Merge branch 'main' into tst-str-gb

Author: jbrockmendel

.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/build_pandas/action.yml

@@ -22,13 +22,6 @@ runs:
         fi
       shell: bash -el {0}
 
-    - name: Uninstall nomkl
-      run: |
-        if conda list nomkl | grep nomkl 1>/dev/null; then
-          conda remove nomkl -y
-        fi
-      shell: bash -el {0}
-
     - name: Build Pandas
       run: |
         if [[ ${{ inputs.editable }} == "true" ]]; then

.github/workflows/code-checks.yml

@@ -4,11 +4,11 @@ on:
   push:
     branches:
       - main
-      - 2.2.x
+      - 2.3.x
   pull_request:
     branches:
       - main
-      - 2.2.x
+      - 2.3.x
 
 env:
   ENV_FILE: environment.yml

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

@@ -4,13 +4,13 @@ on:
   push:
     branches:
       - main
-      - 2.2.x
+      - 2.3.x
     tags:
       - '*'
   pull_request:
     branches:
       - main
-      - 2.2.x
+      - 2.3.x
 
 env:
   ENV_FILE: environment.yml

.github/workflows/package-checks.yml

@@ -4,11 +4,11 @@ on:
   push:
     branches:
       - main
-      - 2.2.x
+      - 2.3.x
   pull_request:
     branches:
       - main
-      - 2.2.x
+      - 2.3.x
     types: [ labeled, opened, synchronize, reopened ]
 
 permissions:
@@ -67,7 +67,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-name: recipe-test
           create-args: >-

.github/workflows/unit-tests.yml

@@ -4,11 +4,11 @@ on:
   push:
     branches:
       - main
-      - 2.2.x
+      - 2.3.x
   pull_request:
     branches:
       - main
-      - 2.2.x
+      - 2.3.x
     paths-ignore:
       - "doc/**"
       - "web/**"
@@ -86,7 +86,6 @@ jobs:
       TEST_ARGS: ${{ matrix.test_args || '' }}
       PYTEST_WORKERS: 'auto'
       PYTEST_TARGET: ${{ matrix.pytest_target || 'pandas' }}
-      NPY_PROMOTION_STATE: ${{ matrix.env_file == 'actions-311-numpydev.yaml' && 'weak' || 'legacy' }}
       # Clipboard tests
       QT_QPA_PLATFORM: offscreen
       REMOVE_PYARROW: ${{ matrix.name == 'Future infer strings (without pyarrow)' && '1' || '0' }}
@@ -380,7 +379,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python Free-threading Version
-        uses: deadsnakes/action@v3.1.0
+        uses: deadsnakes/action@v3.2.0
         with:
           python-version: 3.13-dev
           nogil: true

.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
@@ -158,7 +156,7 @@ jobs:
         run: echo "sdist_name=$(cd ./dist && ls -d */)" >> "$GITHUB_ENV"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.20.0
+        uses: pypa/cibuildwheel@v2.21.3
         with:
          package-dir: ./dist/${{ startsWith(matrix.buildplat[1], 'macosx') && env.sdist_name || needs.build_sdist.outputs.sdist_file }}
         env:
@@ -167,7 +165,7 @@ jobs:
           CIBW_PLATFORM: ${{ matrix.buildplat[1] == 'pyodide_wasm32' && 'pyodide' || 'auto' }}
 
       - name: Set up Python
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-name: wheel-env
           # Use a fixed Python, since we might have an unreleased Python not
@@ -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`\"])`';
           "@

.pre-commit-config.yaml

@@ -2,9 +2,9 @@ minimum_pre_commit_version: 2.15.0
 exclude: ^LICENSES/|\.(html|csv|svg)$
 # reserve "manual" for relatively slow hooks which we still want to run in CI
 default_stages: [
-    commit,
-    merge-commit,
-    push,
+    pre-commit,
+    pre-merge-commit,
+    pre-push,
     prepare-commit-msg,
     commit-msg,
     post-checkout,
@@ -19,7 +19,7 @@ ci:
     skip: [pyright, mypy]
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.6.9
     hooks:
     -   id: ruff
         args: [--exit-non-zero-on-fix]
@@ -34,7 +34,7 @@ repos:
     -   id: ruff-format
         exclude: ^scripts|^pandas/tests/frame/test_query_eval.py
 -   repo: https://github.com/jendrikseipp/vulture
-    rev: 'v2.11'
+    rev: 'v2.13'
     hooks:
       - id: vulture
         entry: python scripts/run_vulture.py
@@ -52,7 +52,7 @@ repos:
     -   id: cython-lint
     -   id: double-quote-cython-strings
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     -   id: check-case-conflict
     -   id: check-toml
@@ -74,7 +74,7 @@ repos:
     hooks:
     -   id: isort
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.16.0
+    rev: v3.17.0
     hooks:
     -   id: pyupgrade
         args: [--py310-plus]
@@ -90,12 +90,12 @@ repos:
         types: [text]  # overwrite types: [rst]
         types_or: [python, rst]
 -   repo: https://github.com/sphinx-contrib/sphinx-lint
-    rev: v0.9.1
+    rev: v1.0.0
     hooks:
     - id: sphinx-lint
       args: ["--enable", "all", "--disable", "line-too-long"]
 -   repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v18.1.8
+    rev: v19.1.1
     hooks:
     - id: clang-format
       files: ^pandas/_libs/src|^pandas/_libs/include
@@ -112,7 +112,7 @@ repos:
         types: [python]
         stages: [manual]
         additional_dependencies: &pyright_dependencies
-        - [email protected].352
+        - [email protected].383
     -   id: pyright
         # note: assumes python env is setup and activated
         name: pyright reportGeneralTypeIssues

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

asv_bench/benchmarks/indexing_engines.py

@@ -87,7 +87,7 @@ def setup(self, engine_and_dtype, index_type, unique, N):
                 arr = np.array([1, 2, 3], dtype=dtype).repeat(N)
 
         self.data = engine(arr)
-        # code belows avoids populating the mapping etc. while timing.
+        # code below avoids populating the mapping etc. while timing.
         self.data.get_loc(2)
 
         self.key_middle = arr[len(arr) // 2]
@@ -140,7 +140,7 @@ def setup(self, engine_and_dtype, index_type, unique, N):
             mask[-1] = True
 
         self.data = engine(BaseMaskedArray(arr, mask))
-        # code belows avoids populating the mapping etc. while timing.
+        # code below avoids populating the mapping etc. while timing.
         self.data.get_loc(2)
 
         self.key_middle = arr[len(arr) // 2]
@@ -169,7 +169,7 @@ def setup(self, index_type):
         }[index_type]
 
         self.data = libindex.ObjectEngine(arr)
-        # code belows avoids populating the mapping etc. while timing.
+        # code below avoids populating the mapping etc. while timing.
         self.data.get_loc("b")
 
     def time_get_loc(self, index_type):