Update numpy to 1.17.1

[pyup-bot]

This PR updates numpy from 1.16.4 to 1.17.1.

Changelog

1.17.0

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

This NumPy release contains a number of new features that should substantially
improve its performance and usefulness, see Highlights below for a summary. The
Python versions supported are 3.5-3.7, note that Python 2.7 has been dropped.
Python 3.8b2 should work with the released source packages, but there are no
future guarantees.

Downstream developers should use Cython >= 0.29.11 for Python 3.8 support and
OpenBLAS >= 3.7 (not currently out) to avoid problems on the Skylake
architecture. The NumPy wheels on PyPI are built from the OpenBLAS development
branch in order to avoid those problems.


Highlights
==========

* A new extensible `random` module along with four selectable `random number
generators <random.BitGenerators>` and improved seeding designed for use in parallel
processes has been added. The currently available bit generators are `MT19937
<random.mt19937.MT19937>`, `PCG64 <random.pcg64.PCG64>`, `Philox
<random.philox.Philox>`, and `SFC64 <random.sfc64.SFC64>`. See below under
New Features.

* NumPy's `FFT <fft>` implementation was changed from fftpack to pocketfft,
resulting in faster, more accurate transforms and better handling of datasets
of prime length. See below under Improvements.

* New radix sort and timsort sorting methods. It is currently not possible to
choose which will be used. They are hardwired to the datatype and used
when either ``stable`` or ``mergesort`` is passed as the method. See below
under Improvements.

* Overriding numpy functions is now possible by default,
see ``__array_function__`` below.


New functions
=============

* `numpy.errstate` is now also a function decorator


Deprecations
============

`numpy.polynomial` functions warn when passed ``float`` in place of ``int``
---------------------------------------------------------------------------
Previously functions in this module would accept ``float`` values provided they
were integral (``1.0``, ``2.0``, etc). For consistency with the rest of numpy,
doing so is now deprecated, and in future will raise a ``TypeError``.

Similarly, passing a float like ``0.5`` in place of an integer will now raise a
``TypeError`` instead of the previous ``ValueError``.

Deprecate `numpy.distutils.exec_command` and ``temp_file_name``
---------------------------------------------------------------
The internal use of these functions has been refactored and there are better
alternatives. Replace ``exec_command`` with `subprocess.Popen` and
`temp_file_name <numpy.distutils.exec_command>` with `tempfile.mkstemp`.

Writeable flag of C-API wrapped arrays
--------------------------------------
When an array is created from the C-API to wrap a pointer to data, the only
indication we have of the read-write nature of the data is the ``writeable``
flag set during creation. It is dangerous to force the flag to writeable.
In the future it will not be possible to switch the writeable flag to ``True``
from python.
This deprecation should not affect many users since arrays created in such
a manner are very rare in practice and only available through the NumPy C-API.

`numpy.nonzero` should no longer be called on 0d arrays
-------------------------------------------------------
The behavior of `numpy.nonzero` on 0d arrays was surprising, making uses of it
almost always incorrect. If the old behavior was intended, it can be preserved
without a warning by using ``nonzero(atleast_1d(arr))`` instead of
``nonzero(arr)``.  In a future release, it is most likely this will raise a
``ValueError``.

Writing to the result of `numpy.broadcast_arrays` will warn
-----------------------------------------------------------

Commonly `numpy.broadcast_arrays` returns a writeable array with internal
overlap, making it unsafe to write to. A future version will set the
``writeable`` flag to ``False``, and require users to manually set it to
``True`` if they are sure that is what they want to do. Now writing to it will
emit a deprecation warning with instructions to set the ``writeable`` flag
``True``.  Note that if one were to inspect the flag before setting it, one
would find it would already be ``True``.  Explicitly setting it, though, as one
will need to do in future versions, clears an internal flag that is used to
produce the deprecation warning. To help alleviate confusion, an additional
`FutureWarning` will be emitted when accessing the ``writeable`` flag state to
clarify the contradiction.

Note that for the C-side buffer protocol such an array will return a
readonly buffer immediately unless a writable buffer is requested. If
a writeable buffer is requested a warning will be given. When using
cython, the ``const`` qualifier should be used with such arrays to avoid
the warning (e.g. ``cdef const double[::1] view``).


Future Changes
==============

Shape-1 fields in dtypes won't be collapsed to scalars in a future version
--------------------------------------------------------------------------

Currently, a field specified as ``[(name, dtype, 1)]`` or ``"1type"`` is
interpreted as a scalar field (i.e., the same as ``[(name, dtype)]`` or
``[(name, dtype, ()]``). This now raises a FutureWarning; in a future version,
it will be interpreted as a shape-(1,) field, i.e. the same as ``[(name,
dtype, (1,))]`` or ``"(1,)type"`` (consistently with ``[(name, dtype, n)]``
/ ``"ntype"`` with ``n>1``, which is already equivalent to ``[(name, dtype,
(n,)]`` / ``"(n,)type"``).


Compatibility notes
===================

``float16`` subnormal rounding
------------------------------
Casting from a different floating point precision to ``float16`` used incorrect
rounding in some edge cases. This means in rare cases, subnormal results will
now be rounded up instead of down, changing the last bit (ULP) of the result.

Signed zero when using divmod
-----------------------------
Starting in version `1.12.0`, numpy incorrectly returned a negatively signed zero
when using the ``divmod`` and ``floor_divide`` functions when the result was
zero. For example::

>>> np.zeros(10)//1
array([-0., -0., -0., -0., -0., -0., -0., -0., -0., -0.])

With this release, the result is correctly returned as a positively signed
zero::

>>> np.zeros(10)//1
array([0., 0., 0., 0., 0., 0., 0., 0., 0., 0.])

``MaskedArray.mask`` now returns a view of the mask, not the mask itself
------------------------------------------------------------------------
Returning the mask itself was unsafe, as it could be reshaped in place which
would violate expectations of the masked array code. The behavior of `mask
<ma.MaskedArray.mask>` is now consistent with `data <ma.MaskedArray.data>`,
which also returns a view.

The underlying mask can still be accessed with ``._mask`` if it is needed.
Tests that contain ``assert x.mask is not y.mask`` or similar will need to be
updated.

Do not lookup ``__buffer__`` attribute in `numpy.frombuffer`
------------------------------------------------------------
Looking up ``__buffer__`` attribute in `numpy.frombuffer` was undocumented and
non-functional. This code was removed. If needed, use
``frombuffer(memoryview(obj), ...)`` instead.

``out`` is buffered for memory overlaps in `take`, `choose`, `put`
------------------------------------------------------------------
If the out argument to these functions is provided and has memory overlap with
the other arguments, it is now buffered to avoid order-dependent behavior.

Unpickling while loading requires explicit opt-in
-------------------------------------------------
The functions `load`, and ``lib.format.read_array`` take an
``allow_pickle`` keyword which now defaults to ``False`` in response to
`CVE-2019-6446 <https://nvd.nist.gov/vuln/detail/CVE-2019-6446>`_.


.. currentmodule:: numpy.random.mtrand

Potential changes to the random stream in old random module
-----------------------------------------------------------
Due to bugs in the application of ``log`` to random floating point numbers,
the stream may change when sampling from `~RandomState.beta`, `~RandomState.binomial`,
`~RandomState.laplace`, `~RandomState.logistic`, `~RandomState.logseries` or
`~RandomState.multinomial` if a ``0`` is generated in the underlying `MT19937
<~numpy.random.mt11937.MT19937>` random stream.  There is a ``1`` in
:math:`10^{53}` chance of this occurring, so the probability that the stream
changes for any given seed is extremely small. If a ``0`` is encountered in the
underlying generator, then the incorrect value produced (either `numpy.inf` or
`numpy.nan`) is now dropped.

.. currentmodule:: numpy

`i0` now always returns a result with the same shape as the input
-----------------------------------------------------------------
Previously, the output was squeezed, such that, e.g., input with just a single
element would lead to an array scalar being returned, and inputs with shapes
such as ``(10, 1)`` would yield results that would not broadcast against the
input.

Note that we generally recommend the SciPy implementation over the numpy one:
it is a proper ufunc written in C, and more than an order of magnitude faster.

`can_cast` no longer assumes all unsafe casting is allowed
----------------------------------------------------------
Previously, `can_cast` returned `True` for almost all inputs for
``casting='unsafe'``, even for cases where casting was not possible, such as
from a structured dtype to a regular one.  This has been fixed, making it
more consistent with actual casting using, e.g., the `.astype <ndarray.astype>`
method.

``ndarray.flags.writeable`` can be switched to true slightly more often
-----------------------------------------------------------------------

In rare cases, it was not possible to switch an array from not writeable
to writeable, although a base array is writeable. This can happen if an
intermediate `ndarray.base` object is writeable. Previously, only the deepest
base object was considered for this decision. However, in rare cases this
object does not have the necessary information. In that case switching to
writeable was never allowed. This has now been fixed.


C API changes
=============

dimension or stride input arguments are now passed by ``npy_intp const*``
-------------------------------------------------------------------------
Previously these function arguments were declared as the more strict
``npy_intp*``, which prevented the caller passing constant data.
This change is backwards compatible, but now allows code like::

 npy_intp const fixed_dims[] = {1, 2, 3};
 // no longer complains that the const-qualifier is discarded
 npy_intp size = PyArray_MultiplyList(fixed_dims, 3);


New Features
============

.. currentmodule:: numpy.random

New extensible `numpy.random` module with selectable random number generators
-----------------------------------------------------------------------------
A new extensible `numpy.random` module along with four selectable random number
generators and improved seeding designed for use in parallel processes has been
added. The currently available :ref:`Bit Generators <bit_generator>` are
`~mt19937.MT19937`, `~pcg64.PCG64`, `~philox.Philox`, and `~sfc64.SFC64`.
``PCG64`` is the new default while ``MT19937`` is retained for backwards
compatibility. Note that the legacy random module is unchanged and is now
frozen, your current results will not change. More information is available in
the :ref:`API change description <new-or-different>` and in the `top-level view
<numpy.random>` documentation.

.. currentmodule:: numpy

libFLAME
--------
Support for building NumPy with the libFLAME linear algebra package as the LAPACK,
implementation, see
`libFLAME <https://www.cs.utexas.edu/~flame/web/libFLAME.html>`_ for details.

User-defined BLAS detection order
---------------------------------
`distutils` now uses an environment variable, comma-separated and case
insensitive, to determine the detection order for BLAS libraries.
By default ``NPY_BLAS_ORDER=mkl,blis,openblas,atlas,accelerate,blas``.
However, to force the use of OpenBLAS simply do::

NPY_BLAS_ORDER=openblas python setup.py build

which forces the use of OpenBLAS.
This may be helpful for users which have a MKL installation but wishes to try
out different implementations.

User-defined LAPACK detection order
-----------------------------------
``numpy.distutils`` now uses an environment variable, comma-separated and case
insensitive, to determine the detection order for LAPACK libraries.
By default ``NPY_LAPACK_ORDER=mkl,openblas,flame,atlas,accelerate,lapack``.
However, to force the use of OpenBLAS simply do::

NPY_LAPACK_ORDER=openblas python setup.py build

which forces the use of OpenBLAS.
This may be helpful for users which have a MKL installation but wishes to try
out different implementations.

`ufunc.reduce` and related functions now accept a ``where`` mask
----------------------------------------------------------------
`ufunc.reduce`, `sum`, `prod`, `min`, `max` all
now accept a ``where`` keyword argument, which can be used to tell which
elements to include in the reduction.  For reductions that do not have an
identity, it is necessary to also pass in an initial value (e.g.,
``initial=np.inf`` for `min`).  For instance, the equivalent of
`nansum` would be ``np.sum(a, where=~np.isnan(a))``.

Timsort and radix sort have replaced mergesort for stable sorting
-----------------------------------------------------------------
Both radix sort and timsort have been implemented and are now used in place of
mergesort. Due to the need to maintain backward compatibility, the sorting
``kind`` options ``"stable"`` and ``"mergesort"`` have been made aliases of
each other with the actual sort implementation depending on the array type.
Radix sort is used for small integer types of 16 bits or less and timsort for
the remaining types.  Timsort features improved performace on data containing
already or nearly sorted data and performs like mergesort on random data and
requires :math:`O(n/2)` working space.  Details of the timsort algorithm can be
found at `CPython listsort.txt
<https://github.com/python/cpython/blob/3.7/Objects/listsort.txt>`_.

`packbits` and `unpackbits` accept an ``order`` keyword
-------------------------------------------------------
The ``order`` keyword defaults to ``big``, and will order the **bits**
accordingly. For ``'order=big'`` 3 will become ``[0, 0, 0, 0, 0, 0, 1, 1]``,
and ``[1, 1, 0, 0, 0, 0, 0, 0]`` for ``order=little``

`unpackbits` now accepts a ``count`` parameter
----------------------------------------------
``count`` allows subsetting the number of bits that will be unpacked up-front,
rather than reshaping and subsetting later, making the `packbits` operation
invertible, and the unpacking less wasteful. Counts larger than the number of
available bits add zero padding. Negative counts trim bits off the end instead
of counting from the beginning. None counts implement the existing behavior of
unpacking everything.

`linalg.svd` and `linalg.pinv` can be faster on hermitian inputs
----------------------------------------------------------------
These functions now accept a ``hermitian`` argument, matching the one added
to `linalg.matrix_rank` in 1.14.0.

divmod operation is now supported for two ``timedelta64`` operands
------------------------------------------------------------------
The divmod operator now handles two ``timedelta64`` operands, with
type signature ``mm->qm``.

`fromfile` now takes an ``offset`` argument
-------------------------------------------
This function now takes an ``offset`` keyword argument for binary files,
which specifics the offset (in bytes) from the file's current position.
Defaults to ``0``.

New mode "empty" for `pad`
--------------------------
This mode pads an array to a desired shape without initializing the new
entries.

`empty_like` and related functions now accept a ``shape`` argument
------------------------------------------------------------------
`empty_like`, `full_like`, `ones_like` and `zeros_like` now accept a ``shape``
keyword argument, which can be used to create a new array
as the prototype, overriding its shape as well. This is particularly useful
when combined with the ``__array_function__`` protocol, allowing the creation
of new arbitrary-shape arrays from NumPy-like libraries when such an array
is used as the prototype.

Floating point scalars implement ``as_integer_ratio`` to match the builtin float
--------------------------------------------------------------------------------
This returns a (numerator, denominator) pair, which can be used to construct a
`fractions.Fraction`.

Structured ``dtype`` objects can be indexed with multiple fields names
----------------------------------------------------------------------
``arr.dtype[['a', 'b']]`` now returns a dtype that is equivalent to
``arr[['a', 'b']].dtype``, for consistency with
``arr.dtype['a'] == arr['a'].dtype``.

Like the dtype of structured arrays indexed with a list of fields, this dtype
has the same ``itemsize`` as the original, but only keeps a subset of the fields.

This means that ``arr[['a', 'b']]`` and ``arr.view(arr.dtype[['a', 'b']])`` are
equivalent.

``.npy`` files support unicode field names
------------------------------------------
A new format version of 3.0 has been introduced, which enables structured types
with non-latin1 field names. This is used automatically when needed.


Improvements
============

Array comparison assertions include maximum differences
-------------------------------------------------------
Error messages from array comparison tests such as
`testing.assert_allclose` now include "max absolute difference" and
"max relative difference," in addition to the previous "mismatch" percentage.
This information makes it easier to update absolute and relative error
tolerances.

Replacement of the fftpack based `fft` module by the pocketfft library
----------------------------------------------------------------------
Both implementations have the same ancestor (Fortran77 FFTPACK by Paul N.
Swarztrauber), but pocketfft contains additional modifications which improve
both accuracy and performance in some circumstances. For FFT lengths containing
large prime factors, pocketfft uses Bluestein's algorithm, which maintains
:math:`O(N log N)` run time complexity instead of deteriorating towards
:math:`O(N*N)` for prime lengths. Also, accuracy for real valued FFTs with near
prime lengths has improved and is on par with complex valued FFTs.

Further improvements to ``ctypes`` support in `numpy.ctypeslib`
---------------------------------------------------------------
A new `numpy.ctypeslib.as_ctypes_type` function has been added, which can be
used to converts a `dtype` into a best-guess `ctypes` type. Thanks to this
new function, `numpy.ctypeslib.as_ctypes` now supports a much wider range of
array types, including structures, booleans, and integers of non-native
endianness.

`numpy.errstate` is now also a function decorator
-------------------------------------------------
Currently, if you have a function like::

 def foo():
     pass

and you want to wrap the whole thing in `errstate`, you have to rewrite it
like so::

 def foo():
     with np.errstate(...):
         pass

but with this change, you can do::

 np.errstate(...)
 def foo():
     pass

thereby saving a level of indentation

`numpy.exp` and `numpy.log` speed up for float32 implementation
---------------------------------------------------------------
float32 implementation of `exp` and `log` now benefit from AVX2/AVX512
instruction set which are detected during runtime. `exp` has a max ulp
error of 2.52 and `log` has a max ulp error or 3.83.

Improve performance of `numpy.pad`
----------------------------------
The performance of the function has been improved for most cases by filling in
a preallocated array with the desired padded shape instead of using
concatenation.

`numpy.interp` handles infinities more robustly
-----------------------------------------------
In some cases where `interp` would previously return `nan`, it now
returns an appropriate infinity.

Pathlib support for `fromfile`, `tofile` and `ndarray.dump`
-----------------------------------------------------------
`fromfile`, `ndarray.ndarray.tofile` and `ndarray.dump` now support
the `pathlib.Path` type for the ``file``/``fid`` parameter.

Specialized `isnan`, `isinf`, and `isfinite` ufuncs for bool and int types
--------------------------------------------------------------------------
The boolean and integer types are incapable of storing `nan` and `inf` values,
which allows us to provide specialized ufuncs that are up to 250x faster than
the previous approach.

`isfinite` supports ``datetime64`` and ``timedelta64`` types
-----------------------------------------------------------------
Previously, `isfinite` used to raise a `TypeError` on being used on these
two types.

New keywords added to `nan_to_num`
----------------------------------
`nan_to_num` now accepts keywords ``nan``, ``posinf`` and ``neginf``
allowing the user to define the value to replace the ``nan``, positive and
negative ``np.inf`` values respectively.

MemoryErrors caused by allocated overly large arrays are more descriptive
-------------------------------------------------------------------------
Often the cause of a MemoryError is incorrect broadcasting, which results in a
very large and incorrect shape. The message of the error now includes this
shape to help diagnose the cause of failure.

`floor`, `ceil`, and `trunc` now respect builtin magic methods
--------------------------------------------------------------
These ufuncs now call the ``__floor__``, ``__ceil__``, and ``__trunc__``
methods when called on object arrays, making them compatible with
`decimal.Decimal` and `fractions.Fraction` objects.

`quantile` now works on `fraction.Fraction` and `decimal.Decimal` objects
-------------------------------------------------------------------------
In general, this handles object arrays more gracefully, and avoids floating-
point operations if exact arithmetic types are used.

Support of object arrays in `matmul`
------------------------------------
It is now possible to use `matmul` (or the ` operator) with object arrays.
For instance, it is now possible to do::

 from fractions import Fraction
 a = np.array([[Fraction(1, 2), Fraction(1, 3)], [Fraction(1, 3), Fraction(1, 2)]])
 b = a  a


Changes
=======

`median` and `percentile` family of functions no longer warn about ``nan``
--------------------------------------------------------------------------
`numpy.median`, `numpy.percentile`, and `numpy.quantile` used to emit a
``RuntimeWarning`` when encountering an `nan`. Since they return the
``nan`` value, the warning is redundant and has been removed.

``timedelta64 % 0`` behavior adjusted to return ``NaT``
-------------------------------------------------------
The modulus operation with two ``np.timedelta64`` operands now returns
``NaT`` in the case of division by zero, rather than returning zero

NumPy functions now always support overrides with ``__array_function__``
------------------------------------------------------------------------
NumPy now always checks the ``__array_function__`` method to implement overrides
of NumPy functions on non-NumPy arrays, as described in `NEP 18`_. The feature
was available for testing with NumPy 1.16 if appropriate environment variables
are set, but is now always enabled.

.. _`NEP 18` : http://www.numpy.org/neps/nep-0018-array-function-protocol.html

``lib.recfunctions.structured_to_unstructured`` does not squeeze single-field views
-----------------------------------------------------------------------------------
Previously ``structured_to_unstructured(arr[['a']])`` would produce a squeezed
result inconsistent with ``structured_to_unstructured(arr[['a', b']])``. This
was accidental. The old behavior can be retained with
``structured_to_unstructured(arr[['a']]).squeeze(axis=-1)`` or far more simply,
``arr['a']``.

`clip` now uses a ufunc under the hood
--------------------------------------
This means that registering clip functions for custom dtypes in C via
``descr->f->fastclip`` is deprecated - they should use the ufunc registration
mechanism instead, attaching to the ``np.core.umath.clip`` ufunc.

It also means that ``clip`` accepts ``where`` and ``casting`` arguments,
and can be override with ``__array_ufunc__``.

A consequence of this change is that some behaviors of the old ``clip`` have
been deprecated:

* Passing ``nan`` to mean "do not clip" as one or both bounds. This didn't work
in all cases anyway, and can be better handled by passing infinities of the
appropriate sign.
* Using "unsafe" casting by default when an ``out`` argument is passed. Using
``casting="unsafe"`` explicitly will silence this warning.

Additionally, there are some corner cases with behavior changes:

* Padding ``max < min`` has changed to be more consistent across dtypes, but
should not be relied upon.
* Scalar ``min`` and ``max`` take part in promotion rules like they do in all
other ufuncs.

``__array_interface__`` offset now works as documented
------------------------------------------------------
The interface may use an ``offset`` value that was mistakenly ignored.

Pickle protocol in `savez` set to 3 for ``force zip64`` flag
-----------------------------------------------------------------
`savez` was not using the ``force_zip64`` flag, which limited the size of
the archive to 2GB. But using the flag requires us to use pickle protocol 3 to
write ``object`` arrays. The protocol used was bumped to 3, meaning the archive
will be unreadable by Python2.

Structured arrays indexed with non-existent fields raise ``KeyError`` not ``ValueError``
----------------------------------------------------------------------------------------
``arr['bad_field']`` on a structured type raises ``KeyError``, for consistency
with ``dict['bad_field']``.



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

Links

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

[pyup-bot]

Closing this in favor of #212