Backport PR #47979 on branch 1.4.x (DEPS: Update cython)

asv_bench/asv.conf.json

@@ -42,7 +42,7 @@
     // followed by the pip installed packages).
     "matrix": {
         "numpy": [],
-        "Cython": ["0.29.30"],
+        "Cython": ["0.29.32"],
         "matplotlib": [],
         "sqlalchemy": [],
         "scipy": [],

ci/deps/actions-310-numpydev.yaml

@@ -16,7 +16,7 @@ dependencies:
   - pytz
   - pip
   - pip:
-    - cython==0.29.30 # GH#34014
+    - cython==0.29.32
     - "--extra-index-url https://pypi.anaconda.org/scipy-wheels-nightly/simple"
     - "--pre"
     - "numpy"

ci/deps/actions-310.yaml

@@ -5,7 +5,7 @@ dependencies:
   - python=3.10
 
   # test dependencies
-  - cython=0.29.30
+  - cython>=0.29.32
   - pytest>=6.0
   - pytest-cov
   - pytest-xdist>=1.31

ci/deps/actions-38-downstream_compat.yaml

@@ -6,7 +6,7 @@ dependencies:
   - python=3.8
 
   # test dependencies
-  - cython=0.29.30
+  - cython>=0.29.32
   - pytest>=6.0
   - pytest-cov
   - pytest-xdist>=1.31

ci/deps/actions-38-minimum_versions.yaml

@@ -7,7 +7,7 @@ dependencies:
   - python=3.8.0
 
   # test dependencies
-  - cython=0.29.30
+  - cython>=0.29.32
   - pytest>=6.0
   - pytest-cov
   - pytest-xdist>=1.31

ci/deps/actions-38.yaml

@@ -5,7 +5,7 @@ dependencies:
   - python=3.8
 
   # test dependencies
-  - cython=0.29.30
+  - cython>=0.29.32
   - pytest>=6.0
   - pytest-cov
   - pytest-xdist>=1.31

ci/deps/actions-39.yaml

@@ -5,7 +5,7 @@ dependencies:
   - python=3.9
 
   # test dependencies
-  - cython=0.29.30
+  - cython>=0.29.32
   - pytest>=6.0
   - pytest-cov
   - pytest-xdist>=1.31

ci/deps/actions-pypy-38.yaml

@@ -8,7 +8,7 @@ dependencies:
   - python=3.8[build=*_pypy] # TODO: use this once pypy3.8 is available
 
   # tools
-  - cython>=0.29.30
+  - cython>=0.29.32
   - pytest>=6.0
   - pytest-cov
   - pytest-asyncio

ci/deps/circle-38-arm64.yaml

@@ -5,7 +5,7 @@ dependencies:
   - python=3.8
 
   # test dependencies
-  - cython=0.29.30
+  - cython>=0.29.32
   - pytest>=6.0
   - pytest-cov
   - pytest-xdist>=1.31

doc/source/whatsnew/v1.4.4.rst

@@ -14,6 +14,7 @@ including other versions of pandas.
 
 Fixed regressions
 ~~~~~~~~~~~~~~~~~
+- Fixed regression in taking NULL :class:`objects` from a :class:`DataFrame` causing a segmentation violation. These NULL values are created by :meth:`numpy.empty_like` (:issue:`46848`)
 - Fixed regression in :func:`concat` materializing :class:`Index` during sorting even if :class:`Index` was already sorted (:issue:`47501`)
 - Fixed regression in :meth:`DataFrame.loc` not updating the cache correctly after values were set (:issue:`47867`)
 - Fixed regression in :meth:`DataFrame.loc` not aligning index in some cases when setting a :class:`DataFrame` (:issue:`47578`)
@@ -36,7 +37,7 @@ Bug fixes
 
 Other
 ~~~~~
--
+- The minimum version of Cython needed to compile pandas is now ``0.29.32`` (:issue:`47978`)
 -
 
 .. ---------------------------------------------------------------------------

environment.yml

@@ -15,7 +15,7 @@ dependencies:
   # The compiler packages are meta-packages and install the correct compiler (activation) packages on the respective platforms.
   - c-compiler
   - cxx-compiler
-  - cython>=0.29.30
+  - cython=0.29.32
 
   # code checks
   - black=22.3.0

pandas/tests/frame/indexing/test_indexing.py

@@ -1227,6 +1227,13 @@ def test_iloc_setitem_nullable_2d_values(self):
         df.iloc[:] = df.iloc[:, :]
         tm.assert_frame_equal(df, orig)
 
+    def test_getitem_segfault_with_empty_like_object(self):
+        # GH#46848
+        df = DataFrame(np.empty((1, 1), dtype=object))
+        df[0] = np.empty_like(df[0])
+        # this produces the segfault
+        df[[0]]
+
     @pytest.mark.parametrize(
         "null", [pd.NaT, pd.NaT.to_numpy("M8[ns]"), pd.NaT.to_numpy("m8[ns]")]
     )

pyproject.toml

@@ -4,7 +4,7 @@
 requires = [
     "setuptools>=51.0.0",
     "wheel",
-    "Cython>=0.29.24,<3",  # Note: sync with setup.py, environment.yml and asv.conf.json
+    "Cython>=0.29.32,<3",  # Note: sync with setup.py, environment.yml and asv.conf.json
     "oldest-supported-numpy>=0.10"
 ]
 # uncomment to enable pep517 after versioneer problem is fixed.

requirements-dev.txt

@@ -5,7 +5,7 @@ numpy>=1.18.5, <=1.22.4
 python-dateutil>=2.8.1
 pytz
 asv
-cython>=0.29.30
+cython==0.29.32
 black==22.3.0
 cpplint
 flake8==4.0.1

setup.py

@@ -38,7 +38,7 @@ def is_platform_mac():
 
 
 # note: sync with pyproject.toml, environment.yml and asv.conf.json
-min_cython_ver = "0.29.30"
+min_cython_ver = "0.29.32"
 
 try:
     from Cython import (