==========================
NumPy 1.11.0 Release Notes
==========================
This release supports Python 2.6 - 2.7 and 3.2 - 3.5 and contains a number
of enhancements and improvements. Note also the build system changes listed
below as they may have subtle effects.
No Windows (TM) binaries are provided for this release due to a broken
toolchain. One of the providers of Python packages for Windows (TM) is your
best bet.
Highlights
==========
Details of these improvements can be found below.
* The datetime64 type is now timezone naive.
* A dtype parameter has been added to ``randint``.
* Improved detection of two arrays possibly sharing memory.
* Automatic bin size estimation for ``np.histogram``.
* Speed optimization of A @ A.T and dot(A, A.T).
* New function ``np.moveaxis`` for reordering array axes.
Build System Changes
====================
* Numpy now uses ``setuptools`` for its builds instead of plain distutils.
This fixes usage of ``install_requires='numpy'`` in the ``setup.py`` files of
projects that depend on Numpy (see gh-6551). It potentially affects the way
that build/install methods for Numpy itself behave though. Please report any
unexpected behavior on the Numpy issue tracker.
* Bento build support and related files have been removed.
* Single file build support and related files have been removed.
Future Changes
==============
The following changes are scheduled for Numpy 1.12.0.
* Support for Python 2.6, 3.2, and 3.3 will be dropped.
* Relaxed stride checking will become the default. See the 1.8.0 release
notes for a more extended discussion of what this change implies.
* The behavior of the datetime64 "not a time" (NaT) value will be changed
to match that of floating point "not a number" (NaN) values: all
comparisons involving NaT will return False, except for NaT != NaT which
will return True.
* Indexing with floats will raise IndexError,
e.g., a[0, 0.0].
* Indexing with non-integer array_like will raise ``IndexError``,
e.g., ``a['1', '2']``
* Indexing with multiple ellipsis will raise ``IndexError``,
e.g., ``a[..., ...]``.
* Non-integers used as index values will raise ``TypeError``,
e.g., in ``reshape``, ``take``, and specifying reduce axis.
In a future release the following changes will be made.
* The ``rand`` function exposed in ``numpy.testing`` will be removed. That
function is left over from early Numpy and was implemented using the
Python random module. The random number generators from ``numpy.random``
should be used instead.
* The ``ndarray.view`` method will only allow c_contiguous arrays to be
viewed using a dtype of different size causing the last dimension to
change. That differs from the current behavior where arrays that are
f_contiguous but not c_contiguous can be viewed as a dtype type of
different size causing the first dimension to change.
* Slicing a ``MaskedArray`` will return views of both data **and** mask.
Currently the mask is copy-on-write and changes to the mask in the slice do
not propagate to the original mask. See the FutureWarnings section below for
details.
Compatibility notes
===================
datetime64 changes
------------------
In prior versions of NumPy the experimental datetime64 type always stored
times in UTC. By default, creating a datetime64 object from a string or
printing it would convert from or to local time::
# old behavior
>>>> np.datetime64('2000-01-01T00:00:00')
numpy.datetime64('2000-01-01T00:00:00-0800') # note the timezone offset -08:00
A consensus of datetime64 users agreed that this behavior is undesirable
and at odds with how datetime64 is usually used (e.g., by `pandas
`__). For most use cases, a timezone naive datetime
type is preferred, similar to the ``datetime.datetime`` type in the Python
standard library. Accordingly, datetime64 no longer assumes that input is in
local time, nor does it print local times::
>>>> np.datetime64('2000-01-01T00:00:00')
numpy.datetime64('2000-01-01T00:00:00')
For backwards compatibility, datetime64 still parses timezone offsets, which
it handles by converting to UTC. However, the resulting datetime is timezone
naive::
>>> np.datetime64('2000-01-01T00:00:00-08')
DeprecationWarning: parsing timezone aware datetimes is deprecated;
this will raise an error in the future
numpy.datetime64('2000-01-01T08:00:00')
As a corollary to this change, we no longer prohibit casting between datetimes
with date units and datetimes with time units. With timezone naive datetimes,
the rule for casting from dates to times is no longer ambiguous.
``linalg.norm`` return type changes
-----------------------------------
The return type of the ``linalg.norm`` function is now floating point without
exception. Some of the norm types previously returned integers.
polynomial fit changes
----------------------
The various fit functions in the numpy polynomial package no longer accept
non-integers for degree specification.
*np.dot* now raises ``TypeError`` instead of ``ValueError``
-----------------------------------------------------------
This behaviour mimics that of other functions such as ``np.inner``. If the two
arguments cannot be cast to a common type, it could have raised a ``TypeError``
or ``ValueError`` depending on their order. Now, ``np.dot`` will now always
raise a ``TypeError``.
FutureWarning to changed behavior
---------------------------------
* In ``np.lib.split`` an empty array in the result always had dimension
``(0,)`` no matter the dimensions of the array being split. This
has been changed so that the dimensions will be preserved. A
``FutureWarning`` for this change has been in place since Numpy 1.9 but,
due to a bug, sometimes no warning was raised and the dimensions were
already preserved.
``%`` and ``//`` operators
--------------------------
These operators are implemented with the ``remainder`` and ``floor_divide``
functions respectively. Those functions are now based around ``fmod`` and are
computed together so as to be compatible with each other and with the Python
versions for float types. The results should be marginally more accurate or
outright bug fixes compared to the previous results, but they may
differ significantly in cases where roundoff makes a difference in the integer
returned by ``floor_divide``. Some corner cases also change, for instance, NaN
is always returned for both functions when the divisor is zero,
``divmod(1.0, inf)`` returns ``(0.0, 1.0)`` except on MSVC 2008, and
``divmod(-1.0, inf)`` returns ``(-1.0, inf)``.
C API
-----
Removed the ``check_return`` and ``inner_loop_selector`` members of
the ``PyUFuncObject`` struct (replacing them with ``reserved`` slots
to preserve struct layout). These were never used for anything, so
it's unlikely that any third-party code is using them either, but we
mention it here for completeness.
object dtype detection for old-style classes
--------------------------------------------
In python 2, objects which are instances of old-style user-defined classes no
longer automatically count as 'object' type in the dtype-detection handler.
Instead, as in python 3, they may potentially count as sequences, but only if
they define both a `__len__` and a `__getitem__` method. This fixes a segfault
and inconsistency between python 2 and 3.
New Features
============
* ``np.histogram`` now provides plugin estimators for automatically
estimating the optimal number of bins. Passing one of ['auto', 'fd',
'scott', 'rice', 'sturges'] as the argument to 'bins' results in the
corresponding estimator being used.
* A benchmark suite using `Airspeed Velocity
`__ has been added, converting the
previous vbench-based one. You can run the suite locally via ``python
runtests.py --bench``. For more details, see ``benchmarks/README.rst``.
* A new function ``np.shares_memory`` that can check exactly whether two
arrays have memory overlap is added. ``np.may_share_memory`` also now has
an option to spend more effort to reduce false positives.
* ``SkipTest`` and ``KnownFailureException`` exception classes are exposed
in the ``numpy.testing`` namespace. Raise them in a test function to mark
the test to be skipped or mark it as a known failure, respectively.
* ``f2py.compile`` has a new ``extension`` keyword parameter that allows the
fortran extension to be specified for generated temp files. For instance,
the files can be specifies to be ``*.f90``. The ``verbose`` argument is
also activated, it was previously ignored.
* A ``dtype`` parameter has been added to ``np.random.randint``
Random ndarrays of the following types can now be generated:
- ``np.bool``,
- ``np.int8``, ``np.uint8``,
- ``np.int16``, ``np.uint16``,
- ``np.int32``, ``np.uint32``,
- ``np.int64``, ``np.uint64``,
- ``np.int_ ``, ``np.intp``
The specification is by precision rather than by C type. Hence, on some
platforms ``np.int64`` may be a ``long`` instead of ``long long`` even if
the specified dtype is ``long long`` because the two may have the same
precision. The resulting type depends on which C type numpy uses for the
given precision. The byteorder specification is also ignored, the
generated arrays are always in native byte order.
* A new ``np.moveaxis`` function allows for moving one or more array axes
to a new position by explicitly providing source and destination axes.
This function should be easier to use than the current ``rollaxis``
function as well as providing more functionality.
* The ``deg`` parameter of the various ``numpy.polynomial`` fits has been
extended to accept a list of the degrees of the terms to be included in
the fit, the coefficients of all other terms being constrained to zero.
The change is backward compatible, passing a scalar ``deg`` will behave
as before.
* A divmod function for float types modeled after the Python version has
been added to the npy_math library.
Improvements
============
``np.gradient`` now supports an ``axis`` argument
-------------------------------------------------
The ``axis`` parameter was added to ``np.gradient`` for consistency. It
allows to specify over which axes the gradient is calculated.
``np.lexsort`` now supports arrays with object data-type
--------------------------------------------------------
The function now internally calls the generic ``npy_amergesort`` when the
type does not implement a merge-sort kind of ``argsort`` method.
``np.ma.core.MaskedArray`` now supports an ``order`` argument
-------------------------------------------------------------
When constructing a new ``MaskedArray`` instance, it can be configured with
an ``order`` argument analogous to the one when calling ``np.ndarray``. The
addition of this argument allows for the proper processing of an ``order``
argument in several MaskedArray-related utility functions such as
``np.ma.core.array`` and ``np.ma.core.asarray``.
Memory and speed improvements for masked arrays
-----------------------------------------------
Creating a masked array with ``mask=True`` (resp. ``mask=False``) now uses
``np.ones`` (resp. ``np.zeros``) to create the mask, which is faster and
avoid a big memory peak. Another optimization was done to avoid a memory
peak and useless computations when printing a masked array.
``ndarray.tofile`` now uses fallocate on linux
----------------------------------------------
The function now uses the fallocate system call to reserve sufficient
disk space on file systems that support it.
Optimizations for operations of the form ``A.T @ A`` and ``A @ A.T``
--------------------------------------------------------------------
Previously, ``gemm`` BLAS operations were used for all matrix products. Now,
if the matrix product is between a matrix and its transpose, it will use
``syrk`` BLAS operations for a performance boost. This optimization has been
extended to ``@``, ``numpy.dot``, ``numpy.inner``, and ``numpy.matmul``.
**Note:** Requires the transposed and non-transposed matrices to share data.
``np.testing.assert_warns`` can now be used as a context manager
----------------------------------------------------------------
This matches the behavior of ``assert_raises``.
Speed improvement for np.random.shuffle
---------------------------------------
``np.random.shuffle`` is now much faster for 1d ndarrays.
Changes
=======
Pyrex support was removed from ``numpy.distutils``
--------------------------------------------------
The method ``build_src.generate_a_pyrex_source`` will remain available; it
has been monkeypatched by users to support Cython instead of Pyrex. It's
recommended to switch to a better supported method of build Cython
extensions though.
``np.broadcast`` can now be called with a single argument
---------------------------------------------------------
The resulting object in that case will simply mimic iteration over
a single array. This change obsoletes distinctions like
if len(x) == 1:
shape = x[0].shape
else:
shape = np.broadcast(\*x).shape
Instead, ``np.broadcast`` can be used in all cases.
``np.trace`` now respects array subclasses
------------------------------------------
This behaviour mimics that of other functions such as ``np.diagonal`` and
ensures, e.g., that for masked arrays ``np.trace(ma)`` and ``ma.trace()`` give
the same result.
``np.dot`` now raises ``TypeError`` instead of ``ValueError``
-------------------------------------------------------------
This behaviour mimics that of other functions such as ``np.inner``. If the two
arguments cannot be cast to a common type, it could have raised a ``TypeError``
or ``ValueError`` depending on their order. Now, ``np.dot`` will now always
raise a ``TypeError``.
``linalg.norm`` return type changes
-----------------------------------
The ``linalg.norm`` function now does all its computations in floating point
and returns floating results. This change fixes bugs due to integer overflow
and the failure of abs with signed integers of minimum value, e.g., int8(-128).
For consistency, floats are used even where an integer might work.
Deprecations
============
Views of arrays in Fortran order
--------------------------------
The F_CONTIGUOUS flag was used to signal that views using a dtype that
changed the element size would change the first index. This was always
problematical for arrays that were both F_CONTIGUOUS and C_CONTIGUOUS
because C_CONTIGUOUS took precedence. Relaxed stride checking results in
more such dual contiguous arrays and breaks some existing code as a result.
Note that this also affects changing the dtype by assigning to the dtype
attribute of an array. The aim of this deprecation is to restrict views to
C_CONTIGUOUS arrays at some future time. A work around that is backward
compatible is to use ``a.T.view(...).T`` instead. A parameter may also be
added to the view method to explicitly ask for Fortran order views, but
that will not be backward compatible.
Invalid arguments for array ordering
------------------------------------
It is currently possible to pass in arguments for the ``order``
parameter in methods like ``array.flatten`` or ``array.ravel``
that were not one of the following: 'C', 'F', 'A', 'K' (note that
all of these possible values are both unicode and case insensitive).
Such behavior will not be allowed in future releases.
Random number generator in the ``testing`` namespace
----------------------------------------------------
The Python standard library random number generator was previously exposed
in the ``testing`` namespace as ``testing.rand``. Using this generator is
not recommended and it will be removed in a future release. Use generators
from ``numpy.random`` namespace instead.
Random integer generation on a closed interval
----------------------------------------------
In accordance with the Python C API, which gives preference to the half-open
interval over the closed one, ``np.random.random_integers`` is being
deprecated in favor of calling ``np.random.randint``, which has been
enhanced with the ``dtype`` parameter as described under "New Features".
However, ``np.random.random_integers`` will not be removed anytime soon.
FutureWarnings
==============
Assigning to slices/views of ``MaskedArray``
--------------------------------------------
Currently a slice of a masked array contains a view of the original data and a
copy-on-write view of the mask. Consequently, any changes to the slice's mask
will result in a copy of the original mask being made and that new mask being
changed rather than the original. For example, if we make a slice of the
original like so, ``view = original[:]``, then modifications to the data in one
array will affect the data of the other but, because the mask will be copied
during assignment operations, changes to the mask will remain local. A similar
situation occurs when explicitly constructing a masked array using
``MaskedArray(data, mask)``, the returned array will contain a view of ``data``
but the mask will be a copy-on-write view of ``mask``.
In the future, these cases will be normalized so that the data and mask arrays
are treated the same way and modifications to either will propagate between
views. In 1.11, numpy will issue a ``MaskedArrayFutureWarning`` warning
whenever user code modifies the mask of a view that in the future may cause
values to propagate back to the original. To silence these warnings and make
your code robust against the upcoming changes, you have two options: if you
want to keep the current behavior, call ``masked_view.unshare_mask()`` before
modifying the mask. If you want to get the future behavior early, use
``masked_view._sharedmask = False``. However, note that setting the
``_sharedmask`` attribute will break following explicit calls to
``masked_view.unshare_mask()``.