "-r", "-q", *fnames)
 
+    def linkcheck(self):
+        """
+        Check for broken links in the documentation.
+        """
+        return self._sphinx_build("linkcheck")
+
 
 def main():
     cmds = [method for method in dir(DocBuilder) if not method.startswith("_")]

doc/redirects.csv

@@ -127,7 +127,6 @@ generated/pandas.api.types.is_number,../reference/api/pandas.api.types.is_number
 generated/pandas.api.types.is_numeric_dtype,../reference/api/pandas.api.types.is_numeric_dtype
 generated/pandas.api.types.is_object_dtype,../reference/api/pandas.api.types.is_object_dtype
 generated/pandas.api.types.is_period_dtype,../reference/api/pandas.api.types.is_period_dtype
-generated/pandas.api.types.is_period,../reference/api/pandas.api.types.is_period
 generated/pandas.api.types.is_re_compilable,../reference/api/pandas.api.types.is_re_compilable
 generated/pandas.api.types.is_re,../reference/api/pandas.api.types.is_re
 generated/pandas.api.types.is_scalar,../reference/api/pandas.api.types.is_scalar

doc/source/conf.py

@@ -162,7 +162,7 @@
 # General information about the project.
 project = "pandas"
 # We have our custom "pandas_footer.html" template, using copyright for the current year
-copyright = f"{datetime.now().year}"
+copyright = f"{datetime.now().year},"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/source/development/contributing_codebase.rst

@@ -528,7 +528,7 @@ If a test is known to fail but the manner in which it fails
 is not meant to be captured, use ``pytest.mark.xfail`` It is common to use this method for a test that
 exhibits buggy behavior or a non-implemented feature. If
 the failing test has flaky behavior, use the argument ``strict=False``. This
-will make it so pytest does not fail if the test happens to pass.
+will make it so pytest does not fail if the test happens to pass. Using ``strict=False`` is highly undesirable, please use it only as a last resort.
 
 Prefer the decorator ``@pytest.mark.xfail`` and the argument ``pytest.param``
 over usage within a test so that the test is appropriately marked during the