Merge branch 'pandas-dev:main' into bug-cov-nat

Author: fbourgey

.github/CODEOWNERS

@@ -4,9 +4,6 @@
 # ci
 ci/                               @mroeschke
 
-# web
-web/                              @datapythonista
-
 # docs
 doc/cheatsheet                    @Dr-Irv
 doc/source/development            @noatamir

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

@@ -14,7 +14,7 @@ runs:
       if: failure()
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         flags: unittests
         name: codecov-pandas

.github/actions/setup-conda/action.yml

@@ -7,7 +7,7 @@ runs:
   using: composite
   steps:
     - name: Install ${{ inputs.environment-file }}
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: ${{ inputs.environment-file }}
         environment-name: test

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

@@ -59,6 +59,10 @@ jobs:
     - name: Build documentation
       run: doc/make.py --warnings-are-errors
 
+    - name: Build the interactive terminal
+      working-directory: web/interactive_terminal
+      run: jupyter lite build
+
     - name: Build documentation zip
       run: doc/make.py zip_html
 

.github/workflows/wheels.yml

@@ -153,7 +153,7 @@ jobs:
         run: echo "sdist_name=$(cd ./dist && ls -d */)" >> "$GITHUB_ENV"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.22.0
+        uses: pypa/cibuildwheel@v2.23.0
         with:
          package-dir: ./dist/${{ startsWith(matrix.buildplat[1], 'macosx') && env.sdist_name || needs.build_sdist.outputs.sdist_file }}
         env:

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ ci:
     skip: [pyright, mypy]
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.4
+    rev: v0.9.9
     hooks:
     -   id: ruff
         args: [--exit-non-zero-on-fix]
@@ -70,7 +70,7 @@ repos:
     -   id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
 -   repo: https://github.com/PyCQA/isort
-    rev: 6.0.0
+    rev: 6.0.1
     hooks:
     -   id: isort
 -   repo: https://github.com/asottile/pyupgrade
@@ -106,6 +106,11 @@ repos:
     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

Dockerfile

@@ -13,5 +13,5 @@ COPY requirements-dev.txt /tmp
 RUN python -m pip install -r /tmp/requirements-dev.txt
 RUN git config --global --add safe.directory /home/pandas
 
-ENV SHELL "/bin/bash"
+ENV SHELL="/bin/bash"
 CMD ["/bin/bash"]

ci/code_checks.sh

@@ -24,15 +24,15 @@ else
 fi
 
 [[ -z "$CHECK" || "$CHECK" == "code" || "$CHECK" == "doctests" || "$CHECK" == "docstrings" || "$CHECK" == "single-docs" || "$CHECK" == "notebooks" ]] || \
-    { echo "Unknown command $1. Usage: $0 [code|doctests|docstrings|single-docs|notebooks]"; exit 9999; }
+    { echo "Unknown command $1. Usage: $0 [code|doctests|docstrings|single-docs|notebooks]"; exit 1; }
 
-BASE_DIR="$(dirname $0)/.."
+BASE_DIR="$(dirname "$0")/.."
 RET=0
 
 ### CODE ###
 if [[ -z "$CHECK" || "$CHECK" == "code" ]]; then
 
-    MSG='Check import. No warnings, and blocklist some optional dependencies' ; echo $MSG
+    MSG='Check import. No warnings, and blocklist some optional dependencies' ; echo "$MSG"
     python -W error -c "
 import sys
 import pandas
@@ -49,24 +49,24 @@ if mods:
     sys.stderr.write('err: pandas should not import: {}\n'.format(', '.join(mods)))
     sys.exit(len(mods))
     "
-    RET=$(($RET + $?)) ; echo $MSG "DONE"
+    RET=$(($RET + $?)) ; echo "$MSG" "DONE"
 
 fi
 
 ### DOCTESTS ###
 if [[ -z "$CHECK" || "$CHECK" == "doctests" ]]; then
 
-    MSG='Python and Cython Doctests' ; echo $MSG
+    MSG='Python and Cython Doctests' ; echo "$MSG"
     python -c 'import pandas as pd; pd.test(run_doctests=True)'
-    RET=$(($RET + $?)) ; echo $MSG "DONE"
+    RET=$(($RET + $?)) ; echo "$MSG" "DONE"
 
 fi
 
 ### DOCSTRINGS ###
 if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then
 
-    MSG='Validate Docstrings' ; echo $MSG
-    $BASE_DIR/scripts/validate_docstrings.py \
+    MSG='Validate Docstrings' ; echo "$MSG"
+    "$BASE_DIR"/scripts/validate_docstrings.py \
         --format=actions \
         -i ES01 `# For now it is ok if docstrings are missing the extended summary` \
         -i "pandas.Series.dt PR01" `# Accessors are implemented as classes, but we do not document the Parameters section` \
@@ -265,7 +265,7 @@ fi
 if [[ -z "$CHECK" || "$CHECK" == "notebooks" ]]; then
 
     MSG='Notebooks' ; echo $MSG
-    jupyter nbconvert --execute $(find doc/source -name '*.ipynb') --to notebook
+    jupyter nbconvert --execute "$(find doc/source -name '*.ipynb')" --to notebook
     RET=$(($RET + $?)) ; echo $MSG "DONE"
 
 fi

ci/run_tests.sh

@@ -3,10 +3,8 @@
 # Workaround for pytest-xdist (it collects different tests in the workers if PYTHONHASHSEED is not set)
 # https://github.com/pytest-dev/pytest/issues/920
 # https://github.com/pytest-dev/pytest/issues/1075
-export PYTHONHASHSEED=$(python -c 'import random; print(random.randint(1, 4294967295))')
-
-# May help reproduce flaky CI builds if set in subsequent runs
-echo PYTHONHASHSEED=$PYTHONHASHSEED
+PYTHONHASHSEED=$(python -c 'import random; print(random.randint(1, 4294967295))')
+export PYTHONHASHSEED
 
 COVERAGE="-s --cov=pandas --cov-report=xml --cov-append --cov-config=pyproject.toml"
 
@@ -16,5 +14,5 @@ if [[ "$PATTERN" ]]; then
   PYTEST_CMD="$PYTEST_CMD -m \"$PATTERN\""
 fi
 
-echo $PYTEST_CMD
+echo "$PYTEST_CMD"
 sh -c "$PYTEST_CMD"

ci/upload_wheels.sh

@@ -1,3 +1,4 @@
+#!/bin/bash
 # Modified from numpy's https://github.com/numpy/numpy/blob/main/tools/wheels/upload_wheels.sh
 
 set_upload_vars() {
@@ -19,20 +20,20 @@ set_upload_vars() {
     fi
 }
 upload_wheels() {
-    echo ${PWD}
+    echo "${PWD}"
     if [[ ${ANACONDA_UPLOAD} == true ]]; then
-        if [ -z ${TOKEN} ]; then
+        if [ -z "${TOKEN}" ]; then
             echo no token set, not uploading
         else
             # sdists are located under dist folder when built through setup.py
             if compgen -G "./dist/*.gz"; then
                 echo "Found sdist"
-                anaconda -q -t ${TOKEN} upload --skip -u ${ANACONDA_ORG} ./dist/*.gz
+                anaconda -q -t "${TOKEN}" upload --skip -u "${ANACONDA_ORG}" ./dist/*.gz
                 echo "Uploaded sdist"
             fi
             if compgen -G "./wheelhouse/*.whl"; then
                 echo "Found wheel"
-                anaconda -q -t ${TOKEN} upload --skip -u ${ANACONDA_ORG} ./wheelhouse/*.whl
+                anaconda -q -t "${TOKEN}" upload --skip -u "${ANACONDA_ORG}" ./wheelhouse/*.whl
                 echo "Uploaded wheel"
             fi
             echo "PyPI-style index: https://pypi.anaconda.org/$ANACONDA_ORG/simple"