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)]
givesarray([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 examplea = 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 setarr[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 generalpositive = a[a > 0]
to work whena
is zero dimensional.In NumPy 1.8 it was possible to use
array(True)
andarray(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 particular, 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.