[SciPy-Dev] Numpy 1.10.0 release

[Charles R Harris]

Hi All,

It is my pleasure to release NumPy 1.10.0. Files may be found at Sourceforge
<http://sourceforge.net/projects/numpy/files/NumPy/1.10.0/> and pypi
<https://pypi.python.org/pypi?%3Aaction=pkg_edit&name=numpy>. This release
is the result of 789 non-merge commits made by 160 developers over a period
of a year and supports Python 2.6 - 2.7 and 3.2 - 3.5.

NumPy 1.10.0 Release Notes
**************************

This release supports Python 2.6 - 2.7 and 3.2 - 3.5.


Highlights
==========
* numpy.distutils now supports parallel compilation via the --parallel/-j
  argument passed to setup.py build
* numpy.distutils now supports additional customization via site.cfg to
  control compilation parameters, i.e. runtime libraries, extra
  linking/compilation flags.
* Addition of *np.linalg.multi_dot*: compute the dot product of two or more
  arrays in a single function call, while automatically selecting the
fastest
  evaluation order.
* The new function `np.stack` provides a general interface for joining a
  sequence of arrays along a new axis, complementing `np.concatenate` for
  joining along an existing axis.
* Addition of `nanprod` to the set of nanfunctions.
* Support for the '@' operator in Python 3.5.

Dropped Support:

* The _dotblas module has been removed. CBLAS Support is now in
  Multiarray.
* The testcalcs.py file has been removed.
* The polytemplate.py file has been removed.
* npy_PyFile_Dup and npy_PyFile_DupClose have been removed from
  npy_3kcompat.h.
* splitcmdline has been removed from numpy/distutils/exec_command.py.
* try_run and get_output have been removed from
  numpy/distutils/command/config.py
* The a._format attribute is no longer supported for array printing.
* Keywords ``skiprows`` and ``missing`` removed from np.genfromtxt.
* Keyword ``old_behavior`` removed from np.correlate.

Future Changes:

* In array comparisons like ``arr1 == arr2``, many corner cases
  involving strings or structured dtypes that used to return scalars
  now issue ``FutureWarning`` or ``DeprecationWarning``, and in the
  future will be change to either perform elementwise comparisons or
  raise an error.
* The SafeEval class will be removed.
* The alterdot and restoredot functions will be removed.

See below for more details on these changes.

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

numpy version string
~~~~~~~~~~~~~~~~~~~~
The numpy version string for development builds has been changed from
``x.y.z.dev-githash`` to ``x.y.z.dev0+githash`` (note the +) in order to
comply
with PEP 440.

relaxed stride checking
~~~~~~~~~~~~~~~~~~~~~~~
NPY_RELAXED_STRIDE_CHECKING is now true by default.

Concatenation of 1d arrays along any but ``axis=0`` raises ``IndexError``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Using axis != 0 has raised a DeprecationWarning since NumPy 1.7, it now
raises an error.

*np.ravel*, *np.diagonal* and *np.diag* now preserve subtypes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
There was inconsistent behavior between *x.ravel()* and *np.ravel(x)*, as
well as between *x.diagonal()* and *np.diagonal(x)*, with the methods
preserving subtypes while the functions did not. This has been fixed and
the functions now behave like the methods, preserving subtypes except in
the case of matrices.  Matrices are special cased for backward
compatibility and still return 1-D arrays as before. If you need to
preserve the matrix subtype, use the methods instead of the functions.

*rollaxis* and *swapaxes* always return a view
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Previously, a view was returned except when no change was made in the order
of the axes, in which case the input array was returned.  A view is now
returned in all cases.

*nonzero* now returns base ndarrays
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Previously, an inconsistency existed between 1-D inputs (returning a
base ndarray) and higher dimensional ones (which preserved subclasses).
Behavior has been unified, and the return will now be a base ndarray.
Subclasses can still override this behavior by providing their own
*nonzero* method.

C API
~~~~~
The changes to *swapaxes* also apply to the *PyArray_SwapAxes* C function,
which now returns a view in all cases.

The changes to *nonzero* also apply to the *PyArray_Nonzero* C function,
which now returns a base ndarray in all cases.

The dtype structure (PyArray_Descr) has a new member at the end to cache
its hash value.  This shouldn't affect any well-written applications.

The change to the concatenation function DeprecationWarning also affects
PyArray_ConcatenateArrays,

recarray field return types
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Previously the returned types for recarray fields accessed by attribute and
by
index were inconsistent, and fields of string type were returned as
chararrays.
Now, fields accessed by either attribute or indexing will return an ndarray
for
fields of non-structured type, and a recarray for fields of structured type.
Notably, this affect recarrays containing strings with whitespace, as
trailing
whitespace is trimmed from chararrays but kept in ndarrays of string type.
Also, the dtype.type of nested structured fields is now inherited.

recarray views
~~~~~~~~~~~~~~
Viewing an ndarray as a recarray now automatically converts the dtype to
np.record. See new record array documentation. Additionally, viewing a
recarray
with a non-structured dtype no longer converts the result's type to ndarray
-
the result will remain a recarray.

'out' keyword argument of ufuncs now accepts tuples of arrays
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When using the 'out' keyword argument of a ufunc, a tuple of arrays, one per
ufunc output, can be provided. For ufuncs with a single output a single
array
is also a valid 'out' keyword argument. Previously a single array could be
provided in the 'out' keyword argument, and it would be used as the first
output for ufuncs with multiple outputs, is deprecated, and will result in a
`DeprecationWarning` now and an error in the future.

byte-array indices now raises an IndexError
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Indexing an ndarray using a byte-string in Python 3 now raises an IndexError
instead of a ValueError.

Masked arrays containing objects with arrays
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
For such (rare) masked arrays, getting a single masked item no longer
returns a
corrupted masked array, but a fully masked version of the item.

Median warns and returns nan when invalid values are encountered
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Similar to mean, median and percentile now emits a Runtime warning and
returns `NaN` in slices where a `NaN` is present.
To compute the median or percentile while ignoring invalid values use the
new `nanmedian` or `nanpercentile` functions.

Functions available from numpy.ma.testutils have changed
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
All functions from numpy.testing were once available from
numpy.ma.testutils but not all of them were redefined to work with masked
arrays. Most of those functions have now been removed from
numpy.ma.testutils with a small subset retained in order to preserve
backward compatibility. In the long run this should help avoid mistaken use
of the wrong functions, but it may cause import problems for some.


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

Reading extra flags from site.cfg
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Previously customization of compilation of dependency libraries and numpy
itself was only accomblishable via code changes in the distutils package.
Now numpy.distutils reads in the following extra flags from each group of
the
*site.cfg*:

* ``runtime_library_dirs/rpath``, sets runtime library directories to
override
    ``LD_LIBRARY_PATH``
* ``extra_compile_args``, add extra flags to the compilation of sources
* ``extra_link_args``, add extra flags when linking libraries

This should, at least partially, complete user customization.

*np.cbrt* to compute cube root for real floats
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*np.cbrt* wraps the C99 cube root function *cbrt*.
Compared to *np.power(x, 1./3.)* it is well defined for negative real floats
and a bit faster.

numpy.distutils now allows parallel compilation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
By passing *--parallel=n* or *-j n* to *setup.py build* the compilation of
extensions is now performed in *n* parallel processes.
The parallelization is limited to files within one extension so projects
using
Cython will not profit because it builds extensions from single files.

*genfromtxt* has a new ``max_rows`` argument
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
A ``max_rows`` argument has been added to *genfromtxt* to limit the
number of rows read in a single call. Using this functionality, it is
possible to read in multiple arrays stored in a single file by making
repeated calls to the function.

New function *np.broadcast_to* for invoking array broadcasting
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*np.broadcast_to* manually broadcasts an array to a given shape according to
numpy's broadcasting rules. The functionality is similar to
broadcast_arrays,
which in fact has been rewritten to use broadcast_to internally, but only a
single array is necessary.

New context manager *clear_and_catch_warnings* for testing warnings
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When Python emits a warning, it records that this warning has been emitted
in
the module that caused the warning, in a module attribute
``__warningregistry__``.  Once this has happened, it is not possible to emit
the warning again, unless you clear the relevant entry in
``__warningregistry__``.  This makes is hard and fragile to test warnings,
because if your test comes after another that has already caused the
warning,
you will not be able to emit the warning or test it. The context manager
``clear_and_catch_warnings`` clears warnings from the module registry on
entry
and resets them on exit, meaning that warnings can be re-raised.

*cov* has new ``fweights`` and ``aweights`` arguments
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The ``fweights`` and ``aweights`` arguments add new functionality to
covariance calculations by applying two types of weighting to observation
vectors. An array of ``fweights`` indicates the number of repeats of each
observation vector, and an array of ``aweights`` provides their relative
importance or probability.

Support for the '@' operator in Python 3.5+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Python 3.5 adds support for a matrix multiplication operator '@' proposed
in PEP465. Preliminary support for that has been implemented, and an
equivalent function ``matmul`` has also been added for testing purposes and
use in earlier Python versions. The function is preliminary and the order
and number of its optional arguments can be expected to change.

New argument ``norm`` to fft functions
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The default normalization has the direct transforms unscaled and the inverse
transforms are scaled by :math:`1/n`. It is possible to obtain unitary
transforms by setting the keyword argument ``norm`` to ``"ortho"`` (default
is
`None`) so that both direct and inverse transforms will be scaled by
:math:`1/\\sqrt{n}`.


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

*np.digitize* using binary search
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*np.digitize* is now implemented in terms of *np.searchsorted*. This means
that a binary search is used to bin the values, which scales much better
for larger number of bins than the previous linear search. It also removes
the requirement for the input array to be 1-dimensional.

*np.poly* now casts integer inputs to float
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*np.poly* will now cast 1-dimensional input arrays of integer type to double
precision floating point, to prevent integer overflow when computing the
monic
polynomial. It is still possible to obtain higher precision results by
passing in an array of object type, filled e.g. with Python ints.

*np.interp* can now be used with periodic functions
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*np.interp* now has a new parameter *period* that supplies the period of the
input data *xp*. In such case, the input data is properly normalized to the
given period and one end point is added to each extremity of *xp* in order
to
close the previous and the next period cycles, resulting in the correct
interpolation behavior.

*np.pad* supports more input types for ``pad_width`` and ``constant_values``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``constant_values`` parameters now accepts NumPy arrays and float values.
NumPy arrays are supported as input for ``pad_width``, and an exception is
raised if its values are not of integral type.

*np.argmax* and *np.argmin* now support an ``out`` argument
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The ``out`` parameter was added to *np.argmax* and *np.argmin* for
consistency
with *ndarray.argmax* and *ndarray.argmin*. The new parameter behaves
exactly
as it does in those methods.

More system C99 complex functions detected and used
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
All of the functions ``in complex.h`` are now detected. There are new
fallback implementations of the following functions.

* npy_ctan,
* npy_cacos, npy_casin, npy_catan
* npy_ccosh, npy_csinh, npy_ctanh,
* npy_cacosh, npy_casinh, npy_catanh

As a result of these improvements, there will be some small changes in
returned values, especially for corner cases.

*np.loadtxt* support for the strings produced by the ``float.hex`` method
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The strings produced by ``float.hex`` look like ``0x1.921fb54442d18p+1``,
so this is not the hex used to represent unsigned integer types.

*np.isclose* properly handles minimal values of integer dtypes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In order to properly handle minimal values of integer types, *np.isclose*
will
now cast to the float dtype during comparisons. This aligns its behavior
with
what was provided by *np.allclose*.

*np.allclose* uses *np.isclose* internally.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*np.allclose* now uses *np.isclose* internally and inherits the ability to
compare NaNs as equal by setting ``equal_nan=True``. Subclasses, such as
*np.ma.MaskedArray*, are also preserved now.

*np.genfromtxt* now handles large integers correctly
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*np.genfromtxt* now correctly handles integers larger than ``2**31-1`` on
32-bit systems and larger than ``2**63-1`` on 64-bit systems (it previously
crashed with an ``OverflowError`` in these cases). Integers larger than
``2**63-1`` are converted to floating-point values.

*np.load*, *np.save* have pickle backward compatibility flags
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The functions *np.load* and *np.save* have additional keyword
arguments for controlling backward compatibility of pickled Python
objects. This enables Numpy on Python 3 to load npy files containing
object arrays that were generated on Python 2.

MaskedArray support for more complicated base classes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Built-in assumptions that the baseclass behaved like a plain array are being
removed. In particular, setting and getting elements and ranges will respect
baseclass overrides of ``__setitem__`` and ``__getitem__``, and arithmetic
will respect overrides of ``__add__``, ``__sub__``, etc.

Changes
=======

dotblas functionality moved to multiarray
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The cblas versions of dot, inner, and vdot have been integrated into
the multiarray module. In particular, vdot is now a multiarray function,
which it was not before.

stricter check of gufunc signature compliance
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Inputs to generalized universal functions are now more strictly checked
against the function's signature: all core dimensions are now required to
be present in input arrays; core dimensions with the same label must have
the exact same size; and output core dimension's must be specified, either
by a same label input core dimension or by a passed-in output array.

views returned from *np.einsum* are writeable
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Views returned by *np.einsum* will now be writeable whenever the input
array is writeable.

*np.argmin* skips NaT values
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

*np.argmin* now skips NaT values in datetime64 and timedelta64 arrays,
making it consistent with *np.min*, *np.argmax* and *np.max*.


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

Array comparisons involving strings or structured dtypes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Normally, comparison operations on arrays perform elementwise
comparisons and return arrays of booleans. But in some corner cases,
especially involving strings are structured dtypes, NumPy has
historically returned a scalar instead. For example::

  ### Current behaviour

  np.arange(2) == "foo"
  # -> False

  np.arange(2) < "foo"
  # -> True on Python 2, error on Python 3

  np.ones(2, dtype="i4,i4") == np.ones(2, dtype="i4,i4,i4")
  # -> False

Continuing work started in 1.9, in 1.10 these comparisons will now
raise ``FutureWarning`` or ``DeprecationWarning``, and in the future
they will be modified to behave more consistently with other
comparison operations, e.g.::

  ### Future behaviour

  np.arange(2) == "foo"
  # -> array([False, False])

  np.arange(2) < "foo"
  # -> error, strings and numbers are not orderable

  np.ones(2, dtype="i4,i4") == np.ones(2, dtype="i4,i4,i4")
  # -> [False, False]

SafeEval
~~~~~~~~
The SafeEval class in numpy/lib/utils.py is deprecated and will be removed
in the next release.

alterdot, restoredot
~~~~~~~~~~~~~~~~~~~~
The alterdot and restoredot functions no longer do anything, and are
deprecated.

pkgload, PackageLoader
~~~~~~~~~~~~~~~~~~~~~~
These ways of loading packages are now deprecated.

bias, ddof arguments to corrcoef
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The values for the ``bias`` and ``ddof`` arguments to the ``corrcoef``
function canceled in the division implied by the correlation coefficient and
so had no effect on the returned values.

We now deprecate these arguments to ``corrcoef`` and the masked array
version
``ma.corrcoef``.

Because we are deprecating the ``bias`` argument to ``ma.corrcoef``, we also
deprecate the use of the ``allow_masked`` argument as a positional argument,
as its position will change with the removal of ``bias``.  ``allow_masked``
will in due course become a keyword-only argument.

dtype string representation changes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Since 1.6, creating a dtype object from its string representation, e.g.
``'f4'``, would issue a deprecation warning if the size did not correspond
to an existing type, and default to creating a dtype of the default size
for the type. Starting with this release, this will now raise a
``TypeError``.

The only exception is object dtypes, where both ``'O4'`` and ``'O8'`` will
still issue a deprecation warning. This platform-dependent representation
will raise an error in the next release.

In preparation for this upcoming change, the string representation of an
object dtype, i.e. ``np.dtype(object).str``, no longer includes the item
size, i.e. will return ``'|O'`` instead of ``'|O4'`` or ``'|O8'`` as
before.


Authors
=======

This release contains work by the following people who contributed at least
one patch to this release. The names are in alphabetical order by first
name.
Names followed by a "+" contributed a patch for the first time.

Abdul Muneer+
Adam Williams+
Alan Briolat+
Alex Griffing
Alex Willmer+
Alexander Belopolsky
Alistair Muldal+
Allan Haldane+
Amir Sarabadani+
Andrea Bedini+
Andrew Dawson+
Andrew Nelson+
Antoine Pitrou+
Anton Ovchinnikov+
Antony Lee+
Behzad Nouri+
Bertrand+
Blake Griffith
Bob Poekert+
Brian Kearns+
CJ Carey
Carl Kleffner+
Chander G+
Charles Harris
Chris Hogan+
Chris Kerr
Chris Lamb+
Chris Laumann+
Christian Brodbeck+
Christian Brueffer
Christoph Gohlke
Cimarron Mittelsteadt
Daniel da Silva
Darsh P. Ranjan+
David Cournapeau
David M Fobes+
David Powell+
Didrik Pinte+
Dimas Abreu Dutra
Dmitry Zagorny+
Eric Firing
Eric Hunsberger+
Eric Martin+
Eric Moore
Eric O. LEBIGOT (EOL)+
Erik M. Bray
Ernest N. Mamikonyan+
Fei Liu+
François Magimel+
Gabor Kovacs+
Gabriel-p+
Garrett-R+
George Castillo+
Gerrit Holl+
Gert-Ludwig Ingold+
Glen Mabey+
Graham Christensen+
Greg Thomsen+
Gregory R. Lee+
Helder Cesar+
Helder Oliveira+
Henning Dickten+
Ian Henriksen+
Jaime Fernandez
James Camel+
James Salter+
Jan Schlüter+
Jarl Haggerty+
Jay Bourque
Joel Nothman+
John Kirkham+
John Tyree+
Joris Van den Bossche+
Joseph Martinot-Lagarde
Josh Warner (Mac)
Juan Luis Cano Rodríguez
Julian Taylor
Kreiswolke+
Lars Buitinck
Leonardo Donelli+
Lev Abalkin
Lev Levitsky+
Malik Woods+
Maniteja Nandana+
Marshall Farrier+
Marten van Kerkwijk
Martin Spacek
Martin Thoma+
Masud Rahman+
Matt Newville+
Mattheus Ueckermann+
Matthew Brett
Matthew Craig+
Michael Currie+
Michael Droettboom
Michele Vallisneri+
Mortada Mehyar+
Nate Jensen+
Nathaniel J. Smith
Nick Papior Andersen+
Nick Papior+
Nils Werner
Oliver Eberle+
Patrick Peglar+
Paul Jacobson
Pauli Virtanen
Peter Iannucci+
Ralf Gommers
Richard Barnes+
Ritta Narita+
Robert Johansson+
Robert LU+
Robert McGibbon+
Ryan Blakemore+
Ryan Nelson+
Sandro Tosi
Saullo Giovani+
Sebastian Berg
Sebastien Gouezel+
Simon Gibbons+
Simon Guillot+
Stefan Eng+
Stefan Otte+
Stefan van der Walt
Stephan Hoyer+
Stuart Berg+
Sturla Molden+
Thomas A Caswell+
Thomas Robitaille
Tim D. Smith+
Tom Krauss+
Tom Poole+
Toon Verstraelen+
Ulrich Seidl
Valentin Haenel
Vraj Mohan+
Warren Weckesser
Wendell Smith+
Yaroslav Halchenko
Yotam Doron
Yousef Hamza+
Yuval Langer+
Yuxiang Wang+
Zbigniew Jędrzejewski-Szmek+
cel+
chebee7i+
empeeu+
endolith
hannaro+
immerrr
jmrosen155+
jnothman
kanhua+
mbyt+
mlai+
styr+
tdihp+
wim glenn+
yolanda15+
Åsmund Hjulstad+


Enjjoy,

Chuck
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