Scheduled monthly dependency update for May by pyup-bot · Pull Request #175 · alimanfoo/pysamstats

pyup-bot · 2025-05-01T15:12:15Z

Update Cython from 0.29.23 to 3.0.12.

Changelog

3.0.12

===================

Bugs fixed
----------

* Release 3.0.11 introduced some incorrect ``noexcept`` warnings.
(Github issue :issue:`6335`)

* Conditional assignments to variables using the walrus operator could crash.
(Github issue :issue:`6094`)

* Dict assignments to struct members with reserved C names could generate invalid C code.

* Fused ctuples with the same entry types but different sizes could fail to compile.
(Github issue :issue:`6328`)

* In Py3, `pyximport` was not searching `sys.path` when looking for importable source files.
(Github issue :issue:`5615`)

* Using `&amp; 0` on integers produced with `int.from_bytes()` could read invalid memory on Python 3.10.
(Github issue :issue:`6480`)

* Modules could fail to compile in PyPy 3.11 due to missing CPython specific header files.
Patch by Matti Picus.  (Github issue :issue:`6482`)

* Minor fix in C++ ``partial_sum()`` declaration.

3.0.11

===================

Features added
--------------

* The C++11 ``emplace*`` methods were added to ``libcpp.deque``.
Patch by Somin An.  (Github issue :issue:`6159`)

Bugs fixed
----------

* The exception check value of functions declared in pxd files was not always applied in 3.0.10.
(Github issue :issue:`6122`)

* A crash on exception deallocations was fixed.
(Github issue :issue:`6022`)

* A crash was fixed when assigning a zero-length slice to a memoryview.
Patch by Michael Man.  (Github issue :issue:`6227`)

* ``libcpp.optional.value()`` could crash if it raised a C++ exception.
Patch by Alexander Condello.  (Github issue :issue:`6190`)

* The return type of ``str()`` was mishandled, leading to crashes with ``language_level=3``.
(Github issue :issue:`6166`)

* ``bytes.startswith/endswith()`` failed for non-bytes substrings (e.g. ``bytearray``).
(Github issue :issue:`6168`)

* Fused ctuples crashed Cython.
(Github issue :issue:`6068`)

* A compiler crash was fixed when using extension types in fused types.
(Github issue :issue:`6204`)

* The module cleanup code was incorrect for globally defined memory view slices.
(Github issue :issue:`6276`)

* Some adaptations were made to enable compilation in Python 3.13.
(Github issues :issue:`5997`, :issue:`6182`, :issue:`6251`)

3.0.10

===================

Bugs fixed
----------

* Cython generated incorrect self-casts when directly calling final methods of subtypes.
Patch by Lisandro Dalcin.  (Github issue :issue:`2747`)

* Internal C names generated from C function signatures could become too long for MSVC.
(Github issue :issue:`6052`)

* The ``noexcept`` warnings could be misleading in some cases.
Patch by Gonzalo Tornaría.  (Github issue :issue:`6087`)

* The ``cython.ufunc`` implementation could generate incomplete C code.
(Github issue :issue:`6064`)

* The ``libcpp.complex`` declarations could result in incorrect C++ code.
Patch by Raffi Enficiaud.  (Github issue :issue:`6037`)

* Several tests were adapted to work with both NumPy 1.x and 2.0.
Patch by Matti Picus.  (Github issues :issue:`6076`, :issue:`6100`)

* C compiler warnings when the freelist implementation is disabled (e.g. on PyPy) were fixed.
It can now be disabled explicitly with the C macro guard ``CYTHON_USE_FREELISTS=0``.
(Github issue :issue:`6099`)

* Some C macro guards for feature flags were missing from the NOGIL Python configuration.

* Some recently added builtins were unconditionally looked up at module import time
(if used by user code) that weren&#x27;t available on all Python versions and could thus
fail the import.

* A performance hint regarding exported pxd declarations was improved.
(Github issue :issue:`6001`)

3.0.9

==================

Features added
--------------

* Assigning ``const`` values to non-const variables now issues a warning.
(Github issue :issue:`5639`)

* Using ``noexcept`` on a function returning Python objects now issues a warning.
(Github issue :issue:`5661`)

* Some C-API usage was updated for the upcoming CPython 3.13.
Patches by Victor Stinner et al.  (Github issues :issue:`6003`, :issue:`6020`)

* The deprecated ``Py_UNICODE`` type is no longer used, unless required by user code.
(Github issue :issue:`5982`)

* ``std::string.replace()`` declarations were added to libcpp.string.
Patch by Kieran Geary.  (Github issue :issue:`6037`)

Bugs fixed
----------

* Cython generates incorrect (but harmless) self-casts when directly calling
final methods of subtypes.  Lacking a better solution, the errors that recent
gcc versions produce have been silenced for the time being.
Original patch by Michał Górny.  (Github issue :issue:`2747`)

* Unused variable warnings about clineno were fixed when C lines in tracebacks are disabled.
(Github issue :issue:`6035`)

* Subclass deallocation of extern classes could crash if the base class uses GC.
Original patch by Jason Fried.  (Github issue :issue:`5971`)

* Type checks for Python ``memoryview`` could use an invalid C function.
Patch by Xenia Lu.  (Github issue :issue:`5988`)

* Calling final fused functions could generate invalid C code.
(Github issue :issue:`5989`)

* Declaring extern enums multiple times could generate invalid C code.
(Github issue :issue:`5905`)

* ``pyximport`` used relative paths incorrectly.
Patch by Stefano Rivera.  (Github issue :issue:`5957`)

* Running Cython with globbing characters (``[]*?``) in the module search path could fail.
Patch by eewanco.  (Github issue :issue:`5942`)

* Literal strings that include braces could change the C code indentation.

Other changes
-------------

* The &quot;enum class not importable&quot; warning is now only issued once per enum type.
(Github issue :issue:`5941`)

3.0.8

==================

Bugs fixed
----------

* Using ``const`` together with defined fused types could fail to compile.
(Github issue :issue:`5230`)

* A &quot;use after free&quot; bug was fixed in parallel sections.
(Github issue :issue:`5922`)

* Several types were not available as ``cython.*`` types in pure Python code.

* The generated code is now correct C89 again, removing some C++ style ``//`` comments
and C99-style declaration-after-code code ordering.  This is still relevant for some
ols C compilers, specifically ones that match old Python 2.7 installations.

3.0.7

==================

Bugs fixed
----------

* In the iterator of generator expressions, ``await`` and ``yield`` were not correctly analysed.
(Github issue :issue:`5851`)

* ``cpdef`` enums with the same name cimported from different modules could lead to
invalid C code.
(Github issue :issue:`5887`)

* Some declarations in ``cpython.unicode`` were fixed and extended.
(Github issue :issue:`5902`)

* Compiling fused types used in pxd files could crash Cython in Python 3.11+.
(Github issues :issue:`5894`,  :issue:`5588`)

* Source files with non-ASCII file names could crash Cython.
(Github issue :issue:`5873`)

* Includes all bug-fixes and features from the 0.29 maintenance branch
up to the :ref:`0.29.37` release.

3.0.6

==================

Features added
--------------

* Fused def function dispatch is a bit faster.

* Declarations for the ``wchar`` PyUnicode API were added.
(Github issue :issue:`5836`)

* The Python &quot;nogil&quot; fork is now also detected with the new ``Py_GIL_DISABLED`` macro.
Patch by Hugo van Kemenade.  (Github issue :issue:`5852`)

Bugs fixed
----------

* Comparing dataclasses could give different results than Python.
(Github issue :issue:`5857`)

* ``float(std::string)`` generated invalid C code.
(Github issue :issue:`5818`)

* Using ``cpdef`` functions with ``cimport_from_pyx`` failed.
(Github issue :issue:`5795`)

* A crash was fixed when string-formatting a Python value fails.
(Github issue :issue:`5787`)

* On item access, Cython could try the sequence protocol before the mapping protocol
in some cases if an object supports both.
(Github issue :issue:`5776`)

* A C compiler warning was resolved.
(Github issue :issue:`5794`)

* Complex numbers failed to compile in MSVC with C11.
Patch by Lysandros Nikolaou.  (Github issue :issue:`5809`)

* Some issues with the Limited API and with PyPy were resolved.
(Github issues :issue:`5695`, :issue:`5696`)

* A C++ issue in Python 3.13 was resolved.
(Github issue :issue:`5790`)

* Several directives are now also available (as no-ops) in Python code.
(Github issue :issue:`5803`)

* An error message was corrected.
Patch by Mads Ynddal.  (Github issue :issue:`5805`)

3.0.5

==================

Features added
--------------

* Preliminary support for CPython 3.13a1 was added to allow early testing.
(Github issue :issue:`5767`)

Bugs fixed
----------

* A compiler crash was fixed.
(Github issue :issue:`5771`)

* A typo in the ``always_allow_keywords`` directive for Python code was fixed.
Patch by lk-1984.  (Github issue :issue:`5772`)

* Some C compiler warnings were resolved.
Patch by Pierre Jolivet.  (Github issue :issue:`5780`)

3.0.4

==================

Features added
--------------

* A new compiler directive ``show_performance_hints`` was added to disable the
newly added performance hint output.
(Github issue :issue:`5748`)

Bugs fixed
----------

* cythonize` required ``distutils`` even for operations that did not build binaries.
(Github issue :issue:`5751`)

* A regression in 3.0.3 was fixed that prevented calling inline functions
from another inline function in ``.pxd`` files.
(Github issue :issue:`5748`)

* Some C compiler warnings were resolved.
Patch by Pierre Jolivet.  (Github issue :issue:`5756`)

3.0.3

==================

Features added
--------------

* More warnings were added to help users migrate and avoid bugs.
(Github issue :issue:`5650`)

* A warning-like category for performance hints was added that bypasses ``-Werror``.
(Github issue :issue:`5673`)

* FastGIL now uses standard ``thread_local`` in C++.
(Github issue :issue:`5640`)

* ``reference_wrapper`` was added to ``libcpp.functional``.
Patch by Vyas Ramasubramani.  (Github issue :issue:`5671`)

* The ``cythonize`` command now supports the ``--cplus`` option known from the ``cython`` command.
(Github issue :issue:`5736`)

Bugs fixed
----------

* Performance regressions where the GIL was needlessly acquired were fixed.
(Github issues :issue:`5670`, :issue:`5700`)

* A reference leak for exceptions in Python 3.12 was resolved.
Patch by Eric Johnson.  (Github issue :issue:`5724`)

* ``fastcall`` calls with keyword arguments generated incorrect C code.
(Github issue :issue:`5665`)

* Assigning the type converted result of a conditional (if-else) expression
to ``int`` or ``bool`` variables could lead to incorrect C code.
(Github issue :issue:`5731`)

* Early (unlikely) failures in Python function wrappers no longer set a
traceback in order to simplify the C code flow.  Being mostly memory
allocation errors, they probably would never have created a traceback anyway.
(Github issue :issue:`5681`)

* Relative cimports from packages with ``__init__.py`` files could fail.
(Github issue :issue:`5715`)

* Several issues with the Limited API support were resolved.
(Github issues :issue:`5641`, :issue:`5648`, :issue:`5689`)

* The code generated for special-casing both Cython functions and PyCFunctions was cleaned up
to avoid calling C-API functions that were not meant for the other type respectively.
This could previously trigger assertions in CPython debug builds and now also plays better
with the Limited API.
(Github issues :issue:`4804`, :issue:`5739`)

* Fix some C compiler warnings.
Patches by Ralf Gommers, Oleksandr Pavlyk, Sebastian Koslowski et al.
(Github issues :issue:`5651`, :issue:`5663`, :issue:`5668`, :issue:`5717`, :issue:`5726`, :issue:`5734`)

* Generating gdb debugging information failed when using generator expressions.
Patch by Oleksandr Pavlyk.  (Github issue :issue:`5552`)

* Passing a ``setuptools.Extension`` into ``cythonize()`` instead of a
``distutils.Extension`` could make it miss the matching extensions.

* ``cython -M`` needlessly required ``distutils``, which made it fail in Python 3.12.
(Github issue :issue:`5681`)

Other changes
-------------

* The visible deprecation warning for ``DEF`` was removed again since it proved
difficult for some users to migrate away from it.  The statement is still
meant to be removed at some point (and thus, like ``IF``, should not be
used in new code), but the time for sunset is probably not around the corner.
(Github issue :issue:`4310`)

* The ``np_pythran`` option raise a ``DeprecationWarning`` if it receives other values
than ``True`` and ``False``.  This will eventually be disallowed (in line with all
other boolean options).

3.0.2

==================

Bugs fixed
----------

* Using ``None`` as default value for arguments annotated as ``int`` could crash Cython.
(Github issue :issue:`5643`)

* Default values of fused types that include ``complex`` could generate invalid C code
with ``-DCYTHON_CCOMPLEX=0``.
(Github issue :issue:`5644`)

* Using C++ enum class types in extension type method signatures could generate invalid C code.
(Github issue :issue:`5637`)

3.0.1

==================

Features added
--------------

* The error messages regarding exception declarations were improved in order to give
better help about possible reasons and fixes.
(Github issue :issue:`5547`)

Bugs fixed
----------

* Memory view types in Python argument annotations no longer accept ``None``.  They now
require an explicit ``Optional[]`` or a ``None`` default value in order to allow ``None``
to be passed.  This was an oversight in the 3.0.0 release and is a BACKWARDS INCOMPATIBLE
change.  However, since it only applies to code using Python syntax, it probably only
applies to newly written code that was written for Cython 3.0 and can easily be adapted.
In most cases, we expect that this change will avoid bugs in user code rather than
produce problems.
(Github issue :issue:`5612`)

* ``nogil`` functions using parallel code could freeze when called with the GIL held.
(Github issues :issue:`5564`, :issue:`5573`)

* Relative cimports could end up searching globally and find the same package installed
elsewhere, potentially in another version.
(Github issue :issue:`5511`)

* Attribute lookups on known standard library modules could accidentally search
in the module namespace instead.
(Github issue :issue:`5536`)

* Using constructed C++ default arguments could generate invalid C++ code.
(Github issue :issue:`5553`)

* ``libcpp.memory.make_unique()`` was lacking C++ exception handling.
(Github issue :issue:`5560`)

* Some non-public and deprecated CAPI usages were replaced by public
(and thus more future proof) API code.

* Many issues with the Limited API support were resolved.
Patches by Lisandro Dalcin et al.
(Github issues :issue:`5549`, :issue:`5550`, :issue:`5556`, :issue:`5605`, :issue:`5617`)

* Some C compiler warnings were resolved.
Patches by Matti Picus et al.  (Github issues :issue:`5557`, :issue:`5555`)

* Large Python integers are now stored in hex instead of decimal strings to work around
security limits in Python and generally speed up their Python object creation.

* ``NULL`` could not be used as default for fused type pointer arguments.
(Github issue :issue:`5554`)

* C functions that return pointer types now return ``NULL`` as default exception value.
Previously, calling code wasn&#x27;t aware of this and always tested for raised exceptions.
(Github issue :issue:`5554`)

* Untyped literal default arguments in fused functions could generate invalid C code.
(Github issue :issue:`5614`)

* C variables declared as ``const`` could generate invalid C code when used in closures,
generator expressions, ctuples, etc.
(Github issues :issue:`5558`,  :issue:`5333`)

* Enums could not refer to previously defined enums in their definition.
(Github issue :issue:`5602`)

* The Python conversion code for anonymous C enums conflicted with regular int conversion.
(Github issue :issue:`5623`)

* Using memory views for property methods (and other special methods) could lead to
refcounting problems.
(Github issue :issue:`5571`)

* Star-imports could generate code that tried to assign to constant C macros like
``PY_SSIZE_T_MAX`` and ``PY_SSIZE_T_MIN``.
Patch by Philipp Wagner.  (Github issue :issue:`5562`)

* ``CYTHON_USE_TYPE_SPECS`` can now be (explicitly) enabled in PyPy.

* The template parameter &quot;delimeters&quot; in the Tempita ``Template`` class was corrected
to &quot;delimiters&quot;.  The old spelling is still available in the main template API but
now issues a ``DeprecationWarning``.
(Github issue :issue:`5608`)

* The ``cython --version`` output is now  less likely to reach both stdout and stderr.
Patch by Eli Schwartz.  (Github issue :issue:`5504`)

* The sdist was missing the `Shadow.pyi` stub file.

3.0.0

==========================

Features added
--------------

* Cython functions now use the `PEP-590`_ vectorcall protocol in Py3.7+.
Patch by Jeroen Demeyer.  (Github issue :issue:`2263`)

* Unicode identifiers are supported in Cython code (`PEP-3131`_).
Patch by David Woods.  (Github issue :issue:`2601`)

* Unicode module names and imports are supported.
Patch by David Woods.  (Github issue :issue:`3119`)

* Annotations are no longer parsed, keeping them as strings following `PEP-563`_.
Patch by David Woods.  (Github issue :issue:`3285`)

* Preliminary support for the CPython&#x27;s ``Py_LIMITED_API`` (stable ABI) is
available by setting the  ``CYTHON_LIMITED_API`` C macro.  Note that the
support is currently in an early stage and many features do not yet work.
You currently still have to define ``Py_LIMITED_API`` externally in order
to restrict the API usage.  This will change when the feature stabilises.
Patches by Eddie Elizondo and David Woods.  (Github issues :issue:`3223`,
:issue:`3311`, :issue:`3501`)

* The dispatch to fused functions is now linear in the number of arguments,
which makes it much faster, often 2x or more, and several times faster for
larger fused types with many specialisations.
Patch by will-ca.  (Github issue :issue:`1385`)

* ``with gil/nogil`` statements can be conditional based on compile-time
constants, e.g. fused type checks.
Patch by Noam Hershtig.  (Github issue :issue:`2579`)

* ``const`` can be used together with fused types.
Patch by Thomas Vincent.  (Github issue :issue:`1772`)

* Reimports of already imported modules are substantially faster.
(Github issue :issue:`2854`)

* Positional-only arguments are supported in Python functions (`PEP-570`_).
Patch by Josh Tobin.  (Github issue :issue:`2915`)

* The ``volatile`` C modifier is supported in Cython code.
Patch by Jeroen Demeyer.  (Github issue :issue:`1667`)

* ``cython.trashcan(True)`` can be used on an extension type to enable the
CPython :ref:`trashcan`. This allows deallocating deeply recursive objects
without overflowing the stack. Patch by Jeroen Demeyer.  (Github issue :issue:`2842`)

* Inlined properties can be defined for external extension types.
Patch by Matti Picus. (Github issue :issue:`2640`, redone later in :issue:`3571`)

* The ``str()`` builtin now calls ``PyObject_Str()`` instead of going
through a Python call.
Patch by William Ayd.  (Github issue :issue:`3279`)

* String concatenation can now happen in place if possible, by extending the
existing string rather than always creating a new one.
Patch by David Woods.  (Github issue :issue:`3453`)

* Multiplication of Python numbers with small constant integers is faster.
(Github issue :issue:`2808`)

* Some list copying is avoided internally when a new list needs to be created
but we already have a fresh one.
(Github issue :issue:`3494`)

* Extension types that do not need their own ``tp_new`` implementation (because
they have no object attributes etc.) directly inherit the implementation of
their parent type if possible.
(Github issue :issue:`1555`)

* The attributes ``gen.gi_frame`` and ``coro.cr_frame`` of Cython compiled
generators and coroutines now return an actual frame object for introspection.
(Github issue :issue:`2306`)

* Several declarations in ``cpython.*``, ``libc.*`` and ``libcpp.*`` were added.
Patches by Jeroen Demeyer, Matthew Edwards, Chris Gyurgyik, Jerome Kieffer
and Zackery Spytz.
(Github issues :issue:`3468`, :issue:`3332`, :issue:`3202`, :issue:`3188`,
:issue:`3179`, :issue:`2891`, :issue:`2826`, :issue:`2713`)

* Deprecated NumPy API usages were removed from ``numpy.pxd``.
Patch by Matti Picus.  (Github issue :issue:`3365`)

* ``cython.inline()`` now sets the ``NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION``
C macro automatically when ``numpy`` is imported in the code, to avoid C compiler
warnings about deprecated NumPy C-API usage.

* The builtin ``abs()`` function can now be used on C numbers in nogil code.
Patch by Elliott Sales de Andrade.  (Github issue :issue:`2748`)

* `PEP-479`_ (``generator_stop``) is now enabled by default with language level 3.
(Github issue :issue:`2580`)

* The ``cython.view.array`` type supports inheritance.
Patch by David Woods.  (Github issue :issue:`3413`)

* Code annotation accepts a new debugging argument ``--annotate-fullc`` that
will include the complete syntax highlighted C file in the HTML output.
(Github issue :issue:`2855`)

* ``--no-capture`` added to ``runtests.py`` to prevent stdout/stderr capturing
during srctree tests.
Patch by Matti Picus.  (Github issue :issue:`2701`)

* ``--no-docstrings`` option added to ``cythonize`` script.
Original patch by mo-han.  (Github issue :issue:`2889`)

* ``cygdb`` gives better error messages when it fails to initialise the
Python runtime support in gdb.
Patch by Volker Weissmann.  (Github issue :issue:`3489`)

* The Pythran ``shape`` attribute is supported.
Patch by Serge Guelton.  (Github issue :issue:`3307`)

Bugs fixed
----------

* The unicode methods ``.upper()``, ``.lower()`` and ``.title()`` were
incorrectly optimised for single character input values and only returned
the first character if multiple characters should have been returned.
They now use the original Python methods again.

* Fused argument types were not correctly handled in type annotations and
``cython.locals()``.
Patch by David Woods.  (Github issues :issue:`3391`, :issue:`3142`)

* Diverging from the usual behaviour, ``len(memoryview)``, ``len(char*)``
and ``len(Py_UNICODE*)`` returned an unsigned ``size_t`` value.  They now
return a signed ``Py_ssize_t``, like other usages of ``len()``.

* Nested dict literals in function call kwargs could incorrectly raise an
error about duplicate keyword arguments, which are allowed when passing
them from dict literals.
(Github issue :issue:`2963`)

* Item access (subscripting) with integer indices/keys always tried the
Sequence protocol before the Mapping protocol, which diverged from Python
semantics.  It now passes through the Mapping protocol first when supported.
(Github issue :issue:`1807`)

* Name lookups in class bodies no longer go through an attribute lookup.
Patch by Jeroen Demeyer.  (Github issue :issue:`3100`)

* Broadcast assignments to a multi-dimensional memory view slice could end
up in the wrong places when the underlying memory view is known to be
contiguous but the slice is not.
(Github issue :issue:`2941`)

* Pickling unbound methods of Python classes failed.
Patch by Pierre Glaser.  (Github issue :issue:`2972`)

* The ``Py_hash_t`` type failed to accept arbitrary &quot;index&quot; values.
(Github issue :issue:`2752`)

* The first function line number of functions with decorators pointed to the
signature line and not the first decorator line, as in Python.
Patch by Felix Kohlgrüber.  (Github issue :issue:`2536`)

* Constant integer expressions that used a negative exponent were evaluated
as integer 0 instead of the expected float value.
Patch by Kryštof Pilnáček.  (Github issue :issue:`2133`)

* The ``cython.declare()`` and ``cython.cast()`` functions could fail in pure mode.
Patch by Dmitry Shesterkin.  (Github issue :issue:`3244`)

* ``__doc__`` was not available inside of the class body during class creation.
(Github issue :issue:`1635`)

* Setting ``language_level=2`` in a file did not work if ``language_level=3``
was enabled globally before.
Patch by Jeroen Demeyer.  (Github issue :issue:`2791`)

* ``__init__.pyx`` files were not always considered as package indicators.
(Github issue :issue:`2665`)

* Compiling package ``__init__`` files could fail under Windows due to an
undefined export symbol.  (Github issue :issue:`2968`)

* A C compiler cast warning was resolved.
Patch by Michael Buesch.  (Github issue :issue:`2775`)

* Binding staticmethods of Cython functions were not behaving like Python methods.
Patch by Jeroen Demeyer.  (Github issue :issue:`3106`, :issue:`3102`)

* Memoryviews failed to compile when the ``cache_builtins`` feature was disabled.
Patch by David Woods.  (Github issue :issue:`3406`)

Other changes
-------------

* The default language level was changed to ``3str``, i.e. Python 3 semantics,
but with ``str`` literals (also in Python 2.7).  This is a backwards incompatible
change from the previous default of Python 2 semantics.  The previous behaviour
is available through the directive ``language_level=2``.
(Github issue :issue:`2565`)

* Cython no longer generates ``__qualname__`` attributes for classes in Python
2.x since they are problematic there and not correctly maintained for subclasses.
Patch by Jeroen Demeyer.  (Github issue :issue:`2772`)

* Source file fingerprinting now uses SHA-1 instead of MD5 since the latter
tends to be slower and less widely supported these days.
(Github issue :issue:`2790`)

* The long deprecated include files ``python_*``, ``stdio``, ``stdlib`` and
``stl`` in ``Cython/Includes/Deprecated/`` were removed.  Use the ``libc.*``
and ``cpython.*`` pxd modules instead.
Patch by Jeroen Demeyer.  (Github issue :issue:`2904`)

* The search order for include files was changed. Previously it was
``include_directories``, ``Cython/Includes``, ``sys.path``. Now it is
``include_directories``, ``sys.path``, ``Cython/Includes``. This was done to
allow third-party ``*.pxd`` files to override the ones in Cython.
Patch by Matti Picus.  (Github issue :issue:`2905`)

* The command line parser was rewritten and modernised using ``argparse``.
Patch by Egor Dranischnikow.  (Github issue :issue:`2952`, :issue:`3001`)

* Dotted filenames for qualified module names (``pkg.mod.pyx``) are deprecated.
Use the normal Python package directory layout instead.
(Github issue :issue:`2686`)

* Binary Linux wheels now follow the manylinux2010 standard.
Patch by Alexey Stepanov.  (Github issue :issue:`3355`)

* Support for Python 2.6 was removed.

.. _`PEP-560`: https://www.python.org/dev/peps/pep-0560
.. _`PEP-570`: https://www.python.org/dev/peps/pep-0570
.. _`PEP-487`: https://www.python.org/dev/peps/pep-0487
.. _`PEP-590`: https://www.python.org/dev/peps/pep-0590
.. _`PEP-3131`: https://www.python.org/dev/peps/pep-3131
.. _`PEP-563`: https://www.python.org/dev/peps/pep-0563
.. _`PEP-479`: https://www.python.org/dev/peps/pep-0479

0.29.37

====================

Bugs fixed
----------

* Fix a potential crash while cleaning up subtypes of externally imported extension
types when terminating Python.  This was introduced in Cython 0.29.35.

* Fix a ``complex`` related compile error on Windows.
(Github issue :issue:`5512`)

* Compiling fused types used in pxd files could crash Cython in Python 3.11+.
(Github issues :issue:`5894`, :issue:`5588`)

* ``cythonize`` failed to consider the ``CYTHON_FORCE_REGEN`` env variable.
Patch by Harmen Stoppels.  (Github issue :issue:`5712`)

0.29.36

====================

Bugs fixed
----------

* Async generators lost their return value in PyPy.
(Github issue :issue:`5465`)

* The outdated C macro ``_PyGC_FINALIZED()`` is no longer used in Py3.9+.

* The deprecated ``Py_OptimizeFlag`` is no longer used in Python 3.9+.
(Github issue :issue:`5343`)

* Using the global ``__debug__`` variable but not assertions could lead to compile errors.

* The broken HTML template support was removed from Tempita.
(Github issue :issue:`3309`)

0.29.35

====================

Bugs fixed
----------

* A garbage collection enabled subtype of a non-GC extension type could call into the
deallocation function of the super type with GC tracking enabled.  This could lead
to crashes during deallocation if GC was triggered on the type at the same time.
(Github issue :issue:`5432`)

* Some C compile failures and crashes in CPython 3.12 were resolved.

* ``except + nogil`` was syntactically not allowed.
``except +nogil`` (i.e. defining a C++ exception handling function called ``nogil``)
is now disallowed to prevent typos.
(Github issue :issue:`5430`)

* A C compile failure in PyPy 3.10 was resolved.
Patch by Matti Picus.  (Github issue :issue:`5408`)

* Cython modules now use PEP-489 multi-phase init by default in PyPy 3.9 and later.
Original patch by Matti Picus.  (Github issue :issue:`5413`)

* API header files generated by different Cython versions can now be included in the
same C file.
(Github issue :issue:`5383`)

* Function signatures containing a type like `tuple[()]` could not be printed.
Patch by Lisandro Dalcin.  (Github issue :issue:`5355`)

0.29.34

====================

Bugs fixed
----------

* A reference leak of the for-loop list/tuple iterable was resolved if the for-loop&#x27;s
``else:`` branch executes a ``break`` for an outer loop.
(Github issue :issue:`5347`)

* Some C compile failures in CPython 3.12 were resolved.

* Some old usages of the deprecated Python ``imp`` module were replaced with ``importlib``.
Patch by Matúš Valo.  (Github issue :issue:`5300`)

* Some issues with ``depfile`` generation were resolved.
Patches by Eli Schwartz.  (Github issues :issue:`5279`, :issue:`5291`)

0.29.33

====================

Features added
--------------

* The ``cythonize`` and ``cython`` commands have a new option ``-M`` / ``--depfile``
to generate ``.dep`` dependency files for the compilation unit.  This can be used
by external build tools to track these dependencies.
The ``cythonize`` option was already available in Cython :ref:`0.29.27`.
Patches by Evgeni Burovski and Eli Schwartz.  (Github issue :issue:`1214`)

Bugs fixed
----------

* ``const`` fused types could not be used with memory views.
Patch by Thomas Vincent.  (Github issue :issue:`1772`)

* ``wstr`` usage was removed in Python 3.12 and later (PEP-623).
(Github issue :issue:`5145`)

* A type check assertion for Cython functions failed in debug Python builds.
(Github issue :issue:`5031`)

* Fixed various compiler warnings.
Patches by Lisandro Dalcin et al.  (Github issues :issue:`4948`, :issue:`5086`)

* Fixed error when calculating complex powers of negative numbers.
(Github issue :issue:`5014`)

* Corrected a small mis-formatting of exception messages on Python 2.
(Github issue :issue:`5018`)

* The ``PyUnicode_AsUTF8AndSize()`` C-API function was missing from the CPython declarations.
(Github issue :issue:`5163`)

* A performance problem in the compiler was resolved when nesting conditional expressions.
(Github issue :issue:`5197`)

* Test suite problems with recent NumPy and CPython versions were resolved.
(Github issues :issue:`5183`, :issue:`5190`)

Other changes
-------------

* The undocumented, untested and apparently useless syntax
``from somemodule cimport class/struct/union somename`` was deprecated
in anticipation of its removal in Cython 3.  The type
modifier is not needed here and a plain ``cimport`` of the name will do.
(Github issue :issue:`4905`)

* Properly disable generation of descriptor docstrings on PyPy since they cause crashes.
It was previously disabled, but only accidentally via a typo.
Patch by Matti Picus.  (Github issue :issue:`5083`)

* The ``cpow`` directive of Cython 3.0 is available as a no-op.
(Github issue :issue:`5016`)

0.29.32

====================

Bugs fixed
----------

* Revert &quot;Using memoryview typed arguments in inner functions is now rejected as unsupported.&quot;
Patch by David Woods.  (Github issue :issue:`4798`)

* ``from module import *`` failed in 0.29.31 when using memoryviews.
Patch by David Woods.  (Github issue :issue:`4927`)

0.29.31

====================

Features added
--------------

* A new argument ``--module-name`` was added to the ``cython`` command to
provide the (one) exact target module name from the command line.
Patch by Matthew Brett and h-vetinari.  (Github issue :issue:`4906`)

* A new keyword ``noexcept`` was added for forward compatibility with Cython 3.
Patch by David Woods.  (Github issue :issue:`4903`)

Bugs fixed
----------

* Use ``importlib.util.find_spec()`` instead of the deprecated ``importlib.find_loader()``
function when setting up the package path at import-time.
Patch by Matti Picus.  (Github issue :issue:`4764`)

* Require the C compiler to support the two-arg form of ``va_start``
on Python 3.10 and higher.
Patch by Thomas Caswell.  (Github issue :issue:`4820`)

* Make ``fused_type`` subscriptable in Shadow.py.
Patch by Pfebrer.  (Github issue :issue:`4842`)

* Fix the incorrect code generation of the target type in ``bytearray`` loops.
Patch by Kenrick Everett.  (Github issue :issue:`4108`)

* Atomic refcounts for memoryviews were not used on some GCC versions by accident.
Patch by Sam Gross.  (Github issue :issue:`4915`)

* Silence some GCC ``-Wconversion`` warnings in C utility code.
Patch by Lisandro Dalcin.  (Github issue :issue:`4854`)

* Tuple multiplication was ignored in expressions such as ``[*(1,) * 2]``.
Patch by David Woods.  (Github issue :issue:`4864`)

* Calling ``append`` methods on extension types could fail to find the method
in some cases.
Patch by David Woods.  (Github issue :issue:`4828`)

* Ensure that object buffers (e.g. ``ndarray[object, ndim=1]``) containing
``NULL``  pointers are safe to use, returning ``None`` instead of the ``NULL``
pointer.
Patch by Sebastian Berg.  (Github issue :issue:`4859`)

* Using memoryview typed arguments in inner functions is now rejected as unsupported.
Patch by David Woods.  (Github issue :issue:`4798`)

* Compilation could fail on systems (e.g. FIPS) that block MD5 checksums at runtime.
(Github issue :issue:`4909`)

* Experimental adaptations for the CPython &quot;nogil&quot; fork was added.
Note that there is no official support for this in Cython 0.x.
Patch by Sam Gross.  (Github issue :issue:`4912`)

0.29.30

====================

Bugs fixed
----------

* The GIL handling changes in 0.29.29 introduced a regression where
objects could be deallocated without holding the GIL.
(Github issue :issue:`4796`)

0.29.29

====================

Features added
--------------

* Avoid acquiring the GIL at the end of nogil functions.
This change was backported in order to avoid generating wrong C code
that would trigger C compiler warnings with tracing support enabled.
Backport by Oleksandr Pavlyk.  (Github issue :issue:`4637`)

Bugs fixed
----------

* Function definitions in ``finally:`` clauses were not correctly generated.
Patch by David Woods.  (Github issue :issue:`4651`)

* A case where C-API functions could be called with a live exception set was fixed.
Patch by Jakub Kulík.  (Github issue :issue:`4722`)

* Pickles can now be exchanged again with those generated from Cython 3.0 modules.
(Github issue :issue:`4680`)

* Cython now correctly generates Python methods for both the provided regular and
reversed special numeric methods of extension types.
Patch by David Woods.  (Github issue :issue:`4750`)

* Calling unbound extension type methods without arguments could raise an
``IndexError`` instead of a ``TypeError``.
Patch by David Woods.  (Github issue :issue:`4779`)

* Calling unbound ``.__contains__()`` super class methods on some builtin base
types could trigger an infinite recursion.
Patch by David Woods.  (Github issue :issue:`4785`)

* The C union type in pure Python mode mishandled some field names.
Patch by Jordan Brière.  (Github issue :issue:`4727`)

* Allow users to overwrite the C macro ``_USE_MATH_DEFINES``.
Patch by Yuriy Chernyshov. (Github issue :issue:`4690`)

* Improved compatibility with CPython 3.10/11.
Patches by Thomas Caswell, David Woods.
(Github issues :issue:`4609`, :issue:`4667`, :issue:`4721`, :issue:`4730`, :issue:`4777`)

* Docstrings of descriptors are now provided in PyPy 7.3.9.
Patch by Matti Picus.  (Github issue :issue:`4701`)

0.29.28

====================

Bugs fixed
----------

* Due to backwards incompatible changes in CPython 3.11a4, the feature flags
``CYTHON_FAST_THREAD_STATE`` and ``CYTHON_USE_EXC_INFO_STACK`` are now disabled
in Python 3.11 and later.  They are enabled again in Cython 3.0.
Patch by David Woods.  (Github issue :issue:`4610`)

* A C compiler warning in older PyPy versions was resolved.
Patch by Matti Picus.  (Github issue :issue:`4236`)

0.29.27

====================

Features added
--------------

* The ``cythonize`` command has a new option ``-M`` to generate ``.dep`` dependency
files for the compilation unit.  This can be used by external build tools to track
these dependencies.
Patch by Evgeni Burovski.  (Github issue :issue:`1214`)

Bugs fixed
----------

* Compilation failures on PyPy were resolved.
Patches by Matti Picus.  (Github issues :issue:`4509`, :issue:`4517`)

* Calls to ``range()`` with more than three arguments did not fail.
Original patch by Max Bachmann.  (Github issue :issue:`4550`)

* Some C compiler warnings about missing type struct initialisers in Py3.10 were resolved.

* Cython no longer warns about using OpenMP 3.0 features since they are now
considered generally available.

0.29.26

====================

Bugs fixed
----------

* An incompatibility with CPython 3.11.0a3 was resolved.
(Github issue :issue:`4499`)

* The ``in`` operator failed on literal lists with starred expressions.
Patch by Arvind Natarajan.  (Github issue :issue:`3938`)

* A C compiler warning in PyPy about a missing struct field initialisation was resolved.

0.29.25

====================

Bugs fixed
----------

* Several incompatibilities with CPython 3.11 were resolved.
Patches by David Woods, Victor Stinner, Thomas Caswell.
(Github issues :issue:`4411`, :issue:`4414`, :issue:`4415`, :issue:`4416`, :issue:`4420`,
:issue:`4428`, :issue:`4473`, :issue:`4479`, :issue:`4480`)

* Some C compiler warnings were resolved.
Patches by Lisandro Dalcin and others.  (Github issue :issue:`4439`)

* C++ ``std::move()`` should only be used automatically in MSVC versions that support it.
Patch by Max Bachmann.  (Github issue :issue:`4191`)

* The ``Py_hash_t`` type failed to accept arbitrary &quot;index&quot; values.
(Github issue :issue:`2752`)

* Avoid copying unaligned 16-bit values since some platforms require them to be aligned.
Use memcpy() instead to let the C compiler decide how to do it.
(Github issue :issue:`4343`)

* Cython crashed on invalid truthiness tests on C++ types without ``operator bool``.
Patch by David Woods.  (Github issue :issue:`4348`)

* The declaration of ``PyUnicode_CompareWithASCIIString()`` in ``cpython.unicode`` was incorrect.
Patch by Max Bachmann.  (Github issue :issue:`4344`)

0.29.24

====================

Bugs fixed
----------

* Inline functions in pxd files that used memory views could lead to invalid
C code if the module that imported from them does not use memory views.
Patch by David Woods.  (Github issue :issue:`1415`)

* Several declarations in ``libcpp.string`` were added and corrected.
Patch by Janek Bevendorff.  (Github issue :issue:`4268`)

* Pickling unbound Cython compiled methods failed.
Patch by Pierre Glaser.  (Github issue :issue:`2972`)

* The tracing code was adapted to work with CPython 3.10.

* The optimised ``in`` operator failed on unicode strings in Py3.9 and later
that were constructed from an external ``wchar_t`` source.
Also, related C compiler warnings about deprecated C-API usage were resolved.
(Github issue :issue:`3925`)

* Some compiler crashes were resolved.
Patch by David Woods.  (Github issues :issue:`4214`, :issue:`2811`)

* An incorrect warning about &#x27;unused&#x27; generator expressions was removed.
(GIthub issue :issue:`1699`)

* The attributes ``gen.gi_frame`` and ``coro.cr_frame`` of Cython compiled
generators and coroutines now return an actual frame object for introspection,
instead of ``None``.
(Github issue :issue:`2306`)

Links

PyPI: https://pypi.org/project/cython
Changelog: https://data.safetycli.com/changelogs/cython/
Homepage: https://cython.org/

Update numpy from 1.21.0 to 2.2.5.

Changelog

2.2.5

release. It has a large number of typing fixes/improvements as well as
the normal bug fixes and some CI maintenance.

This release supports Python versions 3.10-3.13.

Contributors

A total of 7 people contributed to this release. People with a \&quot;+\&quot; by
their names contributed a patch for the first time.

-   Charles Harris
-   Joren Hammudoglu
-   Baskar Gopinath +
-   Nathan Goldbaum
-   Nicholas Christensen +
-   Sayed Adel
-   karl +

Pull requests merged

A total of 19 pull requests were merged for this release.

-   [28545](https://github.com/numpy/numpy/pull/28545): MAINT: Prepare 2.2.x for further development
-   [28582](https://github.com/numpy/numpy/pull/28582): BUG: Fix return type of NpyIter_GetIterNext in Cython declarations
-   [28583](https://github.com/numpy/numpy/pull/28583): BUG: avoid deadlocks with C++ shared mutex in dispatch cache
-   [28585](https://github.com/numpy/numpy/pull/28585): TYP: fix typing errors in `_core.strings`
-   [28631](https://github.com/numpy/numpy/pull/28631): MAINT, CI: Update Ubuntu to 22.04 in azure-pipelines
-   [28632](https://github.com/numpy/numpy/pull/28632): BUG: Set writeable flag for writeable dlpacks.
-   [28633](https://github.com/numpy/numpy/pull/28633): BUG: Fix crackfortran parsing error when a division occurs within\...
-   [28650](https://github.com/numpy/numpy/pull/28650): TYP: fix `ndarray.tolist()` and `.item()` for unknown dtype
-   [28654](https://github.com/numpy/numpy/pull/28654): BUG: fix deepcopying StringDType arrays (#28643)
-   [28661](https://github.com/numpy/numpy/pull/28661): TYP: Accept objects that `write()` to `str` in `savetxt`
-   [28663](https://github.com/numpy/numpy/pull/28663): CI: Replace QEMU armhf with native (32-bit compatibility mode)
-   [28682](https://github.com/numpy/numpy/pull/28682): SIMD: Resolve Highway QSort symbol linking error on aarch32/ASIMD
-   [28683](https://github.com/numpy/numpy/pull/28683): TYP: add missing `&quot;b1&quot;` literals for `dtype[bool]`
-   [28705](https://github.com/numpy/numpy/pull/28705): TYP: Fix false rejection of `NDArray[object_].__abs__()`
-   [28706](https://github.com/numpy/numpy/pull/28706): TYP: Fix inconsistent `NDArray[float64].__[r]truediv__` return\...
-   [28723](https://github.com/numpy/numpy/pull/28723): TYP: fix string-like `ndarray` rich comparison operators
-   [28758](https://github.com/numpy/numpy/pull/28758): TYP: some `[arg]partition` fixes
-   [28772](https://github.com/numpy/numpy/pull/28772): TYP: fix incorrect `random.Generator.integers` return type
-   [28774](https://github.com/numpy/numpy/pull/28774): TYP: fix `count_nonzero` signature

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2.2.4

release. There are a large number of typing improvements, the rest of
the changes are the usual mix of bugfixes and platform maintenace.

This release supports Python versions 3.10-3.13.

Contributors

A total of 15 people contributed to this release. People with a \&quot;+\&quot; by
their names contributed a patch for the first time.

-   Abhishek Kumar
-   Andrej Zhilenkov
-   Andrew Nelson
-   Charles Harris
-   Giovanni Del Monte
-   Guan Ming(Wesley) Chiu +
-   Jonathan Albrecht +
-   Joren Hammudoglu
-   Mark Harfouche
-   Matthieu Darbois
-   Nathan Goldbaum
-   Pieter Eendebak
-   Sebastian Berg
-   Tyler Reddy
-   lvllvl +

Pull requests merged

A total of 17 pull requests were merged for this release.

-   [28333](https://github.com/numpy/numpy/pull/28333): MAINT: Prepare 2.2.x for further development.
-   [28348](https://github.com/numpy/numpy/pull/28348): TYP: fix positional- and keyword-only params in astype, cross\...
-   [28377](https://github.com/numpy/numpy/pull/28377): MAINT: Update FreeBSD version and fix test failure
-   [28379](https://github.com/numpy/numpy/pull/28379): BUG: numpy.loadtxt reads only 50000 lines when skip_rows \&gt;= max_rows
-   [28385](https://github.com/numpy/numpy/pull/28385): BUG: Make np.nonzero threading safe
-   [28420](https://github.com/numpy/numpy/pull/28420): BUG: safer bincount casting (backport to 2.2.x)
-   [28422](https://github.com/numpy/numpy/pull/28422): BUG: Fix building on s390x with clang
-   [28423](https://github.com/numpy/numpy/pull/28423): CI: use QEMU 9.2.2 for Linux Qemu tests
-   [28424](https://github.com/numpy/numpy/pull/28424): BUG: skip legacy dtype multithreaded test on 32 bit runners
-   [28435](https://github.com/numpy/numpy/pull/28435): BUG: Fix searchsorted and CheckFromAny byte-swapping logic
-   [28449](https://github.com/numpy/numpy/pull/28449): BUG: sanity check `__array_interface__` number of dimensions
-   [28510](https://github.com/numpy/numpy/pull/28510): MAINT: Hide decorator from pytest traceback
-   [28512](https://github.com/numpy/numpy/pull/28512): TYP: Typing fixes backported from #28452, 28491, 28494
-   [28521](https://github.com/numpy/numpy/pull/28521): TYP: Backport fixes from #28505, 28506, 28508, and 28511
-   [28533](https://github.com/numpy/numpy/pull/28533): TYP: Backport typing fixes from main (2)
-   [28534](https://github.com/numpy/numpy/pull/28534): TYP: Backport typing fixes from main (3)
-   [28542](https://github.com/numpy/numpy/pull/28542): TYP: Backport typing fixes from main (4)

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pyup-bot · 2025-06-06T21:53:44Z

Closing this in favor of #176

pyup-bot added 4 commits May 1, 2025 16:12

Update cython from 0.29.23 to 3.0.12

f44f0db

Update numpy from 1.21.0 to 2.2.5

fd5320f

Update pysam from 0.16.0.1 to 0.23.0

7337618

Update tables from 3.6.1 to 3.10.2

77bb6ab

pyup-bot mentioned this pull request May 1, 2025

Scheduled monthly dependency update for April #174

Closed

pyup-bot closed this Jun 6, 2025

alimanfoo deleted the pyup-scheduled-update-2025-05-01 branch June 6, 2025 21:53

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Scheduled monthly dependency update for May#175

Scheduled monthly dependency update for May#175
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pyup-bot commented May 1, 2025

Update Cython from 0.29.23 to 3.0.12.

3.0.12

3.0.11

3.0.10

3.0.9

3.0.8

3.0.7

3.0.6

3.0.5

3.0.4

3.0.3

3.0.2

3.0.1

3.0.0

0.29.37

0.29.36

0.29.35

0.29.34

0.29.33

0.29.32

0.29.31

0.29.30

0.29.29

0.29.28

0.29.27

0.29.26

0.29.25

0.29.24

Update numpy from 1.21.0 to 2.2.5.

2.2.5

2.2.4

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pyup-bot commented Jun 6, 2025

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