GH-36730: [Python] Add support for Cython 3.0.0 (#37097)

### Rationale for this change Cython 3.0.0 is the latest release. PyArrow should work with Cython 3.0.0. **Cython 3 is not enabled in this diff.** ### What changes are included in this PR? * Don't use `vector[XXX]&&` * Add a declaration for `postincrement` * See also: https://cython.readthedocs.io/en/latest/src/userguide/migrating_to_cy30.html#c-postincrement-postdecrement-operator * Ignore `C4551` warning (function call missing argument list) with MSVC * See also: cython/cython#4445 * Add missing `const` to `CLocation`'s static methods. * Don't use `StopIteration` to stop generator * See also: https://cython.readthedocs.io/en/latest/src/userguide/migrating_to_cy30.html#python-3-syntax-semantics * non-extern `cdef` functions will now propagate python exceptions automatically unless explicitly labeled `noexcept` * Function binding in cython is now enabled by default. Class methods that are used as wrappers for pickling should be converted to staticmethods. * Numpydocs now validates more Cython 3 objects than Cython <3 * Enum types are now being validated, and some unhelpful validation checks on Enums are now ignored * Added a cython <3 nightly CI job Note: * Cython 3.0.0, 3.0.1, 3.0.2 has an issue when compiling with debug mode cython/cython#5552 ### Are these changes tested? Yes. ### Are there any user-facing changes? Yes. * Closes: #36730 Lead-authored-by: Dane Pitkin <[email protected]> Co-authored-by: Sutou Kouhei <[email protected]> Co-authored-by: Dane Pitkin <[email protected]> Signed-off-by: AlenkaF <[email protected]>
apache · Sep 21, 2023 · e83c23b · e83c23b
1 parent 9d6d501
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diff --git a/ci/docker/conda-python-cython2.dockerfile b/ci/docker/conda-python-cython2.dockerfile
@@ -0,0 +1,24 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+ARG repo
+ARG arch
+ARG python=3.8
+FROM ${repo}:${arch}-conda-python-${python}
+
+RUN mamba install -q -y "cython<3" && \
+    mamba clean --all
diff --git a/dev/archery/archery/lang/python.py b/dev/archery/archery/lang/python.py
@@ -16,6 +16,7 @@
 # under the License.
 
 from contextlib import contextmanager
+from enum import EnumMeta
 import inspect
 import tokenize
 
@@ -112,6 +113,10 @@ def inspect_signature(obj):
 
 
 class NumpyDoc:
+    IGNORE_VALIDATION_ERRORS_FOR_TYPE = {
+        # Enum function signatures should never be documented
+        EnumMeta: ["PR01"]
+    }
 
     def __init__(self, symbols=None):
         if not have_numpydoc:
@@ -229,6 +234,10 @@ def callback(obj):
                     continue
                 if disallow_rules and errcode in disallow_rules:
                     continue
+                if any(isinstance(obj, obj_type) and errcode in errcode_list
+                       for obj_type, errcode_list
+                       in NumpyDoc.IGNORE_VALIDATION_ERRORS_FOR_TYPE.items()):
+                    continue
                 errors.append((errcode, errmsg))
 
             if len(errors):

diff --git a/dev/tasks/tasks.yml b/dev/tasks/tasks.yml
@@ -1286,6 +1286,14 @@ tasks:
         PYTHON: "3.10"
       image: conda-python-substrait
 
+  test-conda-python-3.10-cython2:
+    ci: github
+    template: docker-tests/github.linux.yml
+    params:
+      env:
+        PYTHON: "3.10"
+      image: conda-python-cython2
+
   test-debian-11-python-3:
     ci: azure
     template: docker-tests/azure.linux.yml

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -119,6 +119,7 @@ x-hierarchy:
       - conda-python:
         - conda-python-pandas:
           - conda-python-docs
+        - conda-python-cython2
         - conda-python-dask
         - conda-python-hdfs
         - conda-python-java-integration
@@ -1349,6 +1350,30 @@ services:
           /arrow/ci/scripts/java_build.sh /arrow /build /tmp/dist/java &&
           /arrow/ci/scripts/java_cdata_integration.sh /arrow /tmp/dist/java" ]
 
+  conda-python-cython2:
+    # Usage:
+    #   docker-compose build conda
+    #   docker-compose build conda-cpp
+    #   docker-compose build conda-python
+    #   docker-compose build conda-python-cython2
+    #   docker-compose run --rm conda-python-cython2
+    image: ${REPO}:${ARCH}-conda-python-${PYTHON}-cython2
+    build:
+      context: .
+      dockerfile: ci/docker/conda-python-cython2.dockerfile
+      cache_from:
+        - ${REPO}:${ARCH}-conda-python-${PYTHON}-cython2
+      args:
+        repo: ${REPO}
+        arch: ${ARCH}
+        python: ${PYTHON}
+    shm_size: *shm-size
+    environment:
+      <<: [*common, *ccache]
+      PYTEST_ARGS:  # inherit
+    volumes: *conda-volumes
+    command: *python-conda-command
+
   ################################## R ########################################
 
   ubuntu-r:

diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
@@ -168,37 +168,44 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${PYARROW_CXXFLAGS}")
 
 if(MSVC)
   # MSVC version of -Wno-return-type-c-linkage
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4190")
+  string(APPEND CMAKE_CXX_FLAGS " /wd4190")
 
   # Cython generates some bitshift expressions that MSVC does not like in
   # __Pyx_PyFloat_DivideObjC
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4293")
+  string(APPEND CMAKE_CXX_FLAGS " /wd4293")
 
   # Converting to/from C++ bool is pretty wonky in Cython. The C4800 warning
   # seem harmless, and probably not worth the effort of working around it
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4800")
+  string(APPEND CMAKE_CXX_FLAGS " /wd4800")
 
   # See https://github.com/cython/cython/issues/2731. Change introduced in
   # Cython 0.29.1 causes "unsafe use of type 'bool' in operation"
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4804")
+  string(APPEND CMAKE_CXX_FLAGS " /wd4804")
+
+  # See https://github.com/cython/cython/issues/4445.
+  #
+  # Cython 3 emits "(void)__Pyx_PyObject_CallMethod0;" to suppress a
+  # "unused function" warning but the code emits another "function
+  # call missing argument list" warning.
+  string(APPEND CMAKE_CXX_FLAGS " /wd4551")
 else()
   # Enable perf and other tools to work properly
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-omit-frame-pointer")
+  string(APPEND CMAKE_CXX_FLAGS " -fno-omit-frame-pointer")
 
   # Suppress Cython warnings
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-variable -Wno-maybe-uninitialized")
+  string(APPEND CMAKE_CXX_FLAGS " -Wno-unused-variable -Wno-maybe-uninitialized")
 
   if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang" OR CMAKE_CXX_COMPILER_ID STREQUAL
                                                     "Clang")
     # Cython warnings in clang
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-parentheses-equality")
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-constant-logical-operand")
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-missing-declarations")
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-sometimes-uninitialized")
+    string(APPEND CMAKE_CXX_FLAGS " -Wno-parentheses-equality")
+    string(APPEND CMAKE_CXX_FLAGS " -Wno-constant-logical-operand")
+    string(APPEND CMAKE_CXX_FLAGS " -Wno-missing-declarations")
+    string(APPEND CMAKE_CXX_FLAGS " -Wno-sometimes-uninitialized")
 
     # We have public Cython APIs which return C++ types, which are in an extern
     # "C" blog (no symbol mangling) and clang doesn't like this
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-return-type-c-linkage")
+    string(APPEND CMAKE_CXX_FLAGS " -Wno-return-type-c-linkage")
   endif()
 endif()
 

diff --git a/python/pyarrow/_dataset.pyx b/python/pyarrow/_dataset.pyx
@@ -1078,7 +1078,8 @@ cdef class FileSystemDataset(Dataset):
     @classmethod
     def from_paths(cls, paths, schema=None, format=None,
                    filesystem=None, partitions=None, root_partition=None):
-        """A Dataset created from a list of paths on a particular filesystem.
+        """
+        A Dataset created from a list of paths on a particular filesystem.
 
         Parameters
         ----------

diff --git a/python/pyarrow/_flight.pyx b/python/pyarrow/_flight.pyx
@@ -988,8 +988,10 @@ cdef class _MetadataRecordBatchReader(_Weakrefable, _ReadPandasMixin):
     cdef shared_ptr[CMetadataRecordBatchReader] reader
 
     def __iter__(self):
-        while True:
-            yield self.read_chunk()
+        return self
+
+    def __next__(self):
+        return self.read_chunk()
 
     @property
     def schema(self):
@@ -1699,7 +1701,9 @@ cdef class FlightClient(_Weakrefable):
 
     def close(self):
         """Close the client and disconnect."""
-        check_flight_status(self.client.get().Close())
+        client = self.client.get()
+        if client != NULL:
+            check_flight_status(client.Close())
 
     def __del__(self):
         # Not ideal, but close() wasn't originally present so

diff --git a/python/pyarrow/_substrait.pyx b/python/pyarrow/_substrait.pyx
@@ -27,9 +27,10 @@ from pyarrow.includes.libarrow cimport *
 from pyarrow.includes.libarrow_substrait cimport *
 
 
+# TODO GH-37235: Fix exception handling
 cdef CDeclaration _create_named_table_provider(
     dict named_args, const std_vector[c_string]& names, const CSchema& schema
-):
+) noexcept:
     cdef:
         c_string c_name
         shared_ptr[CTable] c_in_table

diff --git a/python/pyarrow/includes/libarrow_flight.pxd b/python/pyarrow/includes/libarrow_flight.pxd
@@ -118,16 +118,16 @@ cdef extern from "arrow/flight/api.h" namespace "arrow" nogil:
         c_bool Equals(const CLocation& other)
 
         @staticmethod
-        CResult[CLocation] Parse(c_string& uri_string)
+        CResult[CLocation] Parse(const c_string& uri_string)
 
         @staticmethod
-        CResult[CLocation] ForGrpcTcp(c_string& host, int port)
+        CResult[CLocation] ForGrpcTcp(const c_string& host, int port)
 
         @staticmethod
-        CResult[CLocation] ForGrpcTls(c_string& host, int port)
+        CResult[CLocation] ForGrpcTls(const c_string& host, int port)
 
         @staticmethod
-        CResult[CLocation] ForGrpcUnix(c_string& path)
+        CResult[CLocation] ForGrpcUnix(const c_string& path)
 
     cdef cppclass CFlightEndpoint" arrow::flight::FlightEndpoint":
         CFlightEndpoint()
@@ -172,7 +172,9 @@ cdef extern from "arrow/flight/api.h" namespace "arrow" nogil:
         CResult[unique_ptr[CFlightInfo]] Next()
 
     cdef cppclass CSimpleFlightListing" arrow::flight::SimpleFlightListing":
-        CSimpleFlightListing(vector[CFlightInfo]&& info)
+        # This doesn't work with Cython >= 3
+        # CSimpleFlightListing(vector[CFlightInfo]&& info)
+        CSimpleFlightListing(const vector[CFlightInfo]& info)
 
     cdef cppclass CFlightPayload" arrow::flight::FlightPayload":
         shared_ptr[CBuffer] descriptor
@@ -310,7 +312,10 @@ cdef extern from "arrow/flight/api.h" namespace "arrow" nogil:
     cdef cppclass CCallHeaders" arrow::flight::CallHeaders":
         cppclass const_iterator:
             pair[c_string, c_string] operator*()
+            # For Cython < 3
             const_iterator operator++()
+            # For Cython >= 3
+            const_iterator operator++(int)
             bint operator==(const_iterator)
             bint operator!=(const_iterator)
         const_iterator cbegin()

diff --git a/python/pyarrow/ipc.pxi b/python/pyarrow/ipc.pxi
@@ -436,8 +436,10 @@ cdef class MessageReader(_Weakrefable):
         return result
 
     def __iter__(self):
-        while True:
-            yield self.read_next_message()
+        return self
+
+    def __next__(self):
+        return self.read_next_message()
 
     def read_next_message(self):
         """
@@ -656,11 +658,10 @@ cdef class RecordBatchReader(_Weakrefable):
     # cdef block is in lib.pxd
 
     def __iter__(self):
-        while True:
-            try:
-                yield self.read_next_batch()
-            except StopIteration:
-                return
+        return self
+
+    def __next__(self):
+        return self.read_next_batch()
 
     @property
     def schema(self):

diff --git a/python/pyarrow/scalar.pxi b/python/pyarrow/scalar.pxi
@@ -819,8 +819,8 @@ cdef class MapScalar(ListScalar):
         Iterate over this element's values.
         """
         arr = self.values
-        if array is None:
-            raise StopIteration
+        if arr is None:
+            return
         for k, v in zip(arr.field(self.type.key_field.name), arr.field(self.type.item_field.name)):
             yield (k.as_py(), v.as_py())
 

diff --git a/python/pyarrow/tests/test_dataset.py b/python/pyarrow/tests/test_dataset.py
@@ -1615,9 +1615,13 @@ def test_fragments_repr(tempdir, dataset):
     # partitioned parquet dataset
     fragment = list(dataset.get_fragments())[0]
     assert (
+        # Ordering of partition items is non-deterministic
         repr(fragment) ==
         "<pyarrow.dataset.ParquetFileFragment path=subdir/1/xxx/file0.parquet "
-        "partition=[key=xxx, group=1]>"
+        "partition=[key=xxx, group=1]>" or
+        repr(fragment) ==
+        "<pyarrow.dataset.ParquetFileFragment path=subdir/1/xxx/file0.parquet "
+        "partition=[group=1, key=xxx]>"
     )
 
     # single-file parquet dataset (no partition information in repr)

diff --git a/python/pyarrow/tests/test_scalars.py b/python/pyarrow/tests/test_scalars.py
@@ -700,6 +700,10 @@ def test_map(pickle_module):
     for i, j in zip(s, v):
         assert i == j
 
+    # test iteration with missing values
+    for _ in pa.scalar(None, type=ty):
+        pass
+
     assert s.as_py() == v
     assert s[1] == (
         pa.scalar('b', type=pa.string()),