Merge branch 'main' into index-is_unique-slice

.circleci/config.yml

@@ -1,46 +1,66 @@
 version: 2.1
 
 jobs:
-  test-arm:
+  test-linux-arm:
     machine:
       image: default
     resource_class: arm.large
     environment:
-      ENV_FILE: ci/deps/circle-310-arm64.yaml
+      ENV_FILE: ci/deps/circle-311-arm64.yaml
       PYTEST_WORKERS: auto
       PATTERN: "not single_cpu and not slow and not network and not clipboard and not arm_slow and not db"
       PYTEST_TARGET: "pandas"
       PANDAS_CI: "1"
     steps:
       - checkout
-      - run: .circleci/setup_env.sh
-      - run: >
-          PATH=$HOME/miniconda3/envs/pandas-dev/bin:$HOME/miniconda3/condabin:$PATH
-          LD_PRELOAD=$HOME/miniconda3/envs/pandas-dev/lib/libgomp.so.1:$LD_PRELOAD
-          ci/run_tests.sh
-  linux-musl:
+      - run:
+          name: Install Environment and Run Tests
+          shell: /bin/bash -exo pipefail
+          # https://pytest-qt.readthedocs.io/en/latest/troubleshooting.html#github-actions-azure-pipelines-travis-ci-and-gitlab-ci-cd
+          command: |
+            MINI_URL="https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Miniforge3-24.3.0-0-Linux-aarch64.sh"
+            wget -q $MINI_URL -O Miniforge3.sh
+            chmod +x Miniforge3.sh
+            MINI_DIR="$HOME/miniconda3"
+            rm -rf $MINI_DIR
+            ./Miniforge3.sh -b -p $MINI_DIR
+            export PATH=$MINI_DIR/bin:$PATH
+            conda info -a
+            conda env create -q -n pandas-dev -f $ENV_FILE
+            conda list -n pandas-dev
+            source activate pandas-dev
+            if pip show pandas 1>/dev/null; then
+                pip uninstall -y pandas
+            fi
+            python -m pip install --no-build-isolation -ve . --config-settings=setup-args="--werror"
+            PATH=$HOME/miniconda3/envs/pandas-dev/bin:$HOME/miniconda3/condabin:$PATH
+            sudo apt-get update && sudo apt-get install -y libegl1 libopengl0
+            ci/run_tests.sh
+  test-linux-musl:
     docker:
       - image: quay.io/pypa/musllinux_1_1_aarch64
     resource_class: arm.large
     steps:
       # Install pkgs first to have git in the image
       # (needed for checkout)
-      - run: |
-          apk update
-          apk add git
-          apk add musl-locales
+      - run:
+          name: Install System Packages
+          command: |
+            apk update
+            apk add git
+            apk add musl-locales
       - checkout
-      - 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-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 hypothesis>=6.46.1
-          python -m pip install --no-cache-dir --no-build-isolation -e . --config-settings=setup-args="--werror"
-          python -m pip list --no-cache-dir
-      - run: |
-          . ~/virtualenvs/pandas-dev/bin/activate
-          export PANDAS_CI=1
-          python -m pytest -m 'not slow and not network and not clipboard and not single_cpu' pandas --junitxml=test-data.xml
+      - run:
+          name: Install Environment and Run Tests
+          command: |
+            /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>=3.4.0 hypothesis>=6.84.0
+            python -m pip install --no-cache-dir --no-build-isolation -e . --config-settings=setup-args="--werror"
+            python -m pip list --no-cache-dir
+            export PANDAS_CI=1
+            python -m pytest -m 'not slow and not network and not clipboard and not single_cpu' pandas --junitxml=test-data.xml
   build-aarch64:
     parameters:
       cibw-build:
@@ -71,29 +91,24 @@ jobs:
           name: Build aarch64 wheels
           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==2.15.0
+            pip3 install cibuildwheel==2.18.1
             cibuildwheel --prerelease-pythons --output-dir wheelhouse
 
           environment:
             CIBW_BUILD: << parameters.cibw-build >>
 
       - run:
           name: Install Anaconda Client & Upload Wheels
+          shell: /bin/bash -exo pipefail
           command: |
-            echo "Install Mambaforge"
-            MAMBA_URL="https://github.com/conda-forge/miniforge/releases/download/23.1.0-0/Mambaforge-23.1.0-0-Linux-aarch64.sh"
-            echo "Downloading $MAMBA_URL"
-            wget -q $MAMBA_URL -O minimamba.sh
-            chmod +x minimamba.sh
-
-            MAMBA_DIR="$HOME/miniconda3"
-            rm -rf $MAMBA_DIR
-            ./minimamba.sh -b -p $MAMBA_DIR
-
-            export PATH=$MAMBA_DIR/bin:$PATH
-
-            mamba install -y -c conda-forge anaconda-client
-
+            MINI_URL="https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Miniforge3-24.3.0-0-Linux-aarch64.sh"
+            wget -q $MINI_URL -O Miniforge3.sh
+            chmod +x Miniforge3.sh
+            MINI_DIR="$HOME/miniconda3"
+            rm -rf $MINI_DIR
+            ./Miniforge3.sh -b -p $MINI_DIR
+            export PATH=$MINI_DIR/bin:$PATH
+            conda install -y -c conda-forge anaconda-client
             source ci/upload_wheels.sh
             set_upload_vars
             upload_wheels
@@ -107,14 +122,14 @@ workflows:
       not:
         equal: [ scheduled_pipeline, << pipeline.trigger_source >> ]
     jobs:
-      - test-arm
+      - test-linux-arm
   test-musl:
     # Don't run trigger this one when scheduled pipeline runs
     when:
       not:
         equal: [ scheduled_pipeline, << pipeline.trigger_source >> ]
     jobs:
-      - linux-musl
+      - test-linux-musl
   build-wheels:
     jobs:
       - build-aarch64:
@@ -123,11 +138,9 @@ workflows:
               only: /^v.*/
           matrix:
             parameters:
-              cibw-build: ["cp39-manylinux_aarch64",
-                           "cp310-manylinux_aarch64",
+              cibw-build: ["cp310-manylinux_aarch64",
                            "cp311-manylinux_aarch64",
                            "cp312-manylinux_aarch64",
-                           "cp39-musllinux_aarch64",
                            "cp310-musllinux_aarch64",
                            "cp311-musllinux_aarch64",
                            "cp312-musllinux_aarch64",]

.gitattributes

@@ -68,7 +68,7 @@ ci export-ignore
 doc export-ignore
 gitpod export-ignore
 MANIFEST.in export-ignore
-scripts export-ignore
+scripts/** export-ignore
 typings export-ignore
 web export-ignore
 CITATION.cff export-ignore
@@ -82,3 +82,7 @@ setup.py export-ignore
 # csv_dir_path fixture checks the existence of the directory
 # exclude the whole directory to avoid running related tests in sdist
 pandas/tests/io/parser/data export-ignore
+
+# Include cibw script in sdist since it's needed for building wheels
+scripts/cibw_before_build.sh -export-ignore
+scripts/cibw_before_test.sh -export-ignore

.github/actions/build_pandas/action.yml

@@ -4,12 +4,6 @@ inputs:
   editable:
     description: Whether to build pandas in editable mode (default true)
     default: true
-  meson_args:
-    description: Extra flags to pass to meson
-    required: false
-  cflags_adds:
-    description: Items to append to the CFLAGS variable
-    required: false
 runs:
   using: composite
   steps:
@@ -30,12 +24,11 @@ runs:
 
     - name: Build Pandas
       run: |
-        export CFLAGS="$CFLAGS ${{ inputs.cflags_adds }}"
         if [[ ${{ inputs.editable }} == "true" ]]; then
-          pip install -e . --no-build-isolation -v --no-deps ${{ inputs.meson_args }} \
+          pip install -e . --no-build-isolation -v --no-deps \
             --config-settings=setup-args="--werror"
         else
-          pip install . --no-build-isolation -v --no-deps ${{ inputs.meson_args }} \
+          pip install . --no-build-isolation -v --no-deps \
             --config-settings=setup-args="--werror"
         fi
       shell: bash -el {0}

.github/actions/run-tests/action.yml

@@ -7,14 +7,14 @@ runs:
       shell: bash -el {0}
 
     - name: Publish test results
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: Test results
         path: test-data.xml
       if: failure()
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         flags: unittests
         name: codecov-pandas

.github/workflows/code-checks.yml

@@ -51,6 +51,11 @@ jobs:
     # TODO: The doctests have to be run first right now, since the Cython doctests only work
     # with pandas installed in non-editable mode
     # This can be removed once pytest-cython doesn't require C extensions to be installed inplace
+
+    - name: Extra installs
+      # https://pytest-qt.readthedocs.io/en/latest/troubleshooting.html#github-actions-azure-pipelines-travis-ci-and-gitlab-ci-cd
+      run: sudo apt-get update && sudo apt-get install -y libegl1 libopengl0
+
     - name: Run doctests
       run: cd ci && ./code_checks.sh doctests
       if: ${{ steps.build.outcome == 'success' && always() }}

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

@@ -46,6 +46,10 @@ jobs:
     - name: Build Pandas
       uses: ./.github/actions/build_pandas
 
+    - name: Extra installs
+      # https://pytest-qt.readthedocs.io/en/latest/troubleshooting.html#github-actions-azure-pipelines-travis-ci-and-gitlab-ci-cd
+      run: sudo apt-get update && sudo apt-get install -y libegl1 libopengl0
+
     - name: Test website
       run: python -m pytest web/
 

.github/workflows/package-checks.yml

@@ -53,7 +53,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11']
       fail-fast: false
     name: Test Conda Forge Recipe - Python ${{ matrix.python-version }}
     concurrency: