Update numpy to 1.24.1

[pyup-bot]

This PR updates numpy from 1.23.5 to 1.24.1.

Changelog

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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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.

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

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Links

• PyPI: https://pypi.org/project/numpy
• Changelog: https://pyup.io/changelogs/numpy/
• Homepage: https://www.numpy.org

[coveralls]

Coverage: 90.265%. Remained the same when pulling eceb44e on pyup-update-numpy-1.23.5-to-1.24.1 into cce1d95 on develop.