Merge branch 'main' into fix/nat-na-docs

Author: meet-vasita

.github/workflows/code-checks.yml

@@ -175,7 +175,7 @@ jobs:
 
       - name: Setup Python
         id: setup_python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.11'
           cache: 'pip'

.github/workflows/comment-commands.yml

@@ -75,7 +75,7 @@ jobs:
           echo 'EOF' >> $GITHUB_ENV
           echo "REGEX=$REGEX" >> $GITHUB_ENV
 
-      - uses: actions/github-script@v7
+      - uses: actions/github-script@v8
         env:
           BENCH_OUTPUT: ${{env.BENCH_OUTPUT}}
           REGEX: ${{env.REGEX}}

.github/workflows/deprecation-tracking-bot.yml

@@ -21,7 +21,7 @@ jobs:
     env:
       DEPRECATION_TRACKER_ISSUE: 56596
     steps:
-    - uses: actions/github-script@v7
+    - uses: actions/github-script@v8
       id: update-deprecation-issue
       with:
         script: |

.github/workflows/package-checks.yml

@@ -40,7 +40,7 @@ jobs:
 
       - name: Setup Python
         id: setup_python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.11'
 

.github/workflows/stale-pr.yml

@@ -14,7 +14,7 @@ jobs:
     if: github.repository_owner == 'pandas-dev'
     runs-on: ubuntu-24.04
     steps:
-    - uses: actions/stale@v9
+    - uses: actions/stale@v10
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         stale-pr-message: "This pull request is stale because it has been open for thirty days with no activity. Please [update](https://pandas.pydata.org/pandas-docs/stable/development/contributing.html#updating-your-pull-request) and respond to this comment if you're still interested in working on this."

.github/workflows/unit-tests.yml

@@ -243,7 +243,7 @@ jobs:
           . ~/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 numpy -Csetup-args="-Dallow-noblas=true"
-          python -m pip install --no-cache-dir versioneer[toml] cython==3.0.10 python-dateutil pytest>=7.3.2 pytest-xdist>=3.4.0 hypothesis>=6.84.0
+          python -m pip install --no-cache-dir versioneer[toml] cython==3.0.10 python-dateutil pytest>=7.3.2 pytest-xdist>=3.4.0 hypothesis>=6.116.0
           python -m pip install --no-cache-dir --no-build-isolation -e . -Csetup-args="--werror"
           python -m pip list --no-cache-dir
           PANDAS_CI=1 python -m pytest -m 'not slow and not network and not clipboard and not single_cpu' pandas --junitxml=test-data.xml
@@ -280,7 +280,7 @@ jobs:
           /opt/python/cp313-cp313/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 pytest>=7.3.2 pytest-xdist>=3.4.0 hypothesis>=6.84.0
+          python -m pip install --no-cache-dir versioneer[toml] cython numpy python-dateutil pytest>=7.3.2 pytest-xdist>=3.4.0 hypothesis>=6.116.0
           python -m pip install --no-cache-dir --no-build-isolation -e . -Csetup-args="--werror"
           python -m pip list --no-cache-dir
 
@@ -343,7 +343,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python Dev Version
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.13-dev'
 
@@ -352,7 +352,7 @@ jobs:
           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
-          python -m pip install versioneer[toml] python-dateutil tzdata cython hypothesis>=6.84.0 pytest>=7.3.2 pytest-xdist>=3.4.0 pytest-cov
+          python -m pip install versioneer[toml] python-dateutil tzdata cython hypothesis>=6.116.0 pytest>=7.3.2 pytest-xdist>=3.4.0 pytest-cov
           python -m pip install -ve . --no-build-isolation --no-index --no-deps -Csetup-args="--werror"
           python -m pip list
 
@@ -381,7 +381,7 @@ jobs:
 
       - name: Set up Python for pyodide-build
         id: setup-python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.12'
 
@@ -399,7 +399,7 @@ jobs:
           pyodide build
 
       - name: Set up Node.js
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v5
         with:
           node-version: '20'
 

.github/workflows/wheels.yml

@@ -53,7 +53,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.11'
 

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ ci:
     skip: [pyright, mypy]
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.7
+    rev: v0.12.11
     hooks:
     -   id: ruff
         args: [--exit-non-zero-on-fix]
@@ -32,7 +32,7 @@ repos:
         exclude: ^pandas/tests
         args: [--select, "ANN001,ANN2", --fix-only, --exit-non-zero-on-fix]
     -   id: ruff-format
-        exclude: ^scripts|^pandas/tests/frame/test_query_eval.py
+        exclude: ^pandas/tests/frame/test_query_eval.py
 -   repo: https://github.com/jendrikseipp/vulture
     rev: v2.14
     hooks:
@@ -51,7 +51,7 @@ repos:
     -   id: cython-lint
     -   id: double-quote-cython-strings
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     -   id: check-case-conflict
     -   id: check-toml
@@ -64,8 +64,6 @@ repos:
         args: [--fix=auto]
         exclude: ^pandas/tests/io/parser/data/utf16_ex.txt$
     -   id: fix-byte-order-marker
-    -   id: fix-encoding-pragma
-        args: [--remove]
     -   id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
 -   repo: https://github.com/PyCQA/isort
@@ -94,19 +92,19 @@ repos:
     - id: sphinx-lint
       args: ["--enable", "all", "--disable", "line-too-long"]
 -   repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v20.1.8
+    rev: v21.1.0
     hooks:
     - id: clang-format
       files: ^pandas/_libs/src|^pandas/_libs/include
       args: [-i]
       types_or: [c, c++]
 -   repo: https://github.com/trim21/pre-commit-mirror-meson
-    rev: v1.8.3
+    rev: v1.9.0
     hooks:
     - id: meson-fmt
       args: ['--inplace']
 -   repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: v0.10.0.1
+    rev: v0.11.0.1
     hooks:
     -   id: shellcheck
         args: ["--severity=warning"]
@@ -121,7 +119,7 @@ repos:
         types: [python]
         stages: [manual]
         additional_dependencies: &pyright_dependencies
-        - [email protected].383
+        - [email protected].404
     -   id: pyright
         # note: assumes python env is setup and activated
         name: pyright reportGeneralTypeIssues
@@ -266,6 +264,11 @@ repos:
         language: python
         entry: python scripts/validate_unwanted_patterns.py --validation-type="nodefault_used_not_only_for_typing"
         types: [python]
+    -   id: unwanted-patterns-doesnt-use-pandas-warnings
+        name: Check that warning classes for deprecations use pandas' warning classes
+        language: python
+        entry: python scripts/validate_unwanted_patterns.py --validation-type="doesnt_use_pandas_warnings"
+        types: [ python ]
     -   id: no-return-exception
         name: Use raise instead of return for exceptions
         language: pygrep

asv_bench/benchmarks/strings.py

@@ -8,6 +8,7 @@
     DataFrame,
     Index,
     Series,
+    StringDtype,
 )
 from pandas.arrays import StringArray
 
@@ -290,10 +291,10 @@ def setup(self):
         self.series_arr_nan = np.concatenate([self.series_arr, np.array([NA] * 1000)])
 
     def time_string_array_construction(self):
-        StringArray(self.series_arr)
+        StringArray(self.series_arr, dtype=StringDtype())
 
     def time_string_array_with_nan_construction(self):
-        StringArray(self.series_arr_nan)
+        StringArray(self.series_arr_nan, dtype=StringDtype())
 
     def peakmem_stringarray_construction(self):
-        StringArray(self.series_arr)
+        StringArray(self.series_arr, dtype=StringDtype())

ci/code_checks.sh

@@ -73,6 +73,7 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
         -i "pandas.Period.freq GL08" \
         -i "pandas.Period.ordinal GL08" \
         -i "pandas.errors.IncompatibleFrequency SA01,SS06,EX01" \
+        -i "pandas.api.extensions.ExtensionArray.value_counts EX01,RT03,SA01" \
         -i "pandas.core.groupby.DataFrameGroupBy.plot PR02" \
         -i "pandas.core.groupby.SeriesGroupBy.plot PR02" \
         -i "pandas.core.resample.Resampler.quantile PR01,PR07" \