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alimanfoo / pysamstats

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
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Scheduled monthly dependency update for September #152

Closed pyup-bot closed 1 year ago

pyup-bot commented 1 year ago

Update Cython from 0.29.23 to 3.0.2.

Changelog ### 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'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 "delimeters" in the Tempita ``Template`` class was corrected to "delimiters". 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'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 "index" 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 ``` ### 0.29.36 ``` ==================== 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'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 "Using memoryview typed arguments in inner functions is now rejected as unsupported." 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 "nogil" 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 "index" 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 'unused' 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 1.25.2.

Changelog ### 1.25.2 ``` discovered after the 1.25.1 release. This is the last planned release in the 1.25.x series, the next release will be 1.26.0, which will use the meson build system and support Python 3.12. The Python versions supported by this release are 3.9-3.11. Contributors A total of 13 people contributed to this release. People with a \"+\" by their names contributed a patch for the first time. - Aaron Meurer - Andrew Nelson - Charles Harris - Kevin Sheppard - Matti Picus - Nathan Goldbaum - Peter Hawkins - Ralf Gommers - Randy Eckenrode + - Sam James + - Sebastian Berg - Tyler Reddy - dependabot\[bot\] Pull requests merged A total of 19 pull requests were merged for this release. - [24148](https://github.com/numpy/numpy/pull/24148): MAINT: prepare 1.25.x for further development - [24174](https://github.com/numpy/numpy/pull/24174): ENH: Improve clang-cl compliance - [24179](https://github.com/numpy/numpy/pull/24179): MAINT: Upgrade various build dependencies. - [24182](https://github.com/numpy/numpy/pull/24182): BLD: use `-ftrapping-math` with Clang on macOS - [24183](https://github.com/numpy/numpy/pull/24183): BUG: properly handle negative indexes in ufunc_at fast path - [24184](https://github.com/numpy/numpy/pull/24184): BUG: PyObject_IsTrue and PyObject_Not error handling in setflags - [24185](https://github.com/numpy/numpy/pull/24185): BUG: histogram small range robust - [24186](https://github.com/numpy/numpy/pull/24186): MAINT: Update meson.build files from main branch - [24234](https://github.com/numpy/numpy/pull/24234): MAINT: exclude min, max and round from `np.__all__` - [24241](https://github.com/numpy/numpy/pull/24241): MAINT: Dependabot updates - [24242](https://github.com/numpy/numpy/pull/24242): BUG: Fix the signature for np.array_api.take - [24243](https://github.com/numpy/numpy/pull/24243): BLD: update OpenBLAS to an intermeidate commit - [24244](https://github.com/numpy/numpy/pull/24244): BUG: Fix reference count leak in str(scalar). - [24245](https://github.com/numpy/numpy/pull/24245): BUG: fix invalid function pointer conversion error - [24255](https://github.com/numpy/numpy/pull/24255): BUG: Factor out slow `getenv` call used for memory policy warning - [24292](https://github.com/numpy/numpy/pull/24292): CI: correct URL in cirrus.star - [24293](https://github.com/numpy/numpy/pull/24293): BUG: Fix C types in scalartypes - [24294](https://github.com/numpy/numpy/pull/24294): BUG: do not modify the input to ufunc_at - [24295](https://github.com/numpy/numpy/pull/24295): BUG: Further fixes to indexing loop and added tests Checksums MD5 33518ccb4da8ee11f1dee4b9fef1e468 numpy-1.25.2-cp310-cp310-macosx_10_9_x86_64.whl b5cb0c3b33ef6d93ec2888f25b065636 numpy-1.25.2-cp310-cp310-macosx_11_0_arm64.whl ae027dd38bd73f09c07220b2f516f148 numpy-1.25.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 88cf69dc3c0d293492c4c7e75dccf3d8 numpy-1.25.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 3e4e3ad02375ba71ae2cd05ccd97aba4 numpy-1.25.2-cp310-cp310-musllinux_1_1_x86_64.whl f52bb644682deb26c35ddec77198b65c numpy-1.25.2-cp310-cp310-win32.whl 4944cf36652be7560a6bcd0d5d56e8ea numpy-1.25.2-cp310-cp310-win_amd64.whl 5a56e639defebb7b871c8c5613960ca3 numpy-1.25.2-cp311-cp311-macosx_10_9_x86_64.whl 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1a1329e26f46230bf77b02cc19e900db9b52f398d6722ca853349a782d4cff55 numpy-1.25.2-pp39-pypy39_pp73-macosx_10_9_x86_64.whl 4c3abc71e8b6edba80a01a52e66d83c5d14433cbcd26a40c329ec7ed09f37901 numpy-1.25.2-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 1b9735c27cea5d995496f46a8b1cd7b408b3f34b6d50459d9ac8fe3a20cc17bf numpy-1.25.2-pp39-pypy39_pp73-win_amd64.whl fd608e19c8d7c55021dffd43bfe5492fab8cc105cc8986f813f8c3c048b38760 numpy-1.25.2.tar.gz ``` ### 1.25.1 ``` discovered after the 1.25.0 release. The Python versions supported by this release are 3.9-3.11. Contributors A total of 10 people contributed to this release. People with a \"+\" by their names contributed a patch for the first time. - Andrew Nelson - Charles Harris - Developer-Ecosystem-Engineering - Hood Chatham - Nathan Goldbaum - Rohit Goswami - Sebastian Berg - Tim Paine + - dependabot\[bot\] - matoro + Pull requests merged A total of 14 pull requests were merged for this release. - [23968](https://github.com/numpy/numpy/pull/23968): MAINT: prepare 1.25.x for further development - [24036](https://github.com/numpy/numpy/pull/24036): BLD: Port long double identification to C for meson - [24037](https://github.com/numpy/numpy/pull/24037): BUG: Fix reduction `return NULL` to be `goto fail` - [24038](https://github.com/numpy/numpy/pull/24038): BUG: Avoid undefined behavior in array.astype() - [24039](https://github.com/numpy/numpy/pull/24039): BUG: Ensure `__array_ufunc__` works without any kwargs passed - [24117](https://github.com/numpy/numpy/pull/24117): MAINT: Pin urllib3 to avoid anaconda-client bug. - [24118](https://github.com/numpy/numpy/pull/24118): TST: Pin pydantic\<2 in Pyodide workflow - [24119](https://github.com/numpy/numpy/pull/24119): MAINT: Bump pypa/cibuildwheel from 2.13.0 to 2.13.1 - [24120](https://github.com/numpy/numpy/pull/24120): MAINT: Bump actions/checkout from 3.5.2 to 3.5.3 - [24122](https://github.com/numpy/numpy/pull/24122): BUG: Multiply or Divides using SIMD without a full vector can\... - [24127](https://github.com/numpy/numpy/pull/24127): MAINT: testing for IS_MUSL closes #24074 - [24128](https://github.com/numpy/numpy/pull/24128): BUG: Only replace dtype temporarily if dimensions changed - [24129](https://github.com/numpy/numpy/pull/24129): MAINT: Bump actions/setup-node from 3.6.0 to 3.7.0 - [24134](https://github.com/numpy/numpy/pull/24134): BUG: Fix private procedures in f2py modules Checksums MD5 d09d98643db31e892fad11b8c2b7af22 numpy-1.25.1-cp310-cp310-macosx_10_9_x86_64.whl d5b8d3b0424e2af41018f35a087c4500 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numpy-1.25.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 20e1266411120a4f16fad8efa8e0454d21d00b8c7cee5b5ccad7565d95eb42dd numpy-1.25.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl f76aebc3358ade9eacf9bc2bb8ae589863a4f911611694103af05346637df1b7 numpy-1.25.1-cp39-cp39-musllinux_1_1_x86_64.whl 247d3ffdd7775bdf191f848be8d49100495114c82c2bd134e8d5d075fb386a1c numpy-1.25.1-cp39-cp39-win32.whl 1d5d3c68e443c90b38fdf8ef40e60e2538a27548b39b12b73132456847f4b631 numpy-1.25.1-cp39-cp39-win_amd64.whl 35a9527c977b924042170a0887de727cd84ff179e478481404c5dc66b4170009 numpy-1.25.1-pp39-pypy39_pp73-macosx_10_9_x86_64.whl 0d3fe3dd0506a28493d82dc3cf254be8cd0d26f4008a417385cbf1ae95b54004 numpy-1.25.1-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 012097b5b0d00a11070e8f2e261128c44157a8689f7dedcf35576e525893f4fe numpy-1.25.1-pp39-pypy39_pp73-win_amd64.whl 9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf numpy-1.25.1.tar.gz ``` ### 1.25.0 ``` The NumPy 1.25.0 release continues the ongoing work to improve the handling and promotion of dtypes, increase the execution speed, and clarify the documentation. There has also been work to prepare for the future NumPy 2.0.0 release, resulting in a large number of new and expired deprecation. Highlights are: - Support for MUSL, there are now MUSL wheels. - Support the Fujitsu C/C++ compiler. - Object arrays are now supported in einsum - Support for inplace matrix multiplication (`=`). We will be releasing a NumPy 1.26 when Python 3.12 comes out. That is needed because distutils has been dropped by Python 3.12 and we will be switching to using meson for future builds. The next mainline release will be NumPy 2.0.0. We plan that the 2.0 series will still support downstream projects built against earlier versions of NumPy. The Python versions supported in this release are 3.9-3.11. Deprecations - `np.core.MachAr` is deprecated. It is private API. In names defined in `np.core` should generally be considered private. ([gh-22638](https://github.com/numpy/numpy/pull/22638)) - `np.finfo(None)` is deprecated. ([gh-23011](https://github.com/numpy/numpy/pull/23011)) - `np.round_` is deprecated. Use `np.round` instead. ([gh-23302](https://github.com/numpy/numpy/pull/23302)) - `np.product` is deprecated. Use `np.prod` instead. ([gh-23314](https://github.com/numpy/numpy/pull/23314)) - `np.cumproduct` is deprecated. Use `np.cumprod` instead. ([gh-23314](https://github.com/numpy/numpy/pull/23314)) - `np.sometrue` is deprecated. Use `np.any` instead. ([gh-23314](https://github.com/numpy/numpy/pull/23314)) - `np.alltrue` is deprecated. Use `np.all` instead. ([gh-23314](https://github.com/numpy/numpy/pull/23314)) - Only ndim-0 arrays are treated as scalars. NumPy used to treat all arrays of size 1 (e.g., `np.array([3.14])`) as scalars. In the future, this will be limited to arrays of ndim 0 (e.g., `np.array(3.14)`). The following expressions will report a deprecation warning: python a = np.array([3.14]) float(a) better: a[0] to get the numpy.float or a.item() b = np.array([[3.14]]) c = numpy.random.rand(10) c[0] = b better: c[0] = b[0, 0] ([gh-10615](https://github.com/numpy/numpy/pull/10615)) - `numpy.find_common_type` is now deprecated and its use should be replaced with either `numpy.result_type` or `numpy.promote_types`. Most users leave the second `scalar_types` argument to `find_common_type` as `[]` in which case `np.result_type` and `np.promote_types` are both faster and more robust. When not using `scalar_types` the main difference is that the replacement intentionally converts non-native byte-order to native byte order. Further, `find_common_type` returns `object` dtype rather than failing promotion. This leads to differences when the inputs are not all numeric. Importantly, this also happens for e.g. timedelta/datetime for which NumPy promotion rules are currently sometimes surprising. When the `scalar_types` argument is not `[]` things are more complicated. In most cases, using `np.result_type` and passing the Python values `0`, `0.0`, or `0j` has the same result as using `int`, `float`, or `complex` in `scalar_types`. When `scalar_types` is constructed, `np.result_type` is the correct replacement and it may be passed scalar values like `np.float32(0.0)`. Passing values other than 0, may lead to value-inspecting behavior (which `np.find_common_type` never used and NEP 50 may change in the future). The main possible change in behavior in this case, is when the array types are signed integers and scalar types are unsigned. If you are unsure about how to replace a use of `scalar_types` or when non-numeric dtypes are likely, please do not hesitate to open a NumPy issue to ask for help. ([gh-22539](https://github.com/numpy/numpy/pull/22539)) Expired deprecations - `np.core.machar` and `np.finfo.machar` have been removed. ([gh-22638](https://github.com/numpy/numpy/pull/22638)) - `+arr` will now raise an error when the dtype is not numeric (and positive is undefined). ([gh-22998](https://github.com/numpy/numpy/pull/22998)) - A sequence must now be passed into the stacking family of functions (`stack`, `vstack`, `hstack`, `dstack` and `column_stack`). ([gh-23019](https://github.com/numpy/numpy/pull/23019)) - `np.clip` now defaults to same-kind casting. Falling back to unsafe casting was deprecated in NumPy 1.17. ([gh-23403](https://github.com/numpy/numpy/pull/23403)) - `np.clip` will now propagate `np.nan` values passed as `min` or `max`. Previously, a scalar NaN was usually ignored. This was deprecated in NumPy 1.17. ([gh-23403](https://github.com/numpy/numpy/pull/23403)) - The `np.dual` submodule has been removed. ([gh-23480](https://github.com/numpy/numpy/pull/23480)) - NumPy now always ignores sequence behavior for an array-like (defining one of the array protocols). (Deprecation started NumPy 1.20) ([gh-23660](https://github.com/numpy/numpy/pull/23660)) - The niche `FutureWarning` when casting to a subarray dtype in `astype` or the array creation functions such as `asarray` is now finalized. The behavior is now always the same as if the subarray dtype was wrapped into a single field (which was the workaround, previously). (FutureWarning since NumPy 1.20) ([gh-23666](https://github.com/numpy/numpy/pull/23666)) - `==` and `!=` warnings have been finalized. The `==` and `!=` operators on arrays now always: - raise errors that occur during comparisons such as when the arrays have incompatible shapes (`np.array([1, 2]) == np.array([1, 2, 3])`). - return an array of all `True` or all `False` when values are fundamentally not comparable (e.g. have different dtypes). An example is `np.array(["a"]) == np.array([1])`. This mimics the Python behavior of returning `False` and `True` when comparing incompatible types like `"a" == 1` and `"a" != 1`. For a long time these gave `DeprecationWarning` or `FutureWarning`. ([gh-22707](https://github.com/numpy/numpy/pull/22707)) - Nose support has been removed. NumPy switched to using pytest in 2018 and nose has been unmaintained for many years. We have kept NumPy\'s nose support to avoid breaking downstream projects who might have been using it and not yet switched to pytest or some other testing framework. With the arrival of Python 3.12, unpatched nose will raise an error. It is time to move on. *Decorators removed*: - raises - slow - setastest - skipif - knownfailif - deprecated - parametrize - \_needs_refcount These are not to be confused with pytest versions with similar names, e.g., pytest.mark.slow, pytest.mark.skipif, pytest.mark.parametrize. *Functions removed*: - Tester - import_nose - run_module_suite ([gh-23041](https://github.com/numpy/numpy/pull/23041)) - The `numpy.testing.utils` shim has been removed. Importing from the `numpy.testing.utils` shim has been deprecated since 2019, the shim has now been removed. All imports should be made directly from `numpy.testing`. ([gh-23060](https://github.com/numpy/numpy/pull/23060)) - The environment variable to disable dispatching has been removed. Support for the `NUMPY_EXPERIMENTAL_ARRAY_FUNCTION` environment variable has been removed. This variable disabled dispatching with `__array_function__`. ([gh-23376](https://github.com/numpy/numpy/pull/23376)) - Support for `y=` as an alias of `out=` has been removed. The `fix`, `isposinf` and `isneginf` functions allowed using `y=` as a (deprecated) alias for `out=`. This is no longer supported. ([gh-23376](https://github.com/numpy/numpy/pull/23376)) Compatibility notes - The `busday_count` method now correctly handles cases where the `begindates` is later in time than the `enddates`. Previously, the `enddates` was included, even though the documentation states it is always excluded. ([gh-23229](https://github.com/numpy/numpy/pull/23229)) - When comparing datetimes and timedelta using `np.equal` or `np.not_equal` numpy previously allowed the comparison with `casting="unsafe"`. This operation now fails. Forcing the output dtype using the `dtype` kwarg can make the operation succeed, but we do not recommend it. ([gh-22707](https://github.com/numpy/numpy/pull/22707)) - When loading data from a file handle using `np.load`, if the handle is at the end of file, as can happen when reading multiple arrays by calling `np.load` repeatedly, numpy previously raised `ValueError` if `allow_pickle=False`, and `OSError` if `allow_pickle=True`. Now it raises `EOFError` instead, in both cases. ([gh-23105](https://github.com/numpy/numpy/pull/23105)) `np.pad` with `mode=wrap` pads with strict multiples of original data Code based on earlier version of `pad` that uses `mode="wrap"` will return different results when the padding size is larger than initial array. `np.pad` with `mode=wrap` now always fills the space with strict multiples of original data even if the padding size is larger than the initial array. ([gh-22575](https://github.com/numpy/numpy/pull/22575)) Cython `long_t` and `ulong_t` removed `long_t` and `ulong_t` were aliases for `longlong_t` and `ulonglong_t` and confusing (a remainder from of Python 2). This change may lead to the errors: 'long_t' is not a type identifier 'ulong_t' is not a type identifier We recommend use of bit-sized types such as `cnp.int64_t` or the use of `cnp.intp_t` which is 32 bits on 32 bit systems and 64 bits on 64 bit systems (this is most compatible with indexing). If C `long` is desired, use plain `long` or `npy_long`. `cnp.int_t` is also `long` (NumPy\'s default integer). However, `long` is 32 bit on 64 bit windows and we may wish to adjust this even in NumPy. (Please do not hesitate to contact NumPy developers if you are curious about this.) ([gh-22637](https://github.com/numpy/numpy/pull/22637)) Changed error message and type for bad `axes` argument to `ufunc` The error message and type when a wrong `axes` value is passed to `ufunc(..., axes=[...])` has changed. The message is now more indicative of the problem, and if the value is mismatched an `AxisError` will be raised. A `TypeError` will still be raised for invalidinput types. ([gh-22675](https://github.com/numpy/numpy/pull/22675)) Array-likes that define `__array_ufunc__` can now override ufuncs if used as `where` If the `where` keyword argument of a `numpy.ufunc`{.interpreted-text role="class"} is a subclass of `numpy.ndarray`{.interpreted-text role="class"} or is a duck type that defines `numpy.class.__array_ufunc__`{.interpreted-text role="func"} it can override the behavior of the ufunc using the same mechanism as the input and output arguments. Note that for this to work properly, the `where.__array_ufunc__` implementation will have to unwrap the `where` argument to pass it into the default implementation of the `ufunc` or, for `numpy.ndarray`{.interpreted-text role="class"} subclasses before using `super().__array_ufunc__`. ([gh-23240](https://github.com/numpy/numpy/pull/23240)) Compiling against the NumPy C API is now backwards compatible by default NumPy now defaults to exposing a backwards compatible subset of the C-API. This makes the use of `oldest-supported-numpy` unnecessary. Libraries can override the default minimal version to be compatible with using: define NPY_TARGET_VERSION NPY_1_22_API_VERSION before including NumPy or by passing the equivalent `-D` option to the compiler. The NumPy 1.25 default is `NPY_1_19_API_VERSION`. Because the ``` ### 1.24.4 ``` discovered after the 1.24.3 release. It is the last planned release in the 1.24.x cycle. The Python versions supported by this release are 3.8-3.11. Contributors A total of 4 people contributed to this release. 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6620c0acd41dbcb368610bb2f4d83145674040025e5536954782467100aa8835 numpy-1.24.4-cp39-cp39-win32.whl befe2bf740fd8373cf56149a5c23a0f601e82869598d41f8e188a0e9869926f8 numpy-1.24.4-cp39-cp39-win_amd64.whl 31f13e25b4e304632a4619d0e0777662c2ffea99fcae2029556b17d8ff958aef numpy-1.24.4-pp38-pypy38_pp73-macosx_10_9_x86_64.whl 95f7ac6540e95bc440ad77f56e520da5bf877f87dca58bd095288dce8940532a numpy-1.24.4-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl e98f220aa76ca2a977fe435f5b04d7b3470c0a2e6312907b37ba6068f26787f2 numpy-1.24.4-pp38-pypy38_pp73-win_amd64.whl 80f5e3a4e498641401868df4208b74581206afbee7cf7b8329daae82676d9463 numpy-1.24.4.tar.gz ``` ### 1.24.3 ``` discovered after the 1.24.2 release. The Python versions supported by this release are 3.8-3.11. Contributors A total of 12 people contributed to this release. People with a \"+\" by their names contributed a patch for the first time. - Aleksei Nikiforov + - Alexander Heger - Bas van Beek - Bob Eldering - Brock Mendel - Charles Harris - Kyle Sunden - Peter Hawkins - Rohit Goswami - Sebastian Berg - Warren Weckesser - dependabot\[bot\] Pull requests merged A total of 17 pull requests were merged for this release. - [23206](https://github.com/numpy/numpy/pull/23206): BUG: fix for f2py string scalars (#23194) - [23207](https://github.com/numpy/numpy/pull/23207): BUG: datetime64/timedelta64 comparisons return NotImplemented - [23208](https://github.com/numpy/numpy/pull/23208): MAINT: Pin matplotlib to version 3.6.3 for refguide checks - [23221](https://github.com/numpy/numpy/pull/23221): DOC: Fix matplotlib error in documentation - [23226](https://github.com/numpy/numpy/pull/23226): CI: Ensure submodules are initialized in gitpod. - [23341](https://github.com/numpy/numpy/pull/23341): TYP: Replace duplicate reduce in ufunc type signature with reduceat. - [23342](https://github.com/numpy/numpy/pull/23342): TYP: Remove duplicate CLIP/WRAP/RAISE in `__init__.pyi`. - [23343](https://github.com/numpy/numpy/pull/23343): TYP: Mark `d` argument to fftfreq and rfftfreq as optional\... - [23344](https://github.com/numpy/numpy/pull/23344): TYP: Add type annotations for comparison operators to MaskedArray. - [23345](https://github.com/numpy/numpy/pull/23345): TYP: Remove some stray type-check-only imports of `msort` - [23370](https://github.com/numpy/numpy/pull/23370): BUG: Ensure like is only stripped for `like=` dispatched functions - [23543](https://github.com/numpy/numpy/pull/23543): BUG: fix loading and storing big arrays on s390x - [23544](https://github.com/numpy/numpy/pull/23544): MAINT: Bump larsoner/circleci-artifacts-redirector-action - [23634](https://github.com/numpy/numpy/pull/23634): BUG: Ignore invalid and overflow warnings in masked setitem - [23635](https://github.com/numpy/numpy/pull/23635): BUG: Fix masked array raveling when `
pyup-bot commented 1 year ago

Closing this in favor of #153