=========================
NumPy 1.9.0 Release Notes
=========================

This release supports Python 2.6 - 2.7 and 3.2 - 3.4.


Highlights
==========
* Numerous performance improvements in various areas, most notably indexing and
  operations on small arrays are significantly faster.
  Indexing operations now also release the GIL.
* Addition of `nanmedian` and `nanpercentile` rounds out the nanfunction set.


Dropped Support
===============

* The oldnumeric and numarray modules have been removed.
* The doc/pyrex and doc/cython directories have been removed.
* The doc/numpybook directory has been removed.
* The numpy/testing/numpytest.py file has been removed together with
  the importall function it contained.


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

* The numpy/polynomial/polytemplate.py file will be removed in NumPy 1.10.0.
* Default casting for inplace operations will change to 'same_kind' in
  Numpy 1.10.0. This will certainly break some code that is currently
  ignoring the warning.
* Relaxed stride checking will be the default in 1.10.0
* String version checks will break because, e.g., '1.9' > '1.10' is True. A
  NumpyVersion class has been added that can be used for such comparisons.
* The diagonal and diag functions will return writeable views in 1.10.0
* The `S` and/or `a` dtypes may be changed to represent Python strings
  instead of bytes, in Python 3 these two types are very different.


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

The diagonal and diag functions return readonly views.
------------------------------------------------------
In NumPy 1.8, the diagonal and diag functions returned readonly copies, in
NumPy 1.9 they return readonly views, and in 1.10 they will return writeable
views.

Special scalar float values don't cause upcast to double anymore
----------------------------------------------------------------
In previous numpy versions operations involving floating point scalars
containing special values ``NaN``, ``Inf`` and ``-Inf`` caused the result
type to be at least ``float64``.  As the special values can be represented
in the smallest available floating point type, the upcast is not performed
anymore.

For example the dtype of:

    ``np.array([1.], dtype=np.float32) * float('nan')``

now remains ``float32`` instead of being cast to ``float64``.
Operations involving non-special values have not been changed.

Percentile output changes
-------------------------
If given more than one percentile to compute numpy.percentile returns an
array instead of a list. A single percentile still returns a scalar.  The
array is equivalent to converting the list returned in older versions
to an array via ``np.array``.

If the ``overwrite_input`` option is used the input is only partially
instead of fully sorted.

ndarray.tofile exception type
-----------------------------
All ``tofile`` exceptions are now ``IOError``, some were previously
``ValueError``.

Invalid fill value exceptions
-----------------------------
Two changes to numpy.ma.core._check_fill_value:

* When the fill value is a string and the array type is not one of
  'OSUV', TypeError is raised instead of the default fill value being used.

* When the fill value overflows the array type, TypeError is raised instead
  of OverflowError.

Polynomial Classes no longer derived from PolyBase
--------------------------------------------------
This may cause problems with folks who depended on the polynomial classes
being derived from PolyBase. They are now all derived from the abstract
base class ABCPolyBase. Strictly speaking, there should be a deprecation
involved, but no external code making use of the old baseclass could be
found.

Using numpy.random.binomial may change the RNG state vs. numpy < 1.9
--------------------------------------------------------------------
A bug in one of the algorithms to generate a binomial random variate has
been fixed. This change will likely alter the number of random draws
performed, and hence the sequence location will be different after a
call to distribution.c::rk_binomial_btpe. Any tests which rely on the RNG
being in a known state should be checked and/or updated as a result.

Random seed enforced to be a 32 bit unsigned integer
----------------------------------------------------
``np.random.seed`` and ``np.random.RandomState`` now throw a ``ValueError``
if the seed cannot safely be converted to 32 bit unsigned integers.
Applications that now fail can be fixed by masking the higher 32 bit values to
zero: ``seed = seed & 0xFFFFFFFF``. This is what is done silently in older
versions so the random stream remains the same.

Argmin and argmax out argument
------------------------------
The ``out`` argument to ``np.argmin`` and ``np.argmax`` and their
equivalent C-API functions is now checked to match the desired output shape
exactly.  If the check fails a ``ValueError`` instead of ``TypeError`` is
raised.

Einsum
------
Remove unnecessary broadcasting notation restrictions.
``np.einsum('ijk,j->ijk', A, B)`` can also be written as
``np.einsum('ij...,j->ij...', A, B)`` (ellipsis is no longer required on 'j')

Indexing
--------

The NumPy indexing has seen a complete rewrite in this version. This makes
most advanced integer indexing operations much faster and should have no
other implications.  However some subtle changes and deprecations were
introduced in advanced indexing operations:

* Boolean indexing into scalar arrays will always return a new 1-d array.
  This means that ``array(1)[array(True)]`` gives ``array([1])`` and
  not the original array.

* Advanced indexing into one dimensional arrays used to have
  (undocumented) special handling regarding repeating the value array in
  assignments when the shape of the value array was too small or did not
  match.  Code using this will raise an error. For compatibility you can
  use ``arr.flat[index] = values``, which uses the old code branch.  (for
  example ``a = np.ones(10); a[np.arange(10)] = [1, 2, 3]``)

* The iteration order over advanced indexes used to be always C-order.
  In NumPy 1.9. the iteration order adapts to the inputs and is not
  guaranteed (with the exception of a *single* advanced index which is
  never reversed for compatibility reasons). This means that the result
  is undefined if multiple values are assigned to the same element.  An
  example for this is ``arr[[0, 0], [1, 1]] = [1, 2]``, which may set
  ``arr[0, 1]`` to either 1 or 2.

* Equivalent to the iteration order, the memory layout of the advanced
  indexing result is adapted for faster indexing and cannot be predicted.

* All indexing operations return a view or a copy. No indexing operation
  will return the original array object. (For example ``arr[...]``)

* In the future Boolean array-likes (such as lists of python bools) will
  always be treated as Boolean indexes and Boolean scalars (including
  python ``True``) will be a legal *boolean* index. At this time, this is
  already the case for scalar arrays to allow the general
  ``positive = a[a > 0]`` to work when ``a`` is zero dimensional.

* In NumPy 1.8 it was possible to use ``array(True)`` and
  ``array(False)`` equivalent to 1 and 0 if the result of the operation
  was a scalar.  This will raise an error in NumPy 1.9 and, as noted
  above, treated as a boolean index in the future.

* All non-integer array-likes are deprecated, object arrays of custom
  integer like objects may have to be cast explicitly.

* The error reporting for advanced indexing is more informative, however
  the error type has changed in some cases. (Broadcasting errors of
  indexing arrays are reported as ``IndexError``)

* Indexing with more then one ellipsis (``...``) is deprecated.

Non-integer reduction axis indexes are deprecated
-------------------------------------------------
Non-integer axis indexes to reduction ufuncs like `add.reduce` or `sum` are
deprecated.

``promote_types`` and string dtype
----------------------------------
``promote_types`` function now returns a valid string length when given an
integer or float dtype as one argument and a string dtype as another
argument.  Previously it always returned the input string dtype, even if it
wasn't long enough to store the max integer/float value converted to a
string.

``can_cast`` and string dtype
-----------------------------
``can_cast`` function now returns False in "safe" casting mode for
integer/float dtype and string dtype if the string dtype length is not long
enough to store the max integer/float value converted to a string.
Previously ``can_cast`` in "safe" mode returned True for integer/float
dtype and a string dtype of any length.

astype and string dtype
-----------------------
The ``astype`` method now returns an error if the string dtype to cast to
is not long enough in "safe" casting mode to hold the max value of
integer/float array that is being casted. Previously the casting was
allowed even if the result was truncated.

`npyio.recfromcsv` keyword arguments change
-------------------------------------------
`npyio.recfromcsv` no longer accepts the undocumented `update` keyword,
which used to override the `dtype` keyword.

The ``doc/swig`` directory moved
--------------------------------
The ``doc/swig`` directory has been moved to ``tools/swig``.

The ``npy_3kcompat.h`` header changed
-------------------------------------
The unused ``simple_capsule_dtor`` function has been removed from
``npy_3kcompat.h``.  Note that this header is not meant to be used outside
of numpy; other projects should be using their own copy of this file when
needed.

Negative indices in C-Api ``sq_item`` and ``sq_ass_item`` sequence methods
--------------------------------------------------------------------------
When directly accessing the ``sq_item`` or ``sq_ass_item`` PyObject slots
for item getting, negative indices will not be supported anymore.
``PySequence_GetItem`` and ``PySequence_SetItem`` however fix negative
indices so that they can be used there.

NDIter
------
When ``NpyIter_RemoveAxis`` is now called, the iterator range will be reset.

When a multi index is being tracked and an iterator is not buffered, it is
possible to use ``NpyIter_RemoveAxis``. In this case an iterator can shrink
in size. Because the total size of an iterator is limited, the iterator
may be too large before these calls. In this case its size will be set to ``-1``
and an error issued not at construction time but when removing the multi
index, setting the iterator range, or getting the next function.

This has no effect on currently working code, but highlights the necessity
of checking for an error return if these conditions can occur. In most
cases the arrays being iterated are as large as the iterator so that such
a problem cannot occur.

This change was already applied to the 1.8.1 release.

``zeros_like`` for string dtypes now returns empty strings
----------------------------------------------------------
To match the `zeros` function `zeros_like` now returns an array initialized
with empty strings instead of an array filled with `'0'`.


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

Percentile supports more interpolation options
----------------------------------------------
``np.percentile`` now has the interpolation keyword argument to specify in
which way points should be interpolated if the percentiles fall between two
values.  See the documentation for the available options.

Generalized axis support for median and percentile
--------------------------------------------------
``np.median`` and ``np.percentile`` now support generalized axis arguments like
ufunc reductions do since 1.7. One can now say axis=(index, index) to pick a
list of axes for the reduction. The ``keepdims`` keyword argument was also
added to allow convenient broadcasting to arrays of the original shape.

Dtype parameter added to ``np.linspace`` and ``np.logspace``
------------------------------------------------------------
The returned data type from the ``linspace`` and ``logspace`` functions can
now be specified using the dtype parameter.

More general ``np.triu`` and ``np.tril`` broadcasting
-----------------------------------------------------
For arrays with ``ndim`` exceeding 2, these functions will now apply to the
final two axes instead of raising an exception.

``tobytes`` alias for ``tostring`` method
-----------------------------------------
``ndarray.tobytes`` and ``MaskedArray.tobytes`` have been added as aliases
for ``tostring`` which exports arrays as ``bytes``. This is more consistent
in Python 3 where ``str`` and ``bytes`` are not the same.

Build system
------------
Added experimental support for the ppc64le and OpenRISC architecture.

Compatibility to python ``numbers`` module
------------------------------------------
All numerical numpy types are now registered with the type hierarchy in
the python ``numbers`` module.

``increasing`` parameter added to ``np.vander``
-----------------------------------------------
The ordering of the columns of the Vandermonde matrix can be specified with
this new boolean argument.

``unique_counts`` parameter added to ``np.unique``
--------------------------------------------------
The number of times each unique item comes up in the input can now be
obtained as an optional return value.

Support for median and percentile in nanfunctions
-------------------------------------------------
The ``np.nanmedian`` and ``np.nanpercentile`` functions behave like
the median and percentile functions except that NaNs are ignored.

NumpyVersion class added
------------------------
The class may be imported from numpy.lib and can be used for version
comparison when the numpy version goes to 1.10.devel. For example::

    >>> from numpy.lib import NumpyVersion
    >>> if NumpyVersion(np.__version__) < '1.10.0'):
    ...     print('Wow, that is an old NumPy version!')

Allow saving arrays with large number of named columns
------------------------------------------------------
The numpy storage format 1.0 only allowed the array header to have a total size
of 65535 bytes. This can be exceeded by structured arrays with a large number
of columns. A new format 2.0 has been added which extends the header size to 4
GiB. `np.save` will automatically save in 2.0 format if the data requires it,
else it will always use the more compatible 1.0 format.

Full broadcasting support for ``np.cross``
------------------------------------------
``np.cross`` now properly broadcasts its two input arrays, even if they
have different number of dimensions. In earlier versions this would result
in either an error being raised, or wrong results computed.


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

Better numerical stability for sum in some cases
------------------------------------------------
Pairwise summation is now used in the sum method, but only along the fast
axis and for groups of the values <= 8192 in length. This should also
improve the accuracy of var and std in some common cases.

Percentile implemented in terms of ``np.partition``
---------------------------------------------------
``np.percentile`` has been implemented in terms of ``np.partition`` which
only partially sorts the data via a selection algorithm. This improves the
time complexity from ``O(nlog(n))`` to ``O(n)``.

Performance improvement for ``np.array``
----------------------------------------
The performance of converting lists containing arrays to arrays using
``np.array`` has been improved. It is now equivalent in speed to
``np.vstack(list)``.

Performance improvement for ``np.searchsorted``
-----------------------------------------------
For the built-in numeric types, ``np.searchsorted`` no longer relies on the
data type's ``compare`` function to perform the search, but is now
implemented by type specific functions. Depending on the size of the
inputs, this can result in performance improvements over 2x.

Optional reduced verbosity for np.distutils
-------------------------------------------
Set ``numpy.distutils.system_info.system_info.verbosity = 0`` and then
calls to ``numpy.distutils.system_info.get_info('blas_opt')`` will not
print anything on the output. This is mostly for other packages using
numpy.distutils.

Covariance check in ``np.random.multivariate_normal``
-----------------------------------------------------
A ``RuntimeWarning`` warning is raised when the covariance matrix is not
positive-semidefinite.

Polynomial Classes no longer template based
-------------------------------------------
The polynomial classes have been refactored to use an abstract base class
rather than a template in order to implement a common interface. This makes
importing the polynomial package faster as the classes do not need to be
compiled on import.

More GIL releases
-----------------
Several more functions now release the Global Interpreter Lock allowing more
efficient parallelization using the ``threading`` module. Most notably the GIL is
now released for fancy indexing, ``np.where`` and the ``random`` module now
uses a per-state lock instead of the GIL.

MaskedArray support for more complicated base classes
-----------------------------------------------------
Built-in assumptions that the baseclass behaved like a plain array are being
removed. In particalur, ``repr`` and ``str`` should now work more reliably.


C-API
-----


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

Non-integer scalars for sequence repetition
-------------------------------------------
Using non-integer numpy scalars to repeat python sequences is deprecated.
For example ``np.float_(2) * [1]`` will be an error in the future.

``select`` input deprecations
-----------------------------
The integer and empty input to ``select`` is deprecated. In the future only
boolean arrays will be valid conditions and an empty ``condlist`` will be
considered an input error instead of returning the default.

``rank`` function
-----------------
The ``rank`` function has been deprecated to avoid confusion with
``numpy.linalg.matrix_rank``.

Object array equality comparisons
---------------------------------
In the future object array comparisons both `==` and `np.equal` will not
make use of identity checks anymore. For example:

>>> a = np.array([np.array([1, 2, 3]), 1])
>>> b = np.array([np.array([1, 2, 3]), 1])
>>> a == b

will consistently return False (and in the future an error) even if the array
in `a` and `b` was the same object.

The equality operator `==` will in the future raise errors like `np.equal`
if broadcasting or element comparisons, etc. fails.

Comparison with `arr == None` will in the future do an elementwise comparison
instead of just returning False. Code should be using `arr is None`.

All of these changes will give Deprecation- or FutureWarnings at this time.

C-API
-----

The utility function npy_PyFile_Dup and npy_PyFile_DupClose are broken by the
internal buffering python 3 applies to its file objects.
To fix this two new functions npy_PyFile_Dup2 and npy_PyFile_DupClose2 are
declared in npy_3kcompat.h and the old functions are deprecated.
Due to the fragile nature of these functions it is recommended to instead use
the python API when possible.

This change was already applied to the 1.8.1 release.