Merge remote-tracking branch 'upstream/main' into fix_gh55509

Author: aureliobarbosa

Diff for: .circleci/config.yml

@@ -18,6 +18,29 @@ jobs:
           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:
+    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
+      - 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
   build-aarch64:
     parameters:
       cibw-build:
@@ -89,6 +112,13 @@ workflows:
         equal: [ scheduled_pipeline, << pipeline.trigger_source >> ]
     jobs:
       - test-arm
+  test-musl:
+    # Don't run trigger this one when scheduled pipeline runs
+    when:
+      not:
+        equal: [ scheduled_pipeline, << pipeline.trigger_source >> ]
+    jobs:
+      - linux-musl
   build-wheels:
     jobs:
       - build-aarch64:
@@ -97,4 +127,11 @@ workflows:
               only: /^v.*/
           matrix:
             parameters:
-              cibw-build: ["cp39-manylinux_aarch64", "cp310-manylinux_aarch64", "cp311-manylinux_aarch64", "cp312-manylinux_aarch64"]
+              cibw-build: ["cp39-manylinux_aarch64",
+                           "cp310-manylinux_aarch64",
+                           "cp311-manylinux_aarch64",
+                           "cp312-manylinux_aarch64",
+                           "cp39-musllinux_aarch64",
+                           "cp310-musllinux_aarch64",
+                           "cp311-musllinux_aarch64",
+                           "cp312-musllinux_aarch64",]

Diff for: .circleci/setup_env.sh

@@ -55,6 +55,6 @@ if pip show pandas 1>/dev/null; then
 fi
 
 echo "Install pandas"
-python -m pip install --no-build-isolation -ve .
+python -m pip install --no-build-isolation -ve . --config-settings=setup-args="--werror"
 
 echo "done"

Diff for: .github/actions/build_pandas/action.yml

@@ -4,6 +4,12 @@ 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:
@@ -24,9 +30,12 @@ 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
+          pip install -e . --no-build-isolation -v --no-deps ${{ inputs.meson_args }} \
+            --config-settings=setup-args="--werror"
         else
-          pip install . --no-build-isolation -v --no-deps
+          pip install . --no-build-isolation -v --no-deps ${{ inputs.meson_args }} \
+            --config-settings=setup-args="--werror"
         fi
       shell: bash -el {0}

Diff for: .github/actions/run-tests/action.yml

@@ -1,9 +1,16 @@
 name: Run tests and report results
+inputs:
+  preload:
+    description: Preload arguments for sanitizer
+    required: false
+  asan_options:
+    description: Arguments for Address Sanitizer (ASAN)
+    required: false
 runs:
   using: composite
   steps:
     - name: Test
-      run: ci/run_tests.sh
+      run: ${{ inputs.asan_options }} ${{ inputs.preload }} ci/run_tests.sh
       shell: bash -el {0}
 
     - name: Publish test results
@@ -13,11 +20,6 @@ runs:
         path: test-data.xml
       if: failure()
 
-    - name: Report Coverage
-      run: coverage report -m
-      shell: bash -el {0}
-      if: failure()
-
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3
       with:

Diff for: .github/actions/setup-conda/action.yml

@@ -11,6 +11,6 @@ runs:
       with:
         environment-file: ${{ inputs.environment-file }}
         environment-name: test
-        condarc-file: ci/condarc.yml
+        condarc-file: ci/.condarc
         cache-environment: true
         cache-downloads: true

Diff for: .github/workflows/broken-linkcheck.yml

@@ -9,6 +9,7 @@ on:
       - "doc/make.py"
 jobs:
   linkcheck:
+    if: false
     runs-on: ubuntu-latest
     defaults:
       run:

Diff for: .github/workflows/code-checks.yml

@@ -4,11 +4,11 @@ on:
   push:
     branches:
       - main
-      - 2.1.x
+      - 2.2.x
   pull_request:
     branches:
       - main
-      - 2.1.x
+      - 2.2.x
 
 env:
   ENV_FILE: environment.yml
@@ -86,7 +86,7 @@ jobs:
       if: ${{ steps.build.outcome == 'success' && always() }}
 
     - name: Typing + pylint
-      uses: pre-commit/[email protected].0
+      uses: pre-commit/[email protected].1
       with:
         extra_args: --verbose --hook-stage manual --all-files
       if: ${{ steps.build.outcome == 'success' && always() }}
@@ -170,7 +170,7 @@ jobs:
 
       - name: Setup Python
         id: setup_python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           cache: 'pip'

Diff for: .github/workflows/codeql.yml

@@ -28,8 +28,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: github/codeql-action/init@v2
+      - uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
-      - uses: github/codeql-action/autobuild@v2
-      - uses: github/codeql-action/analyze@v2
+      - uses: github/codeql-action/autobuild@v3
+      - uses: github/codeql-action/analyze@v3

Diff for: .github/workflows/comment-commands.yml

@@ -24,12 +24,10 @@ jobs:
     concurrency:
       group: ${{ github.actor }}-preview-docs
     steps:
-      - run: |
-          if curl --output /dev/null --silent --head --fail "https://pandas.pydata.org/preview/${{ github.event.issue.number }}/"; then
-            curl -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -d '{"body": "Website preview of this PR available at: https://pandas.pydata.org/preview/${{ github.event.issue.number }}/"}' https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.issue.number }}/comments
-          else
-            curl -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -d '{"body": "No preview found for PR #${{ github.event.issue.number }}. Did the docs build complete?"}' https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.issue.number }}/comments
-          fi
+      - uses: pandas-dev/[email protected]
+        with:
+          previewer-server: "https://pandas.pydata.org/preview"
+          artifact-job: "Doc Build and Upload"
   asv_run:
     runs-on: ubuntu-22.04
     # TODO: Support more benchmarking options later, against different branches, against self, etc

Diff for: .github/workflows/deprecation-tracking-bot.yml

@@ -19,7 +19,7 @@ jobs:
       issues: write
     runs-on: ubuntu-22.04
     env:
-      DEPRECATION_TRACKER_ISSUE: 50578
+      DEPRECATION_TRACKER_ISSUE: 56596
     steps:
     - uses: actions/github-script@v7
       id: update-deprecation-issue

Diff for: .github/workflows/docbuild-and-upload.yml

@@ -4,13 +4,13 @@ on:
   push:
     branches:
       - main
-      - 2.1.x
+      - 2.2.x
     tags:
       - '*'
   pull_request:
     branches:
       - main
-      - 2.1.x
+      - 2.2.x
 
 env:
   ENV_FILE: environment.yml
@@ -46,6 +46,9 @@ jobs:
     - name: Build Pandas
       uses: ./.github/actions/build_pandas
 
+    - name: Test website
+      run: python -m pytest web/
+
     - name: Build website
       run: python web/pandas_web.py web/pandas --target-path=web/build
 
@@ -82,15 +85,8 @@ jobs:
       run: mv doc/build/html web/build/docs
 
     - name: Save website as an artifact
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: website
         path: web/build
         retention-days: 14
-
-    - name: Trigger web/doc preview
-      run: curl -X POST https://pandas.pydata.org/preview/submit/$RUN_ID/$PR_ID/
-      env:
-        RUN_ID: ${{ github.run_id }}
-        PR_ID: ${{ github.event.pull_request.number }}
-      if: github.event_name == 'pull_request'

Diff for: .github/workflows/package-checks.yml

@@ -4,11 +4,11 @@ on:
   push:
     branches:
       - main
-      - 2.1.x
+      - 2.2.x
   pull_request:
     branches:
       - main
-      - 2.1.x
+      - 2.2.x
     types: [ labeled, opened, synchronize, reopened ]
 
 permissions:
@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        extra: ["test", "performance", "computation", "fss", "aws", "gcp", "excel", "parquet", "feather", "hdf5", "spss", "postgresql", "mysql", "sql-other", "html", "xml", "plot", "output-formatting", "clipboard", "compression", "consortium-standard", "all"]
+        extra: ["test", "performance", "computation", "fss", "aws", "gcp", "excel", "parquet", "feather", "hdf5", "spss", "postgresql", "mysql", "sql-other", "html", "xml", "plot", "output-formatting", "clipboard", "compression", "all"]
       fail-fast: false
     name: Install Extras - ${{ matrix.extra }}
     concurrency:
@@ -40,7 +40,7 @@ jobs:
 
       - name: Setup Python
         id: setup_python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
 

Diff for: .github/workflows/stale-pr.yml

@@ -14,7 +14,7 @@ jobs:
     if: github.repository_owner == 'pandas-dev'
     runs-on: ubuntu-22.04
     steps:
-    - uses: actions/stale@v8
+    - uses: actions/stale@v9
       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."