Merge branch 'main' into feat/add-back-jupyterlite-repl

Author: agriyakhetarpal

.circleci/config.yml

@@ -61,7 +61,6 @@ pandas/_version.py export-subst
 *.pxi export-ignore
 
 # Ignoring stuff from the top level
-.circleci export-ignore
 .github export-ignore
 asv_bench export-ignore
 ci export-ignore

.gitattributes

@@ -107,7 +107,7 @@ jobs:
 
     services:
       mysql:
-        image: mysql:8
+        image: mysql:9
         env:
           MYSQL_ALLOW_EMPTY_PASSWORD: yes
           MYSQL_DATABASE: pandas
@@ -120,7 +120,7 @@ jobs:
           - 3306:3306
 
       postgres:
-        image: postgres:16
+        image: postgres:17
         env:
           PGUSER: postgres
           POSTGRES_USER: postgres
@@ -135,7 +135,7 @@ jobs:
           - 5432:5432
 
       moto:
-        image: motoserver/moto:5.0.0
+        image: motoserver/moto:5.0.27
         env:
           AWS_ACCESS_KEY_ID: foobar_key
           AWS_SECRET_ACCESS_KEY: foobar_secret
@@ -242,15 +242,14 @@ jobs:
       - name: Build environment and Run Tests
         # https://github.com/numpy/numpy/issues/24703#issuecomment-1722379388
         run: |
-          /opt/python/cp311-cp311/bin/python -m venv ~/virtualenvs/pandas-dev
+          /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[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 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
+          PANDAS_CI=1 python -m pytest -m 'not slow and not network and not clipboard and not single_cpu' pandas --junitxml=test-data.xml
     concurrency:
       # https://github.community/t/concurrecy-not-work-for-push/183068/7
       group: ${{ github.event_name == 'push' && github.run_number || github.ref }}-32bit
@@ -259,7 +258,7 @@ jobs:
   Linux-Musl:
     runs-on: ubuntu-22.04
     container:
-      image: quay.io/pypa/musllinux_1_1_x86_64
+      image: quay.io/pypa/musllinux_1_2_x86_64
     steps:
       - name: Checkout pandas Repo
         # actions/checkout does not work since it requires node
@@ -281,7 +280,7 @@ jobs:
           apk add musl-locales
       - name: Build environment
         run: |
-          /opt/python/cp311-cp311/bin/python -m venv ~/virtualenvs/pandas-dev
+          /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
@@ -291,8 +290,7 @@ jobs:
       - name: Run Tests
         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
+          PANDAS_CI=1 python -m pytest -m 'not slow and not network and not clipboard and not single_cpu' pandas --junitxml=test-data.xml
     concurrency:
       # https://github.community/t/concurrecy-not-work-for-push/183068/7
       group: ${{ github.event_name == 'push' && github.run_number || github.ref }}-musl
@@ -357,8 +355,7 @@ jobs:
           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 -m pip install 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>=6.84.0 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
 
@@ -375,7 +372,7 @@ jobs:
 
     concurrency:
       # https://github.community/t/concurrecy-not-work-for-push/183068/7
-      group: ${{ github.event_name == 'push' && github.run_number || github.ref }}-${{ matrix.os }}-python-freethreading-dev
+      group: ${{ github.event_name == 'push' && github.run_number || github.ref }}-python-freethreading-dev
       cancel-in-progress: true
 
     env:
@@ -396,14 +393,11 @@ jobs:
           nogil: true
 
       - name: Build Environment
-        # TODO: Once numpy 2.2.1 is out, don't install nightly version
-        # Tests segfault with numpy 2.2.0: https://github.com/numpy/numpy/pull/27955
         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 cython numpy
-          python -m pip install versioneer[toml]
-          python -m pip install python-dateutil pytz tzdata hypothesis>=6.84.0 pytest>=7.3.2 pytest-xdist>=3.4.0 pytest-cov
+          python -m pip install --upgrade pip setuptools wheel numpy 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 cython
+          python -m pip install versioneer[toml] python-dateutil pytz tzdata hypothesis>=6.84.0 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
 
@@ -430,20 +424,20 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Set up Python for Pyodide
+      - name: Set up Python for pyodide-build
         id: setup-python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11.3'
+          python-version: '3.12'
 
       - name: Set up Emscripten toolchain
         uses: mymindstorm/setup-emsdk@v14
         with:
-          version: '3.1.46'
+          version: '3.1.58'
           actions-cache-folder: emsdk-cache
 
       - name: Install pyodide-build
-        run: pip install "pyodide-build==0.25.1"
+        run: pip install "pyodide-build>=0.29.2"
 
       - name: Build pandas for Pyodide
         run: |
@@ -452,10 +446,13 @@ jobs:
       - name: Set up Node.js
         uses: actions/setup-node@v4
         with:
-          node-version: '18'
+          node-version: '20'
 
       - name: Set up Pyodide virtual environment
+        env:
+          pyodide-version: '0.27.1'
         run: |
+          pyodide xbuildenv install ${{ env.pyodide-version }}
           pyodide venv .venv-pyodide
           source .venv-pyodide/bin/activate
           pip install dist/*.whl

.github/workflows/unit-tests.yml

@@ -137,3 +137,7 @@ doc/source/savefig/
 # Interactive terminal generated files #
 ########################################
 .jupyterlite.doit.db
+
+# Pyodide/WASM related files #
+##############################
+/.pyodide-xbuildenv-*

.gitignore

@@ -19,7 +19,7 @@ ci:
     skip: [pyright, mypy]
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.4
     hooks:
     -   id: ruff
         args: [--exit-non-zero-on-fix]
@@ -41,7 +41,7 @@ repos:
         pass_filenames: true
         require_serial: false
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
     -   id: codespell
         types_or: [python, rst, markdown, cython, c]
@@ -70,7 +70,7 @@ repos:
     -   id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+    rev: 6.0.0
     hooks:
     -   id: isort
 -   repo: https://github.com/asottile/pyupgrade
@@ -95,17 +95,22 @@ repos:
     - id: sphinx-lint
       args: ["--enable", "all", "--disable", "line-too-long"]
 -   repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v19.1.6
+    rev: v19.1.7
     hooks:
     - id: clang-format
       files: ^pandas/_libs/src|^pandas/_libs/include
       args: [-i]
       types_or: [c, c++]
 -   repo: https://github.com/trim21/pre-commit-mirror-meson
-    rev: v1.6.1
+    rev: v1.7.0
     hooks:
     - id: meson-fmt
       args: ['--inplace']
+-   repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.10.0.1
+    hooks:
+    -   id: shellcheck
+        args: ["--severity=warning"]
 -   repo: local
     hooks:
     -   id: pyright

.pre-commit-config.yaml

@@ -13,8 +13,8 @@ class Render:
     def setup(self, cols, rows):
         self.df = DataFrame(
             np.random.randn(rows, cols),
-            columns=[f"float_{i+1}" for i in range(cols)],
-            index=[f"row_{i+1}" for i in range(rows)],
+            columns=[f"float_{i + 1}" for i in range(cols)],
+            index=[f"row_{i + 1}" for i in range(rows)],
         )
 
     def time_apply_render(self, cols, rows):