Merge branch 'main' into include-pyproject

Author: lithomas1

.github/ISSUE_TEMPLATE/bug_report.yaml

@@ -17,7 +17,9 @@ body:
             [latest version](https://pandas.pydata.org/docs/whatsnew/index.html) of pandas.
           required: true
         - label: >
-            I have confirmed this bug exists on the main branch of pandas.
+            I have confirmed this bug exists on the [main branch]
+            (https://pandas.pydata.org/docs/dev/getting_started/install.html#installing-the-development-version-of-pandas)
+            of pandas.
   - type: textarea
     id: example
     attributes:

.github/workflows/32-bit-linux.yml

@@ -39,7 +39,7 @@ jobs:
           . ~/virtualenvs/pandas-dev/bin/activate && \
           python -m pip install --no-deps -U pip wheel 'setuptools<60.0.0' && \
           python -m pip install versioneer[toml] && \
-          python -m pip install cython numpy python-dateutil pytz pytest pytest-xdist pytest-asyncio>=0.17 hypothesis && \
+          python -m pip install cython numpy python-dateutil pytz pytest>=7.0.0 pytest-xdist>=2.2.0 pytest-asyncio>=0.17 hypothesis>=6.34.2 && \
           python setup.py build_ext -q -j1 && \
           python -m pip install --no-build-isolation --no-use-pep517 -e . && \
           python -m pip list && \

.github/workflows/codeql.yml

@@ -8,6 +8,9 @@ concurrency:
   group: ${{ github.repository }}-${{ github.head_ref || github.sha }}-${{ github.workflow }}
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
   analyze:
     runs-on: ubuntu-22.04

.github/workflows/python-dev.yml

@@ -73,10 +73,10 @@ jobs:
       run: |
         python --version
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install -i https://pypi.anaconda.org/scipy-wheels-nightly/simple numpy
+        python -m pip install --pre --extra-index-url https://pypi.anaconda.org/scipy-wheels-nightly/simple numpy
         python -m pip install git+https://github.com/nedbat/coveragepy.git
         python -m pip install versioneer[toml]
-        python -m pip install python-dateutil pytz cython hypothesis==6.52.1 pytest>=6.2.5 pytest-xdist pytest-cov pytest-asyncio>=0.17
+        python -m pip install python-dateutil pytz cython hypothesis>=6.34.2 pytest>=7.0.0 pytest-xdist>=2.2.0 pytest-cov pytest-asyncio>=0.17
         python -m pip list
 
     # GH 47305: Parallel build can cause flaky ImportError from pandas/_libs/tslibs

.github/workflows/wheels.yml

@@ -30,6 +30,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
   build_wheels:
     name: Build wheel for ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}
@@ -165,7 +168,7 @@ jobs:
           # (1. Generate sdist 2. Build wheels from sdist)
           # This tests the sdists, and saves some build time
           python -m pip install dist/*.gz
-          pip install hypothesis==6.52.1 pytest>=6.2.5 pytest-xdist pytest-asyncio>=0.17
+          pip install hypothesis>=6.34.2 pytest>=7.0.0 pytest-xdist>=2.2.0 pytest-asyncio>=0.17
           cd .. # Not a good idea to test within the src tree
           python -c "import pandas; print(pandas.__version__);
           pandas.test(extra_args=['-m not clipboard and not single_cpu', '--skip-slow', '--skip-network', '--skip-db', '-n=2', '--no-strict-data-files']);

.pre-commit-config.yaml

@@ -15,6 +15,10 @@ default_stages: [
 ci:
     autofix_prs: false
 repos:
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.215
+    hooks:
+    -   id: ruff
 -   repo: https://github.com/MarcoGorelli/absolufy-imports
     rev: v0.3.1
     hooks:
@@ -34,7 +38,7 @@ repos:
         types_or: [python, rst, markdown]
         additional_dependencies: [tomli]
 -   repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.9.1
+    rev: v0.10.1
     hooks:
     -   id: cython-lint
     -   id: double-quote-cython-strings
@@ -63,25 +67,16 @@ repos:
             '--extensions=c,h',
             '--headers=h',
             --recursive,
-            '--filter=-readability/casting,-runtime/int,-build/include_subdir'
+            --linelength=88,
+            '--filter=-readability/casting,-runtime/int,-build/include_subdir,-readability/fn_size'
         ]
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-    -   id: flake8
-        # Need to patch os.remove rule in pandas-dev-flaker
-        exclude: ^ci/fix_wheels.py
-        additional_dependencies: &flake8_dependencies
-        - flake8==6.0.0
-        - flake8-bugbear==22.7.1
-        - pandas-dev-flaker==0.5.0
 -   repo: https://github.com/pycqa/pylint
-    rev: v2.15.6
+    rev: v2.15.9
     hooks:
     -   id: pylint
         stages: [manual]
 -   repo: https://github.com/pycqa/pylint
-    rev: v2.15.6
+    rev: v2.15.9
     hooks:
     -   id: pylint
         alias: redefined-outer-name
@@ -94,15 +89,14 @@ repos:
             |^pandas/util/_test_decorators\.py  # keep excluded
             |^pandas/_version\.py  # keep excluded
             |^pandas/conftest\.py  # keep excluded
-            |^pandas/core/generic\.py
         args: [--disable=all, --enable=redefined-outer-name]
         stages: [manual]
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.11.4
     hooks:
     -   id: isort
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.2
+    rev: v3.3.1
     hooks:
     -   id: pyupgrade
         args: [--py38-plus]
@@ -120,12 +114,6 @@ repos:
     rev: v0.6.7
     hooks:
     - id: sphinx-lint
--   repo: https://github.com/asottile/yesqa
-    rev: v1.4.0
-    hooks:
-    -   id: yesqa
-        additional_dependencies: *flake8_dependencies
-        stages: [manual]
 -   repo: local
     hooks:
     # NOTE: we make `black` a local hook because if it's installed from
@@ -183,6 +171,21 @@ repos:
         types: [rst]
         args: [--filename=*.rst]
         additional_dependencies: [flake8-rst==0.7.0, flake8==3.7.9]
+    -   id: inconsistent-namespace-usage
+        name: 'Check for inconsistent use of pandas namespace'
+        entry: python scripts/check_for_inconsistent_pandas_namespace.py
+        exclude: ^pandas/core/interchange/
+        language: python
+        types: [python]
+    -   id: no-os-remove
+        name: Check code for instances of os.remove
+        entry: os\.remove
+        language: pygrep
+        types: [python]
+        files: ^pandas/tests/
+        exclude: |
+            (?x)^
+            pandas/tests/io/pytables/test_store\.py$
     -   id: unwanted-patterns
         name: Unwanted patterns
         language: pygrep
@@ -192,6 +195,20 @@ repos:
             \#\ type:\ (?!ignore)
             |\#\ type:\s?ignore(?!\[)
 
+            # foo._class__ instead of type(foo)
+            |\.__class__
+
+            # np.bool/np.object instead of np.bool_/np.object_
+            |np\.bool[^_8`]
+            |np\.object[^_8`]
+
+            # imports from collections.abc instead of `from collections import abc`
+            |from\ collections\.abc\ import
+
+            # Numpy
+            |from\ numpy\ import\ random
+            |from\ numpy\.random\ import
+
             # Incorrect code-block / IPython directives
             |\.\.\ code-block\ ::
             |\.\.\ ipython\ ::
@@ -200,7 +217,17 @@ repos:
 
             # Check for deprecated messages without sphinx directive
             |(DEPRECATED|DEPRECATE|Deprecated)(:|,|\.)
+
+            # {foo!r} instead of {repr(foo)}
+            |!r}
+
+            # builtin filter function
+            |(?<!def)[\(\s]filter\(
+
+            # exec
+            |[^a-zA-Z0-9_]exec\(
         types_or: [python, cython, rst]
+        exclude: ^doc/source/development/code_style\.rst  # contains examples of patterns to avoid
     -   id: cython-casting
         name: Check Cython casting is `<type>obj`, not `<type> obj`
         language: pygrep
@@ -231,26 +258,103 @@ repos:
         files: ^pandas/tests/extension/base
         types: [python]
         exclude: ^pandas/tests/extension/base/base\.py
+    -   id: unwanted-patterns-in-tests
+        name: Unwanted patterns in tests
+        language: pygrep
+        entry: |
+            (?x)
+            # pytest.xfail instead of pytest.mark.xfail
+            pytest\.xfail
+
+            # imports from pandas._testing instead of `import pandas._testing as tm`
+            |from\ pandas\._testing\ import
+            |from\ pandas\ import\ _testing\ as\ tm
+
+            # No direct imports from conftest
+            |conftest\ import
+            |import\ conftest
+
+            # pandas.testing instead of tm
+            |pd\.testing\.
+
+            # pd.api.types instead of from pandas.api.types import ...
+            |(pd|pandas)\.api\.types\.
+
+            # np.testing, np.array_equal
+            |(numpy|np)(\.testing|\.array_equal)
+
+            # unittest.mock (use pytest builtin monkeypatch fixture instead)
+            |(unittest(\.| import )mock|mock\.Mock\(\)|mock\.patch)
+
+            # pytest raises without context
+            |\s\ pytest.raises
+
+            # pytest.warns (use tm.assert_produces_warning instead)
+            |pytest\.warns
+        files: ^pandas/tests/
+        types_or: [python, cython, rst]
+    -   id: unwanted-patterns-in-ea-tests
+        name: Unwanted patterns in EA tests
+        language: pygrep
+        entry: |
+            (?x)
+            tm.assert_(series|frame)_equal
+        files: ^pandas/tests/extension/base/
+        exclude: ^pandas/tests/extension/base/base\.py$
+        types_or: [python, cython, rst]
+    -   id: unwanted-patterns-in-cython
+        name: Unwanted patterns in Cython code
+        language: pygrep
+        entry: |
+            (?x)
+            # `<type>obj` as opposed to `<type> obj`
+            [a-zA-Z0-9*]>[ ]
+        types: [cython]
     -   id: pip-to-conda
         name: Generate pip dependency from conda
         language: python
         entry: python scripts/generate_pip_deps_from_conda.py
         files: ^(environment.yml|requirements-dev.txt)$
         pass_filenames: false
         additional_dependencies: [pyyaml, toml]
-    -   id: sync-flake8-versions
-        name: Check flake8 version is synced across flake8, yesqa, and environment.yml
-        language: python
-        entry: python scripts/sync_flake8_versions.py
-        files: ^(\.pre-commit-config\.yaml|environment\.yml)$
-        pass_filenames: false
-        additional_dependencies: [pyyaml, toml]
     -   id: title-capitalization
         name: Validate correct capitalization among titles in documentation
         entry: python scripts/validate_rst_title_capitalization.py
         language: python
         types: [rst]
         files: ^doc/source/(development|reference)/
+    -   id: unwanted-patterns-bare-pytest-raises
+        name: Check for use of bare pytest raises
+        language: python
+        entry: python scripts/validate_unwanted_patterns.py --validation-type="bare_pytest_raises"
+        types: [python]
+        files: ^pandas/tests/
+        exclude: ^pandas/tests/extension/
+    -   id: unwanted-patterns-private-function-across-module
+        name: Check for use of private functions across modules
+        language: python
+        entry: python scripts/validate_unwanted_patterns.py --validation-type="private_function_across_module"
+        types: [python]
+        exclude: ^(asv_bench|pandas/tests|doc)/
+    -   id: unwanted-patterns-private-import-across-module
+        name: Check for import of private attributes across modules
+        language: python
+        entry: python scripts/validate_unwanted_patterns.py --validation-type="private_import_across_module"
+        types: [python]
+        exclude: |
+            (?x)
+            ^(asv_bench|pandas/tests|doc)/
+            |scripts/validate_min_versions_in_sync\.py$
+    -   id: unwanted-patterns-strings-to-concatenate
+        name: Check for use of not concatenated strings
+        language: python
+        entry: python scripts/validate_unwanted_patterns.py --validation-type="strings_to_concatenate"
+        types_or: [python, cython]
+    -   id: unwanted-patterns-strings-with-misplaced-whitespace
+        name: Check for strings with misplaced spaces
+        language: python
+        entry: python scripts/validate_unwanted_patterns.py --validation-type="strings_with_wrong_placed_whitespace"
+        types_or: [python, cython]
     -   id: use-pd_array-in-core
         name: Import pandas.array as pd_array in core
         language: python

asv_bench/asv.conf.json

@@ -41,7 +41,7 @@
     // pip (with all the conda available packages installed first,
     // followed by the pip installed packages).
     "matrix": {
-        "numpy": ["1.23.5"],  // https://github.com/pandas-dev/pandas/pull/50356
+        "numpy": [],
         "Cython": ["0.29.32"],
         "matplotlib": [],
         "sqlalchemy": [],

asv_bench/benchmarks/array.py

@@ -44,6 +44,15 @@ def time_from_integer_array(self):
         pd.array(self.values_integer, dtype="Int64")
 
 
+class IntervalArray:
+    def setup(self):
+        N = 10_000
+        self.tuples = [(i, i + 1) for i in range(N)]
+
+    def time_from_tuples(self):
+        pd.arrays.IntervalArray.from_tuples(self.tuples)
+
+
 class StringArray:
     def setup(self):
         N = 100_000

asv_bench/benchmarks/indexing.py

@@ -476,6 +476,19 @@ def time_assign_list_of_columns_concat(self):
         concat([self.df, df], axis=1)
 
 
+class Setitem:
+    def setup(self):
+        N = 500_000
+        cols = 500
+        self.df = DataFrame(np.random.rand(N, cols))
+
+    def time_setitem(self):
+        self.df[100] = 100
+
+    def time_setitem_list(self):
+        self.df[[100, 200, 300]] = 100
+
+
 class ChainIndexing:
 
     params = [None, "warn"]

asv_bench/benchmarks/pandas_vb_common.py

@@ -70,7 +70,7 @@ class BaseIO:
     def remove(self, f):
         """Remove created files"""
         try:
-            os.remove(f)  # noqa: PDF008
+            os.remove(f)
         except OSError:
             # On Windows, attempting to remove a file that is in use
             # causes an exception to be raised

asv_bench/benchmarks/rolling.py

@@ -292,7 +292,7 @@ class Groupby:
         ["sum", "median", "mean", "max", "min", "kurt", "sum"],
         [
             ("rolling", {"window": 2}),
-            ("rolling", {"window": "30s", "on": "C"}),
+            ("rolling", {"window": "30s"}),
             ("expanding", {}),
         ],
     )
@@ -304,9 +304,10 @@ def setup(self, method, window_kwargs):
             {
                 "A": [str(i) for i in range(N)] * 10,
                 "B": list(range(N)) * 10,
-                "C": pd.date_range(start="1900-01-01", freq="1min", periods=N * 10),
             }
         )
+        if isinstance(kwargs.get("window", None), str):
+            df.index = pd.date_range(start="1900-01-01", freq="1min", periods=N * 10)
         self.groupby_window = getattr(df.groupby("A"), window)(**kwargs)
 
     def time_method(self, method, window_kwargs):