SciPy

Release Notes

NumPy 1.12.0 Release Notes

This release supports Python 2.7 and 3.4 - 3.5.

Highlights

Dropped Support

  • Support for Python 2.6, 3.2, and 3.3 has been dropped.

Future Changes

  • In 1.13 NAT will always compare False except for NAT != NAT, which will be True. In short, NAT will behave like NaN

Compatibility notes

DeprecationWarning to error

  • Indexing with floats raises IndexError, e.g., a[0, 0.0].
  • Indexing with non-integer array_like raises IndexError, e.g., a['1', '2']
  • Indexing with multiple ellipsis raises IndexError, e.g., a[..., ...].
  • Non-integers used as index values raise TypeError, e.g., in reshape, take, and specifying reduce axis.

Relaxed stride checking is the default

This will have some impact on code that assumed that F_CONTIGUOUS and C_CONTIGUOUS were mutually exclusive and could be set to determine the default order for arrays that are now both.

MaskedArray takes view of data and mask when slicing

XXX

np.percentile ‘midpoint’ interpolation method fixed for exact indices

‘midpoint’ interpolator now gives the same result as ‘lower’ and ‘higher’ when the two coincide. Previous behavior of ‘lower’ + 0.5 is fixed.

keepdims kwarg is passed through to user-class methods

numpy functions that take a keepdims kwarg now pass the value through to the corresponding methods on ndarray sub-classes. Previously the keepdims keyword would be silently dropped. These functions now have the following behavior:

  1. If user does not provide keepdims, no keyword is passed to the underlying method.
  2. Any user-provided value of keepdims is passed through as a keyword argument to the method.

This will raise in the case where the method does not support a keepdims kwarg and the user explicitly passes in keepdims.

The following functions are changed: sum, product, sometrue, alltrue, any, all, amax, amin, prod, mean, std, var, nanmin, nanmax, nansum, nanprod, nanmean, nanmedian, nanvar, nanstd

bitwise_and identity changed

The previous identity was 1, it is now -1. See entry in `Improvements`_ for more explanation.

FutureWarning to changed behavior

  • np.full now returns an array of the fill-value’s dtype if no dtype is given, instead of defaulting to float.

C API

New Features

Writeable keyword argument for as_strided

np.lib.stride_tricks.as_strided now has a writeable keyword argument. It can be set to False when no write operation to the returned array is expected to avoid accidental unpredictable writes.

Generalized flip

flipud and fliplr reverse the elements of an array along axis=0 and axis=1 respectively. The newly added flip function reverses the elements of an array along any given axis.

BLIS support in numpy.distutils

Building against the BLAS implementation provided by the BLIS library is now supported. See the [blis] section in site.cfg.example (in the root of the numpy repo or source distribution).

Hook in numpy/__init__.py to run distribution-specific checks

Binary distributions of numpy may need to run specific hardware checks or load specific libraries during numpy initialization. For example, if we are distributing numpy with a BLAS library that requires SSE2 instructions, we would like to check the machine on which numpy is running does have SSE2 in order to give an informative error.

Add a hook in numpy/__init__.py to import a numpy/_distributor_init.py file that will remain empty (bar a docstring) in the standard numpy source, but that can be overwritten by people making binary distributions of numpy.

New nanfunctions nancumsum and nancumprod added

Nanfunctions nancumsum and nancumprod have been added to compute cumsum and cumprod by ignoring nans.

np.interp can now interpolate complex values

np.lib.interp(x, xp, fp) now allows the interpolated array fp to be complex and will interpolate at complex128 precision.

Improvements

np.loadtxt now supports a single integer as usecol argument

Instead of using usecol=(n,) to read the nth column of a file it is now allowed to use usecol=n. Also the error message is more user friendly when a non-integer is passed as a column index.

Improved automated bin estimators for histogram

Added ‘doane’ and ‘sqrt’ estimators to histogram via the bins argument. Added support for range-restricted histograms with automated bin estimation.

bitwise_and identity changed

The previous identity was 1 with the result that all bits except the LSB were masked out when the reduce method was used. The new identity is -1, which should work properly on twos complement machines as all bits will be set to one.

Generalized Ufuncs will now unlock the GIL

Generalized Ufuncs, including most of the linalg module, will now unlock the Python global interpreter lock.

np.roll can now roll multiple axes at the same time

The shift and axis arguments to roll are now broadcast against each other, and each specified axis is shifted accordingly.

The __complex__ method has been implemented on the ndarray object

Calling complex() on a size 1 array will now cast to a python complex.

pathlib.Path objects now supported

The standard np.load, np.save, np.loadtxt, np.savez, and similar functions can now take pathlib.Path objects as an argument instead of a filename or open file object.

Changes

All array-like methods are now called with keyword arguments in fromnumeric.py

Internally, many array-like methods in fromnumeric.py were being called with positional arguments instead of keyword arguments as their external signatures were doing. This caused a complication in the downstream ‘pandas’ library that encountered an issue with ‘numpy’ compatibility. Now, all array-like methods in this module are called with keyword arguments instead.

Operations on np.memmap objects return numpy arrays in most cases

Previously operations on a memmap object would misleadingly return a memmap instance even if the result was actually not memmapped. For example, arr + 1 or arr + arr would return memmap instances, although no memory from the output array is memmaped. Version 1.12 returns ordinary numpy arrays from these operations.

Also, reduction of a memmap (e.g. .sum(axis=None) now returns a numpy scalar instead of a 0d memmap.

numpy.sctypes now includes bytes on Python3 too

Previously, it included str (bytes) and unicode on Python2, but only str (unicode) on Python3.

Deprecations

Assignment of ndarray object’s data attribute

Assigning the ‘data’ attribute is an inherently unsafe operation as pointed out in gh-7083. Such a capability will be removed in the future.

Unsafe int casting of the num attribute in linspace

np.linspace now raises DeprecationWarning when num cannot be safely interpreted as an integer.

Insufficient bit width parameter to binary_repr

If a ‘width’ parameter is passed into binary_repr that is insufficient to represent the number in base 2 (positive) or 2’s complement (negative) form, the function used to silently ignore the parameter and return a representation using the minimal number of bits needed for the form in question. Such behavior is now considered unsafe from a user perspective and will raise an error in the future.

NumPy 1.11.1 Release Notes

Numpy 1.11.1 supports Python 2.6 - 2.7 and 3.2 - 3.5. It fixes bugs and regressions found in Numpy 1.11.0 and includes several build related improvements. Wheels for Linux, Windows, and OSX can be found on pypi.

Fixes Merged

  • #7506 BUG: Make sure numpy imports on python 2.6 when nose is unavailable.
  • #7530 BUG: Floating exception with invalid axis in np.lexsort.
  • #7535 BUG: Extend glibc complex trig functions blacklist to glibc < 2.18.
  • #7551 BUG: Allow graceful recovery for no compiler.
  • #7558 BUG: Constant padding expected wrong type in constant_values.
  • #7578 BUG: Fix OverflowError in Python 3.x. in swig interface.
  • #7590 BLD: Fix configparser.InterpolationSyntaxError.
  • #7597 BUG: Make np.ma.take work on scalars.
  • #7608 BUG: linalg.norm(): Don’t convert object arrays to float.
  • #7638 BLD: Correct C compiler customization in system_info.py.
  • #7654 BUG: ma.median of 1d array should return a scalar.
  • #7656 BLD: Remove hardcoded Intel compiler flag -xSSE4.2.
  • #7660 BUG: Temporary fix for str(mvoid) for object field types.
  • #7665 BUG: Fix incorrect printing of 1D masked arrays.
  • #7670 BUG: Correct initial index estimate in histogram.
  • #7671 BUG: Boolean assignment no GIL release when transfer needs API.
  • #7676 BUG: Fix handling of right edge of final histogram bin.
  • #7680 BUG: Fix np.clip bug NaN handling for Visual Studio 2015.

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 consistancy, 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().

NumPy 1.10.4 Release Notes

This release is a bugfix source release motivated by a segfault regression. No windows binaries are provided for this release, as there appear to be bugs in the toolchain we use to generate those files. Hopefully that problem will be fixed for the next release. In the meantime, we suggest using one of the providers of windows binaries.

Compatibility notes

  • The trace function now calls the trace method on subclasses of ndarray, except for matrix, for which the current behavior is preserved. This is to help with the units package of AstroPy and hopefully will not cause problems.

Issues Fixed

  • gh-6922 BUG: numpy.recarray.sort segfaults on Windows.
  • gh-6937 BUG: busday_offset does the wrong thing with modifiedpreceding roll.
  • gh-6949 BUG: Type is lost when slicing a subclass of recarray.

Merged PRs

The following PRs have been merged into 1.10.4. When the PR is a backport, the PR number for the original PR against master is listed.

  • gh-6840 TST: Update travis testing script in 1.10.x
  • gh-6843 BUG: Fix use of python 3 only FileNotFoundError in test_f2py.
  • gh-6884 REL: Update pavement.py and setup.py to reflect current version.
  • gh-6916 BUG: Fix test_f2py so it runs correctly in runtests.py.
  • gh-6924 BUG: Fix segfault gh-6922.
  • gh-6942 Fix datetime roll=’modifiedpreceding’ bug.
  • gh-6943 DOC,BUG: Fix some latex generation problems.
  • gh-6950 BUG trace is not subclass aware, np.trace(ma) != ma.trace().
  • gh-6952 BUG recarray slices should preserve subclass.

NumPy 1.10.3 Release Notes

N/A this release did not happen due to various screwups involving PyPi.

NumPy 1.10.2 Release Notes

This release deals with a number of bugs that turned up in 1.10.1 and adds various build and release improvements.

Numpy 1.10.1 supports Python 2.6 - 2.7 and 3.2 - 3.5.

Compatibility notes

Relaxed stride checking is no longer the default

There were back compatibility problems involving views changing the dtype of multidimensional Fortran arrays that need to be dealt with over a longer timeframe.

Fix swig bug in numpy.i

Relaxed stride checking revealed a bug in array_is_fortran(a), that was using PyArray_ISFORTRAN to check for Fortran contiguity instead of PyArray_IS_F_CONTIGUOUS. You may want to regenerate swigged files using the updated numpy.i

Deprecate views changing dimensions in fortran order

This deprecates assignment of a new descriptor to the dtype attribute of a non-C-contiguous array if it result in changing the shape. This effectively bars viewing a multidimensional Fortran array using a dtype that changes the element size along the first axis.

The reason for the deprecation is that, when relaxed strides checking is enabled, arrays that are both C and Fortran contiguous are always treated as C contiguous which breaks some code that depended the two being mutually exclusive for non-scalar arrays of ndim > 1. This deprecation prepares the way to always enable relaxed stride checking.

Issues Fixed

  • gh-6019 Masked array repr fails for structured array with multi-dimensional column.
  • gh-6462 Median of empty array produces IndexError.
  • gh-6467 Performance regression for record array access.
  • gh-6468 numpy.interp uses ‘left’ value even when x[0]==xp[0].
  • gh-6475 np.allclose returns a memmap when one of its arguments is a memmap.
  • gh-6491 Error in broadcasting stride_tricks array.
  • gh-6495 Unrecognized command line option ‘-ffpe-summary’ in gfortran.
  • gh-6497 Failure of reduce operation on recarrays.
  • gh-6498 Mention change in default casting rule in 1.10 release notes.
  • gh-6530 The partition function errors out on empty input.
  • gh-6532 numpy.inner return wrong inaccurate value sometimes.
  • gh-6563 Intent(out) broken in recent versions of f2py.
  • gh-6569 Cannot run tests after ‘python setup.py build_ext -i’
  • gh-6572 Error in broadcasting stride_tricks array component.
  • gh-6575 BUG: Split produces empty arrays with wrong number of dimensions
  • gh-6590 Fortran Array problem in numpy 1.10.
  • gh-6602 Random __all__ missing choice and dirichlet.
  • gh-6611 ma.dot no longer always returns a masked array in 1.10.
  • gh-6618 NPY_FORTRANORDER in make_fortran() in numpy.i
  • gh-6636 Memory leak in nested dtypes in numpy.recarray
  • gh-6641 Subsetting recarray by fields yields a structured array.
  • gh-6667 ma.make_mask handles ma.nomask input incorrectly.
  • gh-6675 Optimized blas detection broken in master and 1.10.
  • gh-6678 Getting unexpected error from: X.dtype = complex (or Y = X.view(complex))
  • gh-6718 f2py test fail in pip installed numpy-1.10.1 in virtualenv.
  • gh-6719 Error compiling Cython file: Pythonic division not allowed without gil.
  • gh-6771 Numpy.rec.fromarrays losing dtype metadata between versions 1.9.2 and 1.10.1
  • gh-6781 The travis-ci script in maintenance/1.10.x needs fixing.
  • gh-6807 Windows testing errors for 1.10.2

Merged PRs

The following PRs have been merged into 1.10.2. When the PR is a backport, the PR number for the original PR against master is listed.

  • gh-5773 MAINT: Hide testing helper tracebacks when using them with pytest.
  • gh-6094 BUG: Fixed a bug with string representation of masked structured arrays.
  • gh-6208 MAINT: Speedup field access by removing unneeded safety checks.
  • gh-6460 BUG: Replacing the os.environ.clear by less invasive procedure.
  • gh-6470 BUG: Fix AttributeError in numpy distutils.
  • gh-6472 MAINT: Use Python 3.5 instead of 3.5-dev for travis 3.5 testing.
  • gh-6474 REL: Update Paver script for sdist and auto-switch test warnings.
  • gh-6478 BUG: Fix Intel compiler flags for OS X build.
  • gh-6481 MAINT: LIBPATH with spaces is now supported Python 2.7+ and Win32.
  • gh-6487 BUG: Allow nested use of parameters in definition of arrays in f2py.
  • gh-6488 BUG: Extend common blocks rather than overwriting in f2py.
  • gh-6499 DOC: Mention that default casting for inplace operations has changed.
  • gh-6500 BUG: Recarrays viewed as subarrays don’t convert to np.record type.
  • gh-6501 REL: Add “make upload” command for built docs, update “make dist”.
  • gh-6526 BUG: Fix use of __doc__ in setup.py for -OO mode.
  • gh-6527 BUG: Fix the IndexError when taking the median of an empty array.
  • gh-6537 BUG: Make ma.atleast_* with scalar argument return arrays.
  • gh-6538 BUG: Fix ma.masked_values does not shrink mask if requested.
  • gh-6546 BUG: Fix inner product regression for non-contiguous arrays.
  • gh-6553 BUG: Fix partition and argpartition error for empty input.
  • gh-6556 BUG: Error in broadcast_arrays with as_strided array.
  • gh-6558 MAINT: Minor update to “make upload” doc build command.
  • gh-6562 BUG: Disable view safety checks in recarray.
  • gh-6567 BUG: Revert some import * fixes in f2py.
  • gh-6574 DOC: Release notes for Numpy 1.10.2.
  • gh-6577 BUG: Fix for #6569, allowing build_ext –inplace
  • gh-6579 MAINT: Fix mistake in doc upload rule.
  • gh-6596 BUG: Fix swig for relaxed stride checking.
  • gh-6606 DOC: Update 1.10.2 release notes.
  • gh-6614 BUG: Add choice and dirichlet to numpy.random.__all__.
  • gh-6621 BUG: Fix swig make_fortran function.
  • gh-6628 BUG: Make allclose return python bool.
  • gh-6642 BUG: Fix memleak in _convert_from_dict.
  • gh-6643 ENH: make recarray.getitem return a recarray.
  • gh-6653 BUG: Fix ma dot to always return masked array.
  • gh-6668 BUG: ma.make_mask should always return nomask for nomask argument.
  • gh-6686 BUG: Fix a bug in assert_string_equal.
  • gh-6695 BUG: Fix removing tempdirs created during build.
  • gh-6697 MAINT: Fix spurious semicolon in macro definition of PyArray_FROM_OT.
  • gh-6698 TST: test np.rint bug for large integers.
  • gh-6717 BUG: Readd fallback CBLAS detection on linux.
  • gh-6721 BUG: Fix for #6719.
  • gh-6726 BUG: Fix bugs exposed by relaxed stride rollback.
  • gh-6757 BUG: link cblas library if cblas is detected.
  • gh-6756 TST: only test f2py, not f2py2.7 etc, fixes #6718.
  • gh-6747 DEP: Deprecate changing shape of non-C-contiguous array via descr.
  • gh-6775 MAINT: Include from __future__ boilerplate in some files missing it.
  • gh-6780 BUG: metadata is not copied to base_dtype.
  • gh-6783 BUG: Fix travis ci testing for new google infrastructure.
  • gh-6785 BUG: Quick and dirty fix for interp.
  • gh-6813 TST,BUG: Make test_mvoid_multidim_print work for 32 bit systems.
  • gh-6817 BUG: Disable 32-bit msvc9 compiler optimizations for npy_rint.
  • gh-6819 TST: Fix test_mvoid_multidim_print failures on Python 2.x for Windows.

Initial support for mingwpy was reverted as it was causing problems for non-windows builds.

  • gh-6536 BUG: Revert gh-5614 to fix non-windows build problems

A fix for np.lib.split was reverted because it resulted in “fixing” behavior that will be present in the Numpy 1.11 and that was already present in Numpy 1.9. See the discussion of the issue at gh-6575 for clarification.

  • gh-6576 BUG: Revert gh-6376 to fix split behavior for empty arrays.

Relaxed stride checking was reverted. There were back compatibility problems involving views changing the dtype of multidimensional Fortran arrays that need to be dealt with over a longer timeframe.

  • gh-6735 MAINT: Make no relaxed stride checking the default for 1.10.

Notes

A bug in the Numpy 1.10.1 release resulted in exceptions being raised for RuntimeWarning and DeprecationWarning in projects depending on Numpy. That has been fixed.

NumPy 1.10.1 Release Notes

This release deals with a few build problems that showed up in 1.10.0. Most users would not have seen these problems. The differences are:

  • Compiling with msvc9 or msvc10 for 32 bit Windows now requires SSE2. This was the easiest fix for what looked to be some miscompiled code when SSE2 was not used. If you need to compile for 32 bit Windows systems without SSE2 support, mingw32 should still work.
  • Make compiling with VS2008 python2.7 SDK easier
  • Change Intel compiler options so that code will also be generated to support systems without SSE4.2.
  • Some _config test functions needed an explicit integer return in order to avoid the openSUSE rpmlinter erring out.
  • We ran into a problem with pipy not allowing reuse of filenames and a resulting proliferation of ..*.postN releases. Not only were the names getting out of hand, some packages were unable to work with the postN suffix.

Numpy 1.10.1 supports Python 2.6 - 2.7 and 3.2 - 3.5.

Commits:

45a3d84 DEP: Remove warning for full when dtype is set. 0c1a5df BLD: import setuptools to allow compile with VS2008 python2.7 sdk 04211c6 BUG: mask nan to 1 in ordered compare 826716f DOC: Document the reason msvc requires SSE2 on 32 bit platforms. 49fa187 BLD: enable SSE2 for 32-bit msvc 9 and 10 compilers dcbc4cc MAINT: remove Wreturn-type warnings from config checks d6564cb BLD: do not build exclusively for SSE4.2 processors 15cb66f BLD: do not build exclusively for SSE4.2 processors c38bc08 DOC: fix var. reference in percentile docstring 78497f4 DOC: Sync 1.10.0-notes.rst in 1.10.x branch with master.

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.
  • In np.lib.split an empty array in the result always had dimension (0,) no matter the dimensions of the array being split. In Numpy 1.11 that behavior will be 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.
  • The SafeEval class will be removed in Numpy 1.11.
  • The alterdot and restoredot functions will be removed in Numpy 1.11.

See below for more details on these changes.

Compatibility notes

Default casting rule change

Default casting for inplace operations has changed to 'same_kind'. For instance, if n is an array of integers, and f is an array of floats, then n += f will result in a TypeError, whereas in previous Numpy versions the floats would be silently cast to ints. In the unlikely case that the example code is not an actual bug, it can be updated in a backward compatible way by rewriting it as np.add(n, f, out=n, casting='unsafe'). The old 'unsafe' default has been deprecated since Numpy 1.7.

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.

UPDATE: In 1.10.2 the default value of NPY_RELAXED_STRIDE_CHECKING was changed to false for back compatibility reasons. More time is needed before it can be made the default. As part of the roadmap a deprecation of dimension changing views of f_contiguous not c_contiguous arrays was also added.

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 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 1/\\sqrt{n}.

Improvements

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.

NumPy 1.9.2 Release Notes

This is a bugfix only release in the 1.9.x series.

Issues fixed

  • #5316: fix too large dtype alignment of strings and complex types
  • #5424: fix ma.median when used on ndarrays
  • #5481: Fix astype for structured array fields of different byte order
  • #5354: fix segfault when clipping complex arrays
  • #5524: allow np.argpartition on non ndarrays
  • #5612: Fixes ndarray.fill to accept full range of uint64
  • #5155: Fix loadtxt with comments=None and a string None data
  • #4476: Masked array view fails if structured dtype has datetime component
  • #5388: Make RandomState.set_state and RandomState.get_state threadsafe
  • #5390: make seed, randint and shuffle threadsafe
  • #5374: Fixed incorrect assert_array_almost_equal_nulp documentation
  • #5393: Add support for ATLAS > 3.9.33.
  • #5313: PyArray_AsCArray caused segfault for 3d arrays
  • #5492: handle out of memory in rfftf
  • #4181: fix a few bugs in the random.pareto docstring
  • #5359: minor changes to linspace docstring
  • #4723: fix a compile issues on AIX

NumPy 1.9.1 Release Notes

This is a bugfix only release in the 1.9.x series.

Issues fixed

  • gh-5184: restore linear edge behaviour of gradient to as it was in < 1.9. The second order behaviour is available via the edge_order keyword
  • gh-4007: workaround Accelerate sgemv crash on OSX 10.9
  • gh-5100: restore object dtype inference from iterable objects without len()
  • gh-5163: avoid gcc-4.1.2 (red hat 5) miscompilation causing a crash
  • gh-5138: fix nanmedian on arrays containing inf
  • gh-5240: fix not returning out array from ufuncs with subok=False set
  • gh-5203: copy inherited masks in MaskedArray.__array_finalize__
  • gh-2317: genfromtxt did not handle filling_values=0 correctly
  • gh-5067: restore api of npy_PyFile_DupClose in python2
  • gh-5063: cannot convert invalid sequence index to tuple
  • gh-5082: Segmentation fault with argmin() on unicode arrays
  • gh-5095: don’t propagate subtypes from np.where
  • gh-5104: np.inner segfaults with SciPy’s sparse matrices
  • gh-5251: Issue with fromarrays not using correct format for unicode arrays
  • gh-5136: Import dummy_threading if importing threading fails
  • gh-5148: Make numpy import when run with Python flag ‘-OO’
  • gh-5147: Einsum double contraction in particular order causes ValueError
  • gh-479: Make f2py work with intent(in out)
  • gh-5170: Make python2 .npy files readable in python3
  • gh-5027: Use ‘ll’ as the default length specifier for long long
  • gh-4896: fix build error with MSVC 2013 caused by C99 complex support
  • gh-4465: Make PyArray_PutTo respect writeable flag
  • gh-5225: fix crash when using arange on datetime without dtype set
  • gh-5231: fix build in c99 mode

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 parallization 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.

NumPy 1.8.2 Release Notes

This is a bugfix only release in the 1.8.x series.

Issues fixed

  • gh-4836: partition produces wrong results for multiple selections in equal ranges
  • gh-4656: Make fftpack._raw_fft threadsafe
  • gh-4628: incorrect argument order to _copyto in in np.nanmax, np.nanmin
  • gh-4642: Hold GIL for converting dtypes types with fields
  • gh-4733: fix np.linalg.svd(b, compute_uv=False)
  • gh-4853: avoid unaligned simd load on reductions on i386
  • gh-4722: Fix seg fault converting empty string to object
  • gh-4613: Fix lack of NULL check in array_richcompare
  • gh-4774: avoid unaligned access for strided byteswap
  • gh-650: Prevent division by zero when creating arrays from some buffers
  • gh-4602: ifort has issues with optimization flag O2, use O1

NumPy 1.8.1 Release Notes

This is a bugfix only release in the 1.8.x series.

Issues fixed

  • gh-4276: Fix mean, var, std methods for object arrays
  • gh-4262: remove insecure mktemp usage
  • gh-2385: absolute(complex(inf)) raises invalid warning in python3
  • gh-4024: Sequence assignment doesn’t raise exception on shape mismatch
  • gh-4027: Fix chunked reading of strings longer than BUFFERSIZE
  • gh-4109: Fix object scalar return type of 0-d array indices
  • gh-4018: fix missing check for memory allocation failure in ufuncs
  • gh-4156: high order linalg.norm discards imaginary elements of complex arrays
  • gh-4144: linalg: norm fails on longdouble, signed int
  • gh-4094: fix NaT handling in _strided_to_strided_string_to_datetime
  • gh-4051: fix uninitialized use in _strided_to_strided_string_to_datetime
  • gh-4093: Loading compressed .npz file fails under Python 2.6.6
  • gh-4138: segfault with non-native endian memoryview in python 3.4
  • gh-4123: Fix missing NULL check in lexsort
  • gh-4170: fix native-only long long check in memoryviews
  • gh-4187: Fix large file support on 32 bit
  • gh-4152: fromfile: ensure file handle positions are in sync in python3
  • gh-4176: clang compatibility: Typos in conversion_utils
  • gh-4223: Fetching a non-integer item caused array return
  • gh-4197: fix minor memory leak in memoryview failure case
  • gh-4206: fix build with single-threaded python
  • gh-4220: add versionadded:: 1.8.0 to ufunc.at docstring
  • gh-4267: improve handling of memory allocation failure
  • gh-4267: fix use of capi without gil in ufunc.at
  • gh-4261: Detect vendor versions of GNU Compilers
  • gh-4253: IRR was returning nan instead of valid negative answer
  • gh-4254: fix unnecessary byte order flag change for byte arrays
  • gh-3263: numpy.random.shuffle clobbers mask of a MaskedArray
  • gh-4270: np.random.shuffle not work with flexible dtypes
  • gh-3173: Segmentation fault when ‘size’ argument to random.multinomial
  • gh-2799: allow using unique with lists of complex
  • gh-3504: fix linspace truncation for integer array scalar
  • gh-4191: get_info(‘openblas’) does not read libraries key
  • gh-3348: Access violation in _descriptor_from_pep3118_format
  • gh-3175: segmentation fault with numpy.array() from bytearray
  • gh-4266: histogramdd - wrong result for entries very close to last boundary
  • gh-4408: Fix stride_stricks.as_strided function for object arrays
  • gh-4225: fix log1p and exmp1 return for np.inf on windows compiler builds
  • gh-4359: Fix infinite recursion in str.format of flex arrays
  • gh-4145: Incorrect shape of broadcast result with the exponent operator
  • gh-4483: Fix commutativity of {dot,multiply,inner}(scalar, matrix_of_objs)
  • gh-4466: Delay npyiter size check when size may change
  • gh-4485: Buffered stride was erroneously marked fixed
  • gh-4354: byte_bounds fails with datetime dtypes
  • gh-4486: segfault/error converting from/to high-precision datetime64 objects
  • gh-4428: einsum(None, None, None, None) causes segfault
  • gh-4134: uninitialized use for for size 1 object reductions

Changes

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.

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.

Deprecations

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.

NumPy 1.8.0 Release Notes

This release supports Python 2.6 -2.7 and 3.2 - 3.3.

Highlights

  • New, no 2to3, Python 2 and Python 3 are supported by a common code base.
  • New, gufuncs for linear algebra, enabling operations on stacked arrays.
  • New, inplace fancy indexing for ufuncs with the .at method.
  • New, partition function, partial sorting via selection for fast median.
  • New, nanmean, nanvar, and nanstd functions skipping NaNs.
  • New, full and full_like functions to create value initialized arrays.
  • New, PyUFunc_RegisterLoopForDescr, better ufunc support for user dtypes.
  • Numerous performance improvements in many areas.

Dropped Support

Support for Python versions 2.4 and 2.5 has been dropped,

Support for SCons has been removed.

Future Changes

The Datetime64 type remains experimental in this release. In 1.9 there will probably be some changes to make it more useable.

The diagonal method currently returns a new array and raises a FutureWarning. In 1.9 it will return a readonly view.

Multiple field selection from a array of structured type currently returns a new array and raises a FutureWarning. In 1.9 it will return a readonly view.

The numpy/oldnumeric and numpy/numarray compatibility modules will be removed in 1.9.

Compatibility notes

The doc/sphinxext content has been moved into its own github repository, and is included in numpy as a submodule. See the instructions in doc/HOWTO_BUILD_DOCS.rst.txt for how to access the content.

The hash function of numpy.void scalars has been changed. Previously the pointer to the data was hashed as an integer. Now, the hash function uses the tuple-hash algorithm to combine the hash functions of the elements of the scalar, but only if the scalar is read-only.

Numpy has switched its build system to using ‘separate compilation’ by default. In previous releases this was supported, but not default. This should produce the same results as the old system, but if you’re trying to do something complicated like link numpy statically or using an unusual compiler, then it’s possible you will encounter problems. If so, please file a bug and as a temporary workaround you can re-enable the old build system by exporting the shell variable NPY_SEPARATE_COMPILATION=0.

For the AdvancedNew iterator the oa_ndim flag should now be -1 to indicate that no op_axes and itershape are passed in. The oa_ndim == 0 case, now indicates a 0-D iteration and op_axes being NULL and the old usage is deprecated. This does not effect the NpyIter_New or NpyIter_MultiNew functions.

The functions nanargmin and nanargmax now return np.iinfo[‘intp’].min for the index in all-NaN slices. Previously the functions would raise a ValueError for array returns and NaN for scalar returns.

NPY_RELAXED_STRIDES_CHECKING

There is a new compile time environment variable NPY_RELAXED_STRIDES_CHECKING. If this variable is set to 1, then numpy will consider more arrays to be C- or F-contiguous – for example, it becomes possible to have a column vector which is considered both C- and F-contiguous simultaneously. The new definition is more accurate, allows for faster code that makes fewer unnecessary copies, and simplifies numpy’s code internally. However, it may also break third-party libraries that make too-strong assumptions about the stride values of C- and F-contiguous arrays. (It is also currently known that this breaks Cython code using memoryviews, which will be fixed in Cython.) THIS WILL BECOME THE DEFAULT IN A FUTURE RELEASE, SO PLEASE TEST YOUR CODE NOW AGAINST NUMPY BUILT WITH:

NPY_RELAXED_STRIDES_CHECKING=1 python setup.py install

You can check whether NPY_RELAXED_STRIDES_CHECKING is in effect by running:

np.ones((10, 1), order="C").flags.f_contiguous

This will be True if relaxed strides checking is enabled, and False otherwise. The typical problem we’ve seen so far is C code that works with C-contiguous arrays, and assumes that the itemsize can be accessed by looking at the last element in the PyArray_STRIDES(arr) array. When relaxed strides are in effect, this is not true (and in fact, it never was true in some corner cases). Instead, use PyArray_ITEMSIZE(arr).

For more information check the “Internal memory layout of an ndarray” section in the documentation.

Binary operations with non-arrays as second argument

Binary operations of the form <array-or-subclass> * <non-array-subclass> where <non-array-subclass> declares an __array_priority__ higher than that of <array-or-subclass> will now unconditionally return NotImplemented, giving <non-array-subclass> a chance to handle the operation. Previously, NotImplemented would only be returned if <non-array-subclass> actually implemented the reversed operation, and after a (potentially expensive) array conversion of <non-array-subclass> had been attempted. (bug, pull request)

Function median used with overwrite_input only partially sorts array

If median is used with overwrite_input option the input array will now only be partially sorted instead of fully sorted.

Fix to financial.npv

The npv function had a bug. Contrary to what the documentation stated, it summed from indexes 1 to M instead of from 0 to M - 1. The fix changes the returned value. The mirr function called the npv function, but worked around the problem, so that was also fixed and the return value of the mirr function remains unchanged.

Runtime warnings when comparing NaN numbers

Comparing NaN floating point numbers now raises the invalid runtime warning. If a NaN is expected the warning can be ignored using np.errstate. E.g.:

with np.errstate(invalid='ignore'):
    operation()

New Features

Support for linear algebra on stacked arrays

The gufunc machinery is now used for np.linalg, allowing operations on stacked arrays and vectors. For example:

>>> a
array([[[ 1.,  1.],
        [ 0.,  1.]],

       [[ 1.,  1.],
        [ 0.,  1.]]])

>>> np.linalg.inv(a)
array([[[ 1., -1.],
        [ 0.,  1.]],

       [[ 1., -1.],
        [ 0.,  1.]]])

In place fancy indexing for ufuncs

The function at has been added to ufunc objects to allow in place ufuncs with no buffering when fancy indexing is used. For example, the following will increment the first and second items in the array, and will increment the third item twice: numpy.add.at(arr, [0, 1, 2, 2], 1)

This is what many have mistakenly thought arr[[0, 1, 2, 2]] += 1 would do, but that does not work as the incremented value of arr[2] is simply copied into the third slot in arr twice, not incremented twice.

New functions partition and argpartition

New functions to partially sort arrays via a selection algorithm.

A partition by index k moves the k smallest element to the front of an array. All elements before k are then smaller or equal than the value in position k and all elements following k are then greater or equal than the value in position k. The ordering of the values within these bounds is undefined. A sequence of indices can be provided to sort all of them into their sorted position at once iterative partitioning. This can be used to efficiently obtain order statistics like median or percentiles of samples. partition has a linear time complexity of O(n) while a full sort has O(n log(n)).

New functions nanmean, nanvar and nanstd

New nan aware statistical functions are added. In these functions the results are what would be obtained if nan values were ommited from all computations.

New functions full and full_like

New convenience functions to create arrays filled with a specific value; complementary to the existing zeros and zeros_like functions.

IO compatibility with large files

Large NPZ files >2GB can be loaded on 64-bit systems.

Building against OpenBLAS

It is now possible to build numpy against OpenBLAS by editing site.cfg.

New constant

Euler’s constant is now exposed in numpy as euler_gamma.

New modes for qr

New modes ‘complete’, ‘reduced’, and ‘raw’ have been added to the qr factorization and the old ‘full’ and ‘economic’ modes are deprecated. The ‘reduced’ mode replaces the old ‘full’ mode and is the default as was the ‘full’ mode, so backward compatibility can be maintained by not specifying the mode.

The ‘complete’ mode returns a full dimensional factorization, which can be useful for obtaining a basis for the orthogonal complement of the range space. The ‘raw’ mode returns arrays that contain the Householder reflectors and scaling factors that can be used in the future to apply q without needing to convert to a matrix. The ‘economic’ mode is simply deprecated, there isn’t much use for it and it isn’t any more efficient than the ‘raw’ mode.

New invert argument to in1d

The function in1d now accepts a invert argument which, when True, causes the returned array to be inverted.

Advanced indexing using np.newaxis

It is now possible to use np.newaxis/None together with index arrays instead of only in simple indices. This means that array[np.newaxis, [0, 1]] will now work as expected and select the first two rows while prepending a new axis to the array.

C-API

New ufuncs can now be registered with builtin input types and a custom output type. Before this change, NumPy wouldn’t be able to find the right ufunc loop function when the ufunc was called from Python, because the ufunc loop signature matching logic wasn’t looking at the output operand type. Now the correct ufunc loop is found, as long as the user provides an output argument with the correct output type.

runtests.py

A simple test runner script runtests.py was added. It also builds Numpy via setup.py build and can be used to run tests easily during development.

Improvements

IO performance improvements

Performance in reading large files was improved by chunking (see also IO compatibility).

Performance improvements to pad

The pad function has a new implementation, greatly improving performance for all inputs except mode= (retained for backwards compatibility). Scaling with dimensionality is dramatically improved for rank >= 4.

Performance improvements to isnan, isinf, isfinite and byteswap

isnan, isinf, isfinite and byteswap have been improved to take advantage of compiler builtins to avoid expensive calls to libc. This improves performance of these operations by about a factor of two on gnu libc systems.

Performance improvements via SSE2 vectorization

Several functions have been optimized to make use of SSE2 CPU SIMD instructions.

  • Float32 and float64:
    • base math (add, subtract, divide, multiply)
    • sqrt
    • minimum/maximum
    • absolute
  • Bool:
    • logical_or
    • logical_and
    • logical_not

This improves performance of these operations up to 4x/2x for float32/float64 and up to 10x for bool depending on the location of the data in the CPU caches. The performance gain is greatest for in-place operations.

In order to use the improved functions the SSE2 instruction set must be enabled at compile time. It is enabled by default on x86_64 systems. On x86_32 with a capable CPU it must be enabled by passing the appropriate flag to the CFLAGS build variable (-msse2 with gcc).

Performance improvements to median

median is now implemented in terms of partition instead of sort which reduces its time complexity from O(n log(n)) to O(n). If used with the overwrite_input option the array will now only be partially sorted instead of fully sorted.

Overrideable operand flags in ufunc C-API

When creating a ufunc, the default ufunc operand flags can be overridden via the new op_flags attribute of the ufunc object. For example, to set the operand flag for the first input to read/write:

PyObject *ufunc = PyUFunc_FromFuncAndData(...); ufunc->op_flags[0] = NPY_ITER_READWRITE;

This allows a ufunc to perform an operation in place. Also, global nditer flags can be overridden via the new iter_flags attribute of the ufunc object. For example, to set the reduce flag for a ufunc:

ufunc->iter_flags = NPY_ITER_REDUCE_OK;

Changes

General

The function np.take now allows 0-d arrays as indices.

The separate compilation mode is now enabled by default.

Several changes to np.insert and np.delete:

  • Previously, negative indices and indices that pointed past the end of the array were simply ignored. Now, this will raise a Future or Deprecation Warning. In the future they will be treated like normal indexing treats them – negative indices will wrap around, and out-of-bound indices will generate an error.
  • Previously, boolean indices were treated as if they were integers (always referring to either the 0th or 1st item in the array). In the future, they will be treated as masks. In this release, they raise a FutureWarning warning of this coming change.
  • In Numpy 1.7. np.insert already allowed the syntax np.insert(arr, 3, [1,2,3]) to insert multiple items at a single position. In Numpy 1.8. this is also possible for np.insert(arr, [3], [1, 2, 3]).

Padded regions from np.pad are now correctly rounded, not truncated.

C-API Array Additions

Four new functions have been added to the array C-API.

  • PyArray_Partition
  • PyArray_ArgPartition
  • PyArray_SelectkindConverter
  • PyDataMem_NEW_ZEROED

C-API Ufunc Additions

One new function has been added to the ufunc C-API that allows to register an inner loop for user types using the descr.

  • PyUFunc_RegisterLoopForDescr

C-API Developer Improvements

The PyArray_Type instance creation function tp_new now uses tp_basicsize to determine how much memory to allocate. In previous releases only sizeof(PyArrayObject) bytes of memory were allocated, often requiring C-API subtypes to reimplement tp_new.

Deprecations

The ‘full’ and ‘economic’ modes of qr factorization are deprecated.

General

The use of non-integer for indices and most integer arguments has been deprecated. Previously float indices and function arguments such as axes or shapes were truncated to integers without warning. For example arr.reshape(3., -1) or arr[0.] will trigger a deprecation warning in NumPy 1.8., and in some future version of NumPy they will raise an error.

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:

  • 87
  • Adam Ginsburg +
  • Adam Griffiths +
  • Alexander Belopolsky +
  • Alex Barth +
  • Alex Ford +
  • Andreas Hilboll +
  • Andreas Kloeckner +
  • Andreas Schwab +
  • Andrew Horton +
  • argriffing +
  • Arink Verma +
  • Bago Amirbekian +
  • Bartosz Telenczuk +
  • bebert218 +
  • Benjamin Root +
  • Bill Spotz +
  • Bradley M. Froehle
  • Carwyn Pelley +
  • Charles Harris
  • Chris
  • Christian Brueffer +
  • Christoph Dann +
  • Christoph Gohlke
  • Dan Hipschman +
  • Daniel +
  • Dan Miller +
  • daveydave400 +
  • David Cournapeau
  • David Warde-Farley
  • Denis Laxalde
  • dmuellner +
  • Edward Catmur +
  • Egor Zindy +
  • endolith
  • Eric Firing
  • Eric Fode
  • Eric Moore +
  • Eric Price +
  • Fazlul Shahriar +
  • Félix Hartmann +
  • Fernando Perez
  • Frank B +
  • Frank Breitling +
  • Frederic
  • Gabriel
  • GaelVaroquaux
  • Guillaume Gay +
  • Han Genuit
  • HaroldMills +
  • hklemm +
  • jamestwebber +
  • Jason Madden +
  • Jay Bourque
  • jeromekelleher +
  • Jesús Gómez +
  • jmozmoz +
  • jnothman +
  • Johannes Schönberger +
  • John Benediktsson +
  • John Salvatier +
  • John Stechschulte +
  • Jonathan Waltman +
  • Joon Ro +
  • Jos de Kloe +
  • Joseph Martinot-Lagarde +
  • Josh Warner (Mac) +
  • Jostein Bø Fløystad +
  • Juan Luis Cano Rodríguez +
  • Julian Taylor +
  • Julien Phalip +
  • K.-Michael Aye +
  • Kumar Appaiah +
  • Lars Buitinck
  • Leon Weber +
  • Luis Pedro Coelho
  • Marcin Juszkiewicz
  • Mark Wiebe
  • Marten van Kerkwijk +
  • Martin Baeuml +
  • Martin Spacek
  • Martin Teichmann +
  • Matt Davis +
  • Matthew Brett
  • Maximilian Albert +
  • m-d-w +
  • Michael Droettboom
  • mwtoews +
  • Nathaniel J. Smith
  • Nicolas Scheffer +
  • Nils Werner +
  • ochoadavid +
  • Ondřej Čertík
  • ovillellas +
  • Paul Ivanov
  • Pauli Virtanen
  • peterjc
  • Ralf Gommers
  • Raul Cota +
  • Richard Hattersley +
  • Robert Costa +
  • Robert Kern
  • Rob Ruana +
  • Ronan Lamy
  • Sandro Tosi
  • Sascha Peilicke +
  • Sebastian Berg
  • Skipper Seabold
  • Stefan van der Walt
  • Steve +
  • Takafumi Arakaki +
  • Thomas Robitaille +
  • Tomas Tomecek +
  • Travis E. Oliphant
  • Valentin Haenel
  • Vladimir Rutsky +
  • Warren Weckesser
  • Yaroslav Halchenko
  • Yury V. Zaytsev +

A total of 119 people contributed to this release. People with a “+” by their names contributed a patch for the first time.

NumPy 1.7.2 Release Notes

This is a bugfix only release in the 1.7.x series. It supports Python 2.4 - 2.7 and 3.1 - 3.3 and is the last series that supports Python 2.4 - 2.5.

Issues fixed

  • gh-3153: Do not reuse nditer buffers when not filled enough
  • gh-3192: f2py crashes with UnboundLocalError exception
  • gh-442: Concatenate with axis=None now requires equal number of array elements
  • gh-2485: Fix for astype(‘S’) string truncate issue
  • gh-3312: bug in count_nonzero
  • gh-2684: numpy.ma.average casts complex to float under certain conditions
  • gh-2403: masked array with named components does not behave as expected
  • gh-2495: np.ma.compress treated inputs in wrong order
  • gh-576: add __len__ method to ma.mvoid
  • gh-3364: reduce performance regression of mmap slicing
  • gh-3421: fix non-swapping strided copies in GetStridedCopySwap
  • gh-3373: fix small leak in datetime metadata initialization
  • gh-2791: add platform specific python include directories to search paths
  • gh-3168: fix undefined function and add integer divisions
  • gh-3301: memmap does not work with TemporaryFile in python3
  • gh-3057: distutils.misc_util.get_shared_lib_extension returns wrong debug extension
  • gh-3472: add module extensions to load_library search list
  • gh-3324: Make comparison function (gt, ge, ...) respect __array_priority__
  • gh-3497: np.insert behaves incorrectly with argument ‘axis=-1’
  • gh-3541: make preprocessor tests consistent in halffloat.c
  • gh-3458: array_ass_boolean_subscript() writes ‘non-existent’ data to array
  • gh-2892: Regression in ufunc.reduceat with zero-sized index array
  • gh-3608: Regression when filling struct from tuple
  • gh-3701: add support for Python 3.4 ast.NameConstant
  • gh-3712: do not assume that GIL is enabled in xerbla
  • gh-3712: fix LAPACK error handling in lapack_litemodule
  • gh-3728: f2py fix decref on wrong object
  • gh-3743: Hash changed signature in Python 3.3
  • gh-3793: scalar int hashing broken on 64 bit python3
  • gh-3160: SandboxViolation easyinstalling 1.7.0 on Mac OS X 10.8.3
  • gh-3871: npy_math.h has invalid isinf for Solaris with SUNWspro12.2
  • gh-2561: Disable check for oldstyle classes in python3
  • gh-3900: Ensure NotImplemented is passed on in MaskedArray ufunc’s
  • gh-2052: del scalar subscript causes segfault
  • gh-3832: fix a few uninitialized uses and memleaks
  • gh-3971: f2py changed string.lowercase to string.ascii_lowercase for python3
  • gh-3480: numpy.random.binomial raised ValueError for n == 0
  • gh-3992: hypot(inf, 0) shouldn’t raise a warning, hypot(inf, inf) wrong result
  • gh-4018: Segmentation fault dealing with very large arrays
  • gh-4094: fix NaT handling in _strided_to_strided_string_to_datetime
  • gh-4051: fix uninitialized use in _strided_to_strided_string_to_datetime
  • gh-4123: lexsort segfault
  • gh-4141: Fix a few issues that show up with python 3.4b1

NumPy 1.7.1 Release Notes

This is a bugfix only release in the 1.7.x series. It supports Python 2.4 - 2.7 and 3.1 - 3.3 and is the last series that supports Python 2.4 - 2.5.

Issues fixed

  • gh-2973: Fix 1 is printed during numpy.test()
  • gh-2983: BUG: gh-2969: Backport memory leak fix 80b3a34.
  • gh-3007: Backport gh-3006
  • gh-2984: Backport fix complex polynomial fit
  • gh-2982: BUG: Make nansum work with booleans.
  • gh-2985: Backport large sort fixes
  • gh-3039: Backport object take
  • gh-3105: Backport nditer fix op axes initialization
  • gh-3108: BUG: npy-pkg-config ini files were missing after Bento build.
  • gh-3124: BUG: PyArray_LexSort allocates too much temporary memory.
  • gh-3131: BUG: Exported f2py_size symbol prevents linking multiple f2py modules.
  • gh-3117: Backport gh-2992
  • gh-3135: DOC: Add mention of PyArray_SetBaseObject stealing a reference
  • gh-3134: DOC: Fix typo in fft docs (the indexing variable is ‘m’, not ‘n’).
  • gh-3136: Backport #3128

NumPy 1.7.0 Release Notes

This release includes several new features as well as numerous bug fixes and refactorings. It supports Python 2.4 - 2.7 and 3.1 - 3.3 and is the last release that supports Python 2.4 - 2.5.

Highlights

  • where= parameter to ufuncs (allows the use of boolean arrays to choose where a computation should be done)
  • vectorize improvements (added ‘excluded’ and ‘cache’ keyword, general cleanup and bug fixes)
  • numpy.random.choice (random sample generating function)

Compatibility notes

In a future version of numpy, the functions np.diag, np.diagonal, and the diagonal method of ndarrays will return a view onto the original array, instead of producing a copy as they do now. This makes a difference if you write to the array returned by any of these functions. To facilitate this transition, numpy 1.7 produces a FutureWarning if it detects that you may be attempting to write to such an array. See the documentation for np.diagonal for details.

Similar to np.diagonal above, in a future version of numpy, indexing a record array by a list of field names will return a view onto the original array, instead of producing a copy as they do now. As with np.diagonal, numpy 1.7 produces a FutureWarning if it detects that you may be attempting to write to such an array. See the documentation for array indexing for details.

In a future version of numpy, the default casting rule for UFunc out= parameters will be changed from ‘unsafe’ to ‘same_kind’. (This also applies to in-place operations like a += b, which is equivalent to np.add(a, b, out=a).) Most usages which violate the ‘same_kind’ rule are likely bugs, so this change may expose previously undetected errors in projects that depend on NumPy. In this version of numpy, such usages will continue to succeed, but will raise a DeprecationWarning.

Full-array boolean indexing has been optimized to use a different, optimized code path. This code path should produce the same results, but any feedback about changes to your code would be appreciated.

Attempting to write to a read-only array (one with arr.flags.writeable set to False) used to raise either a RuntimeError, ValueError, or TypeError inconsistently, depending on which code path was taken. It now consistently raises a ValueError.

The <ufunc>.reduce functions evaluate some reductions in a different order than in previous versions of NumPy, generally providing higher performance. Because of the nature of floating-point arithmetic, this may subtly change some results, just as linking NumPy to a different BLAS implementations such as MKL can.

If upgrading from 1.5, then generally in 1.6 and 1.7 there have been substantial code added and some code paths altered, particularly in the areas of type resolution and buffered iteration over universal functions. This might have an impact on your code particularly if you relied on accidental behavior in the past.

New features

Reduction UFuncs Generalize axis= Parameter

Any ufunc.reduce function call, as well as other reductions like sum, prod, any, all, max and min support the ability to choose a subset of the axes to reduce over. Previously, one could say axis=None to mean all the axes or axis=# to pick a single axis. Now, one can also say axis=(#,#) to pick a list of axes for reduction.

Reduction UFuncs New keepdims= Parameter

There is a new keepdims= parameter, which if set to True, doesn’t throw away the reduction axes but instead sets them to have size one. When this option is set, the reduction result will broadcast correctly to the original operand which was reduced.

Datetime support

Note

The datetime API is experimental in 1.7.0, and may undergo changes in future versions of NumPy.

There have been a lot of fixes and enhancements to datetime64 compared to NumPy 1.6:

  • the parser is quite strict about only accepting ISO 8601 dates, with a few convenience extensions
  • converts between units correctly
  • datetime arithmetic works correctly
  • business day functionality (allows the datetime to be used in contexts where only certain days of the week are valid)

The notes in doc/source/reference/arrays.datetime.rst (also available in the online docs at arrays.datetime.html) should be consulted for more details.

Custom formatter for printing arrays

See the new formatter parameter of the numpy.set_printoptions function.

New function numpy.random.choice

A generic sampling function has been added which will generate samples from a given array-like. The samples can be with or without replacement, and with uniform or given non-uniform probabilities.

New function isclose

Returns a boolean array where two arrays are element-wise equal within a tolerance. Both relative and absolute tolerance can be specified.

Preliminary multi-dimensional support in the polynomial package

Axis keywords have been added to the integration and differentiation functions and a tensor keyword was added to the evaluation functions. These additions allow multi-dimensional coefficient arrays to be used in those functions. New functions for evaluating 2-D and 3-D coefficient arrays on grids or sets of points were added together with 2-D and 3-D pseudo-Vandermonde matrices that can be used for fitting.

Ability to pad rank-n arrays

A pad module containing functions for padding n-dimensional arrays has been added. The various private padding functions are exposed as options to a public ‘pad’ function. Example:

pad(a, 5, mode='mean')

Current modes are constant, edge, linear_ramp, maximum, mean, median, minimum, reflect, symmetric, wrap, and <function>.

New argument to searchsorted

The function searchsorted now accepts a ‘sorter’ argument that is a permutation array that sorts the array to search.

Build system

Added experimental support for the AArch64 architecture.

C API

New function PyArray_RequireWriteable provides a consistent interface for checking array writeability – any C code which works with arrays whose WRITEABLE flag is not known to be True a priori, should make sure to call this function before writing.

NumPy C Style Guide added (doc/C_STYLE_GUIDE.rst.txt).

Changes

General

The function np.concatenate tries to match the layout of its input arrays. Previously, the layout did not follow any particular reason, and depended in an undesirable way on the particular axis chosen for concatenation. A bug was also fixed which silently allowed out of bounds axis arguments.

The ufuncs logical_or, logical_and, and logical_not now follow Python’s behavior with object arrays, instead of trying to call methods on the objects. For example the expression (3 and ‘test’) produces the string ‘test’, and now np.logical_and(np.array(3, ‘O’), np.array(‘test’, ‘O’)) produces ‘test’ as well.

The .base attribute on ndarrays, which is used on views to ensure that the underlying array owning the memory is not deallocated prematurely, now collapses out references when you have a view-of-a-view. For example:

a = np.arange(10)
b = a[1:]
c = b[1:]

In numpy 1.6, c.base is b, and c.base.base is a. In numpy 1.7, c.base is a.

To increase backwards compatibility for software which relies on the old behaviour of .base, we only ‘skip over’ objects which have exactly the same type as the newly created view. This makes a difference if you use ndarray subclasses. For example, if we have a mix of ndarray and matrix objects which are all views on the same original ndarray:

a = np.arange(10)
b = np.asmatrix(a)
c = b[0, 1:]
d = c[0, 1:]

then d.base will be b. This is because d is a matrix object, and so the collapsing process only continues so long as it encounters other matrix objects. It considers c, b, and a in that order, and b is the last entry in that list which is a matrix object.

Casting Rules

Casting rules have undergone some changes in corner cases, due to the NA-related work. In particular for combinations of scalar+scalar:

  • the longlong type (q) now stays longlong for operations with any other number (? b h i l q p B H I), previously it was cast as int_ (l). The ulonglong type (Q) now stays as ulonglong instead of uint (L).
  • the timedelta64 type (m) can now be mixed with any integer type (b h i l q p B H I L Q P), previously it raised TypeError.

For array + scalar, the above rules just broadcast except the case when the array and scalars are unsigned/signed integers, then the result gets converted to the array type (of possibly larger size) as illustrated by the following examples:

>>> (np.zeros((2,), dtype=np.uint8) + np.int16(257)).dtype
dtype('uint16')
>>> (np.zeros((2,), dtype=np.int8) + np.uint16(257)).dtype
dtype('int16')
>>> (np.zeros((2,), dtype=np.int16) + np.uint32(2**17)).dtype
dtype('int32')

Whether the size gets increased depends on the size of the scalar, for example:

>>> (np.zeros((2,), dtype=np.uint8) + np.int16(255)).dtype
dtype('uint8')
>>> (np.zeros((2,), dtype=np.uint8) + np.int16(256)).dtype
dtype('uint16')

Also a complex128 scalar + float32 array is cast to complex64.

In NumPy 1.7 the datetime64 type (M) must be constructed by explicitly specifying the type as the second argument (e.g. np.datetime64(2000, 'Y')).

Deprecations

General

Specifying a custom string formatter with a _format array attribute is deprecated. The new formatter keyword in numpy.set_printoptions or numpy.array2string can be used instead.

The deprecated imports in the polynomial package have been removed.

concatenate now raises DepractionWarning for 1D arrays if axis != 0. Versions of numpy < 1.7.0 ignored axis argument value for 1D arrays. We allow this for now, but in due course we will raise an error.

C-API

Direct access to the fields of PyArrayObject* has been deprecated. Direct access has been recommended against for many releases. Expect similar deprecations for PyArray_Descr* and other core objects in the future as preparation for NumPy 2.0.

The macros in old_defines.h are deprecated and will be removed in the next major release (>= 2.0). The sed script tools/replace_old_macros.sed can be used to replace these macros with the newer versions.

You can test your code against the deprecated C API by #defining NPY_NO_DEPRECATED_API to the target version number, for example NPY_1_7_API_VERSION, before including any NumPy headers.

The NPY_CHAR member of the NPY_TYPES enum is deprecated and will be removed in NumPy 1.8. See the discussion at gh-2801 for more details.

NumPy 1.6.2 Release Notes

This is a bugfix release in the 1.6.x series. Due to the delay of the NumPy 1.7.0 release, this release contains far more fixes than a regular NumPy bugfix release. It also includes a number of documentation and build improvements.

Issues fixed

numpy.core

  • #2063: make unique() return consistent index
  • #1138: allow creating arrays from empty buffers or empty slices
  • #1446: correct note about correspondence vstack and concatenate
  • #1149: make argmin() work for datetime
  • #1672: fix allclose() to work for scalar inf
  • #1747: make np.median() work for 0-D arrays
  • #1776: make complex division by zero to yield inf properly
  • #1675: add scalar support for the format() function
  • #1905: explicitly check for NaNs in allclose()
  • #1952: allow floating ddof in std() and var()
  • #1948: fix regression for indexing chararrays with empty list
  • #2017: fix type hashing
  • #2046: deleting array attributes causes segfault
  • #2033: a**2.0 has incorrect type
  • #2045: make attribute/iterator_element deletions not segfault
  • #2021: fix segfault in searchsorted()
  • #2073: fix float16 __array_interface__ bug

numpy.lib

  • #2048: break reference cycle in NpzFile
  • #1573: savetxt() now handles complex arrays
  • #1387: allow bincount() to accept empty arrays
  • #1899: fixed histogramdd() bug with empty inputs
  • #1793: fix failing npyio test under py3k
  • #1936: fix extra nesting for subarray dtypes
  • #1848: make tril/triu return the same dtype as the original array
  • #1918: use Py_TYPE to access ob_type, so it works also on Py3

numpy.distutils

  • #1261: change compile flag on AIX from -O5 to -O3
  • #1377: update HP compiler flags
  • #1383: provide better support for C++ code on HPUX
  • #1857: fix build for py3k + pip
  • BLD: raise a clearer warning in case of building without cleaning up first
  • BLD: follow build_ext coding convention in build_clib
  • BLD: fix up detection of Intel CPU on OS X in system_info.py
  • BLD: add support for the new X11 directory structure on Ubuntu & co.
  • BLD: add ufsparse to the libraries search path.
  • BLD: add ‘pgfortran’ as a valid compiler in the Portland Group
  • BLD: update version match regexp for IBM AIX Fortran compilers.

numpy.random

  • BUG: Use npy_intp instead of long in mtrand

Changes

numpy.f2py

  • ENH: Introduce new options extra_f77_compiler_args and extra_f90_compiler_args
  • BLD: Improve reporting of fcompiler value
  • BUG: Fix f2py test_kind.py test

numpy.poly

  • ENH: Add some tests for polynomial printing
  • ENH: Add companion matrix functions
  • DOC: Rearrange the polynomial documents
  • BUG: Fix up links to classes
  • DOC: Add version added to some of the polynomial package modules
  • DOC: Document xxxfit functions in the polynomial package modules
  • BUG: The polynomial convenience classes let different types interact
  • DOC: Document the use of the polynomial convenience classes
  • DOC: Improve numpy reference documentation of polynomial classes
  • ENH: Improve the computation of polynomials from roots
  • STY: Code cleanup in polynomial [*]fromroots functions
  • DOC: Remove references to cast and NA, which were added in 1.7

NumPy 1.6.1 Release Notes

This is a bugfix only release in the 1.6.x series.

Issues Fixed

  • #1834: einsum fails for specific shapes
  • #1837: einsum throws nan or freezes python for specific array shapes
  • #1838: object <-> structured type arrays regression
  • #1851: regression for SWIG based code in 1.6.0
  • #1863: Buggy results when operating on array copied with astype()
  • #1870: Fix corner case of object array assignment
  • #1843: Py3k: fix error with recarray
  • #1885: nditer: Error in detecting double reduction loop
  • #1874: f2py: fix –include_paths bug
  • #1749: Fix ctypes.load_library()
  • #1895/1896: iter: writeonly operands weren’t always being buffered correctly

NumPy 1.6.0 Release Notes

This release includes several new features as well as numerous bug fixes and improved documentation. It is backward compatible with the 1.5.0 release, and supports Python 2.4 - 2.7 and 3.1 - 3.2.

Highlights

  • Re-introduction of datetime dtype support to deal with dates in arrays.
  • A new 16-bit floating point type.
  • A new iterator, which improves performance of many functions.

New features

New 16-bit floating point type

This release adds support for the IEEE 754-2008 binary16 format, available as the data type numpy.half. Within Python, the type behaves similarly to float or double, and C extensions can add support for it with the exposed half-float API.

New iterator

A new iterator has been added, replacing the functionality of the existing iterator and multi-iterator with a single object and API. This iterator works well with general memory layouts different from C or Fortran contiguous, and handles both standard NumPy and customized broadcasting. The buffering, automatic data type conversion, and optional output parameters, offered by ufuncs but difficult to replicate elsewhere, are now exposed by this iterator.

Legendre, Laguerre, Hermite, HermiteE polynomials in numpy.polynomial

Extend the number of polynomials available in the polynomial package. In addition, a new window attribute has been added to the classes in order to specify the range the domain maps to. This is mostly useful for the Laguerre, Hermite, and HermiteE polynomials whose natural domains are infinite and provides a more intuitive way to get the correct mapping of values without playing unnatural tricks with the domain.

Fortran assumed shape array and size function support in numpy.f2py

F2py now supports wrapping Fortran 90 routines that use assumed shape arrays. Before such routines could be called from Python but the corresponding Fortran routines received assumed shape arrays as zero length arrays which caused unpredicted results. Thanks to Lorenz Hüdepohl for pointing out the correct way to interface routines with assumed shape arrays.

In addition, f2py supports now automatic wrapping of Fortran routines that use two argument size function in dimension specifications.

Other new functions

numpy.ravel_multi_index : Converts a multi-index tuple into an array of flat indices, applying boundary modes to the indices.

numpy.einsum : Evaluate the Einstein summation convention. Using the Einstein summation convention, many common multi-dimensional array operations can be represented in a simple fashion. This function provides a way compute such summations.

numpy.count_nonzero : Counts the number of non-zero elements in an array.

numpy.result_type and numpy.min_scalar_type : These functions expose the underlying type promotion used by the ufuncs and other operations to determine the types of outputs. These improve upon the numpy.common_type and numpy.mintypecode which provide similar functionality but do not match the ufunc implementation.

Changes

default error handling

The default error handling has been change from print to warn for all except for underflow, which remains as ignore.

numpy.distutils

Several new compilers are supported for building Numpy: the Portland Group Fortran compiler on OS X, the PathScale compiler suite and the 64-bit Intel C compiler on Linux.

numpy.testing

The testing framework gained numpy.testing.assert_allclose, which provides a more convenient way to compare floating point arrays than assert_almost_equal, assert_approx_equal and assert_array_almost_equal.

C API

In addition to the APIs for the new iterator and half data type, a number of other additions have been made to the C API. The type promotion mechanism used by ufuncs is exposed via PyArray_PromoteTypes, PyArray_ResultType, and PyArray_MinScalarType. A new enumeration NPY_CASTING has been added which controls what types of casts are permitted. This is used by the new functions PyArray_CanCastArrayTo and PyArray_CanCastTypeTo. A more flexible way to handle conversion of arbitrary python objects into arrays is exposed by PyArray_GetArrayParamsFromObject.

Deprecated features

The “normed” keyword in numpy.histogram is deprecated. Its functionality will be replaced by the new “density” keyword.

Removed features

numpy.fft

The functions refft, refft2, refftn, irefft, irefft2, irefftn, which were aliases for the same functions without the ‘e’ in the name, were removed.

numpy.memmap

The sync() and close() methods of memmap were removed. Use flush() and “del memmap” instead.

numpy.lib

The deprecated functions numpy.unique1d, numpy.setmember1d, numpy.intersect1d_nu and numpy.lib.ufunclike.log2 were removed.

numpy.ma

Several deprecated items were removed from the numpy.ma module:

* ``numpy.ma.MaskedArray`` "raw_data" method
* ``numpy.ma.MaskedArray`` constructor "flag" keyword
* ``numpy.ma.make_mask`` "flag" keyword
* ``numpy.ma.allclose`` "fill_value" keyword

numpy.distutils

The numpy.get_numpy_include function was removed, use numpy.get_include instead.

NumPy 1.5.0 Release Notes

Highlights

Python 3 compatibility

This is the first NumPy release which is compatible with Python 3. Support for Python 3 and Python 2 is done from a single code base. Extensive notes on changes can be found at http://projects.scipy.org/numpy/browser/trunk/doc/Py3K.txt.

Note that the Numpy testing framework relies on nose, which does not have a Python 3 compatible release yet. A working Python 3 branch of nose can be found at http://bitbucket.org/jpellerin/nose3/ however.

Porting of SciPy to Python 3 is expected to be completed soon.

PEP 3118 compatibility

The new buffer protocol described by PEP 3118 is fully supported in this version of Numpy. On Python versions >= 2.6 Numpy arrays expose the buffer interface, and array(), asarray() and other functions accept new-style buffers as input.

New features

Warning on casting complex to real

Numpy now emits a numpy.ComplexWarning when a complex number is cast into a real number. For example:

>>> x = np.array([1,2,3])
>>> x[:2] = np.array([1+2j, 1-2j])
ComplexWarning: Casting complex values to real discards the imaginary part

The cast indeed discards the imaginary part, and this may not be the intended behavior in all cases, hence the warning. This warning can be turned off in the standard way:

>>> import warnings
>>> warnings.simplefilter("ignore", np.ComplexWarning)

Dot method for ndarrays

Ndarrays now have the dot product also as a method, which allows writing chains of matrix products as

>>> a.dot(b).dot(c)

instead of the longer alternative

>>> np.dot(a, np.dot(b, c))

linalg.slogdet function

The slogdet function returns the sign and logarithm of the determinant of a matrix. Because the determinant may involve the product of many small/large values, the result is often more accurate than that obtained by simple multiplication.

new header

The new header file ndarraytypes.h contains the symbols from ndarrayobject.h that do not depend on the PY_ARRAY_UNIQUE_SYMBOL and NO_IMPORT/_ARRAY macros. Broadly, these symbols are types, typedefs, and enumerations; the array function calls are left in ndarrayobject.h. This allows users to include array-related types and enumerations without needing to concern themselves with the macro expansions and their side- effects.

Changes

polynomial.polynomial

  • The polyint and polyder functions now check that the specified number integrations or derivations is a non-negative integer. The number 0 is a valid value for both functions.
  • A degree method has been added to the Polynomial class.
  • A trimdeg method has been added to the Polynomial class. It operates like truncate except that the argument is the desired degree of the result, not the number of coefficients.
  • Polynomial.fit now uses None as the default domain for the fit. The default Polynomial domain can be specified by using [] as the domain value.
  • Weights can be used in both polyfit and Polynomial.fit
  • A linspace method has been added to the Polynomial class to ease plotting.
  • The polymulx function was added.

polynomial.chebyshev

  • The chebint and chebder functions now check that the specified number integrations or derivations is a non-negative integer. The number 0 is a valid value for both functions.
  • A degree method has been added to the Chebyshev class.
  • A trimdeg method has been added to the Chebyshev class. It operates like truncate except that the argument is the desired degree of the result, not the number of coefficients.
  • Chebyshev.fit now uses None as the default domain for the fit. The default Chebyshev domain can be specified by using [] as the domain value.
  • Weights can be used in both chebfit and Chebyshev.fit
  • A linspace method has been added to the Chebyshev class to ease plotting.
  • The chebmulx function was added.
  • Added functions for the Chebyshev points of the first and second kind.

histogram

After a two years transition period, the old behavior of the histogram function has been phased out, and the “new” keyword has been removed.

correlate

The old behavior of correlate was deprecated in 1.4.0, the new behavior (the usual definition for cross-correlation) is now the default.

NumPy 1.4.0 Release Notes

This minor includes numerous bug fixes, as well as a few new features. It is backward compatible with 1.3.0 release.

Highlights

  • New datetime dtype support to deal with dates in arrays
  • Faster import time
  • Extended array wrapping mechanism for ufuncs
  • New Neighborhood iterator (C-level only)
  • C99-like complex functions in npymath

New features

Extended array wrapping mechanism for ufuncs

An __array_prepare__ method has been added to ndarray to provide subclasses greater flexibility to interact with ufuncs and ufunc-like functions. ndarray already provided __array_wrap__, which allowed subclasses to set the array type for the result and populate metadata on the way out of the ufunc (as seen in the implementation of MaskedArray). For some applications it is necessary to provide checks and populate metadata on the way in. __array_prepare__ is therefore called just after the ufunc has initialized the output array but before computing the results and populating it. This way, checks can be made and errors raised before operations which may modify data in place.

Automatic detection of forward incompatibilities

Previously, if an extension was built against a version N of NumPy, and used on a system with NumPy M < N, the import_array was successfull, which could cause crashes because the version M does not have a function in N. Starting from NumPy 1.4.0, this will cause a failure in import_array, so the error will be catched early on.

New iterators

A new neighborhood iterator has been added to the C API. It can be used to iterate over the items in a neighborhood of an array, and can handle boundaries conditions automatically. Zero and one padding are available, as well as arbitrary constant value, mirror and circular padding.

New polynomial support

New modules chebyshev and polynomial have been added. The new polynomial module is not compatible with the current polynomial support in numpy, but is much like the new chebyshev module. The most noticeable difference to most will be that coefficients are specified from low to high power, that the low level functions do not work with the Chebyshev and Polynomial classes as arguements, and that the Chebyshev and Polynomial classes include a domain. Mapping between domains is a linear substitution and the two classes can be converted one to the other, allowing, for instance, a Chebyshev series in one domain to be expanded as a polynomial in another domain. The new classes should generally be used instead of the low level functions, the latter are provided for those who wish to build their own classes.

The new modules are not automatically imported into the numpy namespace, they must be explicitly brought in with an “import numpy.polynomial” statement.

New C API

The following C functions have been added to the C API:

  1. PyArray_GetNDArrayCFeatureVersion: return the API version of the loaded numpy.
  2. PyArray_Correlate2 - like PyArray_Correlate, but implements the usual definition of correlation. Inputs are not swapped, and conjugate is taken for complex arrays.
  3. PyArray_NeighborhoodIterNew - a new iterator to iterate over a neighborhood of a point, with automatic boundaries handling. It is documented in the iterators section of the C-API reference, and you can find some examples in the multiarray_test.c.src file in numpy.core.

New ufuncs

The following ufuncs have been added to the C API:

  1. copysign - return the value of the first argument with the sign copied from the second argument.
  2. nextafter - return the next representable floating point value of the first argument toward the second argument.

New defines

The alpha processor is now defined and available in numpy/npy_cpu.h. The failed detection of the PARISC processor has been fixed. The defines are:

  1. NPY_CPU_HPPA: PARISC
  2. NPY_CPU_ALPHA: Alpha

Testing

  1. deprecated decorator: this decorator may be used to avoid cluttering testing output while testing DeprecationWarning is effectively raised by the decorated test.
  2. assert_array_almost_equal_nulps: new method to compare two arrays of floating point values. With this function, two values are considered close if there are not many representable floating point values in between, thus being more robust than assert_array_almost_equal when the values fluctuate a lot.
  3. assert_array_max_ulp: raise an assertion if there are more than N representable numbers between two floating point values.
  4. assert_warns: raise an AssertionError if a callable does not generate a warning of the appropriate class, without altering the warning state.

Reusing npymath

In 1.3.0, we started putting portable C math routines in npymath library, so that people can use those to write portable extensions. Unfortunately, it was not possible to easily link against this library: in 1.4.0, support has been added to numpy.distutils so that 3rd party can reuse this library. See coremath documentation for more information.

Improved set operations

In previous versions of NumPy some set functions (intersect1d, setxor1d, setdiff1d and setmember1d) could return incorrect results if the input arrays contained duplicate items. These now work correctly for input arrays with duplicates. setmember1d has been renamed to in1d, as with the change to accept arrays with duplicates it is no longer a set operation, and is conceptually similar to an elementwise version of the Python operator ‘in’. All of these functions now accept the boolean keyword assume_unique. This is False by default, but can be set True if the input arrays are known not to contain duplicates, which can increase the functions’ execution speed.

Improvements

  1. numpy import is noticeably faster (from 20 to 30 % depending on the platform and computer)

  2. The sort functions now sort nans to the end.

    • Real sort order is [R, nan]
    • Complex sort order is [R + Rj, R + nanj, nan + Rj, nan + nanj]

    Complex numbers with the same nan placements are sorted according to the non-nan part if it exists.

  3. The type comparison functions have been made consistent with the new sort order of nans. Searchsorted now works with sorted arrays containing nan values.

  4. Complex division has been made more resistent to overflow.

  5. Complex floor division has been made more resistent to overflow.

Deprecations

The following functions are deprecated:

  1. correlate: it takes a new keyword argument old_behavior. When True (the default), it returns the same result as before. When False, compute the conventional correlation, and take the conjugate for complex arrays. The old behavior will be removed in NumPy 1.5, and raises a DeprecationWarning in 1.4.
  2. unique1d: use unique instead. unique1d raises a deprecation warning in 1.4, and will be removed in 1.5.
  3. intersect1d_nu: use intersect1d instead. intersect1d_nu raises a deprecation warning in 1.4, and will be removed in 1.5.
  4. setmember1d: use in1d instead. setmember1d raises a deprecation warning in 1.4, and will be removed in 1.5.

The following raise errors:

  1. When operating on 0-d arrays, numpy.max and other functions accept only axis=0, axis=-1 and axis=None. Using an out-of-bounds axes is an indication of a bug, so Numpy raises an error for these cases now.
  2. Specifying axis > MAX_DIMS is no longer allowed; Numpy raises now an error instead of behaving similarly as for axis=None.

Internal changes

Use C99 complex functions when available

The numpy complex types are now guaranteed to be ABI compatible with C99 complex type, if availble on the platform. Moreoever, the complex ufunc now use the platform C99 functions intead of our own.

split multiarray and umath source code

The source code of multiarray and umath has been split into separate logic compilation units. This should make the source code more amenable for newcomers.

Separate compilation

By default, every file of multiarray (and umath) is merged into one for compilation as was the case before, but if NPY_SEPARATE_COMPILATION env variable is set to a non-negative value, experimental individual compilation of each file is enabled. This makes the compile/debug cycle much faster when working on core numpy.

Separate core math library

New functions which have been added:

  • npy_copysign
  • npy_nextafter
  • npy_cpack
  • npy_creal
  • npy_cimag
  • npy_cabs
  • npy_cexp
  • npy_clog
  • npy_cpow
  • npy_csqr
  • npy_ccos
  • npy_csin

NumPy 1.3.0 Release Notes

This minor includes numerous bug fixes, official python 2.6 support, and several new features such as generalized ufuncs.

Highlights

Python 2.6 support

Python 2.6 is now supported on all previously supported platforms, including windows.

http://www.python.org/dev/peps/pep-0361/

Generalized ufuncs

There is a general need for looping over not only functions on scalars but also over functions on vectors (or arrays), as explained on http://scipy.org/scipy/numpy/wiki/GeneralLoopingFunctions. We propose to realize this concept by generalizing the universal functions (ufuncs), and provide a C implementation that adds ~500 lines to the numpy code base. In current (specialized) ufuncs, the elementary function is limited to element-by-element operations, whereas the generalized version supports “sub-array” by “sub-array” operations. The Perl vector library PDL provides a similar functionality and its terms are re-used in the following.

Each generalized ufunc has information associated with it that states what the “core” dimensionality of the inputs is, as well as the corresponding dimensionality of the outputs (the element-wise ufuncs have zero core dimensions). The list of the core dimensions for all arguments is called the “signature” of a ufunc. For example, the ufunc numpy.add has signature “(),()->()” defining two scalar inputs and one scalar output.

Another example is (see the GeneralLoopingFunctions page) the function inner1d(a,b) with a signature of “(i),(i)->()”. This applies the inner product along the last axis of each input, but keeps the remaining indices intact. For example, where a is of shape (3,5,N) and b is of shape (5,N), this will return an output of shape (3,5). The underlying elementary function is called 3*5 times. In the signature, we specify one core dimension “(i)” for each input and zero core dimensions “()” for the output, since it takes two 1-d arrays and returns a scalar. By using the same name “i”, we specify that the two corresponding dimensions should be of the same size (or one of them is of size 1 and will be broadcasted).

The dimensions beyond the core dimensions are called “loop” dimensions. In the above example, this corresponds to (3,5).

The usual numpy “broadcasting” rules apply, where the signature determines how the dimensions of each input/output object are split into core and loop dimensions:

While an input array has a smaller dimensionality than the corresponding number of core dimensions, 1’s are pre-pended to its shape. The core dimensions are removed from all inputs and the remaining dimensions are broadcasted; defining the loop dimensions. The output is given by the loop dimensions plus the output core dimensions.

Experimental Windows 64 bits support

Numpy can now be built on windows 64 bits (amd64 only, not IA64), with both MS compilers and mingw-w64 compilers:

This is highly experimental: DO NOT USE FOR PRODUCTION USE. See INSTALL.txt, Windows 64 bits section for more information on limitations and how to build it by yourself.

New features

Formatting issues

Float formatting is now handled by numpy instead of the C runtime: this enables locale independent formatting, more robust fromstring and related methods. Special values (inf and nan) are also more consistent across platforms (nan vs IND/NaN, etc...), and more consistent with recent python formatting work (in 2.6 and later).

Nan handling in max/min

The maximum/minimum ufuncs now reliably propagate nans. If one of the arguments is a nan, then nan is retured. This affects np.min/np.max, amin/amax and the array methods max/min. New ufuncs fmax and fmin have been added to deal with non-propagating nans.

Nan handling in sign

The ufunc sign now returns nan for the sign of anan.

New ufuncs

  1. fmax - same as maximum for integer types and non-nan floats. Returns the non-nan argument if one argument is nan and returns nan if both arguments are nan.
  2. fmin - same as minimum for integer types and non-nan floats. Returns the non-nan argument if one argument is nan and returns nan if both arguments are nan.
  3. deg2rad - converts degrees to radians, same as the radians ufunc.
  4. rad2deg - converts radians to degrees, same as the degrees ufunc.
  5. log2 - base 2 logarithm.
  6. exp2 - base 2 exponential.
  7. trunc - truncate floats to nearest integer towards zero.
  8. logaddexp - add numbers stored as logarithms and return the logarithm of the result.
  9. logaddexp2 - add numbers stored as base 2 logarithms and return the base 2 logarithm of the result result.

Masked arrays

Several new features and bug fixes, including:

  • structured arrays should now be fully supported by MaskedArray (r6463, r6324, r6305, r6300, r6294...)
  • Minor bug fixes (r6356, r6352, r6335, r6299, r6298)
  • Improved support for __iter__ (r6326)
  • made baseclass, sharedmask and hardmask accesible to the user (but read-only)
  • doc update

gfortran support on windows

Gfortran can now be used as a fortran compiler for numpy on windows, even when the C compiler is Visual Studio (VS 2005 and above; VS 2003 will NOT work). Gfortran + Visual studio does not work on windows 64 bits (but gcc + gfortran does). It is unclear whether it will be possible to use gfortran and visual studio at all on x64.

Arch option for windows binary

Automatic arch detection can now be bypassed from the command line for the superpack installed:

numpy-1.3.0-superpack-win32.exe /arch=nosse

will install a numpy which works on any x86, even if the running computer supports SSE set.

Deprecated features

Histogram

The semantics of histogram has been modified to fix long-standing issues with outliers handling. The main changes concern

  1. the definition of the bin edges, now including the rightmost edge, and
  2. the handling of upper outliers, now ignored rather than tallied in the rightmost bin.

The previous behavior is still accessible using new=False, but this is deprecated, and will be removed entirely in 1.4.0.

Documentation changes

A lot of documentation has been added. Both user guide and references can be built from sphinx.

New C API

Multiarray API

The following functions have been added to the multiarray C API:

  • PyArray_GetEndianness: to get runtime endianness

Ufunc API

The following functions have been added to the ufunc API:

  • PyUFunc_FromFuncAndDataAndSignature: to declare a more general ufunc (generalized ufunc).

New defines

New public C defines are available for ARCH specific code through numpy/npy_cpu.h:

  • NPY_CPU_X86: x86 arch (32 bits)
  • NPY_CPU_AMD64: amd64 arch (x86_64, NOT Itanium)
  • NPY_CPU_PPC: 32 bits ppc
  • NPY_CPU_PPC64: 64 bits ppc
  • NPY_CPU_SPARC: 32 bits sparc
  • NPY_CPU_SPARC64: 64 bits sparc
  • NPY_CPU_S390: S390
  • NPY_CPU_IA64: ia64
  • NPY_CPU_PARISC: PARISC

New macros for CPU endianness has been added as well (see internal changes below for details):

  • NPY_BYTE_ORDER: integer
  • NPY_LITTLE_ENDIAN/NPY_BIG_ENDIAN defines

Those provide portable alternatives to glibc endian.h macros for platforms without it.

Portable NAN, INFINITY, etc...

npy_math.h now makes available several portable macro to get NAN, INFINITY:

  • NPY_NAN: equivalent to NAN, which is a GNU extension
  • NPY_INFINITY: equivalent to C99 INFINITY
  • NPY_PZERO, NPY_NZERO: positive and negative zero respectively

Corresponding single and extended precision macros are available as well. All references to NAN, or home-grown computation of NAN on the fly have been removed for consistency.

Internal changes

numpy.core math configuration revamp

This should make the porting to new platforms easier, and more robust. In particular, the configuration stage does not need to execute any code on the target platform, which is a first step toward cross-compilation.

http://projects.scipy.org/numpy/browser/trunk/doc/neps/math_config_clean.txt

umath refactor

A lot of code cleanup for umath/ufunc code (charris).

Improvements to build warnings

Numpy can now build with -W -Wall without warnings

http://projects.scipy.org/numpy/browser/trunk/doc/neps/warnfix.txt

Separate core math library

The core math functions (sin, cos, etc... for basic C types) have been put into a separate library; it acts as a compatibility layer, to support most C99 maths functions (real only for now). The library includes platform-specific fixes for various maths functions, such as using those versions should be more robust than using your platform functions directly. The API for existing functions is exactly the same as the C99 math functions API; the only difference is the npy prefix (npy_cos vs cos).

The core library will be made available to any extension in 1.4.0.

CPU arch detection

npy_cpu.h defines numpy specific CPU defines, such as NPY_CPU_X86, etc... Those are portable across OS and toolchains, and set up when the header is parsed, so that they can be safely used even in the case of cross-compilation (the values is not set when numpy is built), or for multi-arch binaries (e.g. fat binaries on Max OS X).

npy_endian.h defines numpy specific endianness defines, modeled on the glibc endian.h. NPY_BYTE_ORDER is equivalent to BYTE_ORDER, and one of NPY_LITTLE_ENDIAN or NPY_BIG_ENDIAN is defined. As for CPU archs, those are set when the header is parsed by the compiler, and as such can be used for cross-compilation and multi-arch binaries.

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