Merge remote-tracking branch 'upstream/main' into cow-chained-detection-py314

Author: jorisvandenbossche

.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
 
@@ -313,7 +313,7 @@ jobs:
     #    To freeze this file, uncomment out the ``if: false`` condition, and migrate the jobs
     #    to the corresponding posix/windows-macos/sdist etc. workflows.
     # Feel free to modify this comment as necessary.
-    if: false
+    # if: false
     defaults:
       run:
         shell: bash -eou pipefail {0}
@@ -343,21 +343,23 @@ 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'
+          python-version: '3.14-dev'
 
       - 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
-          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
 
       - name: Run Tests
         uses: ./.github/actions/run-tests
+        # TEMP allow this to fail until we fixed all test failures (related to chained assignment warnings)
+        continue-on-error: true
 
   # NOTE: this job must be kept in sync with the Pyodide build job in wheels.yml
   emscripten:
@@ -381,7 +383,7 @@ 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 +401,7 @@ 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

@@ -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:

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" \

ci/deps/actions-311-minimum_versions.yaml

@@ -28,38 +28,38 @@ dependencies:
   - adbc-driver-postgresql=1.2.0
   - adbc-driver-sqlite=1.2.0
   - beautifulsoup4=4.12.3
-  - bottleneck=1.3.6
-  - fastparquet=2024.2.0
-  - fsspec=2023.12.2
+  - bottleneck=1.4.2
+  - fastparquet=2024.11.0
+  - fsspec=2024.10.0
   - html5lib=1.1
-  - hypothesis=6.84.0
-  - gcsfs=2023.12.2
-  - jinja2=3.1.3
-  - lxml=4.9.2
-  - matplotlib=3.8.3
-  - numba=0.59.0
-  - numexpr=2.9.0
+  - hypothesis=6.116.0
+  - gcsfs=2024.10.0
+  - jinja2=3.1.5
+  - lxml=5.3.0
+  - matplotlib=3.9.3
+  - numba=0.60.0
+  - numexpr=2.10.2
   - odfpy=1.4.1
-  - qtpy=2.3.0
-  - openpyxl=3.1.2
-  - psycopg2=2.9.9
-  - pyarrow=12.0.1
-  - pyiceberg=0.7.1
-  - pymysql=1.1.0
+  - qtpy=2.4.2
+  - openpyxl=3.1.5
+  - psycopg2=2.9.10
+  - pyarrow=13.0.0
+  - pyiceberg=0.8.1
+  - pymysql=1.1.1
   - pyqt=5.15.9
-  - pyreadstat=1.2.6
-  - pytables=3.8.0
-  - python-calamine=0.1.7
-  - pytz=2023.4
+  - pyreadstat=1.2.8
+  - pytables=3.10.1
+  - python-calamine=0.3.0
+  - pytz=2024.2
   - pyxlsb=1.0.10
-  - s3fs=2023.12.2
-  - scipy=1.12.0
-  - sqlalchemy=2.0.0
+  - s3fs=2024.10.0
+  - scipy=1.14.1
+  - sqlalchemy=2.0.36
   - tabulate=0.9.0
-  - xarray=2024.1.1
+  - xarray=2024.10.0
   - xlrd=2.0.1
   - xlsxwriter=3.2.0
-  - zstandard=0.22.0
+  - zstandard=0.23.0
 
   - pip:
     - tzdata==2023.3