Scheduled monthly dependency update for June by pyup-bot · Pull Request #150 · alimanfoo/pysamstats

pyup-bot · 2023-06-01T15:13:04Z

Update Cython from 0.29.23 to 0.29.35.

Changelog

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 refence 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://pyup.io/changelogs/cython/
Homepage: http://cython.org/

Update numpy from 1.21.0 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 \&quot;+\&quot; 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=&quot;A&quot;` or `order=&quot;K&quot;`
-   [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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 ab344f1bf21f140adab8e47fdbc7c35a477dc01408791f8ba00d018dd0bc5155  numpy-1.24.3.tar.gz

1.24.2

discovered after the 1.24.1 release. 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 \&quot;+\&quot; 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 \&lt;type_traits&gt; 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

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SHA256

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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 \&quot;+\&quot; 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`.

Checksums

MD5

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SHA256

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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 \&quot;dtype\&quot; and \&quot;casting\&quot; 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 \&lt; 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 `&quot;int8&quot;` 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=[(&quot;f&quot;, &quot;i&quot;, 3)])
 subarray_fields = arr.astype(object)[0]
 subarray = subarray_fields[0]   &quot;f&quot; 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=&quot;func&quot;} or
:py`asarray()`{.interpreted-text role=&quot;func&quot;}, 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`:

 &gt;&gt;&gt; arr = np.array([1, 2, 3], dtype=&quot;long&quot;)
 &gt;&gt;&gt; new_dtype = np.dtype(&quot;longlong&quot;)
 &gt;&gt;&gt; new = np.asarray(arr, dtype=new_dtype)
 &gt;&gt;&gt; new.dtype is new_dtype
 True
 &gt;&gt;&gt; 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:

 &gt;&gt;&gt; P_y = np.polynomial.Polynomial([1, 0, -1], symbol=&quot;y&quot;)
 &gt;&gt;&gt; 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:

 &gt;&gt;&gt; P = np.polynomial.Polynomial([1, -1])   default symbol is &quot;x&quot;
 &gt;&gt;&gt; P_z = np.polynomial.Polynomial([1, 1], symbol=&quot;z&quot;)
 &gt;&gt;&gt; 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=&#x27;same_kind&#x27;)`.

`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=&#x27;same_kind&#x27;)`.

`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=&#x27;same_kind&#x27;)`.

([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:

 &gt;&gt;&gt; rg = np.random.default_rng(3728973198)
 &gt;&gt;&gt; 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:

 &gt;&gt;&gt; orig_bit_gen = np.random.get_bit_generator()
 &gt;&gt;&gt; np.random.set_bit_generator(rg.bit_generator)
 &gt;&gt;&gt; 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:

 &gt;&gt;&gt; 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\&#x27;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:

 &gt;&gt;&gt; np.arange(2, dtype=str)
 Traceback (most recent call last)
    ...
 TypeError: arange() not supported for inputs with DType &lt;class &#x27;numpy.dtype[str_]&#x27;&gt;.

([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 \&gt;10x faster) when it is passed two integer arrays. This is often
automatically used, but you can use `kind=&quot;sort&quot;` or `kind=&quot;table&quot;` 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:

 &gt;&gt;&gt; np.array([np.iinfo(np.int32).min]*10, dtype=np.int32) // np.int32(-1)
 &lt;stdin&gt;: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\&#x27;s minimum value
and raise the following `RuntimeWarning`:

 &gt;&gt;&gt; np.array([np.iinfo(np.int32).min]*10, dtype=np.int32) // np.int32(-1)
 &lt;stdin&gt;: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 \&quot;common dtype\&quot; cannot be inferred from the other inputs.

([gh-22457](https://github.com/numpy/numpy/pull/22457))

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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 \&quot;+\&quot; 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

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pyup-bot · 2023-07-01T15:13:06Z

Closing this in favor of #151

pyup-bot added 4 commits June 1, 2023 16:13

Update cython from 0.29.23 to 0.29.35

c204ecc

Update numpy from 1.21.0 to 1.24.3

cf51b89

Update pysam from 0.16.0.1 to 0.21.0

cad239f

Update tables from 3.6.1 to 3.8.0

516a21d

pyup-bot mentioned this pull request Jun 1, 2023

Scheduled monthly dependency update for May #149

Closed

pyup-bot closed this Jul 1, 2023

alimanfoo deleted the pyup-scheduled-update-2023-06-01 branch July 1, 2023 15:13

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Scheduled monthly dependency update for June#150

Scheduled monthly dependency update for June#150
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pyup-bot commented Jun 1, 2023

Update Cython from 0.29.23 to 0.29.35.

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 1.24.3.

1.24.3

1.24.2

1.24.1

1.24

1.23.5

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