Merge remote-tracking branch 'upstream/main' into set-__module__-scalars

Author: jorisvandenbossche

.circleci/config.yml

@@ -15,24 +15,26 @@ jobs:
       - checkout
       - run:
           name: Install Environment and Run Tests
-          shell: /bin/bash -exuo pipefail
+          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: |
-            MAMBA_URL="https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Mambaforge-24.3.0-0-Linux-aarch64.sh"
-            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
+            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 $ENV_FILE
             conda list -n pandas-dev
             source activate pandas-dev
             if pip show pandas 1>/dev/null; then
                 pip uninstall -y pandas
             fi
-            python -m pip install --no-build-isolation -ve . --config-settings=setup-args="--werror"
+            python -m pip install --no-build-isolation -ve . -Csetup-args="--werror"
             PATH=$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:
@@ -54,8 +56,8 @@ 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 hypothesis>=6.46.1
-            python -m pip install --no-cache-dir --no-build-isolation -e . --config-settings=setup-args="--werror"
+            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 --no-build-isolation -e . -Csetup-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
@@ -89,29 +91,30 @@ 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==2.18.1
-            cibuildwheel --prerelease-pythons --output-dir wheelhouse
+            pip3 install cibuildwheel==2.20.0
+            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 >>
 
       - 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/24.3.0-0/Mambaforge-24.3.0-0-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
@@ -141,11 +144,13 @@ 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",
+                           "cp313-manylinux_aarch64",
+                           "cp313t-manylinux_aarch64",
                            "cp310-musllinux_aarch64",
                            "cp311-musllinux_aarch64",
-                           "cp312-musllinux_aarch64",]
+                           "cp312-musllinux_aarch64",
+                           "cp313-musllinux_aarch64",
+                           "cp313t-musllinux_aarch64"]

.devcontainer.json

@@ -8,7 +8,6 @@
 	// Use 'settings' to set *default* container specific settings.json values on container create.
 	// You can edit these settings after create using File > Preferences > Settings > Remote.
 	"settings": {
-		"terminal.integrated.shell.linux": "/bin/bash",
 		"python.pythonPath": "/usr/local/bin/python",
 		"python.formatting.provider": "black",
 		"python.linting.enabled": true,

.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 }} \
-            --config-settings=setup-args="--werror"
+          pip install -e . --no-build-isolation -v --no-deps \
+            -Csetup-args="--werror"
         else
-          pip install . --no-build-isolation -v --no-deps ${{ inputs.meson_args }} \
-            --config-settings=setup-args="--werror"
+          pip install . --no-build-isolation -v --no-deps \
+            -Csetup-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/actions/setup-conda/action.yml

@@ -14,3 +14,9 @@ runs:
         condarc-file: ci/.condarc
         cache-environment: true
         cache-downloads: true
+
+    - name: Uninstall pyarrow
+      if: ${{ env.REMOVE_PYARROW == '1' }}
+      run: |
+        micromamba remove -y pyarrow
+      shell: bash -el {0}

.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
@@ -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

@@ -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
@@ -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

@@ -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:
@@ -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:
@@ -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: >-