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cggh / scikit-allel

A Python package for exploring and analysing genetic variation data
MIT License
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Scheduled monthly dependency update for May #394

Closed pyup-bot closed 1 year ago

pyup-bot commented 1 year ago

Update cython from 0.29.24 to 0.29.34.

Changelog ### 0.29.34 ``` ==================== Bugs fixed ---------- * A refence 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`) ```
Links - PyPI: https://pypi.org/project/cython - Changelog: https://pyup.io/changelogs/cython/ - Homepage: http://cython.org/

Update numpy from 1.21.2 to 1.24.3.

Changelog ### 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 `order="A"` or `order="K"` - [23636](https://github.com/numpy/numpy/pull/23636): MAINT: Update conftest for newer hypothesis versions - [23637](https://github.com/numpy/numpy/pull/23637): BUG: Fix bug in parsing F77 style string arrays. 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The Python versions supported by this release are 3.8-3.11. Contributors A total of 14 people contributed to this release. People with a \"+\" by their names contributed a patch for the first time. - Bas van Beek - Charles Harris - Khem Raj + - Mark Harfouche - Matti Picus - Panagiotis Zestanakis + - Peter Hawkins - Pradipta Ghosh - Ross Barnowski - Sayed Adel - Sebastian Berg - Syam Gadde + - dmbelov + - pkubaj + Pull requests merged A total of 17 pull requests were merged for this release. - [22965](https://github.com/numpy/numpy/pull/22965): MAINT: Update python 3.11-dev to 3.11. - [22966](https://github.com/numpy/numpy/pull/22966): DOC: Remove dangling deprecation warning - [22967](https://github.com/numpy/numpy/pull/22967): ENH: Detect CPU features on FreeBSD/powerpc64\* - [22968](https://github.com/numpy/numpy/pull/22968): BUG: np.loadtxt cannot load text file with quoted fields separated\... - [22969](https://github.com/numpy/numpy/pull/22969): TST: Add fixture to avoid issue with randomizing test order. - [22970](https://github.com/numpy/numpy/pull/22970): BUG: Fix fill violating read-only flag. (#22959) - [22971](https://github.com/numpy/numpy/pull/22971): MAINT: Add additional information to missing scalar AttributeError - [22972](https://github.com/numpy/numpy/pull/22972): MAINT: Move export for scipy arm64 helper into main module - [22976](https://github.com/numpy/numpy/pull/22976): BUG, SIMD: Fix spurious invalid exception for sin/cos on arm64/clang - [22989](https://github.com/numpy/numpy/pull/22989): BUG: Ensure correct loop order in sin, cos, and arctan2 - [23030](https://github.com/numpy/numpy/pull/23030): DOC: Add version added information for the strict parameter in\... - [23031](https://github.com/numpy/numpy/pull/23031): BUG: use `_Alignof` rather than `offsetof()` on most compilers - [23147](https://github.com/numpy/numpy/pull/23147): BUG: Fix for npyv\_\_trunc_s32_f32 (VXE) - [23148](https://github.com/numpy/numpy/pull/23148): BUG: Fix integer / float scalar promotion - [23149](https://github.com/numpy/numpy/pull/23149): BUG: Add missing \<type_traits> header. - [23150](https://github.com/numpy/numpy/pull/23150): TYP, MAINT: Add a missing explicit `Any` parameter to the `npt.ArrayLike`\... - [23161](https://github.com/numpy/numpy/pull/23161): BLD: remove redundant definition of npy_nextafter \[wheel build\] Checksums MD5 73fe0b507f56c0baf43171a76ad2003f numpy-1.24.2-cp310-cp310-macosx_10_9_x86_64.whl 2dbbe6f8a14e14978d24de9fcc8b49fe numpy-1.24.2-cp310-cp310-macosx_11_0_arm64.whl 9ddadbf9cac2742318d8b292cb9ca579 numpy-1.24.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 969f4f33baaff53dbbbaf1a146c43534 numpy-1.24.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 6df575dff02feac835d22debb15d190e numpy-1.24.2-cp310-cp310-win32.whl 2f939228a8c33265f2a8a1fce349d6f1 numpy-1.24.2-cp310-cp310-win_amd64.whl c093e61421be01ffff435387839949f1 numpy-1.24.2-cp311-cp311-macosx_10_9_x86_64.whl 03d71e3d9a086b56837c461fd7c9188b numpy-1.24.2-cp311-cp311-macosx_11_0_arm64.whl c0dc33697d156e2b9a029095efeb1b10 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003a9f530e880cb2cd177cba1af7220b9aa42def9c4afc2a2fc3ee6be7eb2b22 numpy-1.24.2.tar.gz ``` ### 1.24.1 ``` discovered after the 1.24.0 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. - Andrew Nelson - Ben Greiner + - Charles Harris - Clément Robert - Matteo Raso - Matti Picus - Melissa Weber Mendonça - Miles Cranmer - Ralf Gommers - Rohit Goswami - Sayed Adel - Sebastian Berg Pull requests merged A total of 18 pull requests were merged for this release. - [22820](https://github.com/numpy/numpy/pull/22820): BLD: add workaround in setup.py for newer setuptools - [22830](https://github.com/numpy/numpy/pull/22830): BLD: CIRRUS_TAG redux - [22831](https://github.com/numpy/numpy/pull/22831): DOC: fix a couple typos in 1.23 notes - [22832](https://github.com/numpy/numpy/pull/22832): BUG: Fix refcounting errors found using pytest-leaks - [22834](https://github.com/numpy/numpy/pull/22834): BUG, SIMD: Fix invalid value encountered in several ufuncs - [22837](https://github.com/numpy/numpy/pull/22837): TST: ignore more np.distutils.log imports - [22839](https://github.com/numpy/numpy/pull/22839): BUG: Do not use getdata() in np.ma.masked_invalid - [22847](https://github.com/numpy/numpy/pull/22847): BUG: Ensure correct behavior for rows ending in delimiter in\... - [22848](https://github.com/numpy/numpy/pull/22848): BUG, SIMD: Fix the bitmask of the boolean comparison - [22857](https://github.com/numpy/numpy/pull/22857): BLD: Help raspian arm + clang 13 about \_\_builtin_mul_overflow - [22858](https://github.com/numpy/numpy/pull/22858): API: Ensure a full mask is returned for masked_invalid - [22866](https://github.com/numpy/numpy/pull/22866): BUG: Polynomials now copy properly (#22669) - [22867](https://github.com/numpy/numpy/pull/22867): BUG, SIMD: Fix memory overlap in ufunc comparison loops - [22868](https://github.com/numpy/numpy/pull/22868): BUG: Fortify string casts against floating point warnings - [22875](https://github.com/numpy/numpy/pull/22875): TST: Ignore nan-warnings in randomized out tests - [22883](https://github.com/numpy/numpy/pull/22883): MAINT: restore npymath implementations needed for freebsd - [22884](https://github.com/numpy/numpy/pull/22884): BUG: Fix integer overflow in in1d for mixed integer dtypes #22877 - [22887](https://github.com/numpy/numpy/pull/22887): BUG: Use whole file for encoding checks with `charset_normalizer`. 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ef85cf1f693c88c1fd229ccd1055570cb41cdf4875873b7728b6301f12cd05bf numpy-1.24.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 87a118968fba001b248aac90e502c0b13606721b1343cdaddbc6e552e8dfb56f numpy-1.24.1-cp39-cp39-win32.whl ddc7ab52b322eb1e40521eb422c4e0a20716c271a306860979d450decbb51b8e numpy-1.24.1-cp39-cp39-win_amd64.whl ed5fb71d79e771ec930566fae9c02626b939e37271ec285e9efaf1b5d4370e7d numpy-1.24.1-pp38-pypy38_pp73-macosx_10_9_x86_64.whl ad2925567f43643f51255220424c23d204024ed428afc5aad0f86f3ffc080086 numpy-1.24.1-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl cfa1161c6ac8f92dea03d625c2d0c05e084668f4a06568b77a25a89111621566 numpy-1.24.1-pp38-pypy38_pp73-win_amd64.whl 2386da9a471cc00a1f47845e27d916d5ec5346ae9696e01a8a34760858fe9dd2 numpy-1.24.1.tar.gz ``` ### 1.24 ``` The NumPy 1.24.0 release continues the ongoing work to improve the handling and promotion of dtypes, increase the execution speed, and clarify the documentation. There are also a large number of new and expired deprecations due to changes in promotion and cleanups. This might be called a deprecation release. Highlights are - Many new deprecations, check them out. - Many expired deprecations, - New F2PY features and fixes. - New \"dtype\" and \"casting\" keywords for stacking functions. See below for the details, Deprecations Deprecate fastCopyAndTranspose and PyArray_CopyAndTranspose The `numpy.fastCopyAndTranspose` function has been deprecated. Use the corresponding copy and transpose methods directly: arr.T.copy() The underlying C function `PyArray_CopyAndTranspose` has also been deprecated from the NumPy C-API. ([gh-22313](https://github.com/numpy/numpy/pull/22313)) Conversion of out-of-bound Python integers Attempting a conversion from a Python integer to a NumPy value will now always check whether the result can be represented by NumPy. This means the following examples will fail in the future and give a `DeprecationWarning` now: np.uint8(-1) np.array([3000], dtype=np.int8) Many of these did succeed before. Such code was mainly useful for unsigned integers with negative values such as `np.uint8(-1)` giving `np.iinfo(np.uint8).max`. Note that conversion between NumPy integers is unaffected, so that `np.array(-1).astype(np.uint8)` continues to work and use C integer overflow logic. ([gh-22393](https://github.com/numpy/numpy/pull/22393)) Deprecate `msort` The `numpy.msort` function is deprecated. Use `np.sort(a, axis=0)` instead. ([gh-22456](https://github.com/numpy/numpy/pull/22456)) `np.str0` and similar are now deprecated The scalar type aliases ending in a 0 bit size: `np.object0`, `np.str0`, `np.bytes0`, `np.void0`, `np.int0`, `np.uint0` as well as `np.bool8` are now deprecated and will eventually be removed. ([gh-22607](https://github.com/numpy/numpy/pull/22607)) Expired deprecations - The `normed` keyword argument has been removed from [np.histogram]{.title-ref}, [np.histogram2d]{.title-ref}, and [np.histogramdd]{.title-ref}. Use `density` instead. If `normed` was passed by position, `density` is now used. ([gh-21645](https://github.com/numpy/numpy/pull/21645)) - Ragged array creation will now always raise a `ValueError` unless `dtype=object` is passed. This includes very deeply nested sequences. ([gh-22004](https://github.com/numpy/numpy/pull/22004)) - Support for Visual Studio 2015 and earlier has been removed. - Support for the Windows Interix POSIX interop layer has been removed. ([gh-22139](https://github.com/numpy/numpy/pull/22139)) - Support for cygwin \< 3.3 has been removed. ([gh-22159](https://github.com/numpy/numpy/pull/22159)) - The mini() method of `np.ma.MaskedArray` has been removed. Use either `np.ma.MaskedArray.min()` or `np.ma.minimum.reduce()`. - The single-argument form of `np.ma.minimum` and `np.ma.maximum` has been removed. Use `np.ma.minimum.reduce()` or `np.ma.maximum.reduce()` instead. ([gh-22228](https://github.com/numpy/numpy/pull/22228)) - Passing dtype instances other than the canonical (mainly native byte-order) ones to `dtype=` or `signature=` in ufuncs will now raise a `TypeError`. We recommend passing the strings `"int8"` or scalar types `np.int8` since the byte-order, datetime/timedelta unit, etc. are never enforced. (Initially deprecated in NumPy 1.21.) ([gh-22540](https://github.com/numpy/numpy/pull/22540)) - The `dtype=` argument to comparison ufuncs is now applied correctly. That means that only `bool` and `object` are valid values and `dtype=object` is enforced. ([gh-22541](https://github.com/numpy/numpy/pull/22541)) - The deprecation for the aliases `np.object`, `np.bool`, `np.float`, `np.complex`, `np.str`, and `np.int` is expired (introduces NumPy 1.20). Some of these will now give a FutureWarning in addition to raising an error since they will be mapped to the NumPy scalars in the future. ([gh-22607](https://github.com/numpy/numpy/pull/22607)) Compatibility notes `array.fill(scalar)` may behave slightly different `numpy.ndarray.fill` may in some cases behave slightly different now due to the fact that the logic is aligned with item assignment: arr = np.array([1]) with any dtype/value arr.fill(scalar) is now identical to: arr[0] = scalar Previously casting may have produced slightly different answers when using values that could not be represented in the target `dtype` or when the target had `object` dtype. ([gh-20924](https://github.com/numpy/numpy/pull/20924)) Subarray to object cast now copies Casting a dtype that includes a subarray to an object will now ensure a copy of the subarray. Previously an unsafe view was returned: arr = np.ones(3, dtype=[("f", "i", 3)]) subarray_fields = arr.astype(object)[0] subarray = subarray_fields[0] "f" field np.may_share_memory(subarray, arr) Is now always false. While previously it was true for the specific cast. ([gh-21925](https://github.com/numpy/numpy/pull/21925)) Returned arrays respect uniqueness of dtype kwarg objects When the `dtype` keyword argument is used with :py`np.array()`{.interpreted-text role="func"} or :py`asarray()`{.interpreted-text role="func"}, the dtype of the returned array now always exactly matches the dtype provided by the caller. In some cases this change means that a *view* rather than the input array is returned. The following is an example for this on 64bit Linux where `long` and `longlong` are the same precision but different `dtypes`: >>> arr = np.array([1, 2, 3], dtype="long") >>> new_dtype = np.dtype("longlong") >>> new = np.asarray(arr, dtype=new_dtype) >>> new.dtype is new_dtype True >>> new is arr False Before the change, the `dtype` did not match because `new is arr` was `True`. ([gh-21995](https://github.com/numpy/numpy/pull/21995)) DLPack export raises `BufferError` When an array buffer cannot be exported via DLPack a `BufferError` is now always raised where previously `TypeError` or `RuntimeError` was raised. This allows falling back to the buffer protocol or `__array_interface__` when DLPack was tried first. ([gh-22542](https://github.com/numpy/numpy/pull/22542)) NumPy builds are no longer tested on GCC-6 Ubuntu 18.04 is deprecated for GitHub actions and GCC-6 is not available on Ubuntu 20.04, so builds using that compiler are no longer tested. We still test builds using GCC-7 and GCC-8. ([gh-22598](https://github.com/numpy/numpy/pull/22598)) New Features New attribute `symbol` added to polynomial classes The polynomial classes in the `numpy.polynomial` package have a new `symbol` attribute which is used to represent the indeterminate of the polynomial. This can be used to change the value of the variable when printing: >>> P_y = np.polynomial.Polynomial([1, 0, -1], symbol="y") >>> print(P_y) 1.0 + 0.0·y¹ - 1.0·y² Note that the polynomial classes only support 1D polynomials, so operations that involve polynomials with different symbols are disallowed when the result would be multivariate: >>> P = np.polynomial.Polynomial([1, -1]) default symbol is "x" >>> P_z = np.polynomial.Polynomial([1, 1], symbol="z") >>> P * P_z Traceback (most recent call last) ... ValueError: Polynomial symbols differ The symbol can be any valid Python identifier. The default is `symbol=x`, consistent with existing behavior. ([gh-16154](https://github.com/numpy/numpy/pull/16154)) F2PY support for Fortran `character` strings F2PY now supports wrapping Fortran functions with: - character (e.g. `character x`) - character array (e.g. `character, dimension(n) :: x`) - character string (e.g. `character(len=10) x`) - and character string array (e.g. `character(len=10), dimension(n, m) :: x`) arguments, including passing Python unicode strings as Fortran character string arguments. ([gh-19388](https://github.com/numpy/numpy/pull/19388)) New function `np.show_runtime` A new function `numpy.show_runtime` has been added to display the runtime information of the machine in addition to `numpy.show_config` which displays the build-related information. ([gh-21468](https://github.com/numpy/numpy/pull/21468)) `strict` option for `testing.assert_array_equal` The `strict` option is now available for `testing.assert_array_equal`. Setting `strict=True` will disable the broadcasting behaviour for scalars and ensure that input arrays have the same data type. ([gh-21595](https://github.com/numpy/numpy/pull/21595)) New parameter `equal_nan` added to `np.unique` `np.unique` was changed in 1.21 to treat all `NaN` values as equal and return a single `NaN`. Setting `equal_nan=False` will restore pre-1.21 behavior to treat `NaNs` as unique. Defaults to `True`. ([gh-21623](https://github.com/numpy/numpy/pull/21623)) `casting` and `dtype` keyword arguments for `numpy.stack` The `casting` and `dtype` keyword arguments are now available for `numpy.stack`. To use them, write `np.stack(..., dtype=None, casting='same_kind')`. `casting` and `dtype` keyword arguments for `numpy.vstack` The `casting` and `dtype` keyword arguments are now available for `numpy.vstack`. To use them, write `np.vstack(..., dtype=None, casting='same_kind')`. `casting` and `dtype` keyword arguments for `numpy.hstack` The `casting` and `dtype` keyword arguments are now available for `numpy.hstack`. To use them, write `np.hstack(..., dtype=None, casting='same_kind')`. ([gh-21627](https://github.com/numpy/numpy/pull/21627)) The bit generator underlying the singleton RandomState can be changed The singleton `RandomState` instance exposed in the `numpy.random` module is initialized at startup with the `MT19937` bit generator. The new function `set_bit_generator` allows the default bit generator to be replaced with a user-provided bit generator. This function has been introduced to provide a method allowing seamless integration of a high-quality, modern bit generator in new code with existing code that makes use of the singleton-provided random variate generating functions. The companion function `get_bit_generator` returns the current bit generator being used by the singleton `RandomState`. This is provided to simplify restoring the original source of randomness if required. The preferred method to generate reproducible random numbers is to use a modern bit generator in an instance of `Generator`. The function `default_rng` simplifies instantiation: >>> rg = np.random.default_rng(3728973198) >>> rg.random() The same bit generator can then be shared with the singleton instance so that calling functions in the `random` module will use the same bit generator: >>> orig_bit_gen = np.random.get_bit_generator() >>> np.random.set_bit_generator(rg.bit_generator) >>> np.random.normal() The swap is permanent (until reversed) and so any call to functions in the `random` module will use the new bit generator. The original can be restored if required for code to run correctly: >>> np.random.set_bit_generator(orig_bit_gen) ([gh-21976](https://github.com/numpy/numpy/pull/21976)) `np.void` now has a `dtype` argument NumPy now allows constructing structured void scalars directly by passing the `dtype` argument to `np.void`. ([gh-22316](https://github.com/numpy/numpy/pull/22316)) Improvements F2PY Improvements - The generated extension modules don\'t use the deprecated NumPy-C API anymore - Improved `f2py` generated exception messages - Numerous bug and `flake8` warning fixes - various CPP macros that one can use within C-expressions of signature files are prefixed with `f2py_`. For example, one should use `f2py_len(x)` instead of `len(x)` - A new construct `character(f2py_len=...)` is introduced to support returning assumed length character strings (e.g. `character(len=*)`) from wrapper functions A hook to support rewriting `f2py` internal data structures after reading all its input files is introduced. This is required, for instance, for BC of SciPy support where character arguments are treated as character strings arguments in `C` expressions. ([gh-19388](https://github.com/numpy/numpy/pull/19388)) IBM zSystems Vector Extension Facility (SIMD) Added support for SIMD extensions of zSystem (z13, z14, z15), through the universal intrinsics interface. This support leads to performance improvements for all SIMD kernels implemented using the universal intrinsics, including the following operations: rint, floor, trunc, ceil, sqrt, absolute, square, reciprocal, tanh, sin, cos, equal, not_equal, greater, greater_equal, less, less_equal, maximum, minimum, fmax, fmin, argmax, argmin, add, subtract, multiply, divide. ([gh-20913](https://github.com/numpy/numpy/pull/20913)) NumPy now gives floating point errors in casts In most cases, NumPy previously did not give floating point warnings or errors when these happened during casts. For examples, casts like: np.array([2e300]).astype(np.float32) overflow for float32 np.array([np.inf]).astype(np.int64) Should now generally give floating point warnings. These warnings should warn that floating point overflow occurred. For errors when converting floating point values to integers users should expect invalid value warnings. Users can modify the behavior of these warnings using `np.errstate`. Note that for float to int casts, the exact warnings that are given may be platform dependent. For example: arr = np.full(100, value=1000, dtype=np.float64) arr.astype(np.int8) May give a result equivalent to (the intermediate cast means no warning is given): arr.astype(np.int64).astype(np.int8) May return an undefined result, with a warning set: RuntimeWarning: invalid value encountered in cast The precise behavior is subject to the C99 standard and its implementation in both software and hardware. ([gh-21437](https://github.com/numpy/numpy/pull/21437)) F2PY supports the value attribute The Fortran standard requires that variables declared with the `value` attribute must be passed by value instead of reference. F2PY now supports this use pattern correctly. So `integer, intent(in), value :: x` in Fortran codes will have correct wrappers generated. ([gh-21807](https://github.com/numpy/numpy/pull/21807)) Added pickle support for third-party BitGenerators The pickle format for bit generators was extended to allow each bit generator to supply its own constructor when during pickling. Previous versions of NumPy only supported unpickling `Generator` instances created with one of the core set of bit generators supplied with NumPy. Attempting to unpickle a `Generator` that used a third-party bit generators would fail since the constructor used during the unpickling was only aware of the bit generators included in NumPy. ([gh-22014](https://github.com/numpy/numpy/pull/22014)) arange() now explicitly fails with dtype=str Previously, the `np.arange(n, dtype=str)` function worked for `n=1` and `n=2`, but would raise a non-specific exception message for other values of `n`. Now, it raises a [TypeError]{.title-ref} informing that `arange` does not support string dtypes: >>> np.arange(2, dtype=str) Traceback (most recent call last) ... TypeError: arange() not supported for inputs with DType <class 'numpy.dtype[str_]'>. ([gh-22055](https://github.com/numpy/numpy/pull/22055)) `numpy.typing` protocols are now runtime checkable The protocols used in `numpy.typing.ArrayLike` and `numpy.typing.DTypeLike` are now properly marked as runtime checkable, making them easier to use for runtime type checkers. ([gh-22357](https://github.com/numpy/numpy/pull/22357)) Performance improvements and changes Faster version of `np.isin` and `np.in1d` for integer arrays `np.in1d` (used by `np.isin`) can now switch to a faster algorithm (up to \>10x faster) when it is passed two integer arrays. This is often automatically used, but you can use `kind="sort"` or `kind="table"` to force the old or new method, respectively. ([gh-12065](https://github.com/numpy/numpy/pull/12065)) Faster comparison operators The comparison functions (`numpy.equal`, `numpy.not_equal`, `numpy.less`, `numpy.less_equal`, `numpy.greater` and `numpy.greater_equal`) are now much faster as they are now vectorized with universal intrinsics. For a CPU with SIMD extension AVX512BW, the performance gain is up to 2.57x, 1.65x and 19.15x for integer, float and boolean data types, respectively (with N=50000). ([gh-21483](https://github.com/numpy/numpy/pull/21483)) Changes Better reporting of integer division overflow Integer division overflow of scalars and arrays used to provide a `RuntimeWarning` and the return value was undefined leading to crashes at rare occasions: >>> np.array([np.iinfo(np.int32).min]*10, dtype=np.int32) // np.int32(-1) <stdin>:1: RuntimeWarning: divide by zero encountered in floor_divide array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0], dtype=int32) Integer division overflow now returns the input dtype\'s minimum value and raise the following `RuntimeWarning`: >>> np.array([np.iinfo(np.int32).min]*10, dtype=np.int32) // np.int32(-1) <stdin>:1: RuntimeWarning: overflow encountered in floor_divide array([-2147483648, -2147483648, -2147483648, -2147483648, -2147483648, -2147483648, -2147483648, -2147483648, -2147483648, -2147483648], dtype=int32) ([gh-21506](https://github.com/numpy/numpy/pull/21506)) `masked_invalid` now modifies the mask in-place When used with `copy=False`, `numpy.ma.masked_invalid` now modifies the input masked array in-place. This makes it behave identically to `masked_where` and better matches the documentation. ([gh-22046](https://github.com/numpy/numpy/pull/22046)) `nditer`/`NpyIter` allows all allocating all operands The NumPy iterator available through `np.nditer` in Python and as `NpyIter` in C now supports allocating all arrays. The iterator shape defaults to `()` in this case. The operands dtype must be provided, since a \"common dtype\" cannot be inferred from the other inputs. 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numpy-1.24.0rc1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 15605b92bf10b10e110a9c0f1c4ef6cd58246532c62a0c3d3188c05e69cdcdb6 numpy-1.24.0rc1-cp39-cp39-win32.whl 8046f5c23769791be8432a592b9881984e0e4abc7f552c7e5c349420a27323e7 numpy-1.24.0rc1-cp39-cp39-win_amd64.whl aa9c4a2f65d669e6559123154da944ad6bd7605cbba5cce81bf6794617870510 numpy-1.24.0rc1-pp38-pypy38_pp73-macosx_10_9_x86_64.whl e44fd1bdfa50979ddec76318e21abc82ee3858e5f45dfc5153b6f660d9d29851 numpy-1.24.0rc1-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 1802199d70d9f8ac11eb63a1ef50d33915b78a84bacacaadb2896175005103d4 numpy-1.24.0rc1-pp38-pypy38_pp73-win_amd64.whl d601180710004799acb8f80e564b84e71490fac9d84e115e2f5b0f6709754f16 numpy-1.24.0rc1.tar.gz ``` ### 1.23.5 ``` the 1.23.4 release and keeps the build infrastructure current. The Python versions supported for this release are 3.8-3.11. Contributors A total of 7 people contributed to this release. People with a \"+\" by their names contributed a patch for the first time. - \DWesl - Aayush Agrawal + - Adam Knapp + - Charles Harris - Navpreet Singh + - Sebastian Berg - Tania Allard Pull requests merged A total of 10 pull requests were merged for this release. - [22489](https://github.com/numpy/numpy/pull/22489): TST, MAINT: Replace most setup with setup_method (also teardown) - [22490](https://github.com/numpy/numpy/pull/22490): MAINT, CI: Switch to cygwin/cygwin-install-actionv2 - [22494](https://github.com/numpy/numpy/pull/22494): TST: Make test_partial_iteration_cleanup robust but require leak\... - [22592](https://github.com/numpy/numpy/pull/22592): MAINT: Ensure graceful handling of large header sizes - [22593](https://github.com/numpy/numpy/pull/22593): TYP: Spelling alignment for array flag literal - [22594](https://github.com/numpy/numpy/pull/22594): BUG: Fix bounds checking for `random.logseries` - [22595](https://github.com/numpy/numpy/pull/22595): DEV: Update GH actions and Dockerfile for Gitpod - [22596](https://github.com/numpy/numpy/pull/22596): CI: Only fetch in actions/checkout - [22597](https://github.com/numpy/numpy/pull/22597): BUG: Decrement ref count in gentype_reduce if allocated memory\... - [22625](https://github.com/numpy/numpy/pull/22625): BUG: Histogramdd breaks on big arrays in Windows Checksums MD5 8a412b79d975199cefadb465279fd569 numpy-1.23.5-cp310-cp310-macosx_10_9_x86_64.whl 1b56e8e6a0516c78473657abf0710538 numpy-1.23.5-cp310-cp310-macosx_11_0_arm64.whl c787f4763c9a5876e86a17f1651ba458 numpy-1.23.5-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl db07645022e56747ba3f00c2d742232e numpy-1.23.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl c63a6fb7cc16a13aabc82ec57ac6bb4d numpy-1.23.5-cp310-cp310-win32.whl 3fea9247e1d812600015641941fa273f numpy-1.23.5-cp310-cp310-win_amd64.whl 4222cfb36e5ac9aec348c81b075e2c05 numpy-1.23.5-cp311-cp311-macosx_10_9_x86_64.whl 6c7102f185b310ac70a62c13d46f04e6 numpy-1.23.5-cp311-cp311-macosx_11_0_arm64.whl 6b7319f66bf7ac01b49e2a32470baf28 numpy-1.23.5-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 3c60928ddb1f55163801f06ac2229eb0 numpy-1.23.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 6936b6bcfd6474acc7a8c162a9393b3c numpy-1.23.5-cp311-cp311-win32.whl 6c9af68b7b56c12c913678cafbdc44d6 numpy-1.23.5-cp311-cp311-win_amd64.whl 699daeac883260d3f182ae4bbbd9bbd2 numpy-1.23.5-cp38-cp38-macosx_10_9_x86_64.whl 6c233a36339de0652139e78ef91504d4 numpy-1.23.5-cp38-cp38-macosx_11_0_arm64.whl 57d5439556ab5078c91bdeffd9c0036e numpy-1.23.5-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl a8045b59187f2e0ccd4294851adbbb8a numpy-1.23.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 7f38f7e560e4bf41490372ab84aa7a38 numpy-1.23.5-cp38-cp38-win32.whl 76095726ba459d7f761b44acf2e56bd1 numpy-1.23.5-cp38-cp38-win_amd64.whl 174befd584bc1b03ed87c8f0d149a58e numpy-1.23.5-cp39-cp39-macosx_10_9_x86_64.whl 9cbac793d77278f5d27a7979b64f6b5b numpy-1.23.5-cp39-cp39-macosx_11_0_arm64.whl 6e417b087044e90562183b33f3049b09 numpy-1.23.5-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 54fa63341eaa6da346d824399e8237f6 numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl cc14d62a158e99c57f925c86551e45f0 numpy-1.23.5-cp39-cp39-win32.whl bad36b81e7e84bd7a028affa0659d235 numpy-1.23.5-cp39-cp39-win_amd64.whl b4d17d6b79a8354a2834047669651963 numpy-1.23.5-pp38-pypy38_pp73-macosx_10_9_x86_64.whl 89f6dc4a4ff63fca6af1223111cd888d numpy-1.23.5-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 633d574a35b8592bab502ef569b0731e numpy-1.23.5-pp38-pypy38_pp73-win_amd64.whl 8b2692a511a3795f3af8af2cd7566a15 numpy-1.23.5.tar.gz SHA256 9c88793f78fca17da0145455f0d7826bcb9f37da4764af27ac945488116efe63 numpy-1.23.5-cp310-cp310-macosx_10_9_x86_64.whl e9f4c4e51567b616be64e05d517c79a8a22f3606499941d97bb76f2ca59f982d numpy-1.23.5-cp310-cp310-macosx_11_0_arm64.whl 7903ba8ab592b82014713c491f6c5d3a1cde5b4a3bf116404e08f5b52f6daf43 numpy-1.23.5-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 5e05b1c973a9f85